From 777a52afda0e2446ec4a07e15b13ba2e4901c13d Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Thu, 19 Jan 2023 10:26:12 +0100
Subject: [PATCH] SSDM-13329 Removed rtd_phosphonetx project
---
.../datastore_server/etc/service.properties | 169 +-
.../datastore_server2/etc/service.properties | 173 +-
openbis_all/build/build.xml | 7 -
openbis_all/source/bash/build/branch.sh | 1 -
rtd_phosphonetx/.gitignore | 11 -
rtd_phosphonetx/.pydevproject | 7 -
rtd_phosphonetx/.shredder | Bin 12 -> 0 bytes
rtd_phosphonetx/build.gradle | 58 -
rtd_phosphonetx/etc/log.xml | 19 -
rtd_phosphonetx/etc/passwd | 4 -
rtd_phosphonetx/etc/passwd.sv | 0
rtd_phosphonetx/etc/passwd.tmp | 0
rtd_phosphonetx/etc/service.properties | 115 -
rtd_phosphonetx/etc/web-client.properties | 12 -
.../gradle/wrapper/gradle-wrapper.jar | Bin 54783 -> 0 bytes
.../gradle/wrapper/gradle-wrapper.properties | 5 -
rtd_phosphonetx/gradlew | 172 -
rtd_phosphonetx/gradlew.bat | 84 -
rtd_phosphonetx/gwtdev.gradle | 95 -
.../resource/dependency-structure.ddf | 50 -
.../Gradle Proteomics compile GWT.launch | 6 -
...Gradle Proteomics openBIS GWT Shell.launch | 37 -
.../Gradle Proteomics prepare GWT.launch | 6 -
.../Proteomics openBIS GWT Shell.launch | 22 -
.../phosphonetx Data Store Server.launch | 13 -
.../resource/server/spring-servlet.xml | 38 -
rtd_phosphonetx/resource/server/web.xml | 30 -
rtd_phosphonetx/settings.gradle | 1 -
.../core-plugins/core-plugins.properties | 16 -
.../plugin.properties | 3 -
.../demo-proteomics-aggregation/script.py | 122 -
.../1/as/initialize-master-data.py | 81 -
.../proteomics-optional/package-to-dist | 0
.../dss-data-sources/DSS1/plugin.properties | 17 -
.../proteomics/1/as/initialize-master-data.py | 42 -
.../proteomics-application/plugin.properties | 1 -
.../proteomics-db/plugin.properties | 25 -
.../drop-boxes/ms-injection/plugin.properties | 18 -
.../drop-boxes/ms-search/plugin.properties | 29 -
.../proteomics-db-clean-up/plugin.properties | 8 -
.../core-plugins/proteomics/package-to-dist | 0
.../source/html/demoapp/body-style.css | 14 -
.../source/html/demoapp/button.css | 52 -
rtd_phosphonetx/source/html/demoapp/d3.js | 4013 ---
.../source/html/demoapp/d3.layout.js | 1865 --
.../source/html/demoapp/d3.time.js | 692 -
.../html/demoapp/images/openBIS_Logo.png | Bin 7229 -> 0 bytes
.../html/demoapp/images/openBIS_Logo.svg | 68 -
.../source/html/demoapp/openbis-demo-app.html | 94 -
.../source/html/demoapp/proteomics-demo.js | 225 -
rtd_phosphonetx/source/html/demoapp/tree.css | 36 -
.../proteomics/server/plugins/APMSReport.java | 559 -
.../server/plugins/DataSetCopier.java | 60 -
.../server/plugins/LocalAndRemoteCopier.java | 191 -
...stractDataSetInfoExtractorWithService.java | 35 -
.../etlserver/proteomics/AbstractHandler.java | 33 -
.../proteomics/AbstractSampleHandler.java | 146 -
.../proteomics/AbundanceHandler.java | 91 -
.../etlserver/proteomics/Constants.java | 27 -
.../DataSetInfoExtractorForMSInjection.java | 237 -
...DataSetInfoExtractorForProteinResults.java | 241 -
.../proteomics/DatabaseVersionHolder.java | 33 -
.../etlserver/proteomics/IProtDAO.java | 105 -
.../proteomics/ModificationFraction.java | 86 -
.../ModificationFractionHandler.java | 71 -
.../etlserver/proteomics/ProtXMLLoader.java | 93 -
.../etlserver/proteomics/ProtXMLUploader.java | 189 -
.../proteomics/ProteinDescription.java | 132 -
...ProteinResultDataSetParentLinkingTask.java | 181 -
.../proteomics/ResultDataSetUploader.java | 477 -
...ageProcessorWithResultDataSetUploader.java | 41 -
.../TypeExtractorForMSInjection.java | 80 -
.../openbis/etlserver/proteomics/Util.java | 128 -
.../proteomics/dto/ASAPRatioPValue.java | 117 -
.../proteomics/dto/AbstractDTOWithID.java | 39 -
.../dto/AbstractDTOWithIDAndPermID.java | 39 -
.../proteomics/dto/AminoAcidMass.java | 78 -
.../proteomics/dto/AnnotatedProtein.java | 63 -
.../etlserver/proteomics/dto/DataSet.java | 64 -
.../etlserver/proteomics/dto/Database.java | 39 -
.../etlserver/proteomics/dto/Experiment.java | 25 -
.../proteomics/dto/ModificationType.java | 95 -
.../etlserver/proteomics/dto/Parameter.java | 67 -
.../proteomics/dto/ParentDataSetCodes.java | 49 -
.../etlserver/proteomics/dto/Peptide.java | 132 -
.../proteomics/dto/PeptideModification.java | 109 -
.../proteomics/dto/ProgramDetails.java | 83 -
.../etlserver/proteomics/dto/Protein.java | 232 -
.../proteomics/dto/ProteinAnnotation.java | 145 -
.../proteomics/dto/ProteinGroup.java | 105 -
.../proteomics/dto/ProteinProphetDetails.java | 66 -
.../proteomics/dto/ProteinReference.java | 51 -
.../proteomics/dto/ProteinSummary.java | 74 -
.../dto/ProteinSummaryDataFilter.java | 68 -
.../proteomics/dto/ProteinSummaryHeader.java | 267 -
.../etlserver/proteomics/dto/Sample.java | 38 -
.../etlserver/proteomics/dto/Sequence.java | 124 -
.../etlserver/proteomics/protXML_v3.xsd | 816 -
.../etlserver/proteomics/protXML_v4.xsd | 820 -
.../etlserver/proteomics/protXML_v5.xsd | 934 -
.../proteomics/BuildAndEnvironmentInfo.java | 45 -
.../openbis/plugin/proteomics/OpenBIS.gwt.xml | 14 -
.../plugin/proteomics/OpenBISFirefox.gwt.xml | 13 -
.../plugin/proteomics/OpenBISSafari.gwt.xml | 13 -
.../client/api/v1/FacadeFactory.java | 103 -
.../api/v1/IProteomicsDataApiFacade.java | 117 -
.../api/v1/ProteomicsDataApiFacade.java | 168 -
.../client/api/v1/ProteomicsDataApiTest.java | 130 -
.../proteomics/client/api/v1/package.html | 5 -
.../client/web/client/Constants.java | 29 -
.../web/client/IPhosphoNetXClientService.java | 119 -
.../IPhosphoNetXClientServiceAsync.java | 137 -
.../AccessionNumberURLCreator.java | 62 -
.../application/ClientPluginFactory.java | 244 -
.../application/DataSetProteinGrid.java | 118 -
.../client/web/client/application/Dict.java | 114 -
.../application/DisplayTypeIDGenerator.java | 50 -
.../client/application/ExperimentViewer.java | 188 -
.../client/application/PhosphoNetXClient.java | 56 -
.../PhosphoNetXDisplayTypeIDGenerator.java | 59 -
.../client/application/PhosphoNetXModule.java | 141 -
.../ProteinByExperimentBrowerToolBar.java | 391 -
.../ProteinByExperimentBrowserGrid.java | 240 -
.../application/ProteinRelatedSampleGrid.java | 133 -
.../client/application/ProteinRenderers.java | 265 -
.../application/ProteinSamplesSection.java | 81 -
.../application/ProteinSequenceGrid.java | 109 -
.../application/ProteinSummaryGrid.java | 112 -
.../ProteinViewLocatorResolver.java | 100 -
.../web/client/application/ProteinViewer.java | 454 -
.../application/RawDataProcessingMenu.java | 175 -
.../client/application/RawDataSampleGrid.java | 157 -
.../web/client/application/ViewContext.java | 60 -
.../web/client/application/columns/.gitignore | 0
.../web/client/application/model/.gitignore | 0
.../wizard/BiologicalSampleChoosingPage.java | 97 -
.../wizard/BiologicalSampleCreatingPage.java | 183 -
.../wizard/BiologicalSampleGrid.java | 87 -
.../MsInjectionAnnotationWizardState.java | 29 -
.../MsInjectionSampleAnnotationModel.java | 120 -
.../MsInjectionSampleAnnotationWizard.java | 41 -
.../wizard/MsInjectionSampleChoosingPage.java | 98 -
.../ParentlessMsInjectionSampleGrid.java | 90 -
.../application/wizard/QuestionPage.java | 67 -
.../dto/BiologicalSampleGridColumnIDs.java | 31 -
.../dto/DataSetProteinGridColumnIDs.java | 33 -
...oteinByExperimentAndReferenceCriteria.java | 56 -
.../dto/ListProteinByExperimentCriteria.java | 94 -
.../dto/ListProteinSequenceCriteria.java | 59 -
...istProteinSummaryByExperimentCriteria.java | 45 -
.../ListSampleAbundanceByProteinCriteria.java | 55 -
...entlessMsInjectionSampleGridColumnIDs.java | 31 -
.../client/dto/ProteinBrowserColumnIDs.java | 29 -
.../ProteinRelatedSampleGridColumnIDs.java | 37 -
.../dto/ProteinSequenceGridColumnIDs.java | 33 -
.../dto/ProteinSummaryGridColumnIDs.java | 35 -
.../proteomics/client/web/public/index.html | 61 -
.../web/public/proteomics-dictionary.js | 101 -
.../web/server/PhosphoNetXClientService.java | 405 -
.../PhosphoNetXClientServiceServlet.java | 55 -
.../web/server/RawDataSampleProvider.java | 79 -
.../resultset/BiologicalSampleProvider.java | 78 -
.../resultset/DataSetProteinProvider.java | 82 -
.../ParentlessMsInjectionSampleProvider.java | 83 -
.../web/server/resultset/ProteinProvider.java | 160 -
.../ProteinRelatedSampleProvider.java | 112 -
.../resultset/ProteinSequenceProvider.java | 77 -
.../resultset/ProteinSummaryProvider.java | 77 -
.../proteomics/server/PhosphoNetXServer.java | 262 -
.../server/PhosphoNetXServerLogger.java | 124 -
.../server/ProteomicsDataServiceInternal.java | 368 -
.../ProteomicsDataServiceInternalLogger.java | 100 -
.../proteomics/server/api/v1/Constants.java | 29 -
.../server/api/v1/ProteomicsDataService.java | 413 -
.../api/v1/ProteomicsDataServiceLogger.java | 142 -
.../api/v1/ProteomicsDataServiceServer.java | 60 -
.../validator/ParentSampleValidator.java | 60 -
.../validator/RawDataSampleValidator.java | 27 -
.../business/AbstractBusinessObject.java | 58 -
.../AbundanceColumnDefinitionTable.java | 142 -
.../server/business/AbundanceManager.java | 84 -
.../business/AccessionNumberBuilder.java | 80 -
.../business/BusinessObjectFactory.java | 120 -
.../server/business/DataSetProteinTable.java | 76 -
.../server/business/ErrorModel.java | 85 -
.../server/business/ExperimentLoader.java | 84 -
.../IAbundanceColumnDefinitionTable.java | 34 -
.../business/IBusinessObjectFactory.java | 51 -
.../server/business/IDataSetProteinTable.java | 34 -
.../server/business/IProteinDetailsBO.java | 32 -
.../server/business/IProteinInfoTable.java | 43 -
.../business/IProteinRelatedSampleTable.java | 35 -
.../business/IProteinSequenceTable.java | 35 -
.../server/business/IProteinSummaryTable.java | 34 -
.../server/business/ISampleIDProvider.java | 38 -
.../server/business/ISampleLoader.java | 31 -
.../server/business/ISampleProvider.java | 42 -
.../server/business/ISampleTable.java | 35 -
.../server/business/ProteinDetailsBO.java | 177 -
.../server/business/ProteinInfoTable.java | 217 -
.../business/ProteinRelatedSampleTable.java | 219 -
.../server/business/ProteinSequenceTable.java | 111 -
.../server/business/ProteinSummaryTable.java | 150 -
.../server/business/SampleIDProvider.java | 69 -
.../server/business/SampleLoader.java | 131 -
.../server/business/SampleProvider.java | 93 -
.../server/business/SampleTable.java | 117 -
.../server/business/TreatmentFinder.java | 147 -
.../dataaccess/IPhosphoNetXDAOFactory.java | 31 -
.../server/dataaccess/IProteinQueryDAO.java | 139 -
.../dataaccess/db/PhosphoNetXDAOFactory.java | 130 -
.../migration/MigrationStepFrom002To003.java | 145 -
.../plugin/proteomics/shared/CacheData.java | 36 -
.../proteomics/shared/IPhosphoNetXServer.java | 76 -
.../IProteomicsDataServiceInternal.java | 65 -
.../shared/ProbabilityToFDRCalculator.java | 83 -
.../proteomics/shared/ResourceNames.java | 38 -
.../shared/api/v1/IProteomicsDataService.java | 133 -
.../proteomics/shared/api/v1/dto/DataSet.java | 114 -
.../DataStoreServerProcessingPluginInfo.java | 73 -
.../shared/api/v1/dto/Experiment.java | 104 -
.../api/v1/dto/MsInjectionDataInfo.java | 172 -
.../shared/api/v1/dto/PropertyKey.java | 90 -
.../proteomics/shared/api/v1/dto/package.html | 5 -
.../shared/basic/CommonConstants.java | 35 -
.../basic/dto/AbundanceColumnDefinition.java | 111 -
.../basic/dto/AccessionNumberProvider.java | 54 -
.../shared/basic/dto/AggregateFunction.java | 114 -
.../shared/basic/dto/AminoAcid.java | 67 -
.../shared/basic/dto/DataSetProtein.java | 103 -
.../shared/basic/dto/IBasicProteinInfo.java | 35 -
.../dto/IndistinguishableProteinInfo.java | 63 -
.../shared/basic/dto/Occurrence.java | 65 -
.../shared/basic/dto/OccurrenceUtil.java | 91 -
.../proteomics/shared/basic/dto/Peptide.java | 53 -
.../shared/basic/dto/PeptideModification.java | 56 -
.../shared/basic/dto/ProteinByExperiment.java | 67 -
.../shared/basic/dto/ProteinDetails.java | 164 -
.../shared/basic/dto/ProteinInfo.java | 119 -
.../basic/dto/ProteinRelatedSample.java | 181 -
.../shared/basic/dto/ProteinSequence.java | 91 -
.../shared/basic/dto/ProteinSummary.java | 90 -
.../basic/dto/RawDataSampleGridIDs.java | 32 -
.../dto/SampleWithPropertiesAndAbundance.java | 138 -
.../shared/basic/dto/Treatment.java | 117 -
.../shared/dto/AbstractDTOWithID.java | 43 -
.../proteomics/shared/dto/AbstractSample.java | 43 -
.../shared/dto/IdentifiedProtein.java | 157 -
.../shared/dto/IndistinguishableProtein.java | 54 -
.../shared/dto/MsInjectionSample.java | 91 -
.../shared/dto/PeptideWithModification.java | 67 -
.../shared/dto/ProbabilityFDRMapping.java | 51 -
.../shared/dto/ProteinAbundance.java | 55 -
.../shared/dto/ProteinReference.java | 56 -
.../dto/ProteinReferenceWithProbability.java | 95 -
...einReferenceWithProbabilityAndPeptide.java | 41 -
.../dto/ProteinReferenceWithProtein.java | 82 -
.../shared/dto/ProteinWithAbundances.java | 69 -
.../shared/dto/SampleAbundance.java | 41 -
.../shared/dto/SamplePeptideModification.java | 80 -
.../proteomics/shared/dto/Sequence.java | 67 -
.../java/proteomics-applicationContext.xml | 13 -
.../proteomics-plugin-applicationContext.xml | 64 -
.../source/java/service.properties | 67 -
.../proteomics/postgresql/001/schema-001.dez | 26083 ---------------
.../proteomics/postgresql/001/schema-001.png | Bin 199097 -> 0 bytes
.../proteomics/postgresql/001/schema-001.sql | 284 -
.../proteomics/postgresql/002/schema-002.png | Bin 199097 -> 0 bytes
.../proteomics/postgresql/002/schema-002.sql | 292 -
.../proteomics/postgresql/003/grant-003.sql | 18 -
.../proteomics/postgresql/003/schema-003.png | Bin 65092 -> 0 bytes
.../proteomics/postgresql/003/schema-003.sql | 293 -
.../proteomics/postgresql/004/grant-004.sql | 18 -
.../proteomics/postgresql/004/schema-004.png | Bin 66176 -> 0 bytes
.../proteomics/postgresql/004/schema-004.sql | 296 -
.../proteomics/postgresql/005/grant-005.sql | 18 -
.../proteomics/postgresql/005/schema-005.png | Bin 66176 -> 0 bytes
.../proteomics/postgresql/005/schema-005.sql | 310 -
.../migration/migration-001-002.sql | 41 -
.../migration/migration-002-003.sql | 4 -
.../migration/migration-003-004.sql | 5 -
.../migration/migration-004-005.sql | 14 -
.../sql/proteomics/postgresql/schema.dez | 26376 ----------------
.../core-plugins/core-plugins.properties | 0
.../server/plugins/APMSReportTest.java | 297 -
.../plugins/LocalAndRemoteCopierTest.java | 392 -
.../proteomics/AbundanceHandlerTest.java | 405 -
...ataSetInfoExtractorForMSInjectionTest.java | 722 -
...SetInfoExtractorForProteinResultsTest.java | 479 -
.../proteomics/ProtXMLLoaderTest.java | 113 -
.../etlserver/proteomics/ProtXMLTestCase.java | 97 -
.../proteomics/ProtXMLUploaderTest.java | 155 -
.../proteomics/ProteinDescriptionTest.java | 182 -
...einResultDataSetParentLinkingTaskTest.java | 178 -
.../proteomics/ResultDataSetUploaderTest.java | 705 -
.../TypeExtractorForMSInjectionTest.java | 84 -
.../etlserver/proteomics/UtilTest.java | 84 -
.../proteomics/DependencyCheckingTest.java | 27 -
.../api/v1/ProteomicsDataApiFacadeTest.java | 223 -
.../application/ProteinRenderersTest.java | 83 -
.../client/web/client/dto/.gitignore | 0
.../server/PhosphoNetXClientServiceTest.java | 302 -
.../web/server/RawDataSampleProviderTest.java | 231 -
.../ProteinSequenceProviderTest.java | 65 -
.../resultset/ProteinSummaryProviderTest.java | 70 -
.../server/PhosphoNetXServerTest.java | 188 -
.../ProteomicsDataServiceInternalTest.java | 449 -
.../server/ServerInterfaceRegressionTest.java | 43 -
.../api/v1/ProteomicsDataServiceTest.java | 426 -
.../api/v1/ServerInterfaceRegressionTest.java | 35 -
.../validator/RawDataSampleValidatorTest.java | 182 -
.../server/business/AbstractBOTestCase.java | 43 -
.../business/AbstractLoaderTestCase.java | 58 -
.../AbundanceColumnDefinitionTableTest.java | 169 -
.../server/business/AbundanceManagerTest.java | 170 -
.../business/AccessionNumberBuilderTest.java | 57 -
.../server/business/ErrorModelTest.java | 159 -
.../server/business/ExperimentLoaderTest.java | 78 -
.../server/business/ProteinInfoTableTest.java | 302 -
.../ProteinRelatedSampleTableTest.java | 182 -
.../business/ProteinSummaryTableTest.java | 206 -
.../server/business/SampleIDProviderTest.java | 122 -
.../server/business/SampleLoaderTest.java | 74 -
.../server/business/SampleProviderTest.java | 180 -
.../server/business/TreatmentFinderTest.java | 196 -
.../dto/AbundanceColumnDefinitionTest.java | 120 -
.../basic/dto/AggregateFunctionTest.java | 74 -
.../shared/basic/dto/OccurrenceUtilTest.java | 61 -
.../AbstractProteomicsSystemTestCase.java | 112 -
.../ProteomicsDataServiceTest.java | 201 -
.../systemtests/ServerAuthorizationTest.java | 108 -
.../CommonValidatorProteomicsSystemTest.java | 33 -
.../ParentSampleValidatorSystemTest.java | 61 -
.../RawDataSampleValidatorSystemTest.java | 62 -
.../SampleValidatorProteomicsTestService.java | 54 -
rtd_phosphonetx/sourceTest/java/tests.xml | 14 -
.../java/tests_project_authorization.xml | 12 -
.../sourceTest/java/tests_system.xml | 7 -
338 files changed, 128 insertions(+), 95214 deletions(-)
delete mode 100644 rtd_phosphonetx/.gitignore
delete mode 100644 rtd_phosphonetx/.pydevproject
delete mode 100644 rtd_phosphonetx/.shredder
delete mode 100644 rtd_phosphonetx/build.gradle
delete mode 100644 rtd_phosphonetx/etc/log.xml
delete mode 100644 rtd_phosphonetx/etc/passwd
delete mode 100644 rtd_phosphonetx/etc/passwd.sv
delete mode 100644 rtd_phosphonetx/etc/passwd.tmp
delete mode 100644 rtd_phosphonetx/etc/service.properties
delete mode 100644 rtd_phosphonetx/etc/web-client.properties
delete mode 100644 rtd_phosphonetx/gradle/wrapper/gradle-wrapper.jar
delete mode 100644 rtd_phosphonetx/gradle/wrapper/gradle-wrapper.properties
delete mode 100755 rtd_phosphonetx/gradlew
delete mode 100644 rtd_phosphonetx/gradlew.bat
delete mode 100644 rtd_phosphonetx/gwtdev.gradle
delete mode 100644 rtd_phosphonetx/resource/dependency-structure.ddf
delete mode 100644 rtd_phosphonetx/resource/eclipse/Gradle Proteomics compile GWT.launch
delete mode 100644 rtd_phosphonetx/resource/eclipse/Gradle Proteomics openBIS GWT Shell.launch
delete mode 100644 rtd_phosphonetx/resource/eclipse/Gradle Proteomics prepare GWT.launch
delete mode 100644 rtd_phosphonetx/resource/eclipse/Proteomics openBIS GWT Shell.launch
delete mode 100644 rtd_phosphonetx/resource/eclipse/phosphonetx Data Store Server.launch
delete mode 100644 rtd_phosphonetx/resource/server/spring-servlet.xml
delete mode 100644 rtd_phosphonetx/resource/server/web.xml
delete mode 100644 rtd_phosphonetx/settings.gradle
delete mode 100644 rtd_phosphonetx/source/core-plugins/core-plugins.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics-optional/package-to-dist
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/as/dss-data-sources/DSS1/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/as/initialize-master-data.py
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/as/miscellaneous/proteomics-application/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/dss/data-sources/proteomics-db/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/1/dss/maintenance-tasks/proteomics-db-clean-up/plugin.properties
delete mode 100644 rtd_phosphonetx/source/core-plugins/proteomics/package-to-dist
delete mode 100644 rtd_phosphonetx/source/html/demoapp/body-style.css
delete mode 100644 rtd_phosphonetx/source/html/demoapp/button.css
delete mode 100755 rtd_phosphonetx/source/html/demoapp/d3.js
delete mode 100755 rtd_phosphonetx/source/html/demoapp/d3.layout.js
delete mode 100644 rtd_phosphonetx/source/html/demoapp/d3.time.js
delete mode 100644 rtd_phosphonetx/source/html/demoapp/images/openBIS_Logo.png
delete mode 100644 rtd_phosphonetx/source/html/demoapp/images/openBIS_Logo.svg
delete mode 100644 rtd_phosphonetx/source/html/demoapp/openbis-demo-app.html
delete mode 100644 rtd_phosphonetx/source/html/demoapp/proteomics-demo.js
delete mode 100644 rtd_phosphonetx/source/html/demoapp/tree.css
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReport.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopier.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractDataSetInfoExtractorWithService.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractHandler.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Constants.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjection.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/IProtDAO.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFraction.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoader.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescription.java
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
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diff --git a/js-test/servers/common/datastore_server/etc/service.properties b/js-test/servers/common/datastore_server/etc/service.properties
index 1ce6fcea983..12f6613e96f 100644
--- a/js-test/servers/common/datastore_server/etc/service.properties
+++ b/js-test/servers/common/datastore_server/etc/service.properties
@@ -1,181 +1,138 @@
# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS1
-
+data-store-server-code=DSS1
# host name of the machine on which the datastore server is running
-host-address = http://localhost
-
+host-address=http://localhost
# parent directory of the store directory and all the dropboxes
-root-dir = data
-
+root-dir=data
# The root directory of the data store
-storeroot-dir = ${root-dir}/store
-
-incoming-root-dir = ${root-dir}
-
+storeroot-dir=${root-dir}/store
+incoming-root-dir=${root-dir}
# Cache for data set files from other Data Store Servers
cache-workspace-folder ${root-dir}/dss-cache
-
-# The directory where the command queue file is located; defaults to storeroot-dir
-commandqueue-dir =
-
+# The directory where the command queue file is located; defaults to storeroot-dir
+commandqueue-dir=
# Port
-port = 20001
-use-ssl = false
-
+port=20001
+use-ssl=false
# Session timeout in minutes
-session-timeout = 720
-
+session-timeout=720
# Path to the keystore
-keystore.path = etc/openBIS.keystore
+keystore.path=etc/openBIS.keystore
# Password of the keystore
-keystore.password = changeit
+keystore.password=changeit
# Key password of the keystore
-keystore.key-password = changeit
-
+keystore.key-password=changeit
# The check interval (in seconds)
-check-interval = 5
-
-quiet-period = 10
-
-data-set-locking-timeout = 1
-
+check-interval=5
+quiet-period=10
+data-set-locking-timeout=1
# The time-out for clean up work in the shutdown sequence (in seconds).
# Note that that the maximal time for the shutdown sequence to complete can be as large
# as twice this time.
# Remark: On a network file system, it is not recommended to turn this value to something
# lower than 180.
-shutdown-timeout = 180
-
+shutdown-timeout=180
# The minimum time (in seconds) of availability of the data stream since moment when user requested
# for the data stream url. If not specified default value (20 seconds) will be used.
# minimum-time-to-keep-streams-in-sec = 20
-
#�If free disk space goes below value defined here, a notification email will be sent.
# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
# specified or if value is negative, the system will not be watching. There are 2 different kinds
# of highwater mark supported: the one that is checking the space on the store, and one that is
# checking the amount of free space for recovery state (on the local filesystem).
-highwater-mark = -1
-recovery-highwater-mark = -1
-
-# If a data set is successfully registered it sends out an email to the registrator.
+highwater-mark=-1
+recovery-highwater-mark=-1
+# If a data set is successfully registered it sends out an email to the registrator.
# If this property is not specified, no email is sent to the registrator. This property
# does not affect the mails which are sent, when the data set could not be registered.
-notify-successful-registration = false
-
+notify-successful-registration=false
# The URL of the openBIS server
-server-url = ${host-address}:20000
-
+server-url=${host-address}:20000
# The username to use when contacting the openBIS server
-username = etlserver
-
+username=etlserver
# The password for the etlserver user who contacts the openBIS server
password=e1AWO4f0ro
-
# The base URL for Web client access to the data store server.
-download-url = ${host-address}:${port}
-
+download-url=${host-address}:${port}
# SMTP properties (must start with 'mail' to be considered).
# The current configuration saves the emails in the file system in the root directory
-mail.smtp.host = file://${root-dir}/email
+mail.smtp.host=file://${root-dir}/email
# mail.smtp.host = localhost
# mail.from = openbis-dss@localhost
# mail.smtp.user =
# mail.smtp.password =
-
-
# Data sources
-data-sources = path-info-db
-
+data-sources=path-info-db
# Data source for pathinfo database
-path-info-db.version-holder-class = ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
-path-info-db.databaseEngineCode = postgresql
-path-info-db.basicDatabaseName = pathinfo
+path-info-db.version-holder-class=ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
+path-info-db.databaseEngineCode=postgresql
+path-info-db.basicDatabaseName=pathinfo
# The host and optionally port. Default is 'localhost'.
# path-info-db.urlHostPart =
-path-info-db.databaseKind = test_js_common
-path-info-db.scriptFolder = ../../../../datastore_server/source/sql
-
+path-info-db.databaseKind=test_js_common
+path-info-db.scriptFolder=../../../../datastore_server/source/sql
# ---------------------------------------------------------------------------
# maintenance plugins configuration
# ---------------------------------------------------------------------------
-
# Comma separated names of maintenance plugins. Each plugin should have configuration properties prefixed with its name.
-maintenance-plugins = post-registration, path-info-deletion
-
-# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database
-post-registration.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
-post-registration.interval = 30
-post-registration.cleanup-tasks-folder = ${root-dir}/post-registration/cleanup-tasks
-post-registration.last-seen-data-set-file = ${root-dir}/post-registration/last-seen-data-set.txt
-post-registration.post-registration-tasks = pathinfo-feeding, notifying
-post-registration.pathinfo-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
-post-registration.pathinfo-feeding.compute-checksum = true
+maintenance-plugins=post-registration, path-info-deletion
+# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database
+post-registration.class=ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
+post-registration.interval=30
+post-registration.cleanup-tasks-folder=${root-dir}/post-registration/cleanup-tasks
+post-registration.last-seen-data-set-file=${root-dir}/post-registration/last-seen-data-set.txt
+post-registration.post-registration-tasks=pathinfo-feeding, notifying
+post-registration.pathinfo-feeding.class=ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
+post-registration.pathinfo-feeding.compute-checksum=true
# The NotifyingTask throws an exception. Thus, post-registration will always fail.
# This is needed to have an example of a data set which isn't post-registered.
-post-registration.notifying.class = ch.systemsx.cisd.etlserver.postregistration.NotifyingTask
-post-registration.notifying.destination-path-template = targets/${unknown-placeholder-preventing-post-registration}
-post-registration.notifying.message-template = hello
-
+post-registration.notifying.class=ch.systemsx.cisd.etlserver.postregistration.NotifyingTask
+post-registration.notifying.destination-path-template=targets/${unknown-placeholder-preventing-post-registration}
+post-registration.notifying.message-template=hello
# Maintenance task for deleting entries from pathinfo database after deletion of a data set
-path-info-deletion.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-path-info-deletion.interval = 120
-path-info-deletion.data-source = path-info-db
-path-info-deletion.data-set-table-name = data_sets
-path-info-deletion.data-set-perm-id = CODE
-
+path-info-deletion.class=ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
+path-info-deletion.interval=120
+path-info-deletion.data-source=path-info-db
+path-info-deletion.data-set-table-name=data_sets
+path-info-deletion.data-set-perm-id=CODE
# ---------------------------------------------------------------------------
# processing plugins configuration
# ---------------------------------------------------------------------------
-
# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
-processing-plugins = path-info-db-consistency-check
-
+processing-plugins=path-info-db-consistency-check
# Processing task that checks the consistency between the data store and the meta information stored in the PathInfoDB.
# It sends out an email which contains all differences found.
-path-info-db-consistency-check.label = Path Info DB consistency check
-path-info-db-consistency-check.dataset-types = .*
-path-info-db-consistency-check.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin
-
+path-info-db-consistency-check.label=Path Info DB consistency check
+path-info-db-consistency-check.dataset-types=.*
+path-info-db-consistency-check.class=ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin
# ---------------------------------------------------------------------------
# dropbox configurations
# ---------------------------------------------------------------------------
-inputs = default-dropbox
-dss-rpc.put-default = default-dropbox
-
-default-dropbox.incoming-dir = ${incoming-root-dir}/incoming-default
-default-dropbox.incoming-data-completeness-condition = auto-detection
-default-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
-default-dropbox.program-class = ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
-default-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+inputs=default-dropbox
+dss-rpc.put-default=default-dropbox
+default-dropbox.incoming-dir=${incoming-root-dir}/incoming-default
+default-dropbox.incoming-data-completeness-condition=auto-detection
+default-dropbox.top-level-data-set-handler=ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
+default-dropbox.program-class=ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
+default-dropbox.storage-processor=ch.systemsx.cisd.etlserver.DefaultStorageProcessor
#default-dropbox.validation-script-path = ../core-plugins/default/default-validation-script.py
-
# ---------------------------------------------------------------------------
# Archiver configuration (optional)
# ---------------------------------------------------------------------------
-
# Configuration of an archiver task. All properties are prefixed with 'archiver.'.
-
# Archiver class specification (together with the list of packages this class belongs to).
-archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
-
+archiver.class=ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
# ---------------------------------------------------------------------------
# Imaging database for screening (optional, only used if screening technology switched on)
# ---------------------------------------------------------------------------
# Format: <host>[:<port>]. Default: localhost
# imaging-database.url-host-part =
# Default: prod.
-
-imaging-database.kind = test_js_common
-proteomics-database-kind = test_js_common
-
-screening-sql-root-folder = ../../../../screening/source/
-proteomics-sql-root-folder = ../../../../rtd_phosphonetx/source/
-
+imaging-database.kind=test_js_common
+proteomics-database-kind=test_js_common
+screening-sql-root-folder=../../../../screening/source/
# ---------------------------------------------------------------------------
# INTERNAL CONFIGURATION,
# Do not change this part unless you are developing openBIS extensions.
# ---------------------------------------------------------------------------
-
-
jython-version=2.7
diff --git a/js-test/servers/common/datastore_server2/etc/service.properties b/js-test/servers/common/datastore_server2/etc/service.properties
index 7bc4758e4fb..646ee8ef193 100644
--- a/js-test/servers/common/datastore_server2/etc/service.properties
+++ b/js-test/servers/common/datastore_server2/etc/service.properties
@@ -1,181 +1,138 @@
# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS2
-
+data-store-server-code=DSS2
# host name of the machine on which the datastore server is running
-host-address = http://localhost
-
+host-address=http://localhost
# parent directory of the store directory and all the dropboxes
-root-dir = data
-
+root-dir=data
# The root directory of the data store
-storeroot-dir = ${root-dir}/store
-
-incoming-root-dir = ${root-dir}
-
+storeroot-dir=${root-dir}/store
+incoming-root-dir=${root-dir}
# Cache for data set files from other Data Store Servers
-cache-workspace-folder = ${root-dir}/dss-cache
-
-# The directory where the command queue file is located; defaults to storeroot-dir
-commandqueue-dir =
-
+cache-workspace-folder=${root-dir}/dss-cache
+# The directory where the command queue file is located; defaults to storeroot-dir
+commandqueue-dir=
# Port
-port = 20002
-use-ssl = false
-
+port=20002
+use-ssl=false
# Session timeout in minutes
-session-timeout = 720
-
+session-timeout=720
# Path to the keystore
-keystore.path = etc/openBIS.keystore
+keystore.path=etc/openBIS.keystore
# Password of the keystore
-keystore.password = changeit
+keystore.password=changeit
# Key password of the keystore
-keystore.key-password = changeit
-
+keystore.key-password=changeit
# The check interval (in seconds)
-check-interval = 5
-
-quiet-period = 10
-
-data-set-locking-timeout = 1
-
+check-interval=5
+quiet-period=10
+data-set-locking-timeout=1
# The time-out for clean up work in the shutdown sequence (in seconds).
# Note that that the maximal time for the shutdown sequence to complete can be as large
# as twice this time.
# Remark: On a network file system, it is not recommended to turn this value to something
# lower than 180.
-shutdown-timeout = 180
-
+shutdown-timeout=180
# The minimum time (in seconds) of availability of the data stream since moment when user requested
# for the data stream url. If not specified default value (20 seconds) will be used.
# minimum-time-to-keep-streams-in-sec = 20
-
#�If free disk space goes below value defined here, a notification email will be sent.
# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
# specified or if value is negative, the system will not be watching. There are 2 different kinds
# of highwater mark supported: the one that is checking the space on the store, and one that is
# checking the amount of free space for recovery state (on the local filesystem).
-highwater-mark = -1
-recovery-highwater-mark = -1
-
-# If a data set is successfully registered it sends out an email to the registrator.
+highwater-mark=-1
+recovery-highwater-mark=-1
+# If a data set is successfully registered it sends out an email to the registrator.
# If this property is not specified, no email is sent to the registrator. This property
# does not affect the mails which are sent, when the data set could not be registered.
-notify-successful-registration = false
-
+notify-successful-registration=false
# The URL of the openBIS server
-server-url = ${host-address}:20000
-
+server-url=${host-address}:20000
# The username to use when contacting the openBIS server
-username = etlserver
-
+username=etlserver
# The password for the etlserver user who contacts the openBIS server
password=e1AWO4f0ro
-
# The base URL for Web client access to the data store server.
-download-url = ${host-address}:${port}
-
+download-url=${host-address}:${port}
# SMTP properties (must start with 'mail' to be considered).
# The current configuration saves the emails in the file system in the root directory
-mail.smtp.host = file://${root-dir}/email
+mail.smtp.host=file://${root-dir}/email
# mail.smtp.host = localhost
# mail.from = openbis-dss@localhost
# mail.smtp.user =
# mail.smtp.password =
-
-
# Data sources
-data-sources = path-info-db
-
+data-sources=path-info-db
# Data source for pathinfo database
-path-info-db.version-holder-class = ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
-path-info-db.databaseEngineCode = postgresql
-path-info-db.basicDatabaseName = pathinfo
+path-info-db.version-holder-class=ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder
+path-info-db.databaseEngineCode=postgresql
+path-info-db.basicDatabaseName=pathinfo
# The host and optionally port. Default is 'localhost'.
# path-info-db.urlHostPart =
-path-info-db.databaseKind = test_js_common2
-path-info-db.scriptFolder = ../../../../datastore_server/source/sql
-
+path-info-db.databaseKind=test_js_common2
+path-info-db.scriptFolder=../../../../datastore_server/source/sql
# ---------------------------------------------------------------------------
# maintenance plugins configuration
# ---------------------------------------------------------------------------
-
# Comma separated names of maintenance plugins. Each plugin should have configuration properties prefixed with its name.
-maintenance-plugins = post-registration, path-info-deletion
-
-# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database
-post-registration.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
-post-registration.interval = 30
-post-registration.cleanup-tasks-folder = ${root-dir}/post-registration/cleanup-tasks
-post-registration.last-seen-data-set-file = ${root-dir}/post-registration/last-seen-data-set.txt
-post-registration.post-registration-tasks = pathinfo-feeding, notifying
-post-registration.pathinfo-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
-post-registration.pathinfo-feeding.compute-checksum = true
+maintenance-plugins=post-registration, path-info-deletion
+# Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database
+post-registration.class=ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask
+post-registration.interval=30
+post-registration.cleanup-tasks-folder=${root-dir}/post-registration/cleanup-tasks
+post-registration.last-seen-data-set-file=${root-dir}/post-registration/last-seen-data-set.txt
+post-registration.post-registration-tasks=pathinfo-feeding, notifying
+post-registration.pathinfo-feeding.class=ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask
+post-registration.pathinfo-feeding.compute-checksum=true
# The NotifyingTask throws an exception. Thus, post-registration will always fail.
# This is needed to have an example of a data set which isn't post-registered.
-post-registration.notifying.class = ch.systemsx.cisd.etlserver.postregistration.NotifyingTask
-post-registration.notifying.destination-path-template = targets/${unknown-placeholder-preventing-post-registration}
-post-registration.notifying.message-template = hello
-
+post-registration.notifying.class=ch.systemsx.cisd.etlserver.postregistration.NotifyingTask
+post-registration.notifying.destination-path-template=targets/${unknown-placeholder-preventing-post-registration}
+post-registration.notifying.message-template=hello
# Maintenance task for deleting entries from pathinfo database after deletion of a data set
-path-info-deletion.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-path-info-deletion.interval = 120
-path-info-deletion.data-source = path-info-db
-path-info-deletion.data-set-table-name = data_sets
-path-info-deletion.data-set-perm-id = CODE
-
+path-info-deletion.class=ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
+path-info-deletion.interval=120
+path-info-deletion.data-source=path-info-db
+path-info-deletion.data-set-table-name=data_sets
+path-info-deletion.data-set-perm-id=CODE
# ---------------------------------------------------------------------------
# processing plugins configuration
# ---------------------------------------------------------------------------
-
# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
-processing-plugins = path-info-db-consistency-check
-
+processing-plugins=path-info-db-consistency-check
# Processing task that checks the consistency between the data store and the meta information stored in the PathInfoDB.
# It sends out an email which contains all differences found.
-path-info-db-consistency-check.label = Path Info DB consistency check
-path-info-db-consistency-check.dataset-types = .*
-path-info-db-consistency-check.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin
-
+path-info-db-consistency-check.label=Path Info DB consistency check
+path-info-db-consistency-check.dataset-types=.*
+path-info-db-consistency-check.class=ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin
# ---------------------------------------------------------------------------
# dropbox configurations
# ---------------------------------------------------------------------------
-inputs = default-dropbox
-dss-rpc.put-default = default-dropbox
-
-default-dropbox.incoming-dir = ${incoming-root-dir}/incoming-default
-default-dropbox.incoming-data-completeness-condition = auto-detection
-default-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
-default-dropbox.program-class = ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
-default-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-default-dropbox.validation-script-path = ../core-plugins/default/default-validation-script.py
-
+inputs=default-dropbox
+dss-rpc.put-default=default-dropbox
+default-dropbox.incoming-dir=${incoming-root-dir}/incoming-default
+default-dropbox.incoming-data-completeness-condition=auto-detection
+default-dropbox.top-level-data-set-handler=ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
+default-dropbox.program-class=ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
+default-dropbox.storage-processor=ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+default-dropbox.validation-script-path=../core-plugins/default/default-validation-script.py
# ---------------------------------------------------------------------------
# Archiver configuration (optional)
# ---------------------------------------------------------------------------
-
# Configuration of an archiver task. All properties are prefixed with 'archiver.'.
-
# Archiver class specification (together with the list of packages this class belongs to).
-archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
-
+archiver.class=ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver
# ---------------------------------------------------------------------------
# Imaging database for screening (optional, only used if screening technology switched on)
# ---------------------------------------------------------------------------
# Format: <host>[:<port>]. Default: localhost
# imaging-database.url-host-part =
# Default: prod.
-
-imaging-database.kind = test_js_common2
-proteomics-database-kind = test_js_common2
-
-screening-sql-root-folder = ../../../../screening/source/
-proteomics-sql-root-folder = ../../../../rtd_phosphonetx/source/
-
+imaging-database.kind=test_js_common2
+proteomics-database-kind=test_js_common2
+screening-sql-root-folder=../../../../screening/source/
# ---------------------------------------------------------------------------
# INTERNAL CONFIGURATION,
# Do not change this part unless you are developing openBIS extensions.
# ---------------------------------------------------------------------------
-
-
jython-version=2.7
diff --git a/openbis_all/build/build.xml b/openbis_all/build/build.xml
index 42907f391a0..c1b51dec44c 100644
--- a/openbis_all/build/build.xml
+++ b/openbis_all/build/build.xml
@@ -20,10 +20,6 @@
<param name="project" value="deep_sequencing_unit" />
<param name="pattern" value="*"/>
</antcall>
- <antcall target="_dist">
- <param name="project" value="rtd_phosphonetx" />
- <param name="pattern" value="*"/>
- </antcall>
<antcall target="_dist">
<param name="project" value="rtd_yeastx" />
<param name="pattern" value="*"/>
@@ -91,9 +87,6 @@
<antcall target="_clean">
<param name="project" value="deep_sequencing_unit"/>
</antcall>
- <antcall target="_clean">
- <param name="project" value="rtd_phosphonetx"/>
- </antcall>
<antcall target="_clean">
<param name="project" value="rtd_yeastx"/>
</antcall>
diff --git a/openbis_all/source/bash/build/branch.sh b/openbis_all/source/bash/build/branch.sh
index 0541401e60c..e046ba9c880 100755
--- a/openbis_all/source/bash/build/branch.sh
+++ b/openbis_all/source/bash/build/branch.sh
@@ -39,7 +39,6 @@ openbis-common \
openbis_standard_technologies \
openbis_api \
plasmid \
-rtd_phosphonetx \
rtd_yeastx \
screening \
ui-test\
diff --git a/rtd_phosphonetx/.gitignore b/rtd_phosphonetx/.gitignore
deleted file mode 100644
index 8186f94570a..00000000000
--- a/rtd_phosphonetx/.gitignore
+++ /dev/null
@@ -1,11 +0,0 @@
-/etc
-/tomcat
-/targets
-/test-output
-/.updater
-/.dynamic_property_evaluator_queue
-/bin
-/build/
-/.idea/
-*.iml
-*.eml
\ No newline at end of file
diff --git a/rtd_phosphonetx/.pydevproject b/rtd_phosphonetx/.pydevproject
deleted file mode 100644
index a9cca037b33..00000000000
--- a/rtd_phosphonetx/.pydevproject
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?eclipse-pydev version="1.0"?>
-
-<pydev_project>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
-</pydev_project>
diff --git a/rtd_phosphonetx/.shredder b/rtd_phosphonetx/.shredder
deleted file mode 100644
index 2e08dce276e43c677d121d627a250d1710fed824..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 12
Rcmeyd#OO5x0|O5T0{|U20@45g
diff --git a/rtd_phosphonetx/build.gradle b/rtd_phosphonetx/build.gradle
deleted file mode 100644
index a53a350ca62..00000000000
--- a/rtd_phosphonetx/build.gradle
+++ /dev/null
@@ -1,58 +0,0 @@
-evaluationDependsOn(':commonbase')
-evaluationDependsOn(':common')
-evaluationDependsOn(':openbis_api')
-evaluationDependsOn(':openbis-common')
-evaluationDependsOn(':authentication')
-evaluationDependsOn(':dbmigration')
-evaluationDependsOn(':openbis')
-evaluationDependsOn(':datastore_server')
-
-apply from: '../gradle/javaproject.gradle'
-
-dependencies {
- compile project(':common'),
- project(':datastore_server')
-
- testCompile project(path: ':datastore_server', configuration: 'tests')
-
-}
-
-sourceSets {
- test {
- resources {
- srcDirs = ['source/java']
- }
- }
-}
-
-jar {
- from('../rtd_phosphonetx/source/sql'){
- into("/sql")
- include "proteomics/**/*.sql"
- }
-}
-
-task systemTestSuite(type: Test) {
- useTestNG()
- options.suites('sourceTest/java/tests_system.xml')
- jvmArgs '-Xmx2048m', '-XX:MaxPermSize=256m'
- reports.html.destination = file("${project.buildDir}/reports/tests-system")
-}
-
-test.dependsOn(systemTestSuite)
-
-task zip(type: Zip) {
- includeEmptyDirs false
- from (jar.archivePath) {
- into 'datastore_server/lib/'
- rename 'datastore_server_plugin-proteomics(.*)\\.jar', 'datastore_server_plugin-proteomics.jar'
- }
-
- from (fileTree(dir: 'source/core-plugins', includes:['proteomics/**', 'proteomics-optional/**'], excludes:['**/as/**', '**/package-to-dist'])) {
- into 'core-plugins'
- }
-}
-zip.dependsOn jar
-build.dependsOn zip
-
-apply from: 'gwtdev.gradle'
diff --git a/rtd_phosphonetx/etc/log.xml b/rtd_phosphonetx/etc/log.xml
deleted file mode 100644
index 5cee0a68436..00000000000
--- a/rtd_phosphonetx/etc/log.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
-
-<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
-
- <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
- <layout class="org.apache.log4j.PatternLayout">
- <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
- </layout>
- </appender>
-
- <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
-
- <root>
- <priority value ="info" />
- <appender-ref ref="STDOUT" />
- </root>
-
-</log4j:configuration>
diff --git a/rtd_phosphonetx/etc/passwd b/rtd_phosphonetx/etc/passwd
deleted file mode 100644
index 6ead36251a5..00000000000
--- a/rtd_phosphonetx/etc/passwd
+++ /dev/null
@@ -1,4 +0,0 @@
-test:a@admins.com:A:The Admin:J3fII6Pex7jnCBwF+uXz2mFuB1QVhPUi
-u:u@users.com:U:The User:dmbGKaGRmbX8YKfslMxUHObmYfjywkuT
-o:o@observers.com:O:The Observer:t53ADCnFnEFhBvHB7FPoHhbHeW2O1KJc
-etlserver::::SHGHSPawL/B3NKXD5nsu4fSrj5LwR2MX
diff --git a/rtd_phosphonetx/etc/passwd.sv b/rtd_phosphonetx/etc/passwd.sv
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/etc/passwd.tmp b/rtd_phosphonetx/etc/passwd.tmp
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
deleted file mode 100644
index 3db2ce8d811..00000000000
--- a/rtd_phosphonetx/etc/service.properties
+++ /dev/null
@@ -1,115 +0,0 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS1
-
-root-dir = targets/playground
-
-# The root directory of the data store
-storeroot-dir = ${root-dir}/data/store
-
-incoming-root-dir = ${root-dir}/data
-
-core-plugins-folder = source/core-plugins
-
-proteomics-database-kind = dev
-proteomics-sql-root-folder = source/
-
-session-workspace-root-dir = ${incoming-root-dir}/session-workspace
-
-dss-rpc.put-default = default-dropbox
-
-# The directory where the command queue file is located; defaults to storeroot-dir
-commandqueue-dir =
-
-# Port
-port = 8889
-
-# Session timeout in minutes
-session-timeout = 720
-
-# Path to the keystore
-keystore.path = ../datastore_server/dist/etc/openBIS.keystore
-
-# Password of the keystore
-keystore.password = changeit
-
-# Key password of the keystore
-keystore.key-password = changeit
-
-# The check interval (in seconds)
-check-interval = 5
-
-# The time-out for clean up work in the shutdown sequence (in seconds).
-# Note that that the maximal time for the shutdown sequence to complete can be as large
-# as twice this time.
-# Remark: On a network file system, it is not recommended to turn this value to something
-# lower than 180.
-shutdown-timeout = 2
-
-# If free disk space goes below value defined here, a notification email will be sent.
-# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
-# specified or if value is negative, the system will not be watching.
-highwater-mark = -1
-
-# If a data set is successfully registered it sends out an email to the registrator.
-# If this property is not specified, no email is sent to the registrator. This property
-# does not affect the mails which are sent, when the data set could not be registered.
-notify-successful-registration = false
-
-dss-temp-dir = ${root-dir}/dss-temp
-dss-registration-log-dir = ${root-dir}/dss-registration-logs
-dss-recovery-state-dir = ${root-dir}/recovery-state
-
-use-ssl = false
-
-# The URL of the openBIS server
-server-url = http://localhost:8888/openbis
-server-timeout-in-minutes = 10
-
-# The username to use when contacting the openBIS server
-username = etlserver
-
-# The password to use when contacting the openBIS server
-password = etlserver
-
-# The base URL for Web client access.
-download-url = http://localhost:8889
-
-# SMTP properties (must start with 'mail' to be considered).
-mail.smtp.host = file://targets/email
-mail.from = datastore_server@localhost
-
-# ---------------- Timing parameters for file system operations on remote shares.
-
-# Time (in seconds) to wait for any file system operation to finish. Operations exceeding this
-# timeout will be terminated.
-timeout = 60
-# Number of times that a timed out operation will be tried again (0 means: every file system
-# operation will only ever be performed once).
-max-retries = 11
-# Time (in seconds) to wait after an operation has been timed out before re-trying.
-failure-interval = 10
-
-# The period of no write access that needs to pass before an incoming data item is considered
-# complete and ready to be processed (in seconds) [default: 300].
-# Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
-quiet-period = 10
-
-# ---------------------------------------------------------------------------
-
-# Globally used separator character which separates entities in a data set file name
-data-set-file-name-entity-separator = _
-
-# ---------------------------------------------------------------------------
-# dropbox configurations
-# ---------------------------------------------------------------------------
-inputs = default-dropbox
-dss-rpc.put-default = default-dropbox
-
-default-dropbox.incoming-dir = ${incoming-root-dir}/incoming-default
-default-dropbox.incoming-data-completeness-condition = auto-detection
-default-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
-default-dropbox.program-class = ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
-default-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-
-
-jython-version=2.7
diff --git a/rtd_phosphonetx/etc/web-client.properties b/rtd_phosphonetx/etc/web-client.properties
deleted file mode 100644
index dc67a8589bc..00000000000
--- a/rtd_phosphonetx/etc/web-client.properties
+++ /dev/null
@@ -1,12 +0,0 @@
-# Maximal number of visible columns in tables. Default: 50.
-max-visible-columns = 15
-enable-trash = true
-
-technologies = proteomics
-
-# Relative path of cache. Default value is 'cache'.
-proteomics.cache-folder = targets/cache
-# Minimum free disk space needed for the cache. Default value is 1 GB.
-#proteomics.minimum-free-disk-space-in-MB = 1024
-# Maximum retention time. Data older than this time will be removed from cache. Default value is a week.
-#proteomics.maximum-retention-time-in-days = 7
diff --git a/rtd_phosphonetx/gradle/wrapper/gradle-wrapper.jar b/rtd_phosphonetx/gradle/wrapper/gradle-wrapper.jar
deleted file mode 100644
index 05a89ea194c2a29cec5f0bd3df21c3e8e1a81b78..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/rtd_phosphonetx/gradle/wrapper/gradle-wrapper.properties b/rtd_phosphonetx/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 3cf832e831f..00000000000
--- a/rtd_phosphonetx/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-distributionUrl=http\://svnsis.ethz.ch/repos/cisd/ivy-repository/trunk/gradle/distribution/5.6.4/gradle-5.6.4-all.zip
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
diff --git a/rtd_phosphonetx/gradlew b/rtd_phosphonetx/gradlew
deleted file mode 100755
index 4453ccea33d..00000000000
--- a/rtd_phosphonetx/gradlew
+++ /dev/null
@@ -1,172 +0,0 @@
-#!/usr/bin/env sh
-
-##############################################################################
-##
-## Gradle start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn ( ) {
- echo "$*"
-}
-
-die ( ) {
- echo
- echo "$*"
- echo
- exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
- fi
- i=$((i+1))
- done
- case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
-fi
-
-# Escape application args
-save ( ) {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
-
-exec "$JAVACMD" "$@"
diff --git a/rtd_phosphonetx/gradlew.bat b/rtd_phosphonetx/gradlew.bat
deleted file mode 100644
index e95643d6a2c..00000000000
--- a/rtd_phosphonetx/gradlew.bat
+++ /dev/null
@@ -1,84 +0,0 @@
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
diff --git a/rtd_phosphonetx/gwtdev.gradle b/rtd_phosphonetx/gwtdev.gradle
deleted file mode 100644
index 072841cf7be..00000000000
--- a/rtd_phosphonetx/gwtdev.gradle
+++ /dev/null
@@ -1,95 +0,0 @@
-configurations.create('gwt')
-if (System.getProperty("openbis.development-build") != null) {
- configurations.gwt {
- transitive = false
- }
-
- dependencies {
- gwt 'reveregroup:gwt-image-loader:1.1.4',
- 'google:gwt-dev:2.4',
- 'google:gwt-user:2.4',
- 'google:gwt-debug-panel:1.0',
- 'sencha:gxt:2.2.5',
- 'sis:sis-base:18.09.0',
- 'fasterxml:jackson-annotations:2.9.10',
- project(':common'),
- project(path:':common', configuration: 'archives'),
- project(path:':openbis_api'),
- project(path:':openbis_api', configuration: 'archives'),
- project(path:':openbis-common'),
- project(path:':openbis-common', configuration: 'archives'),
- project(path:':openbis'),
- project(path:':openbis', configuration: 'archives'),
- project(path:':rtd_phosphonetx', configuration: 'archives')
- }
-}
-
-task deleteGWT(type: Exec) {
- executable "rm"
- args "-rf", "${project.projectDir.absolutePath}/.gwt-cache", "${project.projectDir.absolutePath}/targets/www"
-}
-
-task prepareGWT(type:Copy, dependsOn: [deleteGWT, compileJava]) {
- from 'resource/server'
- from files('../common/resource/server') {
- exclude 'gwt.xml'
- }
- from file('../openbis/resource/server/bis-common.xml')
- into 'targets/www/WEB-INF'
-
- from (project.configurations.runtime.files) {
- into 'lib'
- exclude 'cisd-cifex*'
- exclude 'common-*'
- exclude 'authentication-*'
- exclude 'dbmigration-*'
- exclude 'openbis-common-*'
- exclude 'openbis_api-*'
- exclude 'openbis-*'
- exclude 'datastore_server-*'
- }
-
- from ('source/java/service.properties') {
- into 'classes'
- }
-
- doLast {
- file("targets/www/WEB-INF/gwt.xml").createNewFile()
- }
-}
-
-task compileGWTToTemp(type: JavaExec, dependsOn: prepareGWT) {
- //inputs.source
- sourceSets.main.java.srcDirs
- inputs.dir sourceSets.main.output.resourcesDir
- outputs.dir 'targets/www/gwt-temp'
-
- main = 'com.google.gwt.dev.Compiler'
- maxHeapSize = '1024m'
- classpath {
- [
- sourceSets.main.java.srcDirs,
- project(":openbis").sourceSets.main.java.srcDirs,
- project(":openbis").sourceSets.main.output.resourcesDir,
- project(":openbis").sourceSets.main.output.classesDirs,
- project(":openbis").sourceSets.main.compileClasspath,
- project(":common").sourceSets.main.java.srcDirs,
- project(":openbis_api").sourceSets.main.java.srcDirs,
- project(":rtd_phosphonetx").sourceSets.main.java.srcDirs,
- project(":rtd_phosphonetx").sourceSets.main.output.resourcesDir,
- configurations.gwt
- ]
- }
- args = [ '-war',
- 'targets/www/gwt-temp',
- "ch.systemsx.cisd.openbis.plugin.proteomics.OpenBISSafari",
- '-draftCompile',
- '-style', 'PRETTY',
- '-logLevel', 'INFO']
-}
-
-task compileGWT(type: Copy, dependsOn: compileGWTToTemp) {
- from "targets/www/gwt-temp/ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS"
- into "targets/www/openbis-test-proteomics"
-}
-
diff --git a/rtd_phosphonetx/resource/dependency-structure.ddf b/rtd_phosphonetx/resource/dependency-structure.ddf
deleted file mode 100644
index 5597c17019c..00000000000
--- a/rtd_phosphonetx/resource/dependency-structure.ddf
+++ /dev/null
@@ -1,50 +0,0 @@
-#
-#
-#
-#show allResults
-
-{root} = ch.systemsx.cisd.openbis
-{generic} = ${root}.generic
-{proteomics} = ${root}.plugin.proteomics
-
-######################################################################
-# Check dependencies to openbis
-
-[etlserver] = ${root}.etlserver.proteomics.*
-[private_openbis] = ${root}.* excluding [etlserver] ${root}.dss.generic.shared.* ${root}.generic.shared.* ${proteomics}.shared.* ${root}.common.*
-
-check sets [etlserver]
-
-check [etlserver] independentOf [private_openbis]
-
-######################################################################
-# Check plugin dependencies
-#
-[proteomics.client] = ${proteomics}.client.*
-[proteomics.server] = ${proteomics}.server.*
-[proteomics.shared] = ${proteomics}.shared.*
-[other.client] = ${generic}.client.* ${root}.plugin.*.client excluding [proteomics.client]
-[other.server] = ${generic}.server.* ${root}.plugin.*.server excluding [proteomics.server]
-
-check sets [proteomics.client] [proteomics.server] [proteomics.shared]
-
-layer proteomics.client-server = [proteomics.client] [proteomics.server]
-layer proteomics.shared = [proteomics.shared]
-check layeringOf proteomics.shared proteomics.client-server
-
-check [proteomics.client] independentOf [other.server]
-check [proteomics.server] independentOf [other.client]
-
-######################################################################
-# Check API
-#
-
-[api-shared] = ${root}.generic.shared.api.* ${proteomics}.shared.api.*
-[api-client] = ${proteomics}.client.api.*
-[everything-except-java] = * excluding java* *.annotation.* ch.systemsx.cisd.common.api.IRpcService
-[everything-except-java-and-api-shared] = [everything-except-java] excluding [api-shared] ${root}.common.api.client.* ch.systemsx.cisd.common.api.retry.*
-
-check sets [api-shared] [api-client]
-
-check [api-shared] independentOf [everything-except-java]
-check [api-client] independentOf [everything-except-java-and-api-shared]
diff --git a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics compile GWT.launch b/rtd_phosphonetx/resource/eclipse/Gradle Proteomics compile GWT.launch
deleted file mode 100644
index 5be10595461..00000000000
--- a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics compile GWT.launch
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.springsource.ide.eclipse.gradle.launch">
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.PGM_ARGS" value="-Dopenbis.development-build=true"/>
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.PROJECT" value="gradle"/>
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.TASKTEXT" value=":rtd_phosphonetx:compileGWT "/>
-</launchConfiguration>
diff --git a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics openBIS GWT Shell.launch b/rtd_phosphonetx/resource/eclipse/Gradle Proteomics openBIS GWT Shell.launch
deleted file mode 100644
index 45a3c674d3d..00000000000
--- a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics openBIS GWT Shell.launch
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/rtd_phosphonetx"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
-<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER" javaProject="rtd_phosphonetx" path="1" type="4"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/gwt2.4/gwt-dev.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/authentication/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/common/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/datastore_server/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/dbmigration/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis_api/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis-common/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/rtd_phosphonetx/targets/classes" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/authentication/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/common/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/datastore_server/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/dbmigration/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis_api/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis-common/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/rtd_phosphonetx/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.jdt.launching.classpathentry.defaultClasspath"> <memento exportedEntriesOnly="false" project="rtd_phosphonetx"/> </runtimeClasspathEntry> "/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.google.gwt.dev.DevMode"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-startupUrl ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS/index.html ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS -war targets/www -logLevel WARN"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="rtd_phosphonetx"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Dpython.path=../libraries/jython/jython-lib -Dlog4j.configuration=../openbis/etc/log.xml -Djavax.net.ssl.trustStore=../openbis/dist/server/openBIS.keystore -Dorg.mortbay.util.FileResource.checkAliases=false -Xmx2048m -XX:MaxPermSize=512m -ea"/>
-</launchConfiguration>
diff --git a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics prepare GWT.launch b/rtd_phosphonetx/resource/eclipse/Gradle Proteomics prepare GWT.launch
deleted file mode 100644
index 52ab66e7968..00000000000
--- a/rtd_phosphonetx/resource/eclipse/Gradle Proteomics prepare GWT.launch
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.springsource.ide.eclipse.gradle.launch">
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.PGM_ARGS" value="-Dopenbis.development-build=true"/>
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.PROJECT" value="gradle"/>
-<stringAttribute key="org.springsource.ide.eclipse.gradle.launch.TASKTEXT" value=":rtd_phosphonetx:prepareGWT "/>
-</launchConfiguration>
diff --git a/rtd_phosphonetx/resource/eclipse/Proteomics openBIS GWT Shell.launch b/rtd_phosphonetx/resource/eclipse/Proteomics openBIS GWT Shell.launch
deleted file mode 100644
index 047a0d656b2..00000000000
--- a/rtd_phosphonetx/resource/eclipse/Proteomics openBIS GWT Shell.launch
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/rtd_phosphonetx"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER" javaProject="rtd_phosphonetx" path="1" type="4"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/gwt2.4/gwt-dev.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry id="org.eclipse.jdt.launching.classpathentry.defaultClasspath"> <memento exportedEntriesOnly="false" project="rtd_phosphonetx"/> </runtimeClasspathEntry> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/rtd_phosphonetx/source/java" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/openbis/source/java" path="3" type="2"/> "/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.google.gwt.dev.DevMode"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-startupUrl ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS/index.html ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS -war targets/www -logLevel WARN"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="rtd_phosphonetx"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Dpython.path=../libraries/jython/jython-lib -Dlog4j.configuration=../openbis/etc/log.xml -Djavax.net.ssl.trustStore=../openbis/dist/server/openBIS.keystore -Dorg.mortbay.util.FileResource.checkAliases=false -Xmx2048m -XX:MaxPermSize=512m -ea"/>
-</launchConfiguration>
diff --git a/rtd_phosphonetx/resource/eclipse/phosphonetx Data Store Server.launch b/rtd_phosphonetx/resource/eclipse/phosphonetx Data Store Server.launch
deleted file mode 100644
index 258a7dbb822..00000000000
--- a/rtd_phosphonetx/resource/eclipse/phosphonetx Data Store Server.launch
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="1"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="ch.systemsx.cisd.openbis.dss.generic.DataStoreServer"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="rtd_phosphonetx"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-ea"/>
-</launchConfiguration>
diff --git a/rtd_phosphonetx/resource/server/spring-servlet.xml b/rtd_phosphonetx/resource/server/spring-servlet.xml
deleted file mode 100644
index c209198e6c1..00000000000
--- a/rtd_phosphonetx/resource/server/spring-servlet.xml
+++ /dev/null
@@ -1,38 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xmlns:context="http://www.springframework.org/schema/context"
- xsi:schemaLocation="
- http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/tx
- http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context-2.5.xsd">
-
- <!--
- // Note: obviously it is not possible to have a mix of 'urlMappings' and annotated configuration.
- -->
- <context:annotation-config />
-
- <context:component-scan base-package="ch.systemsx.cisd.openbis" use-default-filters="false">
- <context:include-filter type="annotation"
- expression="org.springframework.stereotype.Controller" />
- </context:component-scan>
-
- <context:component-scan base-package="ch.ethz.sis.openbis" use-default-filters="false">
- <context:include-filter type="annotation"
- expression="org.springframework.stereotype.Controller" />
- </context:component-scan>
-
- <!--
- // Commons-based implementation of the MultipartResolver interface.
- // Needs 'commons-fileupload' library.
- -->
- <bean id="multipartResolver"
- class="org.springframework.web.multipart.commons.CommonsMultipartResolver">
- <!-- Default is 10240 (10kB). Set to 1MB (1048576). -->
- <property name="maxInMemorySize" value="1048576" />
- </bean>
-</beans>
diff --git a/rtd_phosphonetx/resource/server/web.xml b/rtd_phosphonetx/resource/server/web.xml
deleted file mode 100644
index 89daa03c6f5..00000000000
--- a/rtd_phosphonetx/resource/server/web.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE web-app [
- <!ENTITY common SYSTEM "web-common.xml">
- <!ENTITY biscommon SYSTEM "bis-common.xml">
-]>
-<web-app>
-
- <display-name>openBIS</display-name>
- <description>openBIS server</description>
-
- &common;
-
- <context-param>
- <param-name>contextConfigLocation</param-name>
- <param-value>classpath:proteomics-applicationContext.xml</param-value>
- <description>File for Spring beans.</description>
- </context-param>
-
- <context-param>
- <param-name>infoClass</param-name>
- <param-value>ch.systemsx.cisd.openbis.plugin.proteomics.BuildAndEnvironmentInfo</param-value>
- </context-param>
-
- &biscommon;
-
- <!--
- // Additional servlets
- -->
-
-</web-app>
diff --git a/rtd_phosphonetx/settings.gradle b/rtd_phosphonetx/settings.gradle
deleted file mode 100644
index 33440dae995..00000000000
--- a/rtd_phosphonetx/settings.gradle
+++ /dev/null
@@ -1 +0,0 @@
-includeFlat 'commonbase', 'common', 'openbis_api', 'openbis-common', 'authentication', 'dbmigration', 'openbis', 'datastore_server'
diff --git a/rtd_phosphonetx/source/core-plugins/core-plugins.properties b/rtd_phosphonetx/source/core-plugins/core-plugins.properties
deleted file mode 100644
index 5da5ded3e0b..00000000000
--- a/rtd_phosphonetx/source/core-plugins/core-plugins.properties
+++ /dev/null
@@ -1,16 +0,0 @@
-#
-# Properties for enabling/disabling core plugins
-#
-
-#
-# List of comma-separated regular expressions. If a technology (i.e. module) from the core plugins
-# folder is matching one of these regular expressions it is enabled.
-# By default all technologies are disabled.
-#
-enabled-modules = proteomics, dev-.*
-
-#
-# List of comma-separated full core plugin names (or prefixes) of core plugins to be disabled
-# even though they are in an enabled technology.
-#
-#disabled-core-plugins =
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/plugin.properties b/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/plugin.properties
deleted file mode 100644
index ca456755976..00000000000
--- a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/plugin.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-label = Demo Proteomics Aggregation
-class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
-script-path = script.py
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py b/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
deleted file mode 100644
index d9b0b260950..00000000000
--- a/rtd_phosphonetx/source/core-plugins/dev-demo/1/dss/reporting-plugins/demo-proteomics-aggregation/script.py
+++ /dev/null
@@ -1,122 +0,0 @@
-from java.util import ArrayList
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClauseAttribute
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import SearchOperator
-
-BIO_EXPERIMENT = "Biological Experiment"
-BIO_SAMPLE = "Biological Sample"
-MS_SAMPLE = "MS Injection Sample"
-SEARCH_EXPERIMENT = "Search Experiment"
-SEARCH_EXPERIMENT_PERM_ID = "Search Experiment Perm ID"
-ACCESION_NUMBER = "Accession Number"
-DESCRIPTION = "Protein Description"
-
-def countFiles(node):
- sum = 1
- if node.isDirectory():
- for child in node.getChildNodes():
- sum = sum + countFiles(child)
- return sum
-
-
-def gatherExperimentsAndSamples(space):
- bioSample2ExperimentDict = {}
- msInjectionSample2bioSamplesDict = {}
- searchExperiment2msInjectionSamplesDict = {}
- searchExperimentsByPermIdDict = {}
- searchCriteria = SearchCriteria()
- subCriteria = SearchCriteria()
- subCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "BIO*"))
- searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(subCriteria))
- bioSamples = searchService.searchForSamples(searchCriteria)
- searchCriteria = SearchCriteria()
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "MS_INJECTION"))
- subCriteria = SearchCriteria()
- subCriteria.operator = SearchOperator.MATCH_ANY_CLAUSES
- for sample in bioSamples:
- if space == sample.space:
- bioSample2ExperimentDict[sample.sampleIdentifier] = sample.experiment.experimentIdentifier
- subCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, sample.code))
-
- if len(bioSample2ExperimentDict) > 0:
- searchCriteria.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(subCriteria))
- msInjectionSamples = searchService.searchForSamples(searchCriteria)
- if len(msInjectionSamples) > 0:
- searchCriteria = SearchCriteria()
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, "SEARCH"))
- subCriteria = SearchCriteria()
- subCriteria.operator = SearchOperator.MATCH_ANY_CLAUSES
- for sample in msInjectionSamples:
- msInjectionSample2bioSamplesDict[sample.sampleIdentifier] = sample.parentSampleIdentifiers
- subCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, sample.code))
- searchCriteria.addSubCriteria(SearchSubCriteria.createSampleParentCriteria(subCriteria))
- searchSamples = searchService.searchForSamples(searchCriteria)
- for sample in searchSamples:
- experiment = sample.experiment
- searchExperimentsByPermIdDict[experiment.permId] = experiment
- expId = experiment.experimentIdentifier
- for msInjectionSample in sample.parentSampleIdentifiers:
- if expId in searchExperiment2msInjectionSamplesDict:
- searchExperiment2msInjectionSamplesDict[expId].append(msInjectionSample)
- else:
- searchExperiment2msInjectionSamplesDict[expId] = [msInjectionSample]
- return bioSample2ExperimentDict, msInjectionSample2bioSamplesDict, \
- searchExperiment2msInjectionSamplesDict, searchExperimentsByPermIdDict
-
-def createPermIdList(searchExperimentsByPermIdDict):
- permIds = ""
- for exp in searchExperimentsByPermIdDict.values():
- if len(permIds) > 0:
- permIds = permIds + ", "
- permIds = permIds + "'" + exp.permId + "'"
- return permIds
-
-def aggregate(parameters, tableBuilder):
- space = parameters.get('space').upper()
- bioSample2ExperimentDict, msInjectionSample2bioSamplesDict, \
- searchExperiment2msInjectionSamplesDict, searchExperimentsByPermIdDict \
- = gatherExperimentsAndSamples(space)
-
- tableBuilder.addHeader(BIO_EXPERIMENT)
- tableBuilder.addHeader(BIO_SAMPLE)
- tableBuilder.addHeader(MS_SAMPLE)
- tableBuilder.addHeader(SEARCH_EXPERIMENT)
- tableBuilder.addHeader(SEARCH_EXPERIMENT_PERM_ID)
- tableBuilder.addHeader(ACCESION_NUMBER)
- tableBuilder.addHeader(DESCRIPTION)
- if len(searchExperimentsByPermIdDict) == 0:
- return
- protein = '%' + parameters.get('protein') + '%'
- permIds = createPermIdList(searchExperimentsByPermIdDict)
- result = queryService.select("proteomics-db",
- """select e.perm_id, accession_number, description
- from experiments as e join data_sets as d on d.expe_id = e.id
- join proteins as p on p.dase_id = d.id
- join identified_proteins as ip on ip.prot_id = p.id
- join sequences as s on ip.sequ_id = s.id
- join protein_references as pr on s.prre_id = pr.id
- where e.perm_id in ("""
- + permIds +
- """) and (accession_number like ?{1} or description like ?{1})
- order by perm_id""",
- [protein])
- for resultRow in result:
- permId = resultRow.get('perm_id')
- if (permId in searchExperimentsByPermIdDict):
- experiment = searchExperimentsByPermIdDict[permId]
- expId = experiment.experimentIdentifier
- msInjectionSamples = searchExperiment2msInjectionSamplesDict[expId]
- for msInjectionSample in msInjectionSamples:
- bioSamples = msInjectionSample2bioSamplesDict[msInjectionSample]
- for bioSample in bioSamples:
- bioExperiment = bioSample2ExperimentDict[bioSample]
- row = tableBuilder.addRow()
- row.setCell(BIO_EXPERIMENT, bioExperiment)
- row.setCell(BIO_SAMPLE, bioSample)
- row.setCell(MS_SAMPLE, msInjectionSample)
- row.setCell(SEARCH_EXPERIMENT, expId)
- row.setCell(SEARCH_EXPERIMENT_PERM_ID, permId)
- row.setCell(ACCESION_NUMBER, resultRow.get('accession_number'))
- row.setCell(DESCRIPTION, resultRow.get('description'))
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py b/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
deleted file mode 100644
index 0b4de321b86..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics-optional/1/as/initialize-master-data.py
+++ /dev/null
@@ -1,81 +0,0 @@
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-tr = service.transaction()
-
-file_type_HTML = tr.getOrCreateNewFileFormatType('HTML')
-file_type_HTML.setDescription('HTML File')
-
-file_type_MZDATA = tr.getOrCreateNewFileFormatType('MZDATA')
-file_type_MZDATA.setDescription('Mass spectrometry data format.')
-
-file_type_MZML = tr.getOrCreateNewFileFormatType('MZML')
-file_type_MZML.setDescription('Mass spectrometry data format. \
-Unifiying mzXML and mzData formats, as released at the \
-2008 American Society for Mass Spectrometry Meeting.')
-
-file_type_MZXML = tr.getOrCreateNewFileFormatType('MZXML')
-file_type_MZXML.setDescription('Mass spectrometry data format.')
-
-file_type_RAW = tr.getOrCreateNewFileFormatType('RAW')
-file_type_RAW.setDescription('Proprietary file format for Thermo mass sepectrometry data.')
-
-file_type_TGZ = tr.getOrCreateNewFileFormatType('TGZ')
-file_type_TGZ.setDescription('gzipped tar')
-
-file_type_WIFF = tr.getOrCreateNewFileFormatType('WIFF')
-file_type_WIFF.setDescription('Proprieatry file format for Sciex and Agilent mass spectrometry data.')
-
-file_type_ZIP = tr.getOrCreateNewFileFormatType('ZIP')
-file_type_ZIP.setDescription('A zipped package')
-
-vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE')
-
-vocabulary_term_TREATMENT_TYPE_PH = tr.createNewVocabularyTerm('PH')
-vocabulary_term_TREATMENT_TYPE_PH.setDescription(None)
-vocabulary_term_TREATMENT_TYPE_PH.setUrl(None)
-vocabulary_term_TREATMENT_TYPE_PH.setLabel('ph')
-vocabulary_term_TREATMENT_TYPE_PH.setOrdinal(1)
-vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
-
-exp_type_BIOLOGICAL_EXPERIMENT = tr.getOrCreateNewExperimentType('BIOLOGICAL_EXPERIMENT')
-exp_type_BIOLOGICAL_EXPERIMENT.setDescription('A biological experiment')
-
-exp_type_MS_INJECT = tr.getOrCreateNewExperimentType('MS_INJECT')
-exp_type_MS_INJECT.setDescription('MS injection experiment')
-
-exp_type_MS_QUANTIFICATION = tr.getOrCreateNewExperimentType('MS_QUANTIFICATION')
-exp_type_MS_QUANTIFICATION.setDescription('Quantification of LC-MS data')
-
-data_set_type_MZXML_DATA = tr.getOrCreateNewDataSetType('MZXML_DATA')
-data_set_type_MZXML_DATA.setDescription('standardized format for ms data')
-
-data_set_type_RAW_DATA = tr.getOrCreateNewDataSetType('RAW_DATA')
-data_set_type_RAW_DATA.setDescription(None)
-
-prop_type_PARENTDATASETCODES = tr.getOrCreateNewPropertyType('PARENT-DATA-SET-CODES', DataType.VARCHAR)
-prop_type_PARENTDATASETCODES.setLabel('Parent Dataset Codes')
-prop_type_PARENTDATASETCODES.setManagedInternally(False)
-prop_type_PARENTDATASETCODES.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE1 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE1', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE1.setLabel('Treatment Type 1')
-prop_type_TREATMENT_TYPE1.setManagedInternally(False)
-prop_type_TREATMENT_TYPE1.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE1.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-prop_type_TREATMENT_TYPE2 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE2', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE2.setLabel('Treatment Type 2')
-prop_type_TREATMENT_TYPE2.setManagedInternally(False)
-prop_type_TREATMENT_TYPE2.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE2.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-prop_type_TREATMENT_TYPE3 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE3', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE3.setLabel('Treatment Type 3')
-prop_type_TREATMENT_TYPE3.setManagedInternally(False)
-prop_type_TREATMENT_TYPE3.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE3.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics-optional/package-to-dist b/rtd_phosphonetx/source/core-plugins/proteomics-optional/package-to-dist
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/dss-data-sources/DSS1/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/as/dss-data-sources/DSS1/plugin.properties
deleted file mode 100644
index eb43003949a..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/dss-data-sources/DSS1/plugin.properties
+++ /dev/null
@@ -1,17 +0,0 @@
-#
-# Data Store Server data source for the database storing protein identification and quantification results.
-#
-# Variables:
-# proteomics-basic-database-name
-# First part of the database name. Default value is 'proteomics'.
-# proteomics-database-kind
-# Second part of the database name. Default value is 'productive'.
-# proteomics-database-owner
-# Owner of the proteomics database. Default value is an empty string (i.e. the user starting up DSS).
-# proteomics-database-password
-# Password of the owner of the proteomics database. Default value is an empty string.
-#
-database-driver = org.postgresql.Driver
-database-url = jdbc:postgresql://localhost/${proteomics-basic-database-name:proteomics}_${proteomics-database-kind:productive}
-atabase-username = ${proteomics-database-owner:}
-database-password = ${proteomics-database-password:}
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/initialize-master-data.py b/rtd_phosphonetx/source/core-plugins/proteomics/1/as/initialize-master-data.py
deleted file mode 100644
index 1825b0950e3..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/initialize-master-data.py
+++ /dev/null
@@ -1,42 +0,0 @@
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-tr = service.transaction()
-
-vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE')
-vocabulary_TREATMENT_TYPE.setDescription('Type of treatment of a biological sample.')
-vocabulary_TREATMENT_TYPE.setUrlTemplate(None)
-vocabulary_TREATMENT_TYPE.setManagedInternally(False)
-vocabulary_TREATMENT_TYPE.setInternalNamespace(False)
-vocabulary_TREATMENT_TYPE.setChosenFromList(True)
-
-prop_type_NOT_PROCESSED = tr.getOrCreateNewPropertyType('NOT_PROCESSED', DataType.VARCHAR)
-prop_type_NOT_PROCESSED.setLabel('Not Processed')
-prop_type_NOT_PROCESSED.setDescription('Reason why prot.xml file has not been processed.')
-prop_type_NOT_PROCESSED.setManagedInternally(False)
-prop_type_NOT_PROCESSED.setInternalNamespace(False)
-
-exp_type_MS_SEARCH = tr.getOrCreateNewExperimentType('MS_SEARCH')
-exp_type_MS_SEARCH.setDescription('MS_SEARCH experiment')
-
-assignment_MS_SEARCH_NOT_PROCESSED = tr.assignPropertyType(exp_type_MS_SEARCH, prop_type_NOT_PROCESSED)
-assignment_MS_SEARCH_NOT_PROCESSED.setMandatory(False)
-assignment_MS_SEARCH_NOT_PROCESSED.setSection(None)
-assignment_MS_SEARCH_NOT_PROCESSED.setPositionInForms(1)
-
-samp_type_MS_INJECTION = tr.getOrCreateNewSampleType('MS_INJECTION')
-samp_type_MS_INJECTION.setDescription('injection of a biological sample into a MS')
-samp_type_MS_INJECTION.setListable(True)
-samp_type_MS_INJECTION.setSubcodeUnique(False)
-samp_type_MS_INJECTION.setAutoGeneratedCode(False)
-samp_type_MS_INJECTION.setGeneratedCodePrefix('S')
-
-samp_type_SEARCH = tr.getOrCreateNewSampleType('SEARCH')
-samp_type_SEARCH.setDescription('pointer to an MS_INJECTION sample used as placeholder for searches')
-samp_type_SEARCH.setListable(True)
-samp_type_SEARCH.setSubcodeUnique(False)
-samp_type_SEARCH.setAutoGeneratedCode(False)
-samp_type_SEARCH.setGeneratedCodePrefix('S')
-
-data_set_type_PROT_RESULT = tr.getOrCreateNewDataSetType('PROT_RESULT')
-data_set_type_PROT_RESULT.setDescription('protXML file')
-
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/miscellaneous/proteomics-application/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/as/miscellaneous/proteomics-application/plugin.properties
deleted file mode 100644
index 6d34ded45d3..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/as/miscellaneous/proteomics-application/plugin.properties
+++ /dev/null
@@ -1 +0,0 @@
-proteomics-application-context-required = true
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/data-sources/proteomics-db/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/data-sources/proteomics-db/plugin.properties
deleted file mode 100644
index 664b20a45a8..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/data-sources/proteomics-db/plugin.properties
+++ /dev/null
@@ -1,25 +0,0 @@
-#
-# Data source for the database storing protein identification and quantification results.
-#
-# Variables:
-# proteomics-database.url-host-part
-# The host and optionally port. Default is 'localhost'.
-# proteomics-basic-database-name
-# First part of the database name. Default value is 'proteomics'.
-# proteomics-database-kind
-# Second part of the database name. Default value is 'productive'.
-# proteomics-sql-root-folder
-# Path to root folder of SQL scripts. Default value is an empty string.
-# proteomics-database-owner
-# Owner of the proteomics database. Default value is an empty string (i.e. the user starting up DSS).
-# proteomics-database-password
-# Password of the owner of the proteomics database. Default value is an empty string.
-#
-version-holder-class = ch.systemsx.cisd.openbis.etlserver.proteomics.DatabaseVersionHolder
-databaseEngineCode = postgresql
-urlHostPart = ${proteomics-database.url-host-part:localhost}
-basicDatabaseName = ${proteomics-basic-database-name:proteomics}
-databaseKind = ${proteomics-database-kind:productive}
-scriptFolder = ${proteomics-sql-root-folder:}sql/proteomics
-owner = ${proteomics-database-owner:}
-password = ${proteomics-database-password:}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
deleted file mode 100644
index bff82ed31c5..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
+++ /dev/null
@@ -1,18 +0,0 @@
-#
-# Drop box for MS spectra data.
-#
-# Variables:
-# incoming-root-dir
-# Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${incoming-root-dir}/incoming-ms-injection
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values:
-# - auto-detection - when no write access will be detected for a specified 'quite-period'
-# - marker-file - when an appropriate marker file for the data exists.
-# The default value is 'marker-file'.
-incoming-data-completeness-condition = auto-detection
-
-data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection
-storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
deleted file mode 100644
index da2bca2bce8..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
+++ /dev/null
@@ -1,29 +0,0 @@
-#
-# Drop box for protein identification and quantification data.
-#
-# Variables:
-# incoming-root-dir
-# Path to the directory which contains incoming directories for drop boxes.
-#
-# This drop box assumes that data source 'proteomics-db' has been defined.
-#
-incoming-dir = ${incoming-root-dir}/incoming-ms-search
-
-incoming-data-completeness-condition = auto-detection
-
-data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults
-data-set-info-extractor.separator = +
-
-type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
-type-extractor.file-format-type = XML
-type-extractor.locator-type = RELATIVE_LOCATION
-type-extractor.data-set-type = PROT_RESULT
-type-extractor.is-measured = false
-
-storage-processor = ch.systemsx.cisd.openbis.etlserver.proteomics.StorageProcessorWithResultDataSetUploader
-storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-storage-processor.assuming-extended-prot-xml = false
-storage-processor.database.basic-name = ${proteomics-db.basicDatabaseName}
-storage-processor.database.kind = ${proteomics-db.databaseKind}
-storage-processor.database.owner = ${proteomics-db.owner}
-storage-processor.database.password = ${proteomics-db.password}
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/maintenance-tasks/proteomics-db-clean-up/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/maintenance-tasks/proteomics-db-clean-up/plugin.properties
deleted file mode 100644
index 36cd4bae6c2..00000000000
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/maintenance-tasks/proteomics-db-clean-up/plugin.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-#
-# Maintenance task which does a database clean up by deleting all data sets deleted in application server.
-# This task assumes that data source 'proteomics-db' has been defined.
-#
-class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-interval = 300
-data-source = proteomics-db
-data-set-table-name = data_sets
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/package-to-dist b/rtd_phosphonetx/source/core-plugins/proteomics/package-to-dist
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/source/html/demoapp/body-style.css b/rtd_phosphonetx/source/html/demoapp/body-style.css
deleted file mode 100644
index 7a5324bef86..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/body-style.css
+++ /dev/null
@@ -1,14 +0,0 @@
-body { font: 12px "Verdana", sans-serif; }
-
-h1 { font: 16px; }
-h3 { font: 12px; }
-
-div#vis { padding-top: 10px;}
-div#vis div { padding-top: 2px;}
-
-.headers { background-color: #eee; }
-
-div#vis tr:nth-child(even) { background-color: #EEE; }
-div#vis tr:nth-child(odd) { background-color: white; }
-
-#main form { padding-top: 10px;}
diff --git a/rtd_phosphonetx/source/html/demoapp/button.css b/rtd_phosphonetx/source/html/demoapp/button.css
deleted file mode 100644
index b0c9944b189..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/button.css
+++ /dev/null
@@ -1,52 +0,0 @@
-button {
- font: 14px "Trebuchet MS";
- background-color: #222;
- background-image: -moz-linear-gradient(top, rgba(255,255,255,.25), rgba(255,255,255,.11));
- background-image: -webkit-gradient(linear,left top,left bottom,color-stop(0, rgba(255,255,255,.25)),color-stop(1, rgba(255,255,255,.11)));
- background-image: -webkit-linear-gradient(rgba(255,255,255,.25), rgba(255,255,255,.11));
- color: #fff;
- text-rendering: optimizeLegibility;
- text-shadow: 0 -1px 1px #222;
- padding: 3px 5px 3px 5px;
- border: 0;
- border-radius: 0;
- border-bottom: 1px solid #222;
- margin: 0;
- -moz-box-shadow: 0 1px 3px #999;
- -webkit-box-shadow: 0 1px 3px #999;
- box-shadow: 0 1px 3px #999;
-}
-
-button.first {
- border-top-left-radius: 5px;
- border-bottom-left-radius: 5px;
-}
-
-button.last {
- border-top-right-radius: 5px;
- border-bottom-right-radius: 5px;
-}
-
-button.active {
- background-color: rgb(65,102,133);
-}
-
-button:hover {
- background-color: steelblue;
-}
-
-input {
- font: 14px "Trebuchet MS";
- background-image: -moz-linear-gradient(top, rgba(255,255,255,.25), rgba(255,255,255,.11));
- background-image: -webkit-gradient(linear,left top,left bottom,color-stop(0, rgba(255,255,255,.25)),color-stop(1, rgba(255,255,255,.11)));
- background-image: -webkit-linear-gradient(rgba(255,255,255,.5), rgba(255,255,255,.1));
- color: #000;
- text-rendering: optimizeLegibility;
- padding: 3px 5px 3px 5px;
- border: 0;
- border-radius: 0;
- margin: 0;
- -moz-box-shadow: 0 1px 3px #999;
- -webkit-box-shadow: 0 1px 3px #999;
- box-shadow: 0 1px 3px #999;
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/html/demoapp/d3.js b/rtd_phosphonetx/source/html/demoapp/d3.js
deleted file mode 100755
index 13abb6dbc6f..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/d3.js
+++ /dev/null
@@ -1,4013 +0,0 @@
-(function(){if (!Date.now) Date.now = function() {
- return +new Date;
-};
-try {
- document.createElement("div").style.setProperty("opacity", 0, "");
-} catch (error) {
- var d3_style_prototype = CSSStyleDeclaration.prototype,
- d3_style_setProperty = d3_style_prototype.setProperty;
- d3_style_prototype.setProperty = function(name, value, priority) {
- d3_style_setProperty.call(this, name, value + "", priority);
- };
-}
-d3 = {version: "2.1.3"}; // semver
-var d3_arraySubclass = [].__proto__?
-
-// Until ECMAScript supports array subclassing, prototype injection works well.
-function(array, prototype) {
- array.__proto__ = prototype;
-}:
-
-// And if your browser doesn't support __proto__, we'll use direct extension.
-function(array, prototype) {
- for (var property in prototype) array[property] = prototype[property];
-};
-function d3_this() {
- return this;
-}
-d3.functor = function(v) {
- return typeof v === "function" ? v : function() { return v; };
-};
-// A getter-setter method that preserves the appropriate `this` context.
-d3.rebind = function(object, method) {
- return function() {
- var x = method.apply(object, arguments);
- return arguments.length ? object : x;
- };
-};
-d3.ascending = function(a, b) {
- return a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN;
-};
-d3.descending = function(a, b) {
- return b < a ? -1 : b > a ? 1 : b >= a ? 0 : NaN;
-};
-d3.min = function(array, f) {
- var i = -1,
- n = array.length,
- a,
- b;
- if (arguments.length === 1) {
- while (++i < n && ((a = array[i]) == null || a != a)) a = undefined;
- while (++i < n) if ((b = array[i]) != null && a > b) a = b;
- } else {
- while (++i < n && ((a = f.call(array, array[i], i)) == null || a != a)) a = undefined;
- while (++i < n) if ((b = f.call(array, array[i], i)) != null && a > b) a = b;
- }
- return a;
-};
-d3.max = function(array, f) {
- var i = -1,
- n = array.length,
- a,
- b;
- if (arguments.length === 1) {
- while (++i < n && ((a = array[i]) == null || a != a)) a = undefined;
- while (++i < n) if ((b = array[i]) != null && b > a) a = b;
- } else {
- while (++i < n && ((a = f.call(array, array[i], i)) == null || a != a)) a = undefined;
- while (++i < n) if ((b = f.call(array, array[i], i)) != null && b > a) a = b;
- }
- return a;
-};
-d3.sum = function(array, f) {
- var s = 0,
- n = array.length,
- a,
- i = -1;
-
- if (arguments.length === 1) {
- while (++i < n) if (!isNaN(a = +array[i])) s += a;
- } else {
- while (++i < n) if (!isNaN(a = +f.call(array, array[i], i))) s += a;
- }
-
- return s;
-};
-// R-7 per <http://en.wikipedia.org/wiki/Quantile>
-d3.quantile = function(values, p) {
- var H = (values.length - 1) * p + 1,
- h = Math.floor(H),
- v = values[h - 1],
- e = H - h;
- return e ? v + e * (values[h] - v) : v;
-};
-d3.zip = function() {
- if (!(n = arguments.length)) return [];
- for (var i = -1, m = d3.min(arguments, d3_zipLength), zips = new Array(m); ++i < m;) {
- for (var j = -1, n, zip = zips[i] = new Array(n); ++j < n;) {
- zip[j] = arguments[j][i];
- }
- }
- return zips;
-};
-
-function d3_zipLength(d) {
- return d.length;
-}
-// Locate the insertion point for x in a to maintain sorted order. The
-// arguments lo and hi may be used to specify a subset of the array which should
-// be considered; by default the entire array is used. If x is already present
-// in a, the insertion point will be before (to the left of) any existing
-// entries. The return value is suitable for use as the first argument to
-// `array.splice` assuming that a is already sorted.
-//
-// The returned insertion point i partitions the array a into two halves so that
-// all v < x for v in a[lo:i] for the left side and all v >= x for v in a[i:hi]
-// for the right side.
-d3.bisectLeft = function(a, x, lo, hi) {
- if (arguments.length < 3) lo = 0;
- if (arguments.length < 4) hi = a.length;
- while (lo < hi) {
- var mid = (lo + hi) >> 1;
- if (a[mid] < x) lo = mid + 1;
- else hi = mid;
- }
- return lo;
-};
-
-// Similar to bisectLeft, but returns an insertion point which comes after (to
-// the right of) any existing entries of x in a.
-//
-// The returned insertion point i partitions the array into two halves so that
-// all v <= x for v in a[lo:i] for the left side and all v > x for v in a[i:hi]
-// for the right side.
-d3.bisect =
-d3.bisectRight = function(a, x, lo, hi) {
- if (arguments.length < 3) lo = 0;
- if (arguments.length < 4) hi = a.length;
- while (lo < hi) {
- var mid = (lo + hi) >> 1;
- if (x < a[mid]) hi = mid;
- else lo = mid + 1;
- }
- return lo;
-};
-d3.first = function(array, f) {
- var i = 0,
- n = array.length,
- a = array[0],
- b;
- if (arguments.length === 1) f = d3.ascending;
- while (++i < n) {
- if (f.call(array, a, b = array[i]) > 0) {
- a = b;
- }
- }
- return a;
-};
-d3.last = function(array, f) {
- var i = 0,
- n = array.length,
- a = array[0],
- b;
- if (arguments.length === 1) f = d3.ascending;
- while (++i < n) {
- if (f.call(array, a, b = array[i]) <= 0) {
- a = b;
- }
- }
- return a;
-};
-d3.nest = function() {
- var nest = {},
- keys = [],
- sortKeys = [],
- sortValues,
- rollup;
-
- function map(array, depth) {
- if (depth >= keys.length) return rollup
- ? rollup.call(nest, array) : (sortValues
- ? array.sort(sortValues)
- : array);
-
- var i = -1,
- n = array.length,
- key = keys[depth++],
- keyValue,
- object,
- o = {};
-
- while (++i < n) {
- if ((keyValue = key(object = array[i])) in o) {
- o[keyValue].push(object);
- } else {
- o[keyValue] = [object];
- }
- }
-
- for (keyValue in o) {
- o[keyValue] = map(o[keyValue], depth);
- }
-
- return o;
- }
-
- function entries(map, depth) {
- if (depth >= keys.length) return map;
-
- var a = [],
- sortKey = sortKeys[depth++],
- key;
-
- for (key in map) {
- a.push({key: key, values: entries(map[key], depth)});
- }
-
- if (sortKey) a.sort(function(a, b) {
- return sortKey(a.key, b.key);
- });
-
- return a;
- }
-
- nest.map = function(array) {
- return map(array, 0);
- };
-
- nest.entries = function(array) {
- return entries(map(array, 0), 0);
- };
-
- nest.key = function(d) {
- keys.push(d);
- return nest;
- };
-
- // Specifies the order for the most-recently specified key.
- // Note: only applies to entries. Map keys are unordered!
- nest.sortKeys = function(order) {
- sortKeys[keys.length - 1] = order;
- return nest;
- };
-
- // Specifies the order for leaf values.
- // Applies to both maps and entries array.
- nest.sortValues = function(order) {
- sortValues = order;
- return nest;
- };
-
- nest.rollup = function(f) {
- rollup = f;
- return nest;
- };
-
- return nest;
-};
-d3.keys = function(map) {
- var keys = [];
- for (var key in map) keys.push(key);
- return keys;
-};
-d3.values = function(map) {
- var values = [];
- for (var key in map) values.push(map[key]);
- return values;
-};
-d3.entries = function(map) {
- var entries = [];
- for (var key in map) entries.push({key: key, value: map[key]});
- return entries;
-};
-d3.permute = function(array, indexes) {
- var permutes = [],
- i = -1,
- n = indexes.length;
- while (++i < n) permutes[i] = array[indexes[i]];
- return permutes;
-};
-d3.merge = function(arrays) {
- return Array.prototype.concat.apply([], arrays);
-};
-d3.split = function(array, f) {
- var arrays = [],
- values = [],
- value,
- i = -1,
- n = array.length;
- if (arguments.length < 2) f = d3_splitter;
- while (++i < n) {
- if (f.call(values, value = array[i], i)) {
- values = [];
- } else {
- if (!values.length) arrays.push(values);
- values.push(value);
- }
- }
- return arrays;
-};
-
-function d3_splitter(d) {
- return d == null;
-}
-function d3_collapse(s) {
- return s.replace(/(^\s+)|(\s+$)/g, "").replace(/\s+/g, " ");
-}
-/**
- * @param {number} start
- * @param {number=} stop
- * @param {number=} step
- */
-d3.range = function(start, stop, step) {
- if (arguments.length < 3) {
- step = 1;
- if (arguments.length < 2) {
- stop = start;
- start = 0;
- }
- }
- if ((stop - start) / step == Infinity) throw new Error("infinite range");
- var range = [],
- i = -1,
- j;
- if (step < 0) while ((j = start + step * ++i) > stop) range.push(j);
- else while ((j = start + step * ++i) < stop) range.push(j);
- return range;
-};
-d3.requote = function(s) {
- return s.replace(d3_requote_re, "\\$&");
-};
-
-var d3_requote_re = /[\\\^\$\*\+\?\|\[\]\(\)\.\{\}]/g;
-d3.round = function(x, n) {
- return n
- ? Math.round(x * Math.pow(10, n)) * Math.pow(10, -n)
- : Math.round(x);
-};
-d3.xhr = function(url, mime, callback) {
- var req = new XMLHttpRequest;
- if (arguments.length < 3) callback = mime;
- else if (mime && req.overrideMimeType) req.overrideMimeType(mime);
- req.open("GET", url, true);
- req.onreadystatechange = function() {
- if (req.readyState === 4) callback(req.status < 300 ? req : null);
- };
- req.send(null);
-};
-d3.text = function(url, mime, callback) {
- function ready(req) {
- callback(req && req.responseText);
- }
- if (arguments.length < 3) {
- callback = mime;
- mime = null;
- }
- d3.xhr(url, mime, ready);
-};
-d3.json = function(url, callback) {
- d3.text(url, "application/json", function(text) {
- callback(text ? JSON.parse(text) : null);
- });
-};
-d3.html = function(url, callback) {
- d3.text(url, "text/html", function(text) {
- if (text != null) { // Treat empty string as valid HTML.
- var range = document.createRange();
- range.selectNode(document.body);
- text = range.createContextualFragment(text);
- }
- callback(text);
- });
-};
-d3.xml = function(url, mime, callback) {
- function ready(req) {
- callback(req && req.responseXML);
- }
- if (arguments.length < 3) {
- callback = mime;
- mime = null;
- }
- d3.xhr(url, mime, ready);
-};
-d3.ns = {
-
- prefix: {
- svg: "http://www.w3.org/2000/svg",
- xhtml: "http://www.w3.org/1999/xhtml",
- xlink: "http://www.w3.org/1999/xlink",
- xml: "http://www.w3.org/XML/1998/namespace",
- xmlns: "http://www.w3.org/2000/xmlns/"
- },
-
- qualify: function(name) {
- var i = name.indexOf(":");
- return i < 0 ? name : {
- space: d3.ns.prefix[name.substring(0, i)],
- local: name.substring(i + 1)
- };
- }
-
-};
-/** @param {...string} types */
-d3.dispatch = function(types) {
- var dispatch = {},
- type;
- for (var i = 0, n = arguments.length; i < n; i++) {
- type = arguments[i];
- dispatch[type] = d3_dispatch(type);
- }
- return dispatch;
-};
-
-function d3_dispatch(type) {
- var dispatch = {},
- listeners = [];
-
- dispatch.add = function(listener) {
- for (var i = 0; i < listeners.length; i++) {
- if (listeners[i].listener == listener) return dispatch; // already registered
- }
- listeners.push({listener: listener, on: true});
- return dispatch;
- };
-
- dispatch.remove = function(listener) {
- for (var i = 0; i < listeners.length; i++) {
- var l = listeners[i];
- if (l.listener == listener) {
- l.on = false;
- listeners = listeners.slice(0, i).concat(listeners.slice(i + 1));
- break;
- }
- }
- return dispatch;
- };
-
- dispatch.dispatch = function() {
- var ls = listeners; // defensive reference
- for (var i = 0, n = ls.length; i < n; i++) {
- var l = ls[i];
- if (l.on) l.listener.apply(this, arguments);
- }
- };
-
- return dispatch;
-};
-// TODO align
-d3.format = function(specifier) {
- var match = d3_format_re.exec(specifier),
- fill = match[1] || " ",
- sign = match[3] || "",
- zfill = match[5],
- width = +match[6],
- comma = match[7],
- precision = match[8],
- type = match[9],
- percentage = false,
- integer = false;
-
- if (precision) precision = precision.substring(1);
-
- if (zfill) {
- fill = "0"; // TODO align = "=";
- if (comma) width -= Math.floor((width - 1) / 4);
- }
-
- switch (type) {
- case "n": comma = true; type = "g"; break;
- case "%": percentage = true; type = "f"; break;
- case "p": percentage = true; type = "r"; break;
- case "d": integer = true; precision = "0"; break;
- }
-
- type = d3_format_types[type] || d3_format_typeDefault;
-
- return function(value) {
- var number = percentage ? value * 100 : +value,
- negative = (number < 0) && (number = -number) ? "\u2212" : sign;
-
- // Return the empty string for floats formatted as ints.
- if (integer && (number % 1)) return "";
-
- // Convert the input value to the desired precision.
- value = type(number, precision);
-
- // If the fill character is 0, the sign and group is applied after the fill.
- if (zfill) {
- var length = value.length + negative.length;
- if (length < width) value = new Array(width - length + 1).join(fill) + value;
- if (comma) value = d3_format_group(value);
- value = negative + value;
- }
-
- // Otherwise (e.g., space-filling), the sign and group is applied before.
- else {
- if (comma) value = d3_format_group(value);
- value = negative + value;
- var length = value.length;
- if (length < width) value = new Array(width - length + 1).join(fill) + value;
- }
- if (percentage) value += "%";
-
- return value;
- };
-};
-
-// [[fill]align][sign][#][0][width][,][.precision][type]
-var d3_format_re = /(?:([^{])?([<>=^]))?([+\- ])?(#)?(0)?([0-9]+)?(,)?(\.[0-9]+)?([a-zA-Z%])?/;
-
-var d3_format_types = {
- g: function(x, p) { return x.toPrecision(p); },
- e: function(x, p) { return x.toExponential(p); },
- f: function(x, p) { return x.toFixed(p); },
- r: function(x, p) {
- var n = 1 + Math.floor(1e-15 + Math.log(x) / Math.LN10);
- return d3.round(x, p - n).toFixed(Math.max(0, Math.min(20, p - n)));
- }
-};
-
-function d3_format_typeDefault(x) {
- return x + "";
-}
-
-// Apply comma grouping for thousands.
-function d3_format_group(value) {
- var i = value.lastIndexOf("."),
- f = i >= 0 ? value.substring(i) : (i = value.length, ""),
- t = [];
- while (i > 0) t.push(value.substring(i -= 3, i + 3));
- return t.reverse().join(",") + f;
-}
-/*
- * TERMS OF USE - EASING EQUATIONS
- *
- * Open source under the BSD License.
- *
- * Copyright 2001 Robert Penner
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * - Redistributions of source code must retain the above copyright notice, this
- * list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above copyright notice,
- * this list of conditions and the following disclaimer in the documentation
- * and/or other materials provided with the distribution.
- *
- * - Neither the name of the author nor the names of contributors may be used to
- * endorse or promote products derived from this software without specific
- * prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- */
-
-var d3_ease_quad = d3_ease_poly(2),
- d3_ease_cubic = d3_ease_poly(3);
-
-var d3_ease = {
- linear: function() { return d3_ease_linear; },
- poly: d3_ease_poly,
- quad: function() { return d3_ease_quad; },
- cubic: function() { return d3_ease_cubic; },
- sin: function() { return d3_ease_sin; },
- exp: function() { return d3_ease_exp; },
- circle: function() { return d3_ease_circle; },
- elastic: d3_ease_elastic,
- back: d3_ease_back,
- bounce: function() { return d3_ease_bounce; }
-};
-
-var d3_ease_mode = {
- "in": function(f) { return f; },
- "out": d3_ease_reverse,
- "in-out": d3_ease_reflect,
- "out-in": function(f) { return d3_ease_reflect(d3_ease_reverse(f)); }
-};
-
-d3.ease = function(name) {
- var i = name.indexOf("-"),
- t = i >= 0 ? name.substring(0, i) : name,
- m = i >= 0 ? name.substring(i + 1) : "in";
- return d3_ease_clamp(d3_ease_mode[m](d3_ease[t].apply(null, Array.prototype.slice.call(arguments, 1))));
-};
-
-function d3_ease_clamp(f) {
- return function(t) {
- return t <= 0 ? 0 : t >= 1 ? 1 : f(t);
- };
-}
-
-function d3_ease_reverse(f) {
- return function(t) {
- return 1 - f(1 - t);
- };
-}
-
-function d3_ease_reflect(f) {
- return function(t) {
- return .5 * (t < .5 ? f(2 * t) : (2 - f(2 - 2 * t)));
- };
-}
-
-function d3_ease_linear(t) {
- return t;
-}
-
-function d3_ease_poly(e) {
- return function(t) {
- return Math.pow(t, e);
- }
-}
-
-function d3_ease_sin(t) {
- return 1 - Math.cos(t * Math.PI / 2);
-}
-
-function d3_ease_exp(t) {
- return Math.pow(2, 10 * (t - 1));
-}
-
-function d3_ease_circle(t) {
- return 1 - Math.sqrt(1 - t * t);
-}
-
-function d3_ease_elastic(a, p) {
- var s;
- if (arguments.length < 2) p = 0.45;
- if (arguments.length < 1) { a = 1; s = p / 4; }
- else s = p / (2 * Math.PI) * Math.asin(1 / a);
- return function(t) {
- return 1 + a * Math.pow(2, 10 * -t) * Math.sin((t - s) * 2 * Math.PI / p);
- };
-}
-
-function d3_ease_back(s) {
- if (!s) s = 1.70158;
- return function(t) {
- return t * t * ((s + 1) * t - s);
- };
-}
-
-function d3_ease_bounce(t) {
- return t < 1 / 2.75 ? 7.5625 * t * t
- : t < 2 / 2.75 ? 7.5625 * (t -= 1.5 / 2.75) * t + .75
- : t < 2.5 / 2.75 ? 7.5625 * (t -= 2.25 / 2.75) * t + .9375
- : 7.5625 * (t -= 2.625 / 2.75) * t + .984375;
-}
-d3.event = null;
-d3.interpolate = function(a, b) {
- var i = d3.interpolators.length, f;
- while (--i >= 0 && !(f = d3.interpolators[i](a, b)));
- return f;
-};
-
-d3.interpolateNumber = function(a, b) {
- b -= a;
- return function(t) { return a + b * t; };
-};
-
-d3.interpolateRound = function(a, b) {
- b -= a;
- return function(t) { return Math.round(a + b * t); };
-};
-
-d3.interpolateString = function(a, b) {
- var m, // current match
- i, // current index
- j, // current index (for coallescing)
- s0 = 0, // start index of current string prefix
- s1 = 0, // end index of current string prefix
- s = [], // string constants and placeholders
- q = [], // number interpolators
- n, // q.length
- o;
-
- // Reset our regular expression!
- d3_interpolate_number.lastIndex = 0;
-
- // Find all numbers in b.
- for (i = 0; m = d3_interpolate_number.exec(b); ++i) {
- if (m.index) s.push(b.substring(s0, s1 = m.index));
- q.push({i: s.length, x: m[0]});
- s.push(null);
- s0 = d3_interpolate_number.lastIndex;
- }
- if (s0 < b.length) s.push(b.substring(s0));
-
- // Find all numbers in a.
- for (i = 0, n = q.length; (m = d3_interpolate_number.exec(a)) && i < n; ++i) {
- o = q[i];
- if (o.x == m[0]) { // The numbers match, so coallesce.
- if (o.i) {
- if (s[o.i + 1] == null) { // This match is followed by another number.
- s[o.i - 1] += o.x;
- s.splice(o.i, 1);
- for (j = i + 1; j < n; ++j) q[j].i--;
- } else { // This match is followed by a string, so coallesce twice.
- s[o.i - 1] += o.x + s[o.i + 1];
- s.splice(o.i, 2);
- for (j = i + 1; j < n; ++j) q[j].i -= 2;
- }
- } else {
- if (s[o.i + 1] == null) { // This match is followed by another number.
- s[o.i] = o.x;
- } else { // This match is followed by a string, so coallesce twice.
- s[o.i] = o.x + s[o.i + 1];
- s.splice(o.i + 1, 1);
- for (j = i + 1; j < n; ++j) q[j].i--;
- }
- }
- q.splice(i, 1);
- n--;
- i--;
- } else {
- o.x = d3.interpolateNumber(parseFloat(m[0]), parseFloat(o.x));
- }
- }
-
- // Remove any numbers in b not found in a.
- while (i < n) {
- o = q.pop();
- if (s[o.i + 1] == null) { // This match is followed by another number.
- s[o.i] = o.x;
- } else { // This match is followed by a string, so coallesce twice.
- s[o.i] = o.x + s[o.i + 1];
- s.splice(o.i + 1, 1);
- }
- n--;
- }
-
- // Special optimization for only a single match.
- if (s.length === 1) {
- return s[0] == null ? q[0].x : function() { return b; };
- }
-
- // Otherwise, interpolate each of the numbers and rejoin the string.
- return function(t) {
- for (i = 0; i < n; ++i) s[(o = q[i]).i] = o.x(t);
- return s.join("");
- };
-};
-
-d3.interpolateRgb = function(a, b) {
- a = d3.rgb(a);
- b = d3.rgb(b);
- var ar = a.r,
- ag = a.g,
- ab = a.b,
- br = b.r - ar,
- bg = b.g - ag,
- bb = b.b - ab;
- return function(t) {
- return "rgb(" + Math.round(ar + br * t)
- + "," + Math.round(ag + bg * t)
- + "," + Math.round(ab + bb * t)
- + ")";
- };
-};
-
-// interpolates HSL space, but outputs RGB string (for compatibility)
-d3.interpolateHsl = function(a, b) {
- a = d3.hsl(a);
- b = d3.hsl(b);
- var h0 = a.h,
- s0 = a.s,
- l0 = a.l,
- h1 = b.h - h0,
- s1 = b.s - s0,
- l1 = b.l - l0;
- return function(t) {
- return d3_hsl_rgb(h0 + h1 * t, s0 + s1 * t, l0 + l1 * t).toString();
- };
-};
-
-d3.interpolateArray = function(a, b) {
- var x = [],
- c = [],
- na = a.length,
- nb = b.length,
- n0 = Math.min(a.length, b.length),
- i;
- for (i = 0; i < n0; ++i) x.push(d3.interpolate(a[i], b[i]));
- for (; i < na; ++i) c[i] = a[i];
- for (; i < nb; ++i) c[i] = b[i];
- return function(t) {
- for (i = 0; i < n0; ++i) c[i] = x[i](t);
- return c;
- };
-};
-
-d3.interpolateObject = function(a, b) {
- var i = {},
- c = {},
- k;
- for (k in a) {
- if (k in b) {
- i[k] = d3_interpolateByName(k)(a[k], b[k]);
- } else {
- c[k] = a[k];
- }
- }
- for (k in b) {
- if (!(k in a)) {
- c[k] = b[k];
- }
- }
- return function(t) {
- for (k in i) c[k] = i[k](t);
- return c;
- };
-}
-
-var d3_interpolate_number = /[-+]?(?:\d+\.\d+|\d+\.|\.\d+|\d+)(?:[eE][-]?\d+)?/g,
- d3_interpolate_rgb = {background: 1, fill: 1, stroke: 1};
-
-function d3_interpolateByName(n) {
- return n in d3_interpolate_rgb || /\bcolor\b/.test(n)
- ? d3.interpolateRgb
- : d3.interpolate;
-}
-
-d3.interpolators = [
- d3.interpolateObject,
- function(a, b) { return (b instanceof Array) && d3.interpolateArray(a, b); },
- function(a, b) { return (typeof b === "string") && d3.interpolateString(String(a), b); },
- function(a, b) { return (typeof b === "string" ? b in d3_rgb_names || /^(#|rgb\(|hsl\()/.test(b) : b instanceof d3_Rgb || b instanceof d3_Hsl) && d3.interpolateRgb(String(a), b); },
- function(a, b) { return (typeof b === "number") && d3.interpolateNumber(+a, b); }
-];
-function d3_uninterpolateNumber(a, b) {
- b = b - (a = +a) ? 1 / (b - a) : 0;
- return function(x) { return (x - a) * b; };
-}
-
-function d3_uninterpolateClamp(a, b) {
- b = b - (a = +a) ? 1 / (b - a) : 0;
- return function(x) { return Math.max(0, Math.min(1, (x - a) * b)); };
-}
-d3.rgb = function(r, g, b) {
- return arguments.length === 1
- ? d3_rgb_parse("" + r, d3_rgb, d3_hsl_rgb)
- : d3_rgb(~~r, ~~g, ~~b);
-};
-
-function d3_rgb(r, g, b) {
- return new d3_Rgb(r, g, b);
-}
-
-function d3_Rgb(r, g, b) {
- this.r = r;
- this.g = g;
- this.b = b;
-}
-
-d3_Rgb.prototype.brighter = function(k) {
- k = Math.pow(0.7, arguments.length ? k : 1);
- var r = this.r,
- g = this.g,
- b = this.b,
- i = 30;
- if (!r && !g && !b) return d3_rgb(i, i, i);
- if (r && r < i) r = i;
- if (g && g < i) g = i;
- if (b && b < i) b = i;
- return d3_rgb(
- Math.min(255, Math.floor(r / k)),
- Math.min(255, Math.floor(g / k)),
- Math.min(255, Math.floor(b / k)));
-};
-
-d3_Rgb.prototype.darker = function(k) {
- k = Math.pow(0.7, arguments.length ? k : 1);
- return d3_rgb(
- Math.max(0, Math.floor(k * this.r)),
- Math.max(0, Math.floor(k * this.g)),
- Math.max(0, Math.floor(k * this.b)));
-};
-
-d3_Rgb.prototype.hsl = function() {
- return d3_rgb_hsl(this.r, this.g, this.b);
-};
-
-d3_Rgb.prototype.toString = function() {
- return "#" + d3_rgb_hex(this.r) + d3_rgb_hex(this.g) + d3_rgb_hex(this.b);
-};
-
-function d3_rgb_hex(v) {
- return v < 0x10 ? "0" + v.toString(16) : v.toString(16);
-}
-
-function d3_rgb_parse(format, rgb, hsl) {
- var r = 0, // red channel; int in [0, 255]
- g = 0, // green channel; int in [0, 255]
- b = 0, // blue channel; int in [0, 255]
- m1, // CSS color specification match
- m2, // CSS color specification type (e.g., rgb)
- name;
-
- /* Handle hsl, rgb. */
- m1 = /([a-z]+)\((.*)\)/i.exec(format);
- if (m1) {
- m2 = m1[2].split(",");
- switch (m1[1]) {
- case "hsl": {
- return hsl(
- parseFloat(m2[0]), // degrees
- parseFloat(m2[1]) / 100, // percentage
- parseFloat(m2[2]) / 100 // percentage
- );
- }
- case "rgb": {
- return rgb(
- d3_rgb_parseNumber(m2[0]),
- d3_rgb_parseNumber(m2[1]),
- d3_rgb_parseNumber(m2[2])
- );
- }
- }
- }
-
- /* Named colors. */
- if (name = d3_rgb_names[format]) return rgb(name.r, name.g, name.b);
-
- /* Hexadecimal colors: #rgb and #rrggbb. */
- if (format != null && format.charAt(0) === "#") {
- if (format.length === 4) {
- r = format.charAt(1); r += r;
- g = format.charAt(2); g += g;
- b = format.charAt(3); b += b;
- } else if (format.length === 7) {
- r = format.substring(1, 3);
- g = format.substring(3, 5);
- b = format.substring(5, 7);
- }
- r = parseInt(r, 16);
- g = parseInt(g, 16);
- b = parseInt(b, 16);
- }
-
- return rgb(r, g, b);
-}
-
-function d3_rgb_hsl(r, g, b) {
- var min = Math.min(r /= 255, g /= 255, b /= 255),
- max = Math.max(r, g, b),
- d = max - min,
- h,
- s,
- l = (max + min) / 2;
- if (d) {
- s = l < .5 ? d / (max + min) : d / (2 - max - min);
- if (r == max) h = (g - b) / d + (g < b ? 6 : 0);
- else if (g == max) h = (b - r) / d + 2;
- else h = (r - g) / d + 4;
- h *= 60;
- } else {
- s = h = 0;
- }
- return d3_hsl(h, s, l);
-}
-
-function d3_rgb_parseNumber(c) { // either integer or percentage
- var f = parseFloat(c);
- return c.charAt(c.length - 1) === "%" ? Math.round(f * 2.55) : f;
-}
-
-var d3_rgb_names = {
- aliceblue: "#f0f8ff",
- antiquewhite: "#faebd7",
- aqua: "#00ffff",
- aquamarine: "#7fffd4",
- azure: "#f0ffff",
- beige: "#f5f5dc",
- bisque: "#ffe4c4",
- black: "#000000",
- blanchedalmond: "#ffebcd",
- blue: "#0000ff",
- blueviolet: "#8a2be2",
- brown: "#a52a2a",
- burlywood: "#deb887",
- cadetblue: "#5f9ea0",
- chartreuse: "#7fff00",
- chocolate: "#d2691e",
- coral: "#ff7f50",
- cornflowerblue: "#6495ed",
- cornsilk: "#fff8dc",
- crimson: "#dc143c",
- cyan: "#00ffff",
- darkblue: "#00008b",
- darkcyan: "#008b8b",
- darkgoldenrod: "#b8860b",
- darkgray: "#a9a9a9",
- darkgreen: "#006400",
- darkgrey: "#a9a9a9",
- darkkhaki: "#bdb76b",
- darkmagenta: "#8b008b",
- darkolivegreen: "#556b2f",
- darkorange: "#ff8c00",
- darkorchid: "#9932cc",
- darkred: "#8b0000",
- darksalmon: "#e9967a",
- darkseagreen: "#8fbc8f",
- darkslateblue: "#483d8b",
- darkslategray: "#2f4f4f",
- darkslategrey: "#2f4f4f",
- darkturquoise: "#00ced1",
- darkviolet: "#9400d3",
- deeppink: "#ff1493",
- deepskyblue: "#00bfff",
- dimgray: "#696969",
- dimgrey: "#696969",
- dodgerblue: "#1e90ff",
- firebrick: "#b22222",
- floralwhite: "#fffaf0",
- forestgreen: "#228b22",
- fuchsia: "#ff00ff",
- gainsboro: "#dcdcdc",
- ghostwhite: "#f8f8ff",
- gold: "#ffd700",
- goldenrod: "#daa520",
- gray: "#808080",
- green: "#008000",
- greenyellow: "#adff2f",
- grey: "#808080",
- honeydew: "#f0fff0",
- hotpink: "#ff69b4",
- indianred: "#cd5c5c",
- indigo: "#4b0082",
- ivory: "#fffff0",
- khaki: "#f0e68c",
- lavender: "#e6e6fa",
- lavenderblush: "#fff0f5",
- lawngreen: "#7cfc00",
- lemonchiffon: "#fffacd",
- lightblue: "#add8e6",
- lightcoral: "#f08080",
- lightcyan: "#e0ffff",
- lightgoldenrodyellow: "#fafad2",
- lightgray: "#d3d3d3",
- lightgreen: "#90ee90",
- lightgrey: "#d3d3d3",
- lightpink: "#ffb6c1",
- lightsalmon: "#ffa07a",
- lightseagreen: "#20b2aa",
- lightskyblue: "#87cefa",
- lightslategray: "#778899",
- lightslategrey: "#778899",
- lightsteelblue: "#b0c4de",
- lightyellow: "#ffffe0",
- lime: "#00ff00",
- limegreen: "#32cd32",
- linen: "#faf0e6",
- magenta: "#ff00ff",
- maroon: "#800000",
- mediumaquamarine: "#66cdaa",
- mediumblue: "#0000cd",
- mediumorchid: "#ba55d3",
- mediumpurple: "#9370db",
- mediumseagreen: "#3cb371",
- mediumslateblue: "#7b68ee",
- mediumspringgreen: "#00fa9a",
- mediumturquoise: "#48d1cc",
- mediumvioletred: "#c71585",
- midnightblue: "#191970",
- mintcream: "#f5fffa",
- mistyrose: "#ffe4e1",
- moccasin: "#ffe4b5",
- navajowhite: "#ffdead",
- navy: "#000080",
- oldlace: "#fdf5e6",
- olive: "#808000",
- olivedrab: "#6b8e23",
- orange: "#ffa500",
- orangered: "#ff4500",
- orchid: "#da70d6",
- palegoldenrod: "#eee8aa",
- palegreen: "#98fb98",
- paleturquoise: "#afeeee",
- palevioletred: "#db7093",
- papayawhip: "#ffefd5",
- peachpuff: "#ffdab9",
- peru: "#cd853f",
- pink: "#ffc0cb",
- plum: "#dda0dd",
- powderblue: "#b0e0e6",
- purple: "#800080",
- red: "#ff0000",
- rosybrown: "#bc8f8f",
- royalblue: "#4169e1",
- saddlebrown: "#8b4513",
- salmon: "#fa8072",
- sandybrown: "#f4a460",
- seagreen: "#2e8b57",
- seashell: "#fff5ee",
- sienna: "#a0522d",
- silver: "#c0c0c0",
- skyblue: "#87ceeb",
- slateblue: "#6a5acd",
- slategray: "#708090",
- slategrey: "#708090",
- snow: "#fffafa",
- springgreen: "#00ff7f",
- steelblue: "#4682b4",
- tan: "#d2b48c",
- teal: "#008080",
- thistle: "#d8bfd8",
- tomato: "#ff6347",
- turquoise: "#40e0d0",
- violet: "#ee82ee",
- wheat: "#f5deb3",
- white: "#ffffff",
- whitesmoke: "#f5f5f5",
- yellow: "#ffff00",
- yellowgreen: "#9acd32"
-};
-
-for (var d3_rgb_name in d3_rgb_names) {
- d3_rgb_names[d3_rgb_name] = d3_rgb_parse(
- d3_rgb_names[d3_rgb_name],
- d3_rgb,
- d3_hsl_rgb);
-}
-d3.hsl = function(h, s, l) {
- return arguments.length === 1
- ? d3_rgb_parse("" + h, d3_rgb_hsl, d3_hsl)
- : d3_hsl(+h, +s, +l);
-};
-
-function d3_hsl(h, s, l) {
- return new d3_Hsl(h, s, l);
-}
-
-function d3_Hsl(h, s, l) {
- this.h = h;
- this.s = s;
- this.l = l;
-}
-
-d3_Hsl.prototype.brighter = function(k) {
- k = Math.pow(0.7, arguments.length ? k : 1);
- return d3_hsl(this.h, this.s, this.l / k);
-};
-
-d3_Hsl.prototype.darker = function(k) {
- k = Math.pow(0.7, arguments.length ? k : 1);
- return d3_hsl(this.h, this.s, k * this.l);
-};
-
-d3_Hsl.prototype.rgb = function() {
- return d3_hsl_rgb(this.h, this.s, this.l);
-};
-
-d3_Hsl.prototype.toString = function() {
- return "hsl(" + this.h + "," + this.s * 100 + "%," + this.l * 100 + "%)";
-};
-
-function d3_hsl_rgb(h, s, l) {
- var m1,
- m2;
-
- /* Some simple corrections for h, s and l. */
- h = h % 360; if (h < 0) h += 360;
- s = s < 0 ? 0 : s > 1 ? 1 : s;
- l = l < 0 ? 0 : l > 1 ? 1 : l;
-
- /* From FvD 13.37, CSS Color Module Level 3 */
- m2 = l <= .5 ? l * (1 + s) : l + s - l * s;
- m1 = 2 * l - m2;
-
- function v(h) {
- if (h > 360) h -= 360;
- else if (h < 0) h += 360;
- if (h < 60) return m1 + (m2 - m1) * h / 60;
- if (h < 180) return m2;
- if (h < 240) return m1 + (m2 - m1) * (240 - h) / 60;
- return m1;
- }
-
- function vv(h) {
- return Math.round(v(h) * 255);
- }
-
- return d3_rgb(vv(h + 120), vv(h), vv(h - 120));
-}
-function d3_selection(groups) {
- d3_arraySubclass(groups, d3_selectionPrototype);
- return groups;
-}
-
-var d3_select = function(s, n) { return n.querySelector(s); },
- d3_selectAll = function(s, n) { return n.querySelectorAll(s); };
-
-// Prefer Sizzle, if available.
-if (typeof Sizzle === "function") {
- d3_select = function(s, n) { return Sizzle(s, n)[0]; };
- d3_selectAll = function(s, n) { return Sizzle.uniqueSort(Sizzle(s, n)); };
-}
-
-var d3_selectionPrototype = [];
-
-d3.selection = function() {
- return d3_selectionRoot;
-};
-
-d3.selection.prototype = d3_selectionPrototype;
-d3_selectionPrototype.select = function(selector) {
- var subgroups = [],
- subgroup,
- subnode,
- group,
- node;
-
- if (typeof selector !== "function") selector = d3_selection_selector(selector);
-
- for (var j = -1, m = this.length; ++j < m;) {
- subgroups.push(subgroup = []);
- subgroup.parentNode = (group = this[j]).parentNode;
- for (var i = -1, n = group.length; ++i < n;) {
- if (node = group[i]) {
- subgroup.push(subnode = selector.call(node, node.__data__, i));
- if (subnode && "__data__" in node) subnode.__data__ = node.__data__;
- } else {
- subgroup.push(null);
- }
- }
- }
-
- return d3_selection(subgroups);
-};
-
-function d3_selection_selector(selector) {
- return function() {
- return d3_select(selector, this);
- };
-}
-d3_selectionPrototype.selectAll = function(selector) {
- var subgroups = [],
- subgroup,
- node;
-
- if (typeof selector !== "function") selector = d3_selection_selectorAll(selector);
-
- for (var j = -1, m = this.length; ++j < m;) {
- for (var group = this[j], i = -1, n = group.length; ++i < n;) {
- if (node = group[i]) {
- subgroups.push(subgroup = selector.call(node, node.__data__, i));
- subgroup.parentNode = node;
- }
- }
- }
-
- return d3_selection(subgroups);
-};
-
-function d3_selection_selectorAll(selector) {
- return function() {
- return d3_selectAll(selector, this);
- };
-}
-d3_selectionPrototype.attr = function(name, value) {
- name = d3.ns.qualify(name);
-
- // If no value is specified, return the first value.
- if (arguments.length < 2) {
- var node = this.node();
- return name.local
- ? node.getAttributeNS(name.space, name.local)
- : node.getAttribute(name);
- }
-
- function attrNull() {
- this.removeAttribute(name);
- }
-
- function attrNullNS() {
- this.removeAttributeNS(name.space, name.local);
- }
-
- function attrConstant() {
- this.setAttribute(name, value);
- }
-
- function attrConstantNS() {
- this.setAttributeNS(name.space, name.local, value);
- }
-
- function attrFunction() {
- var x = value.apply(this, arguments);
- if (x == null) this.removeAttribute(name);
- else this.setAttribute(name, x);
- }
-
- function attrFunctionNS() {
- var x = value.apply(this, arguments);
- if (x == null) this.removeAttributeNS(name.space, name.local);
- else this.setAttributeNS(name.space, name.local, x);
- }
-
- return this.each(value == null
- ? (name.local ? attrNullNS : attrNull) : (typeof value === "function"
- ? (name.local ? attrFunctionNS : attrFunction)
- : (name.local ? attrConstantNS : attrConstant)));
-};
-d3_selectionPrototype.classed = function(name, value) {
- var re = new RegExp("(^|\\s+)" + d3.requote(name) + "(\\s+|$)", "g");
-
- // If no value is specified, return the first value.
- if (arguments.length < 2) {
- var node = this.node();
- if (c = node.classList) return c.contains(name);
- var c = node.className;
- re.lastIndex = 0;
- return re.test(c.baseVal != null ? c.baseVal : c);
- }
-
- function classedAdd() {
- if (c = this.classList) return c.add(name);
- var c = this.className,
- cb = c.baseVal != null,
- cv = cb ? c.baseVal : c;
- re.lastIndex = 0;
- if (!re.test(cv)) {
- cv = d3_collapse(cv + " " + name);
- if (cb) c.baseVal = cv;
- else this.className = cv;
- }
- }
-
- function classedRemove() {
- if (c = this.classList) return c.remove(name);
- var c = this.className,
- cb = c.baseVal != null,
- cv = cb ? c.baseVal : c;
- cv = d3_collapse(cv.replace(re, " "));
- if (cb) c.baseVal = cv;
- else this.className = cv;
- }
-
- function classedFunction() {
- (value.apply(this, arguments)
- ? classedAdd
- : classedRemove).call(this);
- }
-
- return this.each(typeof value === "function"
- ? classedFunction : value
- ? classedAdd
- : classedRemove);
-};
-d3_selectionPrototype.style = function(name, value, priority) {
- if (arguments.length < 3) priority = "";
-
- // If no value is specified, return the first value.
- if (arguments.length < 2) return window
- .getComputedStyle(this.node(), null)
- .getPropertyValue(name);
-
- function styleNull() {
- this.style.removeProperty(name);
- }
-
- function styleConstant() {
- this.style.setProperty(name, value, priority);
- }
-
- function styleFunction() {
- var x = value.apply(this, arguments);
- if (x == null) this.style.removeProperty(name);
- else this.style.setProperty(name, x, priority);
- }
-
- return this.each(value == null
- ? styleNull : (typeof value === "function"
- ? styleFunction : styleConstant));
-};
-d3_selectionPrototype.property = function(name, value) {
-
- // If no value is specified, return the first value.
- if (arguments.length < 2) return this.node()[name];
-
- function propertyNull() {
- delete this[name];
- }
-
- function propertyConstant() {
- this[name] = value;
- }
-
- function propertyFunction() {
- var x = value.apply(this, arguments);
- if (x == null) delete this[name];
- else this[name] = x;
- }
-
- return this.each(value == null
- ? propertyNull : (typeof value === "function"
- ? propertyFunction : propertyConstant));
-};
-d3_selectionPrototype.text = function(value) {
- return arguments.length < 1 ? this.node().textContent
- : (this.each(typeof value === "function"
- ? function() { this.textContent = value.apply(this, arguments); }
- : function() { this.textContent = value; }));
-};
-d3_selectionPrototype.html = function(value) {
- return arguments.length < 1 ? this.node().innerHTML
- : (this.each(typeof value === "function"
- ? function() { this.innerHTML = value.apply(this, arguments); }
- : function() { this.innerHTML = value; }));
-};
-// TODO append(node)?
-// TODO append(function)?
-d3_selectionPrototype.append = function(name) {
- name = d3.ns.qualify(name);
-
- function append() {
- return this.appendChild(document.createElement(name));
- }
-
- function appendNS() {
- return this.appendChild(document.createElementNS(name.space, name.local));
- }
-
- return this.select(name.local ? appendNS : append);
-};
-// TODO insert(node, function)?
-// TODO insert(function, string)?
-// TODO insert(function, function)?
-d3_selectionPrototype.insert = function(name, before) {
- name = d3.ns.qualify(name);
-
- function insert() {
- return this.insertBefore(
- document.createElement(name),
- d3_select(before, this));
- }
-
- function insertNS() {
- return this.insertBefore(
- document.createElementNS(name.space, name.local),
- d3_select(before, this));
- }
-
- return this.select(name.local ? insertNS : insert);
-};
-// TODO remove(selector)?
-// TODO remove(node)?
-// TODO remove(function)?
-d3_selectionPrototype.remove = function() {
- return this.each(function() {
- var parent = this.parentNode;
- if (parent) parent.removeChild(this);
- });
-};
-// TODO data(null) for clearing data?
-d3_selectionPrototype.data = function(data, join) {
- var enter = [],
- update = [],
- exit = [];
-
- function bind(group, groupData) {
- var i,
- n = group.length,
- m = groupData.length,
- n0 = Math.min(n, m),
- n1 = Math.max(n, m),
- updateNodes = [],
- enterNodes = [],
- exitNodes = [],
- node,
- nodeData;
-
- if (join) {
- var nodeByKey = {},
- keys = [],
- key,
- j = groupData.length;
-
- for (i = -1; ++i < n;) {
- key = join.call(node = group[i], node.__data__, i);
- if (key in nodeByKey) {
- exitNodes[j++] = node; // duplicate key
- } else {
- nodeByKey[key] = node;
- }
- keys.push(key);
- }
-
- for (i = -1; ++i < m;) {
- node = nodeByKey[key = join.call(groupData, nodeData = groupData[i], i)];
- if (node) {
- node.__data__ = nodeData;
- updateNodes[i] = node;
- enterNodes[i] = exitNodes[i] = null;
- } else {
- enterNodes[i] = d3_selection_dataNode(nodeData);
- updateNodes[i] = exitNodes[i] = null;
- }
- delete nodeByKey[key];
- }
-
- for (i = -1; ++i < n;) {
- if (keys[i] in nodeByKey) {
- exitNodes[i] = group[i];
- }
- }
- } else {
- for (i = -1; ++i < n0;) {
- node = group[i];
- nodeData = groupData[i];
- if (node) {
- node.__data__ = nodeData;
- updateNodes[i] = node;
- enterNodes[i] = exitNodes[i] = null;
- } else {
- enterNodes[i] = d3_selection_dataNode(nodeData);
- updateNodes[i] = exitNodes[i] = null;
- }
- }
- for (; i < m; ++i) {
- enterNodes[i] = d3_selection_dataNode(groupData[i]);
- updateNodes[i] = exitNodes[i] = null;
- }
- for (; i < n1; ++i) {
- exitNodes[i] = group[i];
- enterNodes[i] = updateNodes[i] = null;
- }
- }
-
- enterNodes.update
- = updateNodes;
-
- enterNodes.parentNode
- = updateNodes.parentNode
- = exitNodes.parentNode
- = group.parentNode;
-
- enter.push(enterNodes);
- update.push(updateNodes);
- exit.push(exitNodes);
- }
-
- var i = -1,
- n = this.length,
- group;
- if (typeof data === "function") {
- while (++i < n) {
- bind(group = this[i], data.call(group, group.parentNode.__data__, i));
- }
- } else {
- while (++i < n) {
- bind(group = this[i], data);
- }
- }
-
- var selection = d3_selection(update);
- selection.enter = function() { return d3_selection_enter(enter); };
- selection.exit = function() { return d3_selection(exit); };
- return selection;
-};
-
-function d3_selection_dataNode(data) {
- return {__data__: data};
-}
-function d3_selection_enter(selection) {
- d3_arraySubclass(selection, d3_selection_enterPrototype);
- return selection;
-}
-
-var d3_selection_enterPrototype = [];
-
-d3_selection_enterPrototype.append = d3_selectionPrototype.append;
-d3_selection_enterPrototype.insert = d3_selectionPrototype.insert;
-d3_selection_enterPrototype.empty = d3_selectionPrototype.empty;
-d3_selection_enterPrototype.select = function(selector) {
- var subgroups = [],
- subgroup,
- subnode,
- upgroup,
- group,
- node;
-
- for (var j = -1, m = this.length; ++j < m;) {
- upgroup = (group = this[j]).update;
- subgroups.push(subgroup = []);
- subgroup.parentNode = group.parentNode;
- for (var i = -1, n = group.length; ++i < n;) {
- if (node = group[i]) {
- subgroup.push(upgroup[i] = subnode = selector.call(group.parentNode, node.__data__, i));
- subnode.__data__ = node.__data__;
- } else {
- subgroup.push(null);
- }
- }
- }
-
- return d3_selection(subgroups);
-};
-// TODO preserve null elements to maintain index?
-d3_selectionPrototype.filter = function(filter) {
- var subgroups = [],
- subgroup,
- group,
- node;
-
- for (var j = 0, m = this.length; j < m; j++) {
- subgroups.push(subgroup = []);
- subgroup.parentNode = (group = this[j]).parentNode;
- for (var i = 0, n = group.length; i < n; i++) {
- if ((node = group[i]) && filter.call(node, node.__data__, i)) {
- subgroup.push(node);
- }
- }
- }
-
- return d3_selection(subgroups);
-};
-d3_selectionPrototype.map = function(map) {
- return this.each(function() {
- this.__data__ = map.apply(this, arguments);
- });
-};
-d3_selectionPrototype.sort = function(comparator) {
- comparator = d3_selection_sortComparator.apply(this, arguments);
- for (var j = 0, m = this.length; j < m; j++) {
- for (var group = this[j].sort(comparator), i = 1, n = group.length, prev = group[0]; i < n; i++) {
- var node = group[i];
- if (node) {
- if (prev) prev.parentNode.insertBefore(node, prev.nextSibling);
- prev = node;
- }
- }
- }
- return this;
-};
-
-function d3_selection_sortComparator(comparator) {
- if (!arguments.length) comparator = d3.ascending;
- return function(a, b) {
- return comparator(a && a.__data__, b && b.__data__);
- };
-}
-// type can be namespaced, e.g., "click.foo"
-// listener can be null for removal
-d3_selectionPrototype.on = function(type, listener, capture) {
- if (arguments.length < 3) capture = false;
-
- // parse the type specifier
- var name = "__on" + type, i = type.indexOf(".");
- if (i > 0) type = type.substring(0, i);
-
- // if called with only one argument, return the current listener
- if (arguments.length < 2) return (i = this.node()[name]) && i._;
-
- // remove the old event listener, and add the new event listener
- return this.each(function(d, i) {
- var node = this;
-
- if (node[name]) node.removeEventListener(type, node[name], capture);
- if (listener) node.addEventListener(type, node[name] = l, capture);
-
- // wrapped event listener that preserves i
- function l(e) {
- var o = d3.event; // Events can be reentrant (e.g., focus).
- d3.event = e;
- try {
- listener.call(node, node.__data__, i);
- } finally {
- d3.event = o;
- }
- }
-
- // stash the unwrapped listener for retrieval
- l._ = listener;
- });
-};
-d3_selectionPrototype.each = function(callback) {
- for (var j = -1, m = this.length; ++j < m;) {
- for (var group = this[j], i = -1, n = group.length; ++i < n;) {
- var node = group[i];
- if (node) callback.call(node, node.__data__, i, j);
- }
- }
- return this;
-};
-//
-// Note: assigning to the arguments array simultaneously changes the value of
-// the corresponding argument!
-//
-// TODO The `this` argument probably shouldn't be the first argument to the
-// callback, anyway, since it's redundant. However, that will require a major
-// version bump due to backwards compatibility, so I'm not changing it right
-// away.
-//
-d3_selectionPrototype.call = function(callback) {
- callback.apply(this, (arguments[0] = this, arguments));
- return this;
-};
-d3_selectionPrototype.empty = function() {
- return !this.node();
-};
-d3_selectionPrototype.node = function(callback) {
- for (var j = 0, m = this.length; j < m; j++) {
- for (var group = this[j], i = 0, n = group.length; i < n; i++) {
- var node = group[i];
- if (node) return node;
- }
- }
- return null;
-};
-d3_selectionPrototype.transition = function() {
- var subgroups = [],
- subgroup,
- node;
-
- for (var j = -1, m = this.length; ++j < m;) {
- subgroups.push(subgroup = []);
- for (var group = this[j], i = -1, n = group.length; ++i < n;) {
- subgroup.push((node = group[i]) ? {node: node, delay: 0, duration: 250} : null);
- }
- }
-
- return d3_transition(subgroups, d3_transitionInheritId || ++d3_transitionId);
-};
-var d3_selectionRoot = d3_selection([[document]]);
-
-d3_selectionRoot[0].parentNode = document.documentElement;
-
-// TODO fast singleton implementation!
-d3.select = function(selector) {
- return typeof selector === "string"
- ? d3_selectionRoot.select(selector)
- : d3_selection([[selector]]); // assume node
-};
-
-d3.selectAll = function(selector) {
- return typeof selector === "string"
- ? d3_selectionRoot.selectAll(selector)
- : d3_selection([selector]); // assume node[]
-};
-function d3_transition(groups, id) {
- d3_arraySubclass(groups, d3_transitionPrototype);
-
- var tweens = {},
- event = d3.dispatch("start", "end"),
- ease = d3_transitionEase,
- then = Date.now();
-
- groups.id = id;
-
- groups.tween = function(name, tween) {
- if (arguments.length < 2) return tweens[name];
- if (tween == null) delete tweens[name];
- else tweens[name] = tween;
- return groups;
- };
-
- groups.ease = function(value) {
- if (!arguments.length) return ease;
- ease = typeof value === "function" ? value : d3.ease.apply(d3, arguments);
- return groups;
- };
-
- groups.each = function(type, listener) {
- if (arguments.length < 2) return d3_transition_each.call(groups, type);
- event[type].add(listener);
- return groups;
- };
-
- d3.timer(function(elapsed) {
- groups.each(function(d, i, j) {
- var tweened = [],
- node = this,
- delay = groups[j][i].delay,
- duration = groups[j][i].duration,
- lock = node.__transition__ || (node.__transition__ = {active: 0, count: 0});
-
- ++lock.count;
-
- delay <= elapsed ? start(elapsed) : d3.timer(start, delay, then);
-
- function start(elapsed) {
- if (lock.active > id) return stop();
- lock.active = id;
-
- for (var tween in tweens) {
- if (tween = tweens[tween].call(node, d, i)) {
- tweened.push(tween);
- }
- }
-
- event.start.dispatch.call(node, d, i);
- if (!tick(elapsed)) d3.timer(tick, 0, then);
- return 1;
- }
-
- function tick(elapsed) {
- if (lock.active !== id) return stop();
-
- var t = (elapsed - delay) / duration,
- e = ease(t),
- n = tweened.length;
-
- while (n > 0) {
- tweened[--n].call(node, e);
- }
-
- if (t >= 1) {
- stop();
- d3_transitionInheritId = id;
- event.end.dispatch.call(node, d, i);
- d3_transitionInheritId = 0;
- return 1;
- }
- }
-
- function stop() {
- if (!--lock.count) delete node.__transition__;
- return 1;
- }
- });
- return 1;
- }, 0, then);
-
- return groups;
-}
-
-function d3_transitionTween(b) {
- return typeof b === "function"
- ? function(d, i, a) { var v = b.call(this, d, i) + ""; return a != v && d3.interpolate(a, v); }
- : (b = b + "", function(d, i, a) { return a != b && d3.interpolate(a, b); });
-}
-
-var d3_transitionPrototype = [],
- d3_transitionId = 0,
- d3_transitionInheritId = 0,
- d3_transitionEase = d3.ease("cubic-in-out");
-
-d3_transitionPrototype.call = d3_selectionPrototype.call;
-
-d3.transition = function() {
- return d3_selectionRoot.transition();
-};
-
-d3.transition.prototype = d3_transitionPrototype;
-d3_transitionPrototype.select = function(selector) {
- var subgroups = [],
- subgroup,
- subnode,
- node;
-
- if (typeof selector !== "function") selector = d3_selection_selector(selector);
-
- for (var j = -1, m = this.length; ++j < m;) {
- subgroups.push(subgroup = []);
- for (var group = this[j], i = -1, n = group.length; ++i < n;) {
- if ((node = group[i]) && (subnode = selector.call(node.node, node.node.__data__, i))) {
- if ("__data__" in node.node) subnode.__data__ = node.node.__data__;
- subgroup.push({node: subnode, delay: node.delay, duration: node.duration});
- } else {
- subgroup.push(null);
- }
- }
- }
-
- return d3_transition(subgroups, this.id).ease(this.ease());
-};
-d3_transitionPrototype.selectAll = function(selector) {
- var subgroups = [],
- subgroup,
- node;
-
- if (typeof selector !== "function") selector = d3_selection_selectorAll(selector);
-
- for (var j = -1, m = this.length; ++j < m;) {
- for (var group = this[j], i = -1, n = group.length; ++i < n;) {
- if (node = group[i]) {
- subgroups.push(subgroup = selector.call(node.node, node.node.__data__, i));
- for (var k = -1, o = subgroup.length; ++k < o;) {
- subgroup[k] = {node: subgroup[k], delay: node.delay, duration: node.duration};
- }
- }
- }
- }
-
- return d3_transition(subgroups, this.id).ease(this.ease());
-};
-d3_transitionPrototype.attr = function(name, value) {
- return this.attrTween(name, d3_transitionTween(value));
-};
-
-d3_transitionPrototype.attrTween = function(name, tween) {
- name = d3.ns.qualify(name);
-
- function attrTween(d, i) {
- var f = tween.call(this, d, i, this.getAttribute(name));
- return f && function(t) {
- this.setAttribute(name, f(t));
- };
- }
-
- function attrTweenNS(d, i) {
- var f = tween.call(this, d, i, this.getAttributeNS(name.space, name.local));
- return f && function(t) {
- this.setAttributeNS(name.space, name.local, f(t));
- };
- }
-
- return this.tween("attr." + name, name.local ? attrTweenNS : attrTween);
-};
-d3_transitionPrototype.style = function(name, value, priority) {
- if (arguments.length < 3) priority = "";
- return this.styleTween(name, d3_transitionTween(value), priority);
-};
-
-d3_transitionPrototype.styleTween = function(name, tween, priority) {
- if (arguments.length < 3) priority = "";
- return this.tween("style." + name, function(d, i) {
- var f = tween.call(this, d, i, window.getComputedStyle(this, null).getPropertyValue(name));
- return f && function(t) {
- this.style.setProperty(name, f(t), priority);
- };
- });
-};
-d3_transitionPrototype.text = function(value) {
- return this.tween("text", function(d, i) {
- this.textContent = typeof value === "function"
- ? value.call(this, d, i)
- : value;
- });
-};
-d3_transitionPrototype.remove = function() {
- return this.each("end", function() {
- var p;
- if (!this.__transition__ && (p = this.parentNode)) p.removeChild(this);
- });
-};
-d3_transitionPrototype.delay = function(value) {
- var groups = this;
- return groups.each(typeof value === "function"
- ? function(d, i, j) { groups[j][i].delay = +value.apply(this, arguments); }
- : (value = +value, function(d, i, j) { groups[j][i].delay = value; }));
-};
-d3_transitionPrototype.duration = function(value) {
- var groups = this;
- return groups.each(typeof value === "function"
- ? function(d, i, j) { groups[j][i].duration = +value.apply(this, arguments); }
- : (value = +value, function(d, i, j) { groups[j][i].duration = value; }));
-};
-function d3_transition_each(callback) {
- for (var j = 0, m = this.length; j < m; j++) {
- for (var group = this[j], i = 0, n = group.length; i < n; i++) {
- var node = group[i];
- if (node) callback.call(node = node.node, node.__data__, i, j);
- }
- }
- return this;
-}
-d3_transitionPrototype.transition = function() {
- return this.select(d3_this);
-};
-var d3_timer_queue = null,
- d3_timer_interval, // is an interval (or frame) active?
- d3_timer_timeout; // is a timeout active?
-
-// The timer will continue to fire until callback returns true.
-d3.timer = function(callback, delay, then) {
- var found = false,
- t0,
- t1 = d3_timer_queue;
-
- if (arguments.length < 3) {
- if (arguments.length < 2) delay = 0;
- else if (!isFinite(delay)) return;
- then = Date.now();
- }
-
- // See if the callback's already in the queue.
- while (t1) {
- if (t1.callback === callback) {
- t1.then = then;
- t1.delay = delay;
- found = true;
- break;
- }
- t0 = t1;
- t1 = t1.next;
- }
-
- // Otherwise, add the callback to the queue.
- if (!found) d3_timer_queue = {
- callback: callback,
- then: then,
- delay: delay,
- next: d3_timer_queue
- };
-
- // Start animatin'!
- if (!d3_timer_interval) {
- d3_timer_timeout = clearTimeout(d3_timer_timeout);
- d3_timer_interval = 1;
- d3_timer_frame(d3_timer_step);
- }
-}
-
-function d3_timer_step() {
- var elapsed,
- now = Date.now(),
- t1 = d3_timer_queue;
-
- while (t1) {
- elapsed = now - t1.then;
- if (elapsed >= t1.delay) t1.flush = t1.callback(elapsed);
- t1 = t1.next;
- }
-
- var delay = d3_timer_flush() - now;
- if (delay > 24) {
- if (isFinite(delay)) {
- clearTimeout(d3_timer_timeout);
- d3_timer_timeout = setTimeout(d3_timer_step, delay);
- }
- d3_timer_interval = 0;
- } else {
- d3_timer_interval = 1;
- d3_timer_frame(d3_timer_step);
- }
-}
-
-d3.timer.flush = function() {
- var elapsed,
- now = Date.now(),
- t1 = d3_timer_queue;
-
- while (t1) {
- elapsed = now - t1.then;
- if (!t1.delay) t1.flush = t1.callback(elapsed);
- t1 = t1.next;
- }
-
- d3_timer_flush();
-};
-
-// Flush after callbacks, to avoid concurrent queue modification.
-function d3_timer_flush() {
- var t0 = null,
- t1 = d3_timer_queue,
- then = Infinity;
- while (t1) {
- if (t1.flush) {
- t1 = t0 ? t0.next = t1.next : d3_timer_queue = t1.next;
- } else {
- then = Math.min(then, t1.then + t1.delay);
- t1 = (t0 = t1).next;
- }
- }
- return then;
-}
-
-var d3_timer_frame = window.requestAnimationFrame
- || window.webkitRequestAnimationFrame
- || window.mozRequestAnimationFrame
- || window.oRequestAnimationFrame
- || window.msRequestAnimationFrame
- || function(callback) { setTimeout(callback, 17); };
-function d3_noop() {}
-d3.scale = {};
-
-function d3_scaleExtent(domain) {
- var start = domain[0], stop = domain[domain.length - 1];
- return start < stop ? [start, stop] : [stop, start];
-}
-function d3_scale_nice(domain, nice) {
- var i0 = 0,
- i1 = domain.length - 1,
- x0 = domain[i0],
- x1 = domain[i1],
- dx;
-
- if (x1 < x0) {
- dx = i0; i0 = i1; i1 = dx;
- dx = x0; x0 = x1; x1 = dx;
- }
-
- nice = nice(x1 - x0);
- domain[i0] = nice.floor(x0);
- domain[i1] = nice.ceil(x1);
- return domain;
-}
-
-function d3_scale_niceDefault() {
- return Math;
-}
-d3.scale.linear = function() {
- return d3_scale_linear([0, 1], [0, 1], d3.interpolate, false);
-};
-
-function d3_scale_linear(domain, range, interpolate, clamp) {
- var output,
- input;
-
- function rescale() {
- var linear = domain.length == 2 ? d3_scale_bilinear : d3_scale_polylinear,
- uninterpolate = clamp ? d3_uninterpolateClamp : d3_uninterpolateNumber;
- output = linear(domain, range, uninterpolate, interpolate);
- input = linear(range, domain, uninterpolate, d3.interpolate);
- return scale;
- }
-
- function scale(x) {
- return output(x);
- }
-
- // Note: requires range is coercible to number!
- scale.invert = function(y) {
- return input(y);
- };
-
- scale.domain = function(x) {
- if (!arguments.length) return domain;
- domain = x.map(Number);
- return rescale();
- };
-
- scale.range = function(x) {
- if (!arguments.length) return range;
- range = x;
- return rescale();
- };
-
- scale.rangeRound = function(x) {
- return scale.range(x).interpolate(d3.interpolateRound);
- };
-
- scale.clamp = function(x) {
- if (!arguments.length) return clamp;
- clamp = x;
- return rescale();
- };
-
- scale.interpolate = function(x) {
- if (!arguments.length) return interpolate;
- interpolate = x;
- return rescale();
- };
-
- scale.ticks = function(m) {
- return d3_scale_linearTicks(domain, m);
- };
-
- scale.tickFormat = function(m) {
- return d3_scale_linearTickFormat(domain, m);
- };
-
- scale.nice = function() {
- d3_scale_nice(domain, d3_scale_linearNice);
- return rescale();
- };
-
- scale.copy = function() {
- return d3_scale_linear(domain, range, interpolate, clamp);
- };
-
- return rescale();
-};
-
-function d3_scale_linearRebind(scale, linear) {
- scale.range = d3.rebind(scale, linear.range);
- scale.rangeRound = d3.rebind(scale, linear.rangeRound);
- scale.interpolate = d3.rebind(scale, linear.interpolate);
- scale.clamp = d3.rebind(scale, linear.clamp);
- return scale;
-}
-
-function d3_scale_linearNice(dx) {
- dx = Math.pow(10, Math.round(Math.log(dx) / Math.LN10) - 1);
- return {
- floor: function(x) { return Math.floor(x / dx) * dx; },
- ceil: function(x) { return Math.ceil(x / dx) * dx; }
- };
-}
-
-// TODO Dates? Ugh.
-function d3_scale_linearTickRange(domain, m) {
- var extent = d3_scaleExtent(domain),
- span = extent[1] - extent[0],
- step = Math.pow(10, Math.floor(Math.log(span / m) / Math.LN10)),
- err = m / span * step;
-
- // Filter ticks to get closer to the desired count.
- if (err <= .15) step *= 10;
- else if (err <= .35) step *= 5;
- else if (err <= .75) step *= 2;
-
- // Round start and stop values to step interval.
- extent[0] = Math.ceil(extent[0] / step) * step;
- extent[1] = Math.floor(extent[1] / step) * step + step * .5; // inclusive
- extent[2] = step;
- return extent;
-}
-
-function d3_scale_linearTicks(domain, m) {
- return d3.range.apply(d3, d3_scale_linearTickRange(domain, m));
-}
-
-function d3_scale_linearTickFormat(domain, m) {
- return d3.format(",." + Math.max(0, -Math.floor(Math.log(d3_scale_linearTickRange(domain, m)[2]) / Math.LN10 + .01)) + "f");
-}
-function d3_scale_bilinear(domain, range, uninterpolate, interpolate) {
- var u = uninterpolate(domain[0], domain[1]),
- i = interpolate(range[0], range[1]);
- return function(x) {
- return i(u(x));
- };
-}
-function d3_scale_polylinear(domain, range, uninterpolate, interpolate) {
- var u = [],
- i = [],
- j = 0,
- n = domain.length;
-
- while (++j < n) {
- u.push(uninterpolate(domain[j - 1], domain[j]));
- i.push(interpolate(range[j - 1], range[j]));
- }
-
- return function(x) {
- var j = d3.bisect(domain, x, 1, domain.length - 1) - 1;
- return i[j](u[j](x));
- };
-}
-d3.scale.log = function() {
- return d3_scale_log(d3.scale.linear(), d3_scale_logp);
-};
-
-function d3_scale_log(linear, log) {
- var pow = log.pow;
-
- function scale(x) {
- return linear(log(x));
- }
-
- scale.invert = function(x) {
- return pow(linear.invert(x));
- };
-
- scale.domain = function(x) {
- if (!arguments.length) return linear.domain().map(pow);
- log = x[0] < 0 ? d3_scale_logn : d3_scale_logp;
- pow = log.pow;
- linear.domain(x.map(log));
- return scale;
- };
-
- scale.nice = function() {
- linear.domain(d3_scale_nice(linear.domain(), d3_scale_niceDefault));
- return scale;
- };
-
- scale.ticks = function() {
- var extent = d3_scaleExtent(linear.domain()),
- ticks = [];
- if (extent.every(isFinite)) {
- var i = Math.floor(extent[0]),
- j = Math.ceil(extent[1]),
- u = pow(extent[0]),
- v = pow(extent[1]);
- if (log === d3_scale_logn) {
- ticks.push(pow(i));
- for (; i++ < j;) for (var k = 9; k > 0; k--) ticks.push(pow(i) * k);
- } else {
- for (; i < j; i++) for (var k = 1; k < 10; k++) ticks.push(pow(i) * k);
- ticks.push(pow(i));
- }
- for (i = 0; ticks[i] < u; i++) {} // strip small values
- for (j = ticks.length; ticks[j - 1] > v; j--) {} // strip big values
- ticks = ticks.slice(i, j);
- }
- return ticks;
- };
-
- scale.tickFormat = function() {
- return d3_scale_logTickFormat;
- };
-
- scale.copy = function() {
- return d3_scale_log(linear.copy(), log);
- };
-
- return d3_scale_linearRebind(scale, linear);
-};
-
-function d3_scale_logp(x) {
- return Math.log(x) / Math.LN10;
-}
-
-function d3_scale_logn(x) {
- return -Math.log(-x) / Math.LN10;
-}
-
-d3_scale_logp.pow = function(x) {
- return Math.pow(10, x);
-};
-
-d3_scale_logn.pow = function(x) {
- return -Math.pow(10, -x);
-};
-
-function d3_scale_logTickFormat(d) {
- return d.toPrecision(1);
-}
-d3.scale.pow = function() {
- return d3_scale_pow(d3.scale.linear(), 1);
-};
-
-function d3_scale_pow(linear, exponent) {
- var powp = d3_scale_powPow(exponent),
- powb = d3_scale_powPow(1 / exponent);
-
- function scale(x) {
- return linear(powp(x));
- }
-
- scale.invert = function(x) {
- return powb(linear.invert(x));
- };
-
- scale.domain = function(x) {
- if (!arguments.length) return linear.domain().map(powb);
- linear.domain(x.map(powp));
- return scale;
- };
-
- scale.ticks = function(m) {
- return d3_scale_linearTicks(scale.domain(), m);
- };
-
- scale.tickFormat = function(m) {
- return d3_scale_linearTickFormat(scale.domain(), m);
- };
-
- scale.nice = function() {
- return scale.domain(d3_scale_nice(scale.domain(), d3_scale_linearNice));
- };
-
- scale.exponent = function(x) {
- if (!arguments.length) return exponent;
- var domain = scale.domain();
- powp = d3_scale_powPow(exponent = x);
- powb = d3_scale_powPow(1 / exponent);
- return scale.domain(domain);
- };
-
- scale.copy = function() {
- return d3_scale_pow(linear.copy(), exponent);
- };
-
- return d3_scale_linearRebind(scale, linear);
-};
-
-function d3_scale_powPow(e) {
- return function(x) {
- return x < 0 ? -Math.pow(-x, e) : Math.pow(x, e);
- };
-}
-d3.scale.sqrt = function() {
- return d3.scale.pow().exponent(.5);
-};
-d3.scale.ordinal = function() {
- return d3_scale_ordinal([], {t: "range", x: []});
-};
-
-function d3_scale_ordinal(domain, ranger) {
- var index,
- range,
- rangeBand;
-
- function scale(x) {
- return range[((index[x] || (index[x] = domain.push(x))) - 1) % range.length];
- }
-
- scale.domain = function(x) {
- if (!arguments.length) return domain;
- domain = [];
- index = {};
- var i = -1, n = x.length, xi;
- while (++i < n) if (!index[xi = x[i]]) index[xi] = domain.push(xi);
- return scale[ranger.t](ranger.x, ranger.p);
- };
-
- scale.range = function(x) {
- if (!arguments.length) return range;
- range = x;
- rangeBand = 0;
- ranger = {t: "range", x: x};
- return scale;
- };
-
- scale.rangePoints = function(x, padding) {
- if (arguments.length < 2) padding = 0;
- var start = x[0],
- stop = x[1],
- step = (stop - start) / (domain.length - 1 + padding);
- range = domain.length < 2 ? [(start + stop) / 2] : d3.range(start + step * padding / 2, stop + step / 2, step);
- rangeBand = 0;
- ranger = {t: "rangePoints", x: x, p: padding};
- return scale;
- };
-
- scale.rangeBands = function(x, padding) {
- if (arguments.length < 2) padding = 0;
- var start = x[0],
- stop = x[1],
- step = (stop - start) / (domain.length + padding);
- range = d3.range(start + step * padding, stop, step);
- rangeBand = step * (1 - padding);
- ranger = {t: "rangeBands", x: x, p: padding};
- return scale;
- };
-
- scale.rangeRoundBands = function(x, padding) {
- if (arguments.length < 2) padding = 0;
- var start = x[0],
- stop = x[1],
- step = Math.floor((stop - start) / (domain.length + padding)),
- err = stop - start - (domain.length - padding) * step;
- range = d3.range(start + Math.round(err / 2), stop, step);
- rangeBand = Math.round(step * (1 - padding));
- ranger = {t: "rangeRoundBands", x: x, p: padding};
- return scale;
- };
-
- scale.rangeBand = function() {
- return rangeBand;
- };
-
- scale.copy = function() {
- return d3_scale_ordinal(domain, ranger);
- };
-
- return scale.domain(domain);
-};
-/*
- * This product includes color specifications and designs developed by Cynthia
- * Brewer (http://colorbrewer.org/). See lib/colorbrewer for more information.
- */
-
-d3.scale.category10 = function() {
- return d3.scale.ordinal().range(d3_category10);
-};
-
-d3.scale.category20 = function() {
- return d3.scale.ordinal().range(d3_category20);
-};
-
-d3.scale.category20b = function() {
- return d3.scale.ordinal().range(d3_category20b);
-};
-
-d3.scale.category20c = function() {
- return d3.scale.ordinal().range(d3_category20c);
-};
-
-var d3_category10 = [
- "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
- "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"
-];
-
-var d3_category20 = [
- "#1f77b4", "#aec7e8",
- "#ff7f0e", "#ffbb78",
- "#2ca02c", "#98df8a",
- "#d62728", "#ff9896",
- "#9467bd", "#c5b0d5",
- "#8c564b", "#c49c94",
- "#e377c2", "#f7b6d2",
- "#7f7f7f", "#c7c7c7",
- "#bcbd22", "#dbdb8d",
- "#17becf", "#9edae5"
-];
-
-var d3_category20b = [
- "#393b79", "#5254a3", "#6b6ecf", "#9c9ede",
- "#637939", "#8ca252", "#b5cf6b", "#cedb9c",
- "#8c6d31", "#bd9e39", "#e7ba52", "#e7cb94",
- "#843c39", "#ad494a", "#d6616b", "#e7969c",
- "#7b4173", "#a55194", "#ce6dbd", "#de9ed6"
-];
-
-var d3_category20c = [
- "#3182bd", "#6baed6", "#9ecae1", "#c6dbef",
- "#e6550d", "#fd8d3c", "#fdae6b", "#fdd0a2",
- "#31a354", "#74c476", "#a1d99b", "#c7e9c0",
- "#756bb1", "#9e9ac8", "#bcbddc", "#dadaeb",
- "#636363", "#969696", "#bdbdbd", "#d9d9d9"
-];
-d3.scale.quantile = function() {
- return d3_scale_quantile([], []);
-};
-
-function d3_scale_quantile(domain, range) {
- var thresholds;
-
- function rescale() {
- var k = 0,
- n = domain.length,
- q = range.length;
- thresholds = [];
- while (++k < q) thresholds[k - 1] = d3.quantile(domain, k / q);
- return scale;
- }
-
- function scale(x) {
- if (isNaN(x = +x)) return NaN;
- return range[d3.bisect(thresholds, x)];
- }
-
- scale.domain = function(x) {
- if (!arguments.length) return domain;
- domain = x.filter(function(d) { return !isNaN(d); }).sort(d3.ascending);
- return rescale();
- };
-
- scale.range = function(x) {
- if (!arguments.length) return range;
- range = x;
- return rescale();
- };
-
- scale.quantiles = function() {
- return thresholds;
- };
-
- scale.copy = function() {
- return d3_scale_quantile(domain, range); // copy on write!
- };
-
- return rescale();
-};
-d3.scale.quantize = function() {
- return d3_scale_quantize(0, 1, [0, 1]);
-};
-
-function d3_scale_quantize(x0, x1, range) {
- var kx, i;
-
- function scale(x) {
- return range[Math.max(0, Math.min(i, Math.floor(kx * (x - x0))))];
- }
-
- function rescale() {
- kx = range.length / (x1 - x0);
- i = range.length - 1;
- return scale;
- }
-
- scale.domain = function(x) {
- if (!arguments.length) return [x0, x1];
- x0 = +x[0];
- x1 = +x[x.length - 1];
- return rescale();
- };
-
- scale.range = function(x) {
- if (!arguments.length) return range;
- range = x;
- return rescale();
- };
-
- scale.copy = function() {
- return d3_scale_quantize(x0, x1, range); // copy on write
- };
-
- return rescale();
-};
-d3.svg = {};
-d3.svg.arc = function() {
- var innerRadius = d3_svg_arcInnerRadius,
- outerRadius = d3_svg_arcOuterRadius,
- startAngle = d3_svg_arcStartAngle,
- endAngle = d3_svg_arcEndAngle;
-
- function arc() {
- var r0 = innerRadius.apply(this, arguments),
- r1 = outerRadius.apply(this, arguments),
- a0 = startAngle.apply(this, arguments) + d3_svg_arcOffset,
- a1 = endAngle.apply(this, arguments) + d3_svg_arcOffset,
- da = (a1 < a0 && (da = a0, a0 = a1, a1 = da), a1 - a0),
- df = da < Math.PI ? "0" : "1",
- c0 = Math.cos(a0),
- s0 = Math.sin(a0),
- c1 = Math.cos(a1),
- s1 = Math.sin(a1);
- return da >= d3_svg_arcMax
- ? (r0
- ? "M0," + r1
- + "A" + r1 + "," + r1 + " 0 1,1 0," + (-r1)
- + "A" + r1 + "," + r1 + " 0 1,1 0," + r1
- + "M0," + r0
- + "A" + r0 + "," + r0 + " 0 1,0 0," + (-r0)
- + "A" + r0 + "," + r0 + " 0 1,0 0," + r0
- + "Z"
- : "M0," + r1
- + "A" + r1 + "," + r1 + " 0 1,1 0," + (-r1)
- + "A" + r1 + "," + r1 + " 0 1,1 0," + r1
- + "Z")
- : (r0
- ? "M" + r1 * c0 + "," + r1 * s0
- + "A" + r1 + "," + r1 + " 0 " + df + ",1 " + r1 * c1 + "," + r1 * s1
- + "L" + r0 * c1 + "," + r0 * s1
- + "A" + r0 + "," + r0 + " 0 " + df + ",0 " + r0 * c0 + "," + r0 * s0
- + "Z"
- : "M" + r1 * c0 + "," + r1 * s0
- + "A" + r1 + "," + r1 + " 0 " + df + ",1 " + r1 * c1 + "," + r1 * s1
- + "L0,0"
- + "Z");
- }
-
- arc.innerRadius = function(v) {
- if (!arguments.length) return innerRadius;
- innerRadius = d3.functor(v);
- return arc;
- };
-
- arc.outerRadius = function(v) {
- if (!arguments.length) return outerRadius;
- outerRadius = d3.functor(v);
- return arc;
- };
-
- arc.startAngle = function(v) {
- if (!arguments.length) return startAngle;
- startAngle = d3.functor(v);
- return arc;
- };
-
- arc.endAngle = function(v) {
- if (!arguments.length) return endAngle;
- endAngle = d3.functor(v);
- return arc;
- };
-
- arc.centroid = function() {
- var r = (innerRadius.apply(this, arguments)
- + outerRadius.apply(this, arguments)) / 2,
- a = (startAngle.apply(this, arguments)
- + endAngle.apply(this, arguments)) / 2 + d3_svg_arcOffset;
- return [Math.cos(a) * r, Math.sin(a) * r];
- };
-
- return arc;
-};
-
-var d3_svg_arcOffset = -Math.PI / 2,
- d3_svg_arcMax = 2 * Math.PI - 1e-6;
-
-function d3_svg_arcInnerRadius(d) {
- return d.innerRadius;
-}
-
-function d3_svg_arcOuterRadius(d) {
- return d.outerRadius;
-}
-
-function d3_svg_arcStartAngle(d) {
- return d.startAngle;
-}
-
-function d3_svg_arcEndAngle(d) {
- return d.endAngle;
-}
-function d3_svg_line(projection) {
- var x = d3_svg_lineX,
- y = d3_svg_lineY,
- interpolate = "linear",
- interpolator = d3_svg_lineInterpolators[interpolate],
- tension = .7;
-
- function line(d) {
- return d.length < 1 ? null : "M" + interpolator(projection(d3_svg_linePoints(this, d, x, y)), tension);
- }
-
- line.x = function(v) {
- if (!arguments.length) return x;
- x = v;
- return line;
- };
-
- line.y = function(v) {
- if (!arguments.length) return y;
- y = v;
- return line;
- };
-
- line.interpolate = function(v) {
- if (!arguments.length) return interpolate;
- interpolator = d3_svg_lineInterpolators[interpolate = v];
- return line;
- };
-
- line.tension = function(v) {
- if (!arguments.length) return tension;
- tension = v;
- return line;
- };
-
- return line;
-}
-
-d3.svg.line = function() {
- return d3_svg_line(Object);
-};
-
-// Converts the specified array of data into an array of points
-// (x-y tuples), by evaluating the specified `x` and `y` functions on each
-// data point. The `this` context of the evaluated functions is the specified
-// "self" object; each function is passed the current datum and index.
-function d3_svg_linePoints(self, d, x, y) {
- var points = [],
- i = -1,
- n = d.length,
- fx = typeof x === "function",
- fy = typeof y === "function",
- value;
- if (fx && fy) {
- while (++i < n) points.push([
- x.call(self, value = d[i], i),
- y.call(self, value, i)
- ]);
- } else if (fx) {
- while (++i < n) points.push([x.call(self, d[i], i), y]);
- } else if (fy) {
- while (++i < n) points.push([x, y.call(self, d[i], i)]);
- } else {
- while (++i < n) points.push([x, y]);
- }
- return points;
-}
-
-// The default `x` property, which references d[0].
-function d3_svg_lineX(d) {
- return d[0];
-}
-
-// The default `y` property, which references d[1].
-function d3_svg_lineY(d) {
- return d[1];
-}
-
-// The various interpolators supported by the `line` class.
-var d3_svg_lineInterpolators = {
- "linear": d3_svg_lineLinear,
- "step-before": d3_svg_lineStepBefore,
- "step-after": d3_svg_lineStepAfter,
- "basis": d3_svg_lineBasis,
- "basis-open": d3_svg_lineBasisOpen,
- "basis-closed": d3_svg_lineBasisClosed,
- "bundle": d3_svg_lineBundle,
- "cardinal": d3_svg_lineCardinal,
- "cardinal-open": d3_svg_lineCardinalOpen,
- "cardinal-closed": d3_svg_lineCardinalClosed,
- "monotone": d3_svg_lineMonotone
-};
-
-// Linear interpolation; generates "L" commands.
-function d3_svg_lineLinear(points) {
- var path = [],
- i = 0,
- n = points.length,
- p = points[0];
- path.push(p[0], ",", p[1]);
- while (++i < n) path.push("L", (p = points[i])[0], ",", p[1]);
- return path.join("");
-}
-
-// Step interpolation; generates "H" and "V" commands.
-function d3_svg_lineStepBefore(points) {
- var path = [],
- i = 0,
- n = points.length,
- p = points[0];
- path.push(p[0], ",", p[1]);
- while (++i < n) path.push("V", (p = points[i])[1], "H", p[0]);
- return path.join("");
-}
-
-// Step interpolation; generates "H" and "V" commands.
-function d3_svg_lineStepAfter(points) {
- var path = [],
- i = 0,
- n = points.length,
- p = points[0];
- path.push(p[0], ",", p[1]);
- while (++i < n) path.push("H", (p = points[i])[0], "V", p[1]);
- return path.join("");
-}
-
-// Open cardinal spline interpolation; generates "C" commands.
-function d3_svg_lineCardinalOpen(points, tension) {
- return points.length < 4
- ? d3_svg_lineLinear(points)
- : points[1] + d3_svg_lineHermite(points.slice(1, points.length - 1),
- d3_svg_lineCardinalTangents(points, tension));
-}
-
-// Closed cardinal spline interpolation; generates "C" commands.
-function d3_svg_lineCardinalClosed(points, tension) {
- return points.length < 3
- ? d3_svg_lineLinear(points)
- : points[0] + d3_svg_lineHermite((points.push(points[0]), points),
- d3_svg_lineCardinalTangents([points[points.length - 2]]
- .concat(points, [points[1]]), tension));
-}
-
-// Cardinal spline interpolation; generates "C" commands.
-function d3_svg_lineCardinal(points, tension, closed) {
- return points.length < 3
- ? d3_svg_lineLinear(points)
- : points[0] + d3_svg_lineHermite(points,
- d3_svg_lineCardinalTangents(points, tension));
-}
-
-// Hermite spline construction; generates "C" commands.
-function d3_svg_lineHermite(points, tangents) {
- if (tangents.length < 1
- || (points.length != tangents.length
- && points.length != tangents.length + 2)) {
- return d3_svg_lineLinear(points);
- }
-
- var quad = points.length != tangents.length,
- path = "",
- p0 = points[0],
- p = points[1],
- t0 = tangents[0],
- t = t0,
- pi = 1;
-
- if (quad) {
- path += "Q" + (p[0] - t0[0] * 2 / 3) + "," + (p[1] - t0[1] * 2 / 3)
- + "," + p[0] + "," + p[1];
- p0 = points[1];
- pi = 2;
- }
-
- if (tangents.length > 1) {
- t = tangents[1];
- p = points[pi];
- pi++;
- path += "C" + (p0[0] + t0[0]) + "," + (p0[1] + t0[1])
- + "," + (p[0] - t[0]) + "," + (p[1] - t[1])
- + "," + p[0] + "," + p[1];
- for (var i = 2; i < tangents.length; i++, pi++) {
- p = points[pi];
- t = tangents[i];
- path += "S" + (p[0] - t[0]) + "," + (p[1] - t[1])
- + "," + p[0] + "," + p[1];
- }
- }
-
- if (quad) {
- var lp = points[pi];
- path += "Q" + (p[0] + t[0] * 2 / 3) + "," + (p[1] + t[1] * 2 / 3)
- + "," + lp[0] + "," + lp[1];
- }
-
- return path;
-}
-
-// Generates tangents for a cardinal spline.
-function d3_svg_lineCardinalTangents(points, tension) {
- var tangents = [],
- a = (1 - tension) / 2,
- p0,
- p1 = points[0],
- p2 = points[1],
- i = 1,
- n = points.length;
- while (++i < n) {
- p0 = p1;
- p1 = p2;
- p2 = points[i];
- tangents.push([a * (p2[0] - p0[0]), a * (p2[1] - p0[1])]);
- }
- return tangents;
-}
-
-// B-spline interpolation; generates "C" commands.
-function d3_svg_lineBasis(points) {
- if (points.length < 3) return d3_svg_lineLinear(points);
- var path = [],
- i = 1,
- n = points.length,
- pi = points[0],
- x0 = pi[0],
- y0 = pi[1],
- px = [x0, x0, x0, (pi = points[1])[0]],
- py = [y0, y0, y0, pi[1]];
- path.push(x0, ",", y0);
- d3_svg_lineBasisBezier(path, px, py);
- while (++i < n) {
- pi = points[i];
- px.shift(); px.push(pi[0]);
- py.shift(); py.push(pi[1]);
- d3_svg_lineBasisBezier(path, px, py);
- }
- i = -1;
- while (++i < 2) {
- px.shift(); px.push(pi[0]);
- py.shift(); py.push(pi[1]);
- d3_svg_lineBasisBezier(path, px, py);
- }
- return path.join("");
-}
-
-// Open B-spline interpolation; generates "C" commands.
-function d3_svg_lineBasisOpen(points) {
- if (points.length < 4) return d3_svg_lineLinear(points);
- var path = [],
- i = -1,
- n = points.length,
- pi,
- px = [0],
- py = [0];
- while (++i < 3) {
- pi = points[i];
- px.push(pi[0]);
- py.push(pi[1]);
- }
- path.push(d3_svg_lineDot4(d3_svg_lineBasisBezier3, px)
- + "," + d3_svg_lineDot4(d3_svg_lineBasisBezier3, py));
- --i; while (++i < n) {
- pi = points[i];
- px.shift(); px.push(pi[0]);
- py.shift(); py.push(pi[1]);
- d3_svg_lineBasisBezier(path, px, py);
- }
- return path.join("");
-}
-
-// Closed B-spline interpolation; generates "C" commands.
-function d3_svg_lineBasisClosed(points) {
- var path,
- i = -1,
- n = points.length,
- m = n + 4,
- pi,
- px = [],
- py = [];
- while (++i < 4) {
- pi = points[i % n];
- px.push(pi[0]);
- py.push(pi[1]);
- }
- path = [
- d3_svg_lineDot4(d3_svg_lineBasisBezier3, px), ",",
- d3_svg_lineDot4(d3_svg_lineBasisBezier3, py)
- ];
- --i; while (++i < m) {
- pi = points[i % n];
- px.shift(); px.push(pi[0]);
- py.shift(); py.push(pi[1]);
- d3_svg_lineBasisBezier(path, px, py);
- }
- return path.join("");
-}
-
-function d3_svg_lineBundle(points, tension) {
- var n = points.length - 1,
- x0 = points[0][0],
- y0 = points[0][1],
- dx = points[n][0] - x0,
- dy = points[n][1] - y0,
- i = -1,
- p,
- t;
- while (++i <= n) {
- p = points[i];
- t = i / n;
- p[0] = tension * p[0] + (1 - tension) * (x0 + t * dx);
- p[1] = tension * p[1] + (1 - tension) * (y0 + t * dy);
- }
- return d3_svg_lineBasis(points);
-}
-
-// Returns the dot product of the given four-element vectors.
-function d3_svg_lineDot4(a, b) {
- return a[0] * b[0] + a[1] * b[1] + a[2] * b[2] + a[3] * b[3];
-}
-
-// Matrix to transform basis (b-spline) control points to bezier
-// control points. Derived from FvD 11.2.8.
-var d3_svg_lineBasisBezier1 = [0, 2/3, 1/3, 0],
- d3_svg_lineBasisBezier2 = [0, 1/3, 2/3, 0],
- d3_svg_lineBasisBezier3 = [0, 1/6, 2/3, 1/6];
-
-// Pushes a "C" Bézier curve onto the specified path array, given the
-// two specified four-element arrays which define the control points.
-function d3_svg_lineBasisBezier(path, x, y) {
- path.push(
- "C", d3_svg_lineDot4(d3_svg_lineBasisBezier1, x),
- ",", d3_svg_lineDot4(d3_svg_lineBasisBezier1, y),
- ",", d3_svg_lineDot4(d3_svg_lineBasisBezier2, x),
- ",", d3_svg_lineDot4(d3_svg_lineBasisBezier2, y),
- ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, x),
- ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, y));
-}
-
-// Computes the slope from points p0 to p1.
-function d3_svg_lineSlope(p0, p1) {
- return (p1[1] - p0[1]) / (p1[0] - p0[0]);
-}
-
-// Compute three-point differences for the given points.
-// http://en.wikipedia.org/wiki/Cubic_Hermite_spline#Finite_difference
-function d3_svg_lineFiniteDifferences(points) {
- var i = 0,
- j = points.length - 1,
- m = [],
- p0 = points[0],
- p1 = points[1],
- d = m[0] = d3_svg_lineSlope(p0, p1);
- while (++i < j) {
- m[i] = d + (d = d3_svg_lineSlope(p0 = p1, p1 = points[i + 1]));
- }
- m[i] = d;
- return m;
-}
-
-// Interpolates the given points using Fritsch-Carlson Monotone cubic Hermite
-// interpolation. Returns an array of tangent vectors. For details, see
-// http://en.wikipedia.org/wiki/Monotone_cubic_interpolation
-function d3_svg_lineMonotoneTangents(points) {
- var tangents = [],
- d,
- a,
- b,
- s,
- m = d3_svg_lineFiniteDifferences(points),
- i = -1,
- j = points.length - 1;
-
- // The first two steps are done by computing finite-differences:
- // 1. Compute the slopes of the secant lines between successive points.
- // 2. Initialize the tangents at every point as the average of the secants.
-
- // Then, for each segment…
- while (++i < j) {
- d = d3_svg_lineSlope(points[i], points[i + 1]);
-
- // 3. If two successive yk = y{k + 1} are equal (i.e., d is zero), then set
- // mk = m{k + 1} = 0 as the spline connecting these points must be flat to
- // preserve monotonicity. Ignore step 4 and 5 for those k.
-
- if (Math.abs(d) < 1e-6) {
- m[i] = m[i + 1] = 0;
- } else {
- // 4. Let ak = mk / dk and bk = m{k + 1} / dk.
- a = m[i] / d;
- b = m[i + 1] / d;
-
- // 5. Prevent overshoot and ensure monotonicity by restricting the
- // magnitude of vector <ak, bk> to a circle of radius 3.
- s = a * a + b * b;
- if (s > 9) {
- s = d * 3 / Math.sqrt(s);
- m[i] = s * a;
- m[i + 1] = s * b;
- }
- }
- }
-
- // Compute the normalized tangent vector from the slopes. Note that if x is
- // not monotonic, it's possible that the slope will be infinite, so we protect
- // against NaN by setting the coordinate to zero.
- i = -1; while (++i <= j) {
- s = (points[Math.min(j, i + 1)][0] - points[Math.max(0, i - 1)][0])
- / (6 * (1 + m[i] * m[i]));
- tangents.push([s || 0, m[i] * s || 0]);
- }
-
- return tangents;
-}
-
-function d3_svg_lineMonotone(points) {
- return points.length < 3
- ? d3_svg_lineLinear(points)
- : points[0] +
- d3_svg_lineHermite(points, d3_svg_lineMonotoneTangents(points));
-}
-d3.svg.line.radial = function() {
- var line = d3_svg_line(d3_svg_lineRadial);
- line.radius = line.x, delete line.x;
- line.angle = line.y, delete line.y;
- return line;
-};
-
-function d3_svg_lineRadial(points) {
- var point,
- i = -1,
- n = points.length,
- r,
- a;
- while (++i < n) {
- point = points[i];
- r = point[0];
- a = point[1] + d3_svg_arcOffset;
- point[0] = r * Math.cos(a);
- point[1] = r * Math.sin(a);
- }
- return points;
-}
-function d3_svg_area(projection) {
- var x0 = d3_svg_lineX,
- x1 = d3_svg_lineX,
- y0 = 0,
- y1 = d3_svg_lineY,
- interpolate = "linear",
- interpolator = d3_svg_lineInterpolators[interpolate],
- tension = .7;
-
- function area(d) {
- if (d.length < 1) return null;
- var points0 = d3_svg_linePoints(this, d, x0, y0),
- points1 = d3_svg_linePoints(this, d, x0 === x1 ? d3_svg_areaX(points0) : x1, y0 === y1 ? d3_svg_areaY(points0) : y1);
- return "M" + interpolator(projection(points1), tension)
- + "L" + interpolator(projection(points0.reverse()), tension)
- + "Z";
- }
-
- area.x = function(x) {
- if (!arguments.length) return x1;
- x0 = x1 = x;
- return area;
- };
-
- area.x0 = function(x) {
- if (!arguments.length) return x0;
- x0 = x;
- return area;
- };
-
- area.x1 = function(x) {
- if (!arguments.length) return x1;
- x1 = x;
- return area;
- };
-
- area.y = function(y) {
- if (!arguments.length) return y1;
- y0 = y1 = y;
- return area;
- };
-
- area.y0 = function(y) {
- if (!arguments.length) return y0;
- y0 = y;
- return area;
- };
-
- area.y1 = function(y) {
- if (!arguments.length) return y1;
- y1 = y;
- return area;
- };
-
- area.interpolate = function(x) {
- if (!arguments.length) return interpolate;
- interpolator = d3_svg_lineInterpolators[interpolate = x];
- return area;
- };
-
- area.tension = function(x) {
- if (!arguments.length) return tension;
- tension = x;
- return area;
- };
-
- return area;
-}
-
-d3.svg.area = function() {
- return d3_svg_area(Object);
-};
-
-function d3_svg_areaX(points) {
- return function(d, i) {
- return points[i][0];
- };
-}
-
-function d3_svg_areaY(points) {
- return function(d, i) {
- return points[i][1];
- };
-}
-d3.svg.area.radial = function() {
- var area = d3_svg_area(d3_svg_lineRadial);
- area.radius = area.x, delete area.x;
- area.innerRadius = area.x0, delete area.x0;
- area.outerRadius = area.x1, delete area.x1;
- area.angle = area.y, delete area.y;
- area.startAngle = area.y0, delete area.y0;
- area.endAngle = area.y1, delete area.y1;
- return area;
-};
-d3.svg.chord = function() {
- var source = d3_svg_chordSource,
- target = d3_svg_chordTarget,
- radius = d3_svg_chordRadius,
- startAngle = d3_svg_arcStartAngle,
- endAngle = d3_svg_arcEndAngle;
-
- // TODO Allow control point to be customized.
-
- function chord(d, i) {
- var s = subgroup(this, source, d, i),
- t = subgroup(this, target, d, i);
- return "M" + s.p0
- + arc(s.r, s.p1) + (equals(s, t)
- ? curve(s.r, s.p1, s.r, s.p0)
- : curve(s.r, s.p1, t.r, t.p0)
- + arc(t.r, t.p1)
- + curve(t.r, t.p1, s.r, s.p0))
- + "Z";
- }
-
- function subgroup(self, f, d, i) {
- var subgroup = f.call(self, d, i),
- r = radius.call(self, subgroup, i),
- a0 = startAngle.call(self, subgroup, i) + d3_svg_arcOffset,
- a1 = endAngle.call(self, subgroup, i) + d3_svg_arcOffset;
- return {
- r: r,
- a0: a0,
- a1: a1,
- p0: [r * Math.cos(a0), r * Math.sin(a0)],
- p1: [r * Math.cos(a1), r * Math.sin(a1)]
- };
- }
-
- function equals(a, b) {
- return a.a0 == b.a0 && a.a1 == b.a1;
- }
-
- function arc(r, p) {
- return "A" + r + "," + r + " 0 0,1 " + p;
- }
-
- function curve(r0, p0, r1, p1) {
- return "Q 0,0 " + p1;
- }
-
- chord.radius = function(v) {
- if (!arguments.length) return radius;
- radius = d3.functor(v);
- return chord;
- };
-
- chord.source = function(v) {
- if (!arguments.length) return source;
- source = d3.functor(v);
- return chord;
- };
-
- chord.target = function(v) {
- if (!arguments.length) return target;
- target = d3.functor(v);
- return chord;
- };
-
- chord.startAngle = function(v) {
- if (!arguments.length) return startAngle;
- startAngle = d3.functor(v);
- return chord;
- };
-
- chord.endAngle = function(v) {
- if (!arguments.length) return endAngle;
- endAngle = d3.functor(v);
- return chord;
- };
-
- return chord;
-};
-
-function d3_svg_chordSource(d) {
- return d.source;
-}
-
-function d3_svg_chordTarget(d) {
- return d.target;
-}
-
-function d3_svg_chordRadius(d) {
- return d.radius;
-}
-
-function d3_svg_chordStartAngle(d) {
- return d.startAngle;
-}
-
-function d3_svg_chordEndAngle(d) {
- return d.endAngle;
-}
-d3.svg.diagonal = function() {
- var source = d3_svg_chordSource,
- target = d3_svg_chordTarget,
- projection = d3_svg_diagonalProjection;
-
- function diagonal(d, i) {
- var p0 = source.call(this, d, i),
- p3 = target.call(this, d, i),
- m = (p0.y + p3.y) / 2,
- p = [p0, {x: p0.x, y: m}, {x: p3.x, y: m}, p3];
- p = p.map(projection);
- return "M" + p[0] + "C" + p[1] + " " + p[2] + " " + p[3];
- }
-
- diagonal.source = function(x) {
- if (!arguments.length) return source;
- source = d3.functor(x);
- return diagonal;
- };
-
- diagonal.target = function(x) {
- if (!arguments.length) return target;
- target = d3.functor(x);
- return diagonal;
- };
-
- diagonal.projection = function(x) {
- if (!arguments.length) return projection;
- projection = x;
- return diagonal;
- };
-
- return diagonal;
-};
-
-function d3_svg_diagonalProjection(d) {
- return [d.x, d.y];
-}
-d3.svg.diagonal.radial = function() {
- var diagonal = d3.svg.diagonal(),
- projection = d3_svg_diagonalProjection,
- projection_ = diagonal.projection;
-
- diagonal.projection = function(x) {
- return arguments.length
- ? projection_(d3_svg_diagonalRadialProjection(projection = x))
- : projection;
- };
-
- return diagonal;
-};
-
-function d3_svg_diagonalRadialProjection(projection) {
- return function() {
- var d = projection.apply(this, arguments),
- r = d[0],
- a = d[1] + d3_svg_arcOffset;
- return [r * Math.cos(a), r * Math.sin(a)];
- };
-}
-d3.svg.mouse = function(container) {
- return d3_svg_mousePoint(container, d3.event);
-};
-
-// https://bugs.webkit.org/show_bug.cgi?id=44083
-var d3_mouse_bug44083 = /WebKit/.test(navigator.userAgent) ? -1 : 0;
-
-function d3_svg_mousePoint(container, e) {
- var point = (container.ownerSVGElement || container).createSVGPoint();
- if ((d3_mouse_bug44083 < 0) && (window.scrollX || window.scrollY)) {
- var svg = d3.select(document.body)
- .append("svg:svg")
- .style("position", "absolute")
- .style("top", 0)
- .style("left", 0);
- var ctm = svg[0][0].getScreenCTM();
- d3_mouse_bug44083 = !(ctm.f || ctm.e);
- svg.remove();
- }
- if (d3_mouse_bug44083) {
- point.x = e.pageX;
- point.y = e.pageY;
- } else {
- point.x = e.clientX;
- point.y = e.clientY;
- }
- point = point.matrixTransform(container.getScreenCTM().inverse());
- return [point.x, point.y];
-};
-d3.svg.touches = function(container) {
- var touches = d3.event.touches;
- return touches ? Array.prototype.map.call(touches, function(touch) {
- var point = d3_svg_mousePoint(container, touch);
- point.identifier = touch.identifier;
- return point;
- }) : [];
-};
-d3.svg.symbol = function() {
- var type = d3_svg_symbolType,
- size = d3_svg_symbolSize;
-
- function symbol(d, i) {
- return (d3_svg_symbols[type.call(this, d, i)]
- || d3_svg_symbols.circle)
- (size.call(this, d, i));
- }
-
- symbol.type = function(x) {
- if (!arguments.length) return type;
- type = d3.functor(x);
- return symbol;
- };
-
- // size of symbol in square pixels
- symbol.size = function(x) {
- if (!arguments.length) return size;
- size = d3.functor(x);
- return symbol;
- };
-
- return symbol;
-};
-
-function d3_svg_symbolSize() {
- return 64;
-}
-
-function d3_svg_symbolType() {
- return "circle";
-}
-
-// TODO cross-diagonal?
-var d3_svg_symbols = {
- "circle": function(size) {
- var r = Math.sqrt(size / Math.PI);
- return "M0," + r
- + "A" + r + "," + r + " 0 1,1 0," + (-r)
- + "A" + r + "," + r + " 0 1,1 0," + r
- + "Z";
- },
- "cross": function(size) {
- var r = Math.sqrt(size / 5) / 2;
- return "M" + -3 * r + "," + -r
- + "H" + -r
- + "V" + -3 * r
- + "H" + r
- + "V" + -r
- + "H" + 3 * r
- + "V" + r
- + "H" + r
- + "V" + 3 * r
- + "H" + -r
- + "V" + r
- + "H" + -3 * r
- + "Z";
- },
- "diamond": function(size) {
- var ry = Math.sqrt(size / (2 * d3_svg_symbolTan30)),
- rx = ry * d3_svg_symbolTan30;
- return "M0," + -ry
- + "L" + rx + ",0"
- + " 0," + ry
- + " " + -rx + ",0"
- + "Z";
- },
- "square": function(size) {
- var r = Math.sqrt(size) / 2;
- return "M" + -r + "," + -r
- + "L" + r + "," + -r
- + " " + r + "," + r
- + " " + -r + "," + r
- + "Z";
- },
- "triangle-down": function(size) {
- var rx = Math.sqrt(size / d3_svg_symbolSqrt3),
- ry = rx * d3_svg_symbolSqrt3 / 2;
- return "M0," + ry
- + "L" + rx +"," + -ry
- + " " + -rx + "," + -ry
- + "Z";
- },
- "triangle-up": function(size) {
- var rx = Math.sqrt(size / d3_svg_symbolSqrt3),
- ry = rx * d3_svg_symbolSqrt3 / 2;
- return "M0," + -ry
- + "L" + rx +"," + ry
- + " " + -rx + "," + ry
- + "Z";
- }
-};
-
-d3.svg.symbolTypes = d3.keys(d3_svg_symbols);
-
-var d3_svg_symbolSqrt3 = Math.sqrt(3),
- d3_svg_symbolTan30 = Math.tan(30 * Math.PI / 180);
-d3.svg.axis = function() {
- var scale = d3.scale.linear(),
- orient = "bottom",
- tickMajorSize = 6,
- tickMinorSize = 6,
- tickEndSize = 6,
- tickPadding = 3,
- tickArguments_ = [10],
- tickFormat_,
- tickSubdivide = 0;
-
- function axis(selection) {
- selection.each(function(d, i, j) {
- var g = d3.select(this);
-
- // Ticks.
- var ticks = scale.ticks.apply(scale, tickArguments_),
- tickFormat = tickFormat_ == null ? scale.tickFormat.apply(scale, tickArguments_) : tickFormat_;
-
- // Minor ticks.
- var subticks = d3_svg_axisSubdivide(scale, ticks, tickSubdivide),
- subtick = g.selectAll(".minor").data(subticks, String),
- subtickEnter = subtick.enter().insert("svg:line", "g").attr("class", "tick minor").style("opacity", 1e-6),
- subtickExit = transition(subtick.exit()).style("opacity", 1e-6).remove(),
- subtickUpdate = transition(subtick).style("opacity", 1);
-
- // Major ticks.
- var tick = g.selectAll("g").data(ticks, String),
- tickEnter = tick.enter().insert("svg:g", "path").style("opacity", 1e-6),
- tickExit = transition(tick.exit()).style("opacity", 1e-6).remove(),
- tickUpdate = transition(tick).style("opacity", 1),
- tickTransform;
-
- // Domain.
- var range = d3_scaleExtent(scale.range()),
- path = g.selectAll(".domain").data([0]),
- pathEnter = path.enter().append("svg:path").attr("class", "domain"),
- pathUpdate = transition(path);
-
- // Stash the new scale and grab the old scale.
- var scale0 = this.__chart__ || scale;
- this.__chart__ = scale.copy();
-
- tickEnter.append("svg:line").attr("class", "tick");
- tickEnter.append("svg:text");
- tickUpdate.select("text").text(tickFormat);
-
- switch (orient) {
- case "bottom": {
- tickTransform = d3_svg_axisX;
- subtickUpdate.attr("y2", tickMinorSize);
- tickEnter.select("text").attr("dy", ".71em").attr("text-anchor", "middle");
- tickUpdate.select("line").attr("y2", tickMajorSize);
- tickUpdate.select("text").attr("y", Math.max(tickMajorSize, 0) + tickPadding);
- pathUpdate.attr("d", "M" + range[0] + "," + tickEndSize + "V0H" + range[1] + "V" + tickEndSize);
- break;
- }
- case "top": {
- tickTransform = d3_svg_axisX;
- subtickUpdate.attr("y2", -tickMinorSize);
- tickEnter.select("text").attr("text-anchor", "middle");
- tickUpdate.select("line").attr("y2", -tickMajorSize);
- tickUpdate.select("text").attr("y", -(Math.max(tickMajorSize, 0) + tickPadding));
- pathUpdate.attr("d", "M" + range[0] + "," + -tickEndSize + "V0H" + range[1] + "V" + -tickEndSize);
- break;
- }
- case "left": {
- tickTransform = d3_svg_axisY;
- subtickUpdate.attr("x2", -tickMinorSize);
- tickEnter.select("text").attr("dy", ".32em").attr("text-anchor", "end");
- tickUpdate.select("line").attr("x2", -tickMajorSize);
- tickUpdate.select("text").attr("x", -(Math.max(tickMajorSize, 0) + tickPadding));
- pathUpdate.attr("d", "M" + -tickEndSize + "," + range[0] + "H0V" + range[1] + "H" + -tickEndSize);
- break;
- }
- case "right": {
- tickTransform = d3_svg_axisY;
- subtickUpdate.attr("x2", tickMinorSize);
- tickEnter.select("text").attr("dy", ".32em");
- tickUpdate.select("line").attr("x2", tickMajorSize);
- tickUpdate.select("text").attr("x", Math.max(tickMajorSize, 0) + tickPadding);
- pathUpdate.attr("d", "M" + tickEndSize + "," + range[0] + "H0V" + range[1] + "H" + tickEndSize);
- break;
- }
- }
-
- tickEnter.call(tickTransform, scale0);
- tickUpdate.call(tickTransform, scale);
- tickExit.call(tickTransform, scale);
-
- subtickEnter.call(tickTransform, scale0);
- subtickUpdate.call(tickTransform, scale);
- subtickExit.call(tickTransform, scale);
-
- function transition(o) {
- return selection.delay ? o.transition()
- .delay(selection[j][i].delay)
- .duration(selection[j][i].duration)
- .ease(selection.ease()) : o;
- }
- });
- }
-
- axis.scale = function(x) {
- if (!arguments.length) return scale;
- scale = x;
- return axis;
- };
-
- axis.orient = function(x) {
- if (!arguments.length) return orient;
- orient = x;
- return axis;
- };
-
- axis.ticks = function() {
- if (!arguments.length) return tickArguments_;
- tickArguments_ = arguments;
- return axis;
- };
-
- axis.tickFormat = function(x) {
- if (!arguments.length) return tickFormat_;
- tickFormat_ = x;
- return axis;
- };
-
- axis.tickSize = function(x, y, z) {
- if (!arguments.length) return tickMajorSize;
- var n = arguments.length - 1;
- tickMajorSize = +x;
- tickMinorSize = n > 1 ? +y : tickMajorSize;
- tickEndSize = n > 0 ? +arguments[n] : tickMajorSize;
- return axis;
- };
-
- axis.tickPadding = function(x) {
- if (!arguments.length) return tickPadding;
- tickPadding = +x;
- return axis;
- };
-
- axis.tickSubdivide = function(x) {
- if (!arguments.length) return tickSubdivide;
- tickSubdivide = +x;
- return axis;
- };
-
- return axis;
-};
-
-function d3_svg_axisX(selection, x) {
- selection.attr("transform", function(d) { return "translate(" + x(d) + ",0)"; });
-}
-
-function d3_svg_axisY(selection, y) {
- selection.attr("transform", function(d) { return "translate(0," + y(d) + ")"; });
-}
-
-function d3_svg_axisSubdivide(scale, ticks, m) {
- subticks = [];
- if (m && ticks.length > 1) {
- var extent = d3_scaleExtent(scale.domain()),
- subticks,
- i = -1,
- n = ticks.length,
- d = (ticks[1] - ticks[0]) / ++m,
- j,
- v;
- while (++i < n) {
- for (j = m; --j > 0;) {
- if ((v = +ticks[i] - j * d) >= extent[0]) {
- subticks.push(v);
- }
- }
- }
- for (--i, j = 0; ++j < m && (v = +ticks[i] + j * d) < extent[1];) {
- subticks.push(v);
- }
- }
- return subticks;
-}
-d3.behavior = {};
-d3.behavior.drag = function() {
- var event = d3.dispatch("drag", "dragstart", "dragend");
-
- function drag() {
- this
- .on("mousedown.drag", mousedown)
- .on("touchstart.drag", mousedown);
-
- d3.select(window)
- .on("mousemove.drag", d3_behavior_dragMove)
- .on("touchmove.drag", d3_behavior_dragMove)
- .on("mouseup.drag", d3_behavior_dragUp, true)
- .on("touchend.drag", d3_behavior_dragUp, true)
- .on("click.drag", d3_behavior_dragClick, true);
- }
-
- // snapshot the local context for subsequent dispatch
- function start() {
- d3_behavior_dragEvent = event;
- d3_behavior_dragOffset = d3_behavior_dragPoint((d3_behavior_dragTarget = this).parentNode);
- d3_behavior_dragMoved = 0;
- d3_behavior_dragArguments = arguments;
- }
-
- function mousedown() {
- start.apply(this, arguments);
- d3_behavior_dragDispatch("dragstart");
- }
-
- drag.on = function(type, listener) {
- event[type].add(listener);
- return drag;
- };
-
- return drag;
-};
-
-var d3_behavior_dragEvent,
- d3_behavior_dragTarget,
- d3_behavior_dragArguments,
- d3_behavior_dragOffset,
- d3_behavior_dragMoved,
- d3_behavior_dragStopClick;
-
-function d3_behavior_dragDispatch(type) {
- var o = d3.event, p = d3_behavior_dragTarget.parentNode, dx = 0, dy = 0;
-
- if (p) {
- p = d3_behavior_dragPoint(p);
- dx = p[0] - d3_behavior_dragOffset[0];
- dy = p[1] - d3_behavior_dragOffset[1];
- d3_behavior_dragOffset = p;
- d3_behavior_dragMoved |= dx | dy;
- }
-
- try {
- d3.event = {dx: dx, dy: dy};
- d3_behavior_dragEvent[type].dispatch.apply(d3_behavior_dragTarget, d3_behavior_dragArguments);
- } finally {
- d3.event = o;
- }
-
- o.preventDefault();
-}
-
-function d3_behavior_dragPoint(container) {
- return d3.event.touches
- ? d3.svg.touches(container)[0]
- : d3.svg.mouse(container);
-}
-
-function d3_behavior_dragMove() {
- if (!d3_behavior_dragTarget) return;
- var parent = d3_behavior_dragTarget.parentNode;
-
- // O NOES! The drag element was removed from the DOM.
- if (!parent) return d3_behavior_dragUp();
-
- d3_behavior_dragDispatch("drag");
- d3_behavior_dragCancel();
-}
-
-function d3_behavior_dragUp() {
- if (!d3_behavior_dragTarget) return;
- d3_behavior_dragDispatch("dragend");
- d3_behavior_dragTarget = null;
-
- // If the node was moved, prevent the mouseup from propagating.
- // Also prevent the subsequent click from propagating (e.g., for anchors).
- if (d3_behavior_dragMoved) {
- d3_behavior_dragStopClick = true;
- d3_behavior_dragCancel();
- }
-}
-
-function d3_behavior_dragClick() {
- if (d3_behavior_dragStopClick) {
- d3_behavior_dragCancel();
- d3_behavior_dragStopClick = false;
- }
-}
-
-function d3_behavior_dragCancel() {
- d3.event.stopPropagation();
- d3.event.preventDefault();
-}
-// TODO unbind zoom behavior?
-// TODO unbind listener?
-d3.behavior.zoom = function() {
- var xyz = [0, 0, 0],
- event = d3.dispatch("zoom");
-
- function zoom() {
- this
- .on("mousedown.zoom", mousedown)
- .on("mousewheel.zoom", mousewheel)
- .on("DOMMouseScroll.zoom", mousewheel)
- .on("dblclick.zoom", dblclick)
- .on("touchstart.zoom", touchstart);
-
- d3.select(window)
- .on("mousemove.zoom", d3_behavior_zoomMousemove)
- .on("mouseup.zoom", d3_behavior_zoomMouseup)
- .on("touchmove.zoom", d3_behavior_zoomTouchmove)
- .on("touchend.zoom", d3_behavior_zoomTouchup)
- .on("click.zoom", d3_behavior_zoomClick, true);
- }
-
- // snapshot the local context for subsequent dispatch
- function start() {
- d3_behavior_zoomXyz = xyz;
- d3_behavior_zoomDispatch = event.zoom.dispatch;
- d3_behavior_zoomTarget = this;
- d3_behavior_zoomArguments = arguments;
- }
-
- function mousedown() {
- start.apply(this, arguments);
- d3_behavior_zoomPanning = d3_behavior_zoomLocation(d3.svg.mouse(d3_behavior_zoomTarget));
- d3_behavior_zoomMoved = false;
- d3.event.preventDefault();
- window.focus();
- }
-
- // store starting mouse location
- function mousewheel() {
- start.apply(this, arguments);
- if (!d3_behavior_zoomZooming) d3_behavior_zoomZooming = d3_behavior_zoomLocation(d3.svg.mouse(d3_behavior_zoomTarget));
- d3_behavior_zoomTo(d3_behavior_zoomDelta() + xyz[2], d3.svg.mouse(d3_behavior_zoomTarget), d3_behavior_zoomZooming);
- }
-
- function dblclick() {
- start.apply(this, arguments);
- var mouse = d3.svg.mouse(d3_behavior_zoomTarget);
- d3_behavior_zoomTo(d3.event.shiftKey ? Math.ceil(xyz[2] - 1) : Math.floor(xyz[2] + 1), mouse, d3_behavior_zoomLocation(mouse));
- }
-
- // doubletap detection
- function touchstart() {
- start.apply(this, arguments);
- var touches = d3_behavior_zoomTouchup(),
- touch,
- now = Date.now();
- if ((touches.length === 1) && (now - d3_behavior_zoomLast < 300)) {
- d3_behavior_zoomTo(1 + Math.floor(xyz[2]), touch = touches[0], d3_behavior_zoomLocations[touch.identifier]);
- }
- d3_behavior_zoomLast = now;
- }
-
- zoom.on = function(type, listener) {
- event[type].add(listener);
- return zoom;
- };
-
- return zoom;
-};
-
-var d3_behavior_zoomDiv,
- d3_behavior_zoomPanning,
- d3_behavior_zoomZooming,
- d3_behavior_zoomLocations = {}, // identifier -> location
- d3_behavior_zoomLast = 0,
- d3_behavior_zoomXyz,
- d3_behavior_zoomDispatch,
- d3_behavior_zoomTarget,
- d3_behavior_zoomArguments,
- d3_behavior_zoomMoved,
- d3_behavior_zoomStopClick;
-
-function d3_behavior_zoomLocation(point) {
- return [
- point[0] - d3_behavior_zoomXyz[0],
- point[1] - d3_behavior_zoomXyz[1],
- d3_behavior_zoomXyz[2]
- ];
-}
-
-// detect the pixels that would be scrolled by this wheel event
-function d3_behavior_zoomDelta() {
-
- // mousewheel events are totally broken!
- // https://bugs.webkit.org/show_bug.cgi?id=40441
- // not only that, but Chrome and Safari differ in re. to acceleration!
- if (!d3_behavior_zoomDiv) {
- d3_behavior_zoomDiv = d3.select("body").append("div")
- .style("visibility", "hidden")
- .style("top", 0)
- .style("height", 0)
- .style("width", 0)
- .style("overflow-y", "scroll")
- .append("div")
- .style("height", "2000px")
- .node().parentNode;
- }
-
- var e = d3.event, delta;
- try {
- d3_behavior_zoomDiv.scrollTop = 1000;
- d3_behavior_zoomDiv.dispatchEvent(e);
- delta = 1000 - d3_behavior_zoomDiv.scrollTop;
- } catch (error) {
- delta = e.wheelDelta || (-e.detail * 5);
- }
-
- return delta * .005;
-}
-
-// Note: Since we don't rotate, it's possible for the touches to become
-// slightly detached from their original positions. Thus, we recompute the
-// touch points on touchend as well as touchstart!
-function d3_behavior_zoomTouchup() {
- var touches = d3.svg.touches(d3_behavior_zoomTarget),
- i = -1,
- n = touches.length,
- touch;
- while (++i < n) d3_behavior_zoomLocations[(touch = touches[i]).identifier] = d3_behavior_zoomLocation(touch);
- return touches;
-}
-
-function d3_behavior_zoomTouchmove() {
- var touches = d3.svg.touches(d3_behavior_zoomTarget);
- switch (touches.length) {
-
- // single-touch pan
- case 1: {
- var touch = touches[0];
- d3_behavior_zoomTo(d3_behavior_zoomXyz[2], touch, d3_behavior_zoomLocations[touch.identifier]);
- break;
- }
-
- // double-touch pan + zoom
- case 2: {
- var p0 = touches[0],
- p1 = touches[1],
- p2 = [(p0[0] + p1[0]) / 2, (p0[1] + p1[1]) / 2],
- l0 = d3_behavior_zoomLocations[p0.identifier],
- l1 = d3_behavior_zoomLocations[p1.identifier],
- l2 = [(l0[0] + l1[0]) / 2, (l0[1] + l1[1]) / 2, l0[2]];
- d3_behavior_zoomTo(Math.log(d3.event.scale) / Math.LN2 + l0[2], p2, l2);
- break;
- }
- }
-}
-
-function d3_behavior_zoomMousemove() {
- d3_behavior_zoomZooming = null;
- if (d3_behavior_zoomPanning) {
- d3_behavior_zoomMoved = true;
- d3_behavior_zoomTo(d3_behavior_zoomXyz[2], d3.svg.mouse(d3_behavior_zoomTarget), d3_behavior_zoomPanning);
- }
-}
-
-function d3_behavior_zoomMouseup() {
- if (d3_behavior_zoomPanning) {
- if (d3_behavior_zoomMoved) d3_behavior_zoomStopClick = true;
- d3_behavior_zoomMousemove();
- d3_behavior_zoomPanning = null;
- }
-}
-
-function d3_behavior_zoomClick() {
- if (d3_behavior_zoomStopClick) {
- d3.event.stopPropagation();
- d3.event.preventDefault();
- d3_behavior_zoomStopClick = false;
- }
-}
-
-function d3_behavior_zoomTo(z, x0, x1) {
- var K = Math.pow(2, (d3_behavior_zoomXyz[2] = z) - x1[2]),
- x = d3_behavior_zoomXyz[0] = x0[0] - K * x1[0],
- y = d3_behavior_zoomXyz[1] = x0[1] - K * x1[1],
- o = d3.event, // Events can be reentrant (e.g., focus).
- k = Math.pow(2, z);
-
- d3.event = {
- scale: k,
- translate: [x, y],
- transform: function(sx, sy) {
- if (sx) transform(sx, x);
- if (sy) transform(sy, y);
- }
- };
-
- function transform(scale, o) {
- var domain = scale.__domain || (scale.__domain = scale.domain()),
- range = scale.range().map(function(v) { return (v - o) / k; });
- scale.domain(domain).domain(range.map(scale.invert));
- }
-
- try {
- d3_behavior_zoomDispatch.apply(d3_behavior_zoomTarget, d3_behavior_zoomArguments);
- } finally {
- d3.event = o;
- }
-
- o.preventDefault();
-}
-})();
diff --git a/rtd_phosphonetx/source/html/demoapp/d3.layout.js b/rtd_phosphonetx/source/html/demoapp/d3.layout.js
deleted file mode 100755
index 6cc1d716167..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/d3.layout.js
+++ /dev/null
@@ -1,1865 +0,0 @@
-(function(){d3.layout = {};
-// Implements hierarchical edge bundling using Holten's algorithm. For each
-// input link, a path is computed that travels through the tree, up the parent
-// hierarchy to the least common ancestor, and then back down to the destination
-// node. Each path is simply an array of nodes.
-d3.layout.bundle = function() {
- return function(links) {
- var paths = [],
- i = -1,
- n = links.length;
- while (++i < n) paths.push(d3_layout_bundlePath(links[i]));
- return paths;
- };
-};
-
-function d3_layout_bundlePath(link) {
- var start = link.source,
- end = link.target,
- lca = d3_layout_bundleLeastCommonAncestor(start, end),
- points = [start];
- while (start !== lca) {
- start = start.parent;
- points.push(start);
- }
- var k = points.length;
- while (end !== lca) {
- points.splice(k, 0, end);
- end = end.parent;
- }
- return points;
-}
-
-function d3_layout_bundleAncestors(node) {
- var ancestors = [],
- parent = node.parent;
- while (parent != null) {
- ancestors.push(node);
- node = parent;
- parent = parent.parent;
- }
- ancestors.push(node);
- return ancestors;
-}
-
-function d3_layout_bundleLeastCommonAncestor(a, b) {
- if (a === b) return a;
- var aNodes = d3_layout_bundleAncestors(a),
- bNodes = d3_layout_bundleAncestors(b),
- aNode = aNodes.pop(),
- bNode = bNodes.pop(),
- sharedNode = null;
- while (aNode === bNode) {
- sharedNode = aNode;
- aNode = aNodes.pop();
- bNode = bNodes.pop();
- }
- return sharedNode;
-}
-d3.layout.chord = function() {
- var chord = {},
- chords,
- groups,
- matrix,
- n,
- padding = 0,
- sortGroups,
- sortSubgroups,
- sortChords;
-
- function relayout() {
- var subgroups = {},
- groupSums = [],
- groupIndex = d3.range(n),
- subgroupIndex = [],
- k,
- x,
- x0,
- i,
- j;
-
- chords = [];
- groups = [];
-
- // Compute the sum.
- k = 0, i = -1; while (++i < n) {
- x = 0, j = -1; while (++j < n) {
- x += matrix[i][j];
- }
- groupSums.push(x);
- subgroupIndex.push(d3.range(n));
- k += x;
- }
-
- // Sort groups…
- if (sortGroups) {
- groupIndex.sort(function(a, b) {
- return sortGroups(groupSums[a], groupSums[b]);
- });
- }
-
- // Sort subgroups…
- if (sortSubgroups) {
- subgroupIndex.forEach(function(d, i) {
- d.sort(function(a, b) {
- return sortSubgroups(matrix[i][a], matrix[i][b]);
- });
- });
- }
-
- // Convert the sum to scaling factor for [0, 2pi].
- // TODO Allow start and end angle to be specified.
- // TODO Allow padding to be specified as percentage?
- k = (2 * Math.PI - padding * n) / k;
-
- // Compute the start and end angle for each group and subgroup.
- x = 0, i = -1; while (++i < n) {
- x0 = x, j = -1; while (++j < n) {
- var di = groupIndex[i],
- dj = subgroupIndex[i][j],
- v = matrix[di][dj];
- subgroups[di + "-" + dj] = {
- index: di,
- subindex: dj,
- startAngle: x,
- endAngle: x += v * k,
- value: v
- };
- }
- groups.push({
- index: di,
- startAngle: x0,
- endAngle: x,
- value: (x - x0) / k
- });
- x += padding;
- }
-
- // Generate chords for each (non-empty) subgroup-subgroup link.
- i = -1; while (++i < n) {
- j = i - 1; while (++j < n) {
- var source = subgroups[i + "-" + j],
- target = subgroups[j + "-" + i];
- if (source.value || target.value) {
- chords.push(source.value < target.value
- ? {source: target, target: source}
- : {source: source, target: target});
- }
- }
- }
-
- if (sortChords) resort();
- }
-
- function resort() {
- chords.sort(function(a, b) {
- return sortChords(a.target.value, b.target.value);
- });
- }
-
- chord.matrix = function(x) {
- if (!arguments.length) return matrix;
- n = (matrix = x) && matrix.length;
- chords = groups = null;
- return chord;
- };
-
- chord.padding = function(x) {
- if (!arguments.length) return padding;
- padding = x;
- chords = groups = null;
- return chord;
- };
-
- chord.sortGroups = function(x) {
- if (!arguments.length) return sortGroups;
- sortGroups = x;
- chords = groups = null;
- return chord;
- };
-
- chord.sortSubgroups = function(x) {
- if (!arguments.length) return sortSubgroups;
- sortSubgroups = x;
- chords = null;
- return chord;
- };
-
- chord.sortChords = function(x) {
- if (!arguments.length) return sortChords;
- sortChords = x;
- if (chords) resort();
- return chord;
- };
-
- chord.chords = function() {
- if (!chords) relayout();
- return chords;
- };
-
- chord.groups = function() {
- if (!groups) relayout();
- return groups;
- };
-
- return chord;
-};
-// A rudimentary force layout using Gauss-Seidel.
-d3.layout.force = function() {
- var force = {},
- event = d3.dispatch("tick"),
- size = [1, 1],
- drag,
- alpha,
- friction = .9,
- linkDistance = d3_layout_forceLinkDistance,
- linkStrength = d3_layout_forceLinkStrength,
- charge = -30,
- gravity = .1,
- theta = .8,
- interval,
- nodes = [],
- links = [],
- distances,
- strengths;
-
- function repulse(node, kc) {
- return function(quad, x1, y1, x2, y2) {
- if (quad.point !== node) {
- var dx = quad.cx - node.x,
- dy = quad.cy - node.y,
- dn = 1 / Math.sqrt(dx * dx + dy * dy);
-
- /* Barnes-Hut criterion. */
- if ((x2 - x1) * dn < theta) {
- var k = kc * quad.count * dn * dn;
- node.px -= dx * k;
- node.py -= dy * k;
- return true;
- }
-
- if (quad.point && isFinite(dn)) {
- var k = kc * dn * dn;
- node.px -= dx * k;
- node.py -= dy * k;
- }
- }
- };
- }
-
- function tick() {
- var n = nodes.length,
- m = links.length,
- q,
- i, // current index
- o, // current object
- s, // current source
- t, // current target
- l, // current distance
- k, // current force
- x, // x-distance
- y; // y-distance
-
- // gauss-seidel relaxation for links
- for (i = 0; i < m; ++i) {
- o = links[i];
- s = o.source;
- t = o.target;
- x = t.x - s.x;
- y = t.y - s.y;
- if (l = (x * x + y * y)) {
- l = alpha * strengths[i] * ((l = Math.sqrt(l)) - distances[i]) / l;
- x *= l;
- y *= l;
- t.x -= x * (k = s.weight / (t.weight + s.weight));
- t.y -= y * k;
- s.x += x * (k = 1 - k);
- s.y += y * k;
- }
- }
-
- // apply gravity forces
- if (k = alpha * gravity) {
- x = size[0] / 2;
- y = size[1] / 2;
- i = -1; if (k) while (++i < n) {
- o = nodes[i];
- o.x += (x - o.x) * k;
- o.y += (y - o.y) * k;
- }
- }
-
- // compute quadtree center of mass and apply charge forces
- if (k = alpha * charge) {
- d3_layout_forceAccumulate(q = d3.geom.quadtree(nodes));
- i = -1; while (++i < n) {
- if (!(o = nodes[i]).fixed) {
- q.visit(repulse(o, k));
- }
- }
- }
-
- // position verlet integration
- i = -1; while (++i < n) {
- o = nodes[i];
- if (o.fixed) {
- o.x = o.px;
- o.y = o.py;
- } else {
- o.x -= (o.px - (o.px = o.x)) * friction;
- o.y -= (o.py - (o.py = o.y)) * friction;
- }
- }
-
- event.tick.dispatch({type: "tick", alpha: alpha});
-
- // simulated annealing, basically
- return (alpha *= .99) < .005;
- }
-
- force.on = function(type, listener) {
- event[type].add(listener);
- return force;
- };
-
- force.nodes = function(x) {
- if (!arguments.length) return nodes;
- nodes = x;
- return force;
- };
-
- force.links = function(x) {
- if (!arguments.length) return links;
- links = x;
- return force;
- };
-
- force.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return force;
- };
-
- force.linkDistance = function(x) {
- if (!arguments.length) return linkDistance;
- linkDistance = d3.functor(x);
- return force;
- };
-
- // For backwards-compatibility.
- force.distance = force.linkDistance;
-
- force.linkStrength = function(x) {
- if (!arguments.length) return linkStrength;
- linkStrength = d3.functor(x);
- return force;
- };
-
- force.friction = function(x) {
- if (!arguments.length) return friction;
- friction = x;
- return force;
- };
-
- force.charge = function(x) {
- if (!arguments.length) return charge;
- charge = x;
- return force;
- };
-
- force.gravity = function(x) {
- if (!arguments.length) return gravity;
- gravity = x;
- return force;
- };
-
- force.theta = function(x) {
- if (!arguments.length) return theta;
- theta = x;
- return force;
- };
-
- force.start = function() {
- var i,
- j,
- n = nodes.length,
- m = links.length,
- w = size[0],
- h = size[1],
- neighbors,
- o;
-
- for (i = 0; i < n; ++i) {
- (o = nodes[i]).index = i;
- o.weight = 0;
- }
-
- distances = [];
- strengths = [];
- for (i = 0; i < m; ++i) {
- o = links[i];
- if (typeof o.source == "number") o.source = nodes[o.source];
- if (typeof o.target == "number") o.target = nodes[o.target];
- distances[i] = linkDistance.call(this, o, i);
- strengths[i] = linkStrength.call(this, o, i);
- ++o.source.weight;
- ++o.target.weight;
- }
-
- for (i = 0; i < n; ++i) {
- o = nodes[i];
- if (isNaN(o.x)) o.x = position("x", w);
- if (isNaN(o.y)) o.y = position("y", h);
- if (isNaN(o.px)) o.px = o.x;
- if (isNaN(o.py)) o.py = o.y;
- }
-
- // initialize node position based on first neighbor
- function position(dimension, size) {
- var neighbors = neighbor(i),
- j = -1,
- m = neighbors.length,
- x;
- while (++j < m) if (!isNaN(x = neighbors[j][dimension])) return x;
- return Math.random() * size;
- }
-
- // initialize neighbors lazily
- function neighbor() {
- if (!neighbors) {
- neighbors = [];
- for (j = 0; j < n; ++j) {
- neighbors[j] = [];
- }
- for (j = 0; j < m; ++j) {
- var o = links[j];
- neighbors[o.source.index].push(o.target);
- neighbors[o.target.index].push(o.source);
- }
- }
- return neighbors[i];
- }
-
- return force.resume();
- };
-
- force.resume = function() {
- alpha = .1;
- d3.timer(tick);
- return force;
- };
-
- force.stop = function() {
- alpha = 0;
- return force;
- };
-
- // use `node.call(force.drag)` to make nodes draggable
- force.drag = function() {
- if (!drag) drag = d3.behavior.drag()
- .on("dragstart", dragstart)
- .on("drag", d3_layout_forceDrag)
- .on("dragend", d3_layout_forceDragEnd);
-
- this.on("mouseover.force", d3_layout_forceDragOver)
- .on("mouseout.force", d3_layout_forceDragOut)
- .call(drag);
- };
-
- function dragstart(d) {
- d3_layout_forceDragOver(d3_layout_forceDragNode = d);
- d3_layout_forceDragForce = force;
- }
-
- return force;
-};
-
-var d3_layout_forceDragForce,
- d3_layout_forceDragNode;
-
-function d3_layout_forceDragOver(d) {
- d.fixed |= 2;
-}
-
-function d3_layout_forceDragOut(d) {
- if (d !== d3_layout_forceDragNode) d.fixed &= 1;
-}
-
-function d3_layout_forceDragEnd() {
- d3_layout_forceDrag();
- d3_layout_forceDragNode.fixed &= 1;
- d3_layout_forceDragForce = d3_layout_forceDragNode = null;
-}
-
-function d3_layout_forceDrag() {
- d3_layout_forceDragNode.px += d3.event.dx;
- d3_layout_forceDragNode.py += d3.event.dy;
- d3_layout_forceDragForce.resume(); // restart annealing
-}
-
-function d3_layout_forceAccumulate(quad) {
- var cx = 0,
- cy = 0;
- quad.count = 0;
- if (!quad.leaf) {
- var nodes = quad.nodes,
- n = nodes.length,
- i = -1,
- c;
- while (++i < n) {
- c = nodes[i];
- if (c == null) continue;
- d3_layout_forceAccumulate(c);
- quad.count += c.count;
- cx += c.count * c.cx;
- cy += c.count * c.cy;
- }
- }
- if (quad.point) {
- // jitter internal nodes that are coincident
- if (!quad.leaf) {
- quad.point.x += Math.random() - .5;
- quad.point.y += Math.random() - .5;
- }
- quad.count++;
- cx += quad.point.x;
- cy += quad.point.y;
- }
- quad.cx = cx / quad.count;
- quad.cy = cy / quad.count;
-}
-
-function d3_layout_forceLinkDistance(link) {
- return 20;
-}
-
-function d3_layout_forceLinkStrength(link) {
- return 1;
-}
-d3.layout.partition = function() {
- var hierarchy = d3.layout.hierarchy(),
- size = [1, 1]; // width, height
-
- function position(node, x, dx, dy) {
- var children = node.children;
- node.x = x;
- node.y = node.depth * dy;
- node.dx = dx;
- node.dy = dy;
- if (children) {
- var i = -1,
- n = children.length,
- c,
- d;
- dx = node.value ? dx / node.value : 0;
- while (++i < n) {
- position(c = children[i], x, d = c.value * dx, dy);
- x += d;
- }
- }
- }
-
- function depth(node) {
- var children = node.children,
- d = 0;
- if (children) {
- var i = -1,
- n = children.length;
- while (++i < n) d = Math.max(d, depth(children[i]));
- }
- return 1 + d;
- }
-
- function partition(d, i) {
- var nodes = hierarchy.call(this, d, i);
- position(nodes[0], 0, size[0], size[1] / depth(nodes[0]));
- return nodes;
- }
-
- partition.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return partition;
- };
-
- return d3_layout_hierarchyRebind(partition, hierarchy);
-};
-d3.layout.pie = function() {
- var value = Number,
- sort = null,
- startAngle = 0,
- endAngle = 2 * Math.PI;
-
- function pie(data, i) {
-
- // Compute the start angle.
- var a = +(typeof startAngle === "function"
- ? startAngle.apply(this, arguments)
- : startAngle);
-
- // Compute the angular range (end - start).
- var k = (typeof endAngle === "function"
- ? endAngle.apply(this, arguments)
- : endAngle) - startAngle;
-
- // Optionally sort the data.
- var index = d3.range(data.length);
- if (sort != null) index.sort(function(i, j) {
- return sort(data[i], data[j]);
- });
-
- // Compute the numeric values for each data element.
- var values = data.map(value);
-
- // Convert k into a scale factor from value to angle, using the sum.
- k /= values.reduce(function(p, d) { return p + d; }, 0);
-
- // Compute the arcs!
- var arcs = index.map(function(i) {
- return {
- data: data[i],
- value: d = values[i],
- startAngle: a,
- endAngle: a += d * k
- };
- });
-
- // Return the arcs in the original data's order.
- return data.map(function(d, i) {
- return arcs[index[i]];
- });
- }
-
- /**
- * Specifies the value function *x*, which returns a nonnegative numeric value
- * for each datum. The default value function is `Number`. The value function
- * is passed two arguments: the current datum and the current index.
- */
- pie.value = function(x) {
- if (!arguments.length) return value;
- value = x;
- return pie;
- };
-
- /**
- * Specifies a sort comparison operator *x*. The comparator is passed two data
- * elements from the data array, a and b; it returns a negative value if a is
- * less than b, a positive value if a is greater than b, and zero if a equals
- * b.
- */
- pie.sort = function(x) {
- if (!arguments.length) return sort;
- sort = x;
- return pie;
- };
-
- /**
- * Specifies the overall start angle of the pie chart. Defaults to 0. The
- * start angle can be specified either as a constant or as a function; in the
- * case of a function, it is evaluated once per array (as opposed to per
- * element).
- */
- pie.startAngle = function(x) {
- if (!arguments.length) return startAngle;
- startAngle = x;
- return pie;
- };
-
- /**
- * Specifies the overall end angle of the pie chart. Defaults to 2Ï€. The
- * end angle can be specified either as a constant or as a function; in the
- * case of a function, it is evaluated once per array (as opposed to per
- * element).
- */
- pie.endAngle = function(x) {
- if (!arguments.length) return endAngle;
- endAngle = x;
- return pie;
- };
-
- return pie;
-};
-// data is two-dimensional array of x,y; we populate y0
-d3.layout.stack = function() {
- var values = Object,
- order = d3_layout_stackOrders["default"],
- offset = d3_layout_stackOffsets["zero"],
- out = d3_layout_stackOut,
- x = d3_layout_stackX,
- y = d3_layout_stackY;
-
- function stack(data, index) {
-
- // Convert series to canonical two-dimensional representation.
- var series = data.map(function(d, i) {
- return values.call(stack, d, i);
- });
-
- // Convert each series to canonical [[x,y]] representation.
- var points = series.map(function(d, i) {
- return d.map(function(v, i) {
- return [x.call(stack, v, i), y.call(stack, v, i)];
- });
- });
-
- // Compute the order of series, and permute them.
- var orders = order.call(stack, points, index);
- series = d3.permute(series, orders);
- points = d3.permute(points, orders);
-
- // Compute the baseline…
- var offsets = offset.call(stack, points, index);
-
- // And propagate it to other series.
- var n = series.length,
- m = series[0].length,
- i,
- j,
- o;
- for (j = 0; j < m; ++j) {
- out.call(stack, series[0][j], o = offsets[j], points[0][j][1]);
- for (i = 1; i < n; ++i) {
- out.call(stack, series[i][j], o += points[i - 1][j][1], points[i][j][1]);
- }
- }
-
- return data;
- }
-
- stack.values = function(x) {
- if (!arguments.length) return values;
- values = x;
- return stack;
- };
-
- stack.order = function(x) {
- if (!arguments.length) return order;
- order = typeof x === "function" ? x : d3_layout_stackOrders[x];
- return stack;
- };
-
- stack.offset = function(x) {
- if (!arguments.length) return offset;
- offset = typeof x === "function" ? x : d3_layout_stackOffsets[x];
- return stack;
- };
-
- stack.x = function(z) {
- if (!arguments.length) return x;
- x = z;
- return stack;
- };
-
- stack.y = function(z) {
- if (!arguments.length) return y;
- y = z;
- return stack;
- };
-
- stack.out = function(z) {
- if (!arguments.length) return out;
- out = z;
- return stack;
- };
-
- return stack;
-}
-
-function d3_layout_stackX(d) {
- return d.x;
-}
-
-function d3_layout_stackY(d) {
- return d.y;
-}
-
-function d3_layout_stackOut(d, y0, y) {
- d.y0 = y0;
- d.y = y;
-}
-
-var d3_layout_stackOrders = {
-
- "inside-out": function(data) {
- var n = data.length,
- i,
- j,
- max = data.map(d3_layout_stackMaxIndex),
- sums = data.map(d3_layout_stackReduceSum),
- index = d3.range(n).sort(function(a, b) { return max[a] - max[b]; }),
- top = 0,
- bottom = 0,
- tops = [],
- bottoms = [];
- for (i = 0; i < n; ++i) {
- j = index[i];
- if (top < bottom) {
- top += sums[j];
- tops.push(j);
- } else {
- bottom += sums[j];
- bottoms.push(j);
- }
- }
- return bottoms.reverse().concat(tops);
- },
-
- "reverse": function(data) {
- return d3.range(data.length).reverse();
- },
-
- "default": function(data) {
- return d3.range(data.length);
- }
-
-};
-
-var d3_layout_stackOffsets = {
-
- "silhouette": function(data) {
- var n = data.length,
- m = data[0].length,
- sums = [],
- max = 0,
- i,
- j,
- o,
- y0 = [];
- for (j = 0; j < m; ++j) {
- for (i = 0, o = 0; i < n; i++) o += data[i][j][1];
- if (o > max) max = o;
- sums.push(o);
- }
- for (j = 0; j < m; ++j) {
- y0[j] = (max - sums[j]) / 2;
- }
- return y0;
- },
-
- "wiggle": function(data) {
- var n = data.length,
- x = data[0],
- m = x.length,
- max = 0,
- i,
- j,
- k,
- s1,
- s2,
- s3,
- dx,
- o,
- o0,
- y0 = [];
- y0[0] = o = o0 = 0;
- for (j = 1; j < m; ++j) {
- for (i = 0, s1 = 0; i < n; ++i) s1 += data[i][j][1];
- for (i = 0, s2 = 0, dx = x[j][0] - x[j - 1][0]; i < n; ++i) {
- for (k = 0, s3 = (data[i][j][1] - data[i][j - 1][1]) / (2 * dx); k < i; ++k) {
- s3 += (data[k][j][1] - data[k][j - 1][1]) / dx;
- }
- s2 += s3 * data[i][j][1];
- }
- y0[j] = o -= s1 ? s2 / s1 * dx : 0;
- if (o < o0) o0 = o;
- }
- for (j = 0; j < m; ++j) y0[j] -= o0;
- return y0;
- },
-
- "expand": function(data) {
- var n = data.length,
- m = data[0].length,
- k = 1 / n,
- i,
- j,
- o,
- y0 = [];
- for (j = 0; j < m; ++j) {
- for (i = 0, o = 0; i < n; i++) o += data[i][j][1];
- if (o) for (i = 0; i < n; i++) data[i][j][1] /= o;
- else for (i = 0; i < n; i++) data[i][j][1] = k;
- }
- for (j = 0; j < m; ++j) y0[j] = 0;
- return y0;
- },
-
- "zero": function(data) {
- var j = -1,
- m = data[0].length,
- y0 = [];
- while (++j < m) y0[j] = 0;
- return y0;
- }
-
-};
-
-function d3_layout_stackMaxIndex(array) {
- var i = 1,
- j = 0,
- v = array[0][1],
- k,
- n = array.length;
- for (; i < n; ++i) {
- if ((k = array[i][1]) > v) {
- j = i;
- v = k;
- }
- }
- return j;
-}
-
-function d3_layout_stackReduceSum(d) {
- return d.reduce(d3_layout_stackSum, 0);
-}
-
-function d3_layout_stackSum(p, d) {
- return p + d[1];
-}
-d3.layout.histogram = function() {
- var frequency = true,
- valuer = Number,
- ranger = d3_layout_histogramRange,
- binner = d3_layout_histogramBinSturges;
-
- function histogram(data, i) {
- var bins = [],
- values = data.map(valuer, this),
- range = ranger.call(this, values, i),
- thresholds = binner.call(this, range, values, i),
- bin,
- i = -1,
- n = values.length,
- m = thresholds.length - 1,
- k = frequency ? 1 : 1 / n,
- x;
-
- // Initialize the bins.
- while (++i < m) {
- bin = bins[i] = [];
- bin.dx = thresholds[i + 1] - (bin.x = thresholds[i]);
- bin.y = 0;
- }
-
- // Fill the bins, ignoring values outside the range.
- i = -1; while(++i < n) {
- x = values[i];
- if ((x >= range[0]) && (x <= range[1])) {
- bin = bins[d3.bisect(thresholds, x, 1, m) - 1];
- bin.y += k;
- bin.push(data[i]);
- }
- }
-
- return bins;
- }
-
- // Specifies how to extract a value from the associated data. The default
- // value function is `Number`, which is equivalent to the identity function.
- histogram.value = function(x) {
- if (!arguments.length) return valuer;
- valuer = x;
- return histogram;
- };
-
- // Specifies the range of the histogram. Values outside the specified range
- // will be ignored. The argument `x` may be specified either as a two-element
- // array representing the minimum and maximum value of the range, or as a
- // function that returns the range given the array of values and the current
- // index `i`. The default range is the extent (minimum and maximum) of the
- // values.
- histogram.range = function(x) {
- if (!arguments.length) return ranger;
- ranger = d3.functor(x);
- return histogram;
- };
-
- // Specifies how to bin values in the histogram. The argument `x` may be
- // specified as a number, in which case the range of values will be split
- // uniformly into the given number of bins. Or, `x` may be an array of
- // threshold values, defining the bins; the specified array must contain the
- // rightmost (upper) value, thus specifying n + 1 values for n bins. Or, `x`
- // may be a function which is evaluated, being passed the range, the array of
- // values, and the current index `i`, returning an array of thresholds. The
- // default bin function will divide the values into uniform bins using
- // Sturges' formula.
- histogram.bins = function(x) {
- if (!arguments.length) return binner;
- binner = typeof x === "number"
- ? function(range) { return d3_layout_histogramBinFixed(range, x); }
- : d3.functor(x);
- return histogram;
- };
-
- // Specifies whether the histogram's `y` value is a count (frequency) or a
- // probability (density). The default value is true.
- histogram.frequency = function(x) {
- if (!arguments.length) return frequency;
- frequency = !!x;
- return histogram;
- };
-
- return histogram;
-};
-
-function d3_layout_histogramBinSturges(range, values) {
- return d3_layout_histogramBinFixed(range, Math.ceil(Math.log(values.length) / Math.LN2 + 1));
-}
-
-function d3_layout_histogramBinFixed(range, n) {
- var x = -1,
- b = +range[0],
- m = (range[1] - b) / n,
- f = [];
- while (++x <= n) f[x] = m * x + b;
- return f;
-}
-
-function d3_layout_histogramRange(values) {
- return [d3.min(values), d3.max(values)];
-}
-d3.layout.hierarchy = function() {
- var sort = d3_layout_hierarchySort,
- children = d3_layout_hierarchyChildren,
- value = d3_layout_hierarchyValue;
-
- // Recursively compute the node depth and value.
- // Also converts the data representation into a standard hierarchy structure.
- function recurse(data, depth, nodes) {
- var childs = children.call(hierarchy, data, depth),
- node = d3_layout_hierarchyInline ? data : {data: data};
- node.depth = depth;
- nodes.push(node);
- if (childs) {
- var i = -1,
- n = childs.length,
- c = node.children = [],
- v = 0,
- j = depth + 1;
- while (++i < n) {
- d = recurse(childs[i], j, nodes);
- d.parent = node;
- c.push(d);
- v += d.value;
- }
- if (sort) c.sort(sort);
- if (value) node.value = v;
- } else if (value) {
- node.value = +value.call(hierarchy, data, depth) || 0;
- }
- return node;
- }
-
- // Recursively re-evaluates the node value.
- function revalue(node, depth) {
- var children = node.children,
- v = 0;
- if (children) {
- var i = -1,
- n = children.length,
- j = depth + 1;
- while (++i < n) v += revalue(children[i], j);
- } else if (value) {
- v = +value.call(hierarchy, d3_layout_hierarchyInline ? node : node.data, depth) || 0;
- }
- if (value) node.value = v;
- return v;
- }
-
- function hierarchy(d) {
- var nodes = [];
- recurse(d, 0, nodes);
- return nodes;
- }
-
- hierarchy.sort = function(x) {
- if (!arguments.length) return sort;
- sort = x;
- return hierarchy;
- };
-
- hierarchy.children = function(x) {
- if (!arguments.length) return children;
- children = x;
- return hierarchy;
- };
-
- hierarchy.value = function(x) {
- if (!arguments.length) return value;
- value = x;
- return hierarchy;
- };
-
- // Re-evaluates the `value` property for the specified hierarchy.
- hierarchy.revalue = function(root) {
- revalue(root, 0);
- return root;
- };
-
- return hierarchy;
-};
-
-// A method assignment helper for hierarchy subclasses.
-function d3_layout_hierarchyRebind(object, hierarchy) {
- object.sort = d3.rebind(object, hierarchy.sort);
- object.children = d3.rebind(object, hierarchy.children);
- object.links = d3_layout_hierarchyLinks;
- object.value = d3.rebind(object, hierarchy.value);
-
- // If the new API is used, enabling inlining.
- object.nodes = function(d) {
- d3_layout_hierarchyInline = true;
- return (object.nodes = object)(d);
- };
-
- return object;
-}
-
-function d3_layout_hierarchyChildren(d) {
- return d.children;
-}
-
-function d3_layout_hierarchyValue(d) {
- return d.value;
-}
-
-function d3_layout_hierarchySort(a, b) {
- return b.value - a.value;
-}
-
-// Returns an array source+target objects for the specified nodes.
-function d3_layout_hierarchyLinks(nodes) {
- return d3.merge(nodes.map(function(parent) {
- return (parent.children || []).map(function(child) {
- return {source: parent, target: child};
- });
- }));
-}
-
-// For backwards-compatibility, don't enable inlining by default.
-var d3_layout_hierarchyInline = false;
-d3.layout.pack = function() {
- var hierarchy = d3.layout.hierarchy().sort(d3_layout_packSort),
- size = [1, 1];
-
- function pack(d, i) {
- var nodes = hierarchy.call(this, d, i),
- root = nodes[0];
-
- // Recursively compute the layout.
- root.x = 0;
- root.y = 0;
- d3_layout_packTree(root);
-
- // Scale the layout to fit the requested size.
- var w = size[0],
- h = size[1],
- k = 1 / Math.max(2 * root.r / w, 2 * root.r / h);
- d3_layout_packTransform(root, w / 2, h / 2, k);
-
- return nodes;
- }
-
- pack.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return pack;
- };
-
- return d3_layout_hierarchyRebind(pack, hierarchy);
-};
-
-function d3_layout_packSort(a, b) {
- return a.value - b.value;
-}
-
-function d3_layout_packInsert(a, b) {
- var c = a._pack_next;
- a._pack_next = b;
- b._pack_prev = a;
- b._pack_next = c;
- c._pack_prev = b;
-}
-
-function d3_layout_packSplice(a, b) {
- a._pack_next = b;
- b._pack_prev = a;
-}
-
-function d3_layout_packIntersects(a, b) {
- var dx = b.x - a.x,
- dy = b.y - a.y,
- dr = a.r + b.r;
- return (dr * dr - dx * dx - dy * dy) > .001; // within epsilon
-}
-
-function d3_layout_packCircle(nodes) {
- var xMin = Infinity,
- xMax = -Infinity,
- yMin = Infinity,
- yMax = -Infinity,
- n = nodes.length,
- a, b, c, j, k;
-
- function bound(node) {
- xMin = Math.min(node.x - node.r, xMin);
- xMax = Math.max(node.x + node.r, xMax);
- yMin = Math.min(node.y - node.r, yMin);
- yMax = Math.max(node.y + node.r, yMax);
- }
-
- // Create node links.
- nodes.forEach(d3_layout_packLink);
-
- // Create first node.
- a = nodes[0];
- a.x = -a.r;
- a.y = 0;
- bound(a);
-
- // Create second node.
- if (n > 1) {
- b = nodes[1];
- b.x = b.r;
- b.y = 0;
- bound(b);
-
- // Create third node and build chain.
- if (n > 2) {
- c = nodes[2];
- d3_layout_packPlace(a, b, c);
- bound(c);
- d3_layout_packInsert(a, c);
- a._pack_prev = c;
- d3_layout_packInsert(c, b);
- b = a._pack_next;
-
- // Now iterate through the rest.
- for (var i = 3; i < n; i++) {
- d3_layout_packPlace(a, b, c = nodes[i]);
-
- // Search for the closest intersection.
- var isect = 0, s1 = 1, s2 = 1;
- for (j = b._pack_next; j !== b; j = j._pack_next, s1++) {
- if (d3_layout_packIntersects(j, c)) {
- isect = 1;
- break;
- }
- }
- if (isect == 1) {
- for (k = a._pack_prev; k !== j._pack_prev; k = k._pack_prev, s2++) {
- if (d3_layout_packIntersects(k, c)) {
- if (s2 < s1) {
- isect = -1;
- j = k;
- }
- break;
- }
- }
- }
-
- // Update node chain.
- if (isect == 0) {
- d3_layout_packInsert(a, c);
- b = c;
- bound(c);
- } else if (isect > 0) {
- d3_layout_packSplice(a, j);
- b = j;
- i--;
- } else { // isect < 0
- d3_layout_packSplice(j, b);
- a = j;
- i--;
- }
- }
- }
- }
-
- // Re-center the circles and return the encompassing radius.
- var cx = (xMin + xMax) / 2,
- cy = (yMin + yMax) / 2,
- cr = 0;
- for (var i = 0; i < n; i++) {
- var node = nodes[i];
- node.x -= cx;
- node.y -= cy;
- cr = Math.max(cr, node.r + Math.sqrt(node.x * node.x + node.y * node.y));
- }
-
- // Remove node links.
- nodes.forEach(d3_layout_packUnlink);
-
- return cr;
-}
-
-function d3_layout_packLink(node) {
- node._pack_next = node._pack_prev = node;
-}
-
-function d3_layout_packUnlink(node) {
- delete node._pack_next;
- delete node._pack_prev;
-}
-
-function d3_layout_packTree(node) {
- var children = node.children;
- if (children) {
- children.forEach(d3_layout_packTree);
- node.r = d3_layout_packCircle(children);
- } else {
- node.r = Math.sqrt(node.value);
- }
-}
-
-function d3_layout_packTransform(node, x, y, k) {
- var children = node.children;
- node.x = (x += k * node.x);
- node.y = (y += k * node.y);
- node.r *= k;
- if (children) {
- var i = -1, n = children.length;
- while (++i < n) d3_layout_packTransform(children[i], x, y, k);
- }
-}
-
-function d3_layout_packPlace(a, b, c) {
- var da = b.r + c.r,
- db = a.r + c.r,
- dx = b.x - a.x,
- dy = b.y - a.y,
- dc = Math.sqrt(dx * dx + dy * dy),
- cos = (db * db + dc * dc - da * da) / (2 * db * dc),
- theta = Math.acos(cos),
- x = cos * db,
- h = Math.sin(theta) * db;
- dx /= dc;
- dy /= dc;
- c.x = a.x + x * dx + h * dy;
- c.y = a.y + x * dy - h * dx;
-}
-// Implements a hierarchical layout using the cluster (or dendogram) algorithm.
-d3.layout.cluster = function() {
- var hierarchy = d3.layout.hierarchy().sort(null).value(null),
- separation = d3_layout_treeSeparation,
- size = [1, 1]; // width, height
-
- function cluster(d, i) {
- var nodes = hierarchy.call(this, d, i),
- root = nodes[0],
- previousNode,
- x = 0,
- kx,
- ky;
-
- // First walk, computing the initial x & y values.
- d3_layout_treeVisitAfter(root, function(node) {
- if (node.children) {
- node.x = d3_layout_clusterX(node.children);
- node.y = d3_layout_clusterY(node.children);
- } else {
- node.x = previousNode ? x += separation(node, previousNode) : 0;
- node.y = 0;
- previousNode = node;
- }
- });
-
- // Compute the left-most, right-most, and depth-most nodes for extents.
- var left = d3_layout_clusterLeft(root),
- right = d3_layout_clusterRight(root),
- x0 = left.x - separation(left, right) / 2,
- x1 = right.x + separation(right, left) / 2;
-
- // Second walk, normalizing x & y to the desired size.
- d3_layout_treeVisitAfter(root, function(node) {
- node.x = (node.x - x0) / (x1 - x0) * size[0];
- node.y = (1 - node.y / root.y) * size[1];
- });
-
- return nodes;
- }
-
- cluster.separation = function(x) {
- if (!arguments.length) return separation;
- separation = x;
- return cluster;
- };
-
- cluster.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return cluster;
- };
-
- return d3_layout_hierarchyRebind(cluster, hierarchy);
-};
-
-function d3_layout_clusterY(children) {
- return 1 + d3.max(children, function(child) {
- return child.y;
- });
-}
-
-function d3_layout_clusterX(children) {
- return children.reduce(function(x, child) {
- return x + child.x;
- }, 0) / children.length;
-}
-
-function d3_layout_clusterLeft(node) {
- var children = node.children;
- return children ? d3_layout_clusterLeft(children[0]) : node;
-}
-
-function d3_layout_clusterRight(node) {
- var children = node.children;
- return children ? d3_layout_clusterRight(children[children.length - 1]) : node;
-}
-// Node-link tree diagram using the Reingold-Tilford "tidy" algorithm
-d3.layout.tree = function() {
- var hierarchy = d3.layout.hierarchy().sort(null).value(null),
- separation = d3_layout_treeSeparation,
- size = [1, 1]; // width, height
-
- function tree(d, i) {
- var nodes = hierarchy.call(this, d, i),
- root = nodes[0];
-
- function firstWalk(node, previousSibling) {
- var children = node.children,
- layout = node._tree;
- if (children && (n = children.length)) {
- var n,
- firstChild = children[0],
- previousChild,
- ancestor = firstChild,
- child,
- i = -1;
- while (++i < n) {
- child = children[i];
- firstWalk(child, previousChild);
- ancestor = apportion(child, previousChild, ancestor);
- previousChild = child;
- }
- d3_layout_treeShift(node);
- var midpoint = .5 * (firstChild._tree.prelim + child._tree.prelim);
- if (previousSibling) {
- layout.prelim = previousSibling._tree.prelim + separation(node, previousSibling);
- layout.mod = layout.prelim - midpoint;
- } else {
- layout.prelim = midpoint;
- }
- } else {
- if (previousSibling) {
- layout.prelim = previousSibling._tree.prelim + separation(node, previousSibling);
- }
- }
- }
-
- function secondWalk(node, x) {
- node.x = node._tree.prelim + x;
- var children = node.children;
- if (children) {
- var i = -1,
- n = children.length;
- x += node._tree.mod;
- while (++i < n) {
- secondWalk(children[i], x);
- }
- }
- }
-
- function apportion(node, previousSibling, ancestor) {
- if (previousSibling) {
- var vip = node,
- vop = node,
- vim = previousSibling,
- vom = node.parent.children[0],
- sip = vip._tree.mod,
- sop = vop._tree.mod,
- sim = vim._tree.mod,
- som = vom._tree.mod,
- shift;
- while (vim = d3_layout_treeRight(vim), vip = d3_layout_treeLeft(vip), vim && vip) {
- vom = d3_layout_treeLeft(vom);
- vop = d3_layout_treeRight(vop);
- vop._tree.ancestor = node;
- shift = vim._tree.prelim + sim - vip._tree.prelim - sip + separation(vim, vip);
- if (shift > 0) {
- d3_layout_treeMove(d3_layout_treeAncestor(vim, node, ancestor), node, shift);
- sip += shift;
- sop += shift;
- }
- sim += vim._tree.mod;
- sip += vip._tree.mod;
- som += vom._tree.mod;
- sop += vop._tree.mod;
- }
- if (vim && !d3_layout_treeRight(vop)) {
- vop._tree.thread = vim;
- vop._tree.mod += sim - sop;
- }
- if (vip && !d3_layout_treeLeft(vom)) {
- vom._tree.thread = vip;
- vom._tree.mod += sip - som;
- ancestor = node;
- }
- }
- return ancestor;
- }
-
- // Initialize temporary layout variables.
- d3_layout_treeVisitAfter(root, function(node, previousSibling) {
- node._tree = {
- ancestor: node,
- prelim: 0,
- mod: 0,
- change: 0,
- shift: 0,
- number: previousSibling ? previousSibling._tree.number + 1 : 0
- };
- });
-
- // Compute the layout using Buchheim et al.'s algorithm.
- firstWalk(root);
- secondWalk(root, -root._tree.prelim);
-
- // Compute the left-most, right-most, and depth-most nodes for extents.
- var left = d3_layout_treeSearch(root, d3_layout_treeLeftmost),
- right = d3_layout_treeSearch(root, d3_layout_treeRightmost),
- deep = d3_layout_treeSearch(root, d3_layout_treeDeepest),
- x0 = left.x - separation(left, right) / 2,
- x1 = right.x + separation(right, left) / 2,
- y1 = deep.depth || 1;
-
- // Clear temporary layout variables; transform x and y.
- d3_layout_treeVisitAfter(root, function(node) {
- node.x = (node.x - x0) / (x1 - x0) * size[0];
- node.y = node.depth / y1 * size[1];
- delete node._tree;
- });
-
- return nodes;
- }
-
- tree.separation = function(x) {
- if (!arguments.length) return separation;
- separation = x;
- return tree;
- };
-
- tree.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return tree;
- };
-
- return d3_layout_hierarchyRebind(tree, hierarchy);
-};
-
-function d3_layout_treeSeparation(a, b) {
- return a.parent == b.parent ? 1 : 2;
-}
-
-// function d3_layout_treeSeparationRadial(a, b) {
-// return (a.parent == b.parent ? 1 : 2) / a.depth;
-// }
-
-function d3_layout_treeLeft(node) {
- return node.children ? node.children[0] : node._tree.thread;
-}
-
-function d3_layout_treeRight(node) {
- return node.children ? node.children[node.children.length - 1] : node._tree.thread;
-}
-
-function d3_layout_treeSearch(node, compare) {
- var children = node.children;
- if (children) {
- var child,
- n = children.length,
- i = -1;
- while (++i < n) {
- if (compare(child = d3_layout_treeSearch(children[i], compare), node) > 0) {
- node = child;
- }
- }
- }
- return node;
-}
-
-function d3_layout_treeRightmost(a, b) {
- return a.x - b.x;
-}
-
-function d3_layout_treeLeftmost(a, b) {
- return b.x - a.x;
-}
-
-function d3_layout_treeDeepest(a, b) {
- return a.depth - b.depth;
-}
-
-function d3_layout_treeVisitAfter(node, callback) {
- function visit(node, previousSibling) {
- var children = node.children;
- if (children) {
- var child,
- previousChild = null,
- i = -1,
- n = children.length;
- while (++i < n) {
- child = children[i];
- visit(child, previousChild);
- previousChild = child;
- }
- }
- callback(node, previousSibling);
- }
- visit(node, null);
-}
-
-function d3_layout_treeShift(node) {
- var shift = 0,
- change = 0,
- children = node.children,
- i = children.length,
- child;
- while (--i >= 0) {
- child = children[i]._tree;
- child.prelim += shift;
- child.mod += shift;
- shift += child.shift + (change += child.change);
- }
-}
-
-function d3_layout_treeMove(ancestor, node, shift) {
- ancestor = ancestor._tree;
- node = node._tree;
- var change = shift / (node.number - ancestor.number);
- ancestor.change += change;
- node.change -= change;
- node.shift += shift;
- node.prelim += shift;
- node.mod += shift;
-}
-
-function d3_layout_treeAncestor(vim, node, ancestor) {
- return vim._tree.ancestor.parent == node.parent
- ? vim._tree.ancestor
- : ancestor;
-}
-// Squarified Treemaps by Mark Bruls, Kees Huizing, and Jarke J. van Wijk
-// Modified to support a target aspect ratio by Jeff Heer
-d3.layout.treemap = function() {
- var hierarchy = d3.layout.hierarchy(),
- round = Math.round,
- size = [1, 1], // width, height
- padding = null,
- pad = d3_layout_treemapPadNull,
- sticky = false,
- stickies,
- ratio = 0.5 * (1 + Math.sqrt(5)); // golden ratio
-
- // Compute the area for each child based on value & scale.
- function scale(children, k) {
- var i = -1,
- n = children.length,
- child,
- area;
- while (++i < n) {
- area = (child = children[i]).value * (k < 0 ? 0 : k);
- child.area = isNaN(area) || area <= 0 ? 0 : area;
- }
- }
-
- // Recursively arranges the specified node's children into squarified rows.
- function squarify(node) {
- if (!node.children) return;
- var rect = pad(node),
- row = [],
- children = node.children.slice(), // copy-on-write
- child,
- best = Infinity, // the best row score so far
- score, // the current row score
- u = Math.min(rect.dx, rect.dy), // initial orientation
- n;
- scale(children, rect.dx * rect.dy / node.value);
- row.area = 0;
- while ((n = children.length) > 0) {
- row.push(child = children[n - 1]);
- row.area += child.area;
- if ((score = worst(row, u)) <= best) { // continue with this orientation
- children.pop();
- best = score;
- } else { // abort, and try a different orientation
- row.area -= row.pop().area;
- position(row, u, rect, false);
- u = Math.min(rect.dx, rect.dy);
- row.length = row.area = 0;
- best = Infinity;
- }
- }
- if (row.length) {
- position(row, u, rect, true);
- row.length = row.area = 0;
- }
- node.children.forEach(squarify);
- }
-
- // Recursively resizes the specified node's children into existing rows.
- // Preserves the existing layout!
- function stickify(node) {
- if (!node.children) return;
- var rect = pad(node),
- children = node.children.slice(), // copy-on-write
- child,
- row = [];
- scale(children, rect.dx * rect.dy / node.value);
- row.area = 0;
- while (child = children.pop()) {
- row.push(child);
- row.area += child.area;
- if (child.z != null) {
- position(row, child.z ? rect.dx : rect.dy, rect, !children.length);
- row.length = row.area = 0;
- }
- }
- node.children.forEach(stickify);
- }
-
- // Computes the score for the specified row, as the worst aspect ratio.
- function worst(row, u) {
- var s = row.area,
- r,
- rmax = 0,
- rmin = Infinity,
- i = -1,
- n = row.length;
- while (++i < n) {
- if (!(r = row[i].area)) continue;
- if (r < rmin) rmin = r;
- if (r > rmax) rmax = r;
- }
- s *= s;
- u *= u;
- return s
- ? Math.max((u * rmax * ratio) / s, s / (u * rmin * ratio))
- : Infinity;
- }
-
- // Positions the specified row of nodes. Modifies `rect`.
- function position(row, u, rect, flush) {
- var i = -1,
- n = row.length,
- x = rect.x,
- y = rect.y,
- v = u ? round(row.area / u) : 0,
- o;
- if (u == rect.dx) { // horizontal subdivision
- if (flush || v > rect.dy) v = v ? rect.dy : 0; // over+underflow
- while (++i < n) {
- o = row[i];
- o.x = x;
- o.y = y;
- o.dy = v;
- x += o.dx = v ? round(o.area / v) : 0;
- }
- o.z = true;
- o.dx += rect.x + rect.dx - x; // rounding error
- rect.y += v;
- rect.dy -= v;
- } else { // vertical subdivision
- if (flush || v > rect.dx) v = v ? rect.dx : 0; // over+underflow
- while (++i < n) {
- o = row[i];
- o.x = x;
- o.y = y;
- o.dx = v;
- y += o.dy = v ? round(o.area / v) : 0;
- }
- o.z = false;
- o.dy += rect.y + rect.dy - y; // rounding error
- rect.x += v;
- rect.dx -= v;
- }
- }
-
- function treemap(d) {
- var nodes = stickies || hierarchy(d),
- root = nodes[0];
- root.x = 0;
- root.y = 0;
- root.dx = size[0];
- root.dy = size[1];
- if (stickies) hierarchy.revalue(root);
- scale([root], root.dx * root.dy / root.value);
- (stickies ? stickify : squarify)(root);
- if (sticky) stickies = nodes;
- return nodes;
- }
-
- treemap.size = function(x) {
- if (!arguments.length) return size;
- size = x;
- return treemap;
- };
-
- treemap.padding = function(x) {
- if (!arguments.length) return padding;
-
- function padFunction(node) {
- var p = x.call(treemap, node, node.depth);
- return p == null
- ? d3_layout_treemapPadNull(node)
- : d3_layout_treemapPad(node, typeof p === "number" ? [p, p, p, p] : p);
- }
-
- function padConstant(node) {
- return d3_layout_treemapPad(node, x);
- }
-
- var type;
- pad = (padding = x) == null ? d3_layout_treemapPadNull
- : (type = typeof x) === "function" ? padFunction
- : type === "number" ? (x = [x, x, x, x], padConstant)
- : padConstant;
- return treemap;
- };
-
- treemap.round = function(x) {
- if (!arguments.length) return round != Number;
- round = x ? Math.round : Number;
- return treemap;
- };
-
- treemap.sticky = function(x) {
- if (!arguments.length) return sticky;
- sticky = x;
- stickies = null;
- return treemap;
- };
-
- treemap.ratio = function(x) {
- if (!arguments.length) return ratio;
- ratio = x;
- return treemap;
- };
-
- return d3_layout_hierarchyRebind(treemap, hierarchy);
-};
-
-function d3_layout_treemapPadNull(node) {
- return {x: node.x, y: node.y, dx: node.dx, dy: node.dy};
-}
-
-function d3_layout_treemapPad(node, padding) {
- var x = node.x + padding[3],
- y = node.y + padding[0],
- dx = node.dx - padding[1] - padding[3],
- dy = node.dy - padding[0] - padding[2];
- if (dx < 0) { x += dx / 2; dx = 0; }
- if (dy < 0) { y += dy / 2; dy = 0; }
- return {x: x, y: y, dx: dx, dy: dy};
-}
-})();
diff --git a/rtd_phosphonetx/source/html/demoapp/d3.time.js b/rtd_phosphonetx/source/html/demoapp/d3.time.js
deleted file mode 100644
index e1c0831c88e..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/d3.time.js
+++ /dev/null
@@ -1,692 +0,0 @@
-(function(){d3.time = {};
-
-var d3_time = Date;
-d3.time.format = function(template) {
- var n = template.length;
-
- function format(date) {
- var string = [],
- i = -1,
- j = 0,
- c,
- f;
- while (++i < n) {
- if (template.charCodeAt(i) == 37) {
- string.push(
- template.substring(j, i),
- (f = d3_time_formats[c = template.charAt(++i)])
- ? f(date) : c);
- j = i + 1;
- }
- }
- string.push(template.substring(j, i));
- return string.join("");
- }
-
- format.parse = function(string) {
- var date = new d3_time(1900, 0, 1),
- i = d3_time_parse(date, template, string, 0);
- if (i != string.length) return null;
- if (date.hour12) {
- var hours = date.getHours() % 12;
- date.setHours(date.hour12pm ? hours + 12 : hours);
- }
- delete date.hour12;
- delete date.hour12pm;
- return date;
- };
-
- format.toString = function() {
- return template;
- };
-
- return format;
-};
-
-function d3_time_parse(date, template, string, j) {
- var c,
- p,
- i = 0,
- n = template.length,
- m = string.length;
- while (i < n) {
- if (j >= m) return -1;
- c = template.charCodeAt(i++);
- if (c == 37) {
- p = d3_time_parsers[template.charAt(i++)];
- if (!p || ((j = p(date, string, j)) < 0)) return -1;
- } else if (c != string.charCodeAt(j++)) {
- return -1;
- }
- }
- return j;
-}
-
-var d3_time_zfill2 = d3.format("02d"),
- d3_time_zfill3 = d3.format("03d"),
- d3_time_zfill4 = d3.format("04d"),
- d3_time_sfill2 = d3.format("2d");
-
-var d3_time_formats = {
- a: function(d) { return d3_time_weekdays[d.getDay()].substring(0, 3); },
- A: function(d) { return d3_time_weekdays[d.getDay()]; },
- b: function(d) { return d3_time_months[d.getMonth()].substring(0, 3); },
- B: function(d) { return d3_time_months[d.getMonth()]; },
- c: d3.time.format("%a %b %e %H:%M:%S %Y"),
- d: function(d) { return d3_time_zfill2(d.getDate()); },
- e: function(d) { return d3_time_sfill2(d.getDate()); },
- H: function(d) { return d3_time_zfill2(d.getHours()); },
- I: function(d) { return d3_time_zfill2(d.getHours() % 12 || 12); },
- j: d3_time_dayOfYear,
- L: function(d) { return d3_time_zfill3(d.getMilliseconds()); },
- m: function(d) { return d3_time_zfill2(d.getMonth() + 1); },
- M: function(d) { return d3_time_zfill2(d.getMinutes()); },
- p: function(d) { return d.getHours() >= 12 ? "PM" : "AM"; },
- S: function(d) { return d3_time_zfill2(d.getSeconds()); },
- U: d3_time_weekNumberSunday,
- w: function(d) { return d.getDay(); },
- W: d3_time_weekNumberMonday,
- x: d3.time.format("%m/%d/%y"),
- X: d3.time.format("%H:%M:%S"),
- y: function(d) { return d3_time_zfill2(d.getFullYear() % 100); },
- Y: function(d) { return d3_time_zfill4(d.getFullYear() % 10000); },
- Z: d3_time_zone,
- "%": function(d) { return "%"; }
-};
-
-var d3_time_parsers = {
- a: d3_time_parseWeekdayAbbrev,
- A: d3_time_parseWeekday,
- b: d3_time_parseMonthAbbrev,
- B: d3_time_parseMonth,
- c: d3_time_parseLocaleFull,
- d: d3_time_parseDay,
- e: d3_time_parseDay,
- H: d3_time_parseHour24,
- I: d3_time_parseHour12,
- // j: function(d, s, i) { /*TODO day of year [001,366] */ return i; },
- L: d3_time_parseMilliseconds,
- m: d3_time_parseMonthNumber,
- M: d3_time_parseMinutes,
- p: d3_time_parseAmPm,
- S: d3_time_parseSeconds,
- // U: function(d, s, i) { /*TODO week number (sunday) [00,53] */ return i; },
- // w: function(d, s, i) { /*TODO weekday [0,6] */ return i; },
- // W: function(d, s, i) { /*TODO week number (monday) [00,53] */ return i; },
- x: d3_time_parseLocaleDate,
- X: d3_time_parseLocaleTime,
- y: d3_time_parseYear,
- Y: d3_time_parseFullYear
- // ,
- // Z: function(d, s, i) { /*TODO time zone */ return i; },
- // "%": function(d, s, i) { /*TODO literal % */ return i; }
-};
-
-// Note: weekday is validated, but does not set the date.
-function d3_time_parseWeekdayAbbrev(date, string, i) {
- return string.substring(i, i += 3).toLowerCase() in d3_time_weekdayAbbrevLookup ? i : -1;
-}
-
-var d3_time_weekdayAbbrevLookup = {
- sun: 3,
- mon: 3,
- tue: 3,
- wed: 3,
- thu: 3,
- fri: 3,
- sat: 3
-};
-
-// Note: weekday is validated, but does not set the date.
-function d3_time_parseWeekday(date, string, i) {
- d3_time_weekdayRe.lastIndex = 0;
- var n = d3_time_weekdayRe.exec(string.substring(i, i + 10));
- return n ? i += n[0].length : -1;
-}
-
-var d3_time_weekdayRe = /^(?:Sunday|Monday|Tuesday|Wednesday|Thursday|Friday|Saturday)/ig;
-
-var d3_time_weekdays = [
- "Sunday",
- "Monday",
- "Tuesday",
- "Wednesday",
- "Thursday",
- "Friday",
- "Saturday"
-];
-
-function d3_time_parseMonthAbbrev(date, string, i) {
- var n = d3_time_monthAbbrevLookup[string.substring(i, i += 3).toLowerCase()];
- return n == null ? -1 : (date.setMonth(n), i);
-}
-
-var d3_time_monthAbbrevLookup = {
- jan: 0,
- feb: 1,
- mar: 2,
- apr: 3,
- may: 4,
- jun: 5,
- jul: 6,
- aug: 7,
- sep: 8,
- oct: 9,
- nov: 10,
- dec: 11
-};
-
-function d3_time_parseMonth(date, string, i) {
- d3_time_monthRe.lastIndex = 0;
- var n = d3_time_monthRe.exec(string.substring(i, i + 12));
- return n ? (date.setMonth(d3_time_monthLookup[n[0].toLowerCase()]), i += n[0].length) : -1;
-}
-
-var d3_time_monthRe = /^(?:January|February|March|April|May|June|July|August|September|October|November|December)/ig;
-
-var d3_time_monthLookup = {
- january: 0,
- february: 1,
- march: 2,
- april: 3,
- may: 4,
- june: 5,
- july: 6,
- august: 7,
- september: 8,
- october: 9,
- november: 10,
- december: 11
-};
-
-var d3_time_months = [
- "January",
- "February",
- "March",
- "April",
- "May",
- "June",
- "July",
- "August",
- "September",
- "October",
- "November",
- "December"
-];
-
-function d3_time_parseLocaleFull(date, string, i) {
- return d3_time_parse(date, d3_time_formats.c.toString(), string, i);
-}
-
-function d3_time_parseLocaleDate(date, string, i) {
- return d3_time_parse(date, d3_time_formats.x.toString(), string, i);
-}
-
-function d3_time_parseLocaleTime(date, string, i) {
- return d3_time_parse(date, d3_time_formats.X.toString(), string, i);
-}
-
-function d3_time_parseFullYear(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 4));
- return n ? (date.setFullYear(n[0]), i += n[0].length) : -1;
-}
-
-function d3_time_parseYear(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setFullYear(d3_time_century() + +n[0]), i += n[0].length) : -1;
-}
-
-function d3_time_century() {
- return ~~(new Date().getFullYear() / 1000) * 1000;
-}
-
-function d3_time_parseMonthNumber(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setMonth(n[0] - 1), i += n[0].length) : -1;
-}
-
-function d3_time_parseDay(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setDate(+n[0]), i += n[0].length) : -1;
-}
-
-// Note: we don't validate that the hour is in the range [0,23].
-function d3_time_parseHour24(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setHours(+n[0]), i += n[0].length) : -1;
-}
-
-// Note: we don't validate that the hour is in the range [1,12].
-function d3_time_parseHour12(date, string, i) {
- date.hour12 = true;
- return d3_time_parseHour24(date, string, i);
-}
-
-function d3_time_parseMinutes(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setMinutes(+n[0]), i += n[0].length) : -1;
-}
-
-function d3_time_parseSeconds(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 2));
- return n ? (date.setSeconds(+n[0]), i += n[0].length) : -1;
-}
-
-function d3_time_parseMilliseconds(date, string, i) {
- d3_time_numberRe.lastIndex = 0;
- var n = d3_time_numberRe.exec(string.substring(i, i + 3));
- return n ? (date.setMilliseconds(+n[0]), i += n[0].length) : -1;
-}
-
-// Note: we don't look at the next directive.
-var d3_time_numberRe = /\s*\d+/;
-
-function d3_time_parseAmPm(date, string, i) {
- var n = d3_time_amPmLookup[string.substring(i, i += 2).toLowerCase()];
- return n == null ? -1 : (date.hour12pm = n, i);
-}
-
-var d3_time_amPmLookup = {
- am: 0,
- pm: 1
-};
-
-function d3_time_year(d) {
- return new d3_time(d.getFullYear(), 0, 1);
-}
-
-function d3_time_daysElapsed(d0, d1) {
- return ~~((d1 - d0) / 864e5 - (d1.getTimezoneOffset() - d0.getTimezoneOffset()) / 1440);
-}
-
-function d3_time_dayOfYear(d) {
- return d3_time_zfill3(1 + d3_time_daysElapsed(d3_time_year(d), d));
-}
-
-function d3_time_weekNumberSunday(d) {
- var d0 = d3_time_year(d);
- return d3_time_zfill2(~~((d3_time_daysElapsed(d0, d) + d0.getDay()) / 7));
-}
-
-function d3_time_weekNumberMonday(d) {
- var d0 = d3_time_year(d);
- return d3_time_zfill2(~~((d3_time_daysElapsed(d0, d) + (d0.getDay() + 6) % 7) / 7));
-}
-
-// TODO table of time zone offset names?
-function d3_time_zone(d) {
- var z = d.getTimezoneOffset(),
- zs = z > 0 ? "-" : "+",
- zh = ~~(Math.abs(z) / 60),
- zm = Math.abs(z) % 60;
- return zs + d3_time_zfill2(zh) + d3_time_zfill2(zm);
-}
-d3.time.format.utc = function(template) {
- var local = d3.time.format(template);
-
- function format(date) {
- try {
- d3_time = d3_time_format_utc;
- var utc = new d3_time();
- utc._ = date;
- return local(utc);
- } finally {
- d3_time = Date;
- }
- }
-
- format.parse = function(string) {
- try {
- d3_time = d3_time_format_utc;
- var date = local.parse(string);
- return date && date._;
- } finally {
- d3_time = Date;
- }
- };
-
- format.toString = local.toString;
-
- return format;
-};
-
-function d3_time_format_utc() {
- this._ = new Date(Date.UTC.apply(this, arguments));
-}
-
-d3_time_format_utc.prototype = {
- getDate: function() { return this._.getUTCDate(); },
- getDay: function() { return this._.getUTCDay(); },
- getFullYear: function() { return this._.getUTCFullYear(); },
- getHours: function() { return this._.getUTCHours(); },
- getMilliseconds: function() { return this._.getUTCMilliseconds(); },
- getMinutes: function() { return this._.getUTCMinutes(); },
- getMonth: function() { return this._.getUTCMonth(); },
- getSeconds: function() { return this._.getUTCSeconds(); },
- getTimezoneOffset: function() { return 0; },
- valueOf: function() { return this._.getTime(); },
- setDate: function(x) { this._.setUTCDate(x); },
- setDay: function(x) { this._.setUTCDay(x); },
- setFullYear: function(x) { this._.setUTCFullYear(x); },
- setHours: function(x) { this._.setUTCHours(x); },
- setMilliseconds: function(x) { this._.setUTCMilliseconds(x); },
- setMinutes: function(x) { this._.setUTCMinutes(x); },
- setMonth: function(x) { this._.setUTCMonth(x); },
- setSeconds: function(x) { this._.setUTCSeconds(x); }
-};
-var d3_time_formatIso = d3.time.format.utc("%Y-%m-%dT%H:%M:%S.%LZ");
-
-d3.time.format.iso = Date.prototype.toISOString ? d3_time_formatIsoNative : d3_time_formatIso;
-
-function d3_time_formatIsoNative(date) {
- return date.toISOString();
-}
-
-d3_time_formatIsoNative.parse = function(string) {
- return new Date(string);
-};
-
-d3_time_formatIsoNative.toString = d3_time_formatIso.toString;
-function d3_time_range(floor, step, number) {
- return function(t0, t1, dt) {
- var time = floor(t0), times = [];
- if (time < t0) step(time);
- if (dt > 1) {
- while (time < t1) {
- var date = new Date(+time);
- if (!(number(date) % dt)) times.push(date);
- step(time);
- }
- } else {
- while (time < t1) times.push(new Date(+time)), step(time);
- }
- return times;
- };
-}
-d3.time.second = function(date) {
- return new Date(~~(date / 1e3) * 1e3);
-};
-
-d3.time.second.utc = d3.time.second;
-d3.time.seconds = d3_time_range(d3.time.second, function(date) {
- date.setTime(date.getTime() + 1e3);
-}, function(date) {
- return date.getSeconds();
-});
-
-d3.time.seconds.utc = d3.time.seconds;
-d3.time.minute = function(date) {
- return new Date(~~(date / 6e4) * 6e4);
-};
-
-d3.time.minute.utc = d3.time.minute;d3.time.minutes = d3_time_range(d3.time.minute, d3_time_minutesStep, function(date) {
- return date.getMinutes();
-});
-
-d3.time.minutes.utc = d3_time_range(d3.time.minute, d3_time_minutesStep, function(date) {
- return date.getUTCMinutes();
-});
-
-function d3_time_minutesStep(date) {
- date.setTime(date.getTime() + 6e4); // assumes no leap seconds
-}
-d3.time.hour = function(date) {
- var offset = date.getTimezoneOffset() / 60;
- return new Date((~~(date / 36e5 - offset) + offset) * 36e5);
-};
-
-d3.time.hour.utc = function(date) {
- return new Date(~~(date / 36e5) * 36e5);
-};
-d3.time.hours = d3_time_range(d3.time.hour, d3_time_hoursStep, function(date) {
- return date.getHours();
-});
-
-d3.time.hours.utc = d3_time_range(d3.time.hour.utc, d3_time_hoursStep, function(date) {
- return date.getUTCHours();
-});
-
-function d3_time_hoursStep(date) {
- date.setTime(date.getTime() + 36e5);
-}
-d3.time.day = function(date) {
- return new Date(date.getFullYear(), date.getMonth(), date.getDate());
-};
-
-d3.time.day.utc = function(date) {
- return new Date(~~(date / 864e5) * 864e5);
-};
-d3.time.days = d3_time_range(d3.time.day, function(date) {
- date.setDate(date.getDate() + 1);
-}, function(date) {
- return date.getDate() - 1;
-});
-
-d3.time.days.utc = d3_time_range(d3.time.day.utc, function(date) {
- date.setUTCDate(date.getUTCDate() + 1);
-}, function(date) {
- return date.getUTCDate() - 1;
-});
-d3.time.week = function(date) {
- (date = d3.time.day(date)).setDate(date.getDate() - date.getDay());
- return date;
-};
-
-d3.time.week.utc = function(date) {
- (date = d3.time.day.utc(date)).setUTCDate(date.getUTCDate() - date.getUTCDay());
- return date;
-};
-d3.time.weeks = d3_time_range(d3.time.week, function(date) {
- date.setDate(date.getDate() + 7);
-}, function(date) {
- return ~~((date - new Date(date.getFullYear(), 0, 1)) / 6048e5);
-});
-
-d3.time.weeks.utc = d3_time_range(d3.time.week.utc, function(date) {
- date.setUTCDate(date.getUTCDate() + 7);
-}, function(date) {
- return ~~((date - Date.UTC(date.getUTCFullYear(), 0, 1)) / 6048e5);
-});
-d3.time.month = function(date) {
- return new Date(date.getFullYear(), date.getMonth(), 1);
-};
-
-d3.time.month.utc = function(date) {
- return new Date(Date.UTC(date.getUTCFullYear(), date.getUTCMonth(), 1));
-};
-d3.time.months = d3_time_range(d3.time.month, function(date) {
- date.setMonth(date.getMonth() + 1);
-}, function(date) {
- return date.getMonth();
-});
-
-d3.time.months.utc = d3_time_range(d3.time.month.utc, function(date) {
- date.setUTCMonth(date.getUTCMonth() + 1);
-}, function(date) {
- return date.getUTCMonth();
-});
-d3.time.year = function(date) {
- return new Date(date.getFullYear(), 0, 1);
-};
-
-d3.time.year.utc = function(date) {
- return new Date(Date.UTC(date.getUTCFullYear(), 0, 1));
-};
-d3.time.years = d3_time_range(d3.time.year, function(date) {
- date.setFullYear(date.getFullYear() + 1);
-}, function(date) {
- return date.getFullYear();
-});
-
-d3.time.years.utc = d3_time_range(d3.time.year.utc, function(date) {
- date.setUTCFullYear(date.getUTCFullYear() + 1);
-}, function(date) {
- return date.getUTCFullYear();
-});
-// TODO nice
-function d3_time_scale(linear, methods, format) {
-
- function scale(x) {
- return linear(x);
- }
-
- scale.invert = function(x) {
- return d3_time_scaleDate(linear.invert(x));
- };
-
- scale.domain = function(x) {
- if (!arguments.length) return linear.domain().map(d3_time_scaleDate);
- linear.domain(x);
- return scale;
- };
-
- scale.ticks = function(m, k) {
- var extent = d3_time_scaleExtent(scale.domain());
- if (typeof m !== "function") {
- var span = extent[1] - extent[0],
- target = span / m,
- i = d3.bisect(d3_time_scaleSteps, target, 1, d3_time_scaleSteps.length - 1);
- if (Math.log(target / d3_time_scaleSteps[i - 1]) < Math.log(d3_time_scaleSteps[i] / target)) --i;
- m = methods[i];
- k = m[1];
- m = m[0];
- }
- return m(extent[0], extent[1], k);
- };
-
- scale.tickFormat = function() {
- return format;
- };
-
- scale.copy = function() {
- return d3_time_scale(linear.copy(), methods, format);
- };
-
- // TOOD expose d3_scale_linear_rebind?
- scale.range = d3.rebind(scale, linear.range);
- scale.rangeRound = d3.rebind(scale, linear.rangeRound);
- scale.interpolate = d3.rebind(scale, linear.interpolate);
- scale.clamp = d3.rebind(scale, linear.clamp);
-
- return scale;
-}
-
-// TODO expose d3_scaleExtent?
-function d3_time_scaleExtent(domain) {
- var start = domain[0], stop = domain[domain.length - 1];
- return start < stop ? [start, stop] : [stop, start];
-}
-
-function d3_time_scaleDate(t) {
- return new Date(t);
-}
-
-function d3_time_scaleFormat(formats) {
- return function(date) {
- var i = formats.length - 1, f = formats[i];
- while (!f[1](date)) f = formats[--i];
- return f[0](date);
- };
-}
-
-var d3_time_scaleSteps = [
- 1e3, // 1-second
- 5e3, // 5-second
- 15e3, // 15-second
- 3e4, // 30-second
- 6e4, // 1-minute
- 3e5, // 5-minute
- 9e5, // 15-minute
- 18e5, // 30-minute
- 36e5, // 1-hour
- 108e5, // 3-hour
- 216e5, // 6-hour
- 432e5, // 12-hour
- 864e5, // 1-day
- 1728e5, // 2-day
- 6048e5, // 1-week
- 1728e6, // 1-month
- 7776e6, // 3-month
- 31536e6 // 1-year
-];
-
-var d3_time_scaleLocalMethods = [
- [d3.time.seconds, 1],
- [d3.time.seconds, 5],
- [d3.time.seconds, 15],
- [d3.time.seconds, 30],
- [d3.time.minutes, 1],
- [d3.time.minutes, 5],
- [d3.time.minutes, 15],
- [d3.time.minutes, 30],
- [d3.time.hours, 1],
- [d3.time.hours, 3],
- [d3.time.hours, 6],
- [d3.time.hours, 12],
- [d3.time.days, 1],
- [d3.time.days, 2],
- [d3.time.weeks, 1],
- [d3.time.months, 1],
- [d3.time.months, 3],
- [d3.time.years, 1]
-];
-
-var d3_time_scaleLocalFormats = [
- [d3.time.format("%Y"), function(d) { return true; }],
- [d3.time.format("%B"), function(d) { return d.getMonth(); }],
- [d3.time.format("%b %d"), function(d) { return d.getDate() != 1; }],
- [d3.time.format("%a %d"), function(d) { return d.getDay() && d.getDate() != 1; }],
- [d3.time.format("%I %p"), function(d) { return d.getHours(); }],
- [d3.time.format("%I:%M"), function(d) { return d.getMinutes(); }],
- [d3.time.format(":%S"), function(d) { return d.getSeconds() || d.getMilliseconds(); }]
-];
-
-var d3_time_scaleLocalFormat = d3_time_scaleFormat(d3_time_scaleLocalFormats);
-
-d3.time.scale = function() {
- return d3_time_scale(d3.scale.linear(), d3_time_scaleLocalMethods, d3_time_scaleLocalFormat);
-};
-var d3_time_scaleUTCMethods = [
- [d3.time.seconds.utc, 1],
- [d3.time.seconds.utc, 5],
- [d3.time.seconds.utc, 15],
- [d3.time.seconds.utc, 30],
- [d3.time.minutes.utc, 1],
- [d3.time.minutes.utc, 5],
- [d3.time.minutes.utc, 15],
- [d3.time.minutes.utc, 30],
- [d3.time.hours.utc, 1],
- [d3.time.hours.utc, 3],
- [d3.time.hours.utc, 6],
- [d3.time.hours.utc, 12],
- [d3.time.days.utc, 1],
- [d3.time.days.utc, 2],
- [d3.time.weeks.utc, 1],
- [d3.time.months.utc, 1],
- [d3.time.months.utc, 3],
- [d3.time.years.utc, 1]
-];
-
-var d3_time_scaleUTCFormats = [
- [d3.time.format.utc("%Y"), function(d) { return true; }],
- [d3.time.format.utc("%B"), function(d) { return d.getUTCMonth(); }],
- [d3.time.format.utc("%b %d"), function(d) { return d.getUTCDate() != 1; }],
- [d3.time.format.utc("%a %d"), function(d) { return d.getUTCDay() && d.getUTCDate() != 1; }],
- [d3.time.format.utc("%I %p"), function(d) { return d.getUTCHours(); }],
- [d3.time.format.utc("%I:%M"), function(d) { return d.getUTCMinutes(); }],
- [d3.time.format.utc(":%S"), function(d) { return d.getUTCSeconds() || d.getUTCMilliseconds(); }]
-];
-
-var d3_time_scaleUTCFormat = d3_time_scaleFormat(d3_time_scaleUTCFormats);
-
-d3.time.scale.utc = function() {
- return d3_time_scale(d3.scale.linear(), d3_time_scaleUTCMethods, d3_time_scaleUTCFormat);
-};
-})();
diff --git a/rtd_phosphonetx/source/html/demoapp/images/openBIS_Logo.png b/rtd_phosphonetx/source/html/demoapp/images/openBIS_Logo.png
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- <polygon fill="#ADACAF" points="76.131,32.882 92.331,49.084 98.168,43.247 81.969,27.048 76.13,27.048 "/>
- </g>
- <g>
- <g>
- <polygon fill="#ADACAF" points="71.122,32.882 54.921,49.084 49.084,43.247 65.283,27.048 71.123,27.048 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="71.122,16.201 54.921,0 49.084,5.836 65.283,22.036 71.123,22.036 "/>
- </g>
- </g>
- </g>
- </g>
- <g>
- <g>
- <polygon fill="#ADACAF" points="27.046,65.286 43.247,49.084 49.083,54.92 32.884,71.12 27.045,71.12 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="27.046,81.967 43.247,98.167 49.083,92.333 32.884,76.132 27.045,76.132 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="22.038,81.967 5.837,98.167 0,92.333 16.199,76.132 22.038,76.132 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="22.038,65.286 5.837,49.084 0,54.92 16.199,71.12 22.038,71.12 "/>
- </g>
- </g>
- </g>
- </g>
-</g>
-<g id="Layer_2">
-</g>
-</svg>
diff --git a/rtd_phosphonetx/source/html/demoapp/openbis-demo-app.html b/rtd_phosphonetx/source/html/demoapp/openbis-demo-app.html
deleted file mode 100644
index fde4a9f6ce2..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/openbis-demo-app.html
+++ /dev/null
@@ -1,94 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html>
-<head>
- <title>openBIS Proteomics Demo Web App</title>
- <link type="text/css" rel="stylesheet" href="body-style.css" />
- <link type="text/css" rel="stylesheet" href="button.css" />
- <link type="text/css" rel="stylesheet" href="tree.css" />
- <script type="text/javascript" src="d3.js"></script>
- <script type="text/javascript" src="d3.layout.js"></script>
- <script type="text/javascript" src="d3.time.js"></script>
- <script type="text/javascript" src="/openbis/resources/js/jquery.js"></script>
- <script type="text/javascript" src="/openbis/resources/js/openbis.js"></script>
- <script type="text/javascript" src="proteomics-demo.js"></script>
- <!-- To speed development, cache the requests -->
- <!-- <script type="text/javascript" src="/openbis/resources/js/openbis-request-cache.js"></script> -->
-<script>
-
-/// The openbisServer we use for our data
-//var baseURL = 'https://openbis-phosphonetx.ethz.ch'
-var baseURL = 'http://localhost:8888'
-var openbisUrl = baseURL + '/openbis-test-proteomics';
-openbisServer = new openbis(baseURL + '/openbis/openbis', baseURL + '/datastore_server');
-
-
-
-$(document).ready(function() {
- $('#main').hide();
-
- var username = $("#username").value;
- if(username == null || username.length==0) {
- $("#username").focus();
- } else {
- $("#login-button").focus();
- }
-
- $('#logout-button').click(function() {
- openbisServer.logout(function(data) {
- $("#login-form-div").show();
- $("#main").hide();
- $("#username").focus();
- });
- clearTable();
- });
-
- $('#query-button').click(function() {
- var parameters = { "protein" : $.trim($('#protein').val()),
- "space" : $.trim($('#space').val())};
- queryForResults(parameters);
- });
-
- $('#login-form').submit(function() {
- openbisServer.login( $.trim($('#username').val()), $.trim($('#password').val()), function(data) { enterApp(data) })
- });
-
- openbisServer.ifRestoredSessionActive(function(data) { enterApp(data) });
-
- // Make the ENTER key the default button
- $("login-form input").keypress(function (e) {
- if ((e.which && e.which == 13) || (e.keyCode && e.keyCode == 13)) {
- $('button[type=submit].default').click();
- return false;
- } else {
- return true;
- }
- });
-});
-
-</script>
-
-</head>
-<body>
- <img id="openbis-logo" src="images/openBIS_Logo.png" alt="openBIS" style="position: absolute; right: 10px; height: 100px;"/>
- <div id="login-form-div">
- <h1>openBIS Proteomics Demo Web App</h1>
- <form id="login-form" action="javascript:">
- <input id="username" type="text" required="required">
- <input id="password" type="password" required="required">
- <button class="login-button" id="login-button" type="submit">Login</button>
- </form>
- </div>
-
- <div id="main">
- <button id="logout-button">Logout</button>
- <form id="query-form" action="javascript:">
- <table>
- <tr><td>Space</td><td><input id="space" type="text" required="required"></td></tr>
- <tr><td>Protein</td><td><input id="protein" type="text" required="required"></td></tr>
- <tr><td></td><td style="text-align: right"><button class="query-button" id="query-button" type="submit">Search</button></td></tr>
- </table>
- </form>
- <div id="waiting" style="display: none;">Please, wait while loading data.</div>
- </div>
-</body>
-</html>
diff --git a/rtd_phosphonetx/source/html/demoapp/proteomics-demo.js b/rtd_phosphonetx/source/html/demoapp/proteomics-demo.js
deleted file mode 100644
index abda7882c1b..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/proteomics-demo.js
+++ /dev/null
@@ -1,225 +0,0 @@
-/// How much horizontal space do the inspectors take
-var inspectorsWidth = 100;
-
-/// A helper function for drawing the lines between nodes
-var diagonal = d3.svg.diagonal().projection(function(d) { return [d.y, d.x] });
-
-/// The model for the visualization
-var model = null;
-
-/// The visualization, referenced by functions that display content
-var vis;
-
-var didCreateVis = false;
-
-var indexOfLinkedColumn = 3;
-
-/**
- * Create the DOM elements to store the visualization (tree + inspectors)
- */
-function createVis()
-{
- if (didCreateVis) return;
-
- // Create a div to house the tree visualization and the inspectors
- vis = d3.select("#main").append("div").attr("id", "vis");
-
- didCreateVis = true;
-}
-
-function displayReturnedResults(data)
-{
- $("#waiting").hide();
-
- if (data.error) {
- console.log(data.error);
- vis.append("p").text("Could not retrieve data.");
- return;
- }
-
- displayResultsAsGraph(createDataModel(data));
-}
-
-function displayResultsAsGraph(data)
-{
- clearVis();
- if (data.length == 0)
- {
- vis.append("p").text("Nothing found.");
- return;
- }
-
- var delayStep = 20,
- xOffset = 70,
- yOffset = 40,
- xStep = 200,
- yStep = 30,
- xLabel = -30,
- yLabel = 18,
- columnNames = ['Biological Experiment', 'Biological Sample', 'MS Injection Sample', 'Search Experiment', 'Protein'];
-
- var graph = vis.selectAll("svg").data([data]).enter().append("svg:svg")
- .attr("width", $(window).width() - 50)
- .attr("height", $(window).height() - 50);
-
- var g = graph.selectAll("g").data(function(d) { return d; })
- .enter().append("svg:g")
- .attr("transform", function(d,i) { return "translate(" + (xOffset + i * xStep) + ", "
- + yOffset + ")"; });
-
- g.append("svg:text")
- .text(function(d,i) { return columnNames[i]; })
- .attr("class", "columnHeader")
- .attr("text-anchor", "middle")
- .attr("x", 0)
- .attr("y", -10);
-
- g.selectAll("path").data(function(d) { return d[1]; })
- .enter().append("svg:path")
- .attr("class", "line")
- .transition().delay(function(d,i) { return i * delayStep; })
- .attr("d", function(d,i) {
- var y0 = d[0] * yStep;
- var y1 = d[1] * yStep;
- return "M0," + y0
- + "Q" + xStep/4 + "," + y0 + "," + xStep/2 + "," + (y0+y1)/2
- + "L" + xStep/2 + "," + (y0+y1)/2
- + "Q" + 3*xStep/4 + "," + y1 + "," + xStep + "," + y1
- + "L" + xStep + "," + y1;
- })
-
- var node = g.selectAll("g").data(function(d) { return d[0]; })
- .enter().append("svg:g")
- .attr("class", "node")
- .attr("transform", function(d,i) { return "translate(0, " + (i * yStep) + ")"; });
-
- node.append("svg:circle")
- .transition().delay(function(d,i) { return i * delayStep; })
- .attr("r", 5);
-
- node.append("svg:text")
- .on("click", function(d) { if (d.level == indexOfLinkedColumn) {
- window.open(openbisUrl + "/?#entity=EXPERIMENT&permId=" + d.permId, '_blank');
- }
- })
- .transition().delay(function(d,i) { return i * delayStep; })
- .text(function(d) { return d.label; })
- .attr("class", function(d) { return d.level == indexOfLinkedColumn ? "linked" : "notLinked";})
- .attr("text-anchor", "left")
- .attr("x", xLabel)
- .attr("y", yLabel)
-}
-
-
-function Node(level, label, permId) {
- this.level = level;
- this.label = label;
- this.permId = permId;
-}
-
-
-function createDataModel(tableModel)
-{
- var rows = tableModel.result.rows
- var maps = [];
- var permIds = {};
-
- for (n = 0; n < rows.length; n++)
- {
- row = rows[n];
- permIds[row[indexOfLinkedColumn].value] = row[4].value;
- var accessionNumber = row[5].value;
- var splitted = accessionNumber.split("|");
- if (splitted.length > 1)
- {
- accessionNumber = splitted[1];
- }
- row[5].value = accessionNumber + ": " + row[6].value; // concatenate accession number with description
- row.splice(6, 1); // remove description
- row.splice(4, 1); // remove search experiment perm id
- for (i = 0; i < row.length; i++) {
- map = maps[i];
- if (map == null) {
- map = {};
- maps[i] = map;
- }
- cell = row[i].value;
- links = map[cell];
- if (links == null) {
- links = {};
- map[cell] = links;
- }
- if (i < row.length - 1) {
- links[row[i + 1].value] = 0;
- }
- }
- }
- var data = [];
- for (i = 0; i < maps.length; i++) {
- var map = maps[i];
- var elements = [];
- for (element in map) {
- var permId = null;
- if (i == indexOfLinkedColumn)
- {
- permId = permIds[element];
- }
- elements.push(new Node(i, element, permId));
- }
- elements.sort();
- var indexMap = {};
- for (j = 0; j < elements.length; j++) {
- indexMap[elements[j].label] = j;
- }
- data.push([elements, [], indexMap]);
- }
-
- for (i = 0; i < maps.length - 1; i++) {
- var map = maps[i];
- var from = data[i][0];
- var links = data[i][1];
- var indexMap = data[i + 1][2];
- for (j = 0; j < from.length; j++) {
- element = from[j];
- linkedElements = map[element.label];
- for (linkedElement in linkedElements) {
- links.push([j, indexMap[linkedElement]]);
- }
- }
- }
-
- return data;
-}
-
-function clearVis()
-{
- $('#vis > *').remove();
-}
-
-/**
- * Request samples matching some criteria from the server and show them in the Page.
- */
-function queryForResults(parameters)
-{
- $("#waiting").show();
- openbisServer.createReportFromAggregationService("DSS1", "demo-proteomics-aggregation", parameters, displayReturnedResults);
-// openbisServer.createReportFromAggregationService("STANDARD", "demo-proteomics-aggregation", parameters, displayReturnedResults);
-}
-
-
-function enterApp(data)
-{
- if(data.result == null)
- {
- alert("Login or password incorrect");
- $("#username").focus();
- return;
- }
-
- $("#login-form-div").hide();
- $("#main").show();
-
- $('#openbis-logo').height(30);
-
- createVis();
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/html/demoapp/tree.css b/rtd_phosphonetx/source/html/demoapp/tree.css
deleted file mode 100644
index 2d8808b86a6..00000000000
--- a/rtd_phosphonetx/source/html/demoapp/tree.css
+++ /dev/null
@@ -1,36 +0,0 @@
-.node circle {
- fill: #fff;
- stroke: #444444;
- stroke-width: 1.5px;
-}
-
-.columnHeader {
- font: 16px;
- font-weight: bold;
-}
-
-.link {
- fill: none;
- stroke: #ccc;
- stroke-width: 1.5px;
- z-index: -1;
-}
-
-.line {
- fill: none;
- stroke: steelblue;
- stroke-width: 1px;
-}
-
-.node {
- font: 12px "Verdana", sans-serif;
- z-index: 1;
- cursor: pointer;
- position: relative;
- left: -15px;
-}
-
-
-.linked:hover {
- font-weight: bold;
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReport.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReport.java
deleted file mode 100644
index 48e9d481b71..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReport.java
+++ /dev/null
@@ -1,559 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Properties;
-import java.util.Set;
-
-import javax.activation.DataHandler;
-import javax.mail.util.ByteArrayDataSource;
-
-import org.apache.commons.io.IOUtils;
-
-import com.csvreader.CsvReader;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.mail.EMailAddress;
-import ch.systemsx.cisd.common.string.Template;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IProcessingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
-
-/**
- * Creates an APMS report from proteins.csv
- *
- * @author Franz-Josef Elmer
- */
-public class APMSReport extends AbstractTableModelReportingPlugin implements IProcessingPluginTask
-{
- private static final class Header
- {
- private final boolean abundanceHeader;
-
- private final String header;
-
- private String biologicalSample;
-
- private String protein;
-
- Header(String header, String newHeader)
- {
- abundanceHeader = newHeader != null;
- this.header = abundanceHeader ? newHeader : header;
- }
-
- public final String getBiologicalSample()
- {
- return biologicalSample;
- }
-
- public final void setBiologicalSample(String biologicalSample)
- {
- this.biologicalSample = biologicalSample;
- }
-
- public final String getProtein()
- {
- return protein;
- }
-
- public final void setProtein(String protein)
- {
- this.protein = protein;
- }
-
- public final String getHeader()
- {
- return header;
- }
-
- public final boolean isAbundanceHeader()
- {
- return abundanceHeader;
- }
-
- @Override
- public String toString()
- {
- return abundanceHeader ? header + " [" + biologicalSample + ", " + protein + ']'
- : header;
- }
- }
-
- private static final class Row
- {
- private final String[] values;
-
- private final Map<String, Integer> columnIndexMap;
-
- Row(String[] values, Map<String, Integer> columnIndexMap)
- {
- this.values = values;
- this.columnIndexMap = columnIndexMap;
- }
-
- public String getValue(String column)
- {
- Integer index = columnIndexMap.get(column);
- return index == null ? "" : values[index];
- }
-
- @Override
- public String toString()
- {
- return Arrays.asList(values).toString();
- }
- }
-
- private static final class Table
- {
- private final List<Header> headers;
-
- private final Map<String, Integer> columnIndexMap = new HashMap<String, Integer>();
-
- private final List<Row> rows = new ArrayList<Row>();
-
- Table(List<Header> headers)
- {
- this.headers = headers;
- for (int i = 0; i < headers.size(); i++)
- {
- columnIndexMap.put(headers.get(i).getHeader(), i);
- }
- }
-
- void add(String[] row)
- {
- rows.add(new Row(row, columnIndexMap));
- }
-
- public final List<Header> getHeaders()
- {
- return headers;
- }
-
- public final List<Row> getRows()
- {
- return rows;
- }
- }
-
- private static final long serialVersionUID = 1L;
-
- @Private
- static final String PROTEIN_FILE_NAME = "proteins.csv";
-
- private static final String PROTEIN_PROPERTY_CODE_KEY = "protein-property-code";
-
- @Private
- static final String DEFAULT_PROTEIN_PROPERTY_CODE = "PROTEIN";
-
- private static final Template E_MAIL_CONTENT_TEMPLATE =
- new Template(
- "Dear User\n\n"
- + "Enclosed you will find the Protein APMS report file for experiment ${experiment-identifier}.\n"
- + "Data Set: ${data-set}");
-
- private final String proteinPropertyCode;
-
- private IEncapsulatedOpenBISService service;
-
- public APMSReport(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- proteinPropertyCode =
- properties.getProperty(PROTEIN_PROPERTY_CODE_KEY, DEFAULT_PROTEIN_PROPERTY_CODE);
- }
-
- @Override
- public TableModel createReport(List<DatasetDescription> datasets,
- DataSetProcessingContext context)
- {
- if (datasets.size() != 1)
- {
- throw new UserFailureException("Chosen plugin works with exactly one data set. "
- + datasets.size() + " data sets selected.");
- }
- return createTableModel(datasets.get(0), context.getDirectoryProvider());
- }
-
- @Override
- public ProcessingStatus process(List<DatasetDescription> datasets,
- DataSetProcessingContext context)
- {
- ProcessingStatus status = new ProcessingStatus();
- for (DatasetDescription datasetDescription : datasets)
- {
- try
- {
- process(datasetDescription, context);
- status.addDatasetStatus(datasetDescription, Status.OK);
- } catch (Exception ex)
- {
- status.addDatasetStatus(datasetDescription,
- Status.createError("Exception occured: " + ex));
- operationLog.error("Exception occured while processing " + datasetDescription, ex);
- }
- }
- return status;
- }
-
- private void process(DatasetDescription datasetDescription, DataSetProcessingContext context)
- {
- try
- {
- TableModel table =
- createTableModel(datasetDescription, context.getDirectoryProvider());
- String tableAsString = convertTableToCsvString(table);
- String experimentIdentifier =
- datasetDescription.getSpaceCode() + '/' + datasetDescription.getProjectCode()
- + '/' + datasetDescription.getExperimentCode();
- Template template = E_MAIL_CONTENT_TEMPLATE.createFreshCopy();
- template.bind("experiment-identifier", experimentIdentifier);
- template.bind("data-set", datasetDescription.getDataSetCode());
- ByteArrayDataSource dataSource = new ByteArrayDataSource(tableAsString, "text/plain");
- context.getMailClient().sendEmailMessageWithAttachment("Protein APMS Report",
- template.createText(),
- datasetDescription.getExperimentCode() + "-APMS-report.txt",
- new DataHandler(dataSource), null, null,
- new EMailAddress(context.getUserEmailOrNull()));
-
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- private TableModel createTableModel(DatasetDescription datasetDescription,
- IDataSetDirectoryProvider directoryProvider)
- {
- File proteinFile = getProteinFile(datasetDescription, directoryProvider);
- Table table = readTable(proteinFile);
- addHeaderMetaData(table);
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- builder.addHeader("Sample ID");
- builder.addHeader("Bait");
- builder.addHeader("Prey");
- builder.addHeader("freq of obs");
- builder.addHeader("avg MS1 intensities (normalized for the bait)");
- builder.addHeader("STDV MS1 intensity");
- List<Entry<String, List<Header>>> groups = calculateAbundanceColumnGroups(table);
- List<Row> rows = table.getRows();
- for (int i = 0; i < rows.size(); i++)
- {
- Row row = rows.get(i);
- addRowsTo(builder, row, i, groups);
- }
- return builder.getTableModel();
- }
-
- private List<Entry<String, List<Header>>> calculateAbundanceColumnGroups(Table table)
- {
- List<Header> headers = table.getHeaders();
- Map<String, List<Header>> abundanceColumnHeaders = new HashMap<String, List<Header>>();
- for (Header header : headers)
- {
- if (header.isAbundanceHeader())
- {
- String biologicalSample = header.getBiologicalSample();
- List<Header> list = abundanceColumnHeaders.get(biologicalSample);
- if (list == null)
- {
- list = new ArrayList<Header>();
- abundanceColumnHeaders.put(biologicalSample, list);
- }
- list.add(header);
- }
- }
- Set<Entry<String, List<Header>>> entrySet = abundanceColumnHeaders.entrySet();
- List<Entry<String, List<Header>>> entryList =
- new ArrayList<Map.Entry<String, List<Header>>>(entrySet);
- Collections.sort(entryList, new Comparator<Entry<String, List<Header>>>()
- {
- @Override
- public int compare(Entry<String, List<Header>> e1, Entry<String, List<Header>> e2)
- {
- String key1 = e1.getKey();
- String key2 = e2.getKey();
- if (key1 != null && key2 != null)
- {
- return key1.compareTo(key2);
- }
- return key1 == null ? (key2 == null ? 0 : 1) : -1;
- }
- });
- return entryList;
- }
-
- private void addRowsTo(SimpleTableModelBuilder builder, Row row, int i,
- List<Entry<String, List<Header>>> groups)
- {
- String identifiedProtein = row.getValue("protein");
- for (Entry<String, List<Header>> group : groups)
- {
- String biologicalSample = group.getKey();
- List<Header> headers = group.getValue();
- String protein = null;
- double countNonZeroAbundances = 0;
- double sum = 0;
- double sum2 = 0;
- for (Header header : headers)
- {
- if (biologicalSample != null && protein == null)
- {
- protein = header.getProtein();
- }
- String value = row.getValue(header.getHeader());
- try
- {
- double abundance = Double.parseDouble(value);
- sum += abundance;
- sum2 += abundance * abundance;
- if (abundance > 0)
- {
- countNonZeroAbundances++;
- }
- } catch (NumberFormatException ex)
- {
- throw new UserFailureException((i + 5) + ". row has an invalid value (" + value
- + ") for column " + header.getHeader() + ": " + row);
- }
- }
- double averagedAbundance = sum / headers.size();
- double abundanceStandardDeviation =
- Math.sqrt(Math.max(0, sum2 / headers.size() - averagedAbundance
- * averagedAbundance));
- double frequencyOfObservation = countNonZeroAbundances / headers.size();
- StringTableCell biologicalSampleCell = StringTableCell.wrap(biologicalSample);
- StringTableCell proteinCell = StringTableCell.wrap(protein);
- StringTableCell identifiedProteinCell = new StringTableCell(identifiedProtein);
- DoubleTableCell freqOfObsvCell = new DoubleTableCell(frequencyOfObservation);
- DoubleTableCell abundanceCell = new DoubleTableCell(averagedAbundance);
- DoubleTableCell abundanceStdvCell = new DoubleTableCell(abundanceStandardDeviation);
- builder.addRow(Arrays.<ISerializableComparable> asList(biologicalSampleCell,
- proteinCell, identifiedProteinCell, freqOfObsvCell, abundanceCell,
- abundanceStdvCell));
- }
- }
-
- private void addHeaderMetaData(Table table)
- {
- List<Header> headers = table.getHeaders();
- for (Header header : headers)
- {
- if (header.isAbundanceHeader())
- {
- SampleIdentifier sampleIdentifier =
- SampleIdentifierFactory.parse("/MS_DATA/"
- + header.getHeader().toUpperCase());
- Sample sample = getService().tryGetSampleWithExperiment(sampleIdentifier);
- if (sample == null)
- {
- throw new UserFailureException("Unknown sample: " + sampleIdentifier);
- }
- List<Sample> parents =
- getService().listSamples(
- ListSampleCriteria.createForChild(new TechId(sample.getId())));
- if (parents.size() != 1)
- {
- throw new UserFailureException("Exactly one parent sample expected for "
- + sample.getIdentifier() + " instead of " + parents.size());
- }
- Sample biologicalSample = parents.get(0);
- header.setBiologicalSample(biologicalSample.getCode());
- String protein = tryToFindProteinProperty(biologicalSample);
- if (protein != null)
- {
- header.setProtein(protein);
- }
- }
- }
- }
-
- private String tryToFindProteinProperty(Sample sample)
- {
- List<IEntityProperty> sampleProperties = sample.getProperties();
- for (IEntityProperty property : sampleProperties)
- {
- if (property.getPropertyType().getCode().equalsIgnoreCase(proteinPropertyCode))
- {
- Material material = property.getMaterial();
- if (material != null)
- {
- return material.getCode();
- }
- return property.tryGetAsString();
- }
- }
- List<Sample> parents =
- getService().listSamples(
- ListSampleCriteria.createForChild(new TechId(sample.getId())));
- for (Sample parent : parents)
- {
- String proteinProperty = tryToFindProteinProperty(parent);
- if (proteinProperty != null)
- {
- return proteinProperty;
- }
- }
- return null;
- }
-
- private Table readTable(File file)
- {
- FileReader reader = null;
- try
- {
- reader = new FileReader(file);
- CsvReader csvReader = new CsvReader(reader);
- csvReader.readRecord();
- csvReader.readRecord();
- csvReader.readRecord();
- Map<String, String> map = createAbundanceColumnMap(csvReader.getRawRecord());
- csvReader.readRecord();
- String[] columnHeaders = csvReader.getValues();
- List<Header> headers = new ArrayList<Header>();
- for (int i = 0; i < columnHeaders.length; i++)
- {
- String header = columnHeaders[i];
- String newHeader = map.get(header);
- headers.add(new Header(header, newHeader));
- }
- Table table = new Table(headers);
- while (csvReader.readRecord())
- {
- table.add(csvReader.getValues());
- }
- return table;
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(reader);
- }
- }
-
- private Map<String, String> createAbundanceColumnMap(String abundanceColumnMappingDescription)
- {
- int indexOfFirstColon = abundanceColumnMappingDescription.indexOf(':');
- if (indexOfFirstColon < 0)
- {
- throw new UserFailureException("Missing ':' in third line: "
- + abundanceColumnMappingDescription);
- }
- String[] terms =
- abundanceColumnMappingDescription.substring(indexOfFirstColon + 1).split(",");
- Map<String, String> map = new HashMap<String, String>();
- for (String term : terms)
- {
- int indexOfColon = term.indexOf(':');
- if (indexOfColon < 0)
- {
- throw new UserFailureException("Missing ':' in mapping definition: " + term);
- }
- String abundanceColumn = "abundance_" + term.substring(0, indexOfColon).trim();
- String fileName = term.substring(indexOfColon + 1).trim();
- int lastIndexOfSlash = fileName.lastIndexOf('/');
- if (lastIndexOfSlash >= 0)
- {
- fileName = fileName.substring(lastIndexOfSlash + 1);
- }
- int lastIndexOfDot = fileName.lastIndexOf('.');
- if (lastIndexOfDot >= 0)
- {
- fileName = fileName.substring(0, lastIndexOfDot);
- }
- map.put(abundanceColumn, fileName);
- }
- return map;
- }
-
- private File getProteinFile(DatasetDescription datasetDescription,
- IDataSetDirectoryProvider directoryProvider)
- {
- @SuppressWarnings("deprecation")
- File dataSetDir = getDataSubDir(directoryProvider, datasetDescription);
- if (dataSetDir.isDirectory() == false)
- {
- throw new EnvironmentFailureException("Data set folder is not a directory: "
- + dataSetDir);
- }
- File[] files = dataSetDir.listFiles();
- if (files.length == 0)
- {
- throw new EnvironmentFailureException("Empty data set folder: " + dataSetDir);
- }
- File proteinFile = new File(files[0], PROTEIN_FILE_NAME);
- if (proteinFile.exists() == false)
- {
- throw new UserFailureException("File " + PROTEIN_FILE_NAME + " missing.");
- }
- if (proteinFile.isFile() == false)
- {
- throw new UserFailureException("File " + PROTEIN_FILE_NAME + " is a directory.");
- }
- return proteinFile;
- }
-
- private IEncapsulatedOpenBISService getService()
- {
- if (service == null)
- {
- service = ServiceProvider.getOpenBISService();
- }
- return service;
- }
-
- // for tests
- void setService(IEncapsulatedOpenBISService service)
- {
- this.service = service;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
deleted file mode 100644
index 35ea9750c05..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/DataSetCopier.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
-
-import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier.DESTINATION_KEY;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDropboxProcessingPlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierFactory;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.RsyncCopierFactory;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.SshCommandExecutorFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetCopier extends AbstractDropboxProcessingPlugin
-{
- private static final long serialVersionUID = 1L;
-
- public DataSetCopier(Properties properties, File storeRoot)
- {
- this(properties, storeRoot, new RsyncCopierFactory(), new SshCommandExecutorFactory());
- }
-
- @Private
- DataSetCopier(Properties properties, File storeRoot, IPathCopierFactory pathCopierFactory,
- ISshCommandExecutorFactory sshCommandExecutorFactory)
- {
- super(properties, storeRoot, new LocalAndRemoteCopier(properties, pathCopierFactory,
- sshCommandExecutorFactory));
- }
-
- @Override
- protected String getProcessingDescription(DatasetDescription dataset,
- DataSetProcessingContext context)
- {
- return "Copy to " + properties.getProperty(DESTINATION_KEY);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopier.java
deleted file mode 100644
index 6bdf9380721..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopier.java
+++ /dev/null
@@ -1,191 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
-
-import java.io.File;
-import java.io.Serializable;
-import java.util.Map;
-import java.util.Properties;
-
-import org.apache.log4j.Logger;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.ExceptionWithStatus;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.filesystem.BooleanStatus;
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.filesystem.HostAwareFile;
-import ch.systemsx.cisd.common.filesystem.IPathCopier;
-import ch.systemsx.cisd.common.filesystem.highwatermark.HostAwareFileWithHighwaterMark;
-import ch.systemsx.cisd.common.filesystem.ssh.ISshCommandExecutor;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.generic.server.IDataSetFileOperationsExecutor;
-import ch.systemsx.cisd.openbis.dss.generic.server.LocalDataSetFileOperationsExcecutor;
-import ch.systemsx.cisd.openbis.dss.generic.server.RemoteDataSetFileOperationsExecutor;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.Copier;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierFactory;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IPostRegistrationDatasetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.RSyncConfig;
-
-/**
- * @author Franz-Josef Elmer
- */
-class LocalAndRemoteCopier implements Serializable, IPostRegistrationDatasetHandler
-{
-
- @Private
- static final String MARKER_FILE_PREFIX = "marker-file-prefix";
-
- @Private
- static final String SAMPLE_UNKNOWN = "sample-unknown";
-
- private static final long serialVersionUID = 1L;
-
- final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- LocalAndRemoteCopier.class);
-
- private final Properties properties;
-
- private final IPathCopierFactory pathCopierFactory;
-
- private final ISshCommandExecutorFactory sshCommandExecutorFactory;
-
- private transient IDataSetFileOperationsExecutor executor;
-
- private transient String destination;
-
- private String markerFilePrefix;
-
- LocalAndRemoteCopier(Properties properties, IPathCopierFactory pathCopierFactory,
- ISshCommandExecutorFactory sshCommandExecutorFactory)
- {
- this.properties = properties;
- this.pathCopierFactory = pathCopierFactory;
- this.sshCommandExecutorFactory = sshCommandExecutorFactory;
- markerFilePrefix = properties.getProperty(MARKER_FILE_PREFIX);
- if (markerFilePrefix != null && markerFilePrefix.length() == 0)
- {
- throw new ConfigurationFailureException("marker-file-prefix is an empty string.");
- }
- init();
- }
-
- private void init()
- {
- String hostFile =
- PropertyUtils.getMandatoryProperty(properties, DataSetCopier.DESTINATION_KEY);
- HostAwareFile hostAwareFile = HostAwareFileWithHighwaterMark.create(hostFile, -1);
- String hostOrNull = hostAwareFile.tryGetHost();
- destination = hostAwareFile.getPath();
- if (hostOrNull == null)
- {
- File sshExecutable = null; // don't use ssh locally
- File rsyncExecutable = Copier.getExecutable(properties, DataSetCopier.RSYNC_EXEC);
- IPathCopier copier =
- pathCopierFactory.create(rsyncExecutable, sshExecutable,
- DataSetCopier.SSH_TIMEOUT_MILLIS, RSyncConfig.getInstance().getAdditionalCommandLineOptions());
- copier.check();
- String rsyncModule = hostAwareFile.tryGetRsyncModule();
- String rsyncPasswordFile =
- properties.getProperty(DataSetCopier.RSYNC_PASSWORD_FILE_KEY);
- executor =
- new LocalDataSetFileOperationsExcecutor(
- FileOperations.getMonitoredInstanceForCurrentThread(), copier,
- rsyncModule, rsyncPasswordFile);
- } else
- {
- File sshExecutable = Copier.getExecutable(properties, DataSetCopier.SSH_EXEC);
- File rsyncExecutable = Copier.getExecutable(properties, DataSetCopier.RSYNC_EXEC);
- File gfindExecutable = Copier.getExecutable(properties, DataSetCopier.GFIND_EXEC);
- IPathCopier copier =
- pathCopierFactory.create(rsyncExecutable, sshExecutable,
- DataSetCopier.SSH_TIMEOUT_MILLIS, RSyncConfig.getInstance().getAdditionalCommandLineOptions());
- copier.check();
- String rsyncModule = hostAwareFile.tryGetRsyncModule();
- String rsyncPasswordFile =
- properties.getProperty(DataSetCopier.RSYNC_PASSWORD_FILE_KEY);
- FileUtilities.checkPathCopier(copier, hostOrNull, null, rsyncModule, rsyncPasswordFile,
- DataSetCopier.SSH_TIMEOUT_MILLIS);
- ISshCommandExecutor sshCommandExecutor =
- sshCommandExecutorFactory.create(sshExecutable, hostOrNull);
- executor =
- new RemoteDataSetFileOperationsExecutor(sshCommandExecutor, copier,
- gfindExecutable, hostOrNull, rsyncModule, rsyncPasswordFile,
- DataSetCopier.SSH_TIMEOUT_MILLIS);
- }
- }
-
- @Override
- public void undoLastOperation()
- {
- }
-
- /**
- * Copies specified data file/folder to destination specified in constructor. The name of the file/folder at the destination is defined by the
- * data set code.
- */
- @Override
- public Status handle(File originalData, DataSetInformation dataSetInformation,
- Map<String, String> parameterBindings)
- {
- if (destination == null)
- {
- init();
- }
- try
- {
- final File destinationLocalFile = new File(destination);
- String target = dataSetInformation.getDataSetCode();
- File targetFolder = new File(destinationLocalFile, target);
- deleteTargetFolder(targetFolder);
- executor.copyDataSetToDestination(originalData, destinationLocalFile);
- executor.renameTo(targetFolder, new File(destination, originalData.getName()));
- if (markerFilePrefix != null)
- {
- executor.createMarkerFile(new File(destination, markerFilePrefix + target));
- }
- return Status.OK;
-
- } catch (ExceptionWithStatus ex)
- {
- return ex.getStatus();
- }
- }
-
- private void deleteTargetFolder(File targetFolder)
- {
- BooleanStatus targetExists = executor.exists(targetFolder);
- if (targetExists.isError())
- {
- operationLog.error("Could not check existence of '" + targetFolder + "': "
- + targetExists.tryGetMessage());
- throw new ExceptionWithStatus(Status.createError("couldn't check existence"));
- }
- if (targetExists.isSuccess())
- {
- executor.deleteFolder(targetFolder);
- }
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractDataSetInfoExtractorWithService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractDataSetInfoExtractorWithService.java
deleted file mode 100644
index 07158f3b170..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractDataSetInfoExtractorWithService.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractDataSetInfoExtractorWithService implements IDataSetInfoExtractor
-{
- protected final IEncapsulatedOpenBISService service;
-
- protected AbstractDataSetInfoExtractorWithService(IEncapsulatedOpenBISService service)
- {
- this.service = service;
-
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractHandler.java
deleted file mode 100644
index fdf05fc0585..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractHandler.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-/**
- * Abstract super class of classes using {@link IProtDAO}.
- *
- * @author Franz-Josef Elmer
- */
-abstract class AbstractHandler
-{
- protected final IProtDAO dao;
-
- AbstractHandler(IProtDAO dao)
- {
- this.dao = dao;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
deleted file mode 100644
index 9f102974f9a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * Abstract super class of classes getting or creating {@link Sample} instances.
- *
- * @author Franz-Josef Elmer
- */
-abstract class AbstractSampleHandler extends AbstractHandler
-{
- @Private
- static final String MZXML_FILENAME = "MZXML_FILENAME";
-
- protected static final class SampleOrError
- {
- Sample sample;
-
- String error;
- }
-
- protected final IEncapsulatedOpenBISService openbisService;
-
- protected final ExperimentIdentifier experimentIdentifier;
-
- private final Experiment experiment;
-
- private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
-
- private final String delimiter;
-
- private final boolean restrictedSampleResolving;
-
- AbstractSampleHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
- boolean restrictedSampleResolving)
- {
- super(dao);
- this.openbisService = openbisService;
- this.experimentIdentifier = experimentIdentifier;
- this.experiment = experiment;
- this.delimiter = delimiter;
- this.restrictedSampleResolving = restrictedSampleResolving;
- }
-
- protected SampleOrError getOrCreateSampleOrError(String sampleNameAndMore)
- {
- int indexOfDelimiter = sampleNameAndMore.indexOf(delimiter);
- String sampleName;
- if (indexOfDelimiter < 0)
- {
- sampleName = sampleNameAndMore;
- } else
- {
- sampleName = sampleNameAndMore.substring(0, indexOfDelimiter);
- }
- SampleOrError sampleOrError = samplesOrErrors.get(sampleName);
- if (sampleOrError == null)
- {
- // first we look for a sample in space MS_DATA
- SampleIdentifier sampleIdentifier =
- SampleIdentifierFactory.parse(sampleName, "/" + CommonConstants.MS_DATA_SPACE);
- String sampleCode = sampleIdentifier.getSampleCode();
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- openbisService.tryGetSampleWithExperiment(sampleIdentifier);
- sampleOrError = new SampleOrError();
- if (sample != null)
- {
- sampleOrError.sample = getOrCreateSample(sample.getPermId());
- } else if (restrictedSampleResolving == false)
- {
- // second we look for a sample in same space as search experiment with
- // a property specified by 'sampleName'
- String spaceCode = experimentIdentifier.getSpaceCode();
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> list =
- openbisService.listSamplesByCriteria(new ListSamplesByPropertyCriteria(
- MZXML_FILENAME, sampleName, spaceCode, null));
- if (list == null || list.size() == 0)
- {
- sampleOrError.error = "an unidentified sample: " + sampleName;
- } else if (list.size() > 1)
- {
- sampleOrError.error =
- "a not uniquely specified sample (" + list.size()
- + " samples are found): " + sampleName;
- } else
- {
- sample = list.get(0);
- sampleOrError.sample = getOrCreateSample(sample.getPermId());
- }
- } else
- {
- sampleOrError.error = "Couldn't resolve sample: " + sampleIdentifier;
- }
- if (sample != null)
- {
- handleSample(sampleCode, sample);
- }
- samplesOrErrors.put(sampleName, sampleOrError);
- }
- return sampleOrError;
- }
-
- private Sample getOrCreateSample(String samplePermID)
- {
- Sample sample = dao.tryToGetSampleByPermID(samplePermID);
- if (sample == null)
- {
- sample = new Sample();
- sample.setPermID(samplePermID);
- sample.setId(dao.createSample(experiment.getId(), samplePermID));
- }
- return sample;
- }
-
- protected abstract void handleSample(String parameterName,
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
deleted file mode 100644
index 38b3223a0ae..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-
-/**
- * Handler of {@link Parameter} objects of type 'abundance'.
- *
- * @author Franz-Josef Elmer
- */
-class AbundanceHandler extends AbstractSampleHandler
-{
- private final SampleType sampleType;
-
- AbundanceHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
- boolean restrictedSampleResolving)
- {
- super(openbisService, dao, experimentIdentifier, experiment, delimiter,
- restrictedSampleResolving);
- sampleType = new SampleType();
- sampleType.setCode(Constants.SEARCH_SAMPLE_TYPE);
- }
-
- void addAbundancesToDatabase(Parameter parameter, long proteinID, String proteinName)
- {
- Sample sample = getOrCreateSample(parameter.getName(), proteinName);
- try
- {
- double abundance = Double.parseDouble(parameter.getValue());
- dao.createAbundance(proteinID, sample.getId(), abundance);
- } catch (NumberFormatException ex)
- {
- throw new UserFailureException("Abundance of sample '" + parameter.getName()
- + "' of protein '" + proteinName + "' is not a number: " + parameter.getValue());
- }
- }
-
- private Sample getOrCreateSample(String parameterName, String proteinName)
- {
- SampleOrError sampleOrError = getOrCreateSampleOrError(parameterName);
- if (sampleOrError.error != null)
- {
- throw new UserFailureException("Protein '" + proteinName
- + "' has an abundance value for " + sampleOrError.error);
- }
- return sampleOrError.sample;
- }
-
- @Override
- @SuppressWarnings("deprecation")
- protected void handleSample(String parameterName,
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
- {
- NewSample searchSample = new NewSample();
- searchSample.setSampleType(sampleType);
- SpaceIdentifier spaceIdentifier =
- new SpaceIdentifier(experimentIdentifier.getSpaceCode());
- SampleIdentifier identifier =
- new SampleIdentifier(spaceIdentifier, parameterName + "_"
- + experimentIdentifier.getExperimentCode());
- searchSample.setIdentifier(identifier.toString());
- searchSample.setExperimentIdentifier(experimentIdentifier.toString());
- searchSample.setParentIdentifier(sample.getIdentifier());
- openbisService.registerSample(searchSample, null);
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Constants.java
deleted file mode 100644
index b41a7e31782..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Constants.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Constants
-{
- public static final String NAMESPACE = "http://regis-web.systemsbiology.net/protXML";
-
- public static final String SEARCH_SAMPLE_TYPE = "SEARCH";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjection.java
deleted file mode 100644
index a593abbdd80..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjection.java
+++ /dev/null
@@ -1,237 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * Data set info extractor for MS injection data sets. Information is extracted from a properties file (ms-injection.properties) which is expected t
- * be a part of the data set. As a side effect a corresponding sample of type MS_INJECTION is created with the properties of this file.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtractorWithService
-{
- private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- DataSetInfoExtractorForMSInjection.class);
-
- static final String MS_INJECTION_PROPERTIES_FILE = "ms-injection.properties";
-
- static final String DATA_SET_PROPERTIES_FILE = "data-set.properties";
-
- static final String PROJECT_CODE_KEY = "PROJECT_CODE";
-
- static final String EXPERIMENT_CODE_KEY = "EXPERIMENT_CODE";
-
- static final String SAMPLE_CODE_KEY = "SAMPLE_CODE";
-
- static final String BIOLOGICAL_SAMPLE_IDENTIFIER_KEY = "BIOLOGICAL_SAMPLE_IDENTIFIER";
-
- static final String USER_KEY = "USER";
-
- static final String DATA_SET_TYPE_KEY = "DATA_SET_TYPE";
-
- static final String FILE_TYPE_KEY = "FILE_TYPE";
-
- static final String PARENT_TYPE_KEY = "PARENT_TYPE";
-
- static final String EXPERIMENT_TYPE_CODE = "MS_INJECT";
-
- public DataSetInfoExtractorForMSInjection(Properties properties)
- {
- this(ServiceProvider.getOpenBISService());
- }
-
- DataSetInfoExtractorForMSInjection(IEncapsulatedOpenBISService service)
- {
- super(service);
- }
-
- @Override
- public DataSetInformation getDataSetInformation(File incomingDataSetPath,
- IEncapsulatedOpenBISService openbisService) throws UserFailureException,
- EnvironmentFailureException
- {
- Properties sampleProperties =
- Util.loadPropertiesFile(incomingDataSetPath, MS_INJECTION_PROPERTIES_FILE);
- DataSetInformation info = new DataSetInformation();
- info.setSpaceCode(CommonConstants.MS_DATA_SPACE);
- info.setSampleCode(PropertyUtils.getMandatoryProperty(sampleProperties, SAMPLE_CODE_KEY));
- SampleIdentifier sampleIdentifier = info.getSampleIdentifier();
- ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(sampleProperties);
- getOrCreateExperiment(experimentIdentifier);
- info.setExperimentIdentifier(experimentIdentifier);
- long sampleID =
- registerOrUpdateSample(sampleIdentifier, experimentIdentifier, sampleProperties);
-
- Properties dataSetProperties =
- Util.loadPropertiesFile(incomingDataSetPath, DATA_SET_PROPERTIES_FILE);
- String dataSetTypeCode =
- PropertyUtils.getMandatoryProperty(dataSetProperties, DATA_SET_TYPE_KEY);
- String parentTypeOrNull = dataSetProperties.getProperty(PARENT_TYPE_KEY);
- dataSetProperties.remove(DATA_SET_TYPE_KEY);
- dataSetProperties.remove(FILE_TYPE_KEY);
- dataSetProperties.remove(PARENT_TYPE_KEY);
- setDataSetPropertiesFor(info, dataSetProperties, dataSetTypeCode);
- if (parentTypeOrNull != null)
- {
- List<AbstractExternalData> dataSets = service.listDataSetsBySampleID(sampleID, false);
- AbstractExternalData youngestDataSet = null;
- for (AbstractExternalData dataSet : dataSets)
- {
- if (dataSet.getDataSetType().getCode().equals(parentTypeOrNull))
- {
- if (youngestDataSet == null || timeStamp(youngestDataSet) < timeStamp(dataSet))
- {
- youngestDataSet = dataSet;
- }
- }
- }
- if (youngestDataSet != null)
- {
- info.setParentDataSetCodes(Arrays.asList(youngestDataSet.getCode()));
- }
- }
- return info;
- }
-
- private long registerOrUpdateSample(SampleIdentifier sampleIdentifier,
- ExperimentIdentifier experimentIdentifier, Properties properties)
- {
- SampleType sampleType = service.getSampleType(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
- Sample sample = service.tryGetSampleWithExperiment(sampleIdentifier);
- String biologicalSampleIdentifier = tryToGetBiologicalSampleIdentifier(properties);
- if (sample == null)
- {
- NewSample newSample = new NewSample();
- newSample.setSampleType(sampleType);
- newSample.setExperimentIdentifier(experimentIdentifier.toString());
- newSample.setIdentifier(sampleIdentifier.toString());
- if (biologicalSampleIdentifier != null)
- {
- newSample.setParents(biologicalSampleIdentifier);
- }
- IEntityProperty[] sampleProperties = Util.getAndCheckProperties(properties, sampleType);
- newSample.setProperties(sampleProperties);
- return service.registerSample(newSample, properties.getProperty(USER_KEY));
- } else
- {
- TechId sampleID = new TechId(sample.getId());
- List<IEntityProperty> propertiesList =
- Util.getProperties(properties, sampleType, new ArrayList<String>());
- Set<NewAttachment> emptySet = Collections.<NewAttachment> emptySet();
- int version = sample.getVersion();
- service.updateSample(new SampleUpdatesDTO(sampleID, propertiesList,
- experimentIdentifier, null, emptySet, version, sampleIdentifier, null,
- biologicalSampleIdentifier == null ? null : new String[]
- { biologicalSampleIdentifier }));
- return sample.getId();
- }
- }
-
- private String tryToGetBiologicalSampleIdentifier(Properties properties)
- {
- String biologicalSampleIdentifier =
- properties.getProperty(BIOLOGICAL_SAMPLE_IDENTIFIER_KEY);
- if (biologicalSampleIdentifier != null)
- {
- Sample bioSample =
- service.tryGetSampleWithExperiment(SampleIdentifierFactory
- .parse(biologicalSampleIdentifier));
- if (bioSample == null)
- {
- // ignore biological sample if it does not exist.
- biologicalSampleIdentifier = null;
- operationLog.warn("Property " + BIOLOGICAL_SAMPLE_IDENTIFIER_KEY
- + " will be ignored because the specified biological sample "
- + biologicalSampleIdentifier + " does not exist.");
- }
- }
- return biologicalSampleIdentifier;
- }
-
- private long timeStamp(AbstractExternalData dataSet)
- {
- return dataSet.getRegistrationDate().getTime();
- }
-
- private void setDataSetPropertiesFor(DataSetInformation info, Properties dataSetProperties,
- String dataSetTypeCode)
- {
- DataSetType dataSetType = service.getDataSetType(dataSetTypeCode).getDataSetType();
- IEntityProperty[] props = Util.getAndCheckProperties(dataSetProperties, dataSetType);
- List<NewProperty> properties = new ArrayList<NewProperty>();
- for (IEntityProperty p : props)
- {
- properties.add(new NewProperty(p.getPropertyType().getCode(), p.tryGetAsString()));
- }
- info.setDataSetProperties(properties);
- }
-
- private long getOrCreateExperiment(ExperimentIdentifier identifier)
- {
- Experiment experiment = service.tryGetExperiment(identifier);
- if (experiment == null)
- {
- return service.registerExperiment(new NewExperiment(identifier.toString(),
- EXPERIMENT_TYPE_CODE));
- }
- return experiment.getId();
- }
-
- private ExperimentIdentifier getExperimentIdentifier(Properties msInjectionProperties)
- {
- String projectCode =
- PropertyUtils.getMandatoryProperty(msInjectionProperties, PROJECT_CODE_KEY);
- String experimentCode =
- PropertyUtils.getMandatoryProperty(msInjectionProperties, EXPERIMENT_CODE_KEY);
- return new ExperimentIdentifier(CommonConstants.MS_DATA_SPACE, projectCode, experimentCode);
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
deleted file mode 100644
index 4e0c8e6a8fc..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
+++ /dev/null
@@ -1,241 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.io.PropertyIOUtils;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ParentDataSetCodes;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoExtractorWithService
-{
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, DataSetInfoExtractorForProteinResults.class);
-
- static final String NOT_PROCESSED_PROPERTY = "NOT_PROCESSED";
-
- @Private
- static final String PROT_XML_SIZE_THRESHOLD = "prot-xml-size-threshold-in-MB";
-
- private static final int DEFAULT_PROT_XML_SIZE_THRESHOLD = 256;
-
- @Private
- static final String EXPERIMENT_TYPE_CODE_KEY = "experiment-type-code";
-
- @Private
- static final String EXPERIMENT_CODE_KEY = "experiment-code";
-
- @Private
- static final String EXPERIMENT_PROPERTIES_FILE_NAME_KEY = "experiment-properties-file-name";
-
- @Private
- static final String DEFAULT_EXPERIMENT_TYPE_CODE = "MS_SEARCH";
-
- @Private
- static final String SEPARATOR_KEY = "separator";
-
- @Private
- static final String DEFAULT_SEPARATOR = "&";
-
- @Private
- static final String DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME = "search.properties";
-
- static final String PARENT_DATA_SET_CODES = "parent-data-set-codes";
-
- static final String EXPERIMENT_IDENTIFIER_KEY = "base-experiment";
-
- private final String separator;
-
- private final String experimentPropertiesFileName;
-
- private final String experimentTypeCode;
-
- private final long protXmlSizeThreshold;
-
- public DataSetInfoExtractorForProteinResults(Properties properties)
- {
- this(properties, ServiceProvider.getOpenBISService());
- }
-
- DataSetInfoExtractorForProteinResults(Properties properties, IEncapsulatedOpenBISService service)
- {
- super(service);
- separator = properties.getProperty(SEPARATOR_KEY, DEFAULT_SEPARATOR);
- experimentPropertiesFileName =
- properties.getProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY,
- DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME);
- experimentTypeCode =
- properties.getProperty(EXPERIMENT_TYPE_CODE_KEY, DEFAULT_EXPERIMENT_TYPE_CODE);
- protXmlSizeThreshold = PropertyUtils.getInt(properties, PROT_XML_SIZE_THRESHOLD,
- DEFAULT_PROT_XML_SIZE_THRESHOLD) * FileUtils.ONE_MB;
- }
-
- @Override
- public DataSetInformation getDataSetInformation(File incomingDataSetPath,
- IEncapsulatedOpenBISService openbisService) throws UserFailureException,
- EnvironmentFailureException
- {
- String name = incomingDataSetPath.getName();
- String[] items = StringUtils.splitByWholeSeparator(name, separator);
- if (items.length < 2)
- {
- throw new UserFailureException(
- "The name of the data set should have at least two parts separated by '"
- + separator + "': " + name);
- }
- ProjectIdentifier projectIdentifier = new ProjectIdentifier(items[0], items[1]);
- Properties properties =
- loadSearchProperties(new File(incomingDataSetPath, experimentPropertiesFileName));
- String experimentCode = properties.getProperty(EXPERIMENT_CODE_KEY);
- if (experimentCode == null)
- {
- experimentCode = service.generateCodes("E", EntityKind.EXPERIMENT, 1).get(0);
- }
- ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifier(projectIdentifier, experimentCode);
- NewExperiment experiment =
- new NewExperiment(experimentIdentifier.toString(), experimentTypeCode);
- ExperimentType experimentType = service.getExperimentType(experimentTypeCode);
- File protXMLFile = Util.tryGetProtXMLFile(incomingDataSetPath);
- if (protXMLFile == null)
- {
- throw new UserFailureException("No *prot.xml file found in data set '" + incomingDataSetPath + "'.");
- }
- long fileSize = protXMLFile.length();
- if (fileSize > protXmlSizeThreshold)
- {
- String reason = "Size of prot.xml file " + protXMLFile.getName() + " is with "
- + FileUtilities.byteCountToDisplaySize(fileSize) + " too large. Maximum size is "
- + FileUtilities.byteCountToDisplaySize(protXmlSizeThreshold);
- operationLog.warn(reason);
- properties.setProperty(NOT_PROCESSED_PROPERTY, reason);
- }
-
- experiment.setProperties(Util.getAndCheckProperties(properties, experimentType));
- DataSetInformation info = new DataSetInformation();
- info.setExperimentIdentifier(experimentIdentifier);
- String parentDataSetCodesOrNull = getProperty(properties, PARENT_DATA_SET_CODES);
- String baseExperimentIdentifier = getProperty(properties, EXPERIMENT_IDENTIFIER_KEY);
- ParentDataSetCodes parentDataSetCodes =
- getParentDataSetCodes(parentDataSetCodesOrNull, baseExperimentIdentifier, service);
- if (parentDataSetCodes.getErrorMessage() == null)
- {
- info.setParentDataSetCodes(parentDataSetCodes.getDataSetCodes());
- } else
- {
- throw new UserFailureException(parentDataSetCodes.getErrorMessage());
- }
- service.registerExperiment(experiment);
- return info;
- }
-
- /**
- * Returns data set codes either from the first argument or if <code>null</code> from the data sets of the specified experiment.
- */
- static ParentDataSetCodes getParentDataSetCodes(String parentDataSetCodesOrNull,
- String baseExperimentIdentifier, IEncapsulatedOpenBISService service)
- {
- List<AbstractExternalData> parentDataSets = new ArrayList<AbstractExternalData>();
- StringBuilder builder = new StringBuilder();
- if (parentDataSetCodesOrNull != null)
- {
- for (String code : StringUtils.split(parentDataSetCodesOrNull, ", "))
- {
- AbstractExternalData dataSet = service.tryGetDataSet(code);
- if (dataSet != null)
- {
- parentDataSets.add(dataSet);
- } else
- {
- builder.append(builder.length() == 0 ? "Unknown data sets: " : ", ");
- builder.append(code);
- }
- }
- } else if (baseExperimentIdentifier != null)
- {
- ExperimentIdentifier identifier =
- new ExperimentIdentifierFactory(baseExperimentIdentifier).createIdentifier();
- Experiment baseExperiment = service.tryGetExperiment(identifier);
- if (baseExperiment != null)
- {
- parentDataSets.addAll(service.listDataSetsByExperimentID(baseExperiment.getId()));
- } else
- {
- builder.append("Unkown experiment ").append(baseExperimentIdentifier);
- }
- }
- List<String> parentDataSetCodes = new ArrayList<String>();
- for (AbstractExternalData dataSet : parentDataSets)
- {
- parentDataSetCodes.add(dataSet.getCode());
- }
- String errorMessage = builder.length() > 0 ? builder.toString() : null;
- return new ParentDataSetCodes(parentDataSetCodes, errorMessage);
- }
-
- private String getProperty(Properties properties, String key)
- {
- String property = properties.getProperty(key);
- if (property == null)
- {
- property = properties.getProperty(key.toUpperCase());
- }
- return property;
- }
-
- private Properties loadSearchProperties(File propertiesFile)
- {
- Properties properties;
- if (propertiesFile.exists() == false)
- {
- properties = new Properties();
- } else
- {
- properties = PropertyIOUtils.loadProperties(propertiesFile);
- }
- return properties;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java
deleted file mode 100644
index b4499699df4..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.IDatabaseVersionHolder;
-
-/**
- * Holds the version of the proteomics database.
- *
- * @author Franz-Josef Elmer
- */
-public class DatabaseVersionHolder implements IDatabaseVersionHolder
-{
- @Override
- public String getDatabaseVersion()
- {
- return "005"; // changed in S124
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/IProtDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/IProtDAO.java
deleted file mode 100644
index 6b5a3982f5b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/IProtDAO.java
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.List;
-
-import net.lemnik.eodsql.BaseQuery;
-import net.lemnik.eodsql.Select;
-import net.lemnik.eodsql.Update;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Database;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinReference;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProtDAO extends BaseQuery
-{
- @Select("select * from experiments where perm_id = ?{1}")
- public Experiment tryToGetExperimentByPermID(String permID);
-
- @Select("insert into experiments (perm_id) values (?{1}) returning id")
- public long createExperiment(String experimentPermID);
-
- @Select("select * from samples where perm_id = ?{1}")
- public Sample tryToGetSampleByPermID(String permID);
-
- @Select("insert into samples (expe_id, perm_id) values (?{1}, ?{2}) returning id")
- public long createSample(long experimentID, String samplePermID);
-
- @Select("select * from databases where name_and_version = ?{1}")
- public Database tryToGetDatabaseByName(String name);
-
- @Select("insert into databases (name_and_version) values (?{1}) returning id")
- public long createDatabase(String databaseName);
-
- @Select("select * from data_sets where perm_id = ?{1}")
- public ch.systemsx.cisd.openbis.etlserver.proteomics.dto.DataSet tryToGetDataSetByPermID(
- String permID);
-
- @Select("insert into data_sets (expe_id, perm_id, db_id) values (?{1}, ?{2}, ?{3}) returning id")
- public long createDataSet(long experimentID, String dataSetPermID,
- long databaseID);
-
- @Update("insert into probability_fdr_mappings (dase_id, probability, false_discovery_rate) "
- + "values (?{1}, ?{2}, ?{3})")
- public void createProbabilityToFDRMapping(long dataSetID, double probability,
- double falseDiscoveryRate);
-
- @Select("insert into proteins (dase_id, probability) values (?{1}, ?{2}) returning id")
- public long createProtein(long dataSetID, double probability);
-
- @Select("insert into peptides (prot_id, sequence, charge) values (?{1}, ?{2}, ?{3}) returning id")
- public long createPeptide(long proteinID, String sequence, int charge);
-
- @Select("insert into modified_peptides (pept_id, nterm_mass, cterm_mass) values (?{1}, ?{2}, ?{3}) returning id")
- public long createModifiedPeptide(long peptideID, double nTermMass, double cTermMass);
-
- @Select("insert into modifications (mope_id, pos, mass) values (?{1}, ?{2}, ?{3}) returning id")
- public long createModification(long modPeptideID, int position, double mass);
-
- @Select("select * from protein_references where accession_number = ?{1}")
- public ProteinReference tryToGetProteinReference(String accessionNumber);
-
- @Select("insert into protein_references (accession_number, description) values (?{1}, ?{2}) returning id")
- public long createProteinReference(String accessionNumber, String description);
-
- @Update("update protein_references set description = ?{2} where id = ?{1}")
- public void updateProteinReferenceDescription(long proteinReferenceID, String description);
-
- @Select("select * from sequences where prre_id = ?{1} and db_id = ?{2}")
- public List<Sequence> tryToGetSequencesByReferenceAndDatabase(long referenceID, long databaseID);
-
- @Select("insert into sequences (db_id, prre_id, amino_acid_sequence, checksum) "
- + "values (?{1.databaseID}, ?{1.proteinReferenceID}, ?{1.sequence}, ?{1.checksum}) "
- + "returning id")
- public long createSequence(Sequence sequence);
-
- @Update("insert into identified_proteins (prot_id, sequ_id, coverage, is_primary) values (?{1}, ?{2}, ?{3}, ?{4})")
- public void createIdentifiedProtein(long proteinID, long sequenceID, double coverage, boolean primary);
-
- @Update("insert into abundances (prot_id, samp_id, value) values (?{1}, ?{2}, ?{3})")
- public void createAbundance(long proteinID, long sampleID, double value);
-
- @Update("insert into modification_fractions (modi_id, samp_id, fraction) values (?{1}, ?{2}, ?{3})")
- public void createModificationFraction(long modID, long sampleID, double fraction);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFraction.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFraction.java
deleted file mode 100644
index ac20660201b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFraction.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AminoAcidMass;
-
-/**
- * Data class keeping data extracted from a peptide <parameter> element of type 'modification'.
- *
- * @author Franz-Josef Elmer
- */
-final class ModificationFraction
-{
- private final String sample;
-
- private final double fraction;
-
- private final AminoAcidMass aminoAcidMass;
-
- ModificationFraction(String sample, String value)
- {
- this.sample = sample;
- String[] parts = value.split(":");
- if (parts.length != 3)
- {
- throw exception(value, "Three parts separated by ':' expected.");
- }
- aminoAcidMass = new AminoAcidMass();
- try
- {
- aminoAcidMass.setPosition(Integer.parseInt(parts[0]));
- } catch (NumberFormatException ex)
- {
- throw exception(value, "Position part isn't an integer number: " + parts[0]);
- }
- try
- {
- aminoAcidMass.setMass(Double.parseDouble(parts[1]));
- } catch (NumberFormatException ex)
- {
- throw exception(value, "Mass part isn't a floating-point number: " + parts[1]);
- }
- try
- {
- fraction = Double.parseDouble(parts[2]);
- } catch (NumberFormatException ex)
- {
- throw exception(value, "Fraction part isn't a floating-point number: " + parts[2]);
- }
- }
-
- private IllegalArgumentException exception(String value, String message)
- {
- return new IllegalArgumentException("Peptide parameter value [" + value
- + "] for sample '" + sample + "' is invalid: " + message);
- }
-
- public String getSample()
- {
- return sample;
- }
-
- public AminoAcidMass getAminoAcidMass()
- {
- return aminoAcidMass;
- }
-
- public double getFraction()
- {
- return fraction;
- }
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
deleted file mode 100644
index 4927baaebda..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.List;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * Handler of modification fractions.
- *
- * @author Franz-Josef Elmer
- */
-class ModificationFractionHandler extends AbstractSampleHandler
-{
- public ModificationFractionHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
- boolean restrictedSampleResolving)
- {
- super(openbisService, dao, experimentIdentifier, experiment, delimiter,
- restrictedSampleResolving);
- }
-
- @Override
- protected void handleSample(String parameterName,
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
- {
- // Do nothing
- }
-
- public void addModificationFractions(String peptideSequence, long modID,
- List<ModificationFraction> modificationFractions)
- {
- for (ModificationFraction modificationFraction : modificationFractions)
- {
- Sample sample = getOrCreateSample(modificationFraction.getSample(), peptideSequence);
- double fraction = modificationFraction.getFraction();
- dao.createModificationFraction(modID, sample.getId(), fraction);
- }
- }
-
- private Sample getOrCreateSample(String sampleName, String peptideSequence)
- {
- SampleOrError sampleOrError = getOrCreateSampleOrError(sampleName);
- if (sampleOrError.error != null)
- {
- throw new UserFailureException("Protein '" + peptideSequence
- + "' has modification for " + sampleOrError.error);
- }
- return sampleOrError.sample;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoader.java
deleted file mode 100644
index 91ea63764a7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoader.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.Unmarshaller;
-import javax.xml.bind.UnmarshallerHandler;
-
-import org.xml.sax.EntityResolver;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.xml.XMLInfraStructure;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinProphetDetails;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-
-/**
- * Loader of protXML file.
- *
- * @author Franz-Josef Elmer
- */
-class ProtXMLLoader
-{
- private final Unmarshaller unmarshaller;
-
- private final XMLInfraStructure xmlInfraStructure;
-
- ProtXMLLoader(boolean validating)
- {
- try
- {
- JAXBContext context =
- JAXBContext.newInstance(ProteinSummary.class, ProteinProphetDetails.class);
- unmarshaller = context.createUnmarshaller();
- xmlInfraStructure = new XMLInfraStructure(validating);
- xmlInfraStructure.setEntityResolver(new EntityResolver()
- {
- @Override
- public InputSource resolveEntity(String publicId, String systemId) throws SAXException,
- IOException
- {
- String schemaVersion = systemId.substring(systemId.lastIndexOf('/'));
- String resource = "/" + ProtXMLLoader.class.getPackage().getName().replace('.', '/') + schemaVersion;
- InputStream inputStream = ProtXMLLoader.class.getResourceAsStream(resource);
- return inputStream == null ? null : new InputSource(inputStream);
- }
- });
-
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- ProteinSummary readProtXML(File dataSet)
- {
- try
- {
- UnmarshallerHandler unmarshallerHandler = unmarshaller.getUnmarshallerHandler();
- xmlInfraStructure.parse(new FileReader(dataSet), unmarshallerHandler);
- Object object = unmarshallerHandler.getResult();
- if (object instanceof ProteinSummary == false)
- {
- throw new IllegalArgumentException("Wrong type: " + object);
- }
- return (ProteinSummary) object;
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
deleted file mode 100644
index ae8432153ce..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
+++ /dev/null
@@ -1,189 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.List;
-import java.util.Properties;
-
-import javax.sql.DataSource;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.etlserver.IDataSetUploader;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProtXMLUploader implements IDataSetUploader
-{
- private static final String VALIDATING_XML = "validating-xml";
-
- private static final String ASSUMING_EXTENDED_PROT_XML = "assuming-extended-prot-xml";
-
- private static final String MS_INJECTION_SAMPLE_DELIMITER = "delimiter_for_sample_resolving";
-
- private static final String RESTRICTED_SAMPLE_RESOLVING = "restricted_sample_resolving";
-
- private static final String DATABASE_ENGINE = "database.engine";
-
- private static final String DATABASE_URL_HOST_PART = "database.url-host-part";
-
- private static final String DATABASE_BASIC_NAME = "database.basic-name";
-
- private static final String DATABASE_KIND = "database.kind";
-
- private static final String DATABASE_OWNER = "database.owner";
-
- private static final String DATABASE_PASSWORD = "database.password";
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, ProtXMLUploader.class);
-
- private static DataSource createDataSource(Properties properties)
- {
- DatabaseConfigurationContext context = new DatabaseConfigurationContext();
- context.setDatabaseEngineCode(properties.getProperty(DATABASE_ENGINE, "postgresql"));
- context.setUrlHostPart(properties.getProperty(DATABASE_URL_HOST_PART, ""));
- context.setBasicDatabaseName(properties.getProperty(DATABASE_BASIC_NAME, "proteomics"));
- context.setDatabaseKind(PropertyUtils.getMandatoryProperty(properties, DATABASE_KIND));
- context.setOwner(properties.getProperty(DATABASE_OWNER, ""));
- context.setPassword(properties.getProperty(DATABASE_PASSWORD, ""));
- return context.getDataSource();
- }
-
- private final ProtXMLLoader loader;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private final DataSource dataSource;
-
- private final boolean assumingExtendedProtXML;
-
- private final String msInjectionSampleDelimiter;
-
- private final boolean restrictedSampleResolving;
-
- private ResultDataSetUploader currentResultDataSetUploader;
-
- public ProtXMLUploader(Properties properties, IEncapsulatedOpenBISService openbisService)
- {
- dataSource = createDataSource(properties);
- this.openbisService = openbisService;
- assumingExtendedProtXML = PropertyUtils.getBoolean(properties, ASSUMING_EXTENDED_PROT_XML, false);
- msInjectionSampleDelimiter = properties.getProperty(MS_INJECTION_SAMPLE_DELIMITER, "~");
- restrictedSampleResolving = PropertyUtils.getBoolean(properties, RESTRICTED_SAMPLE_RESOLVING, true);
- loader = new ProtXMLLoader(PropertyUtils.getBoolean(properties, VALIDATING_XML, false));
- }
-
- @Override
- public void upload(File dataSet, DataSetInformation dataSetInformation)
- {
- Experiment experiment = dataSetInformation.tryToGetExperiment();
- if (experiment != null)
- {
- List<IEntityProperty> properties = experiment.getProperties();
- for (IEntityProperty property : properties)
- {
- if (property.getPropertyType().getCode().equals(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY))
- {
- return;
- }
- }
- }
- long time = System.currentTimeMillis();
- File protXMLFile = Util.tryGetProtXMLFile(dataSet);
- ProteinSummary summary = loader.readProtXML(protXMLFile);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(summary.getProteinGroups().size()
- + " protein groups are successfully read from '" + protXMLFile + "' in "
- + (System.currentTimeMillis() - time) + " msec");
- }
- time = System.currentTimeMillis();
- if (currentResultDataSetUploader != null)
- {
- throw new IllegalStateException(
- "The previous transaction has been neither commited nor rollbacked.");
- }
- currentResultDataSetUploader = createUploader();
- currentResultDataSetUploader.upload(dataSetInformation, summary);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("Feeding result database took " + (System.currentTimeMillis() - time)
- + " msec.");
- }
- }
-
- @Override
- public void commit()
- {
- try
- {
- if (currentResultDataSetUploader != null)
- {
- currentResultDataSetUploader.commit();
- }
- } finally
- {
- currentResultDataSetUploader = null;
- }
- }
-
- @Override
- public void rollback()
- {
- try
- {
- if (currentResultDataSetUploader != null)
- {
- currentResultDataSetUploader.rollback();
- }
- } finally
- {
- currentResultDataSetUploader = null;
- }
- }
-
- protected ResultDataSetUploader createUploader()
- {
- Connection connection;
- try
- {
- connection = dataSource.getConnection();
- connection.setAutoCommit(false);
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- return new ResultDataSetUploader(connection, openbisService, assumingExtendedProtXML,
- msInjectionSampleDelimiter, restrictedSampleResolving);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescription.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescription.java
deleted file mode 100644
index 3b7db8761f1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescription.java
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinAnnotation;
-
-final class ProteinDescription
-{
- static final String DESCRIPTION_KEY = "DE";
-
- static final String SEQUENCE_KEY = "SEQ";
-
- static String createKeyValuePair(String key, String value)
- {
- return "\\" + key + "=" + value;
- }
-
- private String accessionNumber;
-
- private String description;
-
- private String sequence;
-
- public ProteinDescription(ProteinAnnotation annotation, long proteinID,
- boolean assumingExtendedProtXML)
- {
- String proteinDescription = annotation.getDescription();
- String[] items = proteinDescription.split("\\\\");
- accessionNumber = tryToGetAccessionNumber(items);
- description = tryToGetValue(items, DESCRIPTION_KEY);
- sequence = tryToGetValue(items, SEQUENCE_KEY);
- if (sequence == null)
- {
- if (assumingExtendedProtXML)
- {
- throw new UserFailureException(
- "Can not find a amino-acid sequence in following protein description: "
- + proteinDescription);
- } else
- {
- sequence = "";
- accessionNumber = getAccessionNumber(annotation, proteinID);
- }
- }
- if (description == null && assumingExtendedProtXML == false)
- {
- description = proteinDescription;
- }
- }
-
- private String getAccessionNumber(ProteinAnnotation annotation, long proteinID)
- {
- if (annotation.getSwissprotName() != null)
- {
- return "sp|" + annotation.getSwissprotName();
- }
- if (annotation.getTremblName() != null)
- {
- return "tr|" + annotation.getTremblName();
- }
- if (annotation.getIpiName() != null)
- {
- return "ipi|" + annotation.getIpiName();
- }
- if (annotation.getEnsemblName() != null)
- {
- return "ens|" + annotation.getEnsemblName();
- }
- if (annotation.getRefseqName() != null)
- {
- return "rs|" + annotation.getRefseqName();
- }
- if (annotation.getLocusLinkName() != null)
- {
- return "ll|" + annotation.getLocusLinkName();
- }
- if (annotation.getFlybase() != null)
- {
- return "fb|" + annotation.getFlybase();
- }
- return "unknown|" + proteinID;
- }
-
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-
- public final String getDescription()
- {
- return description;
- }
-
- public final String getSequence()
- {
- return sequence;
- }
-
- private String tryToGetAccessionNumber(String[] items)
- {
- return items == null || items.length == 0 ? null : items[0].trim();
- }
-
- private String tryToGetValue(String[] items, String key)
- {
- for (String item : items)
- {
- int indexOfEqualSign = item.indexOf('=');
- if (indexOfEqualSign > 0
- && item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
- {
- return item.substring(indexOfEqualSign + 1).trim();
- }
- }
- return null;
- }
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
deleted file mode 100644
index eca1c23c62f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetails;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMetaproject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
-{
- private static final String PARENT_DATA_SET_CODES_KEY =
- DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
-
- private static final String BASE_EXPERIMENT_KEY =
- DataSetInfoExtractorForProteinResults.EXPERIMENT_IDENTIFIER_KEY.toUpperCase();
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- ProteinResultDataSetParentLinkingTask.class);
-
- private final IEncapsulatedOpenBISService service;
-
- public ProteinResultDataSetParentLinkingTask()
- {
- this(ServiceProvider.getOpenBISService());
- }
-
- ProteinResultDataSetParentLinkingTask(IEncapsulatedOpenBISService service)
- {
- this.service = service;
-
- }
-
- @Override
- public void setUp(String pluginName, Properties properties)
- {
- }
-
- @Override
- public void execute()
- {
- List<DataSetBatchUpdatesDTO> dataSetUpdates = new ArrayList<DataSetBatchUpdatesDTO>();
- List<Project> projects = service.listProjects();
- for (Project project : projects)
- {
- List<Experiment> experiments =
- service.listExperiments(new ProjectIdentifier(project.getSpace().getCode(),
- project.getCode()));
- for (Experiment experiment : experiments)
- {
- Map<String, IEntityProperty> propertiesMap = getPropertiesMap(experiment);
- String baseExperimentIdentifier =
- tryGetProperty(propertiesMap, BASE_EXPERIMENT_KEY);
- String parentDataSetCodes =
- tryGetProperty(propertiesMap, PARENT_DATA_SET_CODES_KEY);
- List<String> codes =
- DataSetInfoExtractorForProteinResults.getParentDataSetCodes(
- parentDataSetCodes, baseExperimentIdentifier, service)
- .getDataSetCodes();
- if (codes.isEmpty())
- {
- continue;
- }
- List<AbstractExternalData> dataSets =
- service.listDataSetsByExperimentID(experiment.getId());
- if (dataSets.isEmpty())
- {
- continue;
- }
- for (AbstractExternalData ds : dataSets)
- {
- if (ds instanceof PhysicalDataSet == false)
- {
- continue;
- }
- PhysicalDataSet dataSet = (PhysicalDataSet) ds;
- DataSetBatchUpdatesDTO update = new DataSetBatchUpdatesDTO();
- update.setDatasetId(new TechId(dataSet.getId()));
- update.setVersion(dataSet.getVersion());
- update.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(dataSet
- .getExperiment().getIdentifier()));
- update.setFileFormatTypeCode(dataSet.getFileFormatType().getCode());
- update.setProperties(dataSet.getProperties());
-
- // All we want to do is update the parents
- update.setDatasetCode(dataSet.getCode());
- update.setModifiedParentDatasetCodesOrNull(codes.toArray(new String[0]));
- DataSetBatchUpdateDetails details = new DataSetBatchUpdateDetails();
- details.setParentsUpdateRequested(true);
-
- operationLog.info("Parent data set links of data set " + dataSet.getCode()
- + " from experiment " + experiment.getIdentifier()
- + " will be updated.");
- dataSetUpdates.add(update);
- }
- }
- }
- service.performEntityOperations(new AtomicEntityOperationDetails(null, null, Collections
- .<NewSpace> emptyList(), Collections.<NewProject> emptyList(), Collections
- .<ProjectUpdatesDTO> emptyList(), Collections.<NewExperiment> emptyList(),
- Collections.<ExperimentUpdatesDTO> emptyList(),
- Collections.<SampleUpdatesDTO> emptyList(), Collections.<NewSample> emptyList(),
- Collections.<String, List<NewMaterial>> emptyMap(), Collections
- .<MaterialUpdateDTO> emptyList(),
- Collections.<NewExternalData> emptyList(), dataSetUpdates, Collections
- .<NewMetaproject> emptyList(), Collections
- .<MetaprojectUpdatesDTO> emptyList(), Collections
- .<VocabularyUpdatesDTO> emptyList()));
- operationLog.info("Parent data set links for " + dataSetUpdates.size()
- + " data sets have been updated.");
- }
-
- private Map<String, IEntityProperty> getPropertiesMap(Experiment experiment)
- {
- List<IEntityProperty> properties = experiment.getProperties();
- Map<String, IEntityProperty> propertiesMap = new HashMap<String, IEntityProperty>();
- for (IEntityProperty property : properties)
- {
- propertiesMap.put(property.getPropertyType().getCode(), property);
- }
- return propertiesMap;
- }
-
- private String tryGetProperty(Map<String, IEntityProperty> propertiesMap, String key)
- {
- IEntityProperty property = propertiesMap.get(key);
- return property == null ? null : property.tryGetAsString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java
deleted file mode 100644
index 06bec5bded0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java
+++ /dev/null
@@ -1,477 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.apache.commons.lang3.StringUtils;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AminoAcidMass;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AnnotatedProtein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.DataSet;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Database;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Peptide;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.PeptideModification;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Protein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinAnnotation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinGroup;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinProphetDetails;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinReference;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryDataFilter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sequence;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ProbabilityToFDRCalculator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Occurrence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.OccurrenceUtil;
-import net.lemnik.eodsql.QueryTool;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ResultDataSetUploader extends AbstractHandler
-{
- private static final double MAX_FALSE_DISCOVERY_RATE = 0.1;
-
- static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
-
- static final String PARAMETER_TYPE_MODIFICATION = "modification";
-
- private final Connection connection;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private final StringBuffer errorMessages;
-
- private final boolean assumingExtendedProtXML;
-
- private final String delimiter;
-
- private final boolean restrictedSampleResolving;
-
- ResultDataSetUploader(Connection connection, IEncapsulatedOpenBISService openbisService,
- boolean assumingExtendedProtXML, String delimiter,
- boolean restrictedSampleResolving)
- {
- this(QueryTool.getQuery(connection, IProtDAO.class), connection, openbisService,
- assumingExtendedProtXML, delimiter, restrictedSampleResolving);
- }
-
- ResultDataSetUploader(IProtDAO dao, Connection connection,
- IEncapsulatedOpenBISService openbisService, boolean assumingExtendedProtXML,
- String delimiter, boolean restrictedSampleResolving)
- {
- super(dao);
- this.connection = connection;
- this.openbisService = openbisService;
- this.assumingExtendedProtXML = assumingExtendedProtXML;
- this.delimiter = delimiter;
- this.restrictedSampleResolving = restrictedSampleResolving;
- this.errorMessages = new StringBuffer();
- }
-
- void upload(DataSetInformation dataSetInfo, ProteinSummary summary)
- {
- try
- {
- Experiment experiment =
- getOrCreateExperiment(dataSetInfo.tryToGetExperiment().getPermId());
- ExperimentIdentifier experimentIdentifier = dataSetInfo.getExperimentIdentifier();
- String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
- Database database = getOrGreateDatabase(referenceDatabase);
- DataSet ds =
- getOrCreateDataSet(experiment, database, dataSetInfo.getDataSetCode());
- addToDatabase(ds, experiment, experimentIdentifier, summary);
- } catch (Throwable throwable)
- {
- try
- {
- connection.rollback();
- } catch (SQLException ex)
- {
- }
- throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
- }
- if (errorMessages.length() != 0)
- {
- rollback();
- throw UserFailureException.fromTemplate(
- "Following errors occurred while uploading protein information"
- + " to the dataset database from the dataset '%s': %s" + " ",
- dataSetInfo.getDataSetCode(), errorMessages.toString());
- }
- }
-
- /** the uploader should not be used after calling this method */
- public void rollback()
- {
- try
- {
- if (connection.isClosed() == false)
- {
- connection.rollback();
- connection.close();
- }
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- /** the uploader should not be used after calling this method */
- public void commit()
- {
- try
- {
- connection.commit();
- connection.close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- private Database getOrGreateDatabase(String databaseNameAndVersion)
- {
- int indexOfLastSlash = databaseNameAndVersion.lastIndexOf('/');
- String nameOrVersion;
- if (indexOfLastSlash < 0)
- {
- nameOrVersion = databaseNameAndVersion;
- } else
- {
- nameOrVersion = databaseNameAndVersion.substring(indexOfLastSlash + 1);
- }
- Database database = dao.tryToGetDatabaseByName(nameOrVersion);
- if (database == null)
- {
- database = new Database();
- database.setNameAndVersion(nameOrVersion);
- database.setId(dao.createDatabase(database.getNameAndVersion()));
- }
- return database;
- }
-
- private DataSet getOrCreateDataSet(Experiment experiment, Database database,
- String dataSetPermID)
- {
- DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
- if (dataSet == null)
- {
- dataSet = new DataSet();
- dataSet.setPermID(dataSetPermID);
- long experimentID = experiment.getId();
- dataSet.setExperimentID(experimentID);
- long databaseID = database.getId();
- dataSet.setDatabaseID(databaseID);
- dataSet.setId(dao.createDataSet(experimentID, dataSetPermID, databaseID));
- }
- return dataSet;
- }
-
- private Experiment getOrCreateExperiment(String experimentPermID)
- {
- Experiment experiment = dao.tryToGetExperimentByPermID(experimentPermID);
- if (experiment == null)
- {
- experiment = new Experiment();
- experiment.setPermID(experimentPermID);
- experiment.setId(dao.createExperiment(experimentPermID));
- }
- return experiment;
- }
-
- private void addToDatabase(DataSet dataSet, Experiment experiment,
- ExperimentIdentifier experimentIdentifier, ProteinSummary summary)
- {
- long dataSetID = dataSet.getId();
- Long databaseID = dataSet.getDatabaseID();
- AbundanceHandler abundanceHandler =
- new AbundanceHandler(openbisService, dao, experimentIdentifier, experiment,
- delimiter, restrictedSampleResolving);
- ModificationFractionHandler modificationFractionHandler =
- new ModificationFractionHandler(openbisService, dao, experimentIdentifier,
- experiment, delimiter, restrictedSampleResolving);
- ProbabilityToFDRCalculator calculator = createProbabilityToFDRMapping(dataSetID, summary);
- List<ProteinGroup> proteinGroups = summary.getProteinGroups();
- for (ProteinGroup proteinGroup : proteinGroups)
- {
- for (Protein protein : proteinGroup.getProteins())
- {
- try
- {
- double fdr = calculator.calculateFDR(protein.getProbability());
- if (Double.isNaN(fdr) || fdr <= MAX_FALSE_DISCOVERY_RATE)
- {
- addProtein(protein, dataSetID, databaseID, abundanceHandler,
- modificationFractionHandler);
- }
- } catch (Exception e)
- {
- logException(e, "protein", protein.getName());
- }
- }
- }
- }
-
- private void logException(Exception e, String objectType, String instanceDescription)
- {
- StringBuffer sb = new StringBuffer();
- sb.append("Cannot load following '");
- sb.append(objectType);
- sb.append("': ");
- sb.append(instanceDescription);
- sb.append(" because of the following exception: ");
- String message = e.getMessage();
- sb.append(message == null ? e.toString() : message);
- sb.append("\n");
- errorMessages.append(sb.toString());
- }
-
- private void addProtein(Protein protein, long dataSetID, Long databaseID,
- AbundanceHandler abundanceHandler,
- ModificationFractionHandler modificationFractionHandler)
- {
- long proteinID = dao.createProtein(dataSetID, protein.getProbability());
- for (Parameter parameter : protein.getParameters())
- {
- if (PARAMETER_TYPE_ABUNDANCE.equals(parameter.getType()))
- {
- abundanceHandler.addAbundancesToDatabase(parameter, proteinID, protein.getName());
- }
- }
- List<Peptide> peptides = protein.getPeptides();
- Set<String> peptideSequences = new HashSet<String>();
- for (Peptide peptide : peptides)
- {
- try
- {
- addPeptide(proteinID, peptide, modificationFractionHandler);
- peptideSequences.add(peptide.getSequence());
- } catch (Exception e)
- {
- logException(e, "peptide", peptide.getSequence().toString());
- }
- }
- createIdentifiedProtein(proteinID, peptideSequences, databaseID, protein.getAnnotation(), true);
- for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins())
- {
- createIdentifiedProtein(proteinID, peptideSequences, databaseID, annotatedProtein.getAnnotation(), false);
- }
- }
-
- private void addPeptide(long proteinID, Peptide peptide,
- ModificationFractionHandler modificationFractionHandler)
- {
- String peptideSequence = peptide.getSequence();
- int charge = peptide.getCharge();
- long peptideID = dao.createPeptide(proteinID, peptideSequence, charge);
- List<PeptideModification> modifications = peptide.getModifications();
- for (PeptideModification modification : modifications)
- {
- try
- {
- addPeptideModification(peptideID, modification);
- } catch (Exception e)
- {
- logException(e, "modification", modification.toString());
- }
- }
- List<ModificationFraction> modificationFractions = extractModificationFractions(peptide);
- if (modificationFractions.isEmpty())
- {
- return;
- }
- long modPeptideID = dao.createModifiedPeptide(peptideID, 0, 0);
- Map<AminoAcidMass, List<ModificationFraction>> map =
- groupByPositionAndMass(modificationFractions);
- Set<Entry<AminoAcidMass, List<ModificationFraction>>> entrySet = map.entrySet();
- for (Entry<AminoAcidMass, List<ModificationFraction>> entry : entrySet)
- {
- AminoAcidMass positionAndMass = entry.getKey();
- long modID = createModification(modPeptideID, positionAndMass);
- List<ModificationFraction> list = entry.getValue();
- modificationFractionHandler.addModificationFractions(peptideSequence, modID, list);
- }
- }
-
- private Map<AminoAcidMass, List<ModificationFraction>> groupByPositionAndMass(
- List<ModificationFraction> modificationFractions)
- {
- Map<AminoAcidMass, List<ModificationFraction>> result =
- new HashMap<AminoAcidMass, List<ModificationFraction>>();
- for (ModificationFraction modificationFraction : modificationFractions)
- {
- AminoAcidMass positionAndMass = modificationFraction.getAminoAcidMass();
- List<ModificationFraction> list = result.get(positionAndMass);
- if (list == null)
- {
- list = new ArrayList<ModificationFraction>();
- result.put(positionAndMass, list);
- }
- list.add(modificationFraction);
- }
- return result;
- }
-
- private List<ModificationFraction> extractModificationFractions(Peptide peptide)
- {
- List<ModificationFraction> result = new ArrayList<ModificationFraction>();
- for (Parameter parameter : peptide.getParameters())
- {
- if (PARAMETER_TYPE_MODIFICATION.equals(parameter.getType()))
- {
- result.add(new ModificationFraction(parameter.getName(), parameter.getValue()));
- }
- }
- return result;
- }
-
- private void addPeptideModification(long peptideID, PeptideModification modification)
- {
- double ntermMass = modification.getNTermMass();
- double ctermMass = modification.getCTermMass();
- long modPeptideID = dao.createModifiedPeptide(peptideID, ntermMass, ctermMass);
- List<AminoAcidMass> aminoAcidMasses = modification.getAminoAcidMasses();
- for (AminoAcidMass aminoAcidMass : aminoAcidMasses)
- {
- createModification(modPeptideID, aminoAcidMass);
- }
- }
-
- private long createModification(long modPeptideID, AminoAcidMass aminoAcidMass)
- {
- return dao.createModification(modPeptideID, aminoAcidMass.getPosition(),
- aminoAcidMass.getMass());
- }
-
- private void createIdentifiedProtein(long proteinID, Set<String> peptideSequences,
- Long databaseID, ProteinAnnotation annotation, boolean primary)
- {
- ProteinDescription protDesc =
- new ProteinDescription(annotation, proteinID, assumingExtendedProtXML);
- String accessionNumber = protDesc.getAccessionNumber();
- String description = protDesc.getDescription();
- ProteinReference proteinReference = dao.tryToGetProteinReference(accessionNumber);
- if (proteinReference == null)
- {
- proteinReference = new ProteinReference();
- proteinReference.setId(dao.createProteinReference(accessionNumber, description));
- } else if (StringUtils.equals(description, proteinReference.getDescription()) == false)
- {
- dao.updateProteinReferenceDescription(proteinReference.getId(), description);
- }
- Sequence sequence =
- tryFindSequence(proteinReference.getId(), databaseID, protDesc.getSequence());
- if (sequence == null)
- {
- sequence = new Sequence(protDesc.getSequence());
- sequence.setDatabaseID(databaseID);
- sequence.setProteinReferenceID(proteinReference.getId());
- sequence.setId(dao.createSequence(sequence));
- }
- double coverage = calculateCoverage(sequence.getSequence(), peptideSequences);
- dao.createIdentifiedProtein(proteinID, sequence.getId(), coverage, primary);
- }
-
- private double calculateCoverage(String aminoAcidSequence, Set<String> peptideSequences)
- {
- List<Occurrence> list = OccurrenceUtil.getCoverage(aminoAcidSequence, peptideSequences);
- int sumPeptides = 0;
- for (Occurrence occurrence : list)
- {
- sumPeptides += occurrence.getWord().length();
- }
- return sumPeptides / (double) aminoAcidSequence.length();
- }
-
- private Sequence tryFindSequence(long referenceID, Long databaseID, String sequence)
- {
- List<Sequence> sequences =
- dao.tryToGetSequencesByReferenceAndDatabase(referenceID, databaseID);
- if (sequences == null || sequences.isEmpty())
- {
- return null;
- }
- for (Sequence foundSequence : sequences)
- {
- if (sequence.equals(foundSequence.getSequence()))
- {
- return foundSequence;
- }
- }
- return null;
- }
-
- private ProbabilityToFDRCalculator createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
- {
- ProbabilityToFDRCalculator calculator = new ProbabilityToFDRCalculator();
- Object[] s = summary.getSummaryHeader().getProgramDetails().getSummary();
- if (s != null)
- {
- for (Object object : s)
- {
- if (object instanceof ProteinProphetDetails)
- {
- ProteinProphetDetails details = (ProteinProphetDetails) object;
- List<ProteinSummaryDataFilter> filters = details.getDataFilters();
- for (ProteinSummaryDataFilter proteinSummaryDataFilter : filters)
- {
- double probability = proteinSummaryDataFilter.getMinProbability();
- double fdr = proteinSummaryDataFilter.getFalsePositiveErrorRate();
- calculator.add(probability, fdr);
- calculator.init();
- dao.createProbabilityToFDRMapping(dataSetID, probability, fdr);
- }
- return calculator;
- }
- }
- }
- if (assumingExtendedProtXML == false)
- {
- return calculator;
- }
- throw new UserFailureException("Missing Protein Prophet details.");
- }
-
- protected Sample getOrCreateSample(Experiment experiment, String samplePermID)
- {
- Sample sample = dao.tryToGetSampleByPermID(samplePermID);
- if (sample == null)
- {
- sample = new Sample();
- sample.setPermID(samplePermID);
- sample.setId(dao.createSample(experiment.getId(), samplePermID));
- }
- return sample;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/StorageProcessorWithResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/StorageProcessorWithResultDataSetUploader.java
deleted file mode 100644
index 876f138a525..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/StorageProcessorWithResultDataSetUploader.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.etlserver.AbstractStrorageProcessorWithUploader;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class StorageProcessorWithResultDataSetUploader extends AbstractStrorageProcessorWithUploader
-{
-
- public StorageProcessorWithResultDataSetUploader(Properties properties)
- {
- super(properties, new ProtXMLUploader(properties, ServiceProvider.getOpenBISService()));
- }
-
- @Override
- protected void logDataSetFileError(File incomingDataSetDirectory, Throwable exception)
- {
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjection.java
deleted file mode 100644
index 25cc23e08ac..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjection.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.DATA_SET_PROPERTIES_FILE;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.DATA_SET_TYPE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.FILE_TYPE_KEY;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TypeExtractorForMSInjection implements ITypeExtractor
-{
- private static final LocatorType LOCATOR_TYPE = new LocatorType(LocatorType.DEFAULT_LOCATOR_TYPE_CODE);
-
- public TypeExtractorForMSInjection(Properties properties)
- {
- }
-
- @Override
- public DataSetType getDataSetType(File incomingDataSetPath)
- {
- Properties properties = loadProperties(incomingDataSetPath);
- return new DataSetType(PropertyUtils.getMandatoryProperty(properties, DATA_SET_TYPE_KEY));
- }
-
- @Override
- public FileFormatType getFileFormatType(File incomingDataSetPath)
- {
- Properties properties = loadProperties(incomingDataSetPath);
- return new FileFormatType(PropertyUtils.getMandatoryProperty(properties, FILE_TYPE_KEY));
- }
-
- @Override
- public LocatorType getLocatorType(File incomingDataSetPath)
- {
- return LOCATOR_TYPE;
- }
-
- @Override
- public String getProcessorType(File incomingDataSetPath)
- {
- return null;
- }
-
- @Override
- public boolean isMeasuredData(File incomingDataSetPath)
- {
- return true;
- }
-
- private Properties loadProperties(File incomingDataSetPath)
- {
- return Util.loadPropertiesFile(incomingDataSetPath, DATA_SET_PROPERTIES_FILE);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java
deleted file mode 100644
index 564c0196f4d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java
+++ /dev/null
@@ -1,128 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.io.PropertyIOUtils;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-
-/**
- * @author Franz-Josef Elmer
- */
-class Util
-{
- private Util()
- {
- }
-
- /**
- * Tries to return the prot.xml file in the specified data set.
- *
- * @return <code>null</code> if non found.
- */
- static File tryGetProtXMLFile(File dataSet)
- {
- if (dataSet.isDirectory() == false)
- {
- return dataSet;
- }
- File[] files = dataSet.listFiles();
- for (File file : files)
- {
- if (file.getName().endsWith("prot.xml"))
- {
- return file;
- }
- }
- return null;
- }
-
- /**
- * Returns an array of all entity properties defined by the specified entity type for which values are found in the specified {@link Properties}
- * object.
- *
- * @throws UserFailureException if at least one mandatory property were missed.
- */
- static IEntityProperty[] getAndCheckProperties(Properties properties, EntityType entityType)
- {
- List<String> missingMandatoryProperties = new ArrayList<String>();
- List<IEntityProperty> sampleProperties =
- getProperties(properties, entityType, missingMandatoryProperties);
- if (missingMandatoryProperties.isEmpty() == false)
- {
- throw new UserFailureException("The following mandatory properties are missed: "
- + missingMandatoryProperties);
- }
- return sampleProperties.toArray(new IEntityProperty[sampleProperties.size()]);
- }
-
- /**
- * Turns specified properties into a list of {@link IEntityProperty} instances in accordance to the property types assigned to the specified
- * entity type. Keys of missing mandatory properties are added to the specified list.
- */
- static List<IEntityProperty> getProperties(Properties properties,
- EntityType entityType, List<String> missingMandatoryProperties)
- {
- List<IEntityProperty> sampleProperties = new ArrayList<IEntityProperty>();
- List<? extends EntityTypePropertyType<?>> sampleTypePropertyTypes = entityType.getAssignedPropertyTypes();
- for (EntityTypePropertyType<?> entityTypePropertyType : sampleTypePropertyTypes)
- {
- boolean mandatory = entityTypePropertyType.isMandatory();
- PropertyType propertyType = entityTypePropertyType.getPropertyType();
- String key = propertyType.getCode();
- String value = properties.getProperty(key);
- if (value == null)
- {
- if (mandatory)
- {
- missingMandatoryProperties.add(key);
- }
- } else
- {
- EntityProperty property = new EntityProperty();
- property.setPropertyType(propertyType);
- property.setValue(value);
- sampleProperties.add(property);
- }
- }
- return sampleProperties;
- }
-
- static Properties loadPropertiesFile(File incomingDataSetDirectory, String propertiesFileName)
- {
- File propertiesFile = new File(incomingDataSetDirectory, propertiesFileName);
- if (propertiesFile.exists() == false)
- {
- throw new UserFailureException("Missing properties file '" + propertiesFileName + "'.");
- }
- if (propertiesFile.isFile() == false)
- {
- throw new UserFailureException("Properties file '" + propertiesFileName
- + "' is a folder.");
- }
- return PropertyIOUtils.loadProperties(propertiesFile);
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ASAPRatioPValue.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ASAPRatioPValue.java
deleted file mode 100644
index 6c7181a9a23..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ASAPRatioPValue.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlRootElement(name = "ASAPRatio_pvalue", namespace = Constants.NAMESPACE)
-@XmlType
-public class ASAPRatioPValue
-{
- private double adjustedRatioMean;
-
- private double adjustedRatioStandardDeviation;
-
- private double adjustedHeavyToLisghtRatioMean;
-
- private double adjustedHeavyToLisghtRatioStandardDeviation;
-
- private double pValue;
-
- private double decimalPValue;
-
- public ASAPRatioPValue()
- {
- System.out.println("ASAPRatioPValue.ASAPRatioPValue()");
- }
-
- @XmlAttribute(name = "adj_ratio_mean", required = true)
- public final double getAdjustedRatioMean()
- {
- return adjustedRatioMean;
- }
-
- public final void setAdjustedRatioMean(double adjustedRatioMean)
- {
- System.out.println("ASAPRatioPValue.setAdjustedRatioMean(" + adjustedRatioMean + ")");
- this.adjustedRatioMean = adjustedRatioMean;
- }
-
- @XmlAttribute(name = "adj_ratio_standard_dev", required = true)
- public final double getAdjustedRatioStandardDeviation()
- {
- return adjustedRatioStandardDeviation;
- }
-
- public final void setAdjustedRatioStandardDeviation(double adjustedRatioStandardDeviation)
- {
- this.adjustedRatioStandardDeviation = adjustedRatioStandardDeviation;
- }
-
- @XmlAttribute(name = "heavy2light_adj_ratio_mean")
- public final double getAdjustedHeavyToLisghtRatioMean()
- {
- return adjustedHeavyToLisghtRatioMean;
- }
-
- public final void setAdjustedHeavyToLisghtRatioMean(double adjustedHeavyToLisghtRatioMean)
- {
- this.adjustedHeavyToLisghtRatioMean = adjustedHeavyToLisghtRatioMean;
- }
-
- @XmlAttribute(name = "heavy2light_adj_ratio_standard_dev")
- public final double getAdjustedHeavyToLisghtRatioStandardDeviation()
- {
- return adjustedHeavyToLisghtRatioStandardDeviation;
- }
-
- public final void setAdjustedHeavyToLisghtRatioStandardDeviation(
- double adjustedHeavyToLisghtRatioStandardDeviation)
- {
- this.adjustedHeavyToLisghtRatioStandardDeviation = adjustedHeavyToLisghtRatioStandardDeviation;
- }
-
- @XmlAttribute(name = "pvalue")
- public final double getPValue()
- {
- return pValue;
- }
-
- public final void setPValue(double value)
- {
- pValue = value;
- }
-
- @XmlAttribute(name = "decimal_pvalue")
- public final double getDecimalPValue()
- {
- return decimalPValue;
- }
-
- public final void setDecimalPValue(double decimalPValue)
- {
- this.decimalPValue = decimalPValue;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithID.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithID.java
deleted file mode 100644
index a1d9fbf02e3..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithID.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.AutoGeneratedKeys;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractDTOWithID
-{
- @AutoGeneratedKeys
- private long id;
-
- public final long getId()
- {
- return id;
- }
-
- public final void setId(long id)
- {
- this.id = id;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithIDAndPermID.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithIDAndPermID.java
deleted file mode 100644
index 206520bd52a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AbstractDTOWithIDAndPermID.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractDTOWithIDAndPermID extends AbstractDTOWithID
-{
- @ResultColumn("perm_id")
- private String permID;
-
- public final String getPermID()
- {
- return permID;
- }
-
- public final void setPermID(String permID)
- {
- this.permID = permID;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AminoAcidMass.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AminoAcidMass.java
deleted file mode 100644
index b2ab23450f4..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AminoAcidMass.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AminoAcidMass
-{
- private int position;
-
- private double mass;
-
- @XmlAttribute(name = "position", required = true)
- public final int getPosition()
- {
- return position;
- }
-
- public final void setPosition(int position)
- {
- this.position = position;
- }
-
- @XmlAttribute(name = "mass", required = true)
- public final double getMass()
- {
- return mass;
- }
-
- public final void setMass(double mass)
- {
- this.mass = mass;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof AminoAcidMass == false)
- {
- return false;
- }
- AminoAcidMass that = (AminoAcidMass) obj;
- return this.position == that.position && this.mass == that.mass;
- }
-
- @Override
- public int hashCode()
- {
- return (int) (37 * position + mass);
- }
-
- @Override
- public String toString()
- {
- return mass + "@" + position;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AnnotatedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AnnotatedProtein.java
deleted file mode 100644
index 2266b73c965..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/AnnotatedProtein.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class AnnotatedProtein
-{
- protected String name;
-
- protected ProteinAnnotation annotation;
-
- @XmlAttribute(name = "protein_name", required = true)
- public final String getName()
- {
- return name;
- }
-
- public final void setName(String name)
- {
- this.name = name;
- }
-
- @XmlElement(name = "annotation", namespace = Constants.NAMESPACE)
- public final ProteinAnnotation getAnnotation()
- {
- return annotation;
- }
-
- public final void setAnnotation(ProteinAnnotation annotation)
- {
- this.annotation = annotation;
- }
-
- @Override
- public String toString()
- {
- return annotation == null ? name : name + "[" + annotation.getDescription() + "]";
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/DataSet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/DataSet.java
deleted file mode 100644
index 778efdb293b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/DataSet.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSet extends AbstractDTOWithIDAndPermID
-{
- @ResultColumn("samp_id")
- private Long sampleID;
-
- @ResultColumn("expe_id")
- private Long experimentID;
-
- @ResultColumn("db_id")
- private Long databaseID;
-
- public final Long getSampleID()
- {
- return sampleID;
- }
-
- public final void setSampleID(Long sampleID)
- {
- this.sampleID = sampleID;
- }
-
- public final Long getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(Long experimentID)
- {
- this.experimentID = experimentID;
- }
-
- public final Long getDatabaseID()
- {
- return databaseID;
- }
-
- public final void setDatabaseID(Long databaseID)
- {
- this.databaseID = databaseID;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Database.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Database.java
deleted file mode 100644
index 1b16ff40284..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Database.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Database extends AbstractDTOWithID
-{
- @ResultColumn("name_and_version")
- private String nameAndVersion;
-
- public final String getNameAndVersion()
- {
- return nameAndVersion;
- }
-
- public final void setNameAndVersion(String nameAndVersion)
- {
- this.nameAndVersion = nameAndVersion;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Experiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Experiment.java
deleted file mode 100644
index 0959e186f88..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Experiment.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Experiment extends AbstractDTOWithIDAndPermID
-{
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ModificationType.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ModificationType.java
deleted file mode 100644
index b78ea4b8916..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ModificationType.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ModificationType extends AbstractDTOWithID
-{
- private String code;
-
- @ResultColumn("amino_acid")
- private String aminoAcid;
-
- private double mass;
-
- @ResultColumn("mass_tolerance")
- private double massTolerance;
-
- public final String getCode()
- {
- return code;
- }
-
- public final void setCode(String code)
- {
- this.code = code;
- }
-
- public final String getAminoAcid()
- {
- return aminoAcid;
- }
-
- public final void setAminoAcid(String aminoAcid)
- {
- this.aminoAcid = aminoAcid;
- }
-
- public final double getMass()
- {
- return mass;
- }
-
- public final void setMass(double mass)
- {
- this.mass = mass;
- }
-
- public final double getMassTolerance()
- {
- return massTolerance;
- }
-
- public final void setMassTolerance(double deltaMass)
- {
- this.massTolerance = deltaMass;
- }
-
- public boolean matches(char aminoAcidSymbol, double m)
- {
- if (m < mass - massTolerance)
- {
- return false;
- }
- if (m > mass + massTolerance)
- {
- return false;
- }
- return aminoAcid == null || (aminoAcid.length() == 1 && aminoAcid.charAt(0) == aminoAcidSymbol);
- }
-
- @Override
- public String toString()
- {
- return code + "=(" + aminoAcid + ":" + mass + "\u00b1" + massTolerance + ")";
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Parameter.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Parameter.java
deleted file mode 100644
index 92187d45081..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Parameter.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class Parameter
-{
- private String name;
-
- private String value;
-
- private String type;
-
- @XmlAttribute(name = "name", required = true)
- public final String getName()
- {
- return name;
- }
-
- public final void setName(String name)
- {
- this.name = name;
- }
-
- @XmlAttribute(name = "value", required = true)
- public final String getValue()
- {
- return value;
- }
-
- public final void setValue(String value)
- {
- this.value = value;
- }
-
- @XmlAttribute(name = "type")
- public final String getType()
- {
- return type;
- }
-
- public final void setType(String type)
- {
- this.type = type;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ParentDataSetCodes.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ParentDataSetCodes.java
deleted file mode 100644
index 5e013d48f5f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ParentDataSetCodes.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.List;
-
-/**
- * Data transfer object which contains a list of data set codes and an optional error message.
- *
- * @author Franz-Josef Elmer
- */
-public class ParentDataSetCodes
-{
- private final List<String> dataSetCodes;
-
- private final String errorMessage;
-
- public ParentDataSetCodes(List<String> dataSetCodes, String errorMessage)
- {
- super();
- this.dataSetCodes = dataSetCodes;
- this.errorMessage = errorMessage;
- }
-
- public List<String> getDataSetCodes()
- {
- return dataSetCodes;
- }
-
- public String getErrorMessage()
- {
- return errorMessage;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Peptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Peptide.java
deleted file mode 100644
index cea00ffdf20..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Peptide.java
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class Peptide
-{
- private String sequence;
-
- private int charge;
-
- private double initialProbability;
-
- private double weight;
-
- private List<Parameter> parameters = new ArrayList<Parameter>();
-
- private List<PeptideModification> modifications = new ArrayList<PeptideModification>();
-
- @XmlAttribute(name = "peptide_sequence", required = true)
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- @XmlAttribute(name = "charge", required = true)
- public final int getCharge()
- {
- return charge;
- }
-
- public final void setCharge(int charge)
- {
- this.charge = charge;
- }
-
- @XmlAttribute(name = "initial_probability", required = true)
- public final double getInitialProbability()
- {
- return initialProbability;
- }
-
- public final void setInitialProbability(double initialProbability)
- {
- this.initialProbability = initialProbability;
- }
-
- @XmlAttribute(name = "weight")
- public final double getWeight()
- {
- return weight;
- }
-
- public final void setWeight(double weight)
- {
- this.weight = weight;
- }
-
- @XmlElement(name = "modification_info", namespace = Constants.NAMESPACE)
- public final List<PeptideModification> getModifications()
- {
- return modifications;
- }
-
- public final void setModifications(List<PeptideModification> modifications)
- {
- this.modifications = modifications;
- }
-
- @XmlElement(name = "parameter", namespace = Constants.NAMESPACE)
- public final List<Parameter> getParameters()
- {
- return parameters;
- }
-
- public final void setParameters(List<Parameter> parameters)
- {
- this.parameters = parameters;
- }
-
- @Override
- public String toString()
- {
- StringBuilder builder = new StringBuilder();
- builder.append(sequence);
- if (charge > 0)
- {
- builder.append("(");
- for (int i = 0; i < charge; i++)
- {
- builder.append('+');
- }
- builder.append(")");
- }
- builder.append("[initialProbability=").append(initialProbability);
- builder.append(", weight=").append(weight);
- builder.append("]");
- return builder.toString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/PeptideModification.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/PeptideModification.java
deleted file mode 100644
index 6f7f414d3b8..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/PeptideModification.java
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class PeptideModification
-{
- private String modifiedPeptide;
-
- private double nTermMass;
-
- private double cTermMass;
-
- private List<AminoAcidMass> aminoAcidMasses;
-
- @XmlAttribute(name = "modified_peptide")
- public final String getModifiedPeptide()
- {
- return modifiedPeptide;
- }
-
- public final void setModifiedPeptide(String modifiedPeptide)
- {
- this.modifiedPeptide = modifiedPeptide;
- }
-
- @XmlAttribute(name = "mod_nterm_mass")
- public final double getNTermMass()
- {
- return nTermMass;
- }
-
- public final void setNTermMass(double termMass)
- {
- nTermMass = termMass;
- }
-
- @XmlAttribute(name = "mod_cterm_mass")
- public final double getCTermMass()
- {
- return cTermMass;
- }
-
- public final void setCTermMass(double termMass)
- {
- cTermMass = termMass;
- }
-
- @XmlElement(name = "mod_aminoacid_mass", namespace = Constants.NAMESPACE)
- public final List<AminoAcidMass> getAminoAcidMasses()
- {
- return aminoAcidMasses;
- }
-
- public final void setAminoAcidMasses(List<AminoAcidMass> aminoAcidMasses)
- {
- this.aminoAcidMasses = aminoAcidMasses;
- }
-
- @Override
- public String toString()
- {
- StringBuilder builder = new StringBuilder();
- builder.append("Modification[modifiedPeptide=").append(modifiedPeptide);
- builder.append(", nTermMass=").append(nTermMass);
- builder.append(", cTermMass=").append(cTermMass);
- builder.append("]");
- if (aminoAcidMasses != null && aminoAcidMasses.isEmpty() == false)
- {
- builder.append("(");
- for (int i = 0; i < aminoAcidMasses.size(); i++)
- {
- if (i > 0)
- {
- builder.append(", ");
- }
- builder.append(aminoAcidMasses.get(i));
- }
- builder.append(")");
- }
- return builder.toString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProgramDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProgramDetails.java
deleted file mode 100644
index 0832a9bd9f5..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProgramDetails.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.Date;
-
-import javax.xml.bind.annotation.XmlAnyElement;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class ProgramDetails
-{
- private String analysis;
-
- private Date timestamp;
-
- private String version;
-
- private Object[] summary;
-
- @XmlAttribute(name = "analysis", required = true)
- public final String getAnalysis()
- {
- return analysis;
- }
-
- public final void setAnalysis(String analysis)
- {
- this.analysis = analysis;
- }
-
- // @XmlAttribute(name = "time", required = true)
- public final Date getTimestamp()
- {
- return timestamp;
- }
-
- public final void setTimestamp(Date timestamp)
- {
- this.timestamp = timestamp;
- }
-
- @XmlAttribute(name = "version")
- public final String getVersion()
- {
- return version;
- }
-
- public final void setVersion(String version)
- {
- this.version = version;
- }
-
- @XmlAnyElement(lax = true)
- public final Object[] getSummary()
- {
- return summary;
- }
-
- public final void setSummary(Object[] summary)
- {
- this.summary = summary;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Protein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Protein.java
deleted file mode 100644
index 436f04e0586..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Protein.java
+++ /dev/null
@@ -1,232 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class Protein extends AnnotatedProtein
-{
- private double probability;
-
- private double coverage;
-
- private int numberOfIndistinguishableProteins;
-
- private String uniqueStrippedPeptides;
-
- private String groupSiblingID;
-
- private int totalNumberOfPeptides;
-
- private String subsumingProtein;
-
- private String fractionOfCorrectPeptideIdentifications;
-
- private List<Parameter> parameters = new ArrayList<Parameter>();
-
- private List<AnnotatedProtein> indistinguishableProteins = new ArrayList<AnnotatedProtein>();
-
- private List<Peptide> peptides;
-
- @XmlAttribute(name = "probability", required = true)
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- @XmlAttribute(name = "percent_coverage")
- public final double getCoverage()
- {
- return coverage;
- }
-
- public final void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- @XmlAttribute(name = "n_indistinguishable_proteins", required = true)
- public final int getNumberOfIndistinguishableProteins()
- {
- return numberOfIndistinguishableProteins;
- }
-
- public final void setNumberOfIndistinguishableProteins(int numberOfIndistinguishableProteins)
- {
- this.numberOfIndistinguishableProteins = numberOfIndistinguishableProteins;
- }
-
- @XmlAttribute(name = "unique_stripped_peptides")
- public final String getUniqueStrippedPeptides()
- {
- return uniqueStrippedPeptides;
- }
-
- public final void setUniqueStrippedPeptides(String uniqueStrippedPeptides)
- {
- this.uniqueStrippedPeptides = uniqueStrippedPeptides;
- }
-
- @XmlAttribute(name = "group_sibling_id", required = true)
- public final String getGroupSiblingID()
- {
- return groupSiblingID;
- }
-
- public final void setGroupSiblingID(String groupSiblingID)
- {
- this.groupSiblingID = groupSiblingID;
- }
-
- @XmlAttribute(name = "total_number_peptides")
- public final int getTotalNumberOfPeptides()
- {
- return totalNumberOfPeptides;
- }
-
- public final void setTotalNumberOfPeptides(int totalNumberOfPeptides)
- {
- this.totalNumberOfPeptides = totalNumberOfPeptides;
- }
-
- @XmlAttribute(name = "subsuming_protein_entry")
- public final String getSubsumingProtein()
- {
- return subsumingProtein;
- }
-
- public final void setSubsumingProtein(String subsumingProtein)
- {
- this.subsumingProtein = subsumingProtein;
- }
-
- @XmlAttribute(name = "pct_spectrum_ids")
- public final String getFractionOfCorrectPeptideIdentifications()
- {
- return fractionOfCorrectPeptideIdentifications;
- }
-
- public final void setFractionOfCorrectPeptideIdentifications(String fractionOfCorrectPeptideIdentifications)
- {
- this.fractionOfCorrectPeptideIdentifications = fractionOfCorrectPeptideIdentifications;
- }
-
- @XmlElement(name = "parameter", namespace = Constants.NAMESPACE)
- public final List<Parameter> getParameters()
- {
- return parameters;
- }
-
- public final void setParameters(List<Parameter> parameters)
- {
- this.parameters = parameters;
- }
-
- @XmlElement(name = "indistinguishable_protein", namespace = Constants.NAMESPACE)
- public final List<AnnotatedProtein> getIndistinguishableProteins()
- {
- return indistinguishableProteins;
- }
-
- public final void setIndistinguishableProteins(List<AnnotatedProtein> indistinguishableProteins)
- {
- this.indistinguishableProteins = indistinguishableProteins;
- }
-
- @XmlElement(name = "peptide", namespace = Constants.NAMESPACE)
- public final List<Peptide> getPeptides()
- {
- return peptides;
- }
-
- public final void setPeptides(List<Peptide> peptides)
- {
- this.peptides = peptides;
- }
-
- @Override
- public String toString()
- {
- StringBuilder builder = new StringBuilder();
- builder.append(name).append("[probability=").append(probability);
- builder.append(", coverage=").append(coverage);
- builder.append(", indistinguishableProteins=").append(numberOfIndistinguishableProteins);
- if (uniqueStrippedPeptides != null)
- {
- builder.append(", uniqueStrippedPeptides=").append(uniqueStrippedPeptides);
- }
- builder.append(", groupSiblingID=").append(groupSiblingID);
- if (totalNumberOfPeptides > 0)
- {
- builder.append(", totalNumberOfPeptides=").append(totalNumberOfPeptides);
- }
- if (subsumingProtein != null)
- {
- builder.append(", subsumingProtein=").append(subsumingProtein);
- }
- if (fractionOfCorrectPeptideIdentifications != null)
- {
- builder.append(", fractionOfCorrectPeptideIdentifications=").append(fractionOfCorrectPeptideIdentifications);
- }
- builder.append("]");
- if (annotation != null)
- {
- builder.append("\n ").append(annotation);
- }
- if (indistinguishableProteins != null && indistinguishableProteins.isEmpty() == false)
- {
- builder.append("\n indistinguishable proteins:");
- for (AnnotatedProtein protein : indistinguishableProteins)
- {
- builder.append("\n ").append(protein);
- }
- }
- if (peptides != null && peptides.isEmpty() == false)
- {
- builder.append("\n peptides:");
- for (Peptide peptide : peptides)
- {
- builder.append("\n ").append(peptide);
- List<PeptideModification> modifications = peptide.getModifications();
- if (modifications != null && modifications.isEmpty() == false)
- {
- for (PeptideModification modification : modifications)
- {
- builder.append("\n ").append(modification);
- }
- }
- }
- }
- return builder.toString();
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinAnnotation.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinAnnotation.java
deleted file mode 100644
index 06c1344ae69..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinAnnotation.java
+++ /dev/null
@@ -1,145 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class ProteinAnnotation
-{
- private String description;
-
- private String ipiName;
-
- private String refseqName;
-
- private String swissprotName;
-
- private String ensemblName;
-
- private String tremblName;
-
- private String locusLinkName;
-
- private String flybase;
-
- @XmlAttribute(name = "protein_description", required = true)
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-
- @XmlAttribute(name = "ipi_name")
- public final String getIpiName()
- {
- return ipiName;
- }
-
- public final void setIpiName(String ipiName)
- {
- this.ipiName = ipiName;
- }
-
- @XmlAttribute(name = "refseq_name")
- public final String getRefseqName()
- {
- return refseqName;
- }
-
- public final void setRefseqName(String refseqName)
- {
- this.refseqName = refseqName;
- }
-
- @XmlAttribute(name = "swissprot_name")
- public final String getSwissprotName()
- {
- return swissprotName;
- }
-
- public final void setSwissprotName(String swissprotName)
- {
- this.swissprotName = swissprotName;
- }
-
- @XmlAttribute(name = "ensembl_name")
- public final String getEnsemblName()
- {
- return ensemblName;
- }
-
- public final void setEnsemblName(String ensembleName)
- {
- this.ensemblName = ensembleName;
- }
-
- @XmlAttribute(name = "trembl_name")
- public final String getTremblName()
- {
- return tremblName;
- }
-
- public final void setTremblName(String tremblName)
- {
- this.tremblName = tremblName;
- }
-
- @XmlAttribute(name = "locus_link_name")
- public final String getLocusLinkName()
- {
- return locusLinkName;
- }
-
- public final void setLocusLinkName(String locusLinkName)
- {
- this.locusLinkName = locusLinkName;
- }
-
- @XmlAttribute(name = "flybase")
- public final String getFlybase()
- {
- return flybase;
- }
-
- public final void setFlybase(String flybase)
- {
- this.flybase = flybase;
- }
-
- @Override
- public String toString()
- {
- StringBuilder builder = new StringBuilder();
- builder.append("Annotation[description=").append(description);
- if (ipiName != null)
- {
- builder.append(", ipiName=").append(ipiName);
- }
- builder.append("]");
- return builder.toString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinGroup.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinGroup.java
deleted file mode 100644
index 24e0e05ea9a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinGroup.java
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class ProteinGroup
-{
- private String groupNumber;
-
- private String pseudoName;
-
- private double probability;
-
- private List<Protein> proteins;
-
- @XmlAttribute(name = "group_number", required = true)
- public final String getGroupNumber()
- {
- return groupNumber;
- }
-
- public final void setGroupNumber(String groupNumber)
- {
- this.groupNumber = groupNumber;
- }
-
- @XmlAttribute(name = "pseudo_name")
- public final String getPseudoName()
- {
- return pseudoName;
- }
-
- public final void setPseudoName(String pseudoName)
- {
- this.pseudoName = pseudoName;
- }
-
- @XmlAttribute(name = "probability", required = true)
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- @XmlElement(name = "protein", namespace = Constants.NAMESPACE)
- public final List<Protein> getProteins()
- {
- return proteins;
- }
-
- public final void setProteins(List<Protein> proteins)
- {
- this.proteins = proteins;
- }
-
- @Override
- public String toString()
- {
- StringBuilder builder = new StringBuilder();
- builder.append("PG[number=").append(groupNumber);
- if (pseudoName != null)
- {
- builder.append(", pseudoName=").append(pseudoName);
- }
- builder.append(", probability=").append(probability).append("]");
- if (proteins != null && proteins.size() > 0)
- {
- for (Protein protein : proteins)
- {
- builder.append("\n ").append(protein);
- }
- }
- return builder.toString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinProphetDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinProphetDetails.java
deleted file mode 100644
index cc8727dc7f8..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinProphetDetails.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlRootElement(name = "proteinprophet_details", namespace = Constants.NAMESPACE)
-@XmlType
-public class ProteinProphetDetails
-{
- private String occamFlag;
-
- private List<ProteinSummaryDataFilter> dataFilters;
-
- @XmlAttribute(name = "occam_flag", required = true)
- public final String getOccamFlag()
- {
- return occamFlag;
- }
-
- public final void setOccamFlag(String occamFlag)
- {
- this.occamFlag = occamFlag;
- }
-
- @XmlElement(name = "protein_summary_data_filter", namespace = Constants.NAMESPACE)
- public final List<ProteinSummaryDataFilter> getDataFilters()
- {
- return dataFilters;
- }
-
- public final void setDataFilters(List<ProteinSummaryDataFilter> dataFilters)
- {
- this.dataFilters = dataFilters;
- }
-
- @Override
- public String toString()
- {
- return "ProteinProphet[occamFlag=" + occamFlag + "]";
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinReference.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinReference.java
deleted file mode 100644
index 9a3f56fe1bf..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinReference.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinReference extends AbstractDTOWithID
-{
- @ResultColumn("accession_number")
- private String accessionNumber;
-
- @ResultColumn("description")
- private String description;
-
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-
- public final void setAccessionNumber(String accessionNumber)
- {
- this.accessionNumber = accessionNumber;
- }
-
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummary.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummary.java
deleted file mode 100644
index 55a8526b0e6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummary.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlRootElement(name = "protein_summary", namespace = Constants.NAMESPACE)
-@XmlType
-public class ProteinSummary
-{
- private String summaryXML;
-
- private ProteinSummaryHeader summaryHeader;
-
- private List<ProteinGroup> proteinGroups;
-
- @XmlAttribute(name = "summary_xml")
- public final String getSummaryXML()
- {
- return summaryXML;
- }
-
- public final void setSummaryXML(String summaryXML)
- {
- this.summaryXML = summaryXML;
- }
-
- @XmlElement(name = "protein_summary_header", namespace = Constants.NAMESPACE)
- public final ProteinSummaryHeader getSummaryHeader()
- {
- return summaryHeader;
- }
-
- public final void setSummaryHeader(ProteinSummaryHeader summaryHeader)
- {
- this.summaryHeader = summaryHeader;
- }
-
- @XmlElement(name = "protein_group", namespace = Constants.NAMESPACE)
- public final List<ProteinGroup> getProteinGroups()
- {
- return proteinGroups;
- }
-
- public final void setProteinGroups(List<ProteinGroup> proteinGroups)
- {
- this.proteinGroups = proteinGroups;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryDataFilter.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryDataFilter.java
deleted file mode 100644
index db809b28390..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryDataFilter.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * Protein Phrophet section with the mapping between probability and FDR (False Discovery Rate).
- *
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class ProteinSummaryDataFilter
-{
- private double minProbability;
-
- private double sensitivity;
-
- private double falsePositiveErrorRate;
-
- @XmlAttribute(name = "min_probability", required = true)
- public final double getMinProbability()
- {
- return minProbability;
- }
-
- public final void setMinProbability(double minProbability)
- {
- this.minProbability = minProbability;
- }
-
- @XmlAttribute(name = "sensitivity", required = true)
- public final double getSensitivity()
- {
- return sensitivity;
- }
-
- public final void setSensitivity(double sensitivity)
- {
- this.sensitivity = sensitivity;
- }
-
- @XmlAttribute(name = "false_positive_error_rate", required = true)
- public final double getFalsePositiveErrorRate()
- {
- return falsePositiveErrorRate;
- }
-
- public final void setFalsePositiveErrorRate(double falsePositiveErrorRate)
- {
- this.falsePositiveErrorRate = falsePositiveErrorRate;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryHeader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryHeader.java
deleted file mode 100644
index 216543fd617..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/ProteinSummaryHeader.java
+++ /dev/null
@@ -1,267 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlType;
-
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Constants;
-
-/**
- * @author Franz-Josef Elmer
- */
-@XmlType
-public class ProteinSummaryHeader
-{
- private String referenceDatabase;
-
- private String winReferenceDatabase;
-
- private String residueSubstitutions;
-
- private String organism;
-
- private String sourceFiles;
-
- private String sourceFilesAlternative;
-
- private String winSourceFiles;
-
- private String sourceFileType;
-
- private double minimumPeptideProbability;
-
- private double minimumPeptideWeight;
-
- private double numberOfPredictedCorrectProteins;
-
- private int numberOfInput1Spectra;
-
- private int numberOfInput2Spectra;
-
- private int numberOfInput3Spectra;
-
- private double minimumInitialPeptideProbability;
-
- private double totalEstimatedNumberOfCorrectPeptideAssignments;
-
- private String sampleEnzyme;
-
- private ProgramDetails programDetails;
-
- @XmlAttribute(name = "reference_database", required = true)
- public final String getReferenceDatabase()
- {
- return referenceDatabase;
- }
-
- public final void setReferenceDatabase(String referenceDatabase)
- {
- this.referenceDatabase = referenceDatabase;
- }
-
- @XmlAttribute(name = "win-cyg_reference_database")
- public final String getWinReferenceDatabase()
- {
- return winReferenceDatabase;
- }
-
- public final void setWinReferenceDatabase(String winReferenceDatabase)
- {
- this.winReferenceDatabase = winReferenceDatabase;
- }
-
- @XmlAttribute(name = "residue_substitution_list")
- public final String getResidueSubstitutions()
- {
- return residueSubstitutions;
- }
-
- public final void setResidueSubstitutions(String residueSubstitutions)
- {
- this.residueSubstitutions = residueSubstitutions;
- }
-
- @XmlAttribute(name = "organism")
- public final String getOrganism()
- {
- return organism;
- }
-
- public final void setOrganism(String organism)
- {
- this.organism = organism;
- }
-
- @XmlAttribute(name = "source_files", required = true)
- public final String getSourceFiles()
- {
- return sourceFiles;
- }
-
- public final void setSourceFiles(String sourceFiles)
- {
- this.sourceFiles = sourceFiles;
- }
-
- @XmlAttribute(name = "win-cyg_source_files")
- public final String getWinSourceFiles()
- {
- return winSourceFiles;
- }
-
- public final void setWinSourceFiles(String winSourceFiles)
- {
- this.winSourceFiles = winSourceFiles;
- }
-
- @XmlAttribute(name = "source_files_alt", required = true)
- public final String getSourceFilesAlternative()
- {
- return sourceFilesAlternative;
- }
-
- public final void setSourceFilesAlternative(String sourceFilesAlternative)
- {
- this.sourceFilesAlternative = sourceFilesAlternative;
- }
-
- @XmlAttribute(name = "source_file_xtn")
- public final String getSourceFileType()
- {
- return sourceFileType;
- }
-
- public final void setSourceFileType(String sourceFileType)
- {
- this.sourceFileType = sourceFileType;
- }
-
- @XmlAttribute(name = "min_peptide_probability", required = true)
- public final double getMinimumPeptideProbability()
- {
- return minimumPeptideProbability;
- }
-
- public final void setMinimumPeptideProbability(double minimumPeptideProbability)
- {
- this.minimumPeptideProbability = minimumPeptideProbability;
- }
-
- @XmlAttribute(name = "min_peptide_weight", required = true)
- public final double getMinimumPeptideWeight()
- {
- return minimumPeptideWeight;
- }
-
- public final void setMinimumPeptideWeight(double minimumPeptideWeight)
- {
- this.minimumPeptideWeight = minimumPeptideWeight;
- }
-
- @XmlAttribute(name = "num_predicted_correct_prots", required = true)
- public final double getNumberOfPredictedCorrectProteins()
- {
- return numberOfPredictedCorrectProteins;
- }
-
- public final void setNumberOfPredictedCorrectProteins(double numberOfPredictedCorrectProteins)
- {
- this.numberOfPredictedCorrectProteins = numberOfPredictedCorrectProteins;
- }
-
- @XmlAttribute(name = "num_input_1_spectra", required = true)
- public final int getNumberOfInput1Spectra()
- {
- return numberOfInput1Spectra;
- }
-
- public final void setNumberOfInput1Spectra(int numberOfInput1Spectra)
- {
- this.numberOfInput1Spectra = numberOfInput1Spectra;
- }
-
- @XmlAttribute(name = "num_input_2_spectra", required = true)
- public final int getNumberOfInput2Spectra()
- {
- return numberOfInput2Spectra;
- }
-
- public final void setNumberOfInput2Spectra(int numberOfInput2Spectra)
- {
- this.numberOfInput2Spectra = numberOfInput2Spectra;
- }
-
- @XmlAttribute(name = "num_input_3_spectra", required = true)
- public final int getNumberOfInput3Spectra()
- {
- return numberOfInput3Spectra;
- }
-
- public final void setNumberOfInput3Spectra(int numberOfInput3Spectra)
- {
- this.numberOfInput3Spectra = numberOfInput3Spectra;
- }
-
- @XmlAttribute(name = "initial_min_peptide_prob", required = true)
- public final double getMinimumInitialPeptideProbability()
- {
- return minimumInitialPeptideProbability;
- }
-
- public final void setMinimumInitialPeptideProbability(double minimumInitialPeptideProbability)
- {
- this.minimumInitialPeptideProbability = minimumInitialPeptideProbability;
- }
-
- @XmlAttribute(name = "total_no_spectrum_ids")
- public final double getTotalEstimatedNumberOfCorrectPeptideAssignments()
- {
- return totalEstimatedNumberOfCorrectPeptideAssignments;
- }
-
- public final void setTotalEstimatedNumberOfCorrectPeptideAssignments(
- double totalEstimatedNumberOfCorrectPeptideAssignments)
- {
- this.totalEstimatedNumberOfCorrectPeptideAssignments =
- totalEstimatedNumberOfCorrectPeptideAssignments;
- }
-
- @XmlAttribute(name = "sample_enzyme", required = true)
- public final String getSampleEnzyme()
- {
- return sampleEnzyme;
- }
-
- public final void setSampleEnzyme(String sampleEnzyme)
- {
- this.sampleEnzyme = sampleEnzyme;
- }
-
- @XmlElement(name = "program_details", namespace = Constants.NAMESPACE)
- public final ProgramDetails getProgramDetails()
- {
- return programDetails;
- }
-
- public final void setProgramDetails(ProgramDetails programDetails)
- {
- this.programDetails = programDetails;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sample.java
deleted file mode 100644
index debe7356ee5..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sample.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Sample extends AbstractDTOWithIDAndPermID
-{
- @ResultColumn("expe_id")
- private Long experimentID;
-
- public final Long getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(Long experimentID)
- {
- this.experimentID = experimentID;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sequence.java
deleted file mode 100644
index 0be82ad08a6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/dto/Sequence.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Sequence extends AbstractDTOWithID
-{
- @ResultColumn("database_id")
- private long databaseID;
-
- @ResultColumn("protein_reference_id")
- private long proteinReferenceID;
-
- @ResultColumn("amino_acid_sequence")
- private String sequence;
-
- private String checksum;
-
- // Used by eodsql
- @SuppressWarnings("unused")
- private Sequence()
- {
- }
-
- public Sequence(String sequence)
- {
- setSequence(sequence);
- calculateChecksum();
- }
-
- public final long getDatabaseID()
- {
- return databaseID;
- }
-
- public final void setDatabaseID(long databaseID)
- {
- this.databaseID = databaseID;
- }
-
- public final long getProteinReferenceID()
- {
- return proteinReferenceID;
- }
-
- public final void setProteinReferenceID(long proteinDescriptionID)
- {
- this.proteinReferenceID = proteinDescriptionID;
- }
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public void calculateChecksum()
- {
- if (sequence != null)
- {
- setChecksum(Integer.toHexString(sequence.hashCode()));
- }
- }
-
- public final String getChecksum()
- {
- return checksum;
- }
-
- public final void setChecksum(String checksum)
- {
- this.checksum = checksum;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof Sequence == false)
- {
- return false;
- }
- return ((Sequence) obj).toString().equals(toString());
- }
-
- @Override
- public int hashCode()
- {
- return toString().hashCode();
- }
-
- @Override
- public String toString()
- {
- return getDatabaseID() + "-" + getProteinReferenceID() + ":" + sequence
- + "[" + checksum + "]";
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v3.xsd b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v3.xsd
deleted file mode 100644
index 06037477473..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v3.xsd
+++ /dev/null
@@ -1,816 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- edited with XMLSPY v2004 rel. 4 U (http://www.xmlspy.com) by Wei Yan (Institute for Systems Biology) -->
-<!--W3C Schema generated by XMLSPY v2004 rel. 4 U (http://www.xmlspy.com)-->
-<xs:schema targetNamespace="http://regis-web.systemsbiology.net/protXML" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:protx="http://regis-web.systemsbiology.net/protXML" elementFormDefault="qualified">
- <xs:element name="ASAPRatio_pvalue">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="adj_ratio_mean" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="adj_ratio_standard_dev" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_mean" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_standard_dev" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>pvalue (probability of ratio due by chance to 1:1 protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="decimal_pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>decimal representation of pvalue</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAPRatio">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio quantitation of protein</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Peak" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Dta" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="peptide_index" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="light_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="ratio_number_peptides" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double"/>
- <xs:attribute name="description" type="xs:string"/>
- <xs:attribute name="status" type="xs:string"/>
- <xs:attribute name="peptide_inds" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein_summary_header">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="program_details">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>Wildcard for summary info customized for a particular analysis used to infer protein identifications</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>Time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="version" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="reference_database" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>full path database name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="win-cyg_reference_database" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows full path database</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="residue_substitution_list" type="xs:string">
- <xs:annotation>
- <xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="organism" type="xs:string">
- <xs:annotation>
- <xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>input pepXML files</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files_alt" type="xs:string" use="required"/>
- <xs:attribute name="win-cyg_source_files" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows pepXML file names</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_file_xtn" type="xs:string">
- <xs:annotation>
- <xs:documentation>file type (if not pepXML)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_no_spectrum_ids" type="xs:double">
- <xs:annotation>
- <xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sample_enzyme" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein-level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
-
- </xs:complexType>
- </xs:element>
- <xs:element name="dataset_derivation">
- <xs:annotation>
- <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence minOccurs="0" maxOccurs="unbounded">
- <xs:element name="data_filter">
- <xs:complexType>
- <xs:attribute name="number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>generation number (0 is root)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="parent_file" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>File from which derived</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="windows_parent" type="xs:string"/>
- <xs:attribute name="description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>filtering criteria applied to data</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="generation_no" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>number preceding filter generations</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_group" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax">
- <xs:annotation>
- <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
- </xs:annotation>
- </xs:any>
-
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
- <xs:annotation>
- <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- </xs:complexType>
- </xs:element>
- <xs:element name="annotation" minOccurs="0">
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required"/>
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="annotation" minOccurs="0">
- <xs:annotation>
- <xs:documentation>protein description</xs:documentation>
- </xs:annotation>
-
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>description</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>unmodified aa sequence</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="charge" type="xs:positiveInteger" use="required">
- <xs:annotation>
- <xs:documentation>precursor ion charge</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="initial_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>prior to nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>after nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="peptide_group_designator" type="xs:string">
- <xs:annotation>
- <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="weight" type="xs:double" default="1.0"/>
- <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides" type="xs:double">
- <xs:annotation>
- <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
- <xs:annotation>
- <xs:documentation>discretized nsp value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_instances" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
- <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>database protein name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>confidence of protein id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="percent_coverage" type="xs:double">
- <xs:annotation>
- <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
- <xs:attribute name="group_sibling_id" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>protein group id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_number_peptides" type="xs:integer">
- <xs:annotation>
- <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="subsuming_protein_entry" type="xs:string">
- <xs:annotation>
- <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pct_spectrum_ids" type="xs:string">
- <xs:annotation>
- <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_result_analysis_id">
- <xs:annotation>
- <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
- </xs:annotation>
-
- <xs:selector xpath="./protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:unique>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="group_number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>index</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pseudo_name" type="xs:string"/>
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_group_sibling_id">
- <xs:annotation>
- <xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein"/>
- <xs:field xpath="@group_sibling_id"/>
- </xs:unique>
-
- </xs:element>
- </xs:sequence>
- <xs:attribute name="summary_xml" type="xs:string"/>
- </xs:complexType>
- <xs:key name="summary_analysis_id">
- <xs:selector xpath="./protx:analysis_summary"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:key>
- <xs:keyref name="result_analysis_id" refer="summary_analysis_id">
- <xs:annotation>
- <xs:documentation>analysis and id must correspond with those fields in an analysis_summary element</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group/protx:protein/protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:keyref>
- <xs:unique name="unique_group_number">
- <xs:annotation>
- <xs:documentation>Requires group numbers be unique for entire dataset</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group"/>
- <xs:field xpath="@group_number"/>
- </xs:unique>
- </xs:element>
- <xs:element name="proteinprophet_details">
- <xs:annotation>
- <xs:documentation>ProteinProphet analysis details</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_information">
- <xs:annotation>
- <xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_distribution" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="bin_no" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>discretized bin number</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="neg_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
- <xs:annotation>
- <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="min_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>filter setting</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sensitivity" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_correct" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of correct results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_incorrect" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="occam_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not occams razor was used to apportion peptides corresponding to multiple proteins</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="groups_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not related proteins are organized together in common protein groups</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="degen_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not all proteins corresponding to each identified peptide were used in analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not peptide probabilities were adjusted for estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of initial iterations to compute peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_distribution_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of interations used to compute nsp distributions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="final_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of final interations used to compute final peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="run_options" type="xs:string">
- <xs:annotation>
- <xs:documentation>special run options</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="XPress_analysis_summary">
- <xs:complexType>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_prot_analysis_summary">
- <xs:complexType>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="binary_ref_files" type="xs:string"/>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_pvalue_analysis_summary">
- <xs:complexType>
- <xs:attribute name="asapratio_id" type="xs:nonNegativeInteger" default="1"/>
- <xs:attribute name="background_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="background_ratio_stdev" type="xs:double" use="required"/>
- <xs:attribute name="background_fitting_error" type="xs:double" use="required"/>
- <xs:attribute name="analysis_distribution_file" type="xs:string" use="required"/>
- <xs:attribute name="full_analysis_distr_file" type="xs:string"/>
- <xs:attribute name="asap_prot_id" type="xs:nonNegativeInteger" default="1"/>
- </xs:complexType>
- </xs:element>
-
-
- <xs:simpleType name="positiveInt">
- <xs:restriction base="xs:unsignedInt">
- <xs:minInclusive value="1"/>
- </xs:restriction>
- </xs:simpleType>
- <xs:element name="libra_result">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="intensity" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- <xs:attribute name="ratio" type="xs:float" use="required"/>
- <xs:attribute name="error" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
- </xs:complexType>
- <xs:unique name="libra_result_channel_index">
- <xs:selector xpath="."/>
- <xs:field xpath="@channel"/>
- </xs:unique>
-
-
- </xs:element>
- <xs:element name="libra_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="fragment_masses" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="isotopic_contributions" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="contributing_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="affected_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="correction" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mass_tolerance" type="xs:float" use="required"/>
- <xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
- <xs:attribute name="normalization" type="xs:int" use="required"/>
- <xs:attribute name="output_type" type="xs:int" use="required"/>
- <xs:attribute name="channel_code" type="xs:string"/>
- <xs:attribute name="min_pep_prob" type="xs:float" use="required"/>
- <xs:attribute name="min_pep_wt" type="xs:float" use="required"/>
- <xs:attribute name="min_prot_prob" type="xs:float" use="required"/>
- </xs:complexType>
-
- <xs:key name="libra_channel_index">
- <xs:selector xpath="./protx:fragment_masses"/>
- <xs:field xpath="@channel"/>
- </xs:key>
- <xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
- <xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
-
- </xs:element>
-</xs:schema>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v4.xsd b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v4.xsd
deleted file mode 100644
index 26809f124c2..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v4.xsd
+++ /dev/null
@@ -1,820 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- edited with XMLSPY v2004 rel. 4 U (http://www.xmlspy.com) by Wei Yan (Institute for Systems Biology) -->
-<!--W3C Schema generated by XMLSPY v2004 rel. 4 U (http://www.xmlspy.com)-->
-<xs:schema targetNamespace="http://regis-web.systemsbiology.net/protXML" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:protx="http://regis-web.systemsbiology.net/protXML" elementFormDefault="qualified">
- <xs:element name="ASAPRatio_pvalue">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="adj_ratio_mean" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="adj_ratio_standard_dev" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_mean" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_standard_dev" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>pvalue (probability of ratio due by chance to 1:1 protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="decimal_pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>decimal representation of pvalue</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAPRatio">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio quantitation of protein</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Peak" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Dta" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="peptide_index" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="light_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="ratio_number_peptides" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double"/>
- <xs:attribute name="description" type="xs:string"/>
- <xs:attribute name="status" type="xs:string"/>
- <xs:attribute name="peptide_inds" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein_summary_header">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="program_details">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>Wildcard for summary info customized for a particular analysis used to infer protein identifications</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>Time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="version" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="reference_database" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>full path database name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="win-cyg_reference_database" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows full path database</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="residue_substitution_list" type="xs:string">
- <xs:annotation>
- <xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="organism" type="xs:string">
- <xs:annotation>
- <xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>input pepXML files</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files_alt" type="xs:string" use="required"/>
- <xs:attribute name="win-cyg_source_files" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows pepXML file names</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_file_xtn" type="xs:string">
- <xs:annotation>
- <xs:documentation>file type (if not pepXML)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_no_spectrum_ids" type="xs:double">
- <xs:annotation>
- <xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sample_enzyme" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein-level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
-
- </xs:complexType>
- </xs:element>
- <xs:element name="dataset_derivation">
- <xs:annotation>
- <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence minOccurs="0" maxOccurs="unbounded">
- <xs:element name="data_filter">
- <xs:complexType>
- <xs:attribute name="number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>generation number (0 is root)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="parent_file" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>File from which derived</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="windows_parent" type="xs:string"/>
- <xs:attribute name="description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>filtering criteria applied to data</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="generation_no" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>number preceding filter generations</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_group" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax">
- <xs:annotation>
- <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
- </xs:annotation>
- </xs:any>
-
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
- <xs:annotation>
- <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- </xs:complexType>
- </xs:element>
- <xs:element name="annotation" minOccurs="0">
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required"/>
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="annotation" minOccurs="0">
- <xs:annotation>
- <xs:documentation>protein description</xs:documentation>
- </xs:annotation>
-
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>description</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>unmodified aa sequence</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="charge" type="xs:positiveInteger" use="required">
- <xs:annotation>
- <xs:documentation>precursor ion charge</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="initial_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>prior to nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>after nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="peptide_group_designator" type="xs:string">
- <xs:annotation>
- <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="weight" type="xs:double" default="1.0"/>
- <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides" type="xs:double">
- <xs:annotation>
- <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
- <xs:annotation>
- <xs:documentation>discretized nsp value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_instances" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
- <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>database protein name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>confidence of protein id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="percent_coverage" type="xs:double">
- <xs:annotation>
- <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
- <xs:attribute name="group_sibling_id" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>protein group id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_number_peptides" type="xs:integer">
- <xs:annotation>
- <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="subsuming_protein_entry" type="xs:string">
- <xs:annotation>
- <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pct_spectrum_ids" type="xs:string">
- <xs:annotation>
- <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_result_analysis_id">
- <xs:annotation>
- <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
- </xs:annotation>
-
- <xs:selector xpath="./protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:unique>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="group_number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>index</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pseudo_name" type="xs:string"/>
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_group_sibling_id">
- <xs:annotation>
- <xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein"/>
- <xs:field xpath="@group_sibling_id"/>
- </xs:unique>
-
- </xs:element>
- </xs:sequence>
- <xs:attribute name="summary_xml" type="xs:string"/>
- </xs:complexType>
- <xs:key name="summary_analysis_id">
- <xs:selector xpath="./protx:analysis_summary"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:key>
- <xs:keyref name="result_analysis_id" refer="summary_analysis_id">
- <xs:annotation>
- <xs:documentation>analysis and id must correspond with those fields in an analysis_summary element</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group/protx:protein/protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:keyref>
- <xs:unique name="unique_group_number">
- <xs:annotation>
- <xs:documentation>Requires group numbers be unique for entire dataset</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group"/>
- <xs:field xpath="@group_number"/>
- </xs:unique>
- </xs:element>
- <xs:element name="proteinprophet_details">
- <xs:annotation>
- <xs:documentation>ProteinProphet analysis details</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_information">
- <xs:annotation>
- <xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_distribution" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="bin_no" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>discretized bin number</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="neg_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
- <xs:annotation>
- <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="min_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>filter setting</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sensitivity" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_correct" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of correct results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_incorrect" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="occam_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not occams razor was used to apportion peptides corresponding to multiple proteins</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="groups_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not related proteins are organized together in common protein groups</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="degen_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not all proteins corresponding to each identified peptide were used in analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not peptide probabilities were adjusted for estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of initial iterations to compute peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_distribution_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of interations used to compute nsp distributions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="final_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of final interations used to compute final peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="run_options" type="xs:string">
- <xs:annotation>
- <xs:documentation>special run options</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="XPress_analysis_summary">
- <xs:complexType>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_prot_analysis_summary">
- <xs:complexType>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="binary_ref_files" type="xs:string"/>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_pvalue_analysis_summary">
- <xs:complexType>
- <xs:attribute name="asapratio_id" type="xs:nonNegativeInteger" default="1"/>
- <xs:attribute name="background_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="background_ratio_stdev" type="xs:double" use="required"/>
- <xs:attribute name="background_fitting_error" type="xs:double" use="required"/>
- <xs:attribute name="analysis_distribution_file" type="xs:string" use="required"/>
- <xs:attribute name="full_analysis_distr_file" type="xs:string"/>
- <xs:attribute name="asap_prot_id" type="xs:nonNegativeInteger" default="1"/>
- </xs:complexType>
- </xs:element>
-
-
- <xs:simpleType name="positiveInt">
- <xs:restriction base="xs:unsignedInt">
- <xs:minInclusive value="1"/>
- </xs:restriction>
- </xs:simpleType>
- <xs:element name="libra_result">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="intensity" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- <xs:attribute name="ratio" type="xs:float" use="required"/>
- <xs:attribute name="error" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
- </xs:complexType>
- <xs:unique name="libra_result_channel_index">
- <xs:selector xpath="."/>
- <xs:field xpath="@channel"/>
- </xs:unique>
-
-
- </xs:element>
- <xs:element name="libra_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="fragment_masses" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="isotopic_contributions" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="contributing_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="affected_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="correction" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mass_tolerance" type="xs:float" use="required"/>
- <xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
- <xs:attribute name="normalization" type="xs:int" use="required"/>
- <xs:attribute name="output_type" type="xs:int" use="required"/>
- <xs:attribute name="channel_code" type="xs:string"/>
- <xs:attribute name="min_pep_prob" type="xs:float" use="required"/>
- <xs:attribute name="min_pep_wt" type="xs:float" use="required"/>
- <xs:attribute name="min_prot_prob" type="xs:float" use="required"/>
- </xs:complexType>
-
- <xs:key name="libra_channel_index">
- <xs:selector xpath="./protx:fragment_masses"/>
- <xs:field xpath="@channel"/>
- </xs:key>
- <xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
- <xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
-
- </xs:element>
-</xs:schema>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v5.xsd b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v5.xsd
deleted file mode 100644
index 28d1a5eaaf3..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/protXML_v5.xsd
+++ /dev/null
@@ -1,934 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- edited with XMLSPY v2004 rel. 4 U (http://www.xmlspy.com) by Wei Yan (Institute for Systems Biology) -->
-<!--W3C Schema generated by XMLSPY v2004 rel. 4 U (http://www.xmlspy.com)-->
-<xs:schema targetNamespace="http://regis-web.systemsbiology.net/protXML" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:protx="http://regis-web.systemsbiology.net/protXML" elementFormDefault="qualified">
- <xs:element name="ASAPRatio_pvalue">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="adj_ratio_mean" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="adj_ratio_standard_dev" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>Error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_mean" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light ratio adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="heavy2light_adj_ratio_standard_dev" type="xs:double">
- <xs:annotation>
- <xs:documentation>Heavy2light error adjusted for dataset mean value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>pvalue (probability of ratio due by chance to 1:1 protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="decimal_pvalue" type="xs:double">
- <xs:annotation>
- <xs:documentation>decimal representation of pvalue</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAPRatio">
- <xs:annotation>
- <xs:documentation>Results of ASAPRatio quantitation of protein</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Peak" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ASAP_Dta" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="peptide_index" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="status" type="xs:string" use="required"/>
- <xs:attribute name="include" type="xs:string" use="required"/>
- <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="weight" type="xs:double" use="required"/>
- <xs:attribute name="light_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
- <xs:attribute name="ratio_number_peptides" type="xs:nonNegativeInteger" use="required"/>
- <xs:attribute name="heavy2light_ratio_mean" type="xs:double"/>
- <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double"/>
- <xs:attribute name="description" type="xs:string"/>
- <xs:attribute name="status" type="xs:string"/>
- <xs:attribute name="peptide_inds" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein_summary_header">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="program_details">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>Wildcard for summary info customized for a particular analysis used to infer protein identifications</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>Time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="version" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="reference_database" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>full path database name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="win-cyg_reference_database" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows full path database</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="residue_substitution_list" type="xs:string">
- <xs:annotation>
- <xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="organism" type="xs:string">
- <xs:annotation>
- <xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>input pepXML files</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_files_alt" type="xs:string" use="required"/>
- <xs:attribute name="win-cyg_source_files" type="xs:string">
- <xs:annotation>
- <xs:documentation>windows pepXML file names</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="source_file_xtn" type="xs:string">
- <xs:annotation>
- <xs:documentation>file type (if not pepXML)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_4_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 4+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="num_input_5_spectra" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of spectra from 5+ precursor ions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_no_spectrum_ids" type="xs:double">
- <xs:annotation>
- <xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sample_enzyme" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax" minOccurs="0">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:any>
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein-level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="time" type="xs:dateTime" use="required">
- <xs:annotation>
- <xs:documentation>time of analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
-
- </xs:complexType>
- </xs:element>
- <xs:element name="dataset_derivation">
- <xs:annotation>
- <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence minOccurs="0" maxOccurs="unbounded">
- <xs:element name="data_filter">
- <xs:complexType>
- <xs:attribute name="number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>generation number (0 is root)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="parent_file" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>File from which derived</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="windows_parent" type="xs:string"/>
- <xs:attribute name="description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>filtering criteria applied to data</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="generation_no" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>number preceding filter generations</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_group" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="protein" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <!-- note: nameValueType defined below -->
- <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" processContents="lax">
- <xs:annotation>
- <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
- </xs:annotation>
- </xs:any>
-
- </xs:sequence>
- <xs:attribute name="analysis" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>name of protein level analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
- <xs:annotation>
- <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- </xs:complexType>
- </xs:element>
- <xs:element name="annotation" minOccurs="0">
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required"/>
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <!-- note: nameValueType defined below -->
- <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="annotation" minOccurs="0">
- <xs:annotation>
- <xs:documentation>protein description</xs:documentation>
- </xs:annotation>
-
- <xs:complexType>
- <xs:attribute name="protein_description" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>description</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="ipi_name" type="xs:string"/>
- <xs:attribute name="refseq_name" type="xs:string"/>
- <xs:attribute name="swissprot_name" type="xs:string"/>
- <xs:attribute name="ensembl_name" type="xs:string"/>
- <xs:attribute name="trembl_name" type="xs:string"/>
- <xs:attribute name="locus_link_name" type="xs:string"/>
- <xs:attribute name="flybase" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="protein_name" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="position" type="xs:string" use="required"/>
- <xs:attribute name="mass" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mod_nterm_mass" type="xs:string"/>
- <xs:attribute name="mod_cterm_mass" type="xs:string"/>
- <xs:attribute name="modified_peptide" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="peptide_sequence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>unmodified aa sequence</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="charge" type="xs:positiveInteger" use="required">
- <xs:annotation>
- <xs:documentation>precursor ion charge</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="initial_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>prior to nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>after nsp adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="ni_adjusted_probability" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>after ni adjustment</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="exp_sibling_ion_instances" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>expected sibling ion instances</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="exp_sibling_ion_bin" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>expected sibling ion bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="exp_tot_instances" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>expected total instances</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="peptide_group_designator" type="xs:string">
- <xs:annotation>
- <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="weight" type="xs:double" default="1.0"/>
- <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
- <xs:annotation>
- <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides" type="xs:double">
- <xs:annotation>
- <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
- <xs:annotation>
- <xs:documentation>discretized nsp value</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="n_instances" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
- <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="protein_name" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>database protein name</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>confidence of protein id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="percent_coverage" type="xs:double">
- <xs:annotation>
- <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
- <xs:attribute name="group_sibling_id" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>protein group id</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="total_number_peptides" type="xs:integer">
- <xs:annotation>
- <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="subsuming_protein_entry" type="xs:string">
- <xs:annotation>
- <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pct_spectrum_ids" type="xs:string">
- <xs:annotation>
- <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_result_analysis_id">
- <xs:annotation>
- <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
- </xs:annotation>
-
- <xs:selector xpath="./protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:unique>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="group_number" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>index</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pseudo_name" type="xs:string"/>
- <xs:attribute name="probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- <xs:unique name="unique_group_sibling_id">
- <xs:annotation>
- <xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein"/>
- <xs:field xpath="@group_sibling_id"/>
- </xs:unique>
-
- </xs:element>
- </xs:sequence>
- <xs:attribute name="summary_xml" type="xs:string"/>
- </xs:complexType>
- <xs:key name="summary_analysis_id">
- <xs:selector xpath="./protx:analysis_summary"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:key>
- <xs:keyref name="result_analysis_id" refer="summary_analysis_id">
- <xs:annotation>
- <xs:documentation>analysis and id must correspond with those fields in an analysis_summary element</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group/protx:protein/protx:analysis_result"/>
- <xs:field xpath="@analysis"/>
- <xs:field xpath="@id"/>
- </xs:keyref>
- <xs:unique name="unique_group_number">
- <xs:annotation>
- <xs:documentation>Requires group numbers be unique for entire dataset</xs:documentation>
- </xs:annotation>
- <xs:selector xpath="./protx:protein_group"/>
- <xs:field xpath="@group_number"/>
- </xs:unique>
- </xs:element>
- <xs:element name="proteinprophet_details">
- <xs:annotation>
- <xs:documentation>ProteinProphet analysis details</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_information">
- <xs:annotation>
- <xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="nsp_distribution" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="bin_no" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>discretized bin number</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_lower_bound_excl" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_upper_bound_incl" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="neg_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
- <xs:annotation>
- <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ni_information">
- <xs:annotation>
- <xs:documentation>learned distributions of estimated number of peptide instances ("number of instances")</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:sequence>
- <xs:element name="ni_distribution" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="bin_no" type="xs:integer" use="required">
- <xs:annotation>
- <xs:documentation>discretized bin number</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="ni_lower_bound_incl" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="ni_upper_bound_excl" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="ni_lower_bound_excl" type="xs:double" use="optional">
- <xs:annotation>
- <xs:documentation>lower bound nsp value (exclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="ni_upper_bound_incl" type="xs:string" use="optional">
- <xs:annotation>
- <xs:documentation>upper bound nsp value (inclusive)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="neg_freq" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
- <xs:annotation>
- <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <!--
- <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
- -->
- </xs:complexType>
- </xs:element>
- <xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
- <xs:annotation>
- <xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:attribute name="min_probability" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>filter setting</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="sensitivity" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
- <xs:annotation>
- <xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_correct" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of correct results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="predicted_num_incorrect" type="xs:double">
- <xs:annotation>
- <xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="occam_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not occams razor was used to apportion peptides corresponding to multiple proteins</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="groups_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not related proteins are organized together in common protein groups</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="degen_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not all proteins corresponding to each identified peptide were used in analysis</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_flag" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>whether or not peptide probabilities were adjusted for estimated number of sibling peptides</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="initial_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of initial iterations to compute peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="nsp_distribution_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of interations used to compute nsp distributions</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="final_peptide_wt_iters" type="xs:string" use="required">
- <xs:annotation>
- <xs:documentation>proteinprophet number of final interations used to compute final peptide weights</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- <xs:attribute name="run_options" type="xs:string">
- <xs:annotation>
- <xs:documentation>special run options</xs:documentation>
- </xs:annotation>
- </xs:attribute>
- </xs:complexType>
- </xs:element>
- <xs:element name="XPress_analysis_summary">
- <xs:complexType>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_prot_analysis_summary">
- <xs:complexType>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="binary_ref_files" type="xs:string"/>
- <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
- <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
- <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
- <xs:attribute name="reference_isotope" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="ASAP_pvalue_analysis_summary">
- <xs:complexType>
- <xs:attribute name="asapratio_id" type="xs:nonNegativeInteger" default="1"/>
- <xs:attribute name="background_ratio_mean" type="xs:double" use="required"/>
- <xs:attribute name="background_ratio_stdev" type="xs:double" use="required"/>
- <xs:attribute name="background_fitting_error" type="xs:double" use="required"/>
- <xs:attribute name="analysis_distribution_file" type="xs:string" use="required"/>
- <xs:attribute name="full_analysis_distr_file" type="xs:string"/>
- <xs:attribute name="asap_prot_id" type="xs:nonNegativeInteger" default="1"/>
- </xs:complexType>
- </xs:element>
-
-
- <xs:simpleType name="positiveInt">
- <xs:restriction base="xs:unsignedInt">
- <xs:minInclusive value="1"/>
- </xs:restriction>
- </xs:simpleType>
- <xs:element name="libra_result">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="intensity" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- <xs:attribute name="ratio" type="xs:float" use="required"/>
- <xs:attribute name="error" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
- </xs:complexType>
- <xs:unique name="libra_result_channel_index">
- <xs:selector xpath="."/>
- <xs:field xpath="@channel"/>
- </xs:unique>
-
-
- </xs:element>
- <xs:element name="libra_summary">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="fragment_masses" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="mz" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- <xs:element name="isotopic_contributions" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="contributing_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="affected_channel" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- <xs:attribute name="correction" type="xs:float" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="channel" type="positiveInt" use="required"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attribute name="mass_tolerance" type="xs:float" use="required"/>
- <xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
- <xs:attribute name="normalization" type="xs:int" use="required"/>
- <xs:attribute name="output_type" type="xs:int" use="required"/>
- <xs:attribute name="channel_code" type="xs:string"/>
- <xs:attribute name="min_pep_prob" type="xs:float" use="required"/>
- <xs:attribute name="min_pep_wt" type="xs:float" use="required"/>
- <xs:attribute name="min_prot_prob" type="xs:float" use="required"/>
- </xs:complexType>
-
- <xs:key name="libra_channel_index">
- <xs:selector xpath="./protx:fragment_masses"/>
- <xs:field xpath="@channel"/>
- </xs:key>
- <xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
- <xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
- <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel"/>
- <xs:field xpath="@channel"/>
- </xs:keyref>
-
- </xs:element>
-
- <!-- a loosely-defined, general-purpose type used in the "parameter" element, defined above -->
- <xs:complexType name="nameValueType">
- <xs:simpleContent>
- <xs:extension base="xs:anySimpleType">
- <xs:attribute name="name" type="xs:string" use="required"/>
- <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
- <xs:attribute name="type" type="xs:anySimpleType"/>
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
-
-
-</xs:schema>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/BuildAndEnvironmentInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/BuildAndEnvironmentInfo.java
deleted file mode 100644
index 816e57b8fd7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/BuildAndEnvironmentInfo.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics;
-
-import ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo;
-
-/**
- * The build and environment information for PhosphoNetX.
- *
- * @author Franz-Josef Elmer
- */
-public class BuildAndEnvironmentInfo extends AbstractBuildAndEnvironmentInfo
-{
- private final static String BASE = "rtd_phosphonetx";
-
- public final static BuildAndEnvironmentInfo INSTANCE = new BuildAndEnvironmentInfo();
-
- private BuildAndEnvironmentInfo()
- {
- super(BASE);
- }
-
- /**
- * Shows build and environment information on the console.
- */
- public static void main(String[] args)
- {
- System.out.println(INSTANCE);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBIS.gwt.xml b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBIS.gwt.xml
deleted file mode 100644
index 338a32080d0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBIS.gwt.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<module>
- <inherits name='ch.systemsx.cisd.openbis.OpenBIS-without-entry-point'/>
-
- <!--
- // Application entry point
- -->
- <entry-point class='ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.PhosphoNetXClient' />
-
- <script src="proteomics-dictionary.js"/>
- <public path="client/web/public"/>
- <source path="client/web/client"/>
- <source path="shared/basic" />
-
-</module>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISFirefox.gwt.xml b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISFirefox.gwt.xml
deleted file mode 100644
index 28984f69c44..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISFirefox.gwt.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE module PUBLIC "-//Google Inc.//DTD Google Web Toolkit 1.7.1//EN" "http://google-web-toolkit.googlecode.com/svn/tags/1.7.1/distro-source/core/src/gwt-module.dtd">
-<module rename-to="ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS">
- <inherits name='ch.systemsx.cisd.openbis.OpenBIS-without-entry-point' />
- <set-property name="user.agent" value="gecko1_8" />
-
- <entry-point class='ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.PhosphoNetXClient' />
-
- <script src="proteomics-dictionary.js" />
- <public path="client/web/public" />
- <source path="client/web/client" />
- <source path="shared/basic" />
-</module>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISSafari.gwt.xml b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISSafari.gwt.xml
deleted file mode 100644
index 4f39114f92a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/OpenBISSafari.gwt.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE module PUBLIC "-//Google Inc.//DTD Google Web Toolkit 1.7.1//EN" "http://google-web-toolkit.googlecode.com/svn/tags/1.7.1/distro-source/core/src/gwt-module.dtd">
-<module rename-to="ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS">
- <inherits name='ch.systemsx.cisd.openbis.OpenBIS-without-entry-point' />
- <set-property name="user.agent" value="safari" />
-
- <entry-point class='ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.PhosphoNetXClient' />
-
- <script src="proteomics-dictionary.js" />
- <public path="client/web/public" />
- <source path="client/web/client" />
- <source path="shared/basic" />
-</module>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/FacadeFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/FacadeFactory.java
deleted file mode 100644
index 686fe98b785..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/FacadeFactory.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1;
-
-import ch.systemsx.cisd.openbis.common.api.client.ServiceFinder;
-import ch.systemsx.cisd.common.api.retry.RetryCaller;
-import ch.systemsx.cisd.common.api.retry.RetryProxyFactory;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-
-/**
- * Factory of {@link IProteomicsDataApiFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public class FacadeFactory
-{
- private static final ServiceFinder SERVICE_FINDER = new ServiceFinder("openbis",
- IProteomicsDataService.SERVER_URL);
-
- private static final ServiceFinder GENERIC_INFO_SERVICE_FINDER = new ServiceFinder("openbis",
- IGeneralInformationService.SERVICE_URL);
-
- /**
- * Creates a facade for specified server URL, user Id, and password.
- */
- public static IProteomicsDataApiFacade create(final String serverURL, final String userID,
- final String password)
- {
- RetryCaller<IProteomicsDataApiFacade, RuntimeException> caller =
- new RetryCaller<IProteomicsDataApiFacade, RuntimeException>()
- {
- @Override
- protected IProteomicsDataApiFacade call()
- {
- IGeneralInformationService infoService =
- createGenericInfoService(serverURL);
- IProteomicsDataService service = createService(serverURL);
- String sessionToken =
- infoService.tryToAuthenticateForAllServices(userID, password);
- if (sessionToken == null)
- {
- throw new IllegalArgumentException("User " + userID
- + " couldn't be authenticated");
- }
-
- IProteomicsDataApiFacade facade =
- new ProteomicsDataApiFacade(service, infoService, sessionToken);
- return RetryProxyFactory.createProxy(facade);
- }
- };
- return caller.callWithRetry();
- }
-
- /**
- * Creates a facade for specified url and sessionToken.
- */
- public static IProteomicsDataApiFacade create(final String serverURL, final String sessionToken)
- {
- RetryCaller<IProteomicsDataApiFacade, RuntimeException> caller =
- new RetryCaller<IProteomicsDataApiFacade, RuntimeException>()
- {
- @Override
- protected IProteomicsDataApiFacade call()
- {
- IProteomicsDataService service = createService(serverURL);
- IGeneralInformationService infoService =
- createGenericInfoService(serverURL);
-
- IProteomicsDataApiFacade facade =
- new ProteomicsDataApiFacade(service, infoService, sessionToken);
- return RetryProxyFactory.createProxy(facade);
- }
- };
- return caller.callWithRetry();
- }
-
- private static IProteomicsDataService createService(String serverURL)
- {
- return SERVICE_FINDER.createService(IProteomicsDataService.class, serverURL);
- }
-
- private static IGeneralInformationService createGenericInfoService(String serverURL)
- {
- return GENERIC_INFO_SERVICE_FINDER.createService(IGeneralInformationService.class,
- serverURL);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/IProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/IProteomicsDataApiFacade.java
deleted file mode 100644
index 3a2e13a77e1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/IProteomicsDataApiFacade.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1;
-
-import java.util.List;
-
-import ch.systemsx.cisd.common.api.retry.Retry;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * Facade for openBIS proteomics data service to be used by a proteomics pipeline server like p-grade.
- *
- * @author Franz-Josef Elmer
- */
-public interface IProteomicsDataApiFacade
-{
- /**
- * Return the session token for the logged-in user.
- */
- @Retry
- public String getSessionToken();
-
- /**
- * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which the specified user is allow to read.
- */
- @Retry
- public List<MsInjectionDataInfo> listRawDataSamples(String userID);
-
- /**
- * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample.
- */
- @Retry
- public List<MsInjectionDataInfo> listAllRawDataSamples(String userID);
-
- /**
- * Lists all processing plugins on DSS.
- */
- @Retry
- public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos();
-
- /**
- * Processes the data sets of specified samples by the DSS processing plug-in of specified key for the specified user. Only the most recent data
- * sets of specified type are processed.
- */
- @Deprecated
- public void processingRawData(String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType);
-
- /**
- * Processes the specified data sets by the DSS processing plug-in of specified key for the specified user. Implementations should check that the
- * specified user is allowed to read specified data sets.
- */
- public void processDataSets(String userID, String dataSetProcessingKey, List<String> dataSetCodes);
-
- /**
- * Returns all projects where the specified user has USER access rights.
- */
- @Retry
- public List<Project> listProjects(String userID);
-
- /**
- * Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to read.
- */
- @Retry
- public List<Experiment> listSearchExperiments(String userID);
-
- /**
- * Returns all experiments of specified type which the specified user is allowed to read.
- */
- @Retry
- public List<Experiment> listExperiments(String sessionToken, String userID, String experimentTypeCode);
-
- /**
- * Returns all data sets of specified experiment which the specified user is allowed to read.
- */
- @Retry
- public List<DataSet> listDataSetsByExperiment(String userID, long experimentID);
-
- /**
- * Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS processing plug-in of specified key for the specified
- * user. It will be checked if the experiments are of search experiments and if the user has USER access rights.
- */
- @Deprecated
- public void processSearchData(String userID, String dataSetProcessingKey,
- long[] searchExperimentIDs);
-
- /**
- * Processes the data sets of specified experiments by the DSS processing plug-in of specified key for the specified user. It will be checked if
- * the experiments are of specified type and if the user has USER access rights.
- */
- public void processProteinResultDataSets(String sessionToken, String userID,
- String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs);
-
- /**
- * Logs current user out.
- */
- public void logout();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacade.java
deleted file mode 100644
index f80f1569685..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacade.java
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteomicsDataApiFacade implements IProteomicsDataApiFacade
-{
- private static final String USER_ROLE_SET = "SPACE_USER";
-
- private final IProteomicsDataService service;
-
- private final IGeneralInformationService generalInfoService;
-
- private final String sessionToken;
-
- ProteomicsDataApiFacade(IProteomicsDataService service,
- IGeneralInformationService generalInfoService, String sessionToken)
- {
- this.service = service;
- this.generalInfoService = generalInfoService;
- this.sessionToken = sessionToken;
- }
-
- @Override
- public String getSessionToken()
- {
- return sessionToken;
- }
-
- @Override
- public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos()
- {
- return service.listDataStoreServerProcessingPluginInfos(sessionToken);
- }
-
- @Override
- public List<MsInjectionDataInfo> listRawDataSamples(String userID)
- {
- return service.listRawDataSamples(sessionToken, userID);
- }
-
- @Override
- public List<MsInjectionDataInfo> listAllRawDataSamples(String userID)
- {
- return service.listAllRawDataSamples(sessionToken, userID);
- }
-
- @Override
- @SuppressWarnings("deprecation")
- public void processingRawData(String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType)
- {
- service.processingRawData(sessionToken, userID, dataSetProcessingKey, rawDataSampleIDs,
- dataSetType);
- }
-
- @Override
- public void processDataSets(String userID, String dataSetProcessingKey,
- List<String> dataSetCodes)
- {
- service.processDataSets(sessionToken, userID, dataSetProcessingKey, dataSetCodes);
- }
-
- @Override
- public List<Project> listProjects(String userID)
- {
- Map<String, Set<Role>> namedRoleSets = generalInfoService.listNamedRoleSets(sessionToken);
- Set<Role> allowedRoles = namedRoleSets.get(USER_ROLE_SET);
- if (allowedRoles == null)
- {
- throw new IllegalStateException("Role set " + USER_ROLE_SET + " not known.");
- }
-
- List<SpaceWithProjectsAndRoleAssignments> spaces =
- generalInfoService.listSpacesWithProjectsAndRoleAssignments(sessionToken, null);
- List<Project> projects = new ArrayList<Project>();
- for (SpaceWithProjectsAndRoleAssignments space : spaces)
- {
- Set<Role> roles = space.getRoles(userID);
- roles.retainAll(allowedRoles);
- if (roles.isEmpty() == false)
- {
- for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project project : space
- .getProjects())
- {
- projects.add(new Project(project.getId(), project.getPermId(), space.getCode(),
- project.getCode(), project.getDescription()));
- }
- }
- }
- return projects;
- }
-
- @Override
- @SuppressWarnings("deprecation")
- public List<Experiment> listSearchExperiments(String userID)
- {
- return service.listSearchExperiments(sessionToken, userID);
- }
-
- @Override
- public List<Experiment> listExperiments(@SuppressWarnings("hiding") String sessionToken,
- String userID, String experimentTypeCode)
- {
- return service.listExperiments(sessionToken, userID, experimentTypeCode);
- }
-
- @Override
- public List<DataSet> listDataSetsByExperiment(String userID, long experimentID)
- {
- return service.listDataSetsByExperiment(sessionToken, userID, experimentID);
- }
-
- @Override
- @SuppressWarnings("deprecation")
- public void processSearchData(String userID, String dataSetProcessingKey,
- long[] searchExperimentIDs)
- {
- service.processSearchData(sessionToken, userID, dataSetProcessingKey, searchExperimentIDs);
- }
-
- @Override
- public void processProteinResultDataSets(@SuppressWarnings("hiding") String sessionToken,
- String userID, String dataSetProcessingKey, String experimentTypeCode,
- long[] experimentIDs)
- {
- service.processProteinResultDataSets(sessionToken, userID, dataSetProcessingKey,
- experimentTypeCode, experimentIDs);
- }
-
- @Override
- public void logout()
- {
- generalInfoService.logout(sessionToken);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiTest.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiTest.java
deleted file mode 100644
index 548725f59cc..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiTest.java
+++ /dev/null
@@ -1,130 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1;
-
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * Example of usage of Proteomics Data API.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteomicsDataApiTest
-{
- @SuppressWarnings("deprecation")
- public static void main(String[] args)
- {
- if (args.length != 4)
- {
- System.err.println("Usage: <openbis-server-url> <login id> <password> <user id>");
- return;
- }
-
- String serverURL = args[0];
- String loginID = args[1];
- String password = args[2];
- String userID = args[3];
- IProteomicsDataApiFacade facade = FacadeFactory.create(serverURL, loginID, password);
-
- System.out.println("MS_INJECTION samples:");
- List<MsInjectionDataInfo> rawDataSamples = facade.listRawDataSamples(userID);
- for (MsInjectionDataInfo info : rawDataSamples)
- {
- Map<String, Date> latestDataSets = info.getLatestDataSetRegistrationDates();
- if (latestDataSets.isEmpty() == false)
- {
- System.out.println(" " + info.getMsInjectionSampleCode() + " -> "
- + info.getBiologicalSampleIdentifier() + " -> "
- + info.getBiologicalExperimentIdentifier());
- Experiment experiment = info.getBiologicalExperiment();
- if (experiment != null)
- {
- System.out.println(" biological experiment: " + experiment.getCode() + " "
- + experiment.getProperties());
- }
- System.out.println(" latest data sets: "
- + info.getLatestDataSetRegistrationDates());
- Set<DataSet> dataSets = info.getDataSets();
- for (DataSet dataSet : dataSets)
- {
- print(dataSet, " ");
- }
- }
- }
-
- System.out.println("DSS processing plugins:");
- List<DataStoreServerProcessingPluginInfo> infos =
- facade.listDataStoreServerProcessingPluginInfos();
- String dataSetProcessingKey = null;
- for (DataStoreServerProcessingPluginInfo info : infos)
- {
- System.out.println(" key:" + info.getKey() + ", label:'" + info.getLabel()
- + "', data set types:" + info.getDatasetTypeCodes());
- if (info.getDatasetTypeCodes().contains("PROT_RESULT"))
- {
- dataSetProcessingKey = info.getKey();
- }
- }
-
- System.out.println("Projects:");
- List<Project> projects = facade.listProjects(userID);
- for (Project project : projects)
- {
- System.out.println(project);
- }
-
- System.out.println("Search Experiments:");
- List<Experiment> experiments = facade.listSearchExperiments(userID);
- long[] ids = new long[experiments.size()];
- for (int i = 0; i < experiments.size(); i++)
- {
- Experiment experiment = experiments.get(i);
- System.out.println(experiment.getSpaceCode() + "/" + experiment.getProjectCode() + "/"
- + experiment.getCode() + " [" + experiment.getId() + ", "
- + experiment.getRegistrationDate() + "] " + experiment.getProperties());
- ids[i] = experiment.getId();
- }
-
- if (dataSetProcessingKey != null)
- {
- System.out.println("Process search data of " + ids.length + " experiments");
- facade.processSearchData(userID, dataSetProcessingKey, ids);
- }
-
- facade.logout();
- }
-
- private static void print(DataSet dataSet, String indentation)
- {
- System.out.println(indentation + dataSet.getCode() + " " + dataSet.getType() + " "
- + dataSet.getRegistrationDate() + " " + dataSet.getProperties());
- Set<DataSet> children = dataSet.getChildren();
- for (DataSet child : children)
- {
- print(child, indentation + " ");
- }
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/package.html b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/package.html
deleted file mode 100644
index 4dd85ccc624..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/package.html
+++ /dev/null
@@ -1,5 +0,0 @@
-<html>
-<body>
-Proteomics Data API Facade
-</body>
-</html>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/Constants.java
deleted file mode 100644
index e547f038f5e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/Constants.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client;
-
-/**
- * Constants used by client and server of Web presentation layer.
- *
- * @author Franz-Josef Elmer
- */
-public class Constants
-{
-
- public static final String TECHNOLOGY_NAME = "proteomics";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientService.java
deleted file mode 100644
index aeba0b11e81..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientService.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSequenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * * Service interface for the PhosphoNetX GWT client.
- * <p>
- * Each method should declare throwing {@link UserFailureException}. The authorization framework can throw it when the user has insufficient
- * privileges. If it is not marked, the GWT client will report unexpected exception.
- * </p>
- *
- * @author Franz-Josef Elmer
- */
-public interface IPhosphoNetXClientService extends IClientService
-{
- public TypedTableResultSet<Sample> listParentlessMsInjectionSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
- throws UserFailureException;
-
- public TypedTableResultSet<Sample> listBiologicalSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
- throws UserFailureException;
-
- public void linkSamples(Sample parentSample, List<Sample> childSamples) throws UserFailureException;
-
- public void createAndLinkSamples(NewSample newBiologicalSample,
- List<Sample> msInjectionSamples) throws UserFailureException;
-
- public Vocabulary getTreatmentTypeVocabulary() throws UserFailureException;
-
- public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
- TechId experimentID, String treatmentTypeOrNull) throws UserFailureException;
-
- public TypedTableResultSet<ProteinInfo> listProteinsByExperiment(ListProteinByExperimentCriteria criteria)
- throws UserFailureException;
-
- public String prepareExportProteins(TableExportCriteria<TableModelRowWithObject<ProteinInfo>> exportCriteria)
- throws UserFailureException;
-
- public TypedTableResultSet<ProteinSummary> listProteinSummariesByExperiment(
- ListProteinSummaryByExperimentCriteria criteria) throws UserFailureException;
-
- public String prepareExportProteinSummary(TableExportCriteria<TableModelRowWithObject<ProteinSummary>> exportCriteria)
- throws UserFailureException;
-
- public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
- throws UserFailureException;
-
- public TypedTableResultSet<ProteinSequence> listSequencesByProteinReference(
- ListProteinSequenceCriteria criteria) throws UserFailureException;
-
- public String prepareExportProteinSequences(
- TableExportCriteria<TableModelRowWithObject<ProteinSequence>> exportCriteria)
- throws UserFailureException;
-
- public TypedTableResultSet<DataSetProtein> listProteinsByExperimentAndReference(
- ListProteinByExperimentAndReferenceCriteria criteria) throws UserFailureException;
-
- public String prepareExportDataSetProteins(
- TableExportCriteria<TableModelRowWithObject<DataSetProtein>> exportCriteria)
- throws UserFailureException;
-
- public TypedTableResultSet<ProteinRelatedSample> listProteinRelatedSamplesByProtein(
- ListSampleAbundanceByProteinCriteria criteria) throws UserFailureException;
-
- public String prepareExportProteinRelatedSamples(
- TableExportCriteria<TableModelRowWithObject<ProteinRelatedSample>> exportCriteria)
- throws UserFailureException;
-
- public TypedTableResultSet<Sample> listRawDataSamples(
- IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria) throws UserFailureException;
-
- public String prepareExportRawDataSamples(TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria)
- throws UserFailureException;
-
- public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs,
- String dataSetType) throws UserFailureException;
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientServiceAsync.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientServiceAsync.java
deleted file mode 100644
index 7640def96df..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/IPhosphoNetXClientServiceAsync.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client;
-
-import java.util.List;
-
-import com.google.gwt.user.client.rpc.AsyncCallback;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSequenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
-{
- /** @see IPhosphoNetXClientService#listParentlessMsInjectionSamples(DefaultResultSetConfig) */
- public void listParentlessMsInjectionSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
- AsyncCallback<TypedTableResultSet<Sample>> callback);
-
- /** @see IPhosphoNetXClientService#listBiologicalSamples(DefaultResultSetConfig) */
- public void listBiologicalSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
- AsyncCallback<TypedTableResultSet<Sample>> callback);
-
- /** @see IPhosphoNetXClientService#linkSamples(Sample, List) */
- public void linkSamples(Sample parentSample, List<Sample> childSamples, AsyncCallback<Void> callback);
-
- /** @see IPhosphoNetXClientService#createAndLinkSamples(NewSample, List) */
- public void createAndLinkSamples(NewSample newBiologicalSample,
- List<Sample> msInjectionSamples, AsyncCallback<Void> callback);
-
- /** @see IPhosphoNetXClientService#getTreatmentTypeVocabulary() */
- public void getTreatmentTypeVocabulary(AsyncCallback<Vocabulary> callback);
-
- /**
- * @see IPhosphoNetXClientService#getAbundanceColumnDefinitionsForProteinByExperiment(TechId, String)
- */
- public void getAbundanceColumnDefinitionsForProteinByExperiment(TechId experimentID,
- String treatmentTypeOrNull,
- AsyncCallback<List<AbundanceColumnDefinition>> callback);
-
- /** @see IPhosphoNetXClientService#listProteinsByExperiment(ListProteinByExperimentCriteria) */
- public void listProteinsByExperiment(ListProteinByExperimentCriteria criteria,
- AsyncCallback<TypedTableResultSet<ProteinInfo>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportProteins(TableExportCriteria) */
- public void prepareExportProteins(
- TableExportCriteria<TableModelRowWithObject<ProteinInfo>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#listProteinSummariesByExperiment(ListProteinSummaryByExperimentCriteria) */
- public void listProteinSummariesByExperiment(ListProteinSummaryByExperimentCriteria criteria,
- AsyncCallback<TypedTableResultSet<ProteinSummary>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportProteinSummary(TableExportCriteria) */
- public void prepareExportProteinSummary(
- TableExportCriteria<TableModelRowWithObject<ProteinSummary>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#getProteinByExperiment(TechId, TechId) */
- public void getProteinByExperiment(TechId experimentID, TechId proteinReferenceID,
- AsyncCallback<ProteinByExperiment> callback);
-
- /** @see IPhosphoNetXClientService#listSequencesByProteinReference(ListProteinSequenceCriteria) */
- public void listSequencesByProteinReference(ListProteinSequenceCriteria criteria,
- AsyncCallback<TypedTableResultSet<ProteinSequence>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportProteinSequences(TableExportCriteria) */
- public void prepareExportProteinSequences(
- TableExportCriteria<TableModelRowWithObject<ProteinSequence>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#listProteinsByExperimentAndReference(ListProteinByExperimentAndReferenceCriteria) */
- public void listProteinsByExperimentAndReference(
- ListProteinByExperimentAndReferenceCriteria criteria,
- AsyncCallback<TypedTableResultSet<DataSetProtein>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportDataSetProteins(TableExportCriteria) */
- public void prepareExportDataSetProteins(TableExportCriteria<TableModelRowWithObject<DataSetProtein>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#listProteinRelatedSamplesByProtein(ListSampleAbundanceByProteinCriteria) */
- public void listProteinRelatedSamplesByProtein(ListSampleAbundanceByProteinCriteria criteria,
- AsyncCallback<TypedTableResultSet<ProteinRelatedSample>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportProteinRelatedSamples(TableExportCriteria) */
- public void prepareExportProteinRelatedSamples(
- TableExportCriteria<TableModelRowWithObject<ProteinRelatedSample>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#listRawDataSamples(IResultSetConfig) */
- public void listRawDataSamples(IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
- AsyncCallback<TypedTableResultSet<Sample>> callback);
-
- /** @see IPhosphoNetXClientService#prepareExportRawDataSamples(TableExportCriteria) */
- public void prepareExportRawDataSamples(TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
- AsyncCallback<String> callback);
-
- /** @see IPhosphoNetXClientService#processRawData(String, long[], String) */
- public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs, String dataSetType, AsyncCallback<Void> callback);
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/AccessionNumberURLCreator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/AccessionNumberURLCreator.java
deleted file mode 100644
index 9b4caaffd0a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/AccessionNumberURLCreator.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * @author Franz-Josef Elmer
- */
-class AccessionNumberURLCreator
-{
- private static final String UNIPROT_URL_TEMPLATE = "http://www.uniprot.org/uniprot/$id";
-
- private static final String UNIPROT_QUERY_URL_TEMPLATE = "http://www.uniprot.org/uniprot/?query=$id";
-
- private static final Map<String, String> URL_TEMPLATES = createURLTemplates();
-
- private static final Map<String, String> createURLTemplates()
- {
- HashMap<String, String> map = new HashMap<String, String>();
- map.put("sp", UNIPROT_URL_TEMPLATE);
- map.put("tr", UNIPROT_URL_TEMPLATE);
- map.put("ipi", UNIPROT_QUERY_URL_TEMPLATE);
- map.put("ens", UNIPROT_QUERY_URL_TEMPLATE);
- map.put("rs", UNIPROT_QUERY_URL_TEMPLATE);
- map.put("ll", UNIPROT_QUERY_URL_TEMPLATE);
- map.put("fb", UNIPROT_QUERY_URL_TEMPLATE);
- map.put("gi", "http://www.ncbi.nlm.nih.gov/protein/$id");
- map.put("isb", "http://www.ebi.ac.uk/ebisearch/search.ebi?db=proteinSequences&t=$id");
- return map;
- }
-
- static String tryToCreateURL(String typeOrNull, String accessionNumber)
- {
- if (typeOrNull == null)
- {
- return eval(UNIPROT_URL_TEMPLATE, accessionNumber);
- }
- String template = URL_TEMPLATES.get(typeOrNull);
- return template == null ? null : eval(template, accessionNumber);
- }
-
- private static String eval(String template, String value)
- {
- return template.replaceAll("\\$id", value);
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ClientPluginFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ClientPluginFactory.java
deleted file mode 100644
index cfd0dacffd1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ClientPluginFactory.java
+++ /dev/null
@@ -1,244 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractClientPluginFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ActionContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.AbstractTabItemFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageAction;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageDomain;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IClientPlugin;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedInputWidgetDescription;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.AbstractGenericEntityRegistrationForm;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.DelegatedClientPlugin;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.GenericViewContext;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.experiment.GenericExperimentEditForm;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.experiment.GenericExperimentRegistrationForm;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.experiment.GenericExperimentViewer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ClientPluginFactory extends AbstractClientPluginFactory<ViewContext>
-{
-
- public ClientPluginFactory(IViewContext<ICommonClientServiceAsync> originalViewContext)
- {
- super(originalViewContext);
- }
-
- @Override
- protected ViewContext createViewContext(
- IViewContext<ICommonClientServiceAsync> originalViewContext)
- {
- return new ViewContext(originalViewContext);
- }
-
- @Override
- public boolean isEnabled()
- {
- return checkEnabledProperty("proteomics");
- }
-
- @Override
- public IModule maybeCreateModule()
- {
- return new PhosphoNetXModule(getViewContext());
- }
-
- @Override
- public Set<String> getEntityTypeCodes(EntityKind entityKind)
- {
- if (entityKind == EntityKind.EXPERIMENT)
- {
- return new HashSet<String>(Arrays.asList("MS_SEARCH", "MS_QUANTIFICATION"));
- }
- return Collections.emptySet();
- }
-
- @Override
- @SuppressWarnings("unchecked")
- public <T extends BasicEntityType, I extends IIdAndCodeHolder> IClientPlugin<T, I> createClientPlugin(
- EntityKind entityKind)
- {
- if (EntityKind.EXPERIMENT.equals(entityKind))
- {
- return (IClientPlugin<T, I>) new ExperimentClientPlugin(getViewContext());
- }
- throw new UnsupportedOperationException("IClientPlugin for entity kind '" + entityKind
- + "' not implemented yet.");
- }
-
- //
- // Helper classes
- //
-
- private final class ExperimentClientPlugin extends DelegatedClientPlugin<ExperimentType>
- {
- private ExperimentClientPlugin(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(viewContext, EntityKind.EXPERIMENT);
- }
-
- //
- // IViewClientPlugin
- //
-
- @Override
- public final AbstractTabItemFactory createEntityViewer(
- final IEntityInformationHolderWithPermId entity)
- {
- return new AbstractTabItemFactory()
- {
- @Override
- public ITabItem create()
- {
- final DatabaseModificationAwareComponent experimentViewer =
- ExperimentViewer.createComponent(getViewContext(), entity.getEntityType(),
- entity);
- return DefaultTabItem.create(getTabTitle(), experimentViewer,
- getViewContext(), false);
- }
-
- @Override
- public String getId()
- {
- return GenericExperimentViewer.createId(entity);
- }
-
- @Override
- public HelpPageIdentifier getHelpPageIdentifier()
- {
- return new HelpPageIdentifier(HelpPageDomain.EXPERIMENT,
- HelpPageAction.VIEW);
- }
-
- @Override
- public String getTabTitle()
- {
- return getViewerTitle(Dict.EXPERIMENT, entity);
- }
-
- @Override
- public String tryGetLink()
- {
- return LinkExtractor.tryExtract(entity);
- }
- };
- }
-
- @Override
- public DatabaseModificationAwareWidget createRegistrationForEntityType(
- ExperimentType entityType,
- Map<String, List<IManagedInputWidgetDescription>> inputWidgetDescriptions,
- ActionContext context)
- {
- GenericExperimentRegistrationForm form =
- new GenericExperimentRegistrationForm(getGenericViewContext(),
- inputWidgetDescriptions, context, entityType);
- return new DatabaseModificationAwareWidget(form, form);
- }
-
- @Override
- public AbstractTabItemFactory createEntityEditor(final IIdAndCodeHolder identifiable)
- {
- return new AbstractTabItemFactory()
- {
- @Override
- public ITabItem create()
- {
- DatabaseModificationAwareComponent component =
- GenericExperimentEditForm.create(getGenericViewContext(),
- identifiable);
- return DefaultTabItem.create(getTabTitle(), component, getViewContext(),
- true);
- }
-
- @Override
- public String getId()
- {
- return AbstractGenericEntityRegistrationForm.createId(identifiable,
- EntityKind.EXPERIMENT);
- }
-
- @Override
- public HelpPageIdentifier getHelpPageIdentifier()
- {
- return new HelpPageIdentifier(HelpPageDomain.EXPERIMENT,
- HelpPageAction.EDIT);
- }
-
- @Override
- public String getTabTitle()
- {
- return getEditorTitle(Dict.EXPERIMENT, identifiable);
- }
-
- @Override
- public String tryGetLink()
- {
- return null;
- }
- };
- }
-
- private String getViewerTitle(final String entityKindDictKey,
- final IIdAndCodeHolder identifiable)
- {
- return AbstractViewer.getTitle(getViewContext(), entityKindDictKey, identifiable);
- }
-
- private String getEditorTitle(final String entityKindDictKey,
- final IIdAndCodeHolder identifiable)
- {
- return AbstractRegistrationForm.getEditTitle(getViewContext(), entityKindDictKey,
- identifiable);
- }
-
- private IViewContext<IGenericClientServiceAsync> getGenericViewContext()
- {
- return new GenericViewContext(getViewContext().getCommonViewContext());
- }
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DataSetProteinGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DataSetProteinGrid.java
deleted file mode 100644
index 107f6cbbba4..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DataSetProteinGrid.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.DataSetProteinGridColumnIDs;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetProteinGrid extends TypedTableGrid<DataSetProtein>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX + "data-set-protein-browser";
-
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- IIdAndCodeHolder experimentIdOrNull, TechId proteinReferenceID)
- {
- return new DataSetProteinGrid(viewContext, experimentIdOrNull, proteinReferenceID)
- .asDisposableWithoutToolbar();
- }
-
- private static String createWidgetID(IIdAndCodeHolder experimentIdOrNull, TechId proteinReferenceID)
- {
- return "-" + (experimentIdOrNull == null ? "" : experimentIdOrNull.getId() + "-")
- + proteinReferenceID;
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private ListProteinByExperimentAndReferenceCriteria criteria;
-
- private DataSetProteinGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- IIdAndCodeHolder experimentIdOrNull, TechId proteinReferenceID)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID
- + createWidgetID(experimentIdOrNull, proteinReferenceID), true,
- PhosphoNetXDisplayTypeIDGenerator.DATA_SET_PROTEIN_BROWSER_GRID);
- specificViewContext = viewContext;
- criteria = new ListProteinByExperimentAndReferenceCriteria();
- if (experimentIdOrNull != null)
- {
- criteria.setExperimentID(new TechId(experimentIdOrNull));
- }
- criteria.setProteinReferenceID(proteinReferenceID);
- }
-
- @Override
- protected String translateColumnIdToDictionaryKey(String columnID)
- {
- return DataSetProteinGridColumnIDs.FDR.equals(columnID) ? "false_discovery_rate_column"
- : columnID.toLowerCase();
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList();
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<DataSetProtein>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<DataSetProtein>> callback)
- {
- criteria.copyPagingConfig(resultSetConfig);
- specificViewContext.getService().listProteinsByExperimentAndReference(criteria, callback);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<DataSetProtein>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- specificViewContext.getService().prepareExportDataSetProteins(exportCriteria, callback);
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[0];
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/Dict.java
deleted file mode 100644
index 1609b15b473..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/Dict.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Dict
-{
- public static final String QUERY_MENU_TITLE = "query_menu_title";
-
- public static final String SELECTED_EXPERIMENT_LABEL = "selected_experiment_label";
-
- public static final String FDR_FILTER_LABEL = "false_discovery_rate_filter_label";
-
- public static final String AGGREGATE_FUNCTION_LABEL = "aggregate_function_label";
-
- public static final String AGGREGATE_ON_TREATMENT_TYPE_LABEL = "aggregate_on_treatment_type_label";
-
- public static final String AGGREGATE_ORIGINAL_LABEL = "aggregate_original_label";
-
- public static final String ACCESSION_NUMBER = "accession_number";
-
- public static final String PROTEIN_DESCRIPTION = "protein_description";
-
- public static final String COVERAGE = "coverage";
-
- public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate";
-
- public static final String FDR_COMBO_INFO = "fdr_combo_info";
-
- public static final String DATA_SET = "data_set";
-
- public static final String PROTEIN_BROWSER = "protein_browser";
-
- public static final String PROTEIN_SUMMARY = "protein_summary";
-
- // Experiment Viewer
-
- public static final String DATA_SET_PROCESSING_SECTION_TITLE = "data_set_processing_section_title";
-
- // Protein Viewer
- public static final String PROTEIN_DETAILS_WAITING_MESSAGE = "loading_protein_details_waiting_message";
-
- public static final String PROTEINS_SECTION = "proteins_section";
-
- public static final String PRIMARY_PROTEIN = "primary_protein";
-
- public static final String PROTEIN_IN_EXPERIMENT_TAB_LABEL = "protein_in_experiment_tab_label";
-
- public static final String EXPERIMENT_LABEL = "experiment_label";
-
- public static final String SEQUENCE_SHORT_NAME = "sequence_short_name";
-
- public static final String DATABASE_NAME_AND_VERSION = "database_name_and_version";
-
- public static final String INDISTINGUISHABLE_PROTEINS = "indistinguishable_proteins";
-
- public static final String SEQUENCE = "sequence";
-
- public static final String SEQUENCES = "sequences";
-
- public static final String DATA_SET_PROTEINS = "data_set_proteins";
-
- public static final String DATA_SET_PERM_ID = "data_set_perm_id";
-
- public static final String PROTEIN_COUNT = "protein_count";
-
- public static final String PEPTIDE_COUNT = "peptide_count";
-
- public static final String PEPTIDES = "peptides";
-
- public static final String SEQUENCE_NAME = "sequence_name";
-
- public static final String FDR = "false_discovery_rate_column";
-
- // Protein Detail View
- public static final String PROBABILITY = "protein_probability";
-
- public static final String BUTTON_DELETE_PROTEIN = "button_delete_protein";
-
- // SampleAbundance Browser
-
- public static final String ABUNDANCE = "abundance";
-
- // RawDataSample Browser
-
- public static final String BIOLOGICAL_SAMPLE_IDENTIFIER = "biological_sample_identifier";
-
- public static final String MS_INJECTION_SAMPLE_CODE = "ms_injection_sample_code";
-
- public static final String COPY_DATA_SETS_BUTTON_LABEL = "copy_data_sets_button_label";
-
- public static final String COPY_DATA_SETS_TITLE = "copy_data_sets_title";
-
- public static final String COPY_DATA_SETS_MESSAGE = "copy_data_sets_message";
-
- public static final String COPY_DATA_SETS_DATA_SET_TYPE_FIELD = "copy_data_sets_data_set_type_field";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DisplayTypeIDGenerator.java
deleted file mode 100644
index 27246608c0e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/DisplayTypeIDGenerator.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDisplayTypeIDGenerator;
-
-/**
- * Enum for all generic {@link IDisplayTypeIDGenerator}s.
- *
- * @author Franz-Josef Elmer
- */
-public enum DisplayTypeIDGenerator implements IDisplayTypeIDGenerator
-{
- PROTEIN_SECTION("protein-section"),
-
- ;
-
- private final String genericNameOrPrefix;
-
- private DisplayTypeIDGenerator(String genericNameOrPrefix)
- {
- this.genericNameOrPrefix = genericNameOrPrefix;
- }
-
- @Override
- public String createID()
- {
- return genericNameOrPrefix;
- }
-
- @Override
- public String createID(String suffix)
- {
- return genericNameOrPrefix + suffix;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ExperimentViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ExperimentViewer.java
deleted file mode 100644
index 58501159bfb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ExperimentViewer.java
+++ /dev/null
@@ -1,188 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableTabContent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data.ProcessingDisplayCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.lang.StringEscapeUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DisplayedOrSelectedDatasetCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.GenericViewContext;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.experiment.GenericExperimentViewer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Component;
-import com.extjs.gxt.ui.client.widget.ContentPanel;
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.layout.FitLayout;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-import com.extjs.gxt.ui.client.widget.layout.RowLayout;
-import com.google.gwt.event.dom.client.ClickEvent;
-import com.google.gwt.event.dom.client.ClickHandler;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-import com.google.gwt.user.client.ui.Widget;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ExperimentViewer extends GenericExperimentViewer
-{
- public static DatabaseModificationAwareComponent createComponent(
- IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- BasicEntityType experimentType, IIdAndCodeHolder experimentId)
- {
- ExperimentViewer viewer =
- new ExperimentViewer(new GenericViewContext(viewContext.getCommonViewContext()),
- viewContext, experimentType, experimentId);
- return new DatabaseModificationAwareComponent(viewer, viewer);
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- protected ExperimentViewer(IViewContext<IGenericClientServiceAsync> viewContext,
- IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
- BasicEntityType experimentType, IIdAndCodeHolder experimentId)
- {
- super(viewContext, experimentType, experimentId);
- this.specificViewContext = specificViewContext;
- }
-
- @Override
- protected List<DisposableTabContent> createAdditionalBrowserSectionPanels()
- {
- DisposableTabContent section =
- new DisposableTabContent(specificViewContext.getMessage(Dict.PROTEINS_SECTION),
- specificViewContext, experiment)
- {
- @Override
- protected IDisposableComponent createDisposableContent()
- {
- return ProteinByExperimentBrowserGrid.create(specificViewContext,
- experimentType, experiment);
- }
- };
- section.setIds(DisplayTypeIDGenerator.PROTEIN_SECTION);
- return Collections.<DisposableTabContent> singletonList(section);
- }
-
- @Override
- protected Component tryCreateLowerLeftComponent()
- {
- if (viewContext.isSimpleOrEmbeddedMode())
- {
- return null; // no processing in simple view mode
- }
- final ContentPanel contentPanel = new ContentPanel(new RowLayout());
- contentPanel.setHeading(viewContext.getMessage(Dict.DATA_SET_PROCESSING_SECTION_TITLE));
- viewContext.getCommonService().listExperimentDataSets(
- new TechId(experimentId),
- DefaultResultSetConfig
- .<String, TableModelRowWithObject<AbstractExternalData>> createFetchAll(), true,
- new AbstractAsyncCallback<TypedTableResultSet<AbstractExternalData>>(viewContext)
- {
- @Override
- protected void process(TypedTableResultSet<AbstractExternalData> result)
- {
- AsyncCallback<List<DatastoreServiceDescription>> callBack =
- createCallback(contentPanel, result);
- viewContext.getCommonService().listDataStoreServices(
- DataStoreServiceKind.PROCESSING, callBack);
-
- }
- });
- return contentPanel;
- }
-
- private AsyncCallback<List<DatastoreServiceDescription>> createCallback(
- final ContentPanel contentPanel, TypedTableResultSet<AbstractExternalData> result)
- {
- ResultSet<TableModelRowWithObject<AbstractExternalData>> resultSet = result.getResultSet();
- String resultSetKey = resultSet.getResultSetKey();
- viewContext.getCommonService().removeResultSet(resultSetKey,
- new VoidAsyncCallback<Void>(viewContext));
- final List<String> dataSetCodes = new ArrayList<String>();
- for (GridRowModel<TableModelRowWithObject<AbstractExternalData>> gridRowModel : resultSet.getList())
- {
- dataSetCodes.add(gridRowModel.getOriginalObject().getObjectOrNull().getCode());
- }
- final DisplayedOrSelectedDatasetCriteria criteria =
- DisplayedOrSelectedDatasetCriteria.createSelectedItems(dataSetCodes);
- return new AbstractAsyncCallback<List<DatastoreServiceDescription>>(viewContext)
- {
- @Override
- protected void process(List<DatastoreServiceDescription> descriptions)
- {
- for (final DatastoreServiceDescription description : descriptions)
- {
- String[] dataSetTypes = description.getDatasetTypeCodes();
- for (String dataSetType : dataSetTypes)
- {
- if (dataSetType.equals(CommonConstants.PROT_RESULT_DATA_SET_TYPE))
- {
- Widget link = createLink(description, criteria);
- LayoutContainer wrapper = new LayoutContainer(new FitLayout());
- wrapper.add(link);
- contentPanel.add(wrapper, new RowData(1, -1, new Margins(5)));
- }
- }
- }
- contentPanel.layout();
- }
- };
- }
-
- private Widget createLink(final DatastoreServiceDescription description,
- final DisplayedOrSelectedDatasetCriteria criteria)
- {
- String href = "";
- ClickHandler listener = new ClickHandler()
- {
- @Override
- public void onClick(ClickEvent event)
- {
- viewContext.getCommonService().processDatasets(description, criteria,
- new ProcessingDisplayCallback(viewContext));
- }
- };
- String label = StringEscapeUtils.unescapeHtml(description.getLabel());
- return LinkRenderer.getLinkWidget(label, listener, href);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXClient.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXClient.java
deleted file mode 100644
index 5bad10fedb9..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXClient.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Client;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.DefaultClientPluginFactoryProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IClientPluginFactoryProvider;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PhosphoNetXClient extends Client
-{
- private static final class ClientPluginFactoryProvider extends
- DefaultClientPluginFactoryProvider
- {
- ClientPluginFactoryProvider(IViewContext<ICommonClientServiceAsync> originalViewContext)
- {
- super(originalViewContext);
- registerPluginFactory(new ClientPluginFactory(originalViewContext));
- }
-
- }
-
- @Override
- protected IClientPluginFactoryProvider createPluginFactoryProvider(
- final IViewContext<ICommonClientServiceAsync> commonContext)
- {
- return new ClientPluginFactoryProvider(commonContext);
- }
-
- @Override
- protected IClientServiceAsync getServiceForRetrievingApplicationInfo(
- IViewContext<ICommonClientServiceAsync> context)
- {
- return new ViewContext(context).getService();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
deleted file mode 100644
index 6561a789ec1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDisplayTypeIDGenerator;
-
-/**
- * @author Franz-Josef Elmer
- */
-public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
-{
- PROTEIN_BY_EXPERIMENT_BROWSER_GRID("protein-by-experiment-browser-grid"),
-
- PROTEIN_SEQUENCE_BROWSER_GRID("protein-sequence-browser-grid"),
-
- PROTEIN_SUMMARY_BROWSER_GRID("protein-summary-browser-grid"),
-
- DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"),
-
- RAW_DATA_SAMPLE_BROWSER_GRID("raw-data-sample-browser-grid"),
-
- PARENT_LESS_MS_INJECTION_SAMPLE_BROWSER_GRID("parent-less-ms-injection-sample-browser-grid"),
-
- BIOLOGICAL_SAMPLE_BROWSER_GRID("biological-sample-browser-grid"), ;
-
- private final String genericNameOrPrefix;
-
- private PhosphoNetXDisplayTypeIDGenerator(String genericNameOrPrefix)
- {
- this.genericNameOrPrefix = genericNameOrPrefix;
- }
-
- @Override
- public String createID()
- {
- return genericNameOrPrefix;
- }
-
- @Override
- public String createID(String suffix)
- {
- return genericNameOrPrefix + suffix;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXModule.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXModule.java
deleted file mode 100644
index c736783747d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/PhosphoNetXModule.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
-import com.extjs.gxt.ui.client.widget.menu.MenuItem;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableTabContent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ActionMenu;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ITabActionMenuItemDefinition;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.TabActionMenuItemFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.MsInjectionSampleAnnotationWizard;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PhosphoNetXModule implements IModule
-{
- public static final String ID = GenericConstants.ID_PREFIX + "-proteomics-";
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- public PhosphoNetXModule(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- this.viewContext = viewContext;
- }
-
- @Override
- public List<? extends MenuItem> getMenuItems()
- {
- ActionMenu msInjectionSampleAnnotatingMenuItem = TabActionMenuItemFactory.createActionMenu(viewContext, ID,
- new ITabActionMenuItemDefinition<IPhosphoNetXClientServiceAsync>()
- {
-
- @Override
- public String getName()
- {
- return "ANNOTATE_MS_INJECTION_SAMPLES";
- }
-
- @Override
- public String getHelpPageTitle()
- {
- return "Wizard for annotation MS INJECTION " + viewContext.getMessage(
- ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict.SAMPLES).toLowerCase();
- }
-
- @Override
- public DatabaseModificationAwareComponent createComponent(
- IViewContext<IPhosphoNetXClientServiceAsync> context)
- {
- return DatabaseModificationAwareComponent.create(new MsInjectionSampleAnnotationWizard(context));
- }
-
- @Override
- public String tryGetLink()
- {
- URLMethodWithParameters url = new URLMethodWithParameters("");
- url.addParameter((String) BasicConstant.LOCATOR_ACTION_PARAMETER, getName());
- return url.toString().substring(1);
- }
- });
- ActionMenu msInjectionSampleBrowserMenuItem = TabActionMenuItemFactory.createActionMenu(viewContext, ID,
- new ITabActionMenuItemDefinition<IPhosphoNetXClientServiceAsync>()
- {
-
- @Override
- public String getName()
- {
- return "ALL_RAW_DATA_SAMPLES";
- }
-
- @Override
- public String getHelpPageTitle()
- {
- return "MS INJECTION Data Overview";
- }
-
- @Override
- public DatabaseModificationAwareComponent createComponent(
- IViewContext<IPhosphoNetXClientServiceAsync> context)
- {
- return RawDataSampleGrid.create(context);
- }
-
- @Override
- public String tryGetLink()
- {
- return null;
- }
- });
- return Arrays.asList(msInjectionSampleAnnotatingMenuItem, msInjectionSampleBrowserMenuItem);
- }
-
- @Override
- public String getName()
- {
- return viewContext.getMessage(Dict.QUERY_MENU_TITLE);
- }
-
- @Override
- public void initialize(AsyncCallback<Void> callback)
- {
- callback.onSuccess(null);
- }
-
- @Override
- public Collection<? extends DisposableTabContent> getSections(
- IEntityInformationHolderWithIdentifier entity)
- {
- return new ArrayList<DisposableTabContent>();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowerToolBar.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowerToolBar.java
deleted file mode 100644
index d58e10da11f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowerToolBar.java
+++ /dev/null
@@ -1,391 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.List;
-
-import com.extjs.gxt.ui.client.event.BaseEvent;
-import com.extjs.gxt.ui.client.event.Events;
-import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
-import com.extjs.gxt.ui.client.event.SelectionChangedListener;
-import com.extjs.gxt.ui.client.store.ListStore;
-import com.extjs.gxt.ui.client.widget.Label;
-import com.extjs.gxt.ui.client.widget.form.CheckBox;
-import com.extjs.gxt.ui.client.widget.form.ComboBox;
-import com.extjs.gxt.ui.client.widget.form.ComboBox.TriggerAction;
-import com.extjs.gxt.ui.client.widget.toolbar.LabelToolItem;
-import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-import com.google.gwt.user.client.ui.AbstractImagePrototype;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.SimplifiedBaseModelData;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.VocabularyTermModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.VocabularyTermSelectionWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.IDataRefreshCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinByExperimentBrowerToolBar extends ToolBar
-{
- private static final AggregateFunction DEFAULT_AGGREGATE_FUNCTION = AggregateFunction.MEAN;
-
- private static final class AggregateOnTreatmentTypeSelectionWidget extends
- VocabularyTermSelectionWidget
- {
-
- private final VocabularyTermModel nothingTermModel;
-
- AggregateOnTreatmentTypeSelectionWidget(
- IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super("treatmentType", "treatmentType", false, null, viewContext, null, null);
- setAllowBlank(false);
- setForceSelection(true);
- VocabularyTerm nothingTerm = new VocabularyTerm();
- nothingTerm.setLabel("(nothing)");
- nothingTermModel = new VocabularyTermModel(nothingTerm);
- setValue(nothingTermModel);
- viewContext.getService().getTreatmentTypeVocabulary(
- new AbstractAsyncCallback<Vocabulary>(viewContext)
- {
- @Override
- protected void process(Vocabulary vocabulary)
- {
- setVocabulary(vocabulary);
- }
- });
-
- }
-
- @Override
- protected List<VocabularyTermModel> convertItems(List<VocabularyTerm> result)
- {
- List<VocabularyTermModel> terms = super.convertItems(result);
- terms.add(0, nothingTermModel);
- return terms;
- }
-
- }
-
- private abstract static class SimpleModel<T> extends SimplifiedBaseModelData
- {
- private static final long serialVersionUID = 1L;
-
- private static final String PROPERTY = "property";
-
- private final T object;
-
- SimpleModel(T object)
- {
- this.object = object;
- set(PROPERTY, render(object));
- }
-
- public final T getObject()
- {
- return object;
- }
-
- protected abstract String render(T modelObject);
- }
-
- private static final class FalseDiscoveryRateModel extends SimpleModel<Double>
- {
- private static final long serialVersionUID = 1L;
-
- FalseDiscoveryRateModel(Double falseDiscoveryRate)
- {
- super(falseDiscoveryRate);
- }
-
- @Override
- protected String render(Double modelObject)
- {
- int percent = (int) (100 * modelObject);
- int percentFraction = (int) (1000 * modelObject + 0.5) - 10 * percent;
- return Integer.toString(percent)
- + (percentFraction == 0 ? "" : "." + Integer.toString(percentFraction)) + "%";
- }
- }
-
- private static final class AggregateFunctionModel extends SimpleModel<AggregateFunction>
- {
- private static final long serialVersionUID = 1L;
-
- AggregateFunctionModel(AggregateFunction aggregateFunction)
- {
- super(aggregateFunction);
- }
-
- @Override
- protected String render(AggregateFunction modelObject)
- {
- return modelObject.getLabel();
- }
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- private final ComboBox<FalseDiscoveryRateModel> fdrComboBox;
-
- private final ComboBox<AggregateFunctionModel> aggregateFunctionComboBox;
-
- private final VocabularyTermSelectionWidget treatmentTypeComboBox;
-
- private final CheckBox aggregateOriginalCheckBox;
-
- private ProteinByExperimentBrowserGrid browserGrid;
-
- private Experiment experiment;
-
- private ProteinSummaryGrid summaryGrid;
-
- ProteinByExperimentBrowerToolBar(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- Experiment experiment)
- {
- this.viewContext = viewContext;
- this.experiment = experiment;
- setBorders(true);
- // WORKAROUND to get all elements in the toolbar present independent of the original width
- // of the parent
- setWidth(3000);
- add(new LabelToolItem(viewContext.getMessage(Dict.FDR_FILTER_LABEL)
- + GenericConstants.LABEL_SEPARATOR));
- fdrComboBox = createFDRComboBox(new SelectionChangedListener<FalseDiscoveryRateModel>()
- {
-
- @Override
- public void selectionChanged(SelectionChangedEvent<FalseDiscoveryRateModel> se)
- {
- update();
- }
- });
- add(fdrComboBox);
- add(new Label(" "));
- add(new LabelToolItem(viewContext.getMessage(Dict.AGGREGATE_FUNCTION_LABEL)
- + GenericConstants.LABEL_SEPARATOR));
- aggregateFunctionComboBox =
- createAggregateFunctionComboBox(new SelectionChangedListener<AggregateFunctionModel>()
- {
-
- @Override
- public void selectionChanged(
- SelectionChangedEvent<AggregateFunctionModel> se)
- {
- update();
- }
-
- });
- add(aggregateFunctionComboBox);
- add(new LabelToolItem(viewContext.getMessage(Dict.AGGREGATE_ON_TREATMENT_TYPE_LABEL)
- + GenericConstants.LABEL_SEPARATOR));
- treatmentTypeComboBox = new AggregateOnTreatmentTypeSelectionWidget(viewContext);
- treatmentTypeComboBox
- .addSelectionChangedListener(new SelectionChangedListener<VocabularyTermModel>()
- {
-
- @Override
- public void selectionChanged(SelectionChangedEvent<VocabularyTermModel> se)
- {
- update();
-
- }
- });
- add(treatmentTypeComboBox);
- add(new LabelToolItem(viewContext.getMessage(Dict.AGGREGATE_ORIGINAL_LABEL)
- + GenericConstants.LABEL_SEPARATOR));
- aggregateOriginalCheckBox = new CheckBox();
- aggregateOriginalCheckBox.addListener(Events.Change, new Listener<BaseEvent>()
- {
-
- @Override
- public void handleEvent(BaseEvent be)
- {
- update();
- }
- });
- add(aggregateOriginalCheckBox);
- }
-
- private ComboBox<FalseDiscoveryRateModel> createFDRComboBox(
- SelectionChangedListener<FalseDiscoveryRateModel> changedListener)
- {
- ComboBox<FalseDiscoveryRateModel> comboBox = new ComboBox<FalseDiscoveryRateModel>();
- ListStore<FalseDiscoveryRateModel> listStore = new ListStore<FalseDiscoveryRateModel>();
- FalseDiscoveryRateModel fdr0 = new FalseDiscoveryRateModel(0.0);
- listStore.add(fdr0);
- listStore.add(new FalseDiscoveryRateModel(0.01));
- listStore.add(new FalseDiscoveryRateModel(0.025));
- listStore.add(new FalseDiscoveryRateModel(0.05));
- listStore.add(new FalseDiscoveryRateModel(0.1));
- comboBox.setStore(listStore);
- comboBox.setDisplayField(SimpleModel.PROPERTY);
- comboBox.setValue(fdr0);
- comboBox.addSelectionChangedListener(changedListener);
- comboBox.setEnabled(true);
- comboBox.setWidth(70);
- comboBox.setTriggerAction(TriggerAction.ALL);
- AbstractImagePrototype infoIcon =
- AbstractImagePrototype.create(viewContext.getImageBundle().getInfoIcon());
- FieldUtil.addInfoIcon(comboBox, viewContext.getMessage(Dict.FDR_COMBO_INFO),
- infoIcon.createImage(), 3, 3);
- return comboBox;
- }
-
- private ComboBox<AggregateFunctionModel> createAggregateFunctionComboBox(
- SelectionChangedListener<AggregateFunctionModel> changedListener)
- {
- ComboBox<AggregateFunctionModel> comboBox = new ComboBox<AggregateFunctionModel>();
- ListStore<AggregateFunctionModel> store = new ListStore<AggregateFunctionModel>();
- AggregateFunctionModel defaultModel = null;
- for (AggregateFunction aggregateFunction : AggregateFunction.values())
- {
- AggregateFunctionModel model = new AggregateFunctionModel(aggregateFunction);
- store.add(model);
- if (aggregateFunction == DEFAULT_AGGREGATE_FUNCTION)
- {
- defaultModel = model;
- }
- }
- comboBox.setStore(store);
- comboBox.setDisplayField(SimpleModel.PROPERTY);
- comboBox.setValue(defaultModel);
- comboBox.addSelectionChangedListener(changedListener);
- comboBox.setWidth(100);
- comboBox.setEnabled(true);
- comboBox.setTriggerAction(TriggerAction.ALL);
- return comboBox;
- }
-
- Experiment getExperimentOrNull()
- {
- return experiment;
- }
-
- void setBrowserGrid(ProteinByExperimentBrowserGrid browserGrid)
- {
- this.browserGrid = browserGrid;
- }
-
- void setSummaryGrid(ProteinSummaryGrid summaryGrid)
- {
- this.summaryGrid = summaryGrid;
- }
-
- void update()
- {
- if (experiment != null)
- {
- final TechId experimentID = TechId.create(experiment);
- browserGrid.setLoadMaskImmediately(true);
- browserGrid.setPostRefreshCallback(new IDataRefreshCallback()
- {
- @Override
- public void postRefresh(boolean wasSuccessful)
- {
- if (summaryGrid != null)
- {
- summaryGrid.setLoadMaskImmediately(true);
- summaryGrid.update(experimentID);
- }
- }
- });
- double falseDiscoveryRate = getSelection(fdrComboBox, 0.0);
- AggregateFunction aggregateFunction =
- getSelection(aggregateFunctionComboBox, DEFAULT_AGGREGATE_FUNCTION);
- VocabularyTermModel value = treatmentTypeComboBox.getValue();
- String treatmentTypeCode = value == null ? null : value.getTerm().getCode();
- AsyncCallback<List<AbundanceColumnDefinition>> callback =
- new AbundanceColumnDefinitionsCallback(viewContext, browserGrid, experimentID,
- falseDiscoveryRate, aggregateFunction, treatmentTypeCode,
- aggregateOriginalCheckBox.getValue());
- viewContext.getService().getAbundanceColumnDefinitionsForProteinByExperiment(
- experimentID, treatmentTypeCode, callback);
- }
- }
-
- ListProteinByExperimentCriteria getCriteria()
- {
- ListProteinByExperimentCriteria criteria = new ListProteinByExperimentCriteria();
- criteria.setExperimentID(TechId.create(experiment));
- criteria.setFalseDiscoveryRate(getSelection(fdrComboBox, 0.0));
- criteria.setAggregateFunction(getSelection(aggregateFunctionComboBox, DEFAULT_AGGREGATE_FUNCTION));
- VocabularyTermModel value = treatmentTypeComboBox.getValue();
- String treatmentTypeCode = value == null ? null : value.getTerm().getCode();
- criteria.setTreatmentTypeCode(treatmentTypeCode);
- criteria.setAggregateOriginal(aggregateOriginalCheckBox.getValue());
- return criteria;
- }
-
- private <T> T getSelection(ComboBox<? extends SimpleModel<T>> comboBox, T defaultValue)
- {
- List<? extends SimpleModel<T>> selection = comboBox.getSelection();
- return selection.isEmpty() ? defaultValue : selection.get(0).getObject();
- }
-
- private static final class AbundanceColumnDefinitionsCallback extends
- AbstractAsyncCallback<List<AbundanceColumnDefinition>>
- {
- private final ProteinByExperimentBrowserGrid browserGrid;
-
- private final TechId experimentID;
-
- private final double falseDiscoveryRate;
-
- private final AggregateFunction aggregateFunction;
-
- private final String treatmentTypeCode;
-
- private final boolean aggregateOriginal;
-
- public AbundanceColumnDefinitionsCallback(IViewContext<?> viewContext,
- ProteinByExperimentBrowserGrid browserGrid, TechId experimentID, double falseDiscoveryRate,
- AggregateFunction aggregateFunction, String treatmentTypeCode,
- boolean aggregateOriginal)
- {
- super(viewContext);
- this.browserGrid = browserGrid;
- this.experimentID = experimentID;
- this.falseDiscoveryRate = falseDiscoveryRate;
- this.aggregateFunction = aggregateFunction;
- this.treatmentTypeCode = treatmentTypeCode;
- this.aggregateOriginal = aggregateOriginal;
- }
-
- @Override
- protected void process(List<AbundanceColumnDefinition> result)
- {
- browserGrid.update(experimentID, falseDiscoveryRate, aggregateFunction,
- treatmentTypeCode, aggregateOriginal, result);
- }
-
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowserGrid.java
deleted file mode 100644
index 0667f7b297b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinByExperimentBrowserGrid.java
+++ /dev/null
@@ -1,240 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.Set;
-
-import com.extjs.gxt.ui.client.widget.Component;
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.TabItem;
-import com.extjs.gxt.ui.client.widget.TabPanel;
-import com.extjs.gxt.ui.client.widget.layout.FitLayout;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-import com.extjs.gxt.ui.client.widget.layout.RowLayout;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.AbstractTabItemFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListenerAndLinkGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.IDataRefreshCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinBrowserColumnIDs;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinByExperimentBrowserGrid extends TypedTableGrid<ProteinInfo>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX
- + "protein-by-experiment-browser";
-
- // browser consists of the grid and additional toolbars (paging, filtering)
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private final ProteinByExperimentBrowerToolBar toolbar;
-
- private ListProteinByExperimentCriteria criteria;
-
- private IDataRefreshCallback postRefreshCallback = new IDataRefreshCallback()
- {
- @Override
- public void postRefresh(boolean wasSuccessful)
- {
- }
- };
-
- static IDisposableComponent create(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- BasicEntityType experimentType, Experiment experiment)
- {
- final IDisposableComponent summaryGrid = ProteinSummaryGrid.create(viewContext);
- ProteinByExperimentBrowserGrid browserGrid =
- new ProteinByExperimentBrowserGrid(viewContext, experiment);
- final IDisposableComponent disposableBrowerGrid = browserGrid.asDisposableWithoutToolbar();
- final ProteinByExperimentBrowerToolBar toolBar = browserGrid.toolbar;
- toolBar.setSummaryGrid((ProteinSummaryGrid) summaryGrid.getComponent());
- final LayoutContainer container = new LayoutContainer();
- container.setLayout(new RowLayout());
- container.add(toolBar);
- TabPanel tabPanel = new TabPanel();
- tabPanel.add(createTab(disposableBrowerGrid, viewContext, Dict.PROTEIN_BROWSER));
- tabPanel.add(createTab(summaryGrid, viewContext, Dict.PROTEIN_SUMMARY));
- container.add(tabPanel, new RowData(1, 1));
- toolBar.update();
- return new IDisposableComponent()
- {
- @Override
- public void update(Set<DatabaseModificationKind> observedModifications)
- {
- disposableBrowerGrid.update(observedModifications);
- summaryGrid.update(observedModifications);
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return disposableBrowerGrid.getRelevantModifications();
- }
-
- @Override
- public Component getComponent()
- {
- return container;
- }
-
- @Override
- public void dispose()
- {
- disposableBrowerGrid.dispose();
- summaryGrid.dispose();
- }
- };
- }
-
- private static TabItem createTab(IDisposableComponent disposableComponent,
- IMessageProvider messageProvider, String titleKey)
- {
- TabItem tabItem = new TabItem(messageProvider.getMessage(titleKey));
- tabItem.setLayout(new FitLayout());
- Component component = disposableComponent.getComponent();
- component.setHeight("100%");
- tabItem.add(component);
- return tabItem;
- }
-
- private ProteinByExperimentBrowserGrid(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext, final Experiment experiment)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
- specificViewContext = viewContext;
- toolbar = new ProteinByExperimentBrowerToolBar(viewContext, experiment);
- toolbar.setBrowserGrid(this);
- registerListenerAndLinkGenerator(ProteinBrowserColumnIDs.ACCESSION_NUMBER,
- new ICellListenerAndLinkGenerator<ProteinInfo>()
- {
- @Override
- public void handle(TableModelRowWithObject<ProteinInfo> rowItem,
- boolean keyPressed)
- {
- AbstractTabItemFactory tabItemFactory =
- ProteinViewer.createTabItemFactory(viewContext,
- toolbar.getExperimentOrNull(),
- rowItem.getObjectOrNull());
- tabItemFactory.setInBackground(keyPressed);
- DispatcherHelper.dispatchNaviEvent(tabItemFactory);
- }
-
- @Override
- public String tryGetLink(ProteinInfo entity,
- ISerializableComparable comparableValue)
- {
- return ProteinViewLocatorResolver.createLink(experiment, entity);
- }
- });
- }
-
- void update(TechId experimentID, double falseDiscoveryRate,
- AggregateFunction aggregateFunction, String treatmentTypeCode,
- boolean aggregateOriginal, List<AbundanceColumnDefinition> definitions)
- {
- criteria = new ListProteinByExperimentCriteria();
- criteria.setExperimentID(experimentID);
- criteria.setFalseDiscoveryRate(falseDiscoveryRate);
- criteria.setAggregateFunction(aggregateFunction);
- criteria.setTreatmentTypeCode(treatmentTypeCode);
- criteria.setAggregateOriginal(aggregateOriginal);
- refresh(postRefreshCallback, true);
- }
-
- void setPostRefreshCallback(IDataRefreshCallback postRefreshCallback)
- {
- this.postRefreshCallback = postRefreshCallback;
- }
-
- @Override
- protected String translateColumnIdToDictionaryKey(String columnID)
- {
- return columnID.toLowerCase();
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList(ProteinBrowserColumnIDs.PROTEIN_DESCRIPTION);
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinInfo>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<ProteinInfo>> callback)
- {
- if (criteria == null)
- {
- criteria = toolbar.getCriteria();
- }
- criteria.copyPagingConfig(resultSetConfig);
- specificViewContext.getService().listProteinsByExperiment(criteria, callback);
- }
-
- @Override
- protected void prepareExportEntities(TableExportCriteria<TableModelRowWithObject<ProteinInfo>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- specificViewContext.getService().prepareExportProteins(exportCriteria, callback);
- }
-
- @Override
- public void update(Set<DatabaseModificationKind> observedModifications)
- {
- toolbar.update();
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[]
- { DatabaseModificationKind.createOrDelete(ObjectKind.DATA_SET),
- DatabaseModificationKind.edit(ObjectKind.SAMPLE) };
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRelatedSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRelatedSampleGrid.java
deleted file mode 100644
index 0c430904fc7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRelatedSampleGrid.java
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- * Copyright 2008 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.List;
-
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplayTypeIDGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListenerAndLinkGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.SampleWithPropertiesAndAbundance;
-
-/**
- * A {@link LayoutContainer} which contains the grid where {@link SampleWithPropertiesAndAbundance}s of specified Protein are displayed.
- *
- * @author Piotr Buczek
- */
-public class ProteinRelatedSampleGrid extends TypedTableGrid<ProteinRelatedSample>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX + "protein_related_sample_grid";
-
- // browser consists of the grid and additional toolbars (paging, filtering)
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- public static final String EDIT_BUTTON_ID = BROWSER_ID + "_edit-button";
-
- public static final String SHOW_DETAILS_BUTTON_ID = BROWSER_ID + "_show-details-button";
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> phosphoViewContext;
-
- public static IDisposableComponent createGridForProteinSamples(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final TechId proteinReferenceID, Long experimentIDOrNull, final String gridId)
- {
- final ListSampleAbundanceByProteinCriteria criteria =
- new ListSampleAbundanceByProteinCriteria();
- criteria.setProteinReferenceID(proteinReferenceID);
- criteria.setExperimentID(experimentIDOrNull);
- final ProteinRelatedSampleGrid browserGrid =
- new ProteinRelatedSampleGrid(viewContext, criteria, gridId);
- return browserGrid.asDisposableWithoutToolbar();
- }
-
- private ListSampleAbundanceByProteinCriteria criteria;
-
- private ProteinRelatedSampleGrid(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- ListSampleAbundanceByProteinCriteria criteria, String gridId)
- {
- super(viewContext.getCommonViewContext(), gridId, true,
- DisplayTypeIDGenerator.SAMPLE_DETAILS_GRID);
- this.phosphoViewContext = viewContext;
- setId(BROWSER_ID);
- this.criteria = criteria;
- registerListenerAndLinkGenerator(ProteinRelatedSampleGridColumnIDs.SAMPLE_IDENTIFIER,
- new ICellListenerAndLinkGenerator<ProteinRelatedSample>()
- {
-
- @Override
- public void handle(TableModelRowWithObject<ProteinRelatedSample> rowItem,
- boolean specialKeyPressed)
- {
- showEntityInformationHolderViewer(rowItem.getObjectOrNull(), false,
- specialKeyPressed);
- }
-
- @Override
- public String tryGetLink(ProteinRelatedSample entity,
- ISerializableComparable comparableValue)
- {
- return LinkExtractor.tryExtract(entity);
- }
- });
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinRelatedSample>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<ProteinRelatedSample>> callback)
- {
- criteria.copyPagingConfig(resultSetConfig);
- phosphoViewContext.getService().listProteinRelatedSamplesByProtein(criteria, callback);
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList(ProteinRelatedSampleGridColumnIDs.SAMPLE_IDENTIFIER,
- ProteinRelatedSampleGridColumnIDs.ABUNDANCE);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<ProteinRelatedSample>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- phosphoViewContext.getService().prepareExportProteinRelatedSamples(exportCriteria, callback);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderers.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderers.java
deleted file mode 100644
index ce30c2960cf..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderers.java
+++ /dev/null
@@ -1,265 +0,0 @@
-/*
- * Copyright 2007 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.extjs.gxt.ui.client.widget.Text;
-import com.google.gwt.user.client.ui.FlowPanel;
-import com.google.gwt.user.client.ui.InlineHTML;
-import com.google.gwt.user.client.ui.Widget;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.PropertyValueRenderers.EntityInformationHolderPropertyValueRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.AbstractPropertyValueRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.IPropertyValueRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.ExternalHyperlink;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.ProteinViewer.DatasetInformationHolder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AccessionNumberProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Occurrence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.OccurrenceUtil;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Peptide;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.PeptideModification;
-
-/**
- * Utility method for creating {@link IPropertyValueRenderer} instances or directly rendering stuff in {@link ProteinViewer}.
- *
- * @author Tomasz Pylak
- * @author Franz-Josef Elmer
- */
-public final class ProteinRenderers
-{
- private static final class Symbol
- {
- private final char character;
-
- private boolean inPeptide;
-
- private Double mass;
-
- Symbol(char character)
- {
- this.character = character;
- }
-
- public char getCharacter()
- {
- return character;
- }
-
- public boolean isInPeptide()
- {
- return inPeptide;
- }
-
- public void inPeptide()
- {
- this.inPeptide = true;
- }
-
- public Double getMass()
- {
- return mass;
- }
-
- public void setMass(Double mass)
- {
- this.mass = mass;
- }
- }
-
- private ProteinRenderers()
- {
- // Can not be instantiated
- }
-
- /**
- * Allows to render a property identifier which is a link to an external page with a description.
- */
- public final static IPropertyValueRenderer<AccessionNumberProvider> createProteinIdentLinkRenderer(
- final IViewContext<?> viewContext)
- {
- return new AccessionNumberRenderer(viewContext);
- }
-
- public final static IPropertyValueRenderer<Peptide> createPeptideRenderer(
- final IViewContext<?> viewContext)
- {
- return new PeptideRenderer(viewContext);
- }
-
- public final static IPropertyValueRenderer<Experiment> createExperimentPropertyValueRenderer(
- final IViewContext<?> viewContext)
- {
- return ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.PropertyValueRenderers
- .createExperimentPropertyValueRenderer(viewContext);
- }
-
- public final static IPropertyValueRenderer<DatasetInformationHolder> createEntityInformationPropertyValueRenderer(
- final IViewContext<?> viewContext)
- {
- return new EntityInformationHolderPropertyValueRenderer<DatasetInformationHolder>(
- viewContext);
- }
-
- public static String getFixedWidthHTMLString(String text)
- {
- return "<font style='font-family:monospace'>" + text + "</font>";
- }
-
- /** Produces an HTML code with all occurrences properly marked */
- public static String markOccurrencesWithHtml(String proteinSequence, List<Peptide> peptides,
- int blockLength)
- {
- List<Symbol> symbols = createSymbols(proteinSequence, peptides);
- StringBuilder builder = new StringBuilder();
- boolean inPeptide = false;
- for (int i = 0, n = symbols.size(); i < n; i++)
- {
- if (i > 0)
- {
- if (i % blockLength == 0)
- {
- builder.append(" ");
- }
- }
- Symbol symbol = symbols.get(i);
- boolean nextInPeptide = symbol.isInPeptide();
- if (inPeptide != nextInPeptide)
- {
- builder.append(nextInPeptide ? "<font color='red'>" : "</font>");
- }
- inPeptide = nextInPeptide;
- Double mass = symbol.getMass();
- char character = symbol.getCharacter();
- if (mass == null)
- {
- builder.append(character);
- } else
- {
- builder.append(renderAminoAcidSymbol(character, i + 1, mass));
- }
-
- }
- return builder.toString();
- }
-
- public static String renderAminoAcidSymbol(char character, Integer positionOrNull, double mass)
- {
- String tooltip = positionOrNull == null ? "" : "position=" + positionOrNull + ", ";
- tooltip += "mass=" + mass;
-
- return "<font style='text-decoration:underline; cursor:pointer' color='blue' title='"
- + tooltip + "'>" + character + "</font>";
- }
-
- private static List<Symbol> createSymbols(String proteinSequence, List<Peptide> peptides)
- {
- List<Symbol> symbols = new ArrayList<Symbol>();
- for (int i = 0, n = proteinSequence.length(); i < n; i++)
- {
- symbols.add(new Symbol(proteinSequence.charAt(i)));
- }
-
- for (Peptide peptide : peptides)
- {
- List<Occurrence> occurances =
- OccurrenceUtil.findAllOccurrences(proteinSequence, peptide.getSequence());
- List<PeptideModification> modifications = peptide.getModifications();
- for (Occurrence occurrence : occurances)
- {
- int startIndex = occurrence.getStartIndex();
- for (int i = startIndex, n = occurrence.getEndIndex(); i <= n; i++)
- {
- symbols.get(i).inPeptide();
- }
- for (PeptideModification peptideModification : modifications)
- {
- Symbol symbol = symbols.get(startIndex + peptideModification.getPosition() - 1);
- symbol.setMass(peptideModification.getMass());
- }
- }
- }
- return symbols;
- }
-
- private final static class AccessionNumberRenderer extends
- AbstractPropertyValueRenderer<AccessionNumberProvider>
- {
-
- AccessionNumberRenderer(final IMessageProvider messageProvider)
- {
- super(messageProvider);
- }
-
- @Override
- public Widget getAsWidget(AccessionNumberProvider object)
- {
- String accessionNumber = object.getAccessionNumber();
- String type = object.getAccessionNumberType();
- String url = AccessionNumberURLCreator.tryToCreateURL(type, accessionNumber);
- if (url == null)
- {
- return new Text(accessionNumber);
- }
- return new ExternalHyperlink(accessionNumber, url);
- }
- }
-
- private final static class PeptideRenderer extends AbstractPropertyValueRenderer<Peptide>
- {
-
- PeptideRenderer(final IMessageProvider messageProvider)
- {
- super(messageProvider);
- }
-
- @Override
- public Widget getAsWidget(Peptide peptide)
- {
- StringBuilder builder = new StringBuilder();
- String sequence = peptide.getSequence();
- List<PeptideModification> modifications = peptide.getModifications();
- Map<Integer, PeptideModification> modificationsMap = new HashMap<Integer, PeptideModification>();
- for (PeptideModification modification : modifications)
- {
- modificationsMap.put(modification.getPosition(), modification);
- }
- for (int i = 0, n = sequence.length(); i < n; i++)
- {
- char c = sequence.charAt(i);
- PeptideModification peptideModification = modificationsMap.get(i + 1);
- if (peptideModification != null)
- {
- builder.append(renderAminoAcidSymbol(c, null, peptideModification.getMass()));
- } else
- {
- builder.append(c);
- }
- }
- final FlowPanel panel = new FlowPanel();
- panel.add(new InlineHTML(getFixedWidthHTMLString(builder.toString())));
- return panel;
- }
-
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSamplesSection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSamplesSection.java
deleted file mode 100644
index 365c2d64c71..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSamplesSection.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*
- * Copyright 2008 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import com.extjs.gxt.ui.client.widget.ContentPanel;
-import com.extjs.gxt.ui.client.widget.layout.FitLayout;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * {@link TabContent} containing specified protein samples.
- *
- * @author Piotr Buczek
- */
-public class ProteinSamplesSection extends ContentPanel
-{
- private static final String PREFIX = "protein-samples-section_";
-
- public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
-
- private IDisposableComponent disposableComponent;
-
- public ProteinSamplesSection(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final TechId proteinReferenceID, IIdAndCodeHolder experimentOrNull)
- {
- setHeading(viewContext.getMessage(Dict.SAMPLES));
- setHeaderVisible(true);
- setCollapsible(true);
- setAnimCollapse(false);
- setBodyBorder(true);
- setLayout(new FitLayout());
- Long experimentID = experimentOrNull == null ? null : experimentOrNull.getId();
- disposableComponent = ProteinRelatedSampleGrid.createGridForProteinSamples(viewContext,
- proteinReferenceID, experimentID, createGridId(proteinReferenceID));
- add(disposableComponent.getComponent());
- }
-
- // @Private
- static String createGridId(TechId containerId)
- {
- return ID_PREFIX + containerId + "-grid";
- }
-
- @Override
- protected void onDetach()
- {
- if (disposableComponent != null)
- {
- disposableComponent.dispose();
- }
- super.onDetach();
- }
-
- IDatabaseModificationObserver tryGetDatabaseModificationObserver()
- {
- return disposableComponent;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java
deleted file mode 100644
index 05f9e20152d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSequenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSequenceGrid extends TypedTableGrid<ProteinSequence>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX + "protein-sequence-browser";
-
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- Experiment experimentOrNull, TechId proteinReferenceID)
- {
- return new ProteinSequenceGrid(viewContext, experimentOrNull, proteinReferenceID)
- .asDisposableWithoutToolbar();
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private ListProteinSequenceCriteria criteria;
-
- private ProteinSequenceGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- Experiment experimentOrNull, TechId proteinReferenceID)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID + proteinReferenceID, true,
- PhosphoNetXDisplayTypeIDGenerator.PROTEIN_SEQUENCE_BROWSER_GRID);
- specificViewContext = viewContext;
- criteria = new ListProteinSequenceCriteria();
- if (experimentOrNull != null)
- {
- criteria.setExperimentID(new TechId(experimentOrNull.getId()));
- }
- criteria.setProteinReferenceID(proteinReferenceID);
- }
-
- @Override
- protected String translateColumnIdToDictionaryKey(String columnID)
- {
- return columnID.toLowerCase();
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList();
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinSequence>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<ProteinSequence>> callback)
- {
- criteria.copyPagingConfig(resultSetConfig);
- specificViewContext.getService().listSequencesByProteinReference(criteria, callback);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<ProteinSequence>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- specificViewContext.getService().prepareExportProteinSequences(exportCriteria, callback);
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[0];
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSummaryGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSummaryGrid.java
deleted file mode 100644
index 6dc527a0d59..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSummaryGrid.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinSummaryGrid extends TypedTableGrid<ProteinSummary>
-{
- private static final String PREFIX =
- GenericConstants.ID_PREFIX + "protein-summary";
-
- // browser consists of the grid and additional toolbars (paging, filtering)
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- return new ProteinSummaryGrid(viewContext).asDisposableWithoutToolbar();
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private ListProteinSummaryByExperimentCriteria criteria;
-
- ProteinSummaryGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- PhosphoNetXDisplayTypeIDGenerator.PROTEIN_SUMMARY_BROWSER_GRID);
- specificViewContext = viewContext;
- }
-
- void update(TechId experimentID)
- {
- criteria = new ListProteinSummaryByExperimentCriteria();
- criteria.setExperimentID(experimentID);
- refresh(true);
- }
-
- @Override
- protected String translateColumnIdToDictionaryKey(String columnID)
- {
- return ProteinSummaryGridColumnIDs.FDR.equals(columnID) ? "false_discovery_rate_column"
- : columnID.toLowerCase();
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList(ProteinSummaryGridColumnIDs.FDR);
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinSummary>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<ProteinSummary>> callback)
- {
- if (criteria != null)
- {
- criteria.copyPagingConfig(resultSetConfig);
- specificViewContext.getService().listProteinSummariesByExperiment(criteria, callback);
- }
- }
-
- @Override
- protected void prepareExportEntities(TableExportCriteria<TableModelRowWithObject<ProteinSummary>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- specificViewContext.getService().prepareExportProteinSummary(exportCriteria, callback);
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[0];
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewLocatorResolver.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewLocatorResolver.java
deleted file mode 100644
index f6d7f3eea2d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewLocatorResolver.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.AbstractTabItemFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.AbstractViewLocatorResolver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-
-/**
- * Locator resolver for protein details view.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinViewLocatorResolver extends AbstractViewLocatorResolver
-{
- private static final String ACTION = "PROTEIN";
-
- private static final String EXPERIMENT_PERM_ID = "experimentPermId";
-
- private static final String PROTEIN_ID = "id";
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- public ProteinViewLocatorResolver(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(ACTION);
- this.viewContext = viewContext;
- }
-
- @Override
- public void resolve(ViewLocator locator) throws UserFailureException
- {
- String experimentPermID = getMandatoryParameter(locator, EXPERIMENT_PERM_ID);
- final TechId proteinID = new TechId(new Long(getMandatoryParameter(locator, PROTEIN_ID)));
- viewContext.log("resolve protein " + proteinID + " for experiment " + experimentPermID);
- viewContext.getCommonService().getExperimentInfoByPermId(experimentPermID,
- new AbstractAsyncCallback<Experiment>(viewContext)
- {
- @Override
- protected void process(final Experiment experiment)
- {
- IPhosphoNetXClientServiceAsync service =
- ProteinViewLocatorResolver.this.viewContext.getService();
- service.getProteinByExperiment(new TechId(experiment.getId()),
- proteinID, new AbstractAsyncCallback<ProteinByExperiment>(
- viewContext)
- {
- @Override
- protected void process(final ProteinByExperiment protein)
- {
- AbstractTabItemFactory tabItemFactory =
- ProteinViewer
- .createTabItemFactory(
- ProteinViewLocatorResolver.this.viewContext,
- experiment, protein);
- DispatcherHelper.dispatchNaviEvent(tabItemFactory);
- }
-
- });
- }
- });
- }
-
- static String createLink(final Experiment experiment, ProteinInfo entity)
- {
- URLMethodWithParameters url = new URLMethodWithParameters("");
- url.addParameter((String) BasicConstant.LOCATOR_ACTION_PARAMETER, ACTION);
- url.addParameter(ProteinViewLocatorResolver.EXPERIMENT_PERM_ID,
- experiment.getPermId());
- url.addParameter(ProteinViewLocatorResolver.PROTEIN_ID,
- Long.toString(entity.getId().getId()));
- return url.toStringWithoutDelimiterPrefix();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java
deleted file mode 100644
index d061ad1f615..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java
+++ /dev/null
@@ -1,454 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import com.extjs.gxt.ui.client.Style.LayoutRegion;
-import com.extjs.gxt.ui.client.Style.Scroll;
-import com.extjs.gxt.ui.client.widget.ContentPanel;
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.TabItem;
-import com.extjs.gxt.ui.client.widget.TabPanel;
-import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
-import com.extjs.gxt.ui.client.widget.layout.BorderLayoutData;
-import com.extjs.gxt.ui.client.widget.layout.FitLayout;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-import com.extjs.gxt.ui.client.widget.layout.RowLayout;
-
-import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AsyncCallbackWithProgressBar;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableTabContent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.AbstractTabItemFactory;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.CompositeDatabaseModificationObserver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewerWithVerticalSplit;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.RowLayoutManager;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.PropertyGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.IBasicProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.IndistinguishableProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Peptide;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinDetails;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinViewer extends AbstractViewerWithVerticalSplit<IEntityInformationHolder>
- implements IDatabaseModificationObserver
-{
- private static final int AMINOACIDS_IN_ONE_BLOCK = 10;
-
- private static final String PREFIX = "protein-viewer_";
-
- public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
-
- static AbstractTabItemFactory createTabItemFactory(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final Experiment experiment, final IBasicProteinInfo proteinInfo)
- {
- return new AbstractTabItemFactory()
- {
- @Override
- public String getId()
- {
- return createWidgetID(experiment, proteinInfo.getId());
- }
-
- @Override
- public ITabItem create()
- {
- ProteinViewer viewer = new ProteinViewer(viewContext, experiment, proteinInfo);
- DatabaseModificationAwareComponent c =
- new DatabaseModificationAwareComponent(viewer, viewer);
- return DefaultTabItem.create(getTabTitle(), c, viewContext, false);
- }
-
- @Override
- public HelpPageIdentifier getHelpPageIdentifier()
- {
- return HelpPageIdentifier.createSpecific("Protein Viewer");
- }
-
- @Override
- public String getTabTitle()
- {
- String description = getAbbreviatedDescription(proteinInfo);
- String identifier = experiment == null ? "?" : experiment.getCode();
- return viewContext.getMessage(Dict.PROTEIN_IN_EXPERIMENT_TAB_LABEL,
- description, identifier);
- }
-
- @Override
- public String tryGetLink()
- {
- return null;
- }
- };
- }
-
- private static String getAbbreviatedDescription(final IBasicProteinInfo proteinInfo)
- {
- String info = proteinInfo.getDescription();
- if (info == null)
- {
- info = proteinInfo.getAccessionNumber();
- }
- return StringUtils.abbreviate(info, 30);
- }
-
- static String createWidgetID(IIdAndCodeHolder experimentIdOrNull, TechId proteinReferenceID)
- {
- Long experimentID = experimentIdOrNull == null ? null : experimentIdOrNull.getId();
- return ID_PREFIX + experimentID + "_" + proteinReferenceID.getId();
- }
-
- private final Experiment experimentOrNull;
-
- private final IBasicProteinInfo proteinInfo;
-
- private final TechId proteinReferenceID;
-
- private ProteinSamplesSection proteinSamplesSection;
-
- private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- Experiment experiment, IBasicProteinInfo proteinInfo)
- {
- super(viewContext, "", createWidgetID(experiment, proteinInfo.getId()), false);
- this.experimentOrNull = experiment;
- this.proteinInfo = proteinInfo;
- this.proteinReferenceID = proteinInfo.getId();
- reloadAllData();
- }
-
- @Override
- @SuppressWarnings("unchecked")
- protected final IViewContext<IPhosphoNetXClientServiceAsync> getViewContext()
- {
- return (IViewContext<IPhosphoNetXClientServiceAsync>) viewContext;
- }
-
- @Override
- protected void reloadAllData()
- {
- if (experimentOrNull != null)
- {
- final IViewContext<IPhosphoNetXClientServiceAsync> context = getViewContext();
- ProteinByExperimentCallback callback = new ProteinByExperimentCallback(context, this);
- String message =
- context.getMessage(Dict.PROTEIN_DETAILS_WAITING_MESSAGE,
- proteinInfo.getAccessionNumber());
- context.getService().getProteinByExperiment(new TechId(experimentOrNull.getId()),
- proteinReferenceID, AsyncCallbackWithProgressBar.decorate(callback, message));
- }
- }
-
- private void recreateUI(ProteinByExperiment protein)
- {
- setLayout(new BorderLayout());
- removeAll();
- setScrollMode(Scroll.AUTO);
- ContentPanel propertyPanel = createPropertyPanel(protein);
-
- ProteinDetails details = protein.getDetails();
- if (details == null)
- {
- recreateUIWithDatasetTable(protein, propertyPanel);
- } else
- {
- LayoutContainer centerPanel = new LayoutContainer();
- RowLayoutManager rowDataManager = new RowLayoutManager(centerPanel, new RowLayout());
- add(centerPanel, createBorderLayoutData(LayoutRegion.CENTER));
- rowDataManager.addToContainer(propertyPanel, new RowData(1, 0.5f));
- List<IndistinguishableProteinInfo> indistinguishableProteins =
- details.getIndistinguishableProteinInfos();
- if (indistinguishableProteins.isEmpty() == false)
- {
- List<Peptide> peptides = details.getPeptides();
- ContentPanel panel =
- createIndistinguishableProteinsSection(indistinguishableProteins, peptides);
- rowDataManager.addToContainer(panel, new RowData(1, 0.3f));
- }
- proteinSamplesSection =
- new ProteinSamplesSection(getViewContext(), proteinReferenceID,
- experimentOrNull);
- rowDataManager.addToContainer(proteinSamplesSection, new RowData(1, 0.2f));
- layout();
- }
- }
-
- private ContentPanel createIndistinguishableProteinsSection(
- List<IndistinguishableProteinInfo> indistinguishableProteins, List<Peptide> peptides)
- {
- ContentPanel panel = new ContentPanel(new RowLayout());
- panel.setHeading(viewContext.getMessage(Dict.INDISTINGUISHABLE_PROTEINS));
- panel.setCollapsible(true);
- panel.setHeight("100%");
- TabPanel tabPanel = new TabPanel();
- tabPanel.setTabScroll(true);
- for (IndistinguishableProteinInfo info : indistinguishableProteins)
- {
- String accessionNumber = info.getAccessionNumber();
- TabItem item = new TabItem(accessionNumber);
- item.setLayout(new FitLayout());
- PropertyGrid propertyGrid = new PropertyGrid(viewContext, 4, "200");
- final Map<String, Object> properties = new LinkedHashMap<String, Object>();
- properties.put(viewContext.getMessage(Dict.ACCESSION_NUMBER), info);
- propertyGrid.registerPropertyValueRenderer(IndistinguishableProteinInfo.class,
- ProteinRenderers.createProteinIdentLinkRenderer(viewContext));
- properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), info.getDescription());
- String markedSequence = markPeptides(info.getSequence(), peptides);
- properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence);
- properties.put(viewContext.getMessage(Dict.COVERAGE), info.getCoverage());
- propertyGrid.setProperties(properties);
- ContentPanel contentPanel = new ContentPanel();
- contentPanel.setHeight("100%");
- contentPanel.setScrollMode(Scroll.AUTO);
- contentPanel.add(propertyGrid);
- item.add(contentPanel);
- tabPanel.add(item);
- }
- panel.add(tabPanel, new RowData(1, 1));
- return panel;
- }
-
- private void recreateUIWithDatasetTable(ProteinByExperiment protein, ContentPanel propertyPanel)
- {
- BorderLayoutData layoutData = createBorderLayoutData(LayoutRegion.WEST);
- layoutData.setSize(400);
- add(propertyPanel, layoutData);
- DisposableTabContent sequencesSection =
- new DisposableTabContent(viewContext.getMessage(Dict.SEQUENCES), viewContext,
- proteinReferenceID)
- {
- @Override
- protected IDisposableComponent createDisposableContent()
- {
- return ProteinSequenceGrid.create(ProteinViewer.this.getViewContext(),
- experimentOrNull, proteinReferenceID);
- }
- };
- add(sequencesSection, createRightBorderLayoutData());
- DisposableTabContent proteinsSection =
- new DisposableTabContent(viewContext.getMessage(Dict.DATA_SET_PROTEINS),
- viewContext, proteinReferenceID)
- {
- @Override
- protected IDisposableComponent createDisposableContent()
- {
- return DataSetProteinGrid.create(ProteinViewer.this.getViewContext(),
- experimentOrNull, proteinReferenceID);
- }
- };
- add(proteinsSection, createBorderLayoutData(LayoutRegion.SOUTH));
- layout();
- sequencesSection.setContentVisible(true);
- proteinsSection.setContentVisible(true);
- }
-
- private ContentPanel createPropertyPanel(ProteinByExperiment protein)
- {
- PropertyGrid propertyGrid = createPropertyGrid(protein);
- ContentPanel contentPanel = new ContentPanel();
- contentPanel.setHeading(viewContext.getMessage(Dict.PRIMARY_PROTEIN));
- contentPanel.setScrollMode(Scroll.AUTO);
- contentPanel.setCollapsible(true);
- contentPanel.add(propertyGrid);
- return contentPanel;
- }
-
- private PropertyGrid createPropertyGrid(ProteinByExperiment protein)
- {
- final Map<String, Object> properties = new LinkedHashMap<String, Object>();
- PropertyGrid propertyGrid = new PropertyGrid(viewContext, 0, "200");
- if (experimentOrNull != null)
- {
- properties.put(viewContext.getMessage(Dict.EXPERIMENT_LABEL), experimentOrNull);
- }
- properties.put(viewContext.getMessage(Dict.ACCESSION_NUMBER), protein);
- propertyGrid.registerPropertyValueRenderer(ProteinByExperiment.class,
- ProteinRenderers.createProteinIdentLinkRenderer(viewContext));
-
- properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), protein.getDescription());
- if (protein.getDetails() != null)
- {
- addProteinDetails(properties, propertyGrid, protein.getDetails());
- }
-
- propertyGrid.resizeRows(properties.size());
- propertyGrid.setProperties(properties);
- return propertyGrid;
- }
-
- private void addProteinDetails(Map<String, Object> properties, PropertyGrid propertyGrid,
- ProteinDetails proteinDetails)
- {
- properties.put(viewContext.getMessage(Dict.DATABASE_NAME_AND_VERSION),
- proteinDetails.getDatabaseNameAndVersion());
- String markedSequence =
- markPeptides(proteinDetails.getSequence(), proteinDetails.getPeptides());
- properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence);
-
- properties.put(viewContext.getMessage(Dict.COVERAGE), proteinDetails.getCoverage());
-
- propertyGrid.registerPropertyValueRenderer(Peptide.class,
- ProteinRenderers.createPeptideRenderer(viewContext));
- properties.put(viewContext.getMessage(Dict.PEPTIDES, proteinDetails.getPeptides().size()),
- proteinDetails.getPeptides().toArray());
-
- properties.put(viewContext.getMessage(Dict.PROBABILITY), proteinDetails.getProbability());
- properties.put(viewContext.getMessage(Dict.FDR), proteinDetails.getFalseDiscoveryRate());
-
- DatasetInformationHolder dataset = new DatasetInformationHolder(proteinDetails);
- properties.put(viewContext.getMessage(Dict.DATA_SET_PERM_ID), dataset);
- propertyGrid.registerPropertyValueRenderer(DatasetInformationHolder.class,
- ProteinRenderers.createEntityInformationPropertyValueRenderer(viewContext));
- }
-
- private static String markPeptides(String sequence, List<Peptide> peptides)
- {
- String markedSequence =
- ProteinRenderers.markOccurrencesWithHtml(sequence, peptides,
- AMINOACIDS_IN_ONE_BLOCK);
- // the letters should have fixed width
- return ProteinRenderers.getFixedWidthHTMLString(markedSequence);
- }
-
- public static class DatasetInformationHolder implements IEntityInformationHolderWithIdentifier
- {
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private final ProteinDetails proteinDetails;
-
- public DatasetInformationHolder(ProteinDetails proteinDetails)
- {
- this.proteinDetails = proteinDetails;
- }
-
- @Override
- public EntityKind getEntityKind()
- {
- return EntityKind.DATA_SET;
- }
-
- @Override
- public EntityType getEntityType()
- {
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(proteinDetails.getDataSetTypeCode());
- return dataSetType;
- }
-
- @Override
- public String getIdentifier()
- {
- return proteinDetails.getDataSetPermID();
- }
-
- @Override
- public Long getId()
- {
- return proteinDetails.getDataSetTechID();
- }
-
- @Override
- public String getCode()
- {
- return proteinDetails.getDataSetPermID();
- }
-
- @Override
- public String getPermId()
- {
- return getIdentifier();
- }
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return createDatabaseModificationObserver().getRelevantModifications();
- }
-
- @Override
- public void update(Set<DatabaseModificationKind> observedModifications)
- {
- createDatabaseModificationObserver().update(observedModifications);
- }
-
- private CompositeDatabaseModificationObserver createDatabaseModificationObserver()
- {
- CompositeDatabaseModificationObserver observer =
- new CompositeDatabaseModificationObserver();
- if (proteinSamplesSection != null)
- {
- observer.addObserver(proteinSamplesSection.tryGetDatabaseModificationObserver());
- }
- // TODO 2009-07-31, Piotr Buczek: refresh properties panel?
- return observer;
- }
-
- private static final class ProteinByExperimentCallback extends
- AbstractAsyncCallback<ProteinByExperiment>
- {
- private final ProteinViewer viewer;
-
- private ProteinByExperimentCallback(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final ProteinViewer viewer)
- {
- super(viewContext);
- this.viewer = viewer;
- }
-
- @Override
- protected final void process(final ProteinByExperiment result)
- {
- viewer.recreateUI(result);
- }
-
- }
-
- @Override
- protected String getDeleteButtonLabel()
- {
- return viewContext.getMessage(Dict.BUTTON_DELETE_PROTEIN);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataProcessingMenu.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataProcessingMenu.java
deleted file mode 100644
index 4ceb310e652..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataProcessingMenu.java
+++ /dev/null
@@ -1,175 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.Dict.COPY_DATA_SETS_MESSAGE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.Dict.COPY_DATA_SETS_TITLE;
-
-import java.util.List;
-
-import com.extjs.gxt.ui.client.widget.form.TextField;
-import com.extjs.gxt.ui.client.widget.menu.Menu;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ActionMenu;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.IActionMenuItem;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.AbstractDataConfirmationDialog;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedActionWithResult;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.TextToolItem;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class RawDataProcessingMenu extends TextToolItem
-{
- private static final class CopyConfirmationDialog extends
- AbstractDataConfirmationDialog<List<TableModelRowWithObject<Sample>>>
- {
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private final List<TableModelRowWithObject<Sample>> samples;
-
- private final DatastoreServiceDescription datastoreServiceDescription;
-
- private TextField<String> dataSetTypeField;
-
- private CopyConfirmationDialog(
- IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
- DatastoreServiceDescription datastoreServiceDescription,
- List<TableModelRowWithObject<Sample>> samples, String title)
- {
- super(specificViewContext, samples, title);
- this.specificViewContext = specificViewContext;
- this.datastoreServiceDescription = datastoreServiceDescription;
- this.samples = samples;
- setWidth(400);
- }
-
- @Override
- protected String createMessage()
- {
- String list = "[";
- String delim = "";
- for (TableModelRow sample : samples)
- {
- list += delim + sample.getValues().get(0);
- delim = ", ";
- }
- list += "]";
- String label = datastoreServiceDescription.getLabel();
- return specificViewContext.getMessage(COPY_DATA_SETS_MESSAGE, label, list);
- }
-
- @Override
- protected void executeConfirmedAction()
- {
- long[] rawDataSampleIDs = new long[samples.size()];
- for (int i = 0; i < samples.size(); i++)
- {
- rawDataSampleIDs[i] = samples.get(i).getObjectOrNull().getId();
- }
- specificViewContext.getService().processRawData(datastoreServiceDescription.getKey(),
- rawDataSampleIDs, dataSetTypeField.getValue(),
- new VoidAsyncCallback<Void>(specificViewContext));
- }
-
- @Override
- protected void extendForm()
- {
- dataSetTypeField = new TextField<String>();
- dataSetTypeField.setFieldLabel(specificViewContext
- .getMessage(Dict.COPY_DATA_SETS_DATA_SET_TYPE_FIELD));
- dataSetTypeField.setSelectOnFocus(true);
- dataSetTypeField.setWidth(200);
- formPanel.add(dataSetTypeField);
- formPanel.setLabelWidth(100);
- }
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- private final IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>> selectedDataProvider;
-
- public RawDataProcessingMenu(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>> selectedDataProvider)
- {
- super(viewContext.getMessage(Dict.COPY_DATA_SETS_BUTTON_LABEL));
- this.viewContext = viewContext;
- this.selectedDataProvider = selectedDataProvider;
- IViewContext<ICommonClientServiceAsync> commonViewContext =
- viewContext.getCommonViewContext();
- viewContext.getCommonService().listDataStoreServices(DataStoreServiceKind.PROCESSING,
- new AbstractAsyncCallback<List<DatastoreServiceDescription>>(commonViewContext)
- {
- @Override
- public final void process(List<DatastoreServiceDescription> plugins)
- {
- createMenu(plugins);
- }
- });
- }
-
- private void createMenu(List<DatastoreServiceDescription> plugins)
- {
- Menu subMenu = new Menu();
-
- for (final DatastoreServiceDescription datastoreServiceDescription : plugins)
- {
- IActionMenuItem actionMenuItem = new IActionMenuItem()
- {
-
- @Override
- public String getMenuText(IMessageProvider messageProvider)
- {
- return datastoreServiceDescription.getLabel();
- }
-
- @Override
- public String getMenuId()
- {
- return datastoreServiceDescription.getKey();
- }
- };
- IDelegatedAction action = new IDelegatedAction()
- {
-
- @Override
- public void execute()
- {
- String title = viewContext.getMessage(COPY_DATA_SETS_TITLE);
- List<TableModelRowWithObject<Sample>> selectedSamples = selectedDataProvider.execute();
- new CopyConfirmationDialog(viewContext, datastoreServiceDescription,
- selectedSamples, title).show();
- }
- };
- subMenu.add(new ActionMenu(actionMenuItem, viewContext, action));
- }
- setMenu(subMenu);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataSampleGrid.java
deleted file mode 100644
index 67d0e66e6f1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/RawDataSampleGrid.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.createOrDelete;
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.edit;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.DisposableEntityChooser;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListenerAndLinkGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedActionWithResult;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs;
-
-/**
- * @author Franz-Josef Elmer
- */
-class RawDataSampleGrid extends TypedTableGrid<Sample>
-{
- public static final String BROWSER_ID = GenericConstants.ID_PREFIX + "raw_data_sample_browser";
-
- public static DatabaseModificationAwareComponent create(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- RawDataSampleGrid grid = new RawDataSampleGrid(viewContext);
- DisposableEntityChooser<TableModelRowWithObject<Sample>> disposable =
- grid.asDisposableWithoutToolbar();
- return new DatabaseModificationAwareComponent(disposable.getComponent(), disposable);
- }
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- RawDataSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- PhosphoNetXDisplayTypeIDGenerator.RAW_DATA_SAMPLE_BROWSER_GRID);
- specificViewContext = viewContext;
- allowMultipleSelection();
- addEntityOperationsLabel();
- RawDataProcessingMenu button =
- new RawDataProcessingMenu(viewContext,
- new IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>>()
- {
- @Override
- public List<TableModelRowWithObject<Sample>> execute()
- {
- return getSelectedBaseObjects();
- }
- });
- enableButtonOnSelectedItems(button);
- addButton(button);
- linkMSInjectionSample();
- linkBiologicalSample();
- }
-
- private void linkMSInjectionSample()
- {
- registerListenerAndLinkGenerator(RawDataSampleGridIDs.CODE,
- new ICellListenerAndLinkGenerator<Sample>()
- {
-
- @Override
- public void handle(TableModelRowWithObject<Sample> rowItem,
- boolean specialKeyPressed)
- {
- showEntityInformationHolderViewer(rowItem.getObjectOrNull(), false,
- specialKeyPressed);
- }
-
- @Override
- public String tryGetLink(Sample entity, ISerializableComparable value)
- {
- return LinkExtractor.tryExtract(entity);
- }
-
- });
- }
-
- private void linkBiologicalSample()
- {
- registerListenerAndLinkGenerator(RawDataSampleGridIDs.PARENT,
- new ICellListenerAndLinkGenerator<Sample>()
- {
-
- @Override
- public void handle(TableModelRowWithObject<Sample> rowItem,
- boolean specialKeyPressed)
- {
- showEntityInformationHolderViewer(rowItem.getObjectOrNull()
- .getGeneratedFrom(), false, specialKeyPressed);
- }
-
- @Override
- public String tryGetLink(Sample entity,
- ISerializableComparable comparableValue)
- {
- return LinkExtractor.tryExtract(entity.getGeneratedFrom());
- }
- });
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<Sample>> callback)
- {
- specificViewContext.getService().listRawDataSamples(resultSetConfig, callback);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- specificViewContext.getService().prepareExportRawDataSamples(exportCriteria, callback);
- }
-
- @Override
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[]
- { createOrDelete(ObjectKind.SAMPLE_TYPE), edit(ObjectKind.SAMPLE_TYPE),
- edit(ObjectKind.SAMPLE), createOrDelete(ObjectKind.SPACE),
- createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT) };
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ViewContext.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ViewContext.java
deleted file mode 100644
index 45e1ae9cd24..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ViewContext.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import com.google.gwt.core.client.GWT;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractPluginViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocatorResolverRegistry;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.Constants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * View context for technology 'proteomics'.
- *
- * @author Franz-Josef Elmer
- */
-public class ViewContext extends AbstractPluginViewContext<IPhosphoNetXClientServiceAsync>
-{
- public ViewContext(IViewContext<ICommonClientServiceAsync> commonViewContext)
- {
- super(commonViewContext);
- }
-
- @Override
- public String getTechnology()
- {
- return Constants.TECHNOLOGY_NAME;
- }
-
- @Override
- protected IPhosphoNetXClientServiceAsync createClientServiceAsync()
- {
- return GWT.create(IPhosphoNetXClientService.class);
- }
-
- @Override
- protected void initializeLocatorHandlerRegistry(ViewLocatorResolverRegistry handlerRegistry)
- {
- super.initializeLocatorHandlerRegistry(handlerRegistry);
- handlerRegistry.registerHandler(new ProteinViewLocatorResolver(this));
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/columns/.gitignore b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/columns/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/model/.gitignore b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/model/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleChoosingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
deleted file mode 100644
index b945606005c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import java.util.List;
-
-import com.extjs.gxt.ui.client.data.ModelData;
-import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Label;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.demo.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * Wizard for guiding the user to annotate an MS_INJECTION sample.
- *
- * @author Franz-Josef Elmer
- */
-public class BiologicalSampleChoosingPage extends WizardPage<MsInjectionSampleAnnotationModel>
-{
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- private BiologicalSampleGrid sampleGrid;
-
- public BiologicalSampleChoosingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- MsInjectionSampleAnnotationModel model)
- {
- super(viewContext, MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CHOOSING, model);
- this.viewContext = viewContext;
- setLeftContentByDictionary();
- }
-
- @Override
- public void init()
- {
- addToRightContent(
- new Label(
- "Please choose a biological " + viewContext.getMessage(Dict.SAMPLE).toLowerCase()
- + " as annotation of the MS_INJECTION " + viewContext.getMessage(Dict.SAMPLES).toLowerCase()
- + " selected previously:"),
- new RowData(1, -1, new Margins(10)));
-
- sampleGrid = new BiologicalSampleGrid(viewContext);
- sampleGrid.addGridSelectionChangeListener(new Listener<SelectionChangedEvent<ModelData>>()
- {
- @Override
- public void handleEvent(SelectionChangedEvent<ModelData> se)
- {
- List<ModelData> selection = se.getSelection();
- boolean enabled = selection.size() == 1;
- enableNextButton(enabled);
- }
-
- });
- addToRightContent(sampleGrid, new RowData(1, 400, new Margins(20, 10, 10, 10)));
- }
-
- @Override
- public void deactivate()
- {
- List<BaseEntityModel<TableModelRowWithObject<Sample>>> selectedItems =
- sampleGrid.getSelectedItems();
- if (selectedItems.isEmpty() == false)
- {
- model.setBiologicalSample(selectedItems.get(0).getBaseObject().getObjectOrNull());
- }
- }
-
- @Override
- public void destroy()
- {
- sampleGrid.dispose();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleCreatingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
deleted file mode 100644
index 95c8589b386..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
+++ /dev/null
@@ -1,183 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
-import com.extjs.gxt.ui.client.event.SelectionChangedListener;
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-import com.google.gwt.event.dom.client.ClickEvent;
-import com.google.gwt.event.dom.client.ClickHandler;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.SampleTypeDisplayID;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.SampleTypeModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.SpaceSelectionWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CodeFieldWithGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.sample.SampleTypeSelectionWidget;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.ClickableFormPanel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedInputWidgetDescription;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.AbstractGenericSampleRegisterEditForm;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.SamplePropertyEditor;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * Wizard for guiding the user to annotate an MS_INJECTION sample.
- *
- * @author Franz-Josef Elmer
- */
-public class BiologicalSampleCreatingPage extends WizardPage<MsInjectionSampleAnnotationModel>
-{
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- private ClickableFormPanel formPanel;
-
- private SampleTypeSelectionWidget sampleTypeSelectionWidget;
-
- private SampleType sampleType;
-
- private CodeFieldWithGenerator codeField;
-
- private SpaceSelectionWidget spaceSelectionWidget;
-
- private SamplePropertyEditor samplePropertyEditor;
-
- private ExperimentChooserFieldAdaptor experimentField;
-
- private Map<String, List<IManagedInputWidgetDescription>> inputWidgetDescriptions = Collections
- .<String, List<IManagedInputWidgetDescription>> emptyMap();
-
- public BiologicalSampleCreatingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- MsInjectionSampleAnnotationModel model)
- {
- super(viewContext, MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CREATING, model);
- this.viewContext = viewContext;
- setLeftContentByDictionary();
- }
-
- @Override
- public void init()
- {
- formPanel = new ClickableFormPanel();
- formPanel.setHeaderVisible(false);
- sampleTypeSelectionWidget = new SampleTypeSelectionWidget(viewContext, "bio-samp", true,
- SampleTypeDisplayID.SAMPLE_REGISTRATION, null)
- {
-
- @Override
- protected void filterTypes(List<SampleType> types)
- {
- for (Iterator<SampleType> iterator = types.iterator(); iterator.hasNext();)
- {
- SampleType type = iterator.next();
- if (type.getCode().startsWith("BIO") == false)
- {
- iterator.remove();
- }
- }
- }
- };
- sampleTypeSelectionWidget.addSelectionChangedListener(new SelectionChangedListener<SampleTypeModel>()
- {
-
- @Override
- public void selectionChanged(SelectionChangedEvent<SampleTypeModel> se)
- {
- SampleType sampleTypeOrNull = sampleTypeSelectionWidget.tryGetSelectedSampleType();
- if (sampleTypeOrNull != null)
- {
- onSampleTypeChanged(sampleTypeOrNull);
- }
- }
- });
- formPanel.add(sampleTypeSelectionWidget);
- addToRightContent(formPanel, new RowData(1, 600, new Margins(10)));
- }
-
- protected void onSampleTypeChanged(SampleType type)
- {
- this.sampleType = type;
- formPanel.removeAll();
- formPanel.add(sampleTypeSelectionWidget);
- codeField =
- new CodeFieldWithGenerator(viewContext, viewContext.getMessage(Dict.CODE),
- type.getGeneratedCodePrefix(), EntityKind.SAMPLE,
- type.isAutoGeneratedCode());
- boolean codeReadonly = type.isAutoGeneratedCode();
- codeField.setReadOnly(codeReadonly);
- codeField.setHideTrigger(codeReadonly);
- formPanel.add(codeField);
- List<SampleTypePropertyType> types = type.getAssignedPropertyTypes();
- spaceSelectionWidget =
- new SpaceSelectionWidget(viewContext, getId(), true, false, viewContext.getModel()
- .getSessionContext().getUser().getHomeGroupCode());
- FieldUtil.markAsMandatory(spaceSelectionWidget);
- formPanel.add(spaceSelectionWidget);
- String label = viewContext.getMessage(Dict.EXPERIMENT);
- experimentField = ExperimentChooserField.create(label, false, null,
- viewContext.getCommonViewContext());
- formPanel.add(experimentField.getChooserField());
-
- samplePropertyEditor =
- new SamplePropertyEditor("bio-s", inputWidgetDescriptions,
- viewContext.getCommonViewContext());
- samplePropertyEditor.initWithoutProperties(types);
- samplePropertyEditor.addPropertyFieldsWithFieldsetToPanel(formPanel);
- formPanel.layout();
- formPanel.addClickListener(new ClickHandler()
- {
- @Override
- public void onClick(ClickEvent event)
- {
- enableNextButton(formPanel.isValid());
- }
- });
- }
-
- @Override
- public void deactivate()
- {
- String identifier =
- AbstractGenericSampleRegisterEditForm.createSampleIdentifier(spaceSelectionWidget,
- codeField);
- String experimentIdentifierOrNull = experimentField.getChooserField().getValue();
- List<IEntityProperty> properties = samplePropertyEditor.extractProperties();
- model.defineBiologicalSample(sampleType, identifier, experimentIdentifierOrNull, properties);
- }
-
- @Override
- public void destroy()
- {
- spaceSelectionWidget.dispose();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleGrid.java
deleted file mode 100644
index 707918e0db2..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/BiologicalSampleGrid.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.BrowserGridPagingToolBar.PagingToolBarButtonKind;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.PhosphoNetXDisplayTypeIDGenerator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.BiologicalSampleGridColumnIDs;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class BiologicalSampleGrid extends TypedTableGrid<Sample>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX + "biological_sample";
-
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- public BiologicalSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- PhosphoNetXDisplayTypeIDGenerator.BIOLOGICAL_SAMPLE_BROWSER_GRID);
- specificViewContext = viewContext;
- removeButtons(PagingToolBarButtonKind.CONFIG, PagingToolBarButtonKind.EXPORT,
- PagingToolBarButtonKind.FILTERS);
- showFiltersBar();
- setBorders(true);
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<Sample>> callback)
- {
- specificViewContext.getService().listBiologicalSamples(resultSetConfig, callback);
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList(BiologicalSampleGridColumnIDs.IDENTIFIER,
- BiologicalSampleGridColumnIDs.REGISTRATION_DATE);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- }
-
- public void dispose()
- {
- asDisposableWithoutToolbar().dispose();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java
deleted file mode 100644
index aa545172f04..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardState;
-
-/**
- * States of wizard for annotating MS_INJECTION samples.
- *
- * @author Franz-Josef Elmer
- */
-public enum MsInjectionAnnotationWizardState implements IWizardState
-{
- MS_INJECTION_SAMPLE_CHOOSING, CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CHOOSING, BIOLOGICAL_SAMPLE_CREATING;
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
deleted file mode 100644
index 8c9f7d2e410..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CHOOSING;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CREATING;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.MsInjectionAnnotationWizardState.CHOOSE_OR_CREATE_QUESTION;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.MsInjectionAnnotationWizardState.MS_INJECTION_SAMPLE_CHOOSING;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardDataModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardState;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardWorkflowModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class MsInjectionSampleAnnotationModel implements IWizardDataModel
-{
- private final IViewContext<IPhosphoNetXClientServiceAsync> context;
-
- private final WizardWorkflowModel workflowModel;
-
- private List<Sample> msInjectionSamples = new ArrayList<Sample>();
-
- private boolean chooseBiologicalSampleFlag;
-
- private Sample biologicalSample;
-
- private NewSample newBiologicalSample;
-
- public MsInjectionSampleAnnotationModel(IViewContext<IPhosphoNetXClientServiceAsync> context)
- {
- this.context = context;
- workflowModel = new WizardWorkflowModel(this);
- workflowModel.addTransition(MS_INJECTION_SAMPLE_CHOOSING, CHOOSE_OR_CREATE_QUESTION);
- workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CHOOSING);
- workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CREATING);
- }
-
- @Override
- public WizardWorkflowModel getWorkflow()
- {
- return workflowModel;
- }
-
- @Override
- public IWizardState determineNextState(IWizardState currentState)
- {
- return chooseBiologicalSampleFlag ? BIOLOGICAL_SAMPLE_CHOOSING : BIOLOGICAL_SAMPLE_CREATING;
- }
-
- public void setSelectedMsInjectionSample(List<Sample> samples)
- {
- msInjectionSamples = samples;
- }
-
- public List<Sample> getMsInjectionSamples()
- {
- return msInjectionSamples;
- }
-
- public void setChooseBiologicalSampleFlag(boolean flag)
- {
- chooseBiologicalSampleFlag = flag;
- }
-
- public void setBiologicalSample(Sample biologicalSample)
- {
- this.biologicalSample = biologicalSample;
- }
-
- public void defineBiologicalSample(SampleType sampleType, String identifier,
- String experimentIdentifierOrNull, List<IEntityProperty> properties)
- {
- newBiologicalSample = NewSample.createWithParents(identifier, sampleType, null, null);
- newBiologicalSample.setProperties(properties.toArray(IEntityProperty.EMPTY_ARRAY));
- newBiologicalSample.setExperimentIdentifier(experimentIdentifierOrNull);
- }
-
- @Override
- public String finish()
- {
- VoidAsyncCallback<Void> callback = new VoidAsyncCallback<Void>(context);
- if (chooseBiologicalSampleFlag)
- {
- context.getService().linkSamples(biologicalSample, msInjectionSamples, callback);
- } else
- {
- context.getService().createAndLinkSamples(newBiologicalSample, msInjectionSamples, callback);
- }
- return msInjectionSamples.size() + " MS_INJECTION " + context.getMessage(Dict.SAMPLES).toLowerCase()
- + " have been annotated.";
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
deleted file mode 100644
index 42b6377eb3e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.Wizard;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * Wizard for annotation MS_INJECTION samples.
- *
- * @author Franz-Josef Elmer
- */
-public class MsInjectionSampleAnnotationWizard extends Wizard<MsInjectionSampleAnnotationModel>
-{
- public MsInjectionSampleAnnotationWizard(IViewContext<IPhosphoNetXClientServiceAsync> context)
- {
- super(new MsInjectionSampleAnnotationModel(context));
- MsInjectionSampleAnnotationModel wizardDataModel = getWizardDataModel();
- register(new MsInjectionSampleChoosingPage(context, wizardDataModel));
- register(new QuestionPage(context, wizardDataModel));
- register(new BiologicalSampleChoosingPage(context, wizardDataModel));
- register(new BiologicalSampleCreatingPage(context, wizardDataModel));
- start();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
deleted file mode 100644
index 8499af64677..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.extjs.gxt.ui.client.data.ModelData;
-import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Label;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-
-/**
- * Wizard for guiding the user to annotate an MS_INJECTION sample.
- *
- * @author Franz-Josef Elmer
- */
-public class MsInjectionSampleChoosingPage extends WizardPage<MsInjectionSampleAnnotationModel>
-{
- private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
-
- private ParentlessMsInjectionSampleGrid sampleGrid;
-
- public MsInjectionSampleChoosingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- MsInjectionSampleAnnotationModel model)
- {
- super(viewContext, MsInjectionAnnotationWizardState.MS_INJECTION_SAMPLE_CHOOSING, model);
- this.viewContext = viewContext;
- setLeftContentByDictionary();
- }
-
- @Override
- public void init()
- {
- addToRightContent(new Label(
- "Please choose one or more MS_INJECTION " + viewContext.getMessage(Dict.SAMPLES).toLowerCase()
- + " to be annotated:"), new RowData(1,
- -1, new Margins(10)));
-
- sampleGrid = new ParentlessMsInjectionSampleGrid(viewContext);
- sampleGrid.addGridSelectionChangeListener(new Listener<SelectionChangedEvent<ModelData>>()
- {
- @Override
- public void handleEvent(SelectionChangedEvent<ModelData> se)
- {
- List<ModelData> selection = se.getSelection();
- boolean enabled = selection.size() > 0;
- enableNextButton(enabled);
- }
-
- });
- addToRightContent(sampleGrid, new RowData(1, 400, new Margins(20, 10, 10, 10)));
- }
-
- @Override
- public void deactivate()
- {
- List<BaseEntityModel<TableModelRowWithObject<Sample>>> selectedItems =
- sampleGrid.getSelectedItems();
- ArrayList<Sample> samples = new ArrayList<Sample>();
- for (BaseEntityModel<TableModelRowWithObject<Sample>> item : selectedItems)
- {
- samples.add(item.getBaseObject().getObjectOrNull());
- }
- model.setSelectedMsInjectionSample(samples);
- }
-
- @Override
- public void destroy()
- {
- sampleGrid.dispose();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java
deleted file mode 100644
index 9f61b5e643c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.BrowserGridPagingToolBar.PagingToolBarButtonKind;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericConstants;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.PhosphoNetXDisplayTypeIDGenerator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ParentlessMsInjectionSampleGrid extends TypedTableGrid<Sample>
-{
- private static final String PREFIX = GenericConstants.ID_PREFIX
- + "parentless_ms_injection_sample";
-
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
-
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- public ParentlessMsInjectionSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
- {
- super(viewContext.getCommonViewContext(), BROWSER_ID, true,
- PhosphoNetXDisplayTypeIDGenerator.PARENT_LESS_MS_INJECTION_SAMPLE_BROWSER_GRID);
- specificViewContext = viewContext;
- removeButtons(PagingToolBarButtonKind.CONFIG, PagingToolBarButtonKind.EXPORT,
- PagingToolBarButtonKind.FILTERS);
- allowMultipleSelection();
- showFiltersBar();
- setBorders(true);
- }
-
- @Override
- protected void listTableRows(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
- AbstractAsyncCallback<TypedTableResultSet<Sample>> callback)
- {
- specificViewContext.getService()
- .listParentlessMsInjectionSamples(resultSetConfig, callback);
- }
-
- @Override
- protected List<String> getColumnIdsOfFilters()
- {
- return Arrays.asList(ParentlessMsInjectionSampleGridColumnIDs.IDENTIFIER,
- ParentlessMsInjectionSampleGridColumnIDs.REGISTRATION_DATE);
- }
-
- @Override
- protected void prepareExportEntities(
- TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
- AbstractAsyncCallback<String> callback)
- {
- }
-
- public void dispose()
- {
- asDisposableWithoutToolbar().dispose();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/QuestionPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/QuestionPage.java
deleted file mode 100644
index cd739d5702b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/wizard/QuestionPage.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard;
-
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Label;
-import com.extjs.gxt.ui.client.widget.form.Radio;
-import com.extjs.gxt.ui.client.widget.form.RadioGroup;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.query.client.web.client.application.Dict;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class QuestionPage extends WizardPage<MsInjectionSampleAnnotationModel>
-{
-
- private Radio chooseSampleRadioButton;
-
- private RadioGroup radioGroup;
-
- public QuestionPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- MsInjectionSampleAnnotationModel model)
- {
- super(viewContext, MsInjectionAnnotationWizardState.CHOOSE_OR_CREATE_QUESTION, model);
- setLeftContentByDictionary();
- addToRightContent(new Label("How do you want to annotate your "
- + viewContext.getMessage(Dict.SAMPLES).toLowerCase() + "?"), new RowData(1, -1, new Margins(10)));
- radioGroup = new RadioGroup();
- radioGroup.setFieldLabel("choose");
- chooseSampleRadioButton = new Radio();
- String sampleText = viewContext.getMessage(Dict.SAMPLE).toLowerCase();
- chooseSampleRadioButton.setBoxLabel("I want to choose an existing biological " + sampleText + ".");
- chooseSampleRadioButton.setValue(true);
- radioGroup.add(chooseSampleRadioButton);
- Radio createSampleRadioButton = new Radio();
- createSampleRadioButton.setBoxLabel("I want to create a new biological " + sampleText + ".");
- radioGroup.add(createSampleRadioButton);
- addToRightContent(radioGroup, new RowData(1, -1, new Margins(10)));
- enableNextButton(true);
- }
-
- @Override
- public void deactivate()
- {
- model.setChooseBiologicalSampleFlag(radioGroup.getValue().equals(chooseSampleRadioButton));
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/BiologicalSampleGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/BiologicalSampleGridColumnIDs.java
deleted file mode 100644
index cce385f54cc..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/BiologicalSampleGridColumnIDs.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.ParentlessMsInjectionSampleGrid;
-
-/**
- * IDs of columns of {@link ParentlessMsInjectionSampleGrid}.
- *
- * @author Franz-Josef Elmer
- */
-public class BiologicalSampleGridColumnIDs
-{
- public static final String IDENTIFIER = "IDENTIFIER";
-
- public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/DataSetProteinGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/DataSetProteinGridColumnIDs.java
deleted file mode 100644
index dd979dab263..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/DataSetProteinGridColumnIDs.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-/**
- * Column IDs for data set protein grid.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetProteinGridColumnIDs
-{
- public static final String DATA_SET_PERM_ID = "DATA_SET_PERM_ID";
-
- public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
-
- public static final String PEPTIDE_COUNT = "PEPTIDE_COUNT";
-
- public static final String FDR = "FDR";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java
deleted file mode 100644
index 916a69fab85..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ListProteinByExperimentAndReferenceCriteria extends
- DefaultResultSetConfig<String, TableModelRowWithObject<DataSetProtein>> implements IsSerializable
-{
- private TechId experimentID;
-
- private TechId proteinReferenceID;
-
- public final TechId getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(TechId experimentID)
- {
- this.experimentID = experimentID;
- }
-
- public final TechId getProteinReferenceID()
- {
- return proteinReferenceID;
- }
-
- public final void setProteinReferenceID(TechId proteinReferenceID)
- {
- this.proteinReferenceID = proteinReferenceID;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentCriteria.java
deleted file mode 100644
index ff65dae794d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinByExperimentCriteria.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ListProteinByExperimentCriteria extends
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinInfo>> implements
- IsSerializable
-{
- private TechId experimentID;
-
- private double falseDiscoveryRate;
-
- private AggregateFunction aggregateFunction;
-
- private String treatmentTypeCode;
-
- private boolean aggregateOriginal;
-
- public final TechId getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(TechId experimentID)
- {
- this.experimentID = experimentID;
- }
-
- public final double getFalseDiscoveryRate()
- {
- return falseDiscoveryRate;
- }
-
- public final void setFalseDiscoveryRate(double falseDiscoveryRate)
- {
- this.falseDiscoveryRate = falseDiscoveryRate;
- }
-
- public final AggregateFunction getAggregateFunction()
- {
- return aggregateFunction;
- }
-
- public void setAggregateFunction(AggregateFunction aggregateFunction)
- {
- this.aggregateFunction = aggregateFunction;
- }
-
- public final String getTreatmentTypeCode()
- {
- return treatmentTypeCode;
- }
-
- public final void setTreatmentTypeCode(String treatmentTypeCode)
- {
- this.treatmentTypeCode = treatmentTypeCode;
- }
-
- public final boolean isAggregateOriginal()
- {
- return aggregateOriginal;
- }
-
- public final void setAggregateOriginal(boolean aggregateOriginal)
- {
- this.aggregateOriginal = aggregateOriginal;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java
deleted file mode 100644
index 8569e6efc3c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-
-/**
- * Criteria for listing {@link ProteinSequence} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class ListProteinSequenceCriteria extends
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinSequence>> implements
- IsSerializable
-{
- private TechId proteinReferenceID;
-
- private TechId experimentID;
-
- public final TechId getProteinReferenceID()
- {
- return proteinReferenceID;
- }
-
- public final void setProteinReferenceID(TechId proteinReferenceID)
- {
- this.proteinReferenceID = proteinReferenceID;
- }
-
- public void setExperimentID(TechId experimentID)
- {
- this.experimentID = experimentID;
- }
-
- public TechId getExperimentID()
- {
- return experimentID;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java
deleted file mode 100644
index 3944a71acfb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ListProteinSummaryByExperimentCriteria extends
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinSummary>> implements
- IsSerializable
-{
- private TechId experimentID;
-
- public final TechId getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(TechId experimentID)
- {
- this.experimentID = experimentID;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java
deleted file mode 100644
index f191657ee18..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ListSampleAbundanceByProteinCriteria extends
- DefaultResultSetConfig<String, TableModelRowWithObject<ProteinRelatedSample>> implements IsSerializable
-{
- private TechId experimentID;
-
- private TechId proteinReferenceID;
-
- public final TechId getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(Long experimentID)
- {
- this.experimentID = experimentID == null ? null : new TechId(experimentID);
- }
-
- public final TechId getProteinReferenceID()
- {
- return proteinReferenceID;
- }
-
- public final void setProteinReferenceID(TechId proteinReferenceID)
- {
- this.proteinReferenceID = proteinReferenceID;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java
deleted file mode 100644
index 5655e9f62f2..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.wizard.ParentlessMsInjectionSampleGrid;
-
-/**
- * IDs of columns of {@link ParentlessMsInjectionSampleGrid}.
- *
- * @author Franz-Josef Elmer
- */
-public class ParentlessMsInjectionSampleGridColumnIDs
-{
- public static final String IDENTIFIER = "IDENTIFIER";
-
- public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinBrowserColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinBrowserColumnIDs.java
deleted file mode 100644
index faadf66e0ec..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinBrowserColumnIDs.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinBrowserColumnIDs
-{
- public static final String ACCESSION_NUMBER = "ACCESSION_NUMBER";
-
- public static final String PROTEIN_DESCRIPTION = "PROTEIN_DESCRIPTION";
-
- public static final String COVERAGE = "COVERAGE";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinRelatedSampleGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinRelatedSampleGridColumnIDs.java
deleted file mode 100644
index 34c9cff25fa..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinRelatedSampleGridColumnIDs.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinRelatedSampleGridColumnIDs
-{
- public static final String SAMPLE_IDENTIFIER = "SAMPLE_IDENTIFIER";
-
- public static final String SAMPLE_TYPE = "SAMPLE_TYPE";
-
- public static final String ABUNDANCE = "ABUNDANCE";
-
- public static final String MODIFIED_AMINO_ACID = "MODIFIED_AMINO_ACID";
-
- public static final String MODIFICATION_POSITION = "MODIFICATION_POSITION";
-
- public static final String MODIFICATION_MASS = "MODIFICATION_MASS";
-
- public static final String MODIFICATION_FRACTION = "MODIFICATION_FRACTION";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSequenceGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSequenceGridColumnIDs.java
deleted file mode 100644
index 23a88159c15..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSequenceGridColumnIDs.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.ProteinSequenceGrid;
-
-/**
- * Column IDs of {@link ProteinSequenceGrid}.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinSequenceGridColumnIDs
-{
- public static final String SEQUENCE_SHORT_NAME = "SEQUENCE_SHORT_NAME";
-
- public static final String DATABASE_NAME_AND_VERSION = "DATABASE_NAME_AND_VERSION";
-
- public static final String SEQUENCE = "SEQUENCE";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSummaryGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSummaryGridColumnIDs.java
deleted file mode 100644
index 2f94f198755..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ProteinSummaryGridColumnIDs.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto;
-
-/**
- * Column IDs for protein summary grid.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinSummaryGridColumnIDs
-{
- public static final String FDR = "FDR";
-
- public static final String PROTEIN_COUNT = "PROTEIN_COUNT";
-
- public static final String PEPTIDE_COUNT = "PEPTIDE_COUNT";
-
- public static final String DECOY_PROTEIN_COUNT = "DECOY_PROTEIN_COUNT";
-
- public static final String DECOY_PEPTIDE_COUNT = "DECOY_PEPTIDE_COUNT";
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/index.html b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/index.html
deleted file mode 100644
index 0298c05ee9d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/index.html
+++ /dev/null
@@ -1,61 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
-<title>openBIS - Biology Information System for Proteomics</title>
-
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<!-- force IE to go to document mode IE8 standards (and avoid the dreadful quirks-mode) -->
-<meta http-equiv="X-UA-Compatible" content="IE=edge" >
-
-<link rel="shortcut icon" href="images/favicon.ico" />
-<link rel="icon" type="image/png" href="images/favicon.png" />
-<link rel="stylesheet" type="text/css" href="resources/css/gxt-all.css" />
-<!-- New Grey / White Style -->
-<link rel="stylesheet" type="text/css" href="resources/css/gxt-gray.css" />
-<link rel="stylesheet" type="text/css" href="resources/css/debug-panel.css" />
-
-<!--
-// This script loads your compiled module. If you add any GWT meta tags, they must be added before this line.
--->
-<script language="javascript"
- src="ch.systemsx.cisd.openbis.plugin.proteomics.OpenBIS.nocache.js"></script>
-
-<!-- This snippet should be automatically included in all the HTML that wishes to use the debug panel. -->
-<script type="text/javascript" language="javascript">
- var stats = window.__stats = [];
- window.__gwtStatsEvent = function(evt) {
- stats[stats.length] = evt;
- var listener = window.__stats_listener;
- listener && listener(evt);
- return true;
- }
-</script>
-
-</head>
-<!--
-// The body can have arbitrary html, or you can leave the body empty if you want to create a completely dynamic ui.
--->
-<body>
-<!-- Required by IE (GWT 1.7) -->
-<iframe id="__gwt_historyFrame" style="width: 0; height: 0; border: 0"></iframe>
-<div id="openbis_login_div" style="visibility: hidden">
-<form id="openbis_login_form" method="post" action="javascript:;">
-<table cellspacing="5">
- <tbody>
- <tr style="padding-bottom: 5px">
- <td><span>User:</span></td>
- <td><input type="text" id="openbis_login_username"
- name="openbis-username" style="width: 150px;"></td>
- </tr>
- <tr style="padding-bottom: 5px">
- <td><span>Password:</span></td>
- <td><input type="password" id="openbis_login_password"
- name="openbis-password" style="width: 150px;"></td>
- </tr>
- </tbody>
-</table>
-<input style="margin-left: 200px" type="submit" id="openbis_login_submit" value="Login">
-</form>
-</div>
-</body>
-</html>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/proteomics-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/proteomics-dictionary.js
deleted file mode 100644
index d530628ec0e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/public/proteomics-dictionary.js
+++ /dev/null
@@ -1,101 +0,0 @@
-// Proteomics dictionary
-var proteomics = {
- ALL_PROTEINS_OF_AN_EXPERIMENT_menu_item: "All Proteins of an Experiment",
- ALL_PROTEINS_OF_AN_EXPERIMENT_tab_label: "Proteins of an Experiment",
- selected_experiment_label: "Experiment",
- false_discovery_rate_filter_label: "False Discovery Rate",
- aggregate_function_label: "Aggregate Function",
- aggregate_on_treatment_type_label: "Aggregate on",
- aggregate_original_label: "Aggregate original",
-
- // Experiment View
- data_set_processing_section_title: "Available Data Set Processing Tasks",
-
- // Protein grid
- accession_number: "Accession Number",
- protein_description: "Protein",
- coverage: "Protein Coverage (in %)",
- false_discovery_rate: "FDR",
- fdr_combo_info: "<html><div style='width:250px'>This False Discovery Rate determines which ProteinProphet probability " +
- "cut-off is applied to the combined ProteinProphet output. Only proteins above this " +
- "probability are displayed in the table.<br/><br/>" +
- "Note, that the spectral counts are not affected by this threshold and values for individual " +
- "samples stay unchanged as long as the protein is displayed at all.</div></html>",
-
- // Protein in experiment viewer
- loading_protein_details_waiting_message: "Loading details for protein {0}",
- proteins_section: "Proteins",
- protein_in_experiment_tab_label: "{0} in {1}",
- experiment_label: "Experiment",
- sequence_short_name: "Sequence Reference",
- protein_browser: "Proteins",
- protein_summary: "Protein/Peptide Counts",
- database_name_and_version: "Database",
- primary_protein: "Primary Protein and Peptides",
- indistinguishable_proteins: "Indistinguishable Proteins",
- sequence: "Amino Acid Sequence",
- sequences: "Amino Acid Sequences",
- data_set_proteins: "Data Sets",
- data_set_perm_id: "Data Set",
- protein_count: "Proteins (no decoy)",
- peptide_count: "Peptides (no decoy)",
- decoy_protein_count: "Proteins (decoy)",
- decoy_peptide_count: "Peptides (decoy)",
- peptides: "Peptides ({0})",
- sequence_name: "Sequence Reference",
- false_discovery_rate_column: "FDR (Protein Prophet)",
- protein_probability: "Probability (Protein Prophet)",
- button_delete_protein: "Delete Protein",
-
- // ProteinRelatedSampleGrid
- openbis_protein_related_sample_grid_main_SAMPLE_IDENTIFIER: "Identifier",
- openbis_protein_related_sample_grid_main_SAMPLE_TYPE: "Sample Type",
- openbis_protein_related_sample_grid_main_ABUNDANCE: "Abundance",
- openbis_protein_related_sample_grid_main_MODIFIED_AMINO_ACID: "Modified Amino Acid",
- openbis_protein_related_sample_grid_main_MODIFICATION_POSITION: "Modification Position",
- openbis_protein_related_sample_grid_main_MODIFICATION_MASS: "Modification Mass",
- openbis_protein_related_sample_grid_main_MODIFICATION_FRACTION: "Modification Fraction",
-
- // MS_INJECTION annotation wizard
-
- MS_INJECTION_SAMPLE_CHOOSING_left_content: "MS data are added to openBIS in an automated process. "
- + "The corresponding data sets are associated with samples of type <tt>MS_INJECTION</tt>."
- + "<p>Before MS data of such samples can be processed in a protein identification pipeline "
- + "they have to be <b>annotated</b>. In the terminology of openBIS this means: "
- + "An <tt>MS_INJECTION</tt> sample is linked to a biological sample where "
- + "the biological sample is the parent and the <tt>MS_INJECTION</tt> sample is the child. "
- + "The biological sample has all annotations (called properties in openBIS). "
- + "They define the scientific context of proteins found and have to be created "
- + "by the user before the MS_INJECTION sample can be linked to it. "
- + "<p>This wizard helps you adding these important annotations to openBIS.",
- openbis_parentless_ms_injection_sample_main_IDENTIFIER: "MS_INJECTION Sample",
- openbis_parentless_ms_injection_sample_main_REGISTRATION_DATE: "Registration Date",
- CHOOSE_OR_CREATE_QUESTION_left_content: "Annotating the <tt>MS_INJECTION</tt> samples you have chosen "
- + "means to link them to a <b>biological sample</b>. "
- + "You can choose an existing biological sample or you can create a new one.",
- BIOLOGICAL_SAMPLE_CHOOSING_left_content: "Annotating <tt>MS_INJECTION</tt> sample by choosing one biological sample means "
- + "that all properties of the biological sample is also for the <tt>MS_INJECTION</tt> to be annotated.",
- openbis_biological_sample_main_IDENTIFIER: "Biological Sample",
- openbis_biological_sample_main_REGISTRATION_DATE: "Registration Date",
- BIOLOGICAL_SAMPLE_CREATING_left_content: "Annotating <tt>MS_INJECTION</tt> sample by creating a new biological sample means "
- + "mainly specifying properties of a freshly created biological sample in openBIS.",
-
-
- // RawDataSample Browser
-
- ANNOTATE_MS_INJECTION_SAMPLES_menu_item: "Annotate MS INJECTION Samples",
- ANNOTATE_MS_INJECTION_SAMPLES_tab_label: "MS INJECTION Samples Annotation Wizard",
- ALL_RAW_DATA_SAMPLES_menu_item: "All MS INJECTION Samples",
- ALL_RAW_DATA_SAMPLES_tab_label: "MS INJECTION Samples and Related Biological Samples",
- openbis_raw_data_sample_browser_CODE: "MS INJECTION Sample",
- openbis_raw_data_sample_browser_REGISTRATION_DATE: "Registration Date",
- openbis_raw_data_sample_browser_PARENT: "Biological Sample",
- openbis_raw_data_sample_browser_EXPERIMENT: "Biological Experiment",
- copy_data_sets_button_label: "Process Data Sets",
- copy_data_sets_title: "Process Data Sets",
- copy_data_sets_message: "Please, enter the data set type of the data sets of the samples {1} to be processed by '{0}'.",
- copy_data_sets_data_set_type_field: "Data Set Type",
-
- // LAST LINE: KEEP IT AT THE END
- lastline: "" // we need a line without a comma
-};
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java
deleted file mode 100644
index 645c5dc68d3..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java
+++ /dev/null
@@ -1,405 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server;
-
-import static ch.systemsx.cisd.common.utilities.SystemTimeProvider.SYSTEM_TIME_PROVIDER;
-
-import java.io.Serializable;
-import java.lang.reflect.Method;
-import java.util.Collections;
-import java.util.List;
-
-import javax.annotation.Resource;
-
-import org.aopalliance.intercept.MethodInterceptor;
-import org.aopalliance.intercept.MethodInvocation;
-import org.apache.commons.lang3.time.StopWatch;
-import org.springframework.aop.framework.ProxyFactory;
-import org.springframework.aop.support.DefaultPointcutAdvisor;
-import org.springframework.aop.support.annotation.AnnotationMatchingPointcut;
-import org.springframework.beans.factory.InitializingBean;
-import org.springframework.stereotype.Component;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.filesystem.IFreeSpaceProvider;
-import ch.systemsx.cisd.common.filesystem.SimpleFreeSpaceProvider;
-import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
-import ch.systemsx.cisd.common.utilities.ITimeProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.DataProviderAdapter;
-import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.IServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.WebClientConfiguration;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.util.CacheManager;
-import ch.systemsx.cisd.openbis.generic.shared.util.ICacheManager;
-import ch.systemsx.cisd.openbis.generic.shared.util.Key;
-import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.BuildAndEnvironmentInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.Constants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSequenceCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.BiologicalSampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.DataSetProteinProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ParentlessMsInjectionSampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinRelatedSampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinSequenceProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinSummaryProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.CacheData;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Component(value = ResourceNames.PROTEOMICS_PLUGIN_SERVICE)
-public class PhosphoNetXClientService extends AbstractClientService implements
- IPhosphoNetXClientService, InitializingBean
-{
- private static final String CACHE_VERSION = Integer.toString(ServiceVersionHolder.VERSION);
-
- @Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
- private ICommonServer commonServer;
-
- @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
- private IGenericServer genericServer;
-
- @Resource(name = ResourceNames.PROTEOMICS_PLUGIN_SERVER)
- @Private
- IPhosphoNetXServer server;
-
- @Resource(name = ResourceNames.PROTEOMICS_RAW_DATA_SERVICE_WEB)
- private IProteomicsDataServiceInternal proteomicsDataService;
-
- @Private
- ITimeProvider timeProvider = SYSTEM_TIME_PROVIDER;
-
- public PhosphoNetXClientService()
- {
- super();
- }
-
- public PhosphoNetXClientService(IRequestContextProvider requestContextProvider)
- {
- super(requestContextProvider);
- }
-
- @Override
- public void afterPropertiesSet() throws Exception
- {
- WebClientConfiguration webClientConfiguration = getWebClientConfiguration();
- IFreeSpaceProvider freeSpaceProvider = new SimpleFreeSpaceProvider();
- final ICacheManager cacheManager =
- new CacheManager(webClientConfiguration, Constants.TECHNOLOGY_NAME,
- timeProvider, freeSpaceProvider, CACHE_VERSION);
- ProxyFactory proxyFactory = new ProxyFactory(server);
- proxyFactory.addInterface(IPhosphoNetXServer.class);
- AnnotationMatchingPointcut pointcut =
- AnnotationMatchingPointcut.forMethodAnnotation(CacheData.class);
- proxyFactory.addAdvisor(new DefaultPointcutAdvisor(pointcut, new MethodInterceptor()
- {
- @Override
- public Object invoke(MethodInvocation methodInvocation) throws Throwable
- {
- // assuming first argument is sessionToken which shouldn't be a part of the key
- Object[] arguments = methodInvocation.getArguments();
- Object[] keyArguments = new Serializable[arguments.length];
- Method method = methodInvocation.getMethod();
- keyArguments[0] = method.getName();
- for (int i = 1; i < keyArguments.length; i++)
- {
- keyArguments[i] = arguments[i];
- }
- Key key = new Key(keyArguments);
- Object data = cacheManager.tryToGetData(key);
- if (data == null)
- {
- Object serverObject = methodInvocation.getThis();
- data = method.invoke(serverObject, arguments);
- cacheManager.storeData(key, data);
- }
- return data;
- }
- }));
- server = (IPhosphoNetXServer) proxyFactory.getProxy();
- }
-
- @Override
- protected IServer getServer()
- {
- return server;
- }
-
- @Override
- protected String getVersion()
- {
- return BuildAndEnvironmentInfo.INSTANCE.getFullVersion();
- }
-
- @Override
- public TypedTableResultSet<Sample> listParentlessMsInjectionSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- String sessionToken = getSessionToken();
- return listEntities(new ParentlessMsInjectionSampleProvider(commonServer, sessionToken),
- criteria);
- }
-
- @Override
- public TypedTableResultSet<Sample> listBiologicalSamples(
- DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- String sessionToken = getSessionToken();
- return listEntities(new BiologicalSampleProvider(commonServer, sessionToken), criteria);
- }
-
- @Override
- public void linkSamples(Sample parentSample, List<Sample> childSamples)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- String sessionToken = getSessionToken();
- linkSamples(sessionToken, parentSample.getIdentifier(), childSamples);
- }
-
- @Override
- public void createAndLinkSamples(NewSample newBiologicalSample, List<Sample> msInjectionSamples)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- String sessionToken = getSessionToken();
- List<NewAttachment> noAttachments = Collections.<NewAttachment> emptyList();
- genericServer.registerSample(sessionToken, newBiologicalSample, noAttachments);
- linkSamples(sessionToken, newBiologicalSample.getIdentifier(), msInjectionSamples);
- }
-
- private void linkSamples(String sessionToken, String identifier, List<Sample> childSamples)
- {
- String[] parents = new String[]
- { identifier };
- for (Sample childSample : childSamples)
- {
- SampleIdentifier childSampleIdentifier =
- SampleIdentifierFactory.parse(childSample.getIdentifier());
- SampleUpdatesDTO update =
- new SampleUpdatesDTO(new TechId(childSample),
- Collections.<IEntityProperty> emptyList(), null, null,
- Collections.<NewAttachment> emptyList(),
- childSample.getVersion(), childSampleIdentifier, null, parents);
- update.setUpdateExperimentLink(false);
- genericServer.updateSample(sessionToken, update);
- }
- }
-
- @Override
- public Vocabulary getTreatmentTypeVocabulary()
- {
- final String sessionToken = getSessionToken();
- return server.getTreatmentTypeVocabulary(sessionToken);
- }
-
- @Override
- public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
- TechId experimentID, String treatmentTypeOrNull)
- {
- StopWatch stopWatch = new StopWatch();
- stopWatch.start();
- try
- {
- final String sessionToken = getSessionToken();
- return server.getAbundanceColumnDefinitionsForProteinByExperiment(sessionToken,
- experimentID, treatmentTypeOrNull);
- } finally
- {
- operationLog.info(stopWatch.getTime()
- + " msec for getAbundanceColumnDefinitionsForProteinByExperiment");
- }
- }
-
- @Override
- public TypedTableResultSet<ProteinInfo> listProteinsByExperiment(
- ListProteinByExperimentCriteria criteria)
- {
- StopWatch stopWatch = new StopWatch();
- stopWatch.start();
- try
- {
- final String sessionToken = getSessionToken();
- TechId experimentID = criteria.getExperimentID();
- double fdr = criteria.getFalseDiscoveryRate();
- AggregateFunction aggregateFunction = criteria.getAggregateFunction();
- String treatmentTypeCode = criteria.getTreatmentTypeCode();
- boolean aggregateOnOriginal = criteria.isAggregateOriginal();
- return listEntities(new ProteinProvider(server, sessionToken, experimentID, fdr,
- aggregateFunction, treatmentTypeCode, aggregateOnOriginal), criteria);
- } finally
- {
- operationLog.info(stopWatch.getTime() + " msec for listProteinsByExperiment");
- }
- }
-
- @Override
- public String prepareExportProteins(TableExportCriteria<TableModelRowWithObject<ProteinInfo>> exportCriteria)
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- public TypedTableResultSet<ProteinSummary> listProteinSummariesByExperiment(
- ListProteinSummaryByExperimentCriteria criteria)
- {
- StopWatch stopWatch = new StopWatch();
- stopWatch.start();
- try
- {
- final String sessionToken = getSessionToken();
- return listEntities(
- new ProteinSummaryProvider(server, sessionToken, criteria.getExperimentID()),
- criteria);
- } finally
- {
- operationLog.info(stopWatch.getTime() + " msec for listProteinSummariesByExperiment");
- }
- }
-
- @Override
- public String prepareExportProteinSummary(
- TableExportCriteria<TableModelRowWithObject<ProteinSummary>> exportCriteria)
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
- {
- final String sessionToken = getSessionToken();
- return server.getProteinByExperiment(sessionToken, experimentID, proteinReferenceID);
- }
-
- @Override
- public TypedTableResultSet<ProteinSequence> listSequencesByProteinReference(
- ListProteinSequenceCriteria criteria)
- {
- final String sessionToken = getSessionToken();
- return listEntities(
- new ProteinSequenceProvider(server, sessionToken, criteria.getExperimentID(), criteria.getProteinReferenceID()),
- criteria);
- }
-
- @Override
- public String prepareExportProteinSequences(
- TableExportCriteria<TableModelRowWithObject<ProteinSequence>> exportCriteria)
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- public TypedTableResultSet<DataSetProtein> listProteinsByExperimentAndReference(
- ListProteinByExperimentAndReferenceCriteria criteria)
- {
- final String sessionToken = getSessionToken();
- return listEntities(
- new DataSetProteinProvider(server, sessionToken, criteria.getExperimentID(),
- criteria.getProteinReferenceID()), criteria);
- }
-
- @Override
- public String prepareExportDataSetProteins(
- TableExportCriteria<TableModelRowWithObject<DataSetProtein>> exportCriteria)
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- public TypedTableResultSet<ProteinRelatedSample> listProteinRelatedSamplesByProtein(
- ListSampleAbundanceByProteinCriteria criteria)
- {
- final String sessionToken = getSessionToken();
- ProteinRelatedSampleProvider provider =
- new ProteinRelatedSampleProvider(server, sessionToken, criteria.getExperimentID(),
- criteria.getProteinReferenceID());
- return listEntities(provider, criteria);
- }
-
- @Override
- public String prepareExportProteinRelatedSamples(
- TableExportCriteria<TableModelRowWithObject<ProteinRelatedSample>> exportCriteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- public TypedTableResultSet<Sample> listRawDataSamples(
- IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
- {
- final String sessionToken = getSessionToken();
- RawDataSampleProvider rawDataSampleProvider =
- new RawDataSampleProvider(proteomicsDataService, sessionToken);
- DataProviderAdapter<Sample> dataProvider =
- new DataProviderAdapter<Sample>(rawDataSampleProvider);
- ResultSet<TableModelRowWithObject<Sample>> resultSet = listEntities(criteria, dataProvider);
- return new TypedTableResultSet<Sample>(resultSet);
- }
-
- @Override
- public String prepareExportRawDataSamples(
- TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria)
- {
- return prepareExportEntities(exportCriteria);
- }
-
- @Override
- @SuppressWarnings("deprecation")
- public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs,
- String dataSetType)
- {
- proteomicsDataService.processRawData(getSessionToken(), dataSetProcessingKey,
- rawDataSampleIDs, dataSetType);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceServlet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceServlet.java
deleted file mode 100644
index ef4ee6191f3..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceServlet.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server;
-
-import javax.annotation.Resource;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.springframework.stereotype.Controller;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.servlet.ModelAndView;
-
-import ch.systemsx.cisd.common.servlet.GWTRPCServiceExporter;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ResourceNames;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Controller
-public class PhosphoNetXClientServiceServlet extends GWTRPCServiceExporter
-{
- private static final long serialVersionUID = 1L;
-
- @Resource(name = ResourceNames.PROTEOMICS_PLUGIN_SERVICE)
- private IPhosphoNetXClientService service;
-
- @RequestMapping({ "/proteomics", "/openbis/proteomics" })
- public final ModelAndView handleRequestExposed(final HttpServletRequest request,
- final HttpServletResponse response) throws Exception
- {
- return super.handleRequest(request, response);
- }
-
- @Override
- protected Object getService()
- {
- return service;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProvider.java
deleted file mode 100644
index 90fe409c4b9..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProvider.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.CODE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.EXPERIMENT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.PARENT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.REGISTRATION_DATE;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-class RawDataSampleProvider extends AbstractTableModelProvider<Sample>
-{
- private final IProteomicsDataServiceInternal service;
-
- private final String sessionToken;
-
- RawDataSampleProvider(IProteomicsDataServiceInternal service, String sessionToken)
- {
- this.service = service;
- this.sessionToken = sessionToken;
- }
-
- @Override
- public TypedTableModel<Sample> createTableModel()
- {
- List<MsInjectionSample> samples = service.listRawDataSamples(sessionToken);
- TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
- builder.addColumn(CODE).withDataType(DataTypeCode.VARCHAR);
- builder.addColumn(REGISTRATION_DATE).withDataType(DataTypeCode.TIMESTAMP)
- .withDefaultWidth(190);
- builder.addColumn(PARENT).withDataType(DataTypeCode.VARCHAR);
- builder.addColumn(EXPERIMENT).withDataType(DataTypeCode.VARCHAR);
- for (MsInjectionSample msInjectionSample : samples)
- {
- Sample sample = msInjectionSample.getSample();
- builder.addRow(sample);
- builder.column(CODE).addString(sample.getCode());
- builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
- Sample parent = sample.getGeneratedFrom();
- builder.column(PARENT).addString(parent.getIdentifier());
- Experiment experiment = parent.getExperiment();
- if (experiment != null)
- {
- builder.column(EXPERIMENT).addString(experiment.getIdentifier());
- }
- builder.columnGroup("MS").addProperties("", sample.getProperties());
- builder.columnGroup("BIO_").addProperties(parent.getProperties());
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/BiologicalSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/BiologicalSampleProvider.java
deleted file mode 100644
index 8cf8b0eb5d5..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/BiologicalSampleProvider.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.BiologicalSampleGridColumnIDs.IDENTIFIER;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.BiologicalSampleGridColumnIDs.REGISTRATION_DATE;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractCommonTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriterion;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchField;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleAttributeSearchFieldKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * Provider of biological samples registered by the user. A biological sample is a sample with sample type code starting with BIO.
- *
- * @author Franz-Josef Elmer
- */
-public class BiologicalSampleProvider extends AbstractCommonTableModelProvider<Sample>
-{
- public BiologicalSampleProvider(ICommonServer commonServer, String sessionToken)
- {
- super(commonServer, sessionToken);
- }
-
- @Override
- protected TypedTableModel<Sample> createTableModel()
- {
- DetailedSearchCriteria criteria = new DetailedSearchCriteria();
- criteria.setConnection(SearchCriteriaConnection.MATCH_ALL);
- DetailedSearchCriterion typeCriterion = new DetailedSearchCriterion();
- typeCriterion.setField(DetailedSearchField
- .createAttributeField(SampleAttributeSearchFieldKind.SAMPLE_TYPE));
- typeCriterion.setValue(CommonConstants.BIOLOGICAL_SAMPLE_PREFIX + "*");
- DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
- String userName = commonServer.tryGetSession(sessionToken).getUserName();
- registratorCriterion.setField(DetailedSearchField.createRegistratorField());
- registratorCriterion.setValue(userName);
- criteria.setCriteria(Arrays.asList(typeCriterion, registratorCriterion));
- List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
- TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
- builder.addColumn(IDENTIFIER);
- builder.addColumn(REGISTRATION_DATE);
- for (Sample sample : samples)
- {
- builder.addRow(sample);
- builder.column(IDENTIFIER).addString(sample.getIdentifier());
- builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
- builder.columnGroup("PROPERTY").uneditablePropertyColumns()
- .addProperties(sample.getProperties());
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/DataSetProteinProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/DataSetProteinProvider.java
deleted file mode 100644
index 1624dc59835..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/DataSetProteinProvider.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.DataSetProteinGridColumnIDs.DATA_SET_PERM_ID;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.DataSetProteinGridColumnIDs.FDR;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.DataSetProteinGridColumnIDs.PEPTIDE_COUNT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.DataSetProteinGridColumnIDs.SEQUENCE_NAME;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-
-/**
- * Provider of {@link DataSetProtein} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetProteinProvider extends AbstractTableModelProvider<DataSetProtein>
-{
- private final IPhosphoNetXServer server;
-
- private final String sessionToken;
-
- private final TechId experimentID;
-
- private final TechId proteinReferenceID;
-
- public DataSetProteinProvider(IPhosphoNetXServer server, String sessionToken,
- TechId experimentID, TechId proteinReferenceID)
- {
- this.server = server;
- this.sessionToken = sessionToken;
- this.experimentID = experimentID;
- this.proteinReferenceID = proteinReferenceID;
- }
-
- @Override
- protected TypedTableModel<DataSetProtein> createTableModel()
- {
- List<DataSetProtein> proteins =
- server.listProteinsByExperimentAndReference(sessionToken, experimentID,
- proteinReferenceID);
- TypedTableModelBuilder<DataSetProtein> builder =
- new TypedTableModelBuilder<DataSetProtein>();
- builder.addColumn(DATA_SET_PERM_ID).withDefaultWidth(200);
- builder.addColumn(SEQUENCE_NAME).withDefaultWidth(80);
- builder.addColumn(PEPTIDE_COUNT).withDataType(DataTypeCode.INTEGER).withDefaultWidth(80);
- builder.addColumn(FDR).withDefaultWidth(80);
- for (DataSetProtein protein : proteins)
- {
- builder.addRow(protein);
- builder.column(DATA_SET_PERM_ID).addString(protein.getDataSetPermID());
- builder.column(SEQUENCE_NAME).addString(protein.getSequenceName());
- builder.column(PEPTIDE_COUNT).addInteger((long) protein.getPeptideCount());
- int perMille = (int) (1000 * protein.getFalseDiscoveryRate() + 0.5);
- builder.column(FDR).addString((perMille / 10) + "." + (perMille % 10) + " %");
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
deleted file mode 100644
index 3b9feeeef9e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs.IDENTIFIER;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs.REGISTRATION_DATE;
-
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractCommonTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriterion;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchField;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleAttributeSearchFieldKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * Provider of MS_INJECTION samples registered for the user.
- *
- * @author Franz-Josef Elmer
- */
-public class ParentlessMsInjectionSampleProvider extends AbstractCommonTableModelProvider<Sample>
-{
- public ParentlessMsInjectionSampleProvider(ICommonServer commonServer, String sessionToken)
- {
- super(commonServer, sessionToken);
- }
-
- @Override
- protected TypedTableModel<Sample> createTableModel()
- {
- DetailedSearchCriteria criteria = new DetailedSearchCriteria();
- criteria.setConnection(SearchCriteriaConnection.MATCH_ALL);
- DetailedSearchCriterion typeCriterion = new DetailedSearchCriterion();
- typeCriterion.setField(DetailedSearchField
- .createAttributeField(SampleAttributeSearchFieldKind.SAMPLE_TYPE));
- typeCriterion.setValue(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
- DetailedSearchCriterion spaceCriterion = new DetailedSearchCriterion();
- spaceCriterion.setField(DetailedSearchField
- .createAttributeField(SampleAttributeSearchFieldKind.SPACE));
- spaceCriterion.setValue(CommonConstants.MS_DATA_SPACE);
- DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
- String userName = commonServer.tryGetSession(sessionToken).getUserName();
- registratorCriterion.setField(DetailedSearchField.createRegistratorField());
- registratorCriterion.setValue(userName);
- criteria.setCriteria(Arrays.asList(typeCriterion, spaceCriterion, registratorCriterion));
- List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
- TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
- builder.addColumn(IDENTIFIER).withDefaultWidth(300);
- builder.addColumn(REGISTRATION_DATE).withDefaultWidth(300);
- for (Sample sample : samples)
- {
- if (sample.getGeneratedFrom() == null)
- {
- builder.addRow(sample);
- builder.column(IDENTIFIER).addString(sample.getIdentifier());
- builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
- }
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinProvider.java
deleted file mode 100644
index 38513cf59f0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinProvider.java
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinBrowserColumnIDs.ACCESSION_NUMBER;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinBrowserColumnIDs.COVERAGE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinBrowserColumnIDs.PROTEIN_DESCRIPTION;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.HighLevelException;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.IColumn;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * Provider of {@link ProteinInfo} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinProvider extends AbstractTableModelProvider<ProteinInfo>
-{
- private static final String ABUNDANCE_PROPERTY_KEY = "ABUNDANCE";
-
- private final IPhosphoNetXServer server;
-
- private final String sessionToken;
-
- private final TechId experimentID;
-
- private final double falseDiscoveryRate;
-
- private final AggregateFunction aggregateFunction;
-
- private final String treatmentTypeCode;
-
- private final boolean aggregateOnOriginal;
-
- public ProteinProvider(IPhosphoNetXServer server, String sessionToken, TechId experimentID,
- double falseDiscoveryRate, AggregateFunction function, String treatmentTypeCode,
- boolean aggregateOnOriginal)
- {
- this.server = server;
- this.sessionToken = sessionToken;
- this.experimentID = experimentID;
- this.falseDiscoveryRate = falseDiscoveryRate;
- this.aggregateFunction = function;
- this.treatmentTypeCode = treatmentTypeCode;
- this.aggregateOnOriginal = aggregateOnOriginal;
- }
-
- @Override
- protected TypedTableModel<ProteinInfo> createTableModel()
- {
- try
- {
-
- List<AbundanceColumnDefinition> abundanceColumnDefinitions =
- server.getAbundanceColumnDefinitionsForProteinByExperiment(sessionToken,
- experimentID, treatmentTypeCode);
- List<ProteinInfo> proteins =
- server.listProteinsByExperiment(sessionToken, experimentID, falseDiscoveryRate,
- aggregateFunction, treatmentTypeCode, aggregateOnOriginal);
- TypedTableModelBuilder<ProteinInfo> builder = new TypedTableModelBuilder<ProteinInfo>();
- builder.addColumn(ACCESSION_NUMBER);
- builder.addColumn(PROTEIN_DESCRIPTION);
- builder.addColumn(COVERAGE).withDefaultWidth(100);
- Map<Long, IColumn> sampleIdToAbundanceColumnMap = new HashMap<Long, IColumn>();
- for (AbundanceColumnDefinition abundanceColumnDefinition : abundanceColumnDefinitions)
- {
- long sampleID = abundanceColumnDefinition.getID();
- String columnID = "abundance-" + Long.toString(sampleID);
- builder.addColumn(columnID).withDefaultWidth(100);
- IColumn column = builder.column(columnID);
- sampleIdToAbundanceColumnMap.put(sampleID, column);
- String header = abundanceColumnDefinition.getSampleCode();
- Map<String, String> properties = new HashMap<String, String>();
- properties.put(ABUNDANCE_PROPERTY_KEY, header);
- List<Treatment> treatments = abundanceColumnDefinition.getTreatments();
- if (treatments.isEmpty() == false)
- {
- String delim;
- if (header == null)
- {
- header = "";
- delim = "";
- } else
- {
- delim = ": ";
- }
- for (Treatment treatment : treatments)
- {
- header += delim + treatment;
- delim = ", ";
- column.property(treatment.getTypeCode(), treatment.getValue());
- }
- }
- column.withTitle(header);
- }
- for (ProteinInfo protein : proteins)
- {
- builder.addRow(protein);
- builder.column(ACCESSION_NUMBER).addString(protein.getAccessionNumber());
- builder.column(PROTEIN_DESCRIPTION).addString(protein.getDescription());
- builder.column(COVERAGE).addDouble(protein.getCoverage());
- Map<Long, Double> abundances = protein.getAbundances();
- Set<Entry<Long, Double>> entrySet = abundances.entrySet();
- for (Entry<Long, Double> entry : entrySet)
- {
- IColumn column = sampleIdToAbundanceColumnMap.get(entry.getKey());
- if (column != null)
- {
- column.addDouble(entry.getValue());
- }
- }
- }
- return builder.getModel();
- } catch (Exception e)
- {
- Throwable t = e;
- while (t != null)
- {
- if (t instanceof HighLevelException)
- {
- throw (HighLevelException) t;
- }
- t = t.getCause();
- }
- throw CheckedExceptionTunnel.wrapIfNecessary(e);
- }
-
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinRelatedSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinRelatedSampleProvider.java
deleted file mode 100644
index 5cec3d17095..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinRelatedSampleProvider.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode.INTEGER;
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode.REAL;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.ABUNDANCE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.MODIFICATION_FRACTION;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.MODIFICATION_MASS;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.MODIFICATION_POSITION;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.MODIFIED_AMINO_ACID;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.SAMPLE_IDENTIFIER;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinRelatedSampleGridColumnIDs.SAMPLE_TYPE;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AminoAcid;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-
-/**
- * Provider of {@link ProteinRelatedSample}.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinRelatedSampleProvider extends AbstractTableModelProvider<ProteinRelatedSample>
-{
- private static final String PROPERTIES_GROUP = "property-";
-
- private final IPhosphoNetXServer server;
-
- private final String sessionToken;
-
- private final TechId experimentID;
-
- private final TechId proteinReferenceID;
-
- public ProteinRelatedSampleProvider(IPhosphoNetXServer server, String sessionToken,
- TechId experimentID, TechId proteinReferenceID)
- {
- this.server = server;
- this.sessionToken = sessionToken;
- this.experimentID = experimentID;
- this.proteinReferenceID = proteinReferenceID;
- }
-
- @Override
- protected TypedTableModel<ProteinRelatedSample> createTableModel()
- {
- List<ProteinRelatedSample> samples =
- server.listProteinRelatedSamplesByProtein(sessionToken, experimentID,
- proteinReferenceID);
- TypedTableModelBuilder<ProteinRelatedSample> builder =
- new TypedTableModelBuilder<ProteinRelatedSample>();
- builder.column(SAMPLE_IDENTIFIER);
- builder.column(SAMPLE_TYPE);
- builder.column(ABUNDANCE).withDataType(REAL).withDefaultWidth(100);
- builder.column(MODIFIED_AMINO_ACID);
- builder.column(MODIFICATION_POSITION).withDataType(INTEGER).withDefaultWidth(100);
- builder.column(MODIFICATION_MASS).withDataType(REAL).withDefaultWidth(100);
- builder.column(MODIFICATION_FRACTION).withDataType(REAL).withDefaultWidth(100);
- for (ProteinRelatedSample sample : samples)
- {
- builder.addRow(sample);
- builder.column(SAMPLE_IDENTIFIER).addString(sample.getIdentifier());
- builder.column(SAMPLE_TYPE).addString(sample.getEntityType().getCode());
- builder.column(ABUNDANCE).addDouble(sample.getAbundance());
- builder.column(MODIFIED_AMINO_ACID).addString(getAminoAcidName(sample));
- builder.column(MODIFICATION_POSITION).addInteger(sample.getModificationPosition());
- builder.column(MODIFICATION_MASS).addDouble(sample.getModificationMass());
- builder.column(MODIFICATION_FRACTION).addDouble(sample.getModificationFraction());
- builder.columnGroup(PROPERTIES_GROUP).addProperties(sample.getProperties());
- }
- return builder.getModel();
- }
-
- private String getAminoAcidName(ProteinRelatedSample sample)
- {
- char modifiedAminoAcid = sample.getModifiedAminoAcid();
- if (modifiedAminoAcid == 0)
- {
- return null;
- }
- try
- {
- char aminoAcidSymbol = Character.toUpperCase(modifiedAminoAcid);
- return AminoAcid.valueOf(Character.toString(aminoAcidSymbol)).getName();
- } catch (IllegalArgumentException ex)
- {
- return "?";
- }
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java
deleted file mode 100644
index 12bab9a5210..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSequenceGridColumnIDs.DATABASE_NAME_AND_VERSION;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSequenceGridColumnIDs.SEQUENCE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSequenceGridColumnIDs.SEQUENCE_SHORT_NAME;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-
-/**
- * Provider of {@link ProteinSequence} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinSequenceProvider extends AbstractTableModelProvider<ProteinSequence>
-{
- private final IPhosphoNetXServer server;
-
- private final String sessionToken;
-
- private final TechId experimentID;
-
- private final TechId proteinReferenceID;
-
- public ProteinSequenceProvider(IPhosphoNetXServer server, String sessionToken,
- TechId experimentID, TechId proteinReferenceID)
- {
- this.server = server;
- this.sessionToken = sessionToken;
- this.experimentID = experimentID;
- this.proteinReferenceID = proteinReferenceID;
- }
-
- @Override
- protected TypedTableModel<ProteinSequence> createTableModel()
- {
- List<ProteinSequence> sequences =
- server.listProteinSequencesByProteinReference(sessionToken, experimentID, proteinReferenceID);
- TypedTableModelBuilder<ProteinSequence> builder =
- new TypedTableModelBuilder<ProteinSequence>();
- builder.addColumn(SEQUENCE_SHORT_NAME).withDefaultWidth(20);
- builder.addColumn(DATABASE_NAME_AND_VERSION);
- builder.addColumn(SEQUENCE).withDefaultWidth(400);
- for (ProteinSequence sequence : sequences)
- {
- builder.addRow(sequence);
- builder.column(SEQUENCE_SHORT_NAME).addString(sequence.getShortName());
- builder.column(DATABASE_NAME_AND_VERSION).addString(
- sequence.getDatabaseNameAndVersion());
- builder.column(SEQUENCE).addString(sequence.getSequence());
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProvider.java
deleted file mode 100644
index 4f2b5a1093b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProvider.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs.DECOY_PEPTIDE_COUNT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs.DECOY_PROTEIN_COUNT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs.FDR;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs.PEPTIDE_COUNT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ProteinSummaryGridColumnIDs.PROTEIN_COUNT;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * Provider of {@link ProteinSummary} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinSummaryProvider extends AbstractTableModelProvider<ProteinSummary>
-{
- private final IPhosphoNetXServer server;
-
- private final String sessionToken;
-
- private final TechId experimentID;
-
- public ProteinSummaryProvider(IPhosphoNetXServer server, String sessionToken,
- TechId experimentID)
- {
- this.server = server;
- this.sessionToken = sessionToken;
- this.experimentID = experimentID;
- }
-
- @Override
- protected TypedTableModel<ProteinSummary> createTableModel()
- {
- List<ProteinSummary> sumaries = server.listProteinSummariesByExperiment(sessionToken, experimentID);
- TypedTableModelBuilder<ProteinSummary> builder = new TypedTableModelBuilder<ProteinSummary>();
- builder.addColumn(FDR);
- builder.addColumn(PROTEIN_COUNT).withDefaultWidth(100);
- builder.addColumn(PEPTIDE_COUNT).withDefaultWidth(100);
- builder.addColumn(DECOY_PROTEIN_COUNT).withDefaultWidth(100);
- builder.addColumn(DECOY_PEPTIDE_COUNT).withDefaultWidth(100);
- for (ProteinSummary summary : sumaries)
- {
- builder.addRow(summary);
- builder.column(FDR).addDouble(summary.getFDR());
- builder.column(PROTEIN_COUNT).addInteger((long) summary.getProteinCount());
- builder.column(PEPTIDE_COUNT).addInteger((long) summary.getPeptideCount());
- builder.column(DECOY_PROTEIN_COUNT).addInteger((long) summary.getDecoyProteinCount());
- builder.column(DECOY_PEPTIDE_COUNT).addInteger((long) summary.getDecoyPeptideCount());
- }
- return builder.getModel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java
deleted file mode 100644
index 791c9d90ae5..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java
+++ /dev/null
@@ -1,262 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import java.util.List;
-
-import javax.annotation.Resource;
-
-import net.lemnik.eodsql.DataSet;
-
-import org.springframework.stereotype.Component;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
-import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
-import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
-import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
-import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.AccessionNumberBuilder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IAbundanceColumnDefinitionTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IDataSetProteinTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinDetailsBO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinInfoTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinRelatedSampleTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinSequenceTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinSummaryTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinDetails;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReference;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Component(ResourceNames.PROTEOMICS_PLUGIN_SERVER)
-public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implements
- IPhosphoNetXServer
-{
- @Resource(name = ResourceNames.PROTEOMICS_DAO_FACTORY)
- private IPhosphoNetXDAOFactory specificDAOFactory;
-
- @Resource(name = ResourceNames.PROTEOMICS_BO_FACTORY)
- private IBusinessObjectFactory specificBOFactory;
-
- public PhosphoNetXServer()
- {
- super();
- }
-
- @Private
- PhosphoNetXServer(IOpenBisSessionManager sessionManager, IDAOFactory daoFactory,
- IPropertiesBatchManager propertiesBatchManager,
- IPhosphoNetXDAOFactory specificDAOFactory, IBusinessObjectFactory specificBOFactory,
- ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
- IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
- {
- super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
- dataSetTypeSlaveServerPlugin);
- this.specificDAOFactory = specificDAOFactory;
- this.specificBOFactory = specificBOFactory;
- }
-
- @Override
- public IPhosphoNetXServer createLogger(IInvocationLoggerContext context)
- {
- return new PhosphoNetXServerLogger(getSessionManager(), context);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public Vocabulary getTreatmentTypeVocabulary(String sessionToken) throws UserFailureException
- {
- IVocabularyDAO vocabularyDAO = getDAOFactory().getVocabularyDAO();
- VocabularyPE vocabulary = vocabularyDAO.tryFindVocabularyByCode("TREATMENT_TYPE");
- return VocabularyTranslator.translate(vocabulary);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
- String sessionToken, @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentID, String treatmentTypeOrNull)
- throws UserFailureException
- {
- Session session = getSession(sessionToken);
- ISampleProvider sampleProvider = specificBOFactory.createSampleProvider(session);
- sampleProvider.loadByExperimentID(experimentID);
- return getAbundanceColumnDefinitions(session, sampleProvider, experimentID,
- treatmentTypeOrNull);
- }
-
- private List<AbundanceColumnDefinition> getAbundanceColumnDefinitions(Session session,
- ISampleProvider sampleProvider, TechId experimentID, String treatmentTypeOrNull)
- {
- String experimentPermID = getExperimentPermIDFor(experimentID);
- IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO(experimentID);
- DataSet<String> samplePermIDs =
- dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
- try
- {
- IAbundanceColumnDefinitionTable table =
- specificBOFactory.createAbundanceColumnDefinitionTable(session);
- for (String samplePermID : samplePermIDs)
- {
- table.add(sampleProvider.getSample(samplePermID));
- }
- return table.getSortedAndAggregatedDefinitions(treatmentTypeOrNull);
- } finally
- {
- samplePermIDs.close();
- }
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<ProteinInfo> listProteinsByExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId, double falseDiscoveryRate,
- AggregateFunction function,
- String treatmentTypeCode, boolean aggregateOnOriginal) throws UserFailureException
- {
- final Session session = getSession(sessionToken);
- ISampleProvider sampleProvider = specificBOFactory.createSampleProvider(session);
- sampleProvider.loadByExperimentID(experimentId);
- List<AbundanceColumnDefinition> definitions =
- getAbundanceColumnDefinitions(session, sampleProvider, experimentId,
- treatmentTypeCode);
- IProteinInfoTable table = specificBOFactory.createProteinInfoTable(session, sampleProvider);
- table.load(definitions, experimentId, falseDiscoveryRate, function, aggregateOnOriginal);
- return table.getProteinInfos();
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId) throws UserFailureException
- {
- final Session session = getSession(sessionToken);
- IProteinSummaryTable summaryTable = specificBOFactory.createProteinSummaryTable(session);
- summaryTable.load(experimentId);
- return summaryTable.getProteinSummaries();
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public ProteinByExperiment getProteinByExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentID, TechId proteinReferenceID)
- throws UserFailureException
- {
- Session session = getSession(sessionToken);
- IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO(experimentID);
- ProteinByExperiment proteinByExperiment = new ProteinByExperiment();
- ProteinReference proteinReference =
- proteinQueryDAO.tryToGetProteinReference(proteinReferenceID.getId());
- if (proteinReference == null)
- {
- throw new UserFailureException("No protein reference found for ID: "
- + proteinReferenceID);
- }
- proteinByExperiment.setId(proteinReferenceID);
- AccessionNumberBuilder builder =
- new AccessionNumberBuilder(proteinReference.getAccessionNumber());
- proteinByExperiment.setAccessionNumber(builder.getAccessionNumber());
- proteinByExperiment.setAccessionNumberType(builder.getTypeOrNull());
- proteinByExperiment.setDescription(proteinReference.getDescription());
- IProteinDetailsBO proteinDetailsBO = specificBOFactory.createProteinDetailsBO(session);
- proteinDetailsBO.loadByExperimentAndReference(experimentID, proteinReferenceID);
- proteinByExperiment.setDetails(proteinDetailsBO.getDetailsOrNull());
- return proteinByExperiment;
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentID, TechId proteinReferenceID)
- throws UserFailureException
- {
- final Session session = getSession(sessionToken);
- IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
- sequenceTable.loadByReference(experimentID, proteinReferenceID);
- return sequenceTable.getSequences();
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId, TechId proteinReferenceID)
- throws UserFailureException
- {
- final Session session = getSession(sessionToken);
- IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
- sequenceTable.loadByReference(experimentId, proteinReferenceID);
- IDataSetProteinTable dataSetProteinTable =
- specificBOFactory.createDataSetProteinTable(session);
- dataSetProteinTable.load(getExperimentPermIDFor(experimentId), proteinReferenceID,
- sequenceTable);
- return dataSetProteinTable.getDataSetProteins();
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_OBSERVER)
- public List<ProteinRelatedSample> listProteinRelatedSamplesByProtein(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentID, TechId proteinReferenceID)
- throws UserFailureException
- {
- final Session session = getSession(sessionToken);
-
- IProteinDetailsBO proteinDetailsBO = specificBOFactory.createProteinDetailsBO(session);
- proteinDetailsBO.loadByExperimentAndReference(experimentID, proteinReferenceID);
- ProteinDetails detailsOrNull = proteinDetailsBO.getDetailsOrNull();
- String sequenceOrNull = detailsOrNull == null ? null : detailsOrNull.getSequence();
- IProteinRelatedSampleTable proteinRelatedSampleTable =
- specificBOFactory.createProteinRelatedSampleTable(session);
- proteinRelatedSampleTable.load(session, experimentID, proteinReferenceID, sequenceOrNull);
- return proteinRelatedSampleTable.getSamples();
- }
-
- private String getExperimentPermIDFor(TechId experimentId)
- {
- ExperimentPE experiment = getDAOFactory().getExperimentDAO().getByTechId(experimentId);
- return experiment.getPermId();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java
deleted file mode 100644
index 0a3dfe4c53b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import java.util.List;
-
-import ch.systemsx.cisd.authentication.ISessionManager;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPhosphoNetXServer
-{
- PhosphoNetXServerLogger(final ISessionManager<Session> sessionManager,
- IInvocationLoggerContext context)
- {
- super(sessionManager, context);
- }
-
- @Override
- public Vocabulary getTreatmentTypeVocabulary(String sessionToken) throws UserFailureException
- {
- logAccess(sessionToken, "get_treatment_type_vocabulary");
- return null;
- }
-
- @Override
- public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
- String sessionToken, TechId experimentID, String treatmentTypeOrNull)
- throws UserFailureException
- {
- logAccess(sessionToken, "get_abundance_colum_definitions",
- "EXPERIMENT_ID(%s) TREATMENT_TYPE(%s)", experimentID,
- treatmentTypeOrNull);
- return null;
- }
-
- @Override
- public List<ProteinInfo> listProteinsByExperiment(String sessionToken, TechId experimentId,
- double falseDiscoveryRate, AggregateFunction function, String treatmentTypeCode,
- boolean aggregateOnOriginal) throws UserFailureException
- {
- logAccess(sessionToken, "list_proteins_by_experiment",
- "ID(%s) FDR(%s) AGGREGATE_FUNCTION(%s) TREATMENT_TYPE(%s) "
- + "AGGREGATE_ON_ORIGINAL(%s)", experimentId, falseDiscoveryRate, function
- .getLabel(), treatmentTypeCode, aggregateOnOriginal);
- return null;
- }
-
- @Override
- public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
- TechId experimentId) throws UserFailureException
- {
- logAccess(sessionToken, "list_protein_summaries_by_experiment", "EXPERIMENT_ID(%s)",
- experimentId);
- return null;
- }
-
- @Override
- public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
- TechId proteinReferenceID) throws UserFailureException
- {
- logAccess(sessionToken, "get_protein_by_experiment",
- "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentId, proteinReferenceID);
- return null;
- }
-
- @Override
- public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- TechId experimentID, TechId proteinReferenceID) throws UserFailureException
- {
- logAccess(sessionToken, "list_protein_sequences_by_reference",
- "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentID, proteinReferenceID);
- return null;
- }
-
- @Override
- public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
- TechId experimentId, TechId proteinReferenceID) throws UserFailureException
- {
- logAccess(sessionToken, "list_proteins_by_experiment_and_reference",
- "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentId, proteinReferenceID);
- return null;
- }
-
- @Override
- public List<ProteinRelatedSample> listProteinRelatedSamplesByProtein(String sessionToken,
- TechId experimentID, TechId proteinReferenceID) throws UserFailureException
- {
- logAccess(sessionToken, "list_protein_related_samples_by_protein",
- "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentID, proteinReferenceID);
- return null;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java
deleted file mode 100644
index f9d28fd536e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java
+++ /dev/null
@@ -1,368 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import ch.systemsx.cisd.common.collection.CollectionUtils;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
-import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationDataProvider;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SamplePropertyAccessValidator;
-import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.ParentSampleValidator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.RawDataSampleValidator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ExperimentLoader;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleLoader;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDataServiceInternal>
- implements IProteomicsDataServiceInternal
-{
- private ICommonBusinessObjectFactory commonBoFactory;
-
- private IOpenBisSessionManager sessionManagerFromConstructor;
-
- private ExperimentLoader experimentLoader;
-
- private IBusinessObjectFactory boFactory;
-
- private IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
-
- public ProteomicsDataServiceInternal()
- {
- }
-
- public ProteomicsDataServiceInternal(IOpenBisSessionManager sessionManager,
- IDAOFactory daoFactory, ICommonBusinessObjectFactory businessObjectFactory,
- IBusinessObjectFactory boFactory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
- {
- this(sessionManager, daoFactory, null, businessObjectFactory, boFactory,
- managedPropertyEvaluatorFactory);
- }
-
- ProteomicsDataServiceInternal(IOpenBisSessionManager sessionManager, IDAOFactory daoFactory,
- IPropertiesBatchManager propertiesBatchManager,
- ICommonBusinessObjectFactory businessObjectFactory, IBusinessObjectFactory boFactory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
- {
- super(sessionManager, daoFactory, propertiesBatchManager);
- sessionManagerFromConstructor = sessionManager;
- this.commonBoFactory = businessObjectFactory;
- this.boFactory = boFactory;
- experimentLoader = new ExperimentLoader(getDAOFactory(), managedPropertyEvaluatorFactory);
- this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
- }
-
- public void replaceAutoWiredSesseionManagerByConstructorSessionManager()
- {
- sessionManager = sessionManagerFromConstructor;
- }
-
- @Override
- public IProteomicsDataServiceInternal createLogger(IInvocationLoggerContext context)
- {
- return new ProteomicsDataServiceInternalLogger(getSessionManager(), context);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- @ReturnValueFilter(validatorClass = RawDataSampleValidator.class)
- public List<MsInjectionSample> listRawDataSamples(String sessionToken)
- {
- return loadAllRawDataSamples(getSession(sessionToken), true);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- public List<MsInjectionSample> listAllRawDataSamples(String sessionToken)
- {
- return loadAllRawDataSamples(getSession(sessionToken), false);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- public void processRawData(String sessionToken, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType)
- {
- Session session = getSession(sessionToken);
- PersonPE person = session.tryGetPerson();
-
- List<MsInjectionSample> samples = loadAllRawDataSamples(session, true);
- Set<Long> sampleIDs = asSet(rawDataSampleIDs);
- List<String> dataSetCodes = new ArrayList<String>();
- Map<String, String> parameterBindings = new HashMap<String, String>();
-
- RawDataSampleValidator validator = new RawDataSampleValidator();
- validator.init(new AuthorizationDataProvider(getDAOFactory()));
-
- for (MsInjectionSample sample : samples)
- {
- if (validator.isValid(person, sample)
- && sampleIDs.contains(sample.getSample().getId()))
- {
- Map<String, AbstractExternalData> latestDataSets = sample.getLatestDataSets();
- AbstractExternalData latestDataSet = latestDataSets.get(dataSetType);
- if (latestDataSet != null)
- {
- String code = latestDataSet.getCode();
- dataSetCodes.add(code);
- parameterBindings.put(code, sample.getSample().getCode());
- }
- }
- }
-
- processDataSets(session, dataSetProcessingKey, dataSetCodes, parameterBindings);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- public void processDataSets(String sessionToken, String dataSetProcessingKey,
- @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes)
- {
- Session session = getSession(sessionToken);
- processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- @ReturnValueFilter(validatorClass = ExperimentValidator.class)
- public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode)
- {
- Session session = getSession(sessionToken);
-
- IDAOFactory daoFactory = getDAOFactory();
- IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.EXPERIMENT);
- ExperimentTypePE type =
- (ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode(experimentTypeCode);
- List<ExperimentPE> experiments =
- daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null, null);
- final Collection<MetaprojectAssignmentPE> assignmentPEs =
- getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
- session.tryGetPerson(), experiments, EntityKind.EXPERIMENT);
- Map<Long, Set<Metaproject>> assignments =
- MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
- return ExperimentTranslator.translate(experiments, "", assignments,
- managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, getDAOFactory()));
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- public List<AbstractExternalData> listDataSetsByExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentID)
- {
- final Session session = getSession(sessionToken);
-
- IDataSetTable dataSetTable = commonBoFactory.createDataSetTable(session);
- dataSetTable.loadByExperimentTechId(experimentID);
- List<DataPE> dataSetPEs = dataSetTable.getDataSets();
- Collection<MetaprojectAssignmentPE> assignmentPEs =
- getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
- session.tryGetPerson(), dataSetPEs, EntityKind.DATA_SET);
- return DataSetTranslator.translate(dataSetPEs, "", "",
- MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs),
- managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, getDAOFactory()));
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.PROJECT_USER)
- public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
- String experimentType, long[] searchExperimentIDs)
- {
- Session session = getSession(sessionToken);
- PersonPE person = session.tryGetPerson();
-
- List<String> dataSetCodes = new ArrayList<String>();
- IExperimentDAO experimentDAO = getDAOFactory().getExperimentDAO();
- IDataDAO dataSetDAO = getDAOFactory().getDataDAO();
- ExperimentValidator validator = new ExperimentValidator();
-
- validator.init(new AuthorizationDataProvider(getDAOFactory()));
-
- for (long experimentID : searchExperimentIDs)
- {
- ExperimentPE experiment = experimentDAO.tryGetByTechId(new TechId(experimentID));
- String actualExperimentTypeCode = experiment.getExperimentType().getCode();
- if (actualExperimentTypeCode.equals(experimentType) == false)
- {
- throw new UserFailureException("Experiment with technical id " + experimentID
- + " [" + experiment.getIdentifier() + "] is not of type " + experimentType
- + " but of type " + actualExperimentTypeCode + ".");
- }
- Experiment translatedExperiment =
- ExperimentTranslator.translate(experiment, "", null,
- managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, getDAOFactory()));
- if (validator.isValid(person, translatedExperiment))
- {
- List<DataPE> dataSets = dataSetDAO.listDataSets(experiment);
- dataSetCodes.addAll(Code.extractCodes(dataSets));
- }
- }
-
- processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
- }
-
- private List<MsInjectionSample> loadAllRawDataSamples(Session session, boolean parentHasToBeValid)
- {
- List<Sample> samples = loadAccessableSamples(session, parentHasToBeValid);
- List<Sample> parentSamples = new ArrayList<Sample>();
- for (Sample sample : samples)
- {
- Sample parent = sample.getGeneratedFrom();
- if (parent != null)
- {
- parentSamples.add(parent);
- }
- }
- experimentLoader.enrichWithExperiments(session, parentSamples);
- Map<Sample, List<AbstractExternalData>> dataSetsBySamples =
- commonBoFactory.createDatasetLister(session).listAllDataSetsFor(samples);
- List<MsInjectionSample> result = new ArrayList<MsInjectionSample>();
- for (Entry<Sample, List<AbstractExternalData>> entry : dataSetsBySamples.entrySet())
- {
- result.add(new MsInjectionSample(entry.getKey(), entry.getValue()));
- }
- return result;
- }
-
- protected List<Sample> loadAccessableSamples(Session session, boolean parentHasToBeValid)
- {
- ISampleLoader sampleLoader = boFactory.createSampleLoader(session);
- List<Sample> samples =
- sampleLoader.listSamplesWithParentsByTypeAndSpace(
- CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE,
- CommonConstants.MS_DATA_SPACE);
- PersonPE person = session.tryGetPerson();
- List<Sample> validSamples = new ArrayList<Sample>();
-
- ParentSampleValidator validator = new ParentSampleValidator();
- validator.init(new AuthorizationDataProvider(getDAOFactory()));
-
- for (Sample sample : samples)
- {
- if (validator.isValid(person, sample, parentHasToBeValid))
- {
- if (validator.isValid(person, sample) == false)
- {
- sample.setParents(Collections.<Sample> emptySet());
- }
- validSamples.add(sample);
- }
- }
- return validSamples;
- }
-
- private void processDataSets(Session session, String dataSetProcessingKey,
- List<String> dataSetCodes, Map<String, String> parameterBindings)
- {
- try
- {
- String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
- IDataSetTable dataSetTable = commonBoFactory.createDataSetTable(session);
- dataSetTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
- parameterBindings);
- } catch (EnvironmentFailureException ex)
- {
- throw new EnvironmentFailureException("Processing data sets " +
- CollectionUtils.abbreviate(dataSetCodes, 20) + " with processing plugin '"
- + dataSetProcessingKey + "' using bindings " + parameterBindings + " failed.", ex);
- }
- }
-
- private String findDataStoreServer(String dataSetProcessingKey)
- {
- List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
- for (DataStorePE dataStore : dataStores)
- {
- Set<DataStoreServicePE> services = dataStore.getServices();
- for (DataStoreServicePE dataStoreService : services)
- {
- if (DataStoreServiceKind.PROCESSING.equals(dataStoreService.getKind())
- && dataSetProcessingKey.equals(dataStoreService.getKey()))
- {
- return dataStore.getCode();
- }
- }
- }
- throw new EnvironmentFailureException("No data store processing service with key '"
- + dataSetProcessingKey + "' found.");
- }
-
- private Set<Long> asSet(long[] ids)
- {
- Set<Long> result = new HashSet<Long>();
- for (long id : ids)
- {
- result.add(id);
- }
- return result;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalLogger.java
deleted file mode 100644
index 964f3b03c4d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalLogger.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import java.util.List;
-
-import ch.systemsx.cisd.authentication.ISessionManager;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteomicsDataServiceInternalLogger extends AbstractServerLogger implements
- IProteomicsDataServiceInternal
-{
-
- ProteomicsDataServiceInternalLogger(ISessionManager<Session> sessionManager,
- IInvocationLoggerContext context)
- {
- super(sessionManager, context);
- }
-
- @Override
- public List<MsInjectionSample> listRawDataSamples(String sessionToken)
- {
- logAccess(sessionToken, "list_raw_data_samples");
- return null;
- }
-
- @Override
- public List<MsInjectionSample> listAllRawDataSamples(String sessionToken)
- {
- logAccess(sessionToken, "list_all_raw_data_samples");
- return null;
- }
-
- @Override
- public void processRawData(String sessionToken, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType)
- {
- int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
- logAccess(sessionToken, "copy_raw_data", "NUMBER_OF_DATA_SETS(%s), DATA_SET_TYPE(%s)",
- numberOfDataSets, dataSetType);
- }
-
- @Override
- public void processDataSets(String sessionToken, String dataSetProcessingKey,
- List<String> dataSetCodes)
- {
- logAccess(sessionToken, "process_data_sets",
- "DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s)", dataSetProcessingKey,
- dataSetCodes.size());
- }
-
- @Override
- public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode)
- {
- logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
- return null;
- }
-
- @Override
- public List<AbstractExternalData> listDataSetsByExperiment(String sessionToken, TechId experimentID)
- {
- logAccess(sessionToken, "list_data_sets_by_experiments", "EXPERIMENT_ID(%s)", experimentID);
- return null;
- }
-
- @Override
- public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
- String experimentTypeCode, long[] searchExperimentIDs)
- {
- int experimentCount = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
- logAccess(sessionToken, "process_protein_result_data_sets",
- "DSS_PROCESSING_PLUGIN(%s) EXPERIMENT_TYPE(%s) NUMBER_OF_EXPERIMENTS(%s)",
- dataSetProcessingKey, experimentTypeCode, experimentCount);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/Constants.java
deleted file mode 100644
index e55625dd8f0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/Constants.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Constants
-{
- // Spring bean IDs
- public final static String PROTEOMICS_DATA_SERVICE = "proteomics-data-service";
-
- public final static String PROTEOMICS_DATA_SERVICE_INTERNAL = "proteomics-data-service-internal";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataService.java
deleted file mode 100644
index bfabf505a04..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataService.java
+++ /dev/null
@@ -1,413 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import javax.annotation.Resource;
-
-import org.springframework.stereotype.Component;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
-import ch.systemsx.cisd.openbis.generic.shared.util.DataTypeUtils;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.PropertyKey;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * Implementation of {@link IProteomicsDataService}.
- *
- * @author Franz-Josef Elmer
- */
-@Component(Constants.PROTEOMICS_DATA_SERVICE)
-public class ProteomicsDataService extends AbstractServer<IProteomicsDataService> implements
- IProteomicsDataService
-{
- private static final String MS_SEARCH = "MS_SEARCH";
-
- @Resource(name = Constants.PROTEOMICS_DATA_SERVICE_INTERNAL)
- private IProteomicsDataServiceInternal service;
-
- public ProteomicsDataService()
- {
- }
-
- public ProteomicsDataService(final IOpenBisSessionManager sessionManager,
- final IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager,
- IProteomicsDataServiceInternal service)
- {
- super(sessionManager, daoFactory, propertiesBatchManager);
- this.service = service;
- }
-
- @Override
- public String tryToAuthenticateAtRawDataServer(String userID, String userPassword)
- {
- SessionContextDTO session = tryAuthenticate(userID, userPassword);
- return session == null ? null : session.getSessionToken();
- }
-
- @Override
- public IProteomicsDataService createLogger(IInvocationLoggerContext context)
- {
- return new ProteomicsDataServiceLogger(getSessionManager(), context);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- return translateSamples(service.listRawDataSamples(session.getSessionToken()));
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<MsInjectionDataInfo> listAllRawDataSamples(String sessionToken, String userID)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- return translateSamples(service.listAllRawDataSamples(session.getSessionToken()));
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- private List<MsInjectionDataInfo> translateSamples(List<MsInjectionSample> samples)
- {
- ArrayList<MsInjectionDataInfo> result = new ArrayList<MsInjectionDataInfo>();
- for (MsInjectionSample sample : samples)
- {
- result.add(translate(sample));
- }
- return result;
- }
-
- private MsInjectionDataInfo translate(MsInjectionSample sample)
- {
- MsInjectionDataInfo info = new MsInjectionDataInfo();
- Sample msiSample = sample.getSample();
- info.setMsInjectionSampleID(msiSample.getId());
- info.setMsInjectionSampleCode(msiSample.getCode());
- info.setMsInjectionSampleRegistrationDate(msiSample.getRegistrationDate());
- info.setMsInjectionSampleProperties(translate(msiSample.getProperties()));
- Sample bioSample = msiSample.getGeneratedFrom();
- if (bioSample != null)
- {
- info.setBiologicalSampleID(bioSample.getId());
- info.setBiologicalSampleIdentifier(bioSample.getIdentifier());
- Experiment experiment = bioSample.getExperiment();
- if (experiment != null)
- {
- info.setBiologicalExperimentIdentifier(experiment.getIdentifier());
- info.setBiologicalExperiment(translate(experiment));
- }
- info.setBiologicalSampleProperties(translate(bioSample.getProperties()));
- }
- List<AbstractExternalData> dataSets = sample.getDataSets();
- Set<DataSet> transformedDataSets = new HashSet<DataSet>();
- for (AbstractExternalData dataSet : dataSets)
- {
- DataSet transformedDataSet = transform(dataSet);
- transformedDataSets.add(transformedDataSet);
- }
- info.setDataSets(transformedDataSets);
- Map<String, Date> latestDataSetRegistrationDates = new HashMap<String, Date>();
- for (Entry<String, AbstractExternalData> entry : sample.getLatestDataSets().entrySet())
- {
- latestDataSetRegistrationDates.put(entry.getKey(), entry.getValue()
- .getRegistrationDate());
- }
- info.setLatestDataSetRegistrationDates(latestDataSetRegistrationDates);
- return info;
- }
-
- private DataSet transform(AbstractExternalData dataSet)
- {
- DataSet transformedDataSet = new DataSet();
- transformedDataSet.setId(dataSet.getId());
- transformedDataSet.setCode(dataSet.getCode());
- transformedDataSet.setType(dataSet.getDataSetType().getCode());
- transformedDataSet.setRegistrationDate(dataSet.getRegistrationDate());
- transformedDataSet.setProperties(translate(dataSet.getProperties()));
- Collection<AbstractExternalData> children = dataSet.getChildren();
- if (children != null && children.isEmpty() == false)
- {
- for (AbstractExternalData child : children)
- {
- transformedDataSet.addChild(transform(child));
- }
- }
- return transformedDataSet;
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
- String sessionToken)
- {
- checkSession(sessionToken);
-
- List<DataStoreServerProcessingPluginInfo> result =
- new ArrayList<DataStoreServerProcessingPluginInfo>();
- List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
- for (DataStorePE dataStore : dataStores)
- {
- Set<DataStoreServicePE> services = dataStore.getServices();
- for (DataStoreServicePE dataStoreService : services)
- {
- if (dataStoreService.getKind() == DataStoreServiceKind.PROCESSING)
- {
- result.add(translate(dataStoreService));
- }
- }
- }
- return result;
- }
-
- private DataStoreServerProcessingPluginInfo translate(DataStoreServicePE dataStoreService)
- {
- String key = dataStoreService.getKey();
- String label = dataStoreService.getLabel();
- List<String> translatedCodes = new ArrayList<String>();
- Set<DataSetTypePE> datasetTypes = dataStoreService.getDatasetTypes();
- for (DataSetTypePE dataSetType : datasetTypes)
- {
- translatedCodes.add(dataSetType.getCode());
- }
- return new DataStoreServerProcessingPluginInfo(key, label, translatedCodes);
- }
-
- @Override
- @SuppressWarnings("deprecation")
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- service.processRawData(session.getSessionToken(), dataSetProcessingKey,
- rawDataSampleIDs, dataSetType);
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
- List<String> dataSetCodes)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- service.processDataSets(session.getSessionToken(), dataSetProcessingKey, dataSetCodes);
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment> listSearchExperiments(
- String sessionToken, String userID)
- {
- return listExperiments(sessionToken, userID, MS_SEARCH);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment> listExperiments(
- String sessionToken, String userID, String experimentTypeCode)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- List<Experiment> experiments =
- service.listExperiments(session.getSessionToken(), experimentTypeCode);
- List<ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment> result =
- new ArrayList<ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment>();
- for (Experiment experiment : experiments)
- {
- ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment e =
- translate(experiment);
- result.add(e);
- }
- return result;
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- private ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment translate(
- Experiment experiment)
- {
- ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment e =
- new ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment();
- e.setId(experiment.getId());
- e.setCode(experiment.getCode());
- e.setProjectCode(experiment.getProject().getCode());
- e.setSpaceCode(experiment.getProject().getSpace().getCode());
- e.setRegistrationDate(experiment.getRegistrationDate());
- e.setProperties(translate(experiment.getProperties()));
- return e;
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<DataSet> listDataSetsByExperiment(String sessionToken, String userID,
- long experimentID)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- List<DataSet> result = new ArrayList<DataSet>();
- List<AbstractExternalData> dataSets =
- service.listDataSetsByExperiment(session.getSessionToken(), new TechId(
- experimentID));
- for (AbstractExternalData dataSet : dataSets)
- {
- DataSet ds = new DataSet();
- ds.setId(dataSet.getId());
- ds.setCode(dataSet.getCode());
- ds.setType(dataSet.getDataSetType().getCode());
- ds.setProperties(translate(dataSet.getProperties()));
- result.add(ds);
- }
- return result;
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] searchExperimentIDs)
- {
- processProteinResultDataSets(sessionToken, userID, dataSetProcessingKey, MS_SEARCH,
- searchExperimentIDs);
- }
-
- @Override
- @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public void processProteinResultDataSets(String sessionToken, String userID,
- String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs)
- {
- checkSession(sessionToken);
- SessionContextDTO session = login(userID);
- try
- {
- service.processProteinResultDataSets(session.getSessionToken(), dataSetProcessingKey,
- experimentTypeCode, experimentIDs);
- } finally
- {
- service.logout(session.getSessionToken());
- }
- }
-
- private Map<PropertyKey, Serializable> translate(List<IEntityProperty> properties)
- {
- if (properties == null)
- {
- return null;
- }
- HashMap<PropertyKey, Serializable> map = new HashMap<PropertyKey, Serializable>();
- for (IEntityProperty property : properties)
- {
- PropertyType propertyType = property.getPropertyType();
- PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
- DataTypeCode dataTypeCode = propertyType.getDataType().getCode();
- map.put(key, DataTypeUtils.convertValueTo(dataTypeCode, property.tryGetAsString()));
- }
- return map;
- }
-
- private SessionContextDTO login(String userID)
- {
- SessionContextDTO session = service.tryAuthenticate(userID, "dummy-password");
- if (session == null)
- {
- throw new UserFailureException("Unknown user ID: " + userID);
- }
- return session;
- }
-
- @Override
- public int getMajorVersion()
- {
- return 1;
- }
-
- @Override
- public int getMinorVersion()
- {
- return 3;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceLogger.java
deleted file mode 100644
index a779ee526e0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceLogger.java
+++ /dev/null
@@ -1,142 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-import java.util.List;
-
-import ch.systemsx.cisd.authentication.ISessionManager;
-import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProteomicsDataService
-{
-
- ProteomicsDataServiceLogger(ISessionManager<Session> sessionManager, IInvocationLoggerContext context)
- {
- super(sessionManager, context);
- }
-
- @Override
- public String tryToAuthenticateAtRawDataServer(String userID, String userPassword)
- {
- return null;
- }
-
- @Override
- public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID)
- {
- logAccess(sessionToken, "list_raw_data_samples", "USER_ID(%s)", userID);
- return null;
- }
-
- @Override
- public List<MsInjectionDataInfo> listAllRawDataSamples(String sessionToken, String userID)
- {
- logAccess(sessionToken, "list_all_raw_data_samples", "USER_ID(%s)", userID);
- return null;
- }
-
- @Override
- public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
- String sessionToken)
- {
- logAccess(sessionToken, "list_data_store_services", "");
- return null;
- }
-
- @Override
- public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType)
- {
- int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
- logAccess(sessionToken, "copy_raw_data",
- "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s) DATA_SET_TYPE(%s)",
- userID, dataSetProcessingKey, numberOfDataSets, dataSetType);
- }
-
- @Override
- public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
- List<String> dataSetCodes)
- {
- logAccess(sessionToken, "process_data_sets",
- "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) DATA_SETS(%s)", userID,
- dataSetProcessingKey, dataSetCodes);
- }
-
- @Override
- public List<Experiment> listSearchExperiments(String sessionToken, String userID)
- {
- logAccess(sessionToken, "list_search_experiments");
- return null;
- }
-
- @Override
- public List<Experiment> listExperiments(String sessionToken, String userID,
- String experimentTypeCode)
- {
- logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
- return null;
- }
-
- @Override
- public List<DataSet> listDataSetsByExperiment(String sessionToken, String userID,
- long experimentID)
- {
- logAccess(sessionToken, "list_data_sets_by_experiment", "EXPERIMENT_ID(%s)", experimentID);
- return null;
- }
-
- @Override
- public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] searchExperimentIDs)
- {
- int numberOfDataSets = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
- logAccess(sessionToken, "copy_search_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
- }
-
- @Override
- public void processProteinResultDataSets(String sessionToken, String userID,
- String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs)
- {
- int experimentCount = experimentIDs == null ? 0 : experimentIDs.length;
- logAccess(sessionToken, "process_protein_result_data_sets",
- "DSS_PROCESSING_PLUGIN(%s) EXPERIMENT_TYPE(%s) NUMBER_OF_EXPERIMENTS(%s)",
- dataSetProcessingKey, experimentTypeCode, experimentCount);
- }
-
- @Override
- public int getMajorVersion()
- {
- return 1;
- }
-
- @Override
- public int getMinorVersion()
- {
- return 0;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceServer.java
deleted file mode 100644
index a5f5715dbde..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceServer.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-import java.io.IOException;
-
-import javax.annotation.Resource;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.springframework.stereotype.Controller;
-import org.springframework.web.bind.annotation.RequestMapping;
-
-import ch.systemsx.cisd.openbis.common.api.server.AbstractApiServiceExporter;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-
-/**
- * Server wrapping {@link IProteomicsDataService}.
- *
- * @author Franz-Josef Elmer
- */
-@Controller
-public class ProteomicsDataServiceServer extends AbstractApiServiceExporter
-{
- @Resource(name = Constants.PROTEOMICS_DATA_SERVICE)
- private IProteomicsDataService service;
-
- @Override
- public void afterPropertiesSet()
- {
- establishService(IProteomicsDataService.class, service, IProteomicsDataService.SERVICE_NAME,
- IProteomicsDataService.SERVER_URL);
- super.afterPropertiesSet();
- }
-
- @RequestMapping(
- { IProteomicsDataService.SERVER_URL, "/openbis" + IProteomicsDataService.SERVER_URL })
- @Override
- public void handleRequest(HttpServletRequest request, HttpServletResponse response)
- throws ServletException, IOException
- {
- super.handleRequest(request, response);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/ParentSampleValidator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/ParentSampleValidator.java
deleted file mode 100644
index 8d7ad5842d5..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/ParentSampleValidator.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator;
-
-import ch.systemsx.cisd.openbis.generic.server.authorization.project.provider.project.ProjectProviderFromSample;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.AbstractValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.IValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SpaceValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ParentSampleValidator extends AbstractValidator<Sample>
-{
- private IValidator<Space> validator = new SpaceValidator();
-
- @Override
- public boolean doValidation(PersonPE person, Sample value)
- {
- return isValid(person, value, true);
- }
-
- public boolean isValid(PersonPE person, Sample sample, boolean parentHasToBeValid)
- {
- Sample parent = sample.getGeneratedFrom();
-
- if (parent != null)
- {
- Space space = parent.getSpace();
-
- if (parentHasToBeValid == false || space == null || validator.isValid(person, space))
- {
- return true;
- } else
- {
- return isValidPA(person, new ProjectProviderFromSample(parent));
- }
- }
-
- return false;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidator.java
deleted file mode 100644
index 1e280e19880..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidator.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator;
-
-import ch.systemsx.cisd.openbis.generic.server.authorization.IAuthorizationDataProvider;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.IValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public final class RawDataSampleValidator implements IValidator<MsInjectionSample>
-{
- private IValidator<Sample> validator = new ParentSampleValidator();
-
- @Override
- public boolean isValid(PersonPE person, MsInjectionSample sample)
- {
- return validator.isValid(person, sample.getSample());
- }
-
- @Override
- public void init(IAuthorizationDataProvider authorizationDataProvider)
- {
- validator.init(authorizationDataProvider);
- }
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBusinessObject.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBusinessObject.java
deleted file mode 100644
index e32a00999cb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBusinessObject.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractBusinessObject
-{
- private final IDAOFactory daoFactory;
-
- private final IPhosphoNetXDAOFactory specificDAOFactory;
-
- private final Session session;
-
- AbstractBusinessObject(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, Session session)
- {
- this.daoFactory = daoFactory;
- this.specificDAOFactory = specificDAOFactory;
- this.session = session;
- }
-
- protected final PersonPE getRegistrator()
- {
- PersonPE registrator = session.tryGetPerson();
- assert registrator != null : "Session with unknown person: " + session;
- return registrator;
- }
-
- protected final IDAOFactory getDaoFactory()
- {
- return daoFactory;
- }
-
- protected final IPhosphoNetXDAOFactory getSpecificDAOFactory()
- {
- return specificDAOFactory;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTable.java
deleted file mode 100644
index e8544ad2d3c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTable.java
+++ /dev/null
@@ -1,142 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * @author Franz-Josef Elmer
- */
-class AbundanceColumnDefinitionTable extends AbstractBusinessObject implements IAbundanceColumnDefinitionTable
-{
- private final TreatmentFinder treatmentFinder;
-
- private final Map<Long, AbundanceColumnDefinition> columnDefinitions;
-
- AbundanceColumnDefinitionTable(IDAOFactory daoFactory,
- IPhosphoNetXDAOFactory specificDAOFactory, Session session)
- {
- super(daoFactory, specificDAOFactory, session);
- treatmentFinder = new TreatmentFinder();
- columnDefinitions = new TreeMap<Long, AbundanceColumnDefinition>();
- }
-
- @Override
- public void add(Sample sample)
- {
- Sample parent = sample.getGeneratedFrom();
- Sample sampleOrParent = parent == null ? sample : parent;
- Long sampleID = sampleOrParent.getId();
- AbundanceColumnDefinition columnDefinition = columnDefinitions.get(sampleID);
- if (columnDefinition == null)
- {
- columnDefinition = new AbundanceColumnDefinition();
- columnDefinition.addSampleID(sampleID);
- columnDefinition.setSampleCode(sampleOrParent.getCode());
- columnDefinition.setTreatments(treatmentFinder.findTreatmentsOf(sampleOrParent));
- columnDefinitions.put(sampleID, columnDefinition);
- }
- }
-
- @Override
- public List<AbundanceColumnDefinition> getSortedAndAggregatedDefinitions(
- String treatmentTypeOrNull)
- {
- Collection<AbundanceColumnDefinition> values = columnDefinitions.values();
- List<AbundanceColumnDefinition> definitions = new ArrayList<AbundanceColumnDefinition>();
- if (treatmentTypeOrNull == null)
- {
- definitions.addAll(values);
- } else
- {
- Collection<List<AbundanceColumnDefinition>> groupedDefinitions =
- groupDefinitions(values, definitions, treatmentTypeOrNull);
- for (List<AbundanceColumnDefinition> group : groupedDefinitions)
- {
- AbundanceColumnDefinition definition = new AbundanceColumnDefinition();
- AbundanceColumnDefinition firstDefinition = group.get(0);
- Treatment treatment =
- tryToFindTreatmentByTypeCode(firstDefinition, treatmentTypeOrNull);
- definition.setTreatments(Arrays.asList(treatment));
- for (AbundanceColumnDefinition abundanceColumnDefinition : group)
- {
- definition.addSampleIDsOf(abundanceColumnDefinition);
- }
- definitions.add(definition);
- }
- }
-
- Collections.sort(definitions);
- return definitions;
- }
-
- private Collection<List<AbundanceColumnDefinition>> groupDefinitions(
- Collection<AbundanceColumnDefinition> values,
- List<AbundanceColumnDefinition> definitions, String treatmentType)
- {
- Map<String, List<AbundanceColumnDefinition>> groupedDefinitions =
- new HashMap<String, List<AbundanceColumnDefinition>>();
- for (AbundanceColumnDefinition definition : values)
- {
- Treatment treatment = tryToFindTreatmentByTypeCode(definition, treatmentType);
- if (treatment == null)
- {
- definitions.add(definition);
- } else
- {
- String treatmentValue = treatment.getValue();
- List<AbundanceColumnDefinition> list = groupedDefinitions.get(treatmentValue);
- if (list == null)
- {
- list = new ArrayList<AbundanceColumnDefinition>();
- groupedDefinitions.put(treatmentValue, list);
- }
- list.add(definition);
- }
- }
- return groupedDefinitions.values();
- }
-
- private Treatment tryToFindTreatmentByTypeCode(AbundanceColumnDefinition definition,
- String typeCode)
- {
- List<Treatment> treatments = definition.getTreatments();
- for (Treatment treatment : treatments)
- {
- if (treatment.getTypeCode().equals(typeCode))
- {
- return treatment;
- }
- }
- return null;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManager.java
deleted file mode 100644
index 63b8985b5e4..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManager.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinWithAbundances;
-
-/**
- * @author Franz-Josef Elmer
- */
-class AbundanceManager
-{
- private final List<ProteinWithAbundances> proteins = new ArrayList<ProteinWithAbundances>();
-
- private final ISampleProvider sampleProvider;
-
- private final Set<Long> sampleIDs = new TreeSet<Long>();
-
- AbundanceManager(ISampleProvider sampleProvider)
- {
- this.sampleProvider = sampleProvider;
- }
-
- public void handle(ProteinReferenceWithProtein proteinReference, List<ProteinAbundance> listOrNull)
- {
- String accessionNumber = proteinReference.getAccessionNumber();
- ProteinWithAbundances protein = new ProteinWithAbundances();
- protein.setCoverage(proteinReference.getCoverage());
- protein.setId(proteinReference.getId());
- protein.setDescription(proteinReference.getDescription());
- protein.setAccessionNumber(accessionNumber);
- proteins.add(protein);
- if (listOrNull != null)
- {
- for (ProteinAbundance proteinAbundance : listOrNull)
- {
- String samplePermID = proteinAbundance.getSamplePermID();
- Long sampleID = getSampleIDOrParentSampleID(samplePermID);
- sampleIDs.add(sampleID);
- protein.addAbundanceFor(sampleID, proteinAbundance.getAbundance());
- }
- }
- }
-
- private Long getSampleIDOrParentSampleID(String samplePermID)
- {
- Sample sample = sampleProvider.getSample(samplePermID);
- Sample parent = sample.getGeneratedFrom();
- return parent == null ? sample.getId() : parent.getId();
- }
-
- public Collection<ProteinWithAbundances> getProteinsWithAbundances()
- {
- return proteins;
- }
-
- public final Collection<Long> getSampleIDs()
- {
- return sampleIDs;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilder.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilder.java
deleted file mode 100644
index 2e0049c285c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilder.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-/**
- * Parses accession numbers of the form
- *
- * <pre>
- * ['DECOY_'][<type>'|']<accession number>['|'<some string>]
- * </pre>
- *
- * @author Franz-Josef Elmer
- */
-public class AccessionNumberBuilder
-{
- static final String DECOY_PREFIX = "DECOY_";
-
- private static final char SEPARATOR = '|';
-
- private final String typeOrNull;
-
- private final String accessionNumber;
-
- public AccessionNumberBuilder(String fullAccessionNumber)
- {
- int indexOfFirstSeparator = fullAccessionNumber.indexOf(SEPARATOR);
- if (indexOfFirstSeparator < 0)
- {
- typeOrNull = null;
- accessionNumber = fullAccessionNumber;
- } else
- {
- String firstItem = fullAccessionNumber.substring(0, indexOfFirstSeparator);
- int decoyPrefixIndex = firstItem.startsWith(DECOY_PREFIX) ? DECOY_PREFIX.length() : 0;
- String prefix = firstItem.substring(0, decoyPrefixIndex);
- typeOrNull = firstItem.substring(decoyPrefixIndex);
- int startIndex = indexOfFirstSeparator + 1;
- int indexOfSecondSeparator = fullAccessionNumber.indexOf(SEPARATOR, startIndex);
- if (indexOfSecondSeparator < 0)
- {
- accessionNumber =
- addPrefixIfNecessary(prefix, fullAccessionNumber.substring(startIndex));
- } else
- {
- accessionNumber =
- addPrefixIfNecessary(prefix,
- fullAccessionNumber.substring(startIndex, indexOfSecondSeparator));
- }
- }
- }
-
- private String addPrefixIfNecessary(String prefix, String string)
- {
- return string.startsWith(prefix) ? string : prefix + string;
- }
-
- public final String getTypeOrNull()
- {
- return typeOrNull;
- }
-
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/BusinessObjectFactory.java
deleted file mode 100644
index c7b486a1e57..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/BusinessObjectFactory.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.AbstractPluginBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class BusinessObjectFactory extends AbstractPluginBusinessObjectFactory implements
- IBusinessObjectFactory
-{
- private final IDAOFactory daoFactory;
-
- private final IPhosphoNetXDAOFactory specificDAOFactory;
-
- private final ICommonBusinessObjectFactory businessObjectFactory;
-
- public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- ICommonBusinessObjectFactory businessObjectFactory)
- {
- this.daoFactory = daoFactory;
- this.specificDAOFactory = specificDAOFactory;
- this.businessObjectFactory = businessObjectFactory;
- }
-
- @Override
- public ISampleLister createSampleLister(Session session)
- {
- return getCommonBusinessObjectFactory().createSampleLister(session);
- }
-
- @Override
- public IAbundanceColumnDefinitionTable createAbundanceColumnDefinitionTable(Session session)
- {
- return new AbundanceColumnDefinitionTable(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public IProteinInfoTable createProteinInfoTable(Session session, ISampleProvider sampleProvider)
- {
- return new ProteinInfoTable(daoFactory, specificDAOFactory, session, sampleProvider);
- }
-
- @Override
- public IProteinSummaryTable createProteinSummaryTable(Session session)
- {
- return new ProteinSummaryTable(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public IProteinSequenceTable createProteinSequenceTable(Session session)
- {
- return new ProteinSequenceTable(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public IDataSetProteinTable createDataSetProteinTable(Session session)
- {
- return new DataSetProteinTable(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public IProteinDetailsBO createProteinDetailsBO(Session session)
- {
- return new ProteinDetailsBO(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public IProteinRelatedSampleTable createProteinRelatedSampleTable(Session session)
- {
- return new ProteinRelatedSampleTable(daoFactory, specificDAOFactory,
- getManagedPropertyEvaluatorFactory());
- }
-
- @Override
- public ISampleTable createSampleTable(Session session)
- {
- return new SampleTable(daoFactory, specificDAOFactory, session,
- getManagedPropertyEvaluatorFactory());
- }
-
- @Override
- public ISampleIDProvider createSampleIDProvider(Session session)
- {
- return new SampleIDProvider(daoFactory.getSampleDAO());
- }
-
- @Override
- public ISampleProvider createSampleProvider(Session session)
- {
- return new SampleProvider(session, this);
- }
-
- @Override
- public ISampleLoader createSampleLoader(Session session)
- {
- return new SampleLoader(session, daoFactory, businessObjectFactory);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java
deleted file mode 100644
index b1552715903..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.lemnik.eodsql.DataSet;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetProteinTable extends AbstractBusinessObject implements IDataSetProteinTable
-{
- private List<DataSetProtein> dataSetProteins;
-
- DataSetProteinTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- Session session)
- {
- super(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public List<DataSetProtein> getDataSetProteins()
- {
- return dataSetProteins;
- }
-
- @Override
- public void load(String experimentPermID, TechId proteinReferenceID,
- IProteinSequenceTable sequenceTable)
- {
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentPermID);
- ErrorModel errorModel = new ErrorModel(proteinQueryDAO);
- DataSet<IdentifiedProtein> proteins =
- proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
- proteinReferenceID.getId());
- dataSetProteins = new ArrayList<DataSetProtein>();
- for (IdentifiedProtein protein : proteins)
- {
- errorModel.setFalseDiscoveryRateFor(protein);
- DataSetProtein dataSetProtein = new DataSetProtein();
- dataSetProtein.setDataSetID(new TechId(protein.getDataSetID()));
- dataSetProtein.setDataSetPermID(protein.getDataSetPermID());
- dataSetProtein.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
- dataSetProtein.setPeptideCount(protein.getPeptideCount());
- dataSetProtein.setProteinID(new TechId(protein.getProteinID()));
- dataSetProtein.setSequenceName(sequenceTable.getShortName(protein.getDatabaseID()));
- dataSetProteins.add(dataSetProtein);
- }
- proteins.close();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java
deleted file mode 100644
index fbeec454b95..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import net.lemnik.eodsql.DataSet;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ProbabilityToFDRCalculator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ErrorModel
-{
- private final Map<Long, ProbabilityToFDRCalculator> calculators =
- new HashMap<Long, ProbabilityToFDRCalculator>();
-
- private final IProteinQueryDAO dao;
-
- ErrorModel(IProteinQueryDAO dao)
- {
- this.dao = dao;
- }
-
- boolean passProtein(ProteinReferenceWithProtein protein, double falseDiscoveryRate)
- {
- ProbabilityToFDRCalculator calculator = getCalculator(protein.getDataSetID());
- double fdr = calculator.calculateFDR(protein.getProbability());
- return Double.isNaN(fdr) || fdr <= falseDiscoveryRate;
- }
-
- void setFalseDiscoveryRateFor(IdentifiedProtein protein)
- {
- long dataSetID = protein.getDataSetID();
- double probability = protein.getProbability();
- protein.setFalseDiscoveryRate(calculateFalsDiscoveryRate(dataSetID, probability));
- }
-
- double calculateFalsDiscoveryRate(long dataSetID, double probability)
- {
- ProbabilityToFDRCalculator calculator = getCalculator(dataSetID);
- return calculator.calculateFDR(probability);
- }
-
- private ProbabilityToFDRCalculator getCalculator(long dataSetID)
- {
- ProbabilityToFDRCalculator calculator = calculators.get(dataSetID);
- if (calculator == null)
- {
- calculator = new ProbabilityToFDRCalculator();
- DataSet<ProbabilityFDRMapping> mappings = dao.getProbabilityFDRMapping(dataSetID);
- for (ProbabilityFDRMapping probabilityFDRMapping : mappings)
- {
- double probability = probabilityFDRMapping.getProbability();
- double falseDiscoveryRate = probabilityFDRMapping.getFalseDiscoveryRate();
- calculator.add(probability, falseDiscoveryRate);
- }
- mappings.close();
- calculator.init();
- calculators.put(dataSetID, calculator);
- }
- return calculator;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java
deleted file mode 100644
index 50c8f79d2c6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SamplePropertyAccessValidator;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ExperimentLoader
-{
- private final IDAOFactory daoFactory;
-
- private final IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
-
- public ExperimentLoader(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
- {
- this.daoFactory = daoFactory;
- this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
- }
-
- public void enrichWithExperiments(Session session, Collection<Sample> samples)
- {
- Map<Long, List<Sample>> samplesByID = new LinkedHashMap<Long, List<Sample>>();
- for (Sample sample : samples)
- {
- Experiment experiment = sample.getExperiment();
- if (experiment != null)
- {
- Long id = experiment.getId();
- List<Sample> list = samplesByID.get(id);
- if (list == null)
- {
- list = new ArrayList<Sample>();
- samplesByID.put(id, list);
- }
- list.add(sample);
- }
- }
- List<ExperimentPE> experiments =
- daoFactory.getExperimentDAO().listExperimentsWithProperties(samplesByID.keySet());
- for (ExperimentPE experiment : experiments)
- {
- Experiment e =
- ExperimentTranslator.translate(experiment, "", null,
- managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, daoFactory), LoadableFields.PROPERTIES);
- List<Sample> list = samplesByID.get(experiment.getId());
- for (Sample sample : list)
- {
- sample.setExperiment(e);
- }
- }
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IAbundanceColumnDefinitionTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IAbundanceColumnDefinitionTable.java
deleted file mode 100644
index 8b1420e641c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IAbundanceColumnDefinitionTable.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IAbundanceColumnDefinitionTable
-{
- public void add(Sample sample);
-
- public List<AbundanceColumnDefinition> getSortedAndAggregatedDefinitions(
- String treatmentTypeOrNull);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IBusinessObjectFactory.java
deleted file mode 100644
index 2efc9007f38..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IBusinessObjectFactory.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IBusinessObjectFactory
-{
- public ISampleLister createSampleLister(Session session);
-
- public IAbundanceColumnDefinitionTable createAbundanceColumnDefinitionTable(Session session);
-
- public IProteinInfoTable createProteinInfoTable(Session session,
- ISampleProvider sampleProvider);
-
- public IProteinSummaryTable createProteinSummaryTable(Session session);
-
- public IProteinSequenceTable createProteinSequenceTable(Session session);
-
- public IDataSetProteinTable createDataSetProteinTable(Session session);
-
- public IProteinDetailsBO createProteinDetailsBO(Session session);
-
- public IProteinRelatedSampleTable createProteinRelatedSampleTable(Session session);
-
- public ISampleTable createSampleTable(Session session);
-
- public ISampleIDProvider createSampleIDProvider(Session session);
-
- public ISampleProvider createSampleProvider(Session session);
-
- public ISampleLoader createSampleLoader(Session session);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IDataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IDataSetProteinTable.java
deleted file mode 100644
index 6785f2a998d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IDataSetProteinTable.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IDataSetProteinTable
-{
- public List<DataSetProtein> getDataSetProteins();
-
- public void load(String experimentPermID, TechId proteinReferenceID,
- IProteinSequenceTable sequenceTable);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinDetailsBO.java
deleted file mode 100644
index 2aeefffc700..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinDetailsBO.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinDetails;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProteinDetailsBO
-{
-
- public void loadByExperimentAndReference(TechId experimentID, TechId proteinReferenceID);
-
- public ProteinDetails getDetailsOrNull();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinInfoTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinInfoTable.java
deleted file mode 100644
index 97ce2def459..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinInfoTable.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-
-/**
- * Business object for loading proteins together with their abundances.
- *
- * @author Franz-Josef Elmer
- */
-public interface IProteinInfoTable
-{
- /**
- * Loads proteins of all data sets registered for the specified experiment. All proteins are filtered out if their false discovery rate is larger
- * then the specified one. Abundance values are aggregated in accordance with <code>aggregateOnOriginal</code>, abundance column definitions, and
- * aggregate function.
- */
- public void load(List<AbundanceColumnDefinition> definitions, TechId experimentId,
- double falseDiscoveryRate, AggregateFunction function, boolean aggregateOnOriginal);
-
- public List<ProteinInfo> getProteinInfos();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinRelatedSampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinRelatedSampleTable.java
deleted file mode 100644
index 38f02ccfc28..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinRelatedSampleTable.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-
-/**
- * Interface to business object for collection of {@link ProteinRelatedSample} instances.
- *
- * @author Franz-Josef Elmer
- */
-public interface IProteinRelatedSampleTable
-{
- public void load(Session session, TechId experimentID, TechId proteinReferenceID, String sequenceOrNull);
-
- public List<ProteinRelatedSample> getSamples();
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java
deleted file mode 100644
index f19c618ac72..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProteinSequenceTable
-{
-
- public void loadByReference(TechId experimentID, TechId proteinReferenceID);
-
- public List<ProteinSequence> getSequences();
-
- public String getShortName(long databaseID);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSummaryTable.java
deleted file mode 100644
index de570feda6c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSummaryTable.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProteinSummaryTable
-{
-
- public void load(TechId experimentID);
-
- public List<ProteinSummary> getProteinSummaries();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleIDProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleIDProvider.java
deleted file mode 100644
index e363ec393e7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleIDProvider.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-
-/**
- * Provides the ID of a sample or its parent.
- *
- * @author Franz-Josef Elmer
- */
-public interface ISampleIDProvider
-{
- /**
- * Returns the ID of the specified sample or the ID of its parent if it exist.
- *
- * @throws UserFailureException if no sample could be found.
- */
- public long getSampleIDOrParentSampleID(String samplePermID);
-
- public SamplePE getSampleOrParentSample(String samplePermID);
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleLoader.java
deleted file mode 100644
index cfa34fdf1eb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleLoader.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-
-/**
- * Loader for sample having a parent.
- *
- * @author Franz-Josef Elmer
- */
-public interface ISampleLoader
-{
- public List<Sample> listSamplesWithParentsByTypeAndSpace(String sampleTypeCode, String spaceCode);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleProvider.java
deleted file mode 100644
index 47423c1036b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleProvider.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-
-/**
- * Provides samples of an experiments.
- *
- * @author Franz-Josef Elmer
- */
-public interface ISampleProvider
-{
- /**
- * Loads all samples registered for the specified experiment.
- */
- public void loadByExperimentID(TechId experimentID);
-
- /**
- * Returns the sample for specified permID.
- *
- * @throws UserFailureException if sample not found.
- */
- public Sample getSample(String permID);
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleTable.java
deleted file mode 100644
index 08fabca7b1f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ISampleTable.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.SampleWithPropertiesAndAbundance;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface ISampleTable
-{
-
- public void loadSamplesWithAbundance(Session session, TechId experimentID, TechId proteinReferenceID);
-
- public List<SampleWithPropertiesAndAbundance> getSamples();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java
deleted file mode 100644
index c7b94a9afcc..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java
+++ /dev/null
@@ -1,177 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.lemnik.eodsql.DataSet;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.IndistinguishableProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Peptide;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.PeptideModification;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinDetails;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IndistinguishableProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.PeptideWithModification;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetailsBO
-{
- private ProteinDetails details;
-
- ProteinDetailsBO(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- Session session)
- {
- super(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public ProteinDetails getDetailsOrNull()
- {
- return details;
- }
-
- @Override
- public void loadByExperimentAndReference(TechId experimentID, TechId proteinReferenceID)
- {
- String experimentPermID = getExperimentPermIDFor(experimentID);
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
- DataSet<IdentifiedProtein> proteins =
- proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
- proteinReferenceID.getId());
- try
- {
- if (proteins.size() == 1)
- {
- ErrorModel errorModel = new ErrorModel(proteinQueryDAO);
- IdentifiedProtein protein = proteins.get(0);
- errorModel.setFalseDiscoveryRateFor(protein);
- details = new ProteinDetails();
- details.setSequence(protein.getSequence());
- details.setDatabaseNameAndVersion(protein.getDatabaseNameAndVersion());
- details.setProbability(protein.getProbability());
- details.setCoverage(100 * protein.getCoverage());
- details.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
- String dataSetPermID = protein.getDataSetPermID();
- details.setDataSetPermID(dataSetPermID);
- DataPE ds = getDaoFactory().getDataDAO().tryToFindDataSetByCode(dataSetPermID);
- if (ds != null)
- {
- details.setDataSetTechID(ds.getId());
- details.setDataSetTypeCode(ds.getDataSetType().getCode());
- }
- details.setPeptides(loadPeptides(proteinQueryDAO, protein));
- long proteinID = protein.getProteinID();
- details.setProteinID(new TechId(proteinID));
- details.setIndistinguishableProteinInfos(loadIndistinguishableProteinInfos(proteinQueryDAO, proteinID));
- }
- } finally
- {
- proteins.close();
- }
- }
-
- private List<IndistinguishableProteinInfo> loadIndistinguishableProteinInfos(IProteinQueryDAO proteinQueryDAO, long proteinID)
- {
- DataSet<IndistinguishableProtein> proteins =
- proteinQueryDAO.listIndistinguishableProteinsByProteinID(proteinID);
- try
- {
- List<IndistinguishableProteinInfo> infos =
- new ArrayList<IndistinguishableProteinInfo>();
- for (IndistinguishableProtein protein : proteins)
- {
- IndistinguishableProteinInfo info = new IndistinguishableProteinInfo();
- AccessionNumberBuilder builder =
- new AccessionNumberBuilder(protein.getAccessionNumber());
- info.setAccessionNumber(builder.getAccessionNumber());
- info.setAccessionNumberType(builder.getTypeOrNull());
- info.setDescription(protein.getDescription());
- info.setSequence(protein.getSequence());
- info.setCoverage(100 * protein.getCoverage());
- infos.add(info);
- }
- return infos;
- } finally
- {
- proteins.close();
- }
- }
-
- private List<Peptide> loadPeptides(IProteinQueryDAO proteinQueryDAO, IdentifiedProtein protein)
- {
- DataSet<PeptideWithModification> identifiedPeptides =
- proteinQueryDAO.listIdentifiedPeptidesByProtein(protein.getProteinID());
- try
- {
- Map<Long, Peptide> peps = new HashMap<Long, Peptide>();
- for (PeptideWithModification peptidWithModification : identifiedPeptides)
- {
- long id = peptidWithModification.getId();
- Peptide peptide = peps.get(id);
- if (peptide == null)
- {
- peptide = new Peptide();
- peptide.setSequence(peptidWithModification.getSequence());
- peps.put(id, peptide);
- }
- Integer position = peptidWithModification.getPosition();
- Double mass = peptidWithModification.getMass();
- if (position != null && mass != null)
- {
- PeptideModification peptideModification = new PeptideModification();
- peptideModification.setPosition(position);
- peptideModification.setMass(mass);
- peptide.getModifications().add(peptideModification);
- }
- }
- List<Peptide> result = new ArrayList<Peptide>(peps.values());
- Collections.sort(result, new Comparator<Peptide>()
- {
- @Override
- public int compare(Peptide p1, Peptide p2)
- {
- return p1.getSequence().compareTo(p2.getSequence());
- }
- });
- return result;
- } finally
- {
- identifiedPeptides.close();
- }
- }
-
- private String getExperimentPermIDFor(TechId experimentId)
- {
- ExperimentPE experiment = getDaoFactory().getExperimentDAO().getByTechId(experimentId);
- return experiment.getPermId();
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java
deleted file mode 100644
index 6e09f0cc8b3..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java
+++ /dev/null
@@ -1,217 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.lemnik.eodsql.DataSet;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinWithAbundances;
-
-/**
- * Implementation based of {@link IDAOFactory} and {@link IPhosphoNetXDAOFactory}.
- *
- * @author Franz-Josef Elmer
- */
-class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTable
-{
- protected static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, ProteinInfoTable.class);
-
- private List<ProteinInfo> infos;
-
- private final ISampleProvider sampleProvider;
-
- ProteinInfoTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- Session session, ISampleProvider sampleProvider)
- {
- super(daoFactory, specificDAOFactory, session);
- this.sampleProvider = sampleProvider;
- }
-
- @Override
- public List<ProteinInfo> getProteinInfos()
- {
- if (infos == null)
- {
- throw new IllegalStateException("No proteins loaded.");
- }
- return infos;
- }
-
- @Override
- public void load(List<AbundanceColumnDefinition> definitions, TechId experimentID,
- double falseDiscoveryRate, AggregateFunction function, boolean aggregateOnOriginal)
- {
- IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
- String permID = experimentDAO.getByTechId(experimentID).getPermId();
- AbundanceManager abundanceManager = setUpAbundanceManager(permID, falseDiscoveryRate);
- Collection<ProteinWithAbundances> proteins = abundanceManager.getProteinsWithAbundances();
- infos = new ArrayList<ProteinInfo>(proteins.size());
- for (ProteinWithAbundances protein : proteins)
- {
- ProteinInfo proteinInfo = new ProteinInfo();
- proteinInfo.setId(new TechId(protein.getId()));
- AccessionNumberBuilder builder = new AccessionNumberBuilder(protein.getAccessionNumber());
- proteinInfo.setCoverage(100 * protein.getCoverage());
- proteinInfo.setAccessionNumber(builder.getAccessionNumber());
- proteinInfo.setDescription(protein.getDescription());
- proteinInfo.setExperimentID(experimentID);
- Map<Long, Double> abundances = new HashMap<Long, Double>();
- for (AbundanceColumnDefinition abundanceColumnDefinition : definitions)
- {
- double[] abundanceValues = new double[0];
- List<Long> ids = abundanceColumnDefinition.getSampleIDs();
- for (Long sampleID : ids)
- {
- double[] values = protein.getAbundancesForSample(sampleID);
- if (values != null && values.length > 0 && aggregateOnOriginal == false)
- {
- values = new double[] { function.aggregate(values) };
- }
- abundanceValues = concatenate(abundanceValues, values);
- }
- if (abundanceValues.length > 0)
- {
- double aggregatedAbundance = function.aggregate(abundanceValues);
- abundances.put(abundanceColumnDefinition.getID(), aggregatedAbundance);
- }
- }
- proteinInfo.setAbundances(abundances);
- infos.add(proteinInfo);
- }
- Collections.sort(infos, new Comparator<ProteinInfo>()
- {
-
- @Override
- public int compare(ProteinInfo p1, ProteinInfo p2)
- {
- String an1 = p1.getAccessionNumber();
- String an2 = p2.getAccessionNumber();
- return an1 == null ? -1 : (an2 == null ? 1 : an1.compareToIgnoreCase(an2));
- }
- });
- }
-
- private AbundanceManager setUpAbundanceManager(String experimentPermID,
- double falseDiscoveryRate)
- {
- AbundanceManager abundanceManager = new AbundanceManager(sampleProvider);
- IPhosphoNetXDAOFactory specificDAOFactory = getSpecificDAOFactory();
- IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO(experimentPermID);
- long time = System.currentTimeMillis();
- DataSet<ProteinReferenceWithProtein> dataSet =
- dao.listProteinReferencesByExperiment(experimentPermID);
- List<ProteinReferenceWithProtein> proteins = new ArrayList<ProteinReferenceWithProtein>();
- LongOpenHashSet proteinIDs = new LongOpenHashSet();
- try
- {
- for (ProteinReferenceWithProtein protein : dataSet)
- {
- proteins.add(protein);
- proteinIDs.add(protein.getProteinID());
- }
- } finally
- {
- dataSet.close();
- }
- operationLog.info("(" + (System.currentTimeMillis() - time) + "ms) for listProteinReferencesByExperiment");
- Map<Long, List<ProteinAbundance>> abundancesPerProtein = getAbudancesPerProtein(dao, proteinIDs);
- ErrorModel errorModel = new ErrorModel(dao);
- for (ProteinReferenceWithProtein protein : proteins)
- {
- if (errorModel.passProtein(protein, falseDiscoveryRate))
- {
- List<ProteinAbundance> list = abundancesPerProtein.get(protein.getProteinID());
- abundanceManager.handle(protein, list);
- }
- }
- return abundanceManager;
- }
-
- private Map<Long, List<ProteinAbundance>> getAbudancesPerProtein(IProteinQueryDAO dao, LongOpenHashSet proteinIDs)
- {
- long time = System.currentTimeMillis();
- DataSet<ProteinAbundance> dataSet = dao.listProteinWithAbundanceByExperiment(proteinIDs);
- List<ProteinAbundance> proteinAbundances = new ArrayList<ProteinAbundance>();
- try
- {
- for (ProteinAbundance proteinAbundance : dataSet)
- {
- proteinAbundances.add(proteinAbundance);
- }
- } finally
- {
- dataSet.close();
- }
- operationLog.info("(" + (System.currentTimeMillis() - time) + "ms) for listProteinWithAbundanceByExperiment");
- Map<Long, List<ProteinAbundance>> abundancesPerProtein =
- new HashMap<Long, List<ProteinAbundance>>();
- for (ProteinAbundance proteinAbundance : proteinAbundances)
- {
- long proteinID = proteinAbundance.getId();
- List<ProteinAbundance> list = abundancesPerProtein.get(proteinID);
- if (list == null)
- {
- list = new ArrayList<ProteinAbundance>();
- abundancesPerProtein.put(proteinID, list);
- }
- list.add(proteinAbundance);
- }
- return abundancesPerProtein;
- }
-
- private static double[] concatenate(double[] array1OrNull, double[] array2OrNull)
- {
- if (array1OrNull == null || array1OrNull.length == 0)
- {
- return array2OrNull;
- }
- if (array2OrNull == null || array2OrNull.length == 0)
- {
- return array1OrNull;
- }
- double[] newArray = new double[array1OrNull.length + array2OrNull.length];
- System.arraycopy(array1OrNull, 0, newArray, 0, array1OrNull.length);
- System.arraycopy(array2OrNull, 0, newArray, array1OrNull.length, array2OrNull.length);
- return newArray;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java
deleted file mode 100644
index c884b253e98..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java
+++ /dev/null
@@ -1,219 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import net.lemnik.eodsql.DataSet;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SamplePropertyAccessValidator;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Occurrence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.OccurrenceUtil;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.AbstractSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SampleAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SamplePeptideModification;
-
-/**
- * Implementation of {@link IProteinRelatedSampleTable}.
- *
- * @author Franz-Josef Elmer
- */
-class ProteinRelatedSampleTable implements IProteinRelatedSampleTable
-{
- private final IDAOFactory daoFactory;
-
- private final IPhosphoNetXDAOFactory specificDAOFactory;
-
- private final IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
-
- private List<ProteinRelatedSample> result;
-
- ProteinRelatedSampleTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
- {
- this.daoFactory = daoFactory;
- this.specificDAOFactory = specificDAOFactory;
- this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
- }
-
- @Override
- public List<ProteinRelatedSample> getSamples()
- {
- return result;
- }
-
- @Override
- public void load(Session session, TechId experimentID, TechId proteinReferenceID, String sequenceOrNull)
- {
- String experimentPermID =
- daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
- IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO(experimentID);
- Map<String, List<SampleAbundance>> sampleAbundanceMap =
- createSampleMap(proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID,
- proteinReferenceID.getId()));
- Map<String, List<SamplePeptideModification>> samplePeptideModificationMap =
- createSampleMap(proteinQueryDAO.listSamplePeptideModificatioByProtein(
- experimentPermID, proteinReferenceID.getId()));
- result = new ArrayList<ProteinRelatedSample>();
- SampleIDProvider sampleIDProvider = new SampleIDProvider(daoFactory.getSampleDAO());
- Map<PropertyTypePE, PropertyType> cache = new HashMap<PropertyTypePE, PropertyType>();
- Map<MaterialTypePE, MaterialType> materialTypeCache = new HashMap<MaterialTypePE, MaterialType>();
- for (Entry<String, List<SampleAbundance>> entry : sampleAbundanceMap.entrySet())
- {
- String key = entry.getKey();
- SamplePE sample = sampleIDProvider.getSampleOrParentSample(key);
- List<SampleAbundance> sampleAbundances = entry.getValue();
- List<SamplePeptideModification> samplePeptideModifications =
- samplePeptideModificationMap.get(key);
- if (samplePeptideModifications == null)
- {
- for (SampleAbundance sampleAbundance : sampleAbundances)
- {
- ProteinRelatedSample s = createFrom(sample, materialTypeCache, cache, session);
- s.setAbundance(sampleAbundance.getAbundance());
- result.add(s);
- }
- } else
- {
- for (SampleAbundance sampleAbundance : sampleAbundances)
- {
- Double abundance = sampleAbundance.getAbundance();
- result.addAll(createSamplesForPeptideModifications(samplePeptideModifications,
- sample, abundance, sequenceOrNull, materialTypeCache, cache, session));
- }
- }
- }
- for (Entry<String, List<SamplePeptideModification>> entry : samplePeptideModificationMap
- .entrySet())
- {
- String key = entry.getKey();
- if (sampleAbundanceMap.containsKey(key) == false)
- {
- SamplePE sample = sampleIDProvider.getSampleOrParentSample(key);
- List<SamplePeptideModification> samplePeptideModifications = entry.getValue();
- result.addAll(createSamplesForPeptideModifications(samplePeptideModifications,
- sample, null, sequenceOrNull, materialTypeCache, cache, session));
- }
- }
- }
-
- private List<ProteinRelatedSample> createSamplesForPeptideModifications(
- List<SamplePeptideModification> samplePeptideModifications, SamplePE sample,
- Double abundanceOrNull, String sequenceOrNull,
- Map<MaterialTypePE, MaterialType> materialTypeCache, Map<PropertyTypePE, PropertyType> cache
- , Session session)
- {
- List<ProteinRelatedSample> samples = new ArrayList<ProteinRelatedSample>();
- for (SamplePeptideModification samplePeptideModification : samplePeptideModifications)
- {
- int position = samplePeptideModification.getPosition();
- if (sequenceOrNull != null)
- {
- List<Occurrence> occurances =
- OccurrenceUtil.findAllOccurrences(sequenceOrNull,
- samplePeptideModification.getSequence());
- for (Occurrence occurrence : occurances)
- {
- samples.add(createProteinRelatedSample(samplePeptideModification, sample,
- abundanceOrNull, position + occurrence.getStartIndex(), materialTypeCache, cache, session));
- }
- } else
- {
- samples.add(createProteinRelatedSample(samplePeptideModification, sample,
- abundanceOrNull, position, materialTypeCache, cache, session));
- }
- }
- return samples;
- }
-
- private ProteinRelatedSample createProteinRelatedSample(
- SamplePeptideModification samplePeptideModification, SamplePE sample,
- Double abundanceOrNull, int position,
- Map<MaterialTypePE, MaterialType> materialTypeCache, Map<PropertyTypePE, PropertyType> cache
- , Session session)
- {
- ProteinRelatedSample s = createFrom(sample, materialTypeCache, cache, session);
- s.setAbundance(abundanceOrNull);
- int index = samplePeptideModification.getPosition() - 1;
- String sequence = samplePeptideModification.getSequence();
- if (index >= 0 && index < sequence.length())
- {
- s.setModifiedAminoAcid(sequence.charAt(index));
- }
- s.setModificationFraction(samplePeptideModification.getFraction());
- s.setModificationMass(samplePeptideModification.getMass());
- s.setModificationPosition((long) position);
- return s;
- }
-
- private ProteinRelatedSample createFrom(SamplePE sample, Map<MaterialTypePE, MaterialType> materialTypeCache,
- Map<PropertyTypePE, PropertyType> cache, Session session)
- {
- ProteinRelatedSample s = new ProteinRelatedSample();
- s.setCode(sample.getCode());
- s.setEntityType(SampleTypeTranslator.translate(sample.getSampleType(), materialTypeCache, cache));
- s.setId(sample.getId());
- s.setIdentifier(sample.getIdentifier());
- s.setPermId(sample.getPermId());
- s.setProperties(EntityPropertyTranslator.translate(sample.getProperties(), materialTypeCache, cache,
- managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, daoFactory)));
- return s;
- }
-
- private <T extends AbstractSample> Map<String, List<T>> createSampleMap(DataSet<T> items)
- {
- Map<String, List<T>> map = new LinkedHashMap<String, List<T>>();
- try
- {
- for (T item : items)
- {
- String samplePermID = item.getSamplePermID();
- List<T> list = map.get(samplePermID);
- if (list == null)
- {
- list = new ArrayList<T>();
- map.put(samplePermID, list);
- }
- list.add(item);
- }
- } finally
- {
- items.close();
- }
- return map;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java
deleted file mode 100644
index 46492166070..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.lemnik.eodsql.DataSet;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.Sequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinSequenceTable extends AbstractBusinessObject implements IProteinSequenceTable
-{
- private List<ProteinSequence> proteinSequences;
-
- private Map<Long, String> databaseIDToShortNameMap;
-
- ProteinSequenceTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- Session session)
- {
- super(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public List<ProteinSequence> getSequences()
- {
- if (proteinSequences == null)
- {
- throw new IllegalStateException("Sequences not loaded.");
- }
- return proteinSequences;
- }
-
- @Override
- public String getShortName(long databaseID)
- {
- if (databaseIDToShortNameMap == null)
- {
- throw new IllegalStateException("Sequences not loaded.");
- }
- String shortName = databaseIDToShortNameMap.get(databaseID);
- if (shortName == null)
- {
- throw new IllegalArgumentException("No sequence found for databaseID " + databaseID);
- }
- return shortName;
- }
-
- @Override
- public void loadByReference(TechId experimentID, TechId proteinReferenceID)
- {
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
- DataSet<Sequence> sequences =
- proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
- proteinSequences = new ArrayList<ProteinSequence>(sequences.size());
- databaseIDToShortNameMap = new HashMap<Long, String>();
- int number = 0;
- for (Sequence sequence : sequences)
- {
- ProteinSequence proteinSequence = new ProteinSequence();
- proteinSequence.setId(new TechId(sequence.getId()));
- String shortName = createShortName(number++);
- proteinSequence.setShortName(shortName);
- proteinSequence.setSequence(sequence.getSequence());
- long databaseID = sequence.getDatabaseID();
- proteinSequence.setDatabaseID(new TechId(databaseID));
- proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
- proteinSequences.add(proteinSequence);
- databaseIDToShortNameMap.put(databaseID, shortName);
- }
- sequences.close();
- }
-
- private String createShortName(int number)
- {
- StringBuilder builder = new StringBuilder();
- int n = number;
- while (n > 0 || builder.length() == 0)
- {
- builder.insert(0, "ABCEDEFGHIJKLMNOPQRSTUVWXYZ".charAt(n % 26));
- n /= 26;
- }
- return builder.toString();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java
deleted file mode 100644
index 44e994ffdb0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java
+++ /dev/null
@@ -1,150 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import net.lemnik.eodsql.DataSet;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
-
-/**
- * @author Franz-Josef Elmer
- */
-class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSummaryTable
-{
- static final double[] FDR_LEVELS = new double[]
- { 0, 0.01, 0.025, 0.05, 0.1 };
-
- private static final class Counter
- {
-
- private final double fdrLevel;
-
- private final Set<Long> proteins;
-
- private final Set<Long> decoyProteins;
-
- private final Set<String> peptides;
-
- private final Set<String> decoyPeptides;
-
- Counter(double fdrLevel)
- {
- this.fdrLevel = fdrLevel;
- proteins = new HashSet<Long>();
- decoyProteins = new HashSet<Long>();
- peptides = new HashSet<String>();
- decoyPeptides = new HashSet<String>();
- }
-
- public ProteinSummary getProteinSummary()
- {
- ProteinSummary proteinSummary = new ProteinSummary();
- proteinSummary.setFDR(fdrLevel);
- proteinSummary.setProteinCount(proteins.size());
- proteinSummary.setPeptideCount(peptides.size());
- proteinSummary.setDecoyProteinCount(decoyProteins.size());
- proteinSummary.setDecoyPeptideCount(decoyPeptides.size());
- return proteinSummary;
- }
-
- public void handle(double fdr, ProteinReferenceWithProbabilityAndPeptide protein)
- {
- if (Double.isNaN(fdr) || fdr <= fdrLevel)
- {
- String accessionNumber = protein.getAccessionNumber();
- if (accessionNumber.startsWith(AccessionNumberBuilder.DECOY_PREFIX))
- {
- decoyProteins.add(protein.getId());
- decoyPeptides.add(protein.getPeptideSequence());
- } else
- {
- proteins.add(protein.getId());
- peptides.add(protein.getPeptideSequence());
- }
- }
- }
- }
-
- private List<ProteinSummary> summaries;
-
- ProteinSummaryTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
- Session session)
- {
- super(daoFactory, specificDAOFactory, session);
- }
-
- @Override
- public List<ProteinSummary> getProteinSummaries()
- {
- return summaries;
- }
-
- @Override
- public void load(TechId experimentID)
- {
- IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
- String permID = experimentDAO.getByTechId(experimentID).getPermId();
- IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
- ErrorModel errorModel = new ErrorModel(dao);
- DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet =
- dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
- List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
- for (double fdrLevel : FDR_LEVELS)
- {
- counters.add(new Counter(fdrLevel));
- }
- try
- {
- for (ProteinReferenceWithProbabilityAndPeptide protein : resultSet)
- {
- long dataSetID = protein.getDataSetID();
- double probability = protein.getProbability();
- double fdr = errorModel.calculateFalsDiscoveryRate(dataSetID, probability);
- for (Counter counter : counters)
- {
- counter.handle(fdr, protein);
- }
- }
- summaries = getSummaries(counters);
- } finally
- {
- resultSet.close();
- }
- }
-
- private List<ProteinSummary> getSummaries(List<Counter> counters)
- {
- List<ProteinSummary> list = new ArrayList<ProteinSummary>(counters.size());
- for (Counter counter : counters)
- {
- list.add(counter.getProteinSummary());
- }
- return list;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProvider.java
deleted file mode 100644
index 663533f5b4f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProvider.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
-
-/**
- * Implementation based on {@link ISampleDAO}.
- *
- * @author Franz-Josef Elmer
- */
-public class SampleIDProvider implements ISampleIDProvider
-{
- private final ISampleDAO sampleDAO;
-
- private final Map<String, SamplePE> samples = new LinkedHashMap<String, SamplePE>();
-
- public SampleIDProvider(ISampleDAO sampleDAO)
- {
- this.sampleDAO = sampleDAO;
- }
-
- @Override
- public long getSampleIDOrParentSampleID(String samplePermID)
- {
- return HibernateUtils.getId(getSampleOrParentSample(samplePermID));
- }
-
- @Override
- public SamplePE getSampleOrParentSample(String samplePermID)
- {
- SamplePE sample = samples.get(samplePermID);
- if (sample == null)
- {
- sample = sampleDAO.tryToFindByPermID(samplePermID);
- if (sample == null)
- {
- throw new UserFailureException("No sample found for permID " + samplePermID);
- }
- SamplePE parentSample = sample.getGeneratedFrom();
- if (parentSample != null)
- {
- sample = parentSample;
- }
- samples.put(samplePermID, sample);
- }
- return sample;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoader.java
deleted file mode 100644
index cf40e60ebff..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoader.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import ch.systemsx.cisd.common.collection.IValidator;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipSkeleton;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleSkeleton;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SampleLoader implements ISampleLoader
-{
- private final Session session;
-
- private final IDAOFactory daoFactory;
-
- private final ICommonBusinessObjectFactory businessObjectFactory;
-
- public SampleLoader(Session session, IDAOFactory daoFactory,
- ICommonBusinessObjectFactory businessObjectFactory)
- {
- this.session = session;
- this.daoFactory = daoFactory;
- this.businessObjectFactory = businessObjectFactory;
-
- }
-
- @Override
- public List<Sample> listSamplesWithParentsByTypeAndSpace(String sampleTypeCode, String spaceCode)
- {
- ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- Set<Long> filteredSampleIDs = getSampleIDs(sampleLister, sampleTypeCode, spaceCode);
- ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(filteredSampleIDs);
- criteria.setEnrichDependentSamplesWithProperties(true);
- List<Sample> samples = sampleLister.list(criteria);
- ArrayList<Sample> samplesWithParent = new ArrayList<Sample>();
- for (Sample sample : samples)
- {
- if (sample.getParents().size() == 1)
- {
- samplesWithParent.add(sample);
- }
- }
- return samplesWithParent;
- }
-
- private Set<Long> getSampleIDs(ISampleLister sampleLister, String sampleTypeCode,
- String spaceCode)
- {
- SampleTypePE sampleTypePE =
- daoFactory.getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
- if (sampleTypePE == null)
- {
- return Collections.emptySet();
- }
- final Long sampleTypeID = sampleTypePE.getId();
- SpacePE space =
- daoFactory.getSpaceDAO().tryFindSpaceByCode(spaceCode);
- if (space == null)
- {
- return Collections.emptySet();
- }
- final Long spaceID = space.getId();
- List<SampleSkeleton> sampleSkeletons =
- sampleLister.listSampleBy(new IValidator<SampleSkeleton>()
- {
- @Override
- public boolean isValid(SampleSkeleton sampleSkeleton)
- {
- return spaceID.equals(sampleSkeleton.getSpaceID())
- && sampleTypeID.equals(sampleSkeleton.getTypeID());
- }
- });
- final Set<Long> sampleIDs = new HashSet<Long>();
- for (SampleSkeleton sampleSkeleton : sampleSkeletons)
- {
- sampleIDs.add(sampleSkeleton.getId());
- }
- final long relationshipTypeID =
- sampleLister
- .getRelationshipTypeID(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
- @SuppressWarnings("deprecation")
- List<SampleRelationshipSkeleton> relationshipSkeletons =
- sampleLister.listSampleRelationshipsBy(new IValidator<SampleRelationshipSkeleton>()
- {
- @Override
- public boolean isValid(SampleRelationshipSkeleton skeleton)
- {
- return skeleton.getRelationshipTypeID() == relationshipTypeID
- && sampleIDs.contains(skeleton.getChildSampleID());
- }
- });
- Set<Long> filteredSampleIDs = new HashSet<Long>();
- for (SampleRelationshipSkeleton sampleRelationShipSkeleton : relationshipSkeletons)
- {
- filteredSampleIDs.add(sampleRelationShipSkeleton.getChildSampleID());
- }
- return filteredSampleIDs;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProvider.java
deleted file mode 100644
index da9493facb0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProvider.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.HashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-
-/**
- * @author Franz-Josef Elmer
- */
-class SampleProvider implements ISampleProvider
-{
- private final Session session;
-
- private final IBusinessObjectFactory boFactory;
-
- private Map<String, Sample> samplesByPermIDs;
-
- SampleProvider(Session session, IBusinessObjectFactory boFactory)
- {
- this.session = session;
- this.boFactory = boFactory;
- }
-
- @Override
- public void loadByExperimentID(TechId experimentID)
- {
- samplesByPermIDs = new HashMap<String, Sample>();
- ListSampleCriteria criteria = ListSampleCriteria.createForExperiment(experimentID);
- ISampleLister lister = boFactory.createSampleLister(session);
- ListOrSearchSampleCriteria criteria2 = new ListOrSearchSampleCriteria(criteria);
- criteria2.setEnrichDependentSamplesWithProperties(true);
- gatherSamplesAndAncestorsRecursively(lister, criteria2);
- }
-
- private void gatherSamplesAndAncestorsRecursively(ISampleLister lister,
- ListOrSearchSampleCriteria criteria)
- {
- List<Sample> list = lister.list(criteria);
- Set<Long> sampleIDs = new LinkedHashSet<Long>();
- for (Sample sample : list)
- {
- samplesByPermIDs.put(sample.getPermId(), sample);
- sampleIDs.add(sample.getId());
- }
- if (sampleIDs.isEmpty())
- {
- return;
- }
- ListSampleCriteria criteria2 =
- ListSampleCriteria.createForChildren(sampleIDs);
- ListOrSearchSampleCriteria criteria3 = new ListOrSearchSampleCriteria(criteria2);
- criteria3.setEnrichDependentSamplesWithProperties(true);
- gatherSamplesAndAncestorsRecursively(lister, criteria3);
- }
-
- @Override
- public Sample getSample(String permID)
- {
- Sample sample = samplesByPermIDs.get(permID);
- if (sample == null)
- {
- throw new UserFailureException(
- "No sample with following perm ID registered in openBIS: " + permID);
- }
- return sample;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java
deleted file mode 100644
index 7bab99e446a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-import net.lemnik.eodsql.DataSet;
-import ch.systemsx.cisd.common.collection.IValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SamplePropertyAccessValidator;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifierHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.SampleWithPropertiesAndAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SampleAbundance;
-
-/**
- * @author Franz-Josef Elmer
- */
-class SampleTable extends AbstractBusinessObject implements ISampleTable
-{
- private List<SampleWithPropertiesAndAbundance> samples =
- new ArrayList<SampleWithPropertiesAndAbundance>();
-
- private SampleIDProvider sampleIDProvider;
-
- private IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
-
- SampleTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
- {
- super(daoFactory, specificDAOFactory, session);
- sampleIDProvider = new SampleIDProvider(daoFactory.getSampleDAO());
- this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
- }
-
- @Override
- public List<SampleWithPropertiesAndAbundance> getSamples()
- {
- return samples;
- }
-
- @Override
- public void loadSamplesWithAbundance(Session session, TechId experimentID, TechId proteinReferenceID)
- {
- samples = new ArrayList<SampleWithPropertiesAndAbundance>();
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
- IDAOFactory daoFactory = getDaoFactory();
- String experimentPermID =
- daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
- DataSet<SampleAbundance> sampleAbundances =
- proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID,
- proteinReferenceID.getId());
- try
- {
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
- for (SampleAbundance sampleAbundance : sampleAbundances)
- {
- SampleWithPropertiesAndAbundance sample = new SampleWithPropertiesAndAbundance();
- sample.setAbundance(sampleAbundance.getAbundance());
- String samplePermID = sampleAbundance.getSamplePermID();
- long sampleID = sampleIDProvider.getSampleIDOrParentSampleID(samplePermID);
- SamplePE samplePE = sampleDAO.getByTechId(new TechId(sampleID));
- fillSampleData(sample, samplePE, managedPropertyEvaluatorFactory,
- new SamplePropertyAccessValidator(session, daoFactory));
- samples.add(sample);
- }
- } finally
- {
- sampleAbundances.close();
- }
- }
-
- private final static void fillSampleData(final SampleWithPropertiesAndAbundance result,
- final SamplePE samplePE,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- IValidator<IIdentifierHolder> samplePropertyAccessValidator)
- {
- result.setId(HibernateUtils.getId(samplePE));
- result.setPermId(samplePE.getPermId());
- result.setCode(samplePE.getCode());
- result.setIdentifier(samplePE.getIdentifier());
- result.setSampleType(SampleTypeTranslator.translate(samplePE.getSampleType(),
- new HashMap<MaterialTypePE, MaterialType>(), new HashMap<PropertyTypePE, PropertyType>()));
- result.setProperties(EntityPropertyTranslator.translate(samplePE.getProperties(),
- new HashMap<MaterialTypePE, MaterialType>(), new HashMap<PropertyTypePE, PropertyType>(),
- managedPropertyEvaluatorFactory, samplePropertyAccessValidator));
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinder.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinder.java
deleted file mode 100644
index 2aa35c622e4..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinder.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.StringUtils;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * Helper class which gathers properties in a sample and its ancestor samples defining sample treatments. Treatments of the same type will be
- * overridden by descendants.
- *
- * @author Franz-Josef Elmer
- */
-public class TreatmentFinder
-{
- public static final String TREATMENT_TYPE_CODE = "TREATMENT_TYPE";
-
- public static final String TREATMENT_VALUE_CODE = "TREATMENT_VALUE";
-
- /**
- * Returns all treatments found for specified sample and its ancestors.
- */
- public List<Treatment> findTreatmentsOf(Sample sample)
- {
- Map<String, Treatment> treatments = new LinkedHashMap<String, Treatment>();
- findAndAddTreatments(treatments, sample);
- List<Treatment> treatmentList = new ArrayList<Treatment>(treatments.values());
- Collections.sort(treatmentList);
- return treatmentList;
- }
-
- private void findAndAddTreatments(Map<String, Treatment> treatments, Sample sampleOrNull)
- {
- if (sampleOrNull == null)
- {
- return;
- }
- findAndAddTreatments(treatments, sampleOrNull.getGeneratedFrom());
- List<IEntityProperty> properties = sampleOrNull.getProperties();
- Map<String, Treatment> codeTreatmentMap = new HashMap<String, Treatment>();
- for (IEntityProperty property : properties)
- {
- PropertyType propertyType = property.getPropertyType();
- String code = propertyType.getCode();
- if (code.startsWith(TREATMENT_TYPE_CODE))
- {
- String treatmentCode = code.substring(TREATMENT_TYPE_CODE.length());
- VocabularyTerm vocabularyTerm = property.getVocabularyTerm();
- if (vocabularyTerm == null)
- {
- throw new UserFailureException("Data type of property type '" + code
- + "' must be a vocabulary.");
- }
- Treatment treatment = getOrCreateTreatment(codeTreatmentMap, treatmentCode);
- treatment.setType(getLabelOrCode(vocabularyTerm));
- treatment.setTypeCode(vocabularyTerm.getCode());
- } else if (code.startsWith(TREATMENT_VALUE_CODE))
- {
- String treatmentCode = code.substring(TREATMENT_VALUE_CODE.length());
- Treatment treatment = getOrCreateTreatment(codeTreatmentMap, treatmentCode);
- DataTypeCode dataType = propertyType.getDataType().getCode();
- treatment.setValueType(dataType.toString());
- String value = getValue(property);
- treatment.setValue(value);
- }
- }
- Collection<Treatment> treatmentsToBeAdded = codeTreatmentMap.values();
- for (Treatment treatment : treatmentsToBeAdded)
- {
- Treatment superTreatment = treatments.get(treatment.getType());
- if (superTreatment == null)
- {
- treatments.put(treatment.getType(), treatment);
- } else
- {
- superTreatment.setValue(treatment.getValue());
- }
- }
- }
-
- private String getValue(IEntityProperty property)
- {
- Material material = property.getMaterial();
- if (material != null)
- {
- return material.getCode();
- }
- VocabularyTerm vocabularyTerm = property.getVocabularyTerm();
- return vocabularyTerm == null ? property.getValue() : getLabelOrCode(vocabularyTerm);
- }
-
- private String getLabelOrCode(VocabularyTerm vocabularyTerm)
- {
- String label = vocabularyTerm.getLabel();
- if (StringUtils.isBlank(label))
- {
- label = vocabularyTerm.getCode();
- }
- return label;
- }
-
- private Treatment getOrCreateTreatment(Map<String, Treatment> codeTreatmentMap,
- String treatmentCode)
- {
- Treatment treatment = codeTreatmentMap.get(treatmentCode);
- if (treatment == null)
- {
- treatment = new Treatment();
- treatment.setType("");
- treatment.setTypeCode("");
- treatment.setValue("");
- treatment.setValueType(DataTypeCode.VARCHAR.toString());
- codeTreatmentMap.put(treatmentCode, treatment);
- }
- return treatment;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java
deleted file mode 100644
index 22cf326c808..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-
-/**
- * A factory for PhosphoNetX specific DAOs.
- *
- * @author Franz-Josef Elmer
- */
-public interface IPhosphoNetXDAOFactory
-{
- public IProteinQueryDAO getProteinQueryDAO(TechId experimentID);
-
- public IProteinQueryDAO getProteinQueryDAO(String experimentPermID);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IProteinQueryDAO.java
deleted file mode 100644
index 861f24b02ce..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IProteinQueryDAO.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess;
-
-import it.unimi.dsi.fastutil.longs.LongSet;
-import net.lemnik.eodsql.BaseQuery;
-import net.lemnik.eodsql.DataSet;
-import net.lemnik.eodsql.Select;
-
-import ch.systemsx.cisd.common.db.mapper.LongSetMapper;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IndistinguishableProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.PeptideWithModification;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReference;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SampleAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SamplePeptideModification;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.Sequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProteinQueryDAO extends BaseQuery
-{
- @Select(sql = "select * from probability_fdr_mappings where dase_id = ?{1}", disconnected = true)
- public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
-
- @Select("select d.id as data_set_id, p.id as protein_id, probability, coverage, "
- + "pr.id, accession_number, description from protein_references as pr "
- + "left join sequences as s on s.prre_id = pr.id "
- + "left join identified_proteins as ip on ip.sequ_id = s.id "
- + "left join proteins as p on ip.prot_id = p.id "
- + "left join data_sets as d on p.dase_id = d.id "
- + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1} and ip.is_primary = 't'")
- public DataSet<ProteinReferenceWithProtein> listProteinReferencesByExperiment(
- String experimentPermID);
-
- @Select(sql = "select p.id, a.value, s.perm_id "
- + "from proteins as p join abundances as a on p.id = a.prot_id "
- + "left join samples as s on a.samp_id = s.id "
- + "where p.id = any (?{1})", parameterBindings = { LongSetMapper.class })
- public DataSet<ProteinAbundance> listProteinWithAbundanceByExperiment(LongSet proteinIDs);
-
- @Select(sql = "select p.dase_id as data_set_id, p.probability, s.prre_id as id, pr.accession_number, pe.sequence "
- + "from identified_proteins as ip left join sequences as s on ip.sequ_id = s.id "
- + "left join protein_references as pr on s.prre_id = pr.id "
- + "left join proteins as p on ip.prot_id = p.id "
- + "left join peptides as pe on pe.prot_id = p.id "
- + "left join data_sets as d on p.dase_id = d.id "
- + "left join experiments as e on d.expe_id = e.id "
- + "where e.perm_id = ?{1} and ip.is_primary = 't'")
- public DataSet<ProteinReferenceWithProbabilityAndPeptide> listProteinsWithProbabilityAndPeptidesByExperiment(
- String experimentPermID);
-
- @Select("select distinct s.perm_id "
- + "from abundances as a left join proteins as p on a.prot_id = p.id "
- + " left join data_sets as d on p.dase_id = d.id "
- + " left join experiments as e on d.expe_id = e.id "
- + " left join samples as s on a.samp_id = s.id "
- + "where e.perm_id = ?{1} order by s.perm_id")
- public DataSet<String> listAbundanceRelatedSamplePermIDsByExperiment(String experimentPermID);
-
- @Select("select * from protein_references where id = ?{1}")
- public ProteinReference tryToGetProteinReference(long proteinReferenceID);
-
- @Select("select s.id, db_id, amino_acid_sequence, name_and_version "
- + "from sequences as s join databases as d on s.db_id = d.id "
- + "where s.prre_id = ?{1} order by name_and_version")
- public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID);
-
- @Select("select ds.id as data_set_id, ds.perm_id as data_set_perm_id, p.id as protein_id, "
- + "probability, coverage, count(pe.id) as peptide_count, amino_acid_sequence, s.db_id, name_and_version "
- + "from data_sets as ds join experiments as e on ds.expe_id = e.id "
- + " join proteins as p on p.dase_id = ds.id "
- + " join identified_proteins as ip on ip.prot_id = p.id "
- + " join sequences as s on ip.sequ_id = s.id "
- + " join databases as db on s.db_id = db.id "
- + " left join peptides as pe on pe.prot_id = p.id "
- + "where s.prre_id = ?{2} and e.perm_id = ?{1} and ip.is_primary = 't' "
- + "group by data_set_id, data_set_perm_id, protein_id, probability, coverage, "
- + " amino_acid_sequence, s.db_id, name_and_version order by data_set_perm_id")
- public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
- String experimentPermID, long proteinReferenceID);
-
- @Select("select pe.id, sequence, pos, mass "
- + "from peptides as pe left join modified_peptides as mp on mp.pept_id = pe.id "
- + " left join modifications as m on m.mope_id = mp.id "
- + "where prot_id = ?{1} order by pe.id")
- public DataSet<PeptideWithModification> listIdentifiedPeptidesByProtein(long proteinID);
-
- @Select("select accession_number, description, amino_acid_sequence, coverage "
- + "from identified_proteins as ip join sequences as s on ip.sequ_id = s.id "
- + " join protein_references as pr on s.prre_id = pr.id "
- + "where ip.prot_id = ?{1} and ip.is_primary = 'f'")
- public DataSet<IndistinguishableProtein> listIndistinguishableProteinsByProteinID(long proteinID);
-
- @Select("select distinct a.id, samples.perm_id, value "
- + "from abundances as a left join proteins as p on a.prot_id = p.id "
- + " left join data_sets as d on p.dase_id = d.id "
- + " left join experiments as e on d.expe_id = e.id "
- + " left join identified_proteins as ip on ip.prot_id = p.id "
- + " left join sequences as s on ip.sequ_id = s.id "
- + " left join samples on a.samp_id = samples.id "
- + "where e.perm_id = ?{1} and s.prre_id = ?{2} and ip.is_primary = 't'")
- public DataSet<SampleAbundance> listSampleAbundanceByProtein(String experimentPermID,
- long proteinReferenceID);
-
- @Select("select distinct mf.id, samples.perm_id, fraction, pos, mass, sequence "
- + "from modification_fractions as mf left join modifications as m on mf.modi_id = m.id "
- + " left join modified_peptides as mp on m.mope_id = mp.id "
- + " left join peptides as pe on mp.pept_id = pe.id "
- + " left join proteins as p on pe.prot_id = p.id "
- + " left join data_sets as d on p.dase_id = d.id "
- + " left join experiments as e on d.expe_id = e.id "
- + " left join identified_proteins as ip on ip.prot_id = p.id "
- + " left join sequences as s on ip.sequ_id = s.id "
- + " left join samples on mf.samp_id = samples.id "
- + "where e.perm_id = ?{1} and s.prre_id = ?{2} and ip.is_primary = 't'")
- public DataSet<SamplePeptideModification> listSamplePeptideModificatioByProtein(
- String experimentPermID, long proteinReferenceID);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java
deleted file mode 100644
index a9823517b4b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java
+++ /dev/null
@@ -1,130 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.db;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.QueryTool;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSourceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PhosphoNetXDAOFactory implements IPhosphoNetXDAOFactory
-{
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, PhosphoNetXDAOFactory.class);
-
- private final Map<DataSource, IProteinQueryDAO> daos = new HashMap<DataSource, IProteinQueryDAO>();
-
- private final IDAOFactory daoFactory;
-
- private final IDataSourceProvider dataSourceProvider;
-
- public PhosphoNetXDAOFactory(IDataSourceProvider dataSourceProvider, IDAOFactory daoFactory)
- {
- this.dataSourceProvider = dataSourceProvider;
- this.daoFactory = daoFactory;
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("DAO factory for proteomics created.");
- }
- }
-
- @Override
- public IProteinQueryDAO getProteinQueryDAO(String experimentPermID)
- {
- ExperimentPE experiment = daoFactory.getExperimentDAO().tryGetByPermID(experimentPermID);
- if (experiment == null)
- {
- throw new UserFailureException("No experiment with following perm ID found: "
- + experimentPermID);
- }
- return getProteinQueryDAO(experiment);
- }
-
- @Override
- public IProteinQueryDAO getProteinQueryDAO(TechId experimentID)
- {
- ExperimentPE experiment = daoFactory.getExperimentDAO().tryGetByTechId(experimentID);
- if (experiment == null)
- {
- throw new UserFailureException("No experiment with following technical ID found: "
- + experimentID);
- }
- return getProteinQueryDAO(experiment);
- }
-
- public IProteinQueryDAO getProteinQueryDAO(ExperimentPE experiment)
- {
- DataSource dataSource = getDataSource(experiment);
- IProteinQueryDAO dao = daos.get(dataSource);
- if (dao == null)
- {
- dao = QueryTool.getQuery(dataSource, IProteinQueryDAO.class);
- daos.put(dataSource, dao);
- }
- return dao;
- }
-
- private DataSource getDataSource(ExperimentPE experiment)
- {
- IDataDAO dataDAO = daoFactory.getDataDAO();
-
- List<DataPE> dataSets = dataDAO.listDataSets(experiment);
- Set<String> dataStores = new HashSet<String>();
- for (DataPE data : dataSets)
- {
- dataStores.add(data.getDataStore().getCode());
- }
- if (dataStores.isEmpty())
- {
- throw new UserFailureException("Experiment with " + experiment.getIdentifier()
- + " has no data sets.");
- }
- if (dataStores.size() > 1)
- {
- throw new UserFailureException("Experiment with " + experiment.getIdentifier()
- + " has data sets from more than one store. The stores are the following: "
- + dataStores);
- }
- DataSource dataSource =
- dataSourceProvider.getDataSourceByDataStoreServerCode(dataStores.iterator()
- .next(), "proteomics");
- return dataSource;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/migration/MigrationStepFrom002To003.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/migration/MigrationStepFrom002To003.java
deleted file mode 100644
index df1252a3761..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/migration/MigrationStepFrom002To003.java
+++ /dev/null
@@ -1,145 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.db.migration;
-
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.sql.DataSource;
-
-import org.apache.log4j.Logger;
-import org.springframework.dao.DataAccessException;
-import org.springframework.jdbc.core.JdbcOperations;
-import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.core.ResultSetExtractor;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Occurrence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.OccurrenceUtil;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class MigrationStepFrom002To003 extends MigrationStepAdapter
-{
- private static final long MB = 1024 * 1024;
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, MigrationStepFrom002To003.class);
-
- @Override
- public void performPostMigration(JdbcTemplate simpleJdbcTemplate, DataSource dataSource)
- throws DataAccessException
- {
- List<Object[]> coverageValues = calculateCoverageValues(simpleJdbcTemplate);
- operationLog.info("update " + coverageValues.size() + " identified proteins");
- simpleJdbcTemplate.batchUpdate("update identified_proteins set coverage = ? where id = ?",
- coverageValues);
- }
-
- private List<Object[]> calculateCoverageValues(JdbcTemplate simpleJdbcTemplate)
- {
- logMemory();
- JdbcOperations jdbcOperations = simpleJdbcTemplate;
- final Map<Long, List<String>> peptides = getPeptides(jdbcOperations);
- logMemory();
- final List<Object[]> values = new ArrayList<Object[]>();
- jdbcOperations.query("select ip.id, ip.prot_id, s.amino_acid_sequence "
- + "from identified_proteins as ip "
- + "join sequences as s on ip.sequ_id = s.id where coverage is null",
- new ResultSetExtractor()
- {
- @Override
- public Object extractData(ResultSet rs) throws SQLException,
- DataAccessException
- {
- while (rs.next())
- {
- long id = rs.getLong(1);
- long proteinID = rs.getLong(2);
- String sequence = rs.getString(3);
- List<String> peptideSequences = peptides.get(proteinID);
- double coverage = calculateCoverage(sequence, peptideSequences);
- values.add(new Object[] { coverage, id });
- }
- return null;
- }
- });
- logMemory();
- return values;
- }
-
- private Map<Long, List<String>> getPeptides(JdbcOperations jdbcOperations)
- {
- final Map<Long, List<String>> peptides = new HashMap<Long, List<String>>();
- jdbcOperations.query("select prot_id, sequence from peptides order by prot_id",
- new ResultSetExtractor()
- {
- @Override
- public Object extractData(ResultSet rs) throws SQLException,
- DataAccessException
- {
- long currentProteinID = -1;
- ArrayList<String> list = null;
- while (rs.next())
- {
- long proteinID = rs.getLong(1);
- if (list == null || proteinID != currentProteinID)
- {
- if (list != null)
- {
- list.trimToSize();
- }
- currentProteinID = proteinID;
- list = new ArrayList<String>();
- peptides.put(proteinID, list);
- }
- list.add(rs.getString(2));
- }
- return null;
- }
- });
- return peptides;
- }
-
- private double calculateCoverage(String sequence, List<String> peptides)
- {
- Set<String> distinctPeptides = new HashSet<String>(peptides);
- List<Occurrence> list = OccurrenceUtil.getCoverage(sequence, distinctPeptides);
- int sumPeptides = 0;
- for (Occurrence occurrence : list)
- {
- sumPeptides += occurrence.getWord().length();
- }
- return sumPeptides / (double) sequence.length();
- }
-
- private void logMemory()
- {
- Runtime runtime = Runtime.getRuntime();
- long usedMemory = (runtime.totalMemory() - runtime.freeMemory()) / MB;
- operationLog.info(usedMemory + " MB used, " + runtime.totalMemory() / MB + " MB total");
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/CacheData.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/CacheData.java
deleted file mode 100644
index ebaf25b670a..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/CacheData.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared;
-
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-
-/**
- * Annotation for methods to cache their return values.
- *
- * @author Franz-Josef Elmer
- */
-@Retention(RetentionPolicy.RUNTIME)
-@Target(ElementType.METHOD)
-@Inherited
-public @interface CacheData
-{
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java
deleted file mode 100644
index 10215981305..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared;
-
-import java.util.List;
-
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.IServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.DataSetProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinByExperiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IPhosphoNetXServer extends IServer
-{
- @Transactional
- public Vocabulary getTreatmentTypeVocabulary(String sessionToken) throws UserFailureException;
-
- @Transactional
- @CacheData
- public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
- String sessionToken, TechId experimentID, String treatmentTypeOrNull)
- throws UserFailureException;
-
- @Transactional
- @CacheData
- public List<ProteinInfo> listProteinsByExperiment(String sessionToken, TechId experimentId,
- double falseDiscoveryRate, AggregateFunction function, String treatmentTypeCode,
- boolean aggregateOnOriginal) throws UserFailureException;
-
- @Transactional
- @CacheData
- public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
- TechId experimentId) throws UserFailureException;
-
- @Transactional
- public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
- TechId proteinReferenceID) throws UserFailureException;
-
- @Transactional
- public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- TechId experimentID, TechId proteinReferenceID) throws UserFailureException;
-
- @Transactional
- public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
- TechId experimentId, TechId proteinReferenceID) throws UserFailureException;
-
- @Transactional
- public List<ProteinRelatedSample> listProteinRelatedSamplesByProtein(String sessionToken,
- TechId experimentID, TechId proteinReferenceID) throws UserFailureException;
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IProteomicsDataServiceInternal.java
deleted file mode 100644
index 04e941dc98c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IProteomicsDataServiceInternal.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared;
-
-import java.util.List;
-
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.openbis.generic.shared.IServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface IProteomicsDataServiceInternal extends IServer
-{
- /**
- * Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample which the specified user is allow to read.
- */
- @Transactional
- public List<MsInjectionSample> listRawDataSamples(String sessionToken);
-
- /**
- * Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample.
- */
- @Transactional
- public List<MsInjectionSample> listAllRawDataSamples(String sessionToken);
-
- @Deprecated
- @Transactional
- public void processRawData(String sessionToken, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType);
-
- @Transactional
- public void processDataSets(String sessionToken, String dataSetProcessingKey,
- List<String> dataSetCodes);
-
- @Transactional
- public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode);
-
- @Transactional
- public List<AbstractExternalData> listDataSetsByExperiment(String sessionToken, TechId experimentID);
-
- @Transactional
- public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
- String experimentTypeCode, long[] searchExperimentIDs);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ProbabilityToFDRCalculator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ProbabilityToFDRCalculator.java
deleted file mode 100644
index ebb6dbd9dd2..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ProbabilityToFDRCalculator.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-public final class ProbabilityToFDRCalculator
-{
- private static final class MappingEntry implements Comparable<ProbabilityToFDRCalculator.MappingEntry>
- {
- private final double probability;
-
- private final double fdr;
-
- MappingEntry(double probability, double fdr)
- {
- this.probability = probability;
- this.fdr = fdr;
- }
-
- @Override
- public int compareTo(ProbabilityToFDRCalculator.MappingEntry that)
- {
- return probability < that.probability ? -1 : (probability > that.probability ? 1
- : 0);
- }
-
- @Override
- public String toString()
- {
- return probability + " = " + fdr;
- }
- }
-
- private final List<ProbabilityToFDRCalculator.MappingEntry> mappingEntries = new ArrayList<ProbabilityToFDRCalculator.MappingEntry>();
-
- public void add(double probability, double falseDiscoveryRate)
- {
- mappingEntries.add(new MappingEntry(probability, falseDiscoveryRate));
- }
-
- public void init()
- {
- Collections.sort(mappingEntries);
- }
-
- public double calculateFDR(double probability)
- {
- if (mappingEntries.isEmpty())
- {
- return Double.NaN;
- }
- int index = Collections.binarySearch(mappingEntries, new MappingEntry(probability, 0));
- if (index >= 0)
- {
- return mappingEntries.get(index).fdr;
- }
- // calculate by linear interpolation
- int index1 = -index - 1;
- int index0 = index1 - 1;
- assert index0 >= 0;
- ProbabilityToFDRCalculator.MappingEntry m0 = mappingEntries.get(index0);
- ProbabilityToFDRCalculator.MappingEntry m1 = mappingEntries.get(index1);
- double scale = (m1.fdr - m0.fdr) / (m1.probability - m0.probability);
- return m0.fdr + scale * (probability - m0.probability);
- }
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ResourceNames.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ResourceNames.java
deleted file mode 100644
index e1d3f6edb57..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/ResourceNames.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ResourceNames
-{
- private ResourceNames()
- {
- }
-
- public final static String PROTEOMICS_PLUGIN_SERVICE = "proteomics-plugin-service";
-
- public final static String PROTEOMICS_PLUGIN_SERVER = "proteomics-plugin-server";
-
- public final static String PROTEOMICS_RAW_DATA_SERVICE_WEB = "proteomics-data-service-web";
-
- public final static String PROTEOMICS_DAO_FACTORY = "proteomics-dao-factory";
-
- public final static String PROTEOMICS_BO_FACTORY = "proteomics-bo-factory";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/IProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/IProteomicsDataService.java
deleted file mode 100644
index ec18a32bb19..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/IProteomicsDataService.java
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1;
-
-import java.util.List;
-
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.common.api.IRpcService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1.IProteomicsDataApiFacade;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * Interface used by {@link IProteomicsDataApiFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IProteomicsDataService extends IRpcService
-{
- /**
- * Name of this service for which it is registered at the RPC name server.
- */
- public static final String SERVICE_NAME = "proteomics-data";
-
- /**
- * Service part of the URL to access this service remotely.
- */
- public static final String SERVER_URL = "/rmi-" + SERVICE_NAME + "-v1";
-
- /**
- * Tries to authenticate specified user with specified password. Returns session token if succeeded otherwise <code>null</code> is returned.
- */
- @Transactional
- public String tryToAuthenticateAtRawDataServer(String userID, String userPassword);
-
- /**
- * Logout the session with the specified session token.
- */
- @Transactional
- public void logout(String sessionToken);
-
- /**
- * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which the specified user is allowed to read.
- */
- @Transactional
- public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID);
-
- /**
- * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample.
- */
- @Transactional
- public List<MsInjectionDataInfo> listAllRawDataSamples(String sessionToken, String userID);
-
- /**
- * Lists all processing plugins on DSS.
- */
- @Transactional
- public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
- String sessionToken);
-
- /**
- * Processes the data sets of specified samples by the DSS processing plug-in of specified key for the specified user. Implementations should
- * check that the specified user is allowed to read specified samples.
- */
- @Deprecated
- @Transactional
- public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType);
-
- /**
- * Processes the specified data sets by the DSS processing plug-in of specified key for the specified user. Implementations should check that the
- * specified user is allowed to read specified data sets.
- */
- @Transactional
- public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
- List<String> dataSetCodes);
-
- /**
- * Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to read.
- */
- @Deprecated
- @Transactional
- public List<Experiment> listSearchExperiments(String sessionToken, String userID);
-
- /**
- * Returns all experiments of specified type which the specified user is allowed to read.
- */
- @Transactional
- public List<Experiment> listExperiments(String sessionToken, String userID,
- String experimentTypeCode);
-
- /**
- * Returns all data sets of specified experiment which the specified user is allowed to read.
- */
- @Transactional
- public List<DataSet> listDataSetsByExperiment(String sessionToken, String userID,
- long experimentID);
-
- /**
- * Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS processing plug-in of specified key for the specified
- * user. It will be checked if the experiments are of search experiments and if the user is allowed to read them.
- */
- @Deprecated
- @Transactional
- public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] searchExperimentIDs);
-
- /**
- * Processes the data sets of specified experiments by the DSS processing plug-in of specified key for the specified user. It will be checked if
- * the experiments are of specified type and if the user is allowed to read them.
- */
- @Transactional
- public void processProteinResultDataSets(String sessionToken, String userID,
- String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs);
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataSet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataSet.java
deleted file mode 100644
index c26386280c0..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataSet.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto;
-
-import java.io.Serializable;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-/**
- * Date Set bean with properties, children and parents.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSet implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private long id;
-
- private String code;
-
- private String type;
-
- private Date registrationDate;
-
- private Map<PropertyKey, Serializable> properties;
-
- private Set<DataSet> parents = new HashSet<DataSet>();
-
- private Set<DataSet> children = new HashSet<DataSet>();
-
- public final long getId()
- {
- return id;
- }
-
- public final void setId(long id)
- {
- this.id = id;
- }
-
- public final String getCode()
- {
- return code;
- }
-
- public final void setCode(String code)
- {
- this.code = code;
- }
-
- public final String getType()
- {
- return type;
- }
-
- public final void setType(String type)
- {
- this.type = type;
- }
-
- public final Date getRegistrationDate()
- {
- return registrationDate;
- }
-
- public final void setRegistrationDate(Date registrationDate)
- {
- this.registrationDate = registrationDate;
- }
-
- public final Map<PropertyKey, Serializable> getProperties()
- {
- return properties;
- }
-
- public final void setProperties(Map<PropertyKey, Serializable> properties)
- {
- this.properties = properties;
- }
-
- public final Set<DataSet> getParents()
- {
- return parents;
- }
-
- public final Set<DataSet> getChildren()
- {
- return children;
- }
-
- public void addChild(DataSet child)
- {
- getChildren().add(child);
- child.getParents().add(this);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java
deleted file mode 100644
index 2f1ed5b2a11..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * Information about a processing plugin on a Data Store Server (DSS).
- *
- * @author Franz-Josef Elmer
- */
-public class DataStoreServerProcessingPluginInfo implements Serializable
-{
-
- private static final long serialVersionUID = 1L;
-
- private final String key;
-
- private final String label;
-
- private final List<String> datasetTypeCodes;
-
- /**
- * Create a new instance for specified key, label and data set type codes.
- */
- public DataStoreServerProcessingPluginInfo(String key, String label, List<String> datasetTypeCodes)
- {
- this.key = key;
- this.label = label;
- this.datasetTypeCodes = Collections.unmodifiableList(new ArrayList<String>(datasetTypeCodes));
- }
-
- /**
- * Returns a unique key of the plugin.
- */
- public String getKey()
- {
- return key;
- }
-
- /**
- * Returns a human readable name of the plugin.
- */
- public String getLabel()
- {
- return label;
- }
-
- /**
- * Returns a list data set type codes for all data sets for which the plugin is available.
- */
- public List<String> getDatasetTypeCodes()
- {
- return datasetTypeCodes;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/Experiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/Experiment.java
deleted file mode 100644
index 22280ab490f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/Experiment.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto;
-
-import java.io.Serializable;
-import java.util.Date;
-import java.util.Map;
-
-/**
- * Experiment bean with properties.
- *
- * @author Franz-Josef Elmer
- */
-public class Experiment implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private long id;
-
- private String spaceCode;
-
- private String projectCode;
-
- private String code;
-
- private Date registrationDate;
-
- private Map<PropertyKey, Serializable> properties;
-
- public final long getId()
- {
- return id;
- }
-
- public final void setId(long id)
- {
- this.id = id;
- }
-
- public final String getSpaceCode()
- {
- return spaceCode;
- }
-
- public final void setSpaceCode(String spaceCode)
- {
- this.spaceCode = spaceCode;
- }
-
- public final String getProjectCode()
- {
- return projectCode;
- }
-
- public final void setProjectCode(String projectCode)
- {
- this.projectCode = projectCode;
- }
-
- public final String getCode()
- {
- return code;
- }
-
- public final void setCode(String code)
- {
- this.code = code;
- }
-
- public final Date getRegistrationDate()
- {
- return registrationDate;
- }
-
- public final void setRegistrationDate(Date registrationDate)
- {
- this.registrationDate = registrationDate;
- }
-
- public final Map<PropertyKey, Serializable> getProperties()
- {
- return properties;
- }
-
- public final void setProperties(Map<PropertyKey, Serializable> properties)
- {
- this.properties = properties;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/MsInjectionDataInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/MsInjectionDataInfo.java
deleted file mode 100644
index 5ad6c9f5383..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/MsInjectionDataInfo.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto;
-
-import java.io.Serializable;
-import java.util.Date;
-import java.util.Map;
-import java.util.Set;
-
-/**
- * Informations about an MS_INJECTION sample and its related biological sample. There are attributes for
- * <ul>
- * <li>MS_INJECTION sample: ID, properties, code and registration date
- * <li>Biological sample: identifier and properties
- * <li>Biological experiment (i.e. experiment of biological sample) if present: identifier and properties
- * <li>Registration dates of the most recently registered data sets for each data set type
- * <li>All data sets including the derived ones of the MS_INJECTION sample with their type, registration date, and properties.
- * </ul>
- *
- * @author Franz-Josef Elmer
- */
-public class MsInjectionDataInfo implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private long msInjectionSampleID;
-
- private String msInjectionSampleCode;
-
- private Date msInjectionSampleRegistrationDate;
-
- private Map<PropertyKey, Serializable> msInjectionSampleProperties;
-
- private long biologicalSampleID;
-
- private String biologicalSampleIdentifier;
-
- private String biologicalExperimentIdentifier;
-
- private Experiment biologicalExperiment;
-
- private Map<PropertyKey, Serializable> biologicalSampleProperties;
-
- private Set<DataSet> dataSets;
-
- private Map<String, Date> latestDataSetRegistrationDates;
-
- public long getMsInjectionSampleID()
- {
- return msInjectionSampleID;
- }
-
- public void setMsInjectionSampleID(long msInjectionSampleID)
- {
- this.msInjectionSampleID = msInjectionSampleID;
- }
-
- public String getMsInjectionSampleCode()
- {
- return msInjectionSampleCode;
- }
-
- public void setMsInjectionSampleCode(String msInjectionSampleCode)
- {
- this.msInjectionSampleCode = msInjectionSampleCode;
- }
-
- public Date getMsInjectionSampleRegistrationDate()
- {
- return msInjectionSampleRegistrationDate;
- }
-
- public void setMsInjectionSampleRegistrationDate(Date msInjectionSampleRegistrationDate)
- {
- this.msInjectionSampleRegistrationDate = msInjectionSampleRegistrationDate;
- }
-
- public Map<PropertyKey, Serializable> getMsInjectionSampleProperties()
- {
- return msInjectionSampleProperties;
- }
-
- public void setMsInjectionSampleProperties(
- Map<PropertyKey, Serializable> msInjectionSampleProperties)
- {
- this.msInjectionSampleProperties = msInjectionSampleProperties;
- }
-
- public long getBiologicalSampleID()
- {
- return biologicalSampleID;
- }
-
- public void setBiologicalSampleID(long biologicalSampleID)
- {
- this.biologicalSampleID = biologicalSampleID;
- }
-
- public String getBiologicalSampleIdentifier()
- {
- return biologicalSampleIdentifier;
- }
-
- public void setBiologicalSampleIdentifier(String biologicalSampleIdentifier)
- {
- this.biologicalSampleIdentifier = biologicalSampleIdentifier;
- }
-
- public final String getBiologicalExperimentIdentifier()
- {
- return biologicalExperimentIdentifier;
- }
-
- public final void setBiologicalExperimentIdentifier(String biologicalExperimentIdentifier)
- {
- this.biologicalExperimentIdentifier = biologicalExperimentIdentifier;
- }
-
- public final Experiment getBiologicalExperiment()
- {
- return biologicalExperiment;
- }
-
- public final void setBiologicalExperiment(Experiment biologicalExperiment)
- {
- this.biologicalExperiment = biologicalExperiment;
- }
-
- public Map<PropertyKey, Serializable> getBiologicalSampleProperties()
- {
- return biologicalSampleProperties;
- }
-
- public void setBiologicalSampleProperties(Map<PropertyKey, Serializable> biologicalSampleProperties)
- {
- this.biologicalSampleProperties = biologicalSampleProperties;
- }
-
- public final Set<DataSet> getDataSets()
- {
- return dataSets;
- }
-
- public final void setDataSets(Set<DataSet> dataSets)
- {
- this.dataSets = dataSets;
- }
-
- public Map<String, Date> getLatestDataSetRegistrationDates()
- {
- return latestDataSetRegistrationDates;
- }
-
- public void setLatestDataSetRegistrationDates(Map<String, Date> latestDataSetRegistrationDates)
- {
- this.latestDataSetRegistrationDates = latestDataSetRegistrationDates;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/PropertyKey.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/PropertyKey.java
deleted file mode 100644
index e38c444fc02..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/PropertyKey.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto;
-
-import java.io.Serializable;
-
-/**
- * Immutable class of a property key. Two instances are equal if their IDs are equal.
- *
- * @author Franz-Josef Elmer
- */
-public final class PropertyKey implements Serializable
-{
-
- private static final long serialVersionUID = 1L;
-
- private final String id;
-
- private final String label;
-
- /**
- * Creates a new instance for specified ID and label.
- */
- public PropertyKey(String id, String label)
- {
- this.id = id;
- this.label = label;
- }
-
- /**
- * Returns the ID.
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Returns the label.
- */
- public String getLabel()
- {
- return label;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (this == obj)
- {
- return true;
- }
- if (obj instanceof PropertyKey == false)
- {
- return false;
- }
- PropertyKey key = (PropertyKey) obj;
- return key.id.equals(id);
- }
-
- @Override
- public int hashCode()
- {
- return id.hashCode();
- }
-
- /**
- * Renders this key in the form <code><label>[<id>]</code>.
- */
- @Override
- public String toString()
- {
- return label + "[" + id + "]";
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/package.html b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/package.html
deleted file mode 100644
index 0bdd5dde03b..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/api/v1/dto/package.html
+++ /dev/null
@@ -1,5 +0,0 @@
-<html>
-<body>
-Data Transfer Objects
-</body>
-</html>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/CommonConstants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/CommonConstants.java
deleted file mode 100644
index bc01bc3b1d9..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/CommonConstants.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic;
-
-/**
- * Commons constants used in DSS and AS.
- *
- * @author Franz-Josef Elmer
- */
-public class CommonConstants
-{
-
- public static final String MS_INJECTION_SAMPLE_TYPE_CODE = "MS_INJECTION";
-
- public static final String BIOLOGICAL_SAMPLE_PREFIX = "BIO";
-
- public static final String MS_DATA_SPACE = "MS_DATA";
-
- public static final String PROT_RESULT_DATA_SET_TYPE = "PROT_RESULT";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinition.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinition.java
deleted file mode 100644
index b5283af3139..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinition.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AbundanceColumnDefinition implements Serializable,
- Comparable<AbundanceColumnDefinition>
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private List<Long> sampleIDs = new ArrayList<Long>(1);
-
- private String sampleCode;
-
- private List<Treatment> treatments;
-
- public final long getID()
- {
- long id = 0;
- for (Long sampleID : sampleIDs)
- {
- id = 37 * id + sampleID;
- }
- return id;
- }
-
- public final List<Long> getSampleIDs()
- {
- return sampleIDs;
- }
-
- public final void addSampleIDsOf(AbundanceColumnDefinition definition)
- {
- sampleIDs.addAll(definition.getSampleIDs());
- }
-
- public final void addSampleID(long sampleID)
- {
- sampleIDs.add(sampleID);
- }
-
- public final String getSampleCode()
- {
- return sampleCode;
- }
-
- public final void setSampleCode(String sampleCode)
- {
- this.sampleCode = sampleCode;
- }
-
- public final List<Treatment> getTreatments()
- {
- return treatments;
- }
-
- public final void setTreatments(List<Treatment> treatments)
- {
- this.treatments = treatments;
- }
-
- @Override
- public int compareTo(AbundanceColumnDefinition that)
- {
- if (this.treatments != null && that.treatments != null)
- {
- for (int i = 0, n = Math.min(this.treatments.size(), that.treatments.size()); i < n; i++)
- {
- Treatment thisTreatment = this.treatments.get(i);
- Treatment thatTreatment = that.treatments.get(i);
- int diff = thisTreatment.compareTo(thatTreatment);
- if (diff != 0)
- {
- return diff;
- }
- }
- int sizeDiff = this.treatments.size() - that.treatments.size();
- if (sizeDiff != 0)
- {
- return sizeDiff;
- }
- }
- if (this.sampleCode != null && that.sampleCode != null)
- {
- return this.sampleCode.compareTo(that.sampleCode);
- }
- return 0;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AccessionNumberProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AccessionNumberProvider.java
deleted file mode 100644
index 9b3c2dc7d97..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AccessionNumberProvider.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AccessionNumberProvider implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String accessionNumberType;
-
- private String accessionNumber;
-
- public final String getAccessionNumberType()
- {
- return accessionNumberType;
- }
-
- public final void setAccessionNumberType(String accessionNumberType)
- {
- this.accessionNumberType = accessionNumberType;
- }
-
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-
- public final void setAccessionNumber(String accessionNumber)
- {
- this.accessionNumber = accessionNumber;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunction.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunction.java
deleted file mode 100644
index cf515ba4cbb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunction.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.Arrays;
-
-/**
- * Aggregate functions.
- *
- * @author Franz-Josef Elmer
- */
-public enum AggregateFunction implements Serializable
-{
- MEAN("mean")
- {
- @Override
- public double aggregate(double[] values)
- {
- return SUM.aggregate(values) / values.length;
- }
- },
- MEDIAN("median")
- {
- @Override
- public double aggregate(double[] values)
- {
- Arrays.sort(values);
- int i = values.length / 2;
- return values.length % 2 == 0 ? (values[i - 1] + values[i]) / 2 : values[i];
- }
- },
- SUM("sum")
- {
- @Override
- public double aggregate(double[] values)
- {
- double sum = 0;
- for (double value : values)
- {
- sum += value;
- }
- return sum;
- }
- },
- MIN("minimum")
- {
- @Override
- public double aggregate(double[] values)
- {
- double min = Double.MAX_VALUE;
- for (double value : values)
- {
- min = Math.min(min, value);
- }
- return min;
- }
- },
- MAX("maximum")
- {
- @Override
- public double aggregate(double[] values)
- {
- double max = -Double.MAX_VALUE;
- for (double value : values)
- {
- max = Math.max(max, value);
- }
- return max;
- }
- },
- COUNT("count")
- {
- @Override
- public double aggregate(double[] values)
- {
- return values.length;
- }
- },
- ;
-
- private final String label;
-
- private AggregateFunction(String label)
- {
- this.label = label;
- }
-
- public final String getLabel()
- {
- return label;
- }
-
- /**
- * Aggregates the specified array of numbers to one number.
- *
- * @param values an array with at least one value.
- */
- public abstract double aggregate(double[] values);
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AminoAcid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AminoAcid.java
deleted file mode 100644
index 65afabc07f7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AminoAcid.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-/**
- * Amino acid symbols and names.
- *
- * @author Franz-Josef Elmer
- */
-public enum AminoAcid
-{
- A("Alanine", "Ala"),
- R("Arginine", "Arg"),
- N("Asparagine", "Asn"),
- D("Aspartic acid", "Asp"),
- C("Cysteine", "Cys"),
- E("Glutamic acid", "Glu"),
- Q("Glutamine", "Gln"),
- G("Glycine", "Gly"),
- H("Histidine", "His"),
- I("Isoleucine", "Ile"),
- L("Leucine", "Leu"),
- K("Lysine", "Lys"),
- M("Methionine", "Met"),
- F("Phenylalanine", "Phe"),
- P("Proline", "Pro"),
- S("Serine", "Ser"),
- T("Threonine", "Thr"),
- W("Tryptophan", "Trp"),
- Y("Tyrosine", "Tyr"),
- V("Valine", "Val");
-
- private final String name;
-
- private final String longSymbol;
-
- private AminoAcid(String name, String longSymbol)
- {
- this.name = name;
- this.longSymbol = longSymbol;
- }
-
- public String getName()
- {
- return name;
- }
-
- public String getLongSymbol()
- {
- return longSymbol;
- }
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/DataSetProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/DataSetProtein.java
deleted file mode 100644
index 24bcfe9de56..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/DataSetProtein.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetProtein implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String dataSetPermID;
-
- private TechId dataSetID;
-
- private TechId proteinID;
-
- private String sequenceName;
-
- private int peptideCount;
-
- private double falseDiscoveryRate;
-
- public final String getDataSetPermID()
- {
- return dataSetPermID;
- }
-
- public final void setDataSetPermID(String dataSetPermID)
- {
- this.dataSetPermID = dataSetPermID;
- }
-
- public final TechId getDataSetID()
- {
- return dataSetID;
- }
-
- public final void setDataSetID(TechId dataSetID)
- {
- this.dataSetID = dataSetID;
- }
-
- public final TechId getProteinID()
- {
- return proteinID;
- }
-
- public final void setProteinID(TechId proteinID)
- {
- this.proteinID = proteinID;
- }
-
- public final String getSequenceName()
- {
- return sequenceName;
- }
-
- public final void setSequenceName(String sequenceName)
- {
- this.sequenceName = sequenceName;
- }
-
- public final int getPeptideCount()
- {
- return peptideCount;
- }
-
- public final void setPeptideCount(int peptideCount)
- {
- this.peptideCount = peptideCount;
- }
-
- public final double getFalseDiscoveryRate()
- {
- return falseDiscoveryRate;
- }
-
- public final void setFalseDiscoveryRate(double falseDiscoveryRate)
- {
- this.falseDiscoveryRate = falseDiscoveryRate;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IBasicProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IBasicProteinInfo.java
deleted file mode 100644
index 03174e43498..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IBasicProteinInfo.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-
-/**
- * Common interface of DTOs with protein informations.
- *
- * @author Franz-Josef Elmer
- */
-public interface IBasicProteinInfo
-{
-
- public TechId getId();
-
- public String getAccessionNumber();
-
- public String getDescription();
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IndistinguishableProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IndistinguishableProteinInfo.java
deleted file mode 100644
index 2aa9840b46e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/IndistinguishableProteinInfo.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class IndistinguishableProteinInfo extends AccessionNumberProvider
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String sequence;
-
- private String description;
-
- private double coverage;
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Occurrence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Occurrence.java
deleted file mode 100644
index d6d48313e69..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Occurrence.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-/**
- * The occurrence of a word in a text. Occurrences are comparable by their start indexes.
- *
- * @author Tomasz Pylak
- */
-public class Occurrence implements Comparable<Occurrence>
-{
- private final String word;
-
- private final int startIndex;
-
- /**
- * Creates a new instance of the specified word which appears at the specified start index.
- */
- public Occurrence(String word, int startIndex)
- {
- this.word = word;
- this.startIndex = startIndex;
- }
-
- public String getWord()
- {
- return word;
- }
-
- public int getStartIndex()
- {
- return startIndex;
- }
-
- public int getEndIndex()
- {
- return startIndex + word.length() - 1;
- }
-
- @Override
- public int compareTo(Occurrence o)
- {
- return getStartIndex() - o.getStartIndex();
- }
-
- @Override
- public String toString()
- {
- return "[" + word + "@" + startIndex + "]";
- }
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtil.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtil.java
deleted file mode 100644
index 37ec915c463..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtil.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * Helper class for calculating peptide on protein coverage.
- *
- * @author Franz-Josef Elmer
- */
-public class OccurrenceUtil
-{
- /**
- * Returns a list of non-overlapping sequences built by the specified peptides covering the specified protein.
- */
- public static List<Occurrence> getCoverage(String protein, Collection<String> peptides)
- {
- ArrayList<Occurrence> list = new ArrayList<Occurrence>();
- List<Occurrence> sortedList = calcSortedOccurrences(protein, peptides);
- if (sortedList.isEmpty() == false)
- {
- Occurrence current = sortedList.get(0);
- for (int i = 1; i < sortedList.size(); i++)
- {
- String currentPeptide = current.getWord();
- Occurrence next = sortedList.get(i);
- int diff = next.getStartIndex() - current.getStartIndex();
- if (current.getWord().length() < diff)
- {
- list.add(current);
- current = next;
- } else if (current.getEndIndex() < next.getEndIndex())
- {
- String mergedPeptides = currentPeptide.substring(0, diff) + next.getWord();
- current = new Occurrence(mergedPeptides, current.getStartIndex());
- }
- }
- list.add(current);
- }
- return list;
- }
-
- // calculates a list of all words occurences, sorts it be starting position
- private static List<Occurrence> calcSortedOccurrences(String protein, Collection<String> peptides)
- {
- List<Occurrence> result = new ArrayList<Occurrence>();
- for (String word : peptides)
- {
- result.addAll(findAllOccurrences(protein, word));
- }
- Collections.sort(result);
- return result;
- }
-
- public static List<Occurrence> findAllOccurrences(String protein, String peptide)
- {
- List<Occurrence> result = new ArrayList<Occurrence>();
- int startIndex = 0;
- while (true)
- {
- int occurrenceIndex = protein.indexOf(peptide, startIndex);
- if (occurrenceIndex == -1)
- {
- break;
- }
- result.add(new Occurrence(peptide, occurrenceIndex));
- startIndex = occurrenceIndex + 1; // maybe the word overlaps with itself?
- }
- Collections.sort(result);
- return result;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Peptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Peptide.java
deleted file mode 100644
index d38fe54e9d7..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Peptide.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * Peptide sequence and optional modifications.
- *
- * @author Tomasz Pylak
- */
-public class Peptide implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String sequence;
-
- private List<PeptideModification> modifications = new ArrayList<PeptideModification>();
-
- public String getSequence()
- {
- return sequence;
- }
-
- public void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public List<PeptideModification> getModifications()
- {
- return modifications;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/PeptideModification.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/PeptideModification.java
deleted file mode 100644
index 4a16ac6928c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/PeptideModification.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * Position and mass of a modified amino acid in a peptide.
- *
- * @author Franz-Josef Elmer
- */
-public class PeptideModification implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private int position;
-
- private double mass;
-
- public int getPosition()
- {
- return position;
- }
-
- public void setPosition(int position)
- {
- this.position = position;
- }
-
- public double getMass()
- {
- return mass;
- }
-
- public void setMass(double mass)
- {
- this.mass = mass;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinByExperiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinByExperiment.java
deleted file mode 100644
index 842a9de87b6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinByExperiment.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinByExperiment extends AccessionNumberProvider implements IBasicProteinInfo
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private TechId id;
-
- private String description;
-
- private ProteinDetails details;
-
- @Override
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-
- public ProteinDetails getDetails()
- {
- return details;
- }
-
- public void setDetails(ProteinDetails details)
- {
- this.details = details;
- }
-
- @Override
- public final TechId getId()
- {
- return id;
- }
-
- public final void setId(TechId id)
- {
- this.id = id;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinDetails.java
deleted file mode 100644
index 2edd1672ba6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinDetails.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Tomasz Pylak
- */
-public class ProteinDetails implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String sequence;
-
- private String databaseNameAndVersion;
-
- private double probability;
-
- private double coverage;
-
- private double falseDiscoveryRate;
-
- private String dataSetPermID;
-
- private Long dataSetTechID;
-
- private String dataSetTypeCode;
-
- private TechId proteinID;
-
- private List<Peptide> peptides;
-
- private List<IndistinguishableProteinInfo> indistinguishableProteinInfos;
-
- public String getSequence()
- {
- return sequence;
- }
-
- public void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public String getDatabaseNameAndVersion()
- {
- return databaseNameAndVersion;
- }
-
- public void setDatabaseNameAndVersion(String databaseNameAndVersion)
- {
- this.databaseNameAndVersion = databaseNameAndVersion;
- }
-
- public double getFalseDiscoveryRate()
- {
- return falseDiscoveryRate;
- }
-
- public double getProbability()
- {
- return probability;
- }
-
- public void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
- public void setFalseDiscoveryRate(double falseDiscoveryRate)
- {
- this.falseDiscoveryRate = falseDiscoveryRate;
- }
-
- public String getDataSetPermID()
- {
- return dataSetPermID;
- }
-
- public void setDataSetPermID(String dataSetPermID)
- {
- this.dataSetPermID = dataSetPermID;
- }
-
- public final TechId getProteinID()
- {
- return proteinID;
- }
-
- public final void setProteinID(TechId proteinID)
- {
- this.proteinID = proteinID;
- }
-
- public List<Peptide> getPeptides()
- {
- return peptides;
- }
-
- public void setPeptides(List<Peptide> peptides)
- {
- this.peptides = peptides;
- }
-
- public Long getDataSetTechID()
- {
- return dataSetTechID;
- }
-
- public void setDataSetTechID(Long dataSetTechID)
- {
- this.dataSetTechID = dataSetTechID;
- }
-
- public String getDataSetTypeCode()
- {
- return dataSetTypeCode;
- }
-
- public void setDataSetTypeCode(String dataSetTypeCode)
- {
- this.dataSetTypeCode = dataSetTypeCode;
- }
-
- public void setIndistinguishableProteinInfos(
- List<IndistinguishableProteinInfo> indistinguishableProteinInfos)
- {
- this.indistinguishableProteinInfos = indistinguishableProteinInfos;
- }
-
- public List<IndistinguishableProteinInfo> getIndistinguishableProteinInfos()
- {
- return indistinguishableProteinInfos;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinInfo.java
deleted file mode 100644
index 10c4a395c4e..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinInfo.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinInfo implements Serializable, IBasicProteinInfo
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private TechId id;
-
- private String accessionNumber;
-
- private TechId experimentID;
-
- private String dataSetPermID;
-
- private String description;
-
- private double coverage;
-
- private Map<Long, Double> abundances;
-
- @Override
- public final TechId getId()
- {
- return id;
- }
-
- public final void setId(TechId id)
- {
- this.id = id;
- }
-
- public final TechId getExperimentID()
- {
- return experimentID;
- }
-
- public final void setExperimentID(TechId experimentID)
- {
- this.experimentID = experimentID;
- }
-
- public final String getDataSetPermID()
- {
- return dataSetPermID;
- }
-
- public final void setDataSetPermID(String dataSetPermID)
- {
- this.dataSetPermID = dataSetPermID;
- }
-
- @Override
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-
- public final void setAccessionNumber(String accessionNumber)
- {
- this.accessionNumber = accessionNumber;
- }
-
- @Override
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-
- public final Map<Long, Double> getAbundances()
- {
- return abundances;
- }
-
- public final void setAbundances(Map<Long, Double> abundances)
- {
- this.abundances = abundances;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinRelatedSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinRelatedSample.java
deleted file mode 100644
index d1198c0e951..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinRelatedSample.java
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithProperties;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * Sample related to a protein. Contains information about abundance and amino-acid modification.
- *
- * @author Franz-Josef Elmer
- */
-public class ProteinRelatedSample implements Serializable, IEntityInformationHolderWithProperties
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private Long id;
-
- private String permId;
-
- private String code;
-
- private String identifier;
-
- private BasicEntityType entityType;
-
- private List<IEntityProperty> properties;
-
- private Double abundance;
-
- private char modifiedAminoAcid;
-
- private Long modificationPosition;
-
- private Double modificationMass;
-
- private Double modificationFraction;
-
- @Override
- public Long getId()
- {
- return id;
- }
-
- public void setId(Long id)
- {
- this.id = id;
- }
-
- @Override
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId)
- {
- this.permId = permId;
- }
-
- @Override
- public String getCode()
- {
- return code;
- }
-
- public void setCode(String code)
- {
- this.code = code;
- }
-
- @Override
- public BasicEntityType getEntityType()
- {
- return entityType;
- }
-
- public void setEntityType(BasicEntityType entityType)
- {
- this.entityType = entityType;
- }
-
- @Override
- public String getIdentifier()
- {
- return identifier;
- }
-
- public void setIdentifier(String identifier)
- {
- this.identifier = identifier;
- }
-
- public Double getAbundance()
- {
- return abundance;
- }
-
- public void setAbundance(Double abundance)
- {
- this.abundance = abundance;
- }
-
- public char getModifiedAminoAcid()
- {
- return modifiedAminoAcid;
- }
-
- public void setModifiedAminoAcid(char modifiedAminoAcid)
- {
- this.modifiedAminoAcid = modifiedAminoAcid;
- }
-
- public Long getModificationPosition()
- {
- return modificationPosition;
- }
-
- public void setModificationPosition(Long modificationPosition)
- {
- this.modificationPosition = modificationPosition;
- }
-
- public Double getModificationMass()
- {
- return modificationMass;
- }
-
- public void setModificationMass(Double modificationMass)
- {
- this.modificationMass = modificationMass;
- }
-
- public Double getModificationFraction()
- {
- return modificationFraction;
- }
-
- public void setModificationFraction(Double modificationFraction)
- {
- this.modificationFraction = modificationFraction;
- }
-
- @Override
- public EntityKind getEntityKind()
- {
- return EntityKind.SAMPLE;
- }
-
- @Override
- public List<IEntityProperty> getProperties()
- {
- return properties;
- }
-
- public void setProperties(List<IEntityProperty> properties)
- {
- this.properties = properties;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSequence.java
deleted file mode 100644
index 7f9a97bd494..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSequence.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSequence implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String shortName;
-
- private TechId id;
-
- private TechId databaseID;
-
- private String sequence;
-
- private String databaseNameAndVersion;
-
- public final String getShortName()
- {
- return shortName;
- }
-
- public final void setShortName(String version)
- {
- this.shortName = version;
- }
-
- public final TechId getId()
- {
- return id;
- }
-
- public final void setId(TechId id)
- {
- this.id = id;
- }
-
- public final TechId getDatabaseID()
- {
- return databaseID;
- }
-
- public final void setDatabaseID(TechId databaseID)
- {
- this.databaseID = databaseID;
- }
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public final String getDatabaseNameAndVersion()
- {
- return databaseNameAndVersion;
- }
-
- public final void setDatabaseNameAndVersion(String databaseNameAndVersion)
- {
- this.databaseNameAndVersion = databaseNameAndVersion;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSummary.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSummary.java
deleted file mode 100644
index db708980a9f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/ProteinSummary.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSummary implements Serializable
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private double fdr;
-
- private int proteinCount;
-
- private int decoyProteinCount;
-
- private int peptideCount;
-
- private int decoyPeptideCount;
-
- public double getFDR()
- {
- return fdr;
- }
-
- public void setFDR(double fdr)
- {
- this.fdr = fdr;
- }
-
- public int getProteinCount()
- {
- return proteinCount;
- }
-
- public void setProteinCount(int proteinCount)
- {
- this.proteinCount = proteinCount;
- }
-
- public int getPeptideCount()
- {
- return peptideCount;
- }
-
- public void setPeptideCount(int peptideCount)
- {
- this.peptideCount = peptideCount;
- }
-
- public void setDecoyProteinCount(int decoyProteinCount)
- {
- this.decoyProteinCount = decoyProteinCount;
- }
-
- public int getDecoyProteinCount()
- {
- return decoyProteinCount;
- }
-
- public void setDecoyPeptideCount(int decoyPeptideCount)
- {
- this.decoyPeptideCount = decoyPeptideCount;
- }
-
- public int getDecoyPeptideCount()
- {
- return decoyPeptideCount;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/RawDataSampleGridIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/RawDataSampleGridIDs.java
deleted file mode 100644
index 35e9064d0fb..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/RawDataSampleGridIDs.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class RawDataSampleGridIDs
-{
- public static final String EXPERIMENT = "EXPERIMENT";
-
- public static final String PARENT = "PARENT";
-
- public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
-
- public static final String CODE = "CODE";
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/SampleWithPropertiesAndAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/SampleWithPropertiesAndAbundance.java
deleted file mode 100644
index a91dfd0f786..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/SampleWithPropertiesAndAbundance.java
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SampleWithPropertiesAndAbundance implements Serializable,
- IEntityInformationHolderWithPermId, IEntityPropertiesHolder
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private Long id;
-
- private String permId;
-
- private String identifier;
-
- private String code;
-
- private SampleType sampleType;
-
- private List<IEntityProperty> properties;
-
- private double abundance;
-
- @Override
- public final Long getId()
- {
- return id;
- }
-
- public final void setId(Long id)
- {
- this.id = id;
- }
-
- public final String getIdentifier()
- {
- return identifier;
- }
-
- public final void setIdentifier(String identifier)
- {
- this.identifier = identifier;
- }
-
- @Override
- public final String getCode()
- {
- return code;
- }
-
- public void setCode(final String code)
- {
- this.code = code;
- }
-
- @Override
- public EntityType getEntityType()
- {
- return getSampleType();
- }
-
- @Override
- public EntityKind getEntityKind()
- {
- return EntityKind.SAMPLE;
- }
-
- public SampleType getSampleType()
- {
- return sampleType;
- }
-
- public void setSampleType(final SampleType sampleType)
- {
- this.sampleType = sampleType;
- }
-
- @Override
- public List<IEntityProperty> getProperties()
- {
- return properties;
- }
-
- public final void setProperties(List<IEntityProperty> properties)
- {
- this.properties = properties;
- }
-
- public final double getAbundance()
- {
- return abundance;
- }
-
- public final void setAbundance(double abundance)
- {
- this.abundance = abundance;
- }
-
- @Override
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId)
- {
- this.permId = permId;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Treatment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Treatment.java
deleted file mode 100644
index 1b2e630e2b6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/Treatment.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Treatment implements Serializable, Comparable<Treatment>
-{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private String value;
-
- private String type;
-
- private String typeCode;
-
- private String valueType;
-
- public final String getValue()
- {
- return value;
- }
-
- public final void setValue(String value)
- {
- this.value = value;
- }
-
- public final String getValueType()
- {
- return valueType;
- }
-
- public final void setValueType(String valueType)
- {
- this.valueType = valueType;
- }
-
- public final String getType()
- {
- return type;
- }
-
- public final void setType(String type)
- {
- this.type = type;
- }
-
- public final String getTypeCode()
- {
- return typeCode;
- }
-
- public final void setTypeCode(String typeCode)
- {
- this.typeCode = typeCode;
- }
-
- public final String getLabel()
- {
- return value + " " + type;
- }
-
- @Override
- public int compareTo(Treatment that)
- {
- int typeComparisonResult = this.type.toLowerCase().compareTo(that.type.toLowerCase());
- if (typeComparisonResult != 0)
- {
- return typeComparisonResult;
- }
- double thisNumber = convert(this.value);
- double thatNumber = convert(that.value);
- if (Double.isNaN(thisNumber) || Double.isNaN(thatNumber))
- {
- return this.value.compareTo(that.value);
- }
- return Double.compare(thisNumber, thatNumber);
- }
-
- private double convert(String numberOrString)
- {
- try
- {
- return Double.parseDouble(numberOrString);
- } catch (NumberFormatException e)
- {
- return Double.NaN;
- }
- }
-
- @Override
- public String toString()
- {
- return getLabel();
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractDTOWithID.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractDTOWithID.java
deleted file mode 100644
index 1151a854d38..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractDTOWithID.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.io.Serializable;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractDTOWithID implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("id")
- private long id;
-
- public final long getId()
- {
- return id;
- }
-
- public final void setId(long id)
- {
- this.id = id;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractSample.java
deleted file mode 100644
index e1759e519c6..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/AbstractSample.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * Abstract super class of sample.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractSample extends AbstractDTOWithID
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("perm_id")
- private String samplePermID;
-
- public final String getSamplePermID()
- {
- return samplePermID;
- }
-
- public final void setSamplePermID(String samplePermID)
- {
- this.samplePermID = samplePermID;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IdentifiedProtein.java
deleted file mode 100644
index 8ad58fd5700..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IdentifiedProtein.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class IdentifiedProtein extends AbstractDTOWithID
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("data_set_id")
- private long dataSetID;
-
- @ResultColumn("data_set_perm_id")
- private String dataSetPermID;
-
- @ResultColumn("protein_id")
- private long proteinID;
-
- @ResultColumn("peptide_count")
- private int peptideCount;
-
- @ResultColumn("amino_acid_sequence")
- private String sequence;
-
- @ResultColumn("db_id")
- private long databaseID;
-
- @ResultColumn("name_and_version")
- private String databaseNameAndVersion;
-
- @ResultColumn("probability")
- private double probability;
-
- @ResultColumn("coverage")
- private double coverage;
-
- private double falseDiscoveryRate;
-
- public final String getDataSetPermID()
- {
- return dataSetPermID;
- }
-
- public final void setDataSetPermID(String dataSetPermID)
- {
- this.dataSetPermID = dataSetPermID;
- }
-
- public final int getPeptideCount()
- {
- return peptideCount;
- }
-
- public final void setPeptideCount(int accessionNumber)
- {
- this.peptideCount = accessionNumber;
- }
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String description)
- {
- this.sequence = description;
- }
-
- public final long getDataSetID()
- {
- return dataSetID;
- }
-
- public final void setDataSetID(long dataSetID)
- {
- this.dataSetID = dataSetID;
- }
-
- public final long getProteinID()
- {
- return proteinID;
- }
-
- public final void setProteinID(long proteinID)
- {
- this.proteinID = proteinID;
- }
-
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
- public final double getFalseDiscoveryRate()
- {
- return falseDiscoveryRate;
- }
-
- public final void setFalseDiscoveryRate(double falseDiscoveryRate)
- {
- this.falseDiscoveryRate = falseDiscoveryRate;
- }
-
- public final long getDatabaseID()
- {
- return databaseID;
- }
-
- public final void setDatabase(long databaseID)
- {
- this.databaseID = databaseID;
- }
-
- public final String getDatabaseNameAndVersion()
- {
- return databaseNameAndVersion;
- }
-
- public final void setDatabaseNameAndVersion(String databaseNameAndVersion)
- {
- this.databaseNameAndVersion = databaseNameAndVersion;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IndistinguishableProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IndistinguishableProtein.java
deleted file mode 100644
index 874b525c03d..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/IndistinguishableProtein.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class IndistinguishableProtein extends ProteinReference
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("amino_acid_sequence")
- private String sequence;
-
- @ResultColumn("coverage")
- private double coverage;
-
- public void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public String getSequence()
- {
- return sequence;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/MsInjectionSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/MsInjectionSample.java
deleted file mode 100644
index 5f3b22888cc..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/MsInjectionSample.java
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.util.Collection;
-import java.util.Date;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class MsInjectionSample
-{
- private final Sample sample;
-
- private final Map<String, AbstractExternalData> latestDataSets = new LinkedHashMap<String, AbstractExternalData>();
-
- private final List<AbstractExternalData> dataSets;
-
- public MsInjectionSample(Sample sample, List<AbstractExternalData> dataSets)
- {
- this.sample = sample;
- this.dataSets = dataSets;
- add(dataSets);
- }
-
- private void add(Collection<AbstractExternalData> datasets)
- {
- if (datasets != null)
- {
- for (AbstractExternalData dataSet : datasets)
- {
- addLatestDataSet(dataSet);
- add(dataSet.getChildren());
- }
- }
- }
-
- public Sample getSample()
- {
- return sample;
- }
-
- public final List<AbstractExternalData> getDataSets()
- {
- return dataSets;
- }
-
- public Map<String, AbstractExternalData> getLatestDataSets()
- {
- return latestDataSets;
- }
-
- private void addLatestDataSet(AbstractExternalData dataSet)
- {
- String dataSetTypeCode = dataSet.getDataSetType().getCode();
- Date registrationDate = dataSet.getRegistrationDate();
- AbstractExternalData latestDataSet = latestDataSets.get(dataSetTypeCode);
- if (latestDataSet == null
- || latestDataSet.getRegistrationDate().getTime() < registrationDate.getTime())
- {
- latestDataSets.put(dataSetTypeCode, dataSet);
- }
- }
-
- @Override
- public String toString()
- {
- return sample.getIdentifier() + ":" + latestDataSets;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/PeptideWithModification.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/PeptideWithModification.java
deleted file mode 100644
index 9258feb2f41..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/PeptideWithModification.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PeptideWithModification extends AbstractDTOWithID
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("sequence")
- private String sequence;
-
- @ResultColumn("pos")
- private Integer position;
-
- @ResultColumn("mass")
- private Double mass;
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public Integer getPosition()
- {
- return position;
- }
-
- public void setPosition(Integer position)
- {
- this.position = position;
- }
-
- public Double getMass()
- {
- return mass;
- }
-
- public void setMass(Double mass)
- {
- this.mass = mass;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProbabilityFDRMapping.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProbabilityFDRMapping.java
deleted file mode 100644
index f3f365e9495..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProbabilityFDRMapping.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProbabilityFDRMapping
-{
- @ResultColumn("probability")
- private double probability;
-
- @ResultColumn("false_discovery_rate")
- private double falseDiscoveryRate;
-
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- public final double getFalseDiscoveryRate()
- {
- return falseDiscoveryRate;
- }
-
- public final void setFalseDiscoveryRate(double falseDiscoveryRate)
- {
- this.falseDiscoveryRate = falseDiscoveryRate;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinAbundance.java
deleted file mode 100644
index 34875160517..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinAbundance.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.io.Serializable;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinAbundance extends AbstractDTOWithID implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("value")
- private double abundance;
-
- @ResultColumn("perm_id")
- private String samplePermID;
-
- public double getAbundance()
- {
- return abundance;
- }
-
- public void setAbundance(double abundance)
- {
- this.abundance = abundance;
- }
-
- public String getSamplePermID()
- {
- return samplePermID;
- }
-
- public void setSampleID(String samplePermID)
- {
- this.samplePermID = samplePermID;
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReference.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReference.java
deleted file mode 100644
index ef998e95d3c..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReference.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.io.Serializable;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinReference extends AbstractDTOWithID implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("accession_number")
- private String accessionNumber;
-
- @ResultColumn("description")
- private String description;
-
- public final String getAccessionNumber()
- {
- return accessionNumber;
- }
-
- public final void setAccessionNumber(String accessionNumber)
- {
- this.accessionNumber = accessionNumber;
- }
-
- public final String getDescription()
- {
- return description;
- }
-
- public final void setDescription(String description)
- {
- this.description = description;
- }
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbability.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbability.java
deleted file mode 100644
index 8d30c84c290..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbability.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.io.Serializable;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinReferenceWithProbability extends ProteinReference implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("data_set_id")
- private long dataSetID;
-
- @ResultColumn("probability")
- private double probability;
-
- @ResultColumn("coverage")
- private double coverage;
-
- @ResultColumn("abundance")
- private Double abundance;
-
- @ResultColumn("sample_perm_id")
- private String samplePermID;
-
- public final long getDataSetID()
- {
- return dataSetID;
- }
-
- public final void setDataSetID(long dataSetID)
- {
- this.dataSetID = dataSetID;
- }
-
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- public final Double getAbundance()
- {
- return abundance;
- }
-
- public final void setAbundance(Double abundance)
- {
- this.abundance = abundance;
- }
-
- public final String getSamplePermID()
- {
- return samplePermID;
- }
-
- public final void setSamplePermID(String samplePermID)
- {
- this.samplePermID = samplePermID;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java
deleted file mode 100644
index 5f75d2fb2a1..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinReferenceWithProbabilityAndPeptide extends ProteinReferenceWithProbability
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("sequence")
- private String peptideSequence;
-
- public String getPeptideSequence()
- {
- return peptideSequence;
- }
-
- public void setPeptideSequence(String peptideSequence)
- {
- this.peptideSequence = peptideSequence;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProtein.java
deleted file mode 100644
index bf572eea798..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinReferenceWithProtein.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import java.io.Serializable;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinReferenceWithProtein extends ProteinReference implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("data_set_id")
- private long dataSetID;
-
- @ResultColumn("protein_id")
- private long proteinID;
-
- @ResultColumn("probability")
- private double probability;
-
- @ResultColumn("coverage")
- private double coverage;
-
- public final long getDataSetID()
- {
- return dataSetID;
- }
-
- public final void setDataSetID(long dataSetID)
- {
- this.dataSetID = dataSetID;
- }
-
- public long getProteinID()
- {
- return proteinID;
- }
-
- public void setProteinID(long proteinID)
- {
- this.proteinID = proteinID;
- }
-
- public final double getProbability()
- {
- return probability;
- }
-
- public final void setProbability(double probability)
- {
- this.probability = probability;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public double getCoverage()
- {
- return coverage;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinWithAbundances.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinWithAbundances.java
deleted file mode 100644
index 1d12fa3b75f..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/ProteinWithAbundances.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import it.unimi.dsi.fastutil.doubles.DoubleArrayList;
-
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.Set;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinWithAbundances extends ProteinReference
-{
- private static final long serialVersionUID = 1L;
-
- private static final double[] EMPTY_ARRAY = new double[0];
-
- private double coverage;
-
- private final Map<Long, DoubleArrayList> abundances = new LinkedHashMap<Long, DoubleArrayList>();
-
- public double getCoverage()
- {
- return coverage;
- }
-
- public void setCoverage(double coverage)
- {
- this.coverage = coverage;
- }
-
- public void addAbundanceFor(long sampleID, double abundance)
- {
- DoubleArrayList list = abundances.get(sampleID);
- if (list == null)
- {
- list = new DoubleArrayList();
- abundances.put(sampleID, list);
- }
- list.add(abundance);
- }
-
- public Set<Long> getSampleIDs()
- {
- return abundances.keySet();
- }
-
- public double[] getAbundancesForSample(long sampleID)
- {
- DoubleArrayList list = abundances.get(sampleID);
- return list == null ? EMPTY_ARRAY : list.toDoubleArray();
- }
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SampleAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SampleAbundance.java
deleted file mode 100644
index aa93de91f45..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SampleAbundance.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SampleAbundance extends AbstractSample
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("value")
- private double abundance;
-
- public final double getAbundance()
- {
- return abundance;
- }
-
- public final void setAbundance(double abundance)
- {
- this.abundance = abundance;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SamplePeptideModification.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SamplePeptideModification.java
deleted file mode 100644
index 8a4de328d76..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/SamplePeptideModification.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SamplePeptideModification extends AbstractSample
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("fraction")
- private double fraction;
-
- @ResultColumn("pos")
- private int position;
-
- @ResultColumn("mass")
- private double mass;
-
- @ResultColumn("sequence")
- private String sequence;
-
- public double getFraction()
- {
- return fraction;
- }
-
- public void setFraction(double fraction)
- {
- this.fraction = fraction;
- }
-
- public int getPosition()
- {
- return position;
- }
-
- public void setPosition(int position)
- {
- this.position = position;
- }
-
- public double getMass()
- {
- return mass;
- }
-
- public void setMass(double mass)
- {
- this.mass = mass;
- }
-
- public String getSequence()
- {
- return sequence;
- }
-
- public void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/Sequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/Sequence.java
deleted file mode 100644
index 69a91f93655..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/dto/Sequence.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto;
-
-import net.lemnik.eodsql.ResultColumn;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class Sequence extends AbstractDTOWithID
-{
- private static final long serialVersionUID = 1L;
-
- @ResultColumn("amino_acid_sequence")
- private String sequence;
-
- @ResultColumn("db_id")
- private long databaseID;
-
- @ResultColumn("name_and_version")
- private String databaseNameAndVersion;
-
- public final String getSequence()
- {
- return sequence;
- }
-
- public final void setSequence(String sequence)
- {
- this.sequence = sequence;
- }
-
- public final long getDatabaseID()
- {
- return databaseID;
- }
-
- public final void setDatabaseID(long databaseID)
- {
- this.databaseID = databaseID;
- }
-
- public final String getDatabaseNameAndVersion()
- {
- return databaseNameAndVersion;
- }
-
- public final void setDatabaseNameAndVersion(String databaseNameAndVersion)
- {
- this.databaseNameAndVersion = databaseNameAndVersion;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/proteomics-applicationContext.xml b/rtd_phosphonetx/source/java/proteomics-applicationContext.xml
deleted file mode 100644
index a67901501d1..00000000000
--- a/rtd_phosphonetx/source/java/proteomics-applicationContext.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/tx
- http://www.springframework.org/schema/tx/spring-tx-2.5.xsd">
-
- <import resource="applicationContext.xml"/>
- <import resource="proteomics-plugin-applicationContext.xml"/>
-
-</beans>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml b/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml
deleted file mode 100644
index ea3245ffbb5..00000000000
--- a/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml
+++ /dev/null
@@ -1,64 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/tx
- http://www.springframework.org/schema/tx/spring-tx-2.5.xsd">
-
- <bean id="proteomics-dao-factory"
- class="ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.db.PhosphoNetXDAOFactory">
- <constructor-arg ref="dss-based-data-source-provider"/>
- <constructor-arg ref="dao-factory"/>
- </bean>
-
- <bean id="proteomics-bo-factory"
- class="ch.systemsx.cisd.openbis.plugin.proteomics.server.business.BusinessObjectFactory">
- <constructor-arg ref="dao-factory"/>
- <constructor-arg ref="proteomics-dao-factory"/>
- <constructor-arg ref="common-business-object-factory" />
- </bean>
-
- <!--
- // Proteomics Data Server
- -->
-
- <bean id="proteomics-data-service-internal"
- class="ch.systemsx.cisd.openbis.plugin.proteomics.server.ProteomicsDataServiceInternal"
- init-method="replaceAutoWiredSesseionManagerByConstructorSessionManager">
- <constructor-arg>
- <bean class="ch.systemsx.cisd.openbis.generic.server.OpenBisSessionManager">
- <constructor-arg>
- <bean class="ch.systemsx.cisd.openbis.generic.server.SessionFactory" />
- </constructor-arg>
- <constructor-arg>
- <bean class="ch.systemsx.cisd.openbis.generic.shared.LogMessagePrefixGenerator" />
- </constructor-arg>
- <constructor-arg ref="dummy-authentication-service" />
- <constructor-arg>
- <bean class="ch.systemsx.cisd.common.servlet.RequestContextProviderAdapter">
- <constructor-arg ref="request-context-provider" />
- </bean>
- </constructor-arg>
- <constructor-arg value="${session-timeout}" />
- <constructor-arg value="${session-timeout-no-login}" />
- <constructor-arg ref="dao-factory"/>
- </bean>
- </constructor-arg>
- <constructor-arg ref="dao-factory"/>
- <constructor-arg ref="common-business-object-factory" />
- <constructor-arg ref="proteomics-bo-factory" />
- <constructor-arg ref="managed-property-evaluator-factory" />
- </bean>
-
- <bean id="proteomics-data-service-web"
- class="ch.systemsx.cisd.openbis.plugin.proteomics.server.ProteomicsDataServiceInternal">
- <constructor-arg ref="session-manager" />
- <constructor-arg ref="dao-factory"/>
- <constructor-arg ref="common-business-object-factory" />
- <constructor-arg ref="proteomics-bo-factory" />
- <constructor-arg ref="managed-property-evaluator-factory" />
- </bean>
-
-</beans>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/service.properties b/rtd_phosphonetx/source/java/service.properties
deleted file mode 100644
index ecb4704b892..00000000000
--- a/rtd_phosphonetx/source/java/service.properties
+++ /dev/null
@@ -1,67 +0,0 @@
-authentication-service = dummy-authentication-service
-
-# The time after which an inactive session is expired by the service (in minutes).
-session-timeout = 720
-
-# Authorization
-# Supported: 'no-authorization' and 'active-authorization'
-authorization-component-factory = active-authorization
-
-authorization.project-level.enabled = true
-authorization.project-level.users = .*\\_pa\\_on
-
-dss-rpc.put.dss-code = DSS1
-
-script-folder = ../openbis/source/
-
-# Supported: currently only 'postgresql' is supported
-database.engine = postgresql
-database.create-from-scratch = false
-# For debugging set this value to true.
-database.script-single-step-mode = false
-database.url-host-part =
-database.kind = phosphonetx
-# database.kind = system_test
-# database.kind = system_test_strict
-# database.kind = system_test_plates_on_demand
-# database.kind = system_test_multi_groups
-database.owner =
-database.owner-password =
-database.admin-user =
-database.admin-password =
-
-crowd.service.host = crowd.systemsx.ch
-crowd.service.port = 8443
-crowd.application.name = lims
-crowd.application.password =
-
-# The database instance local unique identifier. Used when the new database is created.
-database-instance = CISD
-
-# The URL of the CIFEX server
-cifex-url = https://cifex.ethz.ch:443
-
-trusted-cross-origin-domains= *
-
-# Hibernate Search
-# The working directory.
-hibernate.search.index-base = ./targets/indices_${database.kind}
-# One of NO_INDEX, SKIP_IF_MARKER_FOUND, INDEX_FROM_SCRATCH.
-# If not specified, default (SKIP_IF_MARKER_FOUND) is taken.
-hibernate.search.index-mode = SKIP_IF_MARKER_FOUND
-# Defines the maximum number of elements indexed before flushing the transaction-bound queue.
-# Default is 1000.
-hibernate.search.batch-size = 1000
-# Maximum number of search results
-hibernate.search.maxResults = 100000
-
-web-client-configuration-file = etc/web-client.properties
-
-proteomics-database-kind = dev
-
-core-plugins-folder = source/core-plugins
-
-
-
-
-jython-version=2.7
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.dez b/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.dez
deleted file mode 100644
index 8fb86063bc3..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.dez
+++ /dev/null
@@ -1,26083 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?><dezign>
-
-<FILEFORMATVERSION>51</FILEFORMATVERSION>
-<VERSION>
-<PROJECTSETTINGS>
-<PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME>
-<MODIFIED>2009-09-28</MODIFIED>
-<CREATED>2009-06-29</CREATED>
-<CREATED2></CREATED2>
-<PROJECTNAME></PROJECTNAME>
-<DESCRIPTION></DESCRIPTION>
-<AUTHOR></AUTHOR>
-<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES>N:\user\cisd\felmer\phosphonetx\schema-001.sql;N:\user\cisd\felmer\phosphonetx\drop.sql;C:\Users\felmer\Documents\CreateDBLog_200909281.txt</LASTGENERATEDFILES>
-</PROJECTSETTINGS>
-<CONNECTIONSETTINGS>
-<SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE>
-<CONNECTIONTYPE>SQLFILE</CONNECTIONTYPE>
-<DBID>postgresql8</DBID>
-</CONNECTIONSETTINGS>
-<DATADICT>
-<DBID>postgresql8</DBID>
-<LASTID>175</LASTID>
-<DDSETTINGS>
-<PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE>
-<FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE>
-<CCONNAMETEMPLATE>CC_%table%_%column%</CCONNAMETEMPLATE>
-<NOTNULLCONNAMETEMPLATE>NN_%column%</NOTNULLCONNAMETEMPLATE>
-<DEFAULTCONNAMETEMPLATE>DEF_%table%_%column%</DEFAULTCONNAMETEMPLATE>
-<TUCONNAMETEMPLATE>TUC_%table%_%counter%</TUCONNAMETEMPLATE>
-<TCCONNAMETEMPLATE>TCC_%table%_%counter%</TCCONNAMETEMPLATE>
-<RELNAMETEMPLATE>%parent%_%child%</RELNAMETEMPLATE>
-<INDEXNAMETEMPLATE>IDX_%table%_%counter%</INDEXNAMETEMPLATE>
-<DEFTABLEOPTIONS></DEFTABLEOPTIONS>
-<DEFINDEXOPTIONS></DEFINDEXOPTIONS>
-<BEGINDATABASESCRIPT></BEGINDATABASESCRIPT>
-<ENDDATABASESCRIP></ENDDATABASESCRIP>
-<BEGINALTERDATABASESCRIPT></BEGINALTERDATABASESCRIPT>
-<ENDALTERDATABASESCRIP></ENDALTERDATABASESCRIP>
-<BEGINDROPDATABASESCRIPT></BEGINDROPDATABASESCRIPT>
-<ENDDROPDATABASESCRIP></ENDDROPDATABASESCRIP>
-<GENDIALOGSELECTEDOBJECTS></GENDIALOGSELECTEDOBJECTS>
-<GENTABLES>1</GENTABLES>
-<GENTABLEOPTIONS>1</GENTABLEOPTIONS>
-<GENCONSTRAINTS>1</GENCONSTRAINTS>
-<GENINDEXES>1</GENINDEXES>
-<GENTRIGGERS>1</GENTRIGGERS>
-<GENVIEWS>1</GENVIEWS>
-<GENPROCEDURES>1</GENPROCEDURES>
-<GENSEQUENCES>1</GENSEQUENCES>
-<GENRELATIONSHIPS>1</GENRELATIONSHIPS>
-<GENBEGINENDTABLESCRIPTS>1</GENBEGINENDTABLESCRIPTS>
-<GENBEGINENDDBSCRIPTS>1</GENBEGINENDDBSCRIPTS>
-<GLOBALPREFIX></GLOBALPREFIX>
-<AUTOCREATEINDEXESONKEYS>0</AUTOCREATEINDEXESONKEYS>
-<CONVERTDOMAINS>0</CONVERTDOMAINS>
-<IGNORECOMMENTS>0</IGNORECOMMENTS>
-<USESCHEMANAMES>0</USESCHEMANAMES>
-<UCONNAMETEMPLATE></UCONNAMETEMPLATE>
-<SQLCREATEFILE>N:\user\cisd\felmer\phosphonetx\schema-001.sql</SQLCREATEFILE>
-<SQLDROPFILE>N:\user\cisd\felmer\phosphonetx\drop.sql</SQLDROPFILE>
-</DDSETTINGS>
-<DOMAINS>
-<DOMAIN>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>CODE</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>DESCRIPTION</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>INTEGER_NUMBER</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>REAL_NUMBER</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>LONG_SEQUENCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>SHORT_DESCRIPTION</NAME>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>TECH_ID</NAME>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>SHORT_SEQUENCE</NAME>
-<ID>69</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>ACCESSION_NUMBER</NAME>
-<ID>109</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>256</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>SPECTRUM_REFERENCE</NAME>
-<ID>171</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>100</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-</DOMAINS>
-<ENTITIES>
-<ENT>
-<NAME>EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOPE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_%table%_%counter%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ACCESSION_NUMBER</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>256</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>ACCESSION_NUMBER</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATABASES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>136</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NTERM_MASS</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CTERM_MASS</NAME>
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-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
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-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
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-<SCHEMA></SCHEMA>
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-<DOMAINID>12</DOMAINID>
-<DT>
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-<ATTR>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_STATISTICS</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>2</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
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-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
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-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
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-<ID>5</ID>
-<POSNR>0</POSNR>
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-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
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-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<DOMAINID>12</DOMAINID>
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-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>PRST_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
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-<INDEX>
-<NAME>IX_FK_PROTEINS_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_SEQUENCES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PRST_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IDX_PROTEINS_3</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
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-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
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-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<ATTR>
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-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
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-</NNCON>
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-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
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-<INC>1</INC>
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-<NAME></NAME>
-<ID>1</ID>
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-<VALUE>1</VALUE>
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-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
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-<ATTRIBUTEID>3</ATTRIBUTEID>
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-<CONLEVEL>2</CONLEVEL>
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-<DOMAINID>9</DOMAINID>
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-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_ABUNDANCES_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_ABUNDANCES_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_EXPERIMENTS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>2</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>PRST_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PROTEINS_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_SEQUENCES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PRST_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IDX_PROTEINS_3</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>SPECTRA</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>26</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
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-<CONSTRAINT>
-<NAME>TUC_DATABASES_1</NAME>
-<NAMETEMPLATE>TUC_DATABASES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-</ENTITIES>
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-</SUBCATEGORIES>
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-</TEXTAREAS>
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-</GROUPBOXES>
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-</STAMPS>
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-</PROCEDURES>
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-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
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-<DESC></DESC>
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-<DELETERULE>0</DELETERULE>
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-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
-<ID>1</ID>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<SCHEMA></SCHEMA>
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-<KEYID>2</KEYID>
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-<SCHEMA></SCHEMA>
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-<CHILDOBJECTID>17</CHILDOBJECTID>
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-<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<NAMETEMPLATE>MO_PE_FK</NAMETEMPLATE>
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-<DESC></DESC>
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-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-</DOMAINS>
-<ENTITIES>
-<ENT>
-<NAME>EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_EXPERIMENTS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
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-<NAME></NAME>
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-</NNCON>
-</ATTR>
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-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
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-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
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-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
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-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
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-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<PKCON>
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-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<ATTR>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<DT>
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-<NAME></NAME>
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-<PAIR>
-<NAME></NAME>
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-<PAIR>
-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<PAIR>
-<NAME></NAME>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOPE_ID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATABASES_1</NAME>
-<NAMETEMPLATE>TUC_DATABASES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFIED_PEPTIDES</NAME>
-<ID>136</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_MODIFIED_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NTERM_MASS</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CTERM_MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-</ENTITIES>
-<SUBCATEGORIES>
-</SUBCATEGORIES>
-<TEXTAREAS>
-</TEXTAREAS>
-<GROUPBOXES>
-</GROUPBOXES>
-<STAMPS>
-</STAMPS>
-<SEQUENCES>
-</SEQUENCES>
-<PROCEDURES>
-</PROCEDURES>
-<VIEWS>
-</VIEWS>
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-<REL>
-<NAME>DA_EX_FK</NAME>
-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
-<ID>29</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<PARENTOBJECTID>16</PARENTOBJECTID>
-<CHILDOBJECTID>17</CHILDOBJECTID>
-<CARDINALITY>0</CARDINALITY>
-<RELTYPE>1</RELTYPE>
-<MANDATORYPARENT>1</MANDATORYPARENT>
-<UPDATERULE>0</UPDATERULE>
-<DELETERULE>0</DELETERULE>
-<CONSTRAINT>
-<NAME>DA_EX_FK</NAME>
-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-<PAIRS>
-<PAIR>
-<NAME></NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<KEYID>2</KEYID>
-<FOREIGNKEYID>4</FOREIGNKEYID>
-</PAIR>
-</PAIRS>
-</REL>
-<REL>
-<NAME>DA_SA_FK</NAME>
-<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE>
-<ID>30</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<PARENTOBJECTID>24</PARENTOBJECTID>
-<CHILDOBJECTID>17</CHILDOBJECTID>
-<CARDINALITY>0</CARDINALITY>
-<RELTYPE>1</RELTYPE>
-<MANDATORYPARENT>1</MANDATORYPARENT>
-<UPDATERULE>0</UPDATERULE>
-<DELETERULE>0</DELETERULE>
-<CONSTRAINT>
-<NAME>DA_SA_FK</NAME>
-<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-<PAIRS>
-<PAIR>
-<NAME></NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<KEYID>2</KEYID>
-<FOREIGNKEYID>5</FOREIGNKEYID>
-</PAIR>
-</PAIRS>
-</REL>
-<REL>
-<NAME>PE_PR_FK</NAME>
-<NAMETEMPLATE>PE_PR_FK</NAMETEMPLATE>
-<ID>36</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<PARENTOBJECTID>23</PARENTOBJECTID>
-<CHILDOBJECTID>21</CHILDOBJECTID>
-<CARDINALITY>0</CARDINALITY>
-<RELTYPE>1</RELTYPE>
-<MANDATORYPARENT>1</MANDATORYPARENT>
-<UPDATERULE>0</UPDATERULE>
-<DELETERULE>0</DELETERULE>
-<CONSTRAINT>
-<NAME>PE_PR_FK</NAME>
-<NAMETEMPLATE>PE_PR_FK</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-<PAIRS>
-<PAIR>
-<NAME></NAME>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOPE_ID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
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-<DOMAINID>12</DOMAINID>
-<DT>
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-<INC>1</INC>
-</DT>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<CONSTRAINT>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<NAME>PK_SEQUENCES</NAME>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<ATTR>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
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-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
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-<NAME></NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
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-<NAME>DB_ID</NAME>
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-<SCHEMA></SCHEMA>
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-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
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-<NAME></NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
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-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
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-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
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-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
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-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<VALUE>1</VALUE>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
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-<SCHEMA></SCHEMA>
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-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<CONTYPE>5</CONTYPE>
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-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
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-<SCHEMA></SCHEMA>
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-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
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-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
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-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
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-<CONSTRAINT>
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-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
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-<SCHEMA></SCHEMA>
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-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
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-<INC>1</INC>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.sql
deleted file mode 100644
index 5aaa048555b..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/001/schema-001.sql
+++ /dev/null
@@ -1,284 +0,0 @@
-/* ---------------------------------------------------------------------- */
-/* Script generated with: DeZign for Databases v5.2.3 */
-/* Target DBMS: PostgreSQL 8 */
-/* Project file: schema-001.dez */
-/* Project name: */
-/* Author: */
-/* Script type: Database creation script */
-/* Created on: 2009-09-28 08:43 */
-/* Model version: Version 2009-09-28 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
-
-CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
-
-CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
-
-CREATE DOMAIN LONG_SEQUENCE AS TEXT;
-
-CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
-
-CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EXPERIMENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EXPERIMENTS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
- CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- DB_ID TECH_ID NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
- CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
-);
-
-CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
-
-CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATIONS (
- ID BIGSERIAL NOT NULL,
- MOPE_ID TECH_ID NOT NULL,
- POS INTEGER_NUMBER NOT NULL,
- MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQUENCE SHORT_SEQUENCE NOT NULL,
- CHARGE INTEGER_NUMBER NOT NULL,
- CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEINS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SEQUENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SEQUENCES (
- ID BIGSERIAL NOT NULL,
- DB_ID TECH_ID NOT NULL,
- PRRE_ID TECH_ID NOT NULL,
- AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
- CHECKSUM CHECKSUM NOT NULL,
- CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "IDENTIFIED_PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE IDENTIFIED_PROTEINS (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQU_ID TECH_ID NOT NULL,
- CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ABUNDANCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ABUNDANCES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- VALUE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROBABILITY_FDR_MAPPINGS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROBABILITY_FDR_MAPPINGS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_REFERENCES (
- ID BIGSERIAL NOT NULL,
- ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
- DESCRIPTION DESCRIPTION,
- CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
- CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
-);
-
-CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATABASES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATABASES (
- ID BIGSERIAL NOT NULL,
- NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
- CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
- CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFIED_PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFIED_PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- NTERM_MASS REAL_NUMBER NOT NULL,
- CTERM_MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SPECTRUM_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SPECTRUM_REFERENCES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- REFERENCE SPECTRUM_REFERENCE NOT NULL,
- CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATION_FRACTIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATION_FRACTIONS (
- ID BIGSERIAL NOT NULL,
- MODI_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- FRACTION REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID);
-
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID);
-
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
- FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
- FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID);
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
-
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID);
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/002/schema-002.png b/rtd_phosphonetx/source/sql/proteomics/postgresql/002/schema-002.png
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diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/002/schema-002.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/002/schema-002.sql
deleted file mode 100755
index 4d4128aa57e..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/002/schema-002.sql
+++ /dev/null
@@ -1,292 +0,0 @@
-/* ---------------------------------------------------------------------- */
-/* Script generated with: DeZign for Databases v5.2.3 */
-/* Target DBMS: PostgreSQL 8 */
-/* Project file: schema.dez */
-/* Project name: */
-/* Author: */
-/* Script type: Database creation script */
-/* Created on: 2009-12-07 11:03 */
-/* Model version: Version 2009-12-07 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
-
-CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
-
-CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
-
-CREATE DOMAIN LONG_SEQUENCE AS TEXT;
-
-CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
-
-CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EXPERIMENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EXPERIMENTS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
- CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- DB_ID TECH_ID NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
- CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
-);
-
-CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
-
-CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATIONS (
- ID BIGSERIAL NOT NULL,
- MOPE_ID TECH_ID NOT NULL,
- POS INTEGER_NUMBER NOT NULL,
- MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQUENCE SHORT_SEQUENCE NOT NULL,
- CHARGE INTEGER_NUMBER NOT NULL,
- CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEINS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SEQUENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SEQUENCES (
- ID BIGSERIAL NOT NULL,
- DB_ID TECH_ID NOT NULL,
- PRRE_ID TECH_ID NOT NULL,
- AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
- CHECKSUM CHECKSUM NOT NULL,
- CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "IDENTIFIED_PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE IDENTIFIED_PROTEINS (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQU_ID TECH_ID NOT NULL,
- CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ABUNDANCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ABUNDANCES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- VALUE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROBABILITY_FDR_MAPPINGS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROBABILITY_FDR_MAPPINGS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_REFERENCES (
- ID BIGSERIAL NOT NULL,
- ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
- DESCRIPTION DESCRIPTION,
- CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
- CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
-);
-
-CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATABASES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATABASES (
- ID BIGSERIAL NOT NULL,
- NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
- CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
- CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFIED_PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFIED_PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- NTERM_MASS REAL_NUMBER NOT NULL,
- CTERM_MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SPECTRUM_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SPECTRUM_REFERENCES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- REFERENCE SPECTRUM_REFERENCE NOT NULL,
- CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATION_FRACTIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATION_FRACTIONS (
- ID BIGSERIAL NOT NULL,
- MODI_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- FRACTION REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
- FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
- FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/003/grant-003.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/003/grant-003.sql
deleted file mode 100644
index 2e85f4fb1f6..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/003/grant-003.sql
+++ /dev/null
@@ -1,18 +0,0 @@
--- Granting SELECT privilege to group PHOSPHONETX_READONLY
-
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SAMPLES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SEQUENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE IDENTIFIED_PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE ABUNDANCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROBABILITY_FDR_MAPPINGS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEIN_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATABASES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFIED_PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SPECTRUM_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATION_FRACTIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE EVENTS TO GROUP PHOSPHONETX_READONLY;
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/003/schema-003.png b/rtd_phosphonetx/source/sql/proteomics/postgresql/003/schema-003.png
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diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/003/schema-003.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/003/schema-003.sql
deleted file mode 100755
index 4dd90b2711c..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/003/schema-003.sql
+++ /dev/null
@@ -1,293 +0,0 @@
-/* ---------------------------------------------------------------------- */
-/* Script generated with: DeZign for Databases v5.2.3 */
-/* Target DBMS: PostgreSQL 8 */
-/* Project file: schema.dez */
-/* Project name: */
-/* Author: */
-/* Script type: Database creation script */
-/* Created on: 2010-03-31 16:10 */
-/* Model version: Version 2010-03-31 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
-
-CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
-
-CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
-
-CREATE DOMAIN LONG_SEQUENCE AS TEXT;
-
-CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
-
-CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EXPERIMENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EXPERIMENTS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
- CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- DB_ID TECH_ID NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
- CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
-);
-
-CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
-
-CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATIONS (
- ID BIGSERIAL NOT NULL,
- MOPE_ID TECH_ID NOT NULL,
- POS INTEGER_NUMBER NOT NULL,
- MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQUENCE SHORT_SEQUENCE NOT NULL,
- CHARGE INTEGER_NUMBER NOT NULL,
- CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEINS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SEQUENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SEQUENCES (
- ID BIGSERIAL NOT NULL,
- DB_ID TECH_ID NOT NULL,
- PRRE_ID TECH_ID NOT NULL,
- AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
- CHECKSUM CHECKSUM NOT NULL,
- CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "IDENTIFIED_PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE IDENTIFIED_PROTEINS (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQU_ID TECH_ID NOT NULL,
- COVERAGE REAL_NUMBER,
- CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ABUNDANCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ABUNDANCES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- VALUE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROBABILITY_FDR_MAPPINGS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROBABILITY_FDR_MAPPINGS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_REFERENCES (
- ID BIGSERIAL NOT NULL,
- ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
- DESCRIPTION DESCRIPTION,
- CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
- CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
-);
-
-CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATABASES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATABASES (
- ID BIGSERIAL NOT NULL,
- NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
- CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
- CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFIED_PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFIED_PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- NTERM_MASS REAL_NUMBER NOT NULL,
- CTERM_MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SPECTRUM_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SPECTRUM_REFERENCES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- REFERENCE SPECTRUM_REFERENCE NOT NULL,
- CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATION_FRACTIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATION_FRACTIONS (
- ID BIGSERIAL NOT NULL,
- MODI_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- FRACTION REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
- FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
- FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/004/grant-004.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/004/grant-004.sql
deleted file mode 100644
index 2e85f4fb1f6..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/004/grant-004.sql
+++ /dev/null
@@ -1,18 +0,0 @@
--- Granting SELECT privilege to group PHOSPHONETX_READONLY
-
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SAMPLES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SEQUENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE IDENTIFIED_PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE ABUNDANCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROBABILITY_FDR_MAPPINGS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEIN_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATABASES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFIED_PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SPECTRUM_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATION_FRACTIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE EVENTS TO GROUP PHOSPHONETX_READONLY;
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/004/schema-004.png b/rtd_phosphonetx/source/sql/proteomics/postgresql/004/schema-004.png
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diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/004/schema-004.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/004/schema-004.sql
deleted file mode 100755
index 824269ff55a..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/004/schema-004.sql
+++ /dev/null
@@ -1,296 +0,0 @@
-/* ---------------------------------------------------------------------- */
-/* Script generated with: DeZign for Databases v5.2.3 */
-/* Target DBMS: PostgreSQL 8 */
-/* Project file: schema.dez */
-/* Project name: */
-/* Author: */
-/* Script type: Database creation script */
-/* Created on: 2010-05-27 14:26 */
-/* Model version: Version 2010-05-27 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
-
-CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
-
-CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
-
-CREATE DOMAIN LONG_SEQUENCE AS TEXT;
-
-CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
-
-CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
-
-CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EXPERIMENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EXPERIMENTS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
- CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- DB_ID TECH_ID NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
- CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
-);
-
-CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
-
-CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATIONS (
- ID BIGSERIAL NOT NULL,
- MOPE_ID TECH_ID NOT NULL,
- POS INTEGER_NUMBER NOT NULL,
- MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQUENCE SHORT_SEQUENCE NOT NULL,
- CHARGE INTEGER_NUMBER NOT NULL,
- CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEINS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SEQUENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SEQUENCES (
- ID BIGSERIAL NOT NULL,
- DB_ID TECH_ID NOT NULL,
- PRRE_ID TECH_ID NOT NULL,
- AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
- CHECKSUM CHECKSUM NOT NULL,
- CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "IDENTIFIED_PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE IDENTIFIED_PROTEINS (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQU_ID TECH_ID NOT NULL,
- COVERAGE REAL_NUMBER,
- IS_PRIMARY BOOLEAN_CHAR NOT NULL,
- CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ABUNDANCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ABUNDANCES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- VALUE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROBABILITY_FDR_MAPPINGS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROBABILITY_FDR_MAPPINGS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_REFERENCES (
- ID BIGSERIAL NOT NULL,
- ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
- DESCRIPTION DESCRIPTION,
- CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
- CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
-);
-
-CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATABASES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATABASES (
- ID BIGSERIAL NOT NULL,
- NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
- CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
- CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFIED_PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFIED_PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- NTERM_MASS REAL_NUMBER NOT NULL,
- CTERM_MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SPECTRUM_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SPECTRUM_REFERENCES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- REFERENCE SPECTRUM_REFERENCE NOT NULL,
- CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATION_FRACTIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATION_FRACTIONS (
- ID BIGSERIAL NOT NULL,
- MODI_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- FRACTION REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
- FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
- FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/005/grant-005.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/005/grant-005.sql
deleted file mode 100644
index 2e85f4fb1f6..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/005/grant-005.sql
+++ /dev/null
@@ -1,18 +0,0 @@
--- Granting SELECT privilege to group PHOSPHONETX_READONLY
-
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SAMPLES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SEQUENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE IDENTIFIED_PROTEINS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE ABUNDANCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROBABILITY_FDR_MAPPINGS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE PROTEIN_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE DATABASES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFIED_PEPTIDES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE SPECTRUM_REFERENCES TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE MODIFICATION_FRACTIONS TO GROUP PHOSPHONETX_READONLY;
-GRANT SELECT ON TABLE EVENTS TO GROUP PHOSPHONETX_READONLY;
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/005/schema-005.png b/rtd_phosphonetx/source/sql/proteomics/postgresql/005/schema-005.png
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diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/005/schema-005.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/005/schema-005.sql
deleted file mode 100755
index ac882b6f7f9..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/005/schema-005.sql
+++ /dev/null
@@ -1,310 +0,0 @@
-/* ---------------------------------------------------------------------- */
-/* Script generated with: DeZign for Databases v5.2.3 */
-/* Target DBMS: PostgreSQL 8 */
-/* Project file: schema.dez */
-/* Project name: */
-/* Author: */
-/* Script type: Database creation script */
-/* Created on: 2011-06-08 08:28 */
-/* Model version: Version 2011-06-08 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
-
-CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
-
-CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
-
-CREATE DOMAIN LONG_SEQUENCE AS TEXT;
-
-CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
-
-CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
-
-CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EXPERIMENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EXPERIMENTS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
- CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- DB_ID TECH_ID NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
- CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
-);
-
-CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
-
-CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATIONS (
- ID BIGSERIAL NOT NULL,
- MOPE_ID TECH_ID NOT NULL,
- POS INTEGER_NUMBER NOT NULL,
- MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_MODIFICATIONS_MODIFIED_PEPTIDES ON MODIFICATIONS (MOPE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQUENCE SHORT_SEQUENCE NOT NULL,
- CHARGE INTEGER_NUMBER NOT NULL,
- CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEINS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- EXPE_ID TECH_ID NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SEQUENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SEQUENCES (
- ID BIGSERIAL NOT NULL,
- DB_ID TECH_ID NOT NULL,
- PRRE_ID TECH_ID NOT NULL,
- AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
- CHECKSUM CHECKSUM NOT NULL,
- CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_SEQUENCES_PROTEIN_REFERENCES ON SEQUENCES (PRRE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "IDENTIFIED_PROTEINS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE IDENTIFIED_PROTEINS (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SEQU_ID TECH_ID NOT NULL,
- COVERAGE REAL_NUMBER,
- IS_PRIMARY BOOLEAN_CHAR NOT NULL,
- CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_IDENTIFIED_PROTEINS_PROTEINS ON IDENTIFIED_PROTEINS (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ABUNDANCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ABUNDANCES (
- ID BIGSERIAL NOT NULL,
- PROT_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- VALUE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_ABUNDANCES_PROTEINS ON ABUNDANCES (PROT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROBABILITY_FDR_MAPPINGS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROBABILITY_FDR_MAPPINGS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- PROBABILITY REAL_NUMBER NOT NULL,
- FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
- CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_PROBABILITY_FDR_MAPPINGS_DATA_SETS ON PROBABILITY_FDR_MAPPINGS (DASE_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_REFERENCES (
- ID BIGSERIAL NOT NULL,
- ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
- DESCRIPTION DESCRIPTION,
- CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
- CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
-);
-
-CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATABASES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATABASES (
- ID BIGSERIAL NOT NULL,
- NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
- CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
- CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFIED_PEPTIDES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFIED_PEPTIDES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- NTERM_MASS REAL_NUMBER NOT NULL,
- CTERM_MASS REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_MODIFIED_PEPTIDES_PEPTIDES ON MODIFIED_PEPTIDES (PEPT_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SPECTRUM_REFERENCES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SPECTRUM_REFERENCES (
- ID BIGSERIAL NOT NULL,
- PEPT_ID TECH_ID NOT NULL,
- REFERENCE SPECTRUM_REFERENCE NOT NULL,
- CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "MODIFICATION_FRACTIONS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE MODIFICATION_FRACTIONS (
- ID BIGSERIAL NOT NULL,
- MODI_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID,
- FRACTION REAL_NUMBER NOT NULL,
- CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
-);
-
-CREATE INDEX IX_FK_MODIFICATION_FRACTIONS_MODIFICATIONS ON MODIFICATION_FRACTIONS (MODI_ID);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
- FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
-
-ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
- FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
- FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-001-002.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-001-002.sql
deleted file mode 100644
index 36900c0353f..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-001-002.sql
+++ /dev/null
@@ -1,41 +0,0 @@
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
-);
-
-
-ALTER TABLE MODIFICATIONS DROP CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS;
-ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
- FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE PEPTIDES DROP CONSTRAINT PE_PR_FK;
-ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROTEINS DROP CONSTRAINT DATA_SETS_PROTEINS;
-ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE IDENTIFIED_PROTEINS DROP CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS;
-ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE ABUNDANCES DROP CONSTRAINT PROTEINS_ABUNDANCES;
-ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
- FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
-
-ALTER TABLE PROBABILITY_FDR_MAPPINGS DROP CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS;
-ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFIED_PEPTIDES DROP CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES;
-ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE SPECTRUM_REFERENCES DROP CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES;
-ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
- FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
-
-ALTER TABLE MODIFICATION_FRACTIONS DROP CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS;
-ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
- FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
-
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-002-003.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-002-003.sql
deleted file mode 100644
index 639f94657a5..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-002-003.sql
+++ /dev/null
@@ -1,4 +0,0 @@
--- JAVA ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.db.migration.MigrationStepFrom002To003
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD COLUMN COVERAGE REAL_NUMBER;
-
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-003-004.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-003-004.sql
deleted file mode 100644
index 84d3d8a841b..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-003-004.sql
+++ /dev/null
@@ -1,5 +0,0 @@
-CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
-
-ALTER TABLE IDENTIFIED_PROTEINS ADD COLUMN IS_PRIMARY BOOLEAN_CHAR NOT NULL;
-
-UPDATE IDENTIFIED_PROTEINS SET IS_PRIMARY = 'T' WHERE ID = ANY(SELECT MIN(ID) FROM IDENTIFIED_PROTEINS GROUP BY PROT_ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-004-005.sql b/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-004-005.sql
deleted file mode 100644
index fb183f726ad..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/migration/migration-004-005.sql
+++ /dev/null
@@ -1,14 +0,0 @@
-DROP INDEX IF EXISTS IX_FK_MODIFICATION_FRACTIONS_MODIFICATIONS;
-CREATE INDEX IX_FK_MODIFICATION_FRACTIONS_MODIFICATIONS ON MODIFICATION_FRACTIONS (MODI_ID);
-DROP INDEX IF EXISTS IX_FK_MODIFICATIONS_MODIFIED_PEPTIDES;
-CREATE INDEX IX_FK_MODIFICATIONS_MODIFIED_PEPTIDES ON MODIFICATIONS (MOPE_ID);
-DROP INDEX IF EXISTS IX_FK_MODIFIED_PEPTIDES_PEPTIDES;
-CREATE INDEX IX_FK_MODIFIED_PEPTIDES_PEPTIDES ON MODIFIED_PEPTIDES (PEPT_ID);
-DROP INDEX IF EXISTS IX_FK_ABUNDANCES_PROTEINS;
-CREATE INDEX IX_FK_ABUNDANCES_PROTEINS ON ABUNDANCES (PROT_ID);
-DROP INDEX IF EXISTS IX_FK_IDENTIFIED_PROTEINS_PROTEINS;
-CREATE INDEX IX_FK_IDENTIFIED_PROTEINS_PROTEINS ON IDENTIFIED_PROTEINS (PROT_ID);
-DROP INDEX IF EXISTS IX_FK_SEQUENCES_PROTEIN_REFERENCES;
-CREATE INDEX IX_FK_SEQUENCES_PROTEIN_REFERENCES ON SEQUENCES (PRRE_ID);
-DROP INDEX IF EXISTS IX_FK_PROBABILITY_FDR_MAPPINGS_DATA_SETS;
-CREATE INDEX IX_FK_PROBABILITY_FDR_MAPPINGS_DATA_SETS ON PROBABILITY_FDR_MAPPINGS (DASE_ID);
diff --git a/rtd_phosphonetx/source/sql/proteomics/postgresql/schema.dez b/rtd_phosphonetx/source/sql/proteomics/postgresql/schema.dez
deleted file mode 100755
index 4c8ebf447f3..00000000000
--- a/rtd_phosphonetx/source/sql/proteomics/postgresql/schema.dez
+++ /dev/null
@@ -1,26376 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?><dezign>
-
-<FILEFORMATVERSION>51</FILEFORMATVERSION>
-<VERSION>
-<PROJECTSETTINGS>
-<PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME>
-<MODIFIED>2011-06-08</MODIFIED>
-<CREATED>2009-06-29</CREATED>
-<CREATED2></CREATED2>
-<PROJECTNAME></PROJECTNAME>
-<DESCRIPTION></DESCRIPTION>
-<AUTHOR></AUTHOR>
-<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES>G:\phosphonetx\datamodel\schema.sql;G:\phosphonetx\datamodel\drop.sql;\CreateDBLog_201106081.txt</LASTGENERATEDFILES>
-</PROJECTSETTINGS>
-<CONNECTIONSETTINGS>
-<SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE>
-<CONNECTIONTYPE>SQLFILE</CONNECTIONTYPE>
-<DBID>postgresql8</DBID>
-</CONNECTIONSETTINGS>
-<DATADICT>
-<DBID>postgresql8</DBID>
-<LASTID>236</LASTID>
-<DDSETTINGS>
-<PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE>
-<FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE>
-<CCONNAMETEMPLATE>CC_%table%_%column%</CCONNAMETEMPLATE>
-<NOTNULLCONNAMETEMPLATE>NN_%column%</NOTNULLCONNAMETEMPLATE>
-<DEFAULTCONNAMETEMPLATE>DEF_%table%_%column%</DEFAULTCONNAMETEMPLATE>
-<TUCONNAMETEMPLATE>TUC_%table%_%counter%</TUCONNAMETEMPLATE>
-<TCCONNAMETEMPLATE>TCC_%table%_%counter%</TCCONNAMETEMPLATE>
-<RELNAMETEMPLATE>%parent%_%child%</RELNAMETEMPLATE>
-<INDEXNAMETEMPLATE>IDX_%table%_%counter%</INDEXNAMETEMPLATE>
-<DEFTABLEOPTIONS></DEFTABLEOPTIONS>
-<DEFINDEXOPTIONS></DEFINDEXOPTIONS>
-<BEGINDATABASESCRIPT></BEGINDATABASESCRIPT>
-<ENDDATABASESCRIP></ENDDATABASESCRIP>
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-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_%table%_%counter%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_SEQUENCES_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>IX_FK_SEQUENCES_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PRRE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>COVERAGE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IS_PRIMARY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>188</DOMAINID>
-<DT>
-<DTLISTNAME>BOOLEAN</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-<DEFCON>
-<NAME></NAME>
-<NAMETEMPLATE>DEF_%table%_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>FALSE</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>6</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</DEFCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFIED_PROTEINS_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFIED_PROTEINS_PROTEINS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_ABUNDANCES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_ABUNDANCES_PROTEINS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PROBABILITY_FDR_MAPPINGS_DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_PROBABILITY_FDR_MAPPINGS_DATA_SETS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ACCESSION_NUMBER</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>256</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>ACCESSION_NUMBER</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATABASES_1</NAME>
-<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>136</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NTERM_MASS</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CTERM_MASS</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFIED_PEPTIDES_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFIED_PEPTIDES_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SPECTRUM_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>160</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SPECTRUM_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>REFERENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>171</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>100</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_STATISTICS</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>2</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_STATISTICS</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>2</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>PRST_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PROTEINS_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_SEQUENCES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PRST_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IDX_PROTEINS_3</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
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-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
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-<SD>0</SD>
-<INC>1</INC>
-</DT>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
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-<NAME>SEQUENCES</NAME>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
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-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
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-<DTLISTNAME>TEXT</DTLISTNAME>
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-<INC>1</INC>
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-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
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-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<NAME>SPECTRA</NAME>
-<ID>26</ID>
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-<SCHEMA></SCHEMA>
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-<CONTYPE>3</CONTYPE>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<ATTR>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<DOMAINID>-1</DOMAINID>
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-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
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-<ID>1</ID>
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-<SCHEMA></SCHEMA>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
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-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_ABUNDANCES_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_ABUNDANCES_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_EXPERIMENTS</NAME>
-<NAMETEMPLATE>PK_EXPERIMENTS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SPEC_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>SPECTRA_COUNT</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME>
-<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SPEC_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>9</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>IDDA_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDDA_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>2</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>PRST_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ABUNDANCE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PROTEINS_SEQUENCES</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_SEQUENCES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SEQU_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PRST_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IDX_PROTEINS_3</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>SPECTRA</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>26</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SPECTRA</NAME>
-<NAMETEMPLATE>PK_SPECTRA</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>DELTA_MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
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-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>ABTY_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
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-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
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-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
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-<CONLASTID>2</CONLASTID>
-<PKCON>
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-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
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-<ATTR>
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-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
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-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
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-</ATTRIBUTEIDS>
-</NNCON>
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-<ID>3</ID>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
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-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>3</ATTRIBUTEID>
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-<NAMETEMPLATE>TUC_DATABASES_1</NAMETEMPLATE>
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-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
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-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
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-</SUBCATEGORIES>
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-</TEXTAREAS>
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-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PEPT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOTY_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PEPT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>MOTY_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATION_TYPES</NAME>
-<NAMETEMPLATE>PK_MODIFICATION_TYPES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CODE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER</DTLISTNAME>
-<LE>1</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MASS_TOLERANCE</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_MODIFICATION_TYPES_1</NAME>
-<NAMETEMPLATE>TUC_MODIFICATION_TYPES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
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-</NNCON>
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-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEID>2</ATTRIBUTEID>
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-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
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-</DT>
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-<NAME></NAME>
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-<ATTRIBUTEID>3</ATTRIBUTEID>
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-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
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-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<RELID>0</RELID>
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-<IDXCOL>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
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-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
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-</ENT>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-</ATTRIBUTEIDS>
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-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
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-<CONLASTID>1</CONLASTID>
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-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATABASES_1</NAME>
-<NAMETEMPLATE>TUC_DATABASES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFIED_PEPTIDES</NAME>
-<ID>136</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
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-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFIED_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_MODIFIED_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<SD>0</SD>
-<INC>1</INC>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<SCHEMA></SCHEMA>
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-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
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-<NNCON>
-<NAME></NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
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-<SCHEMA></SCHEMA>
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-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
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-</SUBCATEGORIES>
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-</TEXTAREAS>
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-</GROUPBOXES>
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-</STAMPS>
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-</PROCEDURES>
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-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
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-<PAIR>
-<NAME></NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<KEYID>2</KEYID>
-<FOREIGNKEYID>4</FOREIGNKEYID>
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-</PAIRS>
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-<REL>
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-<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE>
-<ID>30</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CHILDOBJECTID>17</CHILDOBJECTID>
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-<RELTYPE>1</RELTYPE>
-<MANDATORYPARENT>1</MANDATORYPARENT>
-<UPDATERULE>0</UPDATERULE>
-<DELETERULE>0</DELETERULE>
-<CONSTRAINT>
-<NAME>DA_SA_FK</NAME>
-<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
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-<PAIR>
-<NAME></NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<KEYID>2</KEYID>
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-<REL>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<CHILDOBJECTID>21</CHILDOBJECTID>
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-<DELETERULE>0</DELETERULE>
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-<NAMETEMPLATE>PE_PR_FK</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
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-<PAIR>
-<NAME></NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<SCHEMA></SCHEMA>
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-<DELETERULE>0</DELETERULE>
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-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_EXPERIMENTS_1</NAME>
-<NAMETEMPLATE>TUC_EXPERIMENTS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>3</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATA_SETS</NAME>
-<NAMETEMPLATE>PK_DATA_SETS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_EXPERIMENTS</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_EXPERIMENTS</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>4</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>IX_FK_DATA_SETS_SAMPLES</NAME>
-<NAMETEMPLATE>IX_FK_DATA_SETS_SAMPLES</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SAMP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>5</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_DATA_SETS_1</NAME>
-<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>MODIFICATIONS</NAME>
-<NAMETEMPLATE>IX_FK_MODIFICATIONS_PEPTIDES</NAMETEMPLATE>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>7</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_MODIFICATIONS</NAME>
-<NAMETEMPLATE>PK_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MOPE_ID</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>POS</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>MASS</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PEPTIDES</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_ABUNDANCES</NAMETEMPLATE>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>10</ATTRLASTID>
-<IDXLASTID>5</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PEPTIDES</NAME>
-<NAMETEMPLATE>PK_PEPTIDES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQUENCE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>69</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHARGE</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>7</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IX_FK_PEPTIDES_PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>PROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>PROTEINS</NAME>
-<NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>11</ATTRLASTID>
-<IDXLASTID>7</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEINS</NAME>
-<NAMETEMPLATE>PK_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>10</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>9</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEINS_1</NAME>
-<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DASE_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>10</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>SAMPLES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_SAMPLES</NAME>
-<NAMETEMPLATE>PK_SAMPLES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PERM_ID</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXPE_ID</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_SAMPLES_1</NAME>
-<NAMETEMPLATE>TUC_SAMPLES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>SEQUENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_SEQUENCES</NAME>
-<NAMETEMPLATE>PK_SEQUENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DB_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PRRE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>AMINO_ACID_SEQUENCE</NAME>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>9</DOMAINID>
-<DT>
-<DTLISTNAME>TEXT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHECKSUM</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>8</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>47</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_IDENTIFIED_PROTEINS</NAME>
-<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SEQU_ID</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>91</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_ABUNDANCES</NAME>
-<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SAMP_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>96</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME>
-<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DASE_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>12</DOMAINID>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>PROBABILITY</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>FALSE_DISCOVERY_RATE</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>8</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-</ENT>
-<ENT>
-<NAME>PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>98</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>4</ATTRLASTID>
-<IDXLASTID>2</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_PROTEIN_REFERENCES</NAME>
-<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIPROT_ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>109</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>40</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DESCRIPTION</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>2000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>IDX_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIPROT_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>TUC_PROTEIN_REFERENCES_1</NAME>
-<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>2</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>3</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-</CONSTRAINTS>
-</ENT>
-<ENT>
-<NAME>DATABASES</NAME>
-<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
-<ID>110</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>3</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>PK_DATABASES</NAME>
-<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>3</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</PKCON>
-<ATTRIBUTES>
-<ATTR>
-<NAME>ID</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
-<DTLISTNAME>BIGSERIAL</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>2</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>NAME_AND_VERSION</NAME>
-<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>11</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>200</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
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-<DELETERULE>0</DELETERULE>
-<CONSTRAINT>
-<NAME>MODIFIED_PEPTIDES_MODIFICATIONS</NAME>
-<NAMETEMPLATE>MODIFIED_PEPTIDES_MODIFICATIONS</NAMETEMPLATE>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<CONLEVEL>2</CONLEVEL>
-<CONTYPE>4</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</CONSTRAINT>
-<PAIRS>
-<PAIR>
-<NAME></NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<KEYID>2</KEYID>
-<FOREIGNKEYID>7</FOREIGNKEYID>
-</PAIR>
-</PAIRS>
-</REL>
-</RELATIONSHIPS>
-<SUBCATEGORYCONNECTIONS>
-</SUBCATEGORYCONNECTIONS>
-</DATADICT>
-</VERSION>
-
-</dezign>
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/core-plugins/core-plugins.properties b/rtd_phosphonetx/sourceTest/core-plugins/core-plugins.properties
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java
deleted file mode 100644
index 84e93ffbf16..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/APMSReportTest.java
+++ /dev/null
@@ -1,297 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
-
-import static ch.systemsx.cisd.openbis.dss.proteomics.server.plugins.APMSReport.DEFAULT_PROTEIN_PROPERTY_CODE;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-import java.util.Set;
-
-import javax.activation.DataHandler;
-
-import org.apache.commons.io.IOUtils;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hamcrest.core.IsNull;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.mail.EMailAddress;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.MockDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.Constants;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = APMSReport.class)
-public class APMSReportTest extends AbstractFileSystemTestCase
-{
- private static final String EXAMPLE_PROTEINS =
- "# Protein abundances computed from file 'result.consensusXML'\n"
- + "# Parameters (relevant only): top=3, average=median, include_all, consensus:normalize\n"
- + "# Files/samples associated with abundance values below:"
- + " 0: '/cluster/s1.featureXML',"
- + " 1: '/cluster/s2.featureXML',"
- + " 2: '/cluster/s3.featureXML'\n"
- + "\"protein\",\"n_proteins\",\"protein_score\",\"n_peptides\",\"abundance_0\",\"abundance_1\",\"abundance_2\"\n"
- + "\"P1\",1,1,5,1.5,2.5,3.5\n" + "\"P2\",1,1,6,11.5,0,13.5\n"
- + "\"P3\",1,1,14,21.5,22.5,0\n";
-
- private Mockery context;
-
- private APMSReport report;
-
- private IEncapsulatedOpenBISService service;
-
- private IMailClient mailClient;
-
- private DataSetProcessingContext processingContext;
-
- @BeforeMethod
- public void beforeMethod()
- {
- File dataSetFolder = createDataSet("1");
- FileUtilities.writeToFile(new File(dataSetFolder, APMSReport.PROTEIN_FILE_NAME),
- EXAMPLE_PROTEINS);
- createDataSet("2");
-
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- mailClient = context.mock(IMailClient.class);
- report = new APMSReport(new Properties(), workingDirectory);
- report.setService(service);
- MockDataSetDirectoryProvider directoryProvider =
- new MockDataSetDirectoryProvider(workingDirectory, Constants.DEFAULT_SHARE_ID);
- processingContext =
- new DataSetProcessingContext(null, directoryProvider,
- Collections.<String, String> emptyMap(), mailClient, "test-user", "a@bc.de");
- }
-
- private File createDataSet(String location)
- {
- File share = new File(workingDirectory, Constants.DEFAULT_SHARE_ID);
- File originalFolder = new File(new File(share, location), "original");
- originalFolder.mkdirs();
- File dataSetFolder = new File(originalFolder, "data-set-folder");
- dataSetFolder.mkdirs();
- return dataSetFolder;
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcess() throws IOException
- {
- Sample b2 = new SampleBuilder("/S/B2").id(12).getSample();
- prepareGetSample(new SampleBuilder("/MS_DATA/S1").id(1).childOf(b2).getSample());
- prepareGetSample(new SampleBuilder("/MS_DATA/S2").id(2).childOf(b2).getSample());
- prepareGetSample(new SampleBuilder("/MS_DATA/S3").id(3).childOf(b2).getSample());
- DatasetDescriptionBuilder ds1 =
- new DatasetDescriptionBuilder("ds1").location("1").space("s").project("p")
- .experiment("e");
- DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location("2");
- List<DatasetDescription> dataSets =
- Arrays.asList(ds1.getDatasetDescription(), ds2.getDatasetDescription());
- final RecordingMatcher<String> subjectMatcher = new RecordingMatcher<String>();
- final RecordingMatcher<String> contentMatcher = new RecordingMatcher<String>();
- final RecordingMatcher<String> fileNameMatcher = new RecordingMatcher<String>();
- final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
- final RecordingMatcher<EMailAddress[]> addressesMatcher =
- new RecordingMatcher<EMailAddress[]>();
- context.checking(new Expectations()
- {
- {
- one(mailClient).sendEmailMessageWithAttachment(with(subjectMatcher),
- with(contentMatcher), with(fileNameMatcher), with(attachmentMatcher),
- with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
- with(addressesMatcher));
- }
- });
-
- ProcessingStatus status = report.process(dataSets, processingContext);
- assertEquals("Protein APMS Report", subjectMatcher.recordedObject());
- assertEquals("Dear User\n\n"
- + "Enclosed you will find the Protein APMS report file for experiment s/p/e.\n"
- + "Data Set: ds1", contentMatcher.recordedObject());
- @SuppressWarnings("unchecked")
- List<String> fileLines =
- IOUtils.readLines(attachmentMatcher.recordedObject().getInputStream());
- assertEquals("Sample ID,Bait,Prey,freq of obs,"
- + "avg MS1 intensities (normalized for the bait),STDV MS1 intensity",
- fileLines.get(0));
- assertEquals(4, fileLines.size());
- assertEquals("[ERROR: \"Exception occured: "
- + UserFailureException.class.getName() + ": File "
- + APMSReport.PROTEIN_FILE_NAME + " missing.\"]", status.getErrorStatuses()
- .toString());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCreateReport()
- {
- Sample master =
- new SampleBuilder("/master").property(DEFAULT_PROTEIN_PROPERTY_CODE, "Q1")
- .getSample();
- Sample b1 = new SampleBuilder("/S/B1").id(11).childOf(master).getSample();
- Sample b2 = new SampleBuilder("/S/B2").id(12).getSample();
- prepareGetSample(new SampleBuilder("/MS_DATA/S1").id(1).childOf(b1).getSample());
- prepareGetSample(new SampleBuilder("/MS_DATA/S2").id(2).childOf(b1).getSample());
- prepareGetSample(new SampleBuilder("/MS_DATA/S3").id(3).childOf(b2).getSample());
- DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
- List<DatasetDescription> dataSets = Arrays.asList(ds1.getDatasetDescription());
-
- TableModel table = report.createReport(dataSets, processingContext);
-
- List<TableModelColumnHeader> headers = table.getHeader();
- assertEquals("[Sample ID, Bait, Prey, freq of obs, "
- + "avg MS1 intensities (normalized for the bait), STDV MS1 intensity]",
- headers.toString());
- List<TableModelRow> rows = table.getRows();
- assertEquals("[B1, Q1, P1, 1.0, 2.0, 0.5]", rows.get(0).getValues().toString());
- assertEquals("[B2, , P1, 1.0, 3.5, 0.0]", rows.get(1).getValues().toString());
- assertEquals("[B1, Q1, P2, 0.5, 5.75, 5.75]", rows.get(2).getValues().toString());
- assertEquals("[B2, , P2, 1.0, 13.5, 0.0]", rows.get(3).getValues().toString());
- assertEquals("[B1, Q1, P3, 1.0, 22.0, 0.5]", rows.get(4).getValues().toString());
- assertEquals("[B2, , P3, 0.0, 0.0, 0.0]", rows.get(5).getValues().toString());
- assertEquals(3 * 2, rows.size());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCreateReportForMissingProteinsFile()
- {
- DatasetDescriptionBuilder ds = new DatasetDescriptionBuilder("ds2").location("2");
- try
- {
- report.createReport(Arrays.asList(ds.getDatasetDescription()), processingContext);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("File " + APMSReport.PROTEIN_FILE_NAME + " missing.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCreateReportForTwoDataSets()
- {
- DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
- DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location("2");
- try
- {
- report.createReport(
- Arrays.asList(ds1.getDatasetDescription(), ds2.getDatasetDescription()), null);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Chosen plugin works with exactly one data set. 2 data sets selected.",
- ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private void prepareGetSample(final Sample sample)
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- SampleIdentifierFactory.parse(sample.getIdentifier()));
- will(returnValue(sample));
- }
- });
- prepareGetAncestors(sample);
- }
-
- protected void prepareGetAncestors(final Sample sample)
- {
- List<IEntityProperty> properties = sample.getProperties();
- for (IEntityProperty property : properties)
- {
- if (property.getPropertyType().getCode().equals(DEFAULT_PROTEIN_PROPERTY_CODE))
- {
- return;
- }
- }
- final Set<Sample> parents = sample.getParents();
- context.checking(new Expectations()
- {
- {
- one(service).listSamples(with(new BaseMatcher<ListSampleCriteria>()
- {
- @Override
- public boolean matches(Object item)
- {
- return sample.getId() == ((ListSampleCriteria) item)
- .getChildSampleId().getId();
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendText("parents of " + sample.getIdentifier());
- }
- }));
- will(returnValue(new ArrayList<Sample>(parents)));
- }
- });
- for (Sample parent : parents)
- {
- prepareGetAncestors(parent);
- }
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java
deleted file mode 100644
index cf6469dc431..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/proteomics/server/plugins/LocalAndRemoteCopierTest.java
+++ /dev/null
@@ -1,392 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.dss.proteomics.server.plugins;
-
-import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier.SSH_TIMEOUT_MILLIS;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.io.FileUtils;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.concurrent.ExecutionResult;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.filesystem.BooleanStatus;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.filesystem.IPathCopier;
-import ch.systemsx.cisd.common.filesystem.ssh.ISshCommandExecutor;
-import ch.systemsx.cisd.common.process.ProcessResult;
-import ch.systemsx.cisd.common.utilities.ITextHandler;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierFactory;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.RSyncConfig;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = LocalAndRemoteCopier.class)
-public class LocalAndRemoteCopierTest extends AbstractFileSystemTestCase
-{
- private static final ProcessResult OK_RESULT = new ProcessResult(Arrays.asList(""), 0, null,
- ExecutionResult.create(null), null, 0, (List<String>) null, null, null, null);
-
- private static final String SAMPLE_CODE = "my-sample";
-
- private static final DataSetType DATA_SET_TYPE = new DataSetType("MY");
-
- private static final DataSetKind DATA_SET_KIND = DataSetKind.PHYSICAL;
-
- private static final String DATA_SET_CODE = "my-dataset-123";
-
- private static final String FOLDER_NAME = DATA_SET_CODE;
-
- private static final String DATA = "hello test";
-
- private Mockery context;
-
- private File dataSet;
-
- private IPathCopierFactory copierFactory;
-
- private IPathCopier copier;
-
- private ISshCommandExecutorFactory sshExecutorFactory;
-
- private ISshCommandExecutor sshExecutor;
-
- private File destination;
-
- private File dataFile;
-
- private File rsyncExec;
-
- private File sshExec;
-
- @BeforeMethod
- public void beforeMethod() throws Exception
- {
- context = new Mockery();
- copierFactory = context.mock(IPathCopierFactory.class);
- copier = context.mock(IPathCopier.class);
- sshExecutorFactory = context.mock(ISshCommandExecutorFactory.class);
- sshExecutor = context.mock(ISshCommandExecutor.class);
- dataSet = new File(workingDirectory, "data-set");
- dataSet.mkdirs();
- dataFile = new File(dataSet, "data.txt");
- FileUtilities.writeToFile(dataFile, DATA);
- destination = new File(workingDirectory, "destination");
- destination.mkdirs();
- rsyncExec = new File(workingDirectory, "my-rsync");
- rsyncExec.createNewFile();
- sshExec = new File(workingDirectory, "my-rssh");
- sshExec.createNewFile();
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLocalWithKnownSample()
- {
- Properties properties = new Properties();
- prepareCopier(properties);
- properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
- LocalAndRemoteCopier msInjectionCopier =
- new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
- prepareForCheckingLastModifiedDate();
-
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetType(DATA_SET_TYPE);
- dataSetInformation.setDataSetKind(DATA_SET_KIND);
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put(DATA_SET_CODE, SAMPLE_CODE);
- Status status = msInjectionCopier.handle(dataSet, dataSetInformation, parameterBindings);
-
- assertEquals(Status.OK, status);
- File copiedDataSet = new File(destination, FOLDER_NAME);
- assertEquals(true, copiedDataSet.isDirectory());
- assertEquals(dataSet.lastModified(), copiedDataSet.lastModified());
- assertEquals(DATA, FileUtilities.loadToString(new File(copiedDataSet, dataFile.getName()))
- .trim());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLocalWithUnknownSample()
- {
- Properties properties = new Properties();
- prepareCopier(properties);
- properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
- LocalAndRemoteCopier msInjectionCopier =
- new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
-
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetType(DATA_SET_TYPE);
- dataSetInformation.setDataSetKind(DATA_SET_KIND);
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- Status status = msInjectionCopier.handle(dataSet, dataSetInformation, parameterBindings);
-
- assertEquals(Status.OK, status);
- File copiedDataSet = new File(destination, DATA_SET_CODE);
- assertEquals(true, copiedDataSet.isDirectory());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLocalWithAlreadyExistingDestination()
- {
- Properties properties = new Properties();
- prepareCopier(properties);
- properties.setProperty(DataSetCopier.DESTINATION_KEY, destination.getPath());
- LocalAndRemoteCopier msInjectionCopier =
- new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
- File copiedDataSet = new File(destination, FOLDER_NAME);
- copiedDataSet.mkdirs();
- File dummy = new File(copiedDataSet, "dummy");
- FileUtilities.writeToFile(dummy, "hello");
-
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetType(DATA_SET_TYPE);
- dataSetInformation.setDataSetKind(DATA_SET_KIND);
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put(DATA_SET_CODE, SAMPLE_CODE);
- Status status = msInjectionCopier.handle(dataSet, dataSetInformation, parameterBindings);
-
- assertEquals(Status.OK, status);
- assertEquals(true, copiedDataSet.isDirectory());
- assertEquals(DATA, FileUtilities.loadToString(new File(copiedDataSet, dataFile.getName()))
- .trim());
- assertEquals(false, dummy.exists());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRemoteWithMarkerFile()
- {
- Properties properties = new Properties();
- properties.setProperty(LocalAndRemoteCopier.MARKER_FILE_PREFIX, "MARKER-");
- properties.setProperty(DataSetCopier.DESTINATION_KEY, "localhost:" + destination.getPath());
- properties.setProperty(DataSetCopier.RSYNC_EXEC + "-executable", rsyncExec.getPath());
- properties.setProperty(DataSetCopier.SSH_EXEC + "-executable", sshExec.getPath());
- context.checking(new Expectations()
- {
- {
- one(copierFactory).create(rsyncExec, sshExec, DataSetCopier.SSH_TIMEOUT_MILLIS,
- RSyncConfig.getInstance().getAdditionalCommandLineOptions());
- will(returnValue(copier));
-
- one(copier).check();
- one(copier).checkRsyncConnectionViaSsh("localhost", null,
- DataSetCopier.SSH_TIMEOUT_MILLIS);
- will(returnValue(true));
-
- one(sshExecutorFactory).create(sshExec, "localhost");
- will(returnValue(sshExecutor));
-
- final String copiedDataSet = new File(destination, FOLDER_NAME).getPath();
- one(sshExecutor).exists(copiedDataSet, SSH_TIMEOUT_MILLIS);
- will(returnValue(BooleanStatus.createTrue()));
-
- one(sshExecutor).executeCommandRemotely("rm -rf " + copiedDataSet,
- SSH_TIMEOUT_MILLIS);
- will(returnValue(OK_RESULT));
-
- one(copier).copyToRemote(dataSet, destination.getPath(), "localhost", null, null, null, null);
- will(returnValue(Status.OK));
-
- one(sshExecutor).executeCommandRemotely(
- "mv " + new File(destination, dataSet.getName()) + " " + copiedDataSet,
- SSH_TIMEOUT_MILLIS);
- will(returnValue(OK_RESULT));
-
- one(sshExecutor).executeCommandRemotely(
- "touch " + new File(destination, "MARKER-" + FOLDER_NAME),
- SSH_TIMEOUT_MILLIS);
- will(returnValue(OK_RESULT));
- }
- });
- LocalAndRemoteCopier msInjectionCopier =
- new LocalAndRemoteCopier(properties, copierFactory, sshExecutorFactory);
-
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetType(DATA_SET_TYPE);
- dataSetInformation.setDataSetKind(DATA_SET_KIND);
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put(DATA_SET_CODE, SAMPLE_CODE);
- Status status = msInjectionCopier.handle(dataSet, dataSetInformation, parameterBindings);
-
- assertEquals(Status.OK, status);
- context.assertIsSatisfied();
- }
-
- private void prepareForCheckingLastModifiedDate()
- {
- // Sleep long enough to test last modified date of target will be same as of source.
- try
- {
- Thread.sleep(2000);
- } catch (InterruptedException ex)
- {
- // ignored
- }
- }
-
- private void prepareCopier(Properties properties)
- {
- properties.setProperty(DataSetCopier.RSYNC_EXEC + "-executable", rsyncExec.getPath());
- context.checking(new Expectations()
- {
- {
- one(copierFactory).create(rsyncExec, null, DataSetCopier.SSH_TIMEOUT_MILLIS,
- RSyncConfig.getInstance().getAdditionalCommandLineOptions());
- will(returnValue(new MockCopier()));
- }
- });
- }
-
- private final class MockCopier implements IPathCopier
- {
-
- @Override
- public boolean isProgressEnabled()
- {
- return false;
- }
-
- @Override
- public boolean terminate()
- {
- return false;
- }
-
- @Override
- public boolean isRemote()
- {
- return false;
- }
-
- @Override
- public void check() throws EnvironmentFailureException, ConfigurationFailureException
- {
- }
-
- @Override
- public Status copy(File sourcePath, File destinationDirectory,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- return null;
- }
-
- @Override
- public Status copyContent(File sourcePath, File destinationDirectory,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- return null;
- }
-
- @Override
- public Status copyToRemote(File sourcePath, String destinationDirectory,
- String destinationHostOrNull, String rsyncModuleNameOrNull,
- String rsyncPasswordFileOrNull,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- try
- {
- FileUtils.copyDirectoryToDirectory(dataSet, new File(destinationDirectory));
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- File file = new File(destinationDirectory, dataSet.getName());
- file.setLastModified(dataSet.lastModified());
- return Status.OK;
- }
-
- @Override
- public Status copyContentToRemote(File sourcePath, String destinationDirectory,
- String destinationHostOrNull, String rsyncModuleNameOrNull,
- String rsyncPasswordFileOrNull,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- return null;
- }
-
- @Override
- public Status copyFromRemote(String sourcePath, String sourceHost,
- File destinationDirectory, String rsyncModuleNameOrNull,
- String rsyncPasswordFileOrNull,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- return null;
- }
-
- @Override
- public Status copyContentFromRemote(String sourcePath, String sourceHost,
- File destinationDirectory, String rsyncModuleNameOrNull,
- String rsyncPasswordFileOrNull,
- ITextHandler stdoutHandlerOrNull, ITextHandler stderrHandlerOrNull)
- {
- return null;
- }
-
- @Override
- public boolean checkRsyncConnectionViaSsh(String host, String rsyncExecutableOnHostOrNull,
- long millisToWaitForCompletion)
- {
- return false;
- }
-
- @Override
- public boolean checkRsyncConnectionViaRsyncServer(String host, String rsyncModule,
- String rsyncPassworFileOrNull, long millisToWaitForCompletion)
- {
- return false;
- }
-
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java
deleted file mode 100644
index 2f71d9dd3a5..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java
+++ /dev/null
@@ -1,405 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hamcrest.core.IsNull;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AbundanceHandlerTest extends AssertJUnit
-{
- private static final String SPACE_CODE = "G1";
-
- private static final SpaceIdentifier SPACE_IDENTIFIER = new SpaceIdentifier(SPACE_CODE);
-
- private static final String EXPERIMENT_CODE = "E1";
-
- private static final SpaceIdentifier SPACE_IDENTIFIER_MS = new SpaceIdentifier(
- CommonConstants.MS_DATA_SPACE);
-
- private static final String PARAMETER_VALUE = "1234.5";
-
- private static final double ABUNDANCE = 1234.5;
-
- private static final String PARAMETER_NAME = "ABC12";
-
- private static final SampleIdentifier SAMPLE_IDENTIFER = new SampleIdentifier(SPACE_IDENTIFIER_MS,
- PARAMETER_NAME);
-
- private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER = new ExperimentIdentifier(
- new ProjectIdentifier(SPACE_CODE, "P1"), EXPERIMENT_CODE);
-
- private static final String SAMPLE_PERM_ID = "s12-34";
-
- private static final String EXPERIMENT_PERM_ID = "e12345-42";
-
- private static final long EXPERIMENT_ID = 42;
-
- private static final long SAMPLE_ID = 43;
-
- private static final long PROTEIN_ID = 4711;
-
- private static final String PROTEIN_NAME = "my protein";
-
- private static final ListSamplesByPropertyCriteria CRITERIA =
- new ListSamplesByPropertyCriteria(AbundanceHandler.MZXML_FILENAME, PARAMETER_NAME,
- SPACE_CODE, null);
-
- private Mockery context;
-
- private IProtDAO dao;
-
- private IEncapsulatedOpenBISService service;
-
- private Experiment experiment;
-
- private AbundanceHandler handler;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- dao = context.mock(IProtDAO.class);
- service = context.mock(IEncapsulatedOpenBISService.class);
- experiment = new Experiment();
- experiment.setPermID(EXPERIMENT_PERM_ID);
- experiment.setId(EXPERIMENT_ID);
- handler = new AbundanceHandler(service, dao, EXPERIMENT_IDENTIFIER, experiment, "+", false);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddAbundanceValueWhichIsNotANumber()
- {
- prepareCreateSampleIdentifiedByCode();
-
- try
- {
- handler.addAbundancesToDatabase(createParameter("blabla"), PROTEIN_ID, PROTEIN_NAME);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Abundance of sample '" + PARAMETER_NAME + "' of protein '" + PROTEIN_NAME
- + "' is not a number: blabla", e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddTwoAbundanceValuesForASampleIdentifiedByCode()
- {
- prepareCreateSampleIdentifiedByCode();
- context.checking(new Expectations()
- {
- {
- one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
- one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, 1.5);
- }
- });
-
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
- handler.addAbundancesToDatabase(createParameter("1.5"), PROTEIN_ID, PROTEIN_NAME);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddTwoAbundanceValuesForASampleIdentifiedByCodeAndSpace()
- {
- String sampleIdentifier = "/" + SPACE_CODE + "/" + PARAMETER_NAME;
- prepareCreateSampleIdentifiedByIdentifier(sampleIdentifier);
- context.checking(new Expectations()
- {
- {
- one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
- one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, 1.5);
- }
- });
-
- handler.addAbundancesToDatabase(createParameter(sampleIdentifier, PARAMETER_VALUE),
- PROTEIN_ID, PROTEIN_NAME);
- handler.addAbundancesToDatabase(createParameter(sampleIdentifier, "1.5"), PROTEIN_ID,
- PROTEIN_NAME);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddTwoAbundanceValuesForASampleIdentifiedByPropertyButNoSampleFound()
- {
- prepareCreateSampleIdentifiedByProperty(Arrays.<Sample> asList());
-
- try
- {
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID,
- PROTEIN_NAME);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Protein '" + PROTEIN_NAME
- + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME,
- e.getMessage());
- }
-
- try
- {
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID,
- PROTEIN_NAME);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Protein '" + PROTEIN_NAME
- + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME,
- e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddAbundanceValuesForASampleIdentifiedByPropertyButTwoSamplesFound()
- {
- Sample sample = new Sample();
- sample.setPermId(SAMPLE_PERM_ID);
- prepareCreateSampleIdentifiedByProperty(Arrays.<Sample> asList(sample, sample));
-
- try
- {
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID,
- PROTEIN_NAME);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Protein '" + PROTEIN_NAME
- + "' has an abundance value for a not uniquely specified sample "
- + "(2 samples are found): " + PARAMETER_NAME, e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddAbundanceValuesForASampleIdentifiedByProperty()
- {
- final Sample sample = new Sample();
- sample.setPermId(SAMPLE_PERM_ID);
- sample.setIdentifier("blabla");
- prepareCreateSampleIdentifiedByProperty(Arrays.<Sample> asList(sample));
- prepareCreateSample();
- context.checking(new Expectations()
- {
- {
- one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
- one(service).registerSample(with(new BaseMatcher<NewSample>()
- {
-
- @Override
- @SuppressWarnings("deprecation")
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample newSample = (NewSample) item;
- assertEquals(SPACE_IDENTIFIER + "/" + PARAMETER_NAME + "_"
- + EXPERIMENT_CODE, newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(),
- newSample.getExperimentIdentifier());
- assertEquals(sample.getIdentifier(),
- newSample.getParentIdentifier());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
-
- }
- }), with(new IsNull<String>()));
- }
- });
-
- handler.addAbundancesToDatabase(
- createParameter(PARAMETER_NAME + "+blabla.xml", PARAMETER_VALUE), PROTEIN_ID,
- PROTEIN_NAME);
-
- context.assertIsSatisfied();
- }
-
- private Parameter createParameter(String value)
- {
- return createParameter(PARAMETER_NAME, value);
- }
-
- Parameter createParameter(String parameterName, String value)
- {
- Parameter parameter = new Parameter();
- parameter.setName(parameterName);
- parameter.setValue(value);
- return parameter;
- }
-
- private void prepareCreateSampleIdentifiedByCode()
- {
- prepareCreateSampleIdentifiedByIdentifier(PARAMETER_NAME);
- }
-
- void prepareCreateSampleIdentifiedByIdentifier(final String sampleIdentifier)
- {
- Sample sample = new Sample();
- sample.setPermId(SAMPLE_PERM_ID);
- sample.setIdentifier(sampleIdentifier);
- prepareGetSample(
- SampleIdentifierFactory
- .parse(sampleIdentifier, "/" + CommonConstants.MS_DATA_SPACE).toString(),
- sample);
- prepareCreateSample();
- context.checking(new Expectations()
- {
- {
- one(service).registerSample(with(new BaseMatcher<NewSample>()
- {
- @Override
- @SuppressWarnings("deprecation")
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample newSample = (NewSample) item;
- assertEquals(SPACE_IDENTIFIER + "/" + PARAMETER_NAME + "_"
- + EXPERIMENT_CODE, newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(),
- newSample.getExperimentIdentifier());
- assertEquals(sampleIdentifier, newSample.getParentIdentifier());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
-
- }
- }), with(new IsNull<String>()));
- }
- });
- }
-
- private void prepareCreateSample()
- {
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetSampleByPermID(SAMPLE_PERM_ID);
- will(returnValue(null));
-
- one(dao).createSample(EXPERIMENT_ID, SAMPLE_PERM_ID);
- will(returnValue(SAMPLE_ID));
- }
- });
- }
-
- private void prepareCreateSampleIdentifiedByProperty(final List<Sample> samples)
- {
- prepareGetSample(SAMPLE_IDENTIFER.toString(), null);
- context.checking(new Expectations()
- {
- {
- one(service).listSamplesByCriteria(
- with(new BaseMatcher<ListSamplesByPropertyCriteria>()
- {
- @Override
- public boolean matches(Object item)
- {
- return CRITERIA.toString().equals(item.toString());
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendValue(CRITERIA);
-
- }
- }));
- will(returnValue(samples));
- }
- });
- }
-
- private void prepareGetSample(final String expectedSampleIdentifier, final Sample sample)
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- with(new BaseMatcher<SampleIdentifier>()
- {
-
- @Override
- public boolean matches(Object item)
- {
- return expectedSampleIdentifier.equals(item.toString());
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendValue(expectedSampleIdentifier);
-
- }
- }));
- will(returnValue(sample));
- }
- });
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjectionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjectionTest.java
deleted file mode 100644
index d6c11894cb1..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForMSInjectionTest.java
+++ /dev/null
@@ -1,722 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.BIOLOGICAL_SAMPLE_IDENTIFIER_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.DATA_SET_PROPERTIES_FILE;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.DATA_SET_TYPE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.EXPERIMENT_CODE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.EXPERIMENT_TYPE_CODE;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.MS_INJECTION_PROPERTIES_FILE;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.PARENT_TYPE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.PROJECT_CODE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.SAMPLE_CODE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.USER_KEY;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-
-import org.apache.commons.io.IOUtils;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.Assert;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTestCase
-{
- private static final String PROJECT_CODE = "MS2";
-
- private static final String EXPERIMENT_CODE = "2010-02";
-
- private static final String SAMPLE_CODE = "U09-1242";
-
- private static final String SAMPLE_IDENTIFIER =
- SpaceIdentifier.Constants.IDENTIFIER_SEPARATOR + CommonConstants.MS_DATA_SPACE
- + SpaceIdentifier.Constants.IDENTIFIER_SEPARATOR + SAMPLE_CODE;
-
- private static final String EXPERIMENT_IDENTIFIER =
- SpaceIdentifier.Constants.IDENTIFIER_SEPARATOR + CommonConstants.MS_DATA_SPACE
- + SpaceIdentifier.Constants.IDENTIFIER_SEPARATOR + PROJECT_CODE
- + SpaceIdentifier.Constants.IDENTIFIER_SEPARATOR + EXPERIMENT_CODE;
-
- private static final long EXPERIMENT_ID = 42;
-
- private static final long SAMPLE_ID = 43;
-
- private static final String SAMPLE_PROPERTY = "name";
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService service;
-
- private IDataSetInfoExtractor extractor;
-
- private File dataSet;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- extractor = new DataSetInfoExtractorForMSInjection(service);
- dataSet = new File(workingDirectory, "data-set");
- dataSet.mkdirs();
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingPropertiesFile()
- {
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Missing properties file '" + MS_INJECTION_PROPERTIES_FILE + "'.", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testPropertiesFileIsAFolder()
- {
- new File(dataSet, MS_INJECTION_PROPERTIES_FILE).mkdir();
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Properties file '" + MS_INJECTION_PROPERTIES_FILE + "' is a folder.", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingSampleCode()
- {
- Properties properties = new Properties();
- save(properties, MS_INJECTION_PROPERTIES_FILE);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Given key '" + SAMPLE_CODE_KEY + "' not found in properties '[]'", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingProjectCode()
- {
- Properties properties = new Properties();
-
- properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- save(properties, MS_INJECTION_PROPERTIES_FILE);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Given key '" + PROJECT_CODE_KEY + "' not found in properties '["
- + SAMPLE_CODE_KEY + "]'", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingExperimentCode()
- {
- Properties properties = new Properties();
- properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- save(properties, MS_INJECTION_PROPERTIES_FILE);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Given key '" + EXPERIMENT_CODE_KEY + "' not found in properties '["
- + PROJECT_CODE_KEY + ", " + SAMPLE_CODE_KEY + "]'", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingDataSetPropertiesFile()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(USER_KEY, "user1");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- SampleTypePropertyType pt = createPropertyType(SAMPLE_CODE_KEY, true);
- prepareGetExperimentAndGetSampleType(true, pt);
- prepareRegisterSample(null);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Missing properties file '" + DATA_SET_PROPERTIES_FILE + "'.", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingDataSetType()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(USER_KEY, "user1");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- SampleTypePropertyType pt = createPropertyType(SAMPLE_CODE_KEY, true);
- prepareGetExperimentAndGetSampleType(true, pt);
- prepareRegisterSample(null);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Given key '" + DATA_SET_TYPE_KEY + "' not found in properties '[]'", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterRawData()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(USER_KEY, "user1");
- sampleProperties.setProperty("TEMPERATURE", "47.11");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "RAW_DATA");
- dataSetProperties.setProperty("CENTROID", "true");
- dataSetProperties.setProperty("BLABLA", "blub");
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
- SampleTypePropertyType pt2 = createPropertyType("VOLUME", false);
- prepareGetExperimentAndGetSampleType(false, pt1, pt2);
- prepareRegisterSample(null);
- prepareGetDataSetType("RAW_DATA", createDataSetPropertyType("CENTROID", false));
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
- assertEquals(SAMPLE_CODE, info.getSampleCode());
- assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
- List<NewProperty> dProps = info.getDataSetProperties();
- assertEquals(1, dProps.size());
- assertEquals("CENTROID", dProps.get(0).getPropertyCode());
- assertEquals("true", dProps.get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterRawDataAndLinkToBiologicalSampe()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(BIOLOGICAL_SAMPLE_IDENTIFIER_KEY, "bio-sample");
- sampleProperties.setProperty(USER_KEY, "user1");
- sampleProperties.setProperty("TEMPERATURE", "47.11");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "RAW_DATA");
- dataSetProperties.setProperty("CENTROID", "true");
- dataSetProperties.setProperty("BLABLA", "blub");
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
- SampleTypePropertyType pt2 = createPropertyType("VOLUME", false);
- prepareGetExperimentAndGetSampleType(false, pt1, pt2);
- prepareRegisterSample("bio-sample");
- prepareGetDataSetType("RAW_DATA", createDataSetPropertyType("CENTROID", false));
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(SampleIdentifierFactory.parse("bio-sample"));
- will(returnValue(new Sample()));
- }
- });
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
- assertEquals(SAMPLE_CODE, info.getSampleCode());
- assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
- List<NewProperty> dProps = info.getDataSetProperties();
- assertEquals(1, dProps.size());
- assertEquals("CENTROID", dProps.get(0).getPropertyCode());
- assertEquals("true", dProps.get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterSupersedingRawDataWhichUpdatesSampleProperties()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(SAMPLE_PROPERTY, "Isaac");
- sampleProperties.setProperty("TEMPERATURE", "47.11");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "RAW_DATA");
- dataSetProperties.setProperty("CENTROID", "true");
- dataSetProperties.setProperty("BLABLA", "blub");
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- prepareGetExperimentAndGetSampleType(false, createPropertyType(SAMPLE_PROPERTY, true));
- prepareUpdateSample("Isaac", null);
- prepareGetDataSetType("RAW_DATA", createDataSetPropertyType("CENTROID", false));
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
- assertEquals(SAMPLE_CODE, info.getSampleCode());
- assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
- List<NewProperty> dProps = info.getDataSetProperties();
- assertEquals(1, dProps.size());
- assertEquals("CENTROID", dProps.get(0).getPropertyCode());
- assertEquals("true", dProps.get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterSupersedingRawDataWhichUpdatesSampleParent()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(BIOLOGICAL_SAMPLE_IDENTIFIER_KEY, "bio-sample");
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(SAMPLE_PROPERTY, "Isaac");
- sampleProperties.setProperty("TEMPERATURE", "47.11");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "RAW_DATA");
- dataSetProperties.setProperty("CENTROID", "true");
- dataSetProperties.setProperty("BLABLA", "blub");
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- prepareGetExperimentAndGetSampleType(false, createPropertyType(SAMPLE_PROPERTY, true));
- prepareUpdateSample("Isaac", new String[] { "bio-sample" });
- prepareGetDataSetType("RAW_DATA", createDataSetPropertyType("CENTROID", false));
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- SampleIdentifierFactory.parse("bio-sample"));
- will(returnValue(new Sample()));
- }
- });
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
- assertEquals(SAMPLE_CODE, info.getSampleCode());
- assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
- List<NewProperty> dProps = info.getDataSetProperties();
- assertEquals(1, dProps.size());
- assertEquals("CENTROID", dProps.get(0).getPropertyCode());
- assertEquals("true", dProps.get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegisterParentDataSet()
- {
- Properties sampleProperties = new Properties();
- sampleProperties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- sampleProperties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- sampleProperties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- sampleProperties.setProperty(SAMPLE_PROPERTY, "Albert");
- save(sampleProperties, MS_INJECTION_PROPERTIES_FILE);
- Properties dataSetProperties = new Properties();
- dataSetProperties.setProperty(DATA_SET_TYPE_KEY, "MZXML_DATA");
- dataSetProperties.setProperty(PARENT_TYPE_KEY, "RAW_DATA");
- save(dataSetProperties, DATA_SET_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(SAMPLE_PROPERTY, false);
- SampleTypePropertyType pt2 = createPropertyType("VOLUME", false);
- SampleTypePropertyType pt3 = createPropertyType("TEMPERATURE", false);
- prepareGetExperimentAndGetSampleType(true, pt1, pt2, pt3);
- prepareUpdateSample(null, null);
- prepareGetDataSetType("MZXML_DATA");
- context.checking(new Expectations()
- {
- {
- one(service).listDataSetsBySampleID(SAMPLE_ID, false);
- AbstractExternalData ds1 = createDataSet("RAW_DATA", "raw1", 11);
- AbstractExternalData ds2 = createDataSet("MZXML_DATA", "mzxml1", 13);
- AbstractExternalData ds3 = createDataSet("RAW_DATA", "raw2", 12);
- will(returnValue(Arrays.asList(ds1, ds2, ds3)));
- }
- });
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
- assertEquals(SAMPLE_CODE, info.getSampleCode());
- assertEquals(new SampleIdentifier(new SpaceIdentifier(CommonConstants.MS_DATA_SPACE),
- SAMPLE_CODE), info.getSampleIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
- assertEquals(0, info.getDataSetProperties().size());
- List<String> parentDataSetCodes = info.getParentDataSetCodes();
- assertEquals("raw2", parentDataSetCodes.get(0));
- assertEquals(1, parentDataSetCodes.size());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingMandatoryProperties()
- {
- Properties properties = new Properties();
- properties.setProperty(PROJECT_CODE_KEY, PROJECT_CODE);
- properties.setProperty(SAMPLE_CODE_KEY, SAMPLE_CODE);
- properties.setProperty(EXPERIMENT_CODE_KEY, EXPERIMENT_CODE);
- save(properties, MS_INJECTION_PROPERTIES_FILE);
- SampleTypePropertyType pt1 = createPropertyType(SAMPLE_CODE_KEY, true);
- SampleTypePropertyType pt2 = createPropertyType("VOLUME", true);
- SampleTypePropertyType pt3 = createPropertyType("TEMPERATURE", true);
- prepareGetExperimentAndGetSampleType(true, pt1, pt2, pt3);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- SampleIdentifierFactory.parse(SAMPLE_IDENTIFIER));
- will(returnValue(null));
- }
- });
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("The following mandatory properties are missed: [VOLUME, TEMPERATURE]", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private void prepareGetExperimentAndGetSampleType(final boolean experimentExists,
- final SampleTypePropertyType... sampleTypePropertyTypes)
- {
- context.checking(new Expectations()
- {
- {
- ExperimentIdentifier identifier =
- new ExperimentIdentifier(CommonConstants.MS_DATA_SPACE, PROJECT_CODE,
- EXPERIMENT_CODE);
- one(service).tryGetExperiment(identifier);
- Experiment experiment = new Experiment();
- experiment.setId(EXPERIMENT_ID);
- will(returnValue(experimentExists ? experiment : null));
-
- if (experimentExists == false)
- {
- one(service).registerExperiment(
- new NewExperiment(identifier.toString(), EXPERIMENT_TYPE_CODE));
- }
- }
- });
- prepareGetSampleType(sampleTypePropertyTypes);
- }
-
- private void prepareGetSampleType(final SampleTypePropertyType... sampleTypePropertyTypes)
- {
- context.checking(new Expectations()
- {
- {
- one(service).getSampleType(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
- SampleType sampleType = new SampleType();
- sampleType.setCode(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
- sampleType.setSampleTypePropertyTypes(Arrays.asList(sampleTypePropertyTypes));
- will(returnValue(sampleType));
- }
- });
- }
-
- private void prepareGetDataSetType(final String dataSetType,
- final DataSetTypePropertyType... types)
- {
- context.checking(new Expectations()
- {
- {
- one(service).getDataSetType(dataSetType);
- DataSetTypeWithVocabularyTerms result = new DataSetTypeWithVocabularyTerms();
- DataSetType type = new DataSetType(dataSetType);
- type.setDataSetTypePropertyTypes(Arrays.asList(types));
- result.setDataSetType(type);
- will(returnValue(result));
- }
- });
- }
-
- private void prepareRegisterSample(final String parentIdentifier)
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- SampleIdentifierFactory.parse(SAMPLE_IDENTIFIER));
- will(returnValue(null));
-
- one(service).registerSample(with(new BaseMatcher<NewSample>()
- {
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample sample = (NewSample) item;
- assertEquals(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE, sample.getSampleType().getCode());
- assertEquals(SAMPLE_IDENTIFIER, sample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER, sample
- .getExperimentIdentifier());
- String[] parents = sample.getParentsOrNull();
- assertEquals(parentIdentifier, parents == null ? null : parents[0]);
- IEntityProperty[] properties = sample.getProperties();
- Map<String, IEntityProperty> map =
- new HashMap<String, IEntityProperty>();
- for (IEntityProperty property : properties)
- {
- map.put(property.getPropertyType().getCode(), property);
- }
-
- assertEquals(SAMPLE_CODE, map.get(SAMPLE_CODE_KEY).getValue());
- assertEquals(1, map.size());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendText(SAMPLE_IDENTIFIER);
- }
- }), with("user1"));
- }
- });
- }
-
- private void prepareUpdateSample(final String newName, final String[] expectedModifiedParentCodesOrNull)
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- SampleIdentifierFactory.parse(SAMPLE_IDENTIFIER));
- Sample sample = new Sample();
- sample.setId(SAMPLE_ID);
- sample.setModificationDate(new Date(4711));
- sample.setProperties(Arrays.<IEntityProperty> asList(createProperty(
- SAMPLE_PROPERTY, "Albert")));
- SampleType sampleType = new SampleType();
- sampleType.setSampleTypePropertyTypes(Arrays.asList(createPropertyType(
- SAMPLE_PROPERTY, true)));
- sample.setSampleType(sampleType);
- will(returnValue(sample));
-
- one(service).updateSample(with(new BaseMatcher<SampleUpdatesDTO>()
- {
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof SampleUpdatesDTO)
- {
- SampleUpdatesDTO sampleUpdate = (SampleUpdatesDTO) item;
- assertEquals(SAMPLE_ID, sampleUpdate.getSampleIdOrNull()
- .getId().longValue());
- assertEquals(0, sampleUpdate.getAttachments().size());
- assertEquals(null, sampleUpdate.getContainerIdentifierOrNull());
- Assert.assertEquals(
- sampleUpdate.getModifiedParentCodesOrNull(),
- expectedModifiedParentCodesOrNull);
- assertEquals(EXPERIMENT_IDENTIFIER, sampleUpdate
- .getExperimentIdentifierOrNull().toString());
- assertEquals(SAMPLE_IDENTIFIER, sampleUpdate
- .getSampleIdentifier().toString());
- List<IEntityProperty> properties = sampleUpdate.getProperties();
- assertEquals(SAMPLE_PROPERTY, properties.get(0)
- .getPropertyType().getCode());
- assertEquals(newName == null ? "Albert" : newName, properties
- .get(0).getValue());
- assertEquals(1, properties.size());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- }
- }));
- }
- });
- }
-
- private void save(Properties properties, String fileName)
- {
- File propertiesFile = new File(dataSet, fileName);
- FileOutputStream outputStream = null;
- try
- {
- outputStream = new FileOutputStream(propertiesFile);
- properties.store(outputStream, null);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(outputStream);
- }
- }
-
- private SampleTypePropertyType createPropertyType(String key, boolean mandatory)
- {
- SampleTypePropertyType stpt = new SampleTypePropertyType();
- stpt.setMandatory(mandatory);
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(key);
- stpt.setPropertyType(propertyType);
- return stpt;
- }
-
- private DataSetTypePropertyType createDataSetPropertyType(String key, boolean mandatory)
- {
- DataSetTypePropertyType etpt = new DataSetTypePropertyType();
- etpt.setMandatory(mandatory);
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(key);
- etpt.setPropertyType(propertyType);
- return etpt;
- }
-
- private EntityProperty createProperty(String name, String value)
- {
- EntityProperty entityProperty = new EntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(name);
- entityProperty.setPropertyType(propertyType);
- entityProperty.setValue(value);
- return entityProperty;
- }
-
- private AbstractExternalData createDataSet(String type, String code, int timestamp)
- {
- PhysicalDataSet ds = new PhysicalDataSet();
- ds.setDataSetType(new DataSetType(type));
- ds.setCode(code);
- ds.setRegistrationDate(new Date(timestamp));
- return ds;
- }
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
deleted file mode 100644
index a6d4275ff7f..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
+++ /dev/null
@@ -1,479 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_TYPE_CODE;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults.EXPERIMENT_IDENTIFIER_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults.EXPERIMENT_PROPERTIES_FILE_NAME_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults.EXPERIMENT_TYPE_CODE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = DataSetInfoExtractorForProteinResults.class)
-public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSystemTestCase
-{
- private static final String PARENT_DATA_SET_CODES_KEY =
- DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService service;
-
- private File dataSet;
-
- private File protXmlFile;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- dataSet = new File(workingDirectory, "space1&project1");
- dataSet.mkdirs();
- protXmlFile = new File(dataSet, "prot.xml");
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithNonDefaultExperimentTypeAndPropertiesFileName()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP_TO_BE_IGNORED\n"
- + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepareGetDataSet("1");
- prepareGetDataSet("2");
- prepareGetDataSet("3");
- prepareGetDataSet("4");
- prepare(experimentType);
- context.checking(new Expectations()
- {
- {
- one(service).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
- assertEquals("[1, 2, 3, 4]", info.getParentDataSetCodes().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithProvidedExperimentCode()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + DataSetInfoExtractorForProteinResults.EXPERIMENT_CODE_KEY + "= MY_EXP1\n");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepare(experimentType, false);
- context.checking(new Expectations()
- {
- {
- one(service).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/MY_EXP1", info.getExperimentIdentifier().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegistrationWithOneMandatoryProperty()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- FileUtilities.writeToFile(new File(dataSet,
- DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME),
- "answer=42\nblabla=blub\n" + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
- prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
- prepareGetDataSet("1");
- prepareGetDataSet("2");
- prepareGetDataSet("3");
- prepareGetDataSet("4");
-
- context.checking(new Expectations()
- {
- {
- one(service).registerExperiment(with(new BaseMatcher<NewExperiment>()
- {
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof NewExperiment)
- {
- NewExperiment experiment = (NewExperiment) item;
- assertEquals(DEFAULT_EXPERIMENT_TYPE_CODE,
- experiment.getExperimentTypeCode());
- IEntityProperty[] properties = experiment.getProperties();
- assertEquals(1, properties.length);
- assertEquals("answer", properties[0].getPropertyType()
- .getCode());
- assertEquals("42", properties[0].tryGetAsString());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- }
- }));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(new Properties());
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
- assertEquals("[1, 2, 3, 4]", info.getParentDataSetCodes().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegistrationWithMissingProtXmlFile()
- {
- prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
-
- IDataSetInfoExtractor extractor = createExtractor(new Properties());
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("No *prot.xml file found in data set '" + dataSet + "'.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testRegistrationWithMissingMandatoryProperty()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
-
- IDataSetInfoExtractor extractor = createExtractor(new Properties());
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("The following mandatory properties are missed: [answer]", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithParentDataSetsDefinedByBaseExperimentAndProtXmlFileTooLarge()
- {
- FileUtilities.writeToFile(protXmlFile, "abc");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- properties.setProperty(DataSetInfoExtractorForProteinResults.PROT_XML_SIZE_THRESHOLD, "0");
- prepare(experimentType);
- final RecordingMatcher<NewExperiment> experimentMatcher = new RecordingMatcher<NewExperiment>();
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(new ProjectIdentifier("TEST", "PROJECT"),
- "EXP1"));
- Experiment experiment = new ExperimentBuilder().id(123789L).getExperiment();
- will(returnValue(experiment));
-
- one(service).listDataSetsByExperimentID(experiment.getId());
- AbstractExternalData ds1 = new DataSetBuilder().code("ds1").getDataSet();
- AbstractExternalData ds2 = new DataSetBuilder().code("ds2").getDataSet();
- will(returnValue(Arrays.asList(ds1, ds2)));
-
- one(service).registerExperiment(with(experimentMatcher));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
- assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
- IEntityProperty[] expProps = experimentMatcher.recordedObject().getProperties();
- assertEquals("Size of prot.xml file prot.xml is with 3 bytes too large. Maximum size is 0 bytes",
- asMap(expProps).get(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY).getValue());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithUnkownBaseExperiment()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepare(experimentType);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(new ProjectIdentifier("TEST", "PROJECT"),
- "EXP1"));
- will(returnValue(null));
-
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected.");
- } catch (UserFailureException ex)
- {
- assertEquals("Unkown experiment /TEST/PROJECT/EXP1", ex.getMessage());
- }
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithUnkownParentDataSets()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n" + PARENT_DATA_SET_CODES_KEY
- + " = ds1 ds2, ds3");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepare(experimentType);
- prepareGetDataSet("ds1");
- prepareGetDataSet("ds2", null);
- prepareGetDataSet("ds3", null);
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- try
- {
- extractor.getDataSetInformation(dataSet, service);
- fail("UserFailureException expected.");
- } catch (UserFailureException ex)
- {
- assertEquals("Unknown data sets: ds2, ds3", ex.getMessage());
- }
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithParentDataSetsSeparatedBySpaces()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n" + PARENT_DATA_SET_CODES_KEY
- + " = ds1 ds2");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepare(experimentType);
- prepareGetDataSet("ds1");
- prepareGetDataSet("ds2");
- context.checking(new Expectations()
- {
- {
- one(service).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
- assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWithParentDataSetsSeparatedByComma()
- {
- FileUtilities.writeToFile(protXmlFile, "");
- String propertiesFile = "my.properties";
- FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
- + PARENT_DATA_SET_CODES_KEY + " = ds1,ds2");
- Properties properties = new Properties();
- String experimentType = "MY_EXPERIMENT";
- properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
- properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
- prepare(experimentType);
- prepareGetDataSet("ds1");
- prepareGetDataSet("ds2");
- context.checking(new Expectations()
- {
- {
- one(service).registerExperiment(with(any(NewExperiment.class)));
- }
- });
-
- IDataSetInfoExtractor extractor = createExtractor(properties);
-
- DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
-
- assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
- assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
- context.assertIsSatisfied();
- }
-
- private void prepare(final String experimentType)
- {
- prepare(experimentType, true);
- }
-
- private void prepare(final String experimentType, final boolean experimentCodeGenerated)
- {
- context.checking(new Expectations()
- {
- {
- if (experimentCodeGenerated)
- {
- one(service).generateCodes("E", EntityKind.EXPERIMENT, 1);
- will(returnValue(Collections.singletonList("E4711")));
- }
-
- one(service).getExperimentType(experimentType);
- ExperimentType type = new ExperimentType();
- ExperimentTypePropertyType etpt1 = new ExperimentTypePropertyType();
- PropertyType propertyType1 = new PropertyType();
- propertyType1.setCode("answer");
- etpt1.setPropertyType(propertyType1);
- etpt1.setMandatory(true);
- ExperimentTypePropertyType etpt2 = new ExperimentTypePropertyType();
- PropertyType propertyType2 = new PropertyType();
- propertyType2.setCode(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY);
- etpt2.setPropertyType(propertyType2);
- type.setExperimentTypePropertyTypes(Arrays.asList(etpt1, etpt2));
- will(returnValue(type));
- }
- });
- }
-
- private void prepareGetDataSet(final String dataSetCode)
- {
- prepareGetDataSet(dataSetCode, new DataSetBuilder().code(dataSetCode).getDataSet());
- }
-
- private void prepareGetDataSet(final String dataSetCode, final AbstractExternalData data)
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetDataSet(dataSetCode);
- will(returnValue(data));
- }
- });
- }
-
- private Map<String, IEntityProperty> asMap(IEntityProperty[] properties)
- {
- Map<String, IEntityProperty> result = new HashMap<String, IEntityProperty>();
- for (IEntityProperty property : properties)
- {
- result.put(property.getPropertyType().getCode(), property);
- }
- return result;
- }
-
- private IDataSetInfoExtractor createExtractor(Properties properties)
- {
- return new DataSetInfoExtractorForProteinResults(properties, service);
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoaderTest.java
deleted file mode 100644
index a9664abc6a8..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLLoaderTest.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.ProtXMLLoader;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AminoAcidMass;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AnnotatedProtein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Peptide;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.PeptideModification;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Protein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinGroup;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinProphetDetails;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryDataFilter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryHeader;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProtXMLLoaderTest extends ProtXMLTestCase
-{
- @Test
- public void test()
- {
- File file = new File(workingDirectory, "test.xml");
- FileUtilities.writeToFile(file, EXAMPLE);
- ProteinSummary summary = new ProtXMLLoader(true).readProtXML(file);
-
- ProteinSummaryHeader header = summary.getSummaryHeader();
- assertEquals("some/path/uniprot.HUMAN.v125.fasta", header.getReferenceDatabase());
- ProteinProphetDetails proteinProphet =
- (ProteinProphetDetails) summary.getSummaryHeader().getProgramDetails().getSummary()[0];
- List<ProteinSummaryDataFilter> dataFilters = proteinProphet.getDataFilters();
- assertEquals(1, dataFilters.size());
- assertEquals(0.25, dataFilters.get(0).getMinProbability());
- assertEquals(1.0, dataFilters.get(0).getSensitivity());
- assertEquals(0.5, dataFilters.get(0).getFalsePositiveErrorRate());
-
- List<ProteinGroup> groups = summary.getProteinGroups();
- assertEquals(2, groups.size());
- assertEquals(1.0, groups.get(0).getProbability());
- List<Protein> proteins = groups.get(0).getProteins();
- assertEquals(2, proteins.size());
- Protein protein1 = proteins.get(0);
- assertEquals(1.0, protein1.getProbability());
- List<Parameter> parameters = protein1.getParameters();
- assertEquals(2, parameters.size());
- assertEquals("key1", parameters.get(0).getName());
- assertEquals("value1", parameters.get(0).getValue());
- assertEquals("type1", parameters.get(0).getType());
- assertEquals("key2", parameters.get(1).getName());
- assertEquals("value2", parameters.get(1).getValue());
- assertEquals("type2", parameters.get(1).getType());
- assertEquals("P42", protein1.getAnnotation().getDescription());
- List<AnnotatedProtein> indistinguishableProteins = protein1.getIndistinguishableProteins();
- assertEquals(2, indistinguishableProteins.size());
- assertEquals("P43", indistinguishableProteins.get(0).getAnnotation().getDescription());
- assertEquals("P44", indistinguishableProteins.get(1).getAnnotation().getDescription());
- List<Peptide> peptides = protein1.getPeptides();
- assertEquals(2, peptides.size());
- assertEquals("VYQIDGNYSR", peptides.get(0).getSequence());
- assertEquals(1, peptides.get(0).getModifications().size());
- PeptideModification peptideModification = peptides.get(0).getModifications().get(0);
- assertEquals(42.0, peptideModification.getNTermMass());
- assertEquals(24.25, peptideModification.getCTermMass());
- List<AminoAcidMass> masses = peptideModification.getAminoAcidMasses();
- assertEquals(2, masses.size());
- assertEquals(1, masses.get(0).getPosition());
- assertEquals(115.25, masses.get(0).getMass());
- assertEquals(4, masses.get(1).getPosition());
- assertEquals(31.75, masses.get(1).getMass());
- assertEquals("ITSN", peptides.get(1).getSequence());
- assertEquals(0, peptides.get(1).getModifications().size());
- Protein protein2 = proteins.get(1);
- assertEquals(0.0, protein2.getProbability());
- assertEquals("Q42", protein2.getAnnotation().getDescription());
- assertEquals(0, protein2.getIndistinguishableProteins().size());
- assertEquals(1, protein2.getPeptides().size());
- assertEquals("YSR", protein2.getPeptides().get(0).getSequence());
- assertEquals(0, protein2.getPeptides().get(0).getModifications().size());
-
- assertEquals(0.75, groups.get(1).getProbability());
- assertEquals(1, groups.get(1).getProteins().size());
- Protein protein = groups.get(1).getProteins().get(0);
- assertEquals(0.75, protein.getProbability());
- assertEquals("R42", protein.getAnnotation().getDescription());
- assertEquals(0, protein.getIndistinguishableProteins().size());
- assertEquals(1, protein.getPeptides().size());
- assertEquals("IYSR", protein.getPeptides().get(0).getSequence());
- assertEquals(0, protein.getPeptides().get(0).getModifications().size());
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLTestCase.java
deleted file mode 100644
index d94493700d8..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLTestCase.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class ProtXMLTestCase extends AbstractFileSystemTestCase
-{
-
- protected static final String EXAMPLE =
- "<?xml version='1.0' encoding='UTF-8'?>\n"
- + "<protein_summary xmlns='http://regis-web.systemsbiology.net/protXML' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' "
- +
- "xsi:schemaLocation='http://regis-web.systemsbiology.net/protXML http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v5.xsd'>\n"
- + "<protein_summary_header reference_database='some/path/uniprot.HUMAN.v125.fasta' residue_substitution_list='I -> L' "
- +
- "source_files='/home/lars/tmp/interact.pep.xml' source_files_alt='/home/lars/tmp/interact.pep.xml' min_peptide_probability='0.20' min_peptide_weight='0.50' num_predicted_correct_prots='755.6' num_input_1_spectra='0' num_input_2_spectra='77824' num_input_3_spectra='38201' num_input_4_spectra='0' num_input_5_spectra='0' initial_min_peptide_prob='0.05' total_no_spectrum_ids='104665.2' sample_enzyme='trypsin'>\n"
- + " <program_details analysis='' time='2009-08-12T09:08:07'>\n"
- + " <proteinprophet_details occam_flag='true' groups_flag='Y' degen_flag='Y' nsp_flag='Y' initial_peptide_wt_iters='2' "
- +
- "nsp_distribution_iters='2' final_peptide_wt_iters='4' run_options='XML'>\n"
- + " <nsp_information neighboring_bin_smoothing='Y'>\n"
- + " <nsp_distribution bin_no='0' nsp_lower_bound_incl='0.00' nsp_upper_bound_incl='0.00' pos_freq='0.003' neg_freq='0.320' pos_to_neg_ratio='0.01'/>\n"
- + " </nsp_information>\n"
- + " <ni_information>\n"
- + " <ni_distribution bin_no='1' pos_freq='42' neg_freq='42' pos_to_neg_ratio='1'/>\n"
- + " </ni_information>\n"
- + " <protein_summary_data_filter min_probability='0.25' sensitivity='1' false_positive_error_rate='0.5' predicted_num_correct='9' "
- +
- "predicted_num_incorrect='4'/>\n"
- + " </proteinprophet_details>\n"
- + " </program_details>\n"
- + "</protein_summary_header>\n"
- + "<dataset_derivation generation_no='1'/>\n"
- + "<protein_group probability='1' group_number='1'>\n"
- + " <protein probability='1' protein_name='a' n_indistinguishable_proteins='3' group_sibling_id='0'>\n"
- + " <parameter name='key1' value='value1' type='type1'/>\n"
- + " <parameter name='key2' value='value2' type='type2'/>\n"
- + " <annotation protein_description='P42'/>\n"
- + " <indistinguishable_protein protein_name='a'><annotation protein_description='P43'/></indistinguishable_protein>\n"
- + " <indistinguishable_protein protein_name='a'><annotation protein_description='P44'/></indistinguishable_protein>\n"
- + " <peptide peptide_sequence='VYQIDGNYSR' charge='1' initial_probability='0' is_nondegenerate_evidence='true' n_enzymatic_termini='1' n_instances='1' is_contributing_evidence='N'>\n"
- + " <modification_info mod_nterm_mass='42' mod_cterm_mass='24.25'>\n"
- + " <mod_aminoacid_mass position='1' mass='115.25'/>\n"
- + " <mod_aminoacid_mass position='4' mass='31.75'/>\n"
- + " </modification_info>\n"
- + " </peptide>\n"
- + " <peptide peptide_sequence='ITSN' charge='1' initial_probability='0' is_nondegenerate_evidence='Y' n_enzymatic_termini='1' n_instances='1' is_contributing_evidence='N'/>\n"
- + " </protein>\n"
- + " <protein probability='0' protein_name='a' n_indistinguishable_proteins='1' group_sibling_id='1'>\n"
- + " <annotation protein_description='Q42'/>\n"
- + " <peptide peptide_sequence='YSR' charge='1' initial_probability='0' is_nondegenerate_evidence='Y' n_enzymatic_termini='1' n_instances='1' is_contributing_evidence='N'/>\n"
- + " </protein>\n"
- + "</protein_group>\n"
- + "<protein_group probability='0.75' group_number='2'>\n"
- + " <protein probability='0.75' protein_name='a' n_indistinguishable_proteins='1' group_sibling_id='2'>\n"
- + " <annotation protein_description='R42'/>\n"
- + " <peptide peptide_sequence='IYSR' charge='1' initial_probability='0' is_nondegenerate_evidence='Y' n_enzymatic_termini='1' n_instances='1' is_contributing_evidence='N'/>\n"
- + " </protein>\n"
- + "</protein_group>\n"
- + "</protein_summary>\n";
-
- /**
- *
- *
- */
- public ProtXMLTestCase()
- {
- super();
- }
-
- /**
- * @param cleanAfterMethod
- */
- public ProtXMLTestCase(boolean cleanAfterMethod)
- {
- super(cleanAfterMethod);
- }
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
deleted file mode 100644
index 28a17c1fff1..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
+++ /dev/null
@@ -1,155 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.io.File;
-import java.util.Properties;
-
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryHeader;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProtXMLUploaderTest extends ProtXMLTestCase
-{
- private static final class MockUploader extends ProtXMLUploader
- {
- private final IEncapsulatedOpenBISService openbisService;
-
- private DataSetInformation dataSetInformation;
-
- private ProteinSummary proteinSummary;
-
- public MockUploader(Properties properties, IEncapsulatedOpenBISService openbisService)
- {
- super(properties, openbisService);
- this.openbisService = openbisService;
- }
-
- @Override
- protected ResultDataSetUploader createUploader()
- {
- return new ResultDataSetUploader(null, null, null, true, "+", false)
- {
- @Override
- void upload(DataSetInformation dataSetInfo, ProteinSummary summary)
- {
- dataSetInformation = dataSetInfo;
- proteinSummary = summary;
- }
- };
- }
-
- public IEncapsulatedOpenBISService getService()
- {
- return openbisService;
- }
-
- public DataSetInformation getDataSetInformation()
- {
- return dataSetInformation;
- }
-
- public ProteinSummary getProteinSummary()
- {
- return proteinSummary;
- }
- }
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService service;
-
- private MockUploader uploader;
-
- @BeforeMethod
- public void startUp()
- {
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- Properties properties = new Properties();
- properties.setProperty("database.kind", "test");
- uploader = new MockUploader(properties, service);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDataSetIsProtXMLFile()
- {
- File file = new File(workingDirectory, "test.xml");
- FileUtilities.writeToFile(file, EXAMPLE);
- DataSetInformation dataSetInformation = new DataSetInformation();
-
- uploader.upload(file, dataSetInformation);
-
- assertSame(service, uploader.getService());
- assertSame(dataSetInformation, uploader.getDataSetInformation());
- ProteinSummaryHeader header = uploader.getProteinSummary().getSummaryHeader();
- assertEquals("some/path/uniprot.HUMAN.v125.fasta", header.getReferenceDatabase());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDataSetIsFolderWithProtXMLFile()
- {
- File dataSet = new File(workingDirectory, "data-set");
- dataSet.mkdir();
- FileUtilities.writeToFile(new File(dataSet, "test-prot.xml"), EXAMPLE);
- DataSetInformation dataSetInformation = new DataSetInformation();
-
- uploader.upload(dataSet, dataSetInformation);
-
- assertSame(service, uploader.getService());
- assertSame(dataSetInformation, uploader.getDataSetInformation());
- ProteinSummaryHeader header = uploader.getProteinSummary().getSummaryHeader();
- assertEquals("some/path/uniprot.HUMAN.v125.fasta", header.getReferenceDatabase());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDataSetIsFolderWithProtXMLFileToBeTooLarge()
- {
- File dataSet = new File(workingDirectory, "data-set");
- dataSet.mkdir();
- FileUtilities.writeToFile(new File(dataSet, "test-prot.xml"), EXAMPLE);
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setExperiment(new ExperimentBuilder().property(
- DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY, "too large").getExperiment());
-
- uploader.upload(dataSet, dataSetInformation);
-
- assertEquals(null, uploader.getDataSetInformation());
- context.assertIsSatisfied();
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescriptionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescriptionTest.java
deleted file mode 100644
index 977515a90c1..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinDescriptionTest.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.ProteinDescription;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinAnnotation;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinDescriptionTest extends AssertJUnit
-{
- @Test
- public void testWithOutAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("Q92902");
- try
- {
- new ProteinDescription(annotation, 0, true);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Can not find a amino-acid sequence in following protein description: Q92902", ex.getMessage());
- }
- }
-
- @Test
- public void testWithAccessionNumberAndSequence()
- {
- ProteinAnnotation annotation =
- createAnnotation("Q92902 \\ID=HPS1_HUMAN \\MODRES= "
- + "\\VARIANT=(55|.|)(100|E|D)(186|A|V)(283|G|W)(480|A|T) "
- + "\\NCBITAXID=9606 \\DE=Hermansky-Pudlak syndrome 1 protein "
- + "\\SEQ=MKCVLVATEGAEVLFYWTDQEFEESLRLKFGQSENEEEELPA");
- ProteinDescription description = new ProteinDescription(annotation, 0, true);
- assertEquals("Q92902", description.getAccessionNumber());
- assertEquals("Hermansky-Pudlak syndrome 1 protein", description.getDescription());
- assertEquals("MKCVLVATEGAEVLFYWTDQEFEESLRLKFGQSENEEEELPA", description.getSequence());
- }
-
- @Test
- public void testWithSwissProtNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("sp|swissprot-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithTremblNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("tr|trembl-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithIpiNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- annotation.setTremblName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("ipi|ipi-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithEnsemblNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- annotation.setTremblName(null);
- annotation.setIpiName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("ens|ensembl-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithRefSeqNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- annotation.setTremblName(null);
- annotation.setIpiName(null);
- annotation.setEnsemblName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("rs|refseq-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithLocusLinkNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- annotation.setTremblName(null);
- annotation.setIpiName(null);
- annotation.setEnsemblName(null);
- annotation.setRefseqName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("ll|locus-link-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithFlybaseNameAsAccessionNumber()
- {
- ProteinAnnotation annotation = createAnnotation("my protein");
- annotation.setSwissprotName(null);
- annotation.setTremblName(null);
- annotation.setIpiName(null);
- annotation.setEnsemblName(null);
- annotation.setRefseqName(null);
- annotation.setLocusLinkName(null);
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("my protein", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("fb|flybase-42", description.getAccessionNumber());
- }
-
- @Test
- public void testWithNoAccessionNumber()
- {
- ProteinAnnotation annotation = new ProteinAnnotation();
- annotation.setDescription("");
- ProteinDescription description = new ProteinDescription(annotation, 4711, false);
-
- assertEquals("", description.getDescription());
- assertEquals("", description.getSequence());
- assertEquals("unknown|4711", description.getAccessionNumber());
- }
-
- private ProteinAnnotation createAnnotation(String description)
- {
- ProteinAnnotation proteinAnnotation = new ProteinAnnotation();
- proteinAnnotation.setDescription(description);
- proteinAnnotation.setEnsemblName("ensembl-42");
- proteinAnnotation.setFlybase("flybase-42");
- proteinAnnotation.setIpiName("ipi-42");
- proteinAnnotation.setLocusLinkName("locus-link-42");
- proteinAnnotation.setRefseqName("refseq-42");
- proteinAnnotation.setSwissprotName("swissprot-42");
- proteinAnnotation.setTremblName("trembl-42");
- return proteinAnnotation;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java
deleted file mode 100644
index 9392844d0da..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java
+++ /dev/null
@@ -1,178 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.log4j.Level;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
-{
- private static final String PARENT_DATA_SET_CODES_KEY =
- DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
-
- private static final String BASE_EXPERIMENT_KEY =
- DataSetInfoExtractorForProteinResults.EXPERIMENT_IDENTIFIER_KEY.toUpperCase();
-
- private BufferedAppender logRecorder;
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService service;
-
- private ProteinResultDataSetParentLinkingTask task;
-
- @BeforeMethod
- public void beforeMethod()
- {
- logRecorder = LogRecordingUtils.createRecorder("%-5p %c - %m%n", Level.DEBUG);
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- task = new ProteinResultDataSetParentLinkingTask(service);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- logRecorder.reset();
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void test()
- {
- final Experiment e1 =
- new ExperimentBuilder().id(1).identifier("/S/P1/E1").property("ABC", "non-sense")
- .getExperiment();
- final Experiment e2 =
- new ExperimentBuilder().id(2).identifier("/A/P2/E2")
- .property(PARENT_DATA_SET_CODES_KEY, "non-sense2").getExperiment();
- final Experiment e3 =
- new ExperimentBuilder().id(3).identifier("/A/P2/E3")
- .property(PARENT_DATA_SET_CODES_KEY, "ds1, ds3").getExperiment();
- final Experiment e4 =
- new ExperimentBuilder().id(4).identifier("/S/P1/E4")
- .property(BASE_EXPERIMENT_KEY, "/S/P1/E1").getExperiment();
- final PhysicalDataSet ds1 =
- new DataSetBuilder(1).code("ds1").fileFormat("A").experiment(e1)
- .version(11).getDataSet();
- final PhysicalDataSet ds2 =
- new DataSetBuilder(2).code("ds2").fileFormat("B").experiment(e4)
- .version(22).getDataSet();
- final PhysicalDataSet ds3 =
- new DataSetBuilder(3).code("ds3").fileFormat("C").experiment(e3)
- .version(33).property("ALPHA", "3.1").getDataSet();
- final RecordingMatcher<AtomicEntityOperationDetails> operationRecorder =
- new RecordingMatcher<AtomicEntityOperationDetails>();
- context.checking(new Expectations()
- {
- {
- one(service).listProjects();
- will(returnValue(Arrays.asList(e1.getProject(), e2.getProject())));
-
- one(service).listExperiments(new ProjectIdentifier("S", "P1"));
- will(returnValue(Arrays.asList(e1, e4)));
-
- one(service).listExperiments(new ProjectIdentifier("A", "P2"));
- will(returnValue(Arrays.asList(e2, e3)));
-
- one(service).tryGetExperiment(ExperimentIdentifierFactory.parse("/S/P1/E1"));
- will(returnValue(e1));
-
- one(service).tryGetDataSet("non-sense2");
- will(returnValue(null));
-
- one(service).tryGetDataSet("ds1");
- will(returnValue(ds1));
-
- one(service).tryGetDataSet("ds3");
- will(returnValue(ds3));
-
- one(service).listDataSetsByExperimentID(e1.getId());
- will(returnValue(Arrays.asList(ds1)));
-
- one(service).listDataSetsByExperimentID(e3.getId());
- will(returnValue(Arrays.asList(ds3)));
-
- one(service).listDataSetsByExperimentID(e4.getId());
- will(returnValue(Arrays.asList(ds2)));
-
- one(service).performEntityOperations(with(operationRecorder));
- }
- });
-
- task.execute();
-
- assertEquals("INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
- + "Parent data set links of data set ds2 "
- + "from experiment /S/P1/E4 will be updated.\n"
- + "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
- + "Parent data set links of data set ds3 "
- + "from experiment /A/P2/E3 will be updated.\n"
- + "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
- + "Parent data set links for 2 data sets have been updated.",
- logRecorder.getLogContent());
- List<DataSetBatchUpdatesDTO> dataSetUpdates =
- operationRecorder.recordedObject().getDataSetUpdates();
- assertEquals(2L, dataSetUpdates.get(0).getDatasetId().getId().longValue());
- assertEquals(22, dataSetUpdates.get(0).getVersion());
- assertEquals("B", dataSetUpdates.get(0).getFileFormatTypeCode());
- assertEquals("[]", dataSetUpdates.get(0).getProperties().toString());
- assertEquals(e4.getIdentifier(), dataSetUpdates.get(0).getExperimentIdentifierOrNull()
- .toString());
- assertEquals("[ds1]",
- Arrays.asList(dataSetUpdates.get(0).getModifiedParentDatasetCodesOrNull())
- .toString());
- assertEquals(3L, dataSetUpdates.get(1).getDatasetId().getId().longValue());
- assertEquals(33, dataSetUpdates.get(1).getVersion());
- assertEquals("C", dataSetUpdates.get(1).getFileFormatTypeCode());
- assertEquals("[ALPHA: 3.1]", dataSetUpdates.get(1).getProperties().toString());
- assertEquals(e3.getIdentifier(), dataSetUpdates.get(1).getExperimentIdentifierOrNull()
- .toString());
- assertEquals("[ds1, ds3]",
- Arrays.asList(dataSetUpdates.get(1).getModifiedParentDatasetCodesOrNull())
- .toString());
- assertEquals(2, dataSetUpdates.size());
- context.assertIsSatisfied();
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java
deleted file mode 100644
index fb70ac7b248..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java
+++ /dev/null
@@ -1,705 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hamcrest.core.IsNull;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.test.AssertionUtil;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AminoAcidMass;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.AnnotatedProtein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.DataSet;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Database;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Peptide;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.PeptideModification;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProgramDetails;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Protein;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinAnnotation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinGroup;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinProphetDetails;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinReference;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryDataFilter;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryHeader;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sequence;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ResultDataSetUploaderTest extends AssertJUnit
-{
- private static final long MOD_PEPTIDE_ID = 101L;
-
- private static final long PEPTIDE_ID = 99L;
-
- private static final long CELL_LYSATE_ID1 = 88L;
-
- private static final String CELL_LYSATE1 = "cell_lysate1";
-
- private static final String CELL_LYSATE_PERM_ID1 = "c1";
-
- private static final long SEQUENCE_ID = 77L;
-
- private static final long PROTEIN_REFERENCE_ID = 66L;
-
- private static final String UNIPROT_ID1 = "unipr1";
-
- private static final String PROTEIN_NAME1 = "my protein";
-
- private static final String SEQUENCE1 = "seq";
-
- private static final String UNIPROT_ID2 = "unipr2";
-
- private static final String PROTEIN_NAME2 = "my 2. protein";
-
- private static final String SEQUENCE2 = "seqe";
-
- private static final long PROTEIN1_ID = 55L;
-
- private static final long DATA_SET_ID = 42L;
-
- private static final String DATA_SET_CODE = "ds1";
-
- private static final long DATABASE_ID = 33l;
-
- private static final String NAME_AND_VERSION = "uniprot.HUMAN.v123.fasta";
-
- private static final String REFERENCE_DATABASE = "/here/and/there/" + NAME_AND_VERSION;
-
- private static final String EXPERIMENT_CODE = "E1";
-
- private static final long EXPERIMENT_ID = 11l;
-
- private static final String EXPERIMENT_PERM_ID = "e1234";
-
- private static final String SAMPLE_PERM_ID = "s1234";
-
- private static final String DB_INSTANCE = "DB";
-
- private static final String SPACE_CODE = "S1";
-
- private static final String PROJECT_CODE = "P1";
-
- private Mockery context;
-
- private Connection connection;
-
- private IEncapsulatedOpenBISService service;
-
- private IProtDAO dao;
-
- private ResultDataSetUploader uploader;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- connection = context.mock(Connection.class);
- dao = context.mock(IProtDAO.class);
- service = context.mock(IEncapsulatedOpenBISService.class);
-
- uploader = new ResultDataSetUploader(dao, connection, service, true, "+", false);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNoProteinsGetExperimentSampleDatabaseAndDataSet()
- {
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetExperimentByPermID(EXPERIMENT_PERM_ID);
- Experiment experiment = new Experiment();
- experiment.setPermID(EXPERIMENT_PERM_ID);
- experiment.setId(EXPERIMENT_ID);
- will(returnValue(experiment));
-
- one(dao).tryToGetDatabaseByName(NAME_AND_VERSION);
- Database database = new Database();
- database.setNameAndVersion(NAME_AND_VERSION);
- database.setId(DATABASE_ID);
- will(returnValue(database));
-
- one(dao).tryToGetDataSetByPermID(DATA_SET_CODE);
- DataSet dataSet = new DataSet();
- dataSet.setId(DATA_SET_ID);
- dataSet.setDatabaseID(DATABASE_ID);
- will(returnValue(dataSet));
- }
- });
-
- uploader.upload(createDataSetInfo(), createProteinSummary());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNoProteinsCreateExperimentSampleDatabaseAndDataSet()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
-
- uploader.upload(createDataSetInfo(), createProteinSummary());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testEmptyProteinGroup()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
-
- ProteinSummary summary = createProteinSummary();
- summary.getProteinGroups().add(createProteinGroup());
- uploader.upload(createDataSetInfo(), summary);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProteinWithIndistiguishableProtein()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 1.0;
- prepareForCreatingProtein(probability);
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false, true);
- ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
- prepareForCreatingIdentifiedProtein(a2, true, false);
-
- ProteinSummary summary = createProteinSummary();
- Protein p1 = createProtein(probability, a1, a2);
- p1.setPeptides(Collections.<Peptide> emptyList());
- summary.getProteinGroups().add(createProteinGroup(p1));
-
- uploader.upload(createDataSetInfo(), summary);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProteinGroupWithTwoProteins()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 1.0;
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingProtein(probability);
- prepareForCreatingIdentifiedProtein(a1, false, true);
- Protein p1 = createProtein(probability, a1);
- p1.setPeptides(Collections.<Peptide> emptyList());
- ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
- probability = 0.99;
- prepareForCreatingProtein(probability);
- prepareForCreatingIdentifiedProtein(a2, false, true);
- Protein p2 = createProtein(probability, a2);
- p2.setPeptides(Collections.<Peptide> emptyList());
-
- ProteinSummary summary = createProteinSummary();
- summary.getProteinGroups().add(createProteinGroup(p1, p2));
-
- uploader.upload(createDataSetInfo(), summary);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAbundancesForSameSampleInTwoDifferentProteins()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 0.75;
- ProteinSummary summary = createProteinSummary();
- prepareForCreatingProtein(probability);
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false, true);
- Protein p1 = createProtein(probability, a1);
- p1.setName(PROTEIN_NAME1);
- p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
- p1.getParameters().add(new Parameter());
- prepareCreateSample();
- context.checking(new Expectations()
- {
- {
- one(service).registerSample(with(any(NewSample.class)), with(new IsNull<String>()));
-
- one(dao).createAbundance(PROTEIN1_ID, CELL_LYSATE_ID1, 2.5);
- }
- });
- p1.setPeptides(Collections.<Peptide> emptyList());
-
- prepareForCreatingProtein(probability);
- summary.getProteinGroups().add(createProteinGroup(p1));
- ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
- prepareForCreatingIdentifiedProtein(a2, false, true);
- Protein p2 = createProtein(probability, a2);
- p2.setName(PROTEIN_NAME1);
- p2.getParameters().add(createAbundance(CELL_LYSATE1, 42.5));
- context.checking(new Expectations()
- {
- {
- one(dao).createAbundance(PROTEIN1_ID, CELL_LYSATE_ID1, 42.5);
- }
- });
- p2.setPeptides(Collections.<Peptide> emptyList());
- summary.getProteinGroups().add(createProteinGroup(p2));
- prepareForCommit();
-
- uploader.upload(createDataSetInfo(), summary);
- uploader.commit();
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAbundancesForNonExistingSample()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 0.75;
- prepareForCreatingProtein(probability);
- ProteinSummary summary = createProteinSummary();
- Protein p1 = createProtein(probability);
- p1.setName(PROTEIN_NAME1);
- p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
- p1.getParameters().add(new Parameter());
- final SpaceIdentifier groupIdentifier = new SpaceIdentifier(CommonConstants.MS_DATA_SPACE);
- final SampleIdentifier sampleIdentifier =
- new SampleIdentifier(groupIdentifier, CELL_LYSATE1);
- final ListSamplesByPropertyCriteria criteria =
- new ListSamplesByPropertyCriteria(AbstractSampleHandler.MZXML_FILENAME, CELL_LYSATE1,
- SPACE_CODE, null);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(sampleIdentifier);
- will(returnValue(null));
-
- one(service).listSamplesByCriteria(
- with(new BaseMatcher<ListSamplesByPropertyCriteria>()
- {
- @Override
- public boolean matches(Object item)
- {
- return criteria.toString().equals(item.toString());
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendValue(criteria);
- }
- }));
- }
- });
- p1.setPeptides(Collections.<Peptide> emptyList());
- summary.getProteinGroups().add(createProteinGroup(p1));
- prepareForRollback();
-
- try
- {
- uploader.upload(createDataSetInfo(), summary);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- AssertionUtil.assertContains("Protein '" + PROTEIN_NAME1
- + "' has an abundance value for an unidentified sample: " + CELL_LYSATE1, ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProteinWithUnmodifiedPeptide()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 1.0;
- prepareForCreatingProtein(probability);
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false, true);
-
- ProteinSummary summary = createProteinSummary();
- Protein p1 = createProtein(probability, a1);
- final Peptide peptide = new Peptide();
- peptide.setSequence("abcd");
- peptide.setCharge(3);
- p1.setPeptides(Arrays.asList(peptide));
- summary.getProteinGroups().add(createProteinGroup(p1));
- context.checking(new Expectations()
- {
- {
- one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
- will(returnValue(PEPTIDE_ID));
- }
- });
-
- uploader.upload(createDataSetInfo(), summary);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProteinWithModifiedPeptide()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 1.0;
- prepareForCreatingProtein(probability);
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false, true);
-
- ProteinSummary summary = createProteinSummary();
- Protein p1 = createProtein(probability, a1);
- final Peptide peptide = new Peptide();
- peptide.setSequence("abcd");
- peptide.setCharge(3);
- final PeptideModification modification = new PeptideModification();
- modification.setNTermMass(42);
- modification.setCTermMass(4711);
- final AminoAcidMass mass = new AminoAcidMass();
- mass.setMass(123);
- mass.setPosition(1);
- modification.setAminoAcidMasses(Arrays.asList(mass));
- peptide.getModifications().add(modification);
- p1.setPeptides(Arrays.asList(peptide));
- summary.getProteinGroups().add(createProteinGroup(p1));
- context.checking(new Expectations()
- {
- {
- one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
- will(returnValue(PEPTIDE_ID));
-
- one(dao).createModifiedPeptide(PEPTIDE_ID, modification.getNTermMass(),
- modification.getCTermMass());
- will(returnValue(MOD_PEPTIDE_ID));
-
- one(dao).createModification(MOD_PEPTIDE_ID, mass.getPosition(), mass.getMass());
- }
- });
-
- uploader.upload(createDataSetInfo(), summary);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProteinWithPeptideWithModificationParameter()
- {
- prepareForCreatingExperimentSampleDatabaseAndDataSet();
- double probability = 1.0;
- prepareForCreatingProtein(probability);
- ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false, true);
-
- ProteinSummary summary = createProteinSummary();
- Protein p1 = createProtein(probability, a1);
- final Peptide peptide = new Peptide();
- Parameter parameter = new Parameter();
- parameter.setName(CELL_LYSATE1);
- parameter.setValue("2:9.5:0.125");
- parameter.setType(ResultDataSetUploader.PARAMETER_TYPE_MODIFICATION);
- peptide.setParameters(Arrays.asList(parameter));
- peptide.setSequence("abcd");
- peptide.setCharge(3);
- p1.setPeptides(Arrays.asList(peptide));
- summary.getProteinGroups().add(createProteinGroup(p1));
- prepareCreateSample();
- context.checking(new Expectations()
- {
- {
- one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
- will(returnValue(PEPTIDE_ID));
-
- one(dao).createModifiedPeptide(PEPTIDE_ID, 0, 0);
- will(returnValue(MOD_PEPTIDE_ID));
-
- one(dao).createModification(MOD_PEPTIDE_ID, 2, 9.5);
- will(returnValue(157L));
-
- one(dao).createModificationFraction(157L, CELL_LYSATE_ID1, 0.125);
- }
- });
-
- uploader.upload(createDataSetInfo(), summary);
-
- context.assertIsSatisfied();
- }
-
- private Parameter createAbundance(String sampleCode, double value)
- {
- Parameter parameter = new Parameter();
- parameter.setName(sampleCode);
- parameter.setValue(Double.toString(value));
- parameter.setType(ResultDataSetUploader.PARAMETER_TYPE_ABUNDANCE);
- return parameter;
- }
-
- private Protein createProtein(double probability, ProteinAnnotation... annotations)
- {
- Protein protein = new Protein();
- protein.setProbability(probability);
- if (annotations.length > 0)
- {
- protein.setAnnotation(annotations[0]);
- }
- List<AnnotatedProtein> indistinguishableProteins = new ArrayList<AnnotatedProtein>();
- for (int i = 1; i < annotations.length; i++)
- {
- AnnotatedProtein annotatedProtein = new AnnotatedProtein();
- annotatedProtein.setAnnotation(annotations[i]);
- indistinguishableProteins.add(annotatedProtein);
- }
- protein.setIndistinguishableProteins(indistinguishableProteins);
- return protein;
- }
-
- private ProteinAnnotation createAnnotation(String uniprotID, String description, String sequence)
- {
- ProteinAnnotation proteinAnnotation = new ProteinAnnotation();
- proteinAnnotation.setDescription(uniprotID
- + " "
- + ProteinDescription.createKeyValuePair(ProteinDescription.DESCRIPTION_KEY,
- description) + " "
- + ProteinDescription.createKeyValuePair(ProteinDescription.SEQUENCE_KEY, sequence));
- return proteinAnnotation;
- }
-
- private ProteinGroup createProteinGroup(Protein... proteins)
- {
- ProteinGroup proteinGroup = new ProteinGroup();
- proteinGroup.setProteins(Arrays.asList(proteins));
- return proteinGroup;
- }
-
- private void prepareForCreatingProtein(final double probability)
- {
- context.checking(new Expectations()
- {
- {
- one(dao).createProtein(DATA_SET_ID, probability);
- will(returnValue(PROTEIN1_ID));
- }
- });
- }
-
- private void prepareCreateSample()
- {
- context.checking(new Expectations()
- {
- {
- one(service).tryGetSampleWithExperiment(
- new SampleIdentifier(new SpaceIdentifier(
- CommonConstants.MS_DATA_SPACE), CELL_LYSATE1));
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
- sample.setPermId(CELL_LYSATE_PERM_ID1);
- will(returnValue(sample));
- one(dao).tryToGetSampleByPermID(CELL_LYSATE_PERM_ID1);
- will(returnValue(null));
- one(dao).createSample(EXPERIMENT_ID, CELL_LYSATE_PERM_ID1);
- will(returnValue(CELL_LYSATE_ID1));
- }
- });
- }
-
- private void prepareForCreatingIdentifiedProtein(ProteinAnnotation annotation,
- final boolean referenceExist, final boolean primary)
- {
- ProteinDescription proteinDescription = new ProteinDescription(annotation, 0, true);
- final String uniprotID = proteinDescription.getAccessionNumber();
- final String description = proteinDescription.getDescription();
- final String sequence = proteinDescription.getSequence();
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetProteinReference(uniprotID);
- if (referenceExist == false)
- {
- will(returnValue(null));
-
- one(dao).createProteinReference(uniprotID, description);
- will(returnValue(PROTEIN_REFERENCE_ID));
- } else
- {
- ProteinReference proteinReference = new ProteinReference();
- proteinReference.setId(PROTEIN_REFERENCE_ID);
- will(returnValue(proteinReference));
-
- one(dao).updateProteinReferenceDescription(PROTEIN_REFERENCE_ID,
- description);
- }
-
- one(dao).tryToGetSequencesByReferenceAndDatabase(PROTEIN_REFERENCE_ID,
- DATABASE_ID);
- Sequence seq = new Sequence(sequence);
- seq.setId(SEQUENCE_ID);
- if (referenceExist == false)
- {
- will(returnValue(null));
-
- seq.setDatabaseID(DATABASE_ID);
- seq.setProteinReferenceID(PROTEIN_REFERENCE_ID);
- one(dao).createSequence(seq);
- will(returnValue(SEQUENCE_ID));
- } else
- {
- will(returnValue(Arrays.asList(seq)));
- }
-
- one(dao).createIdentifiedProtein(PROTEIN1_ID, SEQUENCE_ID, 0, primary);
- }
- });
- }
-
- private void prepareForCreatingExperimentSampleDatabaseAndDataSet()
- {
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetExperimentByPermID(EXPERIMENT_PERM_ID);
- will(returnValue(null));
- one(dao).createExperiment(EXPERIMENT_PERM_ID);
- will(returnValue(EXPERIMENT_ID));
-
- one(dao).tryToGetDatabaseByName(NAME_AND_VERSION);
- will(returnValue(null));
- one(dao).createDatabase(NAME_AND_VERSION);
- will(returnValue(DATABASE_ID));
-
- one(dao).tryToGetDataSetByPermID(DATA_SET_CODE);
- will(returnValue(null));
- one(dao).createDataSet(EXPERIMENT_ID, DATA_SET_CODE, DATABASE_ID);
- will(returnValue(DATA_SET_ID));
- }
- });
- }
-
- private void prepareForCommit()
- {
- context.checking(new Expectations()
- {
- {
- try
- {
- one(connection).commit();
- one(connection).close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
- });
- }
-
- private void prepareForRollback()
- {
- context.checking(new Expectations()
- {
- {
- try
- {
- one(connection).isClosed();
- will(returnValue(false));
- one(connection).rollback();
- one(connection).close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
- });
- }
-
- private DataSetInformation createDataSetInfo()
- {
- DataSetInformation info = new DataSetInformation();
- info.setExperimentIdentifier(new ExperimentIdentifier(SPACE_CODE, PROJECT_CODE, EXPERIMENT_CODE));
- info.setDataSetCode(DATA_SET_CODE);
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
- sample.setPermId(SAMPLE_PERM_ID);
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
- new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment();
- experiment.setPermId(EXPERIMENT_PERM_ID);
- sample.setExperiment(experiment);
- Space space = new Space();
- space.setCode(SPACE_CODE);
- sample.setSpace(space);
- info.setSample(sample);
- return info;
- }
-
- private ProteinSummary createProteinSummary()
- {
- ProteinSummary proteinSummary = new ProteinSummary();
- ProteinSummaryHeader proteinSummaryHeader = new ProteinSummaryHeader();
- proteinSummaryHeader.setReferenceDatabase(REFERENCE_DATABASE);
- ProgramDetails programDetails = new ProgramDetails();
- ProteinProphetDetails proteinProphetDetails = new ProteinProphetDetails();
- ProteinSummaryDataFilter m1 = createFilter(0.5, 0.125);
- ProteinSummaryDataFilter m2 = createFilter(1.0, 0.0);
- proteinProphetDetails.setDataFilters(Arrays.asList(m1, m2));
- programDetails.setSummary(new Object[]
- { proteinProphetDetails });
- proteinSummaryHeader.setProgramDetails(programDetails);
- proteinSummary.setSummaryHeader(proteinSummaryHeader);
- proteinSummary.setProteinGroups(new ArrayList<ProteinGroup>());
- return proteinSummary;
- }
-
- private ProteinSummaryDataFilter createFilter(final double probability, final double fdr)
- {
- context.checking(new Expectations()
- {
- {
- one(dao).createProbabilityToFDRMapping(DATA_SET_ID, probability, fdr);
- }
- });
- ProteinSummaryDataFilter mapping = new ProteinSummaryDataFilter();
- mapping.setMinProbability(probability);
- mapping.setFalsePositiveErrorRate(fdr);
- return mapping;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjectionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjectionTest.java
deleted file mode 100644
index d1ec3a35ec2..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/TypeExtractorForMSInjectionTest.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection.DATA_SET_PROPERTIES_FILE;
-
-import java.io.File;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TypeExtractorForMSInjectionTest extends AbstractFileSystemTestCase
-{
- @Test
- public void testMissingDataSetPropertiesFile()
- {
- TypeExtractorForMSInjection extractor = new TypeExtractorForMSInjection(new Properties());
- try
- {
- extractor.getDataSetType(workingDirectory);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Missing properties file '" + DATA_SET_PROPERTIES_FILE + "'.", ex.getMessage());
- }
- }
-
- @Test
- public void testGetDataSetType()
- {
- FileUtilities.writeToFile(new File(workingDirectory, DATA_SET_PROPERTIES_FILE), "DATA_SET_TYPE = RAW");
- TypeExtractorForMSInjection extractor = new TypeExtractorForMSInjection(new Properties());
- DataSetType dataSetType = extractor.getDataSetType(workingDirectory);
- assertEquals("RAW", dataSetType.getCode());
- }
-
- @Test
- public void testGetProcessorType()
- {
- FileUtilities.writeToFile(new File(workingDirectory, DATA_SET_PROPERTIES_FILE), "DATA_SET_TYPE = RAW");
- TypeExtractorForMSInjection extractor = new TypeExtractorForMSInjection(new Properties());
- assertEquals(null, extractor.getProcessorType(workingDirectory));
- }
-
- @Test
- public void testGetFileFormatType()
- {
- FileUtilities.writeToFile(new File(workingDirectory, DATA_SET_PROPERTIES_FILE), "FILE_TYPE = XML");
- TypeExtractorForMSInjection extractor = new TypeExtractorForMSInjection(new Properties());
- assertEquals("XML", extractor.getFileFormatType(workingDirectory).getCode());
- }
-
- @Test
- public void testGetLocatorType()
- {
- FileUtilities.writeToFile(new File(workingDirectory, DATA_SET_PROPERTIES_FILE), "FILE_TYPE = XML");
- TypeExtractorForMSInjection extractor = new TypeExtractorForMSInjection(new Properties());
- assertEquals(LocatorType.DEFAULT_LOCATOR_TYPE_CODE, extractor.getLocatorType(workingDirectory).getCode());
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/UtilTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/UtilTest.java
deleted file mode 100644
index 7742a5a902d..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/UtilTest.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.etlserver.proteomics;
-
-import java.util.Arrays;
-import java.util.Properties;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.Util;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class UtilTest extends AssertJUnit
-{
- @Test
- public void testGetAndCheckProperties()
- {
- SampleType entityType = new SampleType();
- SampleTypePropertyType etpt1 = createETPT("answer", false);
- SampleTypePropertyType etpt2 = createETPT("greetings", true);
- entityType.setSampleTypePropertyTypes(Arrays.asList(etpt1, etpt2));
- Properties properties = new Properties();
- properties.setProperty("greetings", "hello");
- properties.setProperty("blabla", "blub");
-
- IEntityProperty[] entityProperties = Util.getAndCheckProperties(properties, entityType);
-
- assertEquals(1, entityProperties.length);
- assertEquals("greetings", entityProperties[0].getPropertyType().getCode());
- assertEquals("hello", entityProperties[0].tryGetAsString());
- }
-
- @Test
- public void testGetAndCheckPropertiesForMissingMandatoryProperty()
- {
- SampleType entityType = new SampleType();
- SampleTypePropertyType etpt1 = createETPT("answer", true);
- SampleTypePropertyType etpt2 = createETPT("greetings", true);
- entityType.setSampleTypePropertyTypes(Arrays.asList(etpt1, etpt2));
- Properties properties = new Properties();
- properties.setProperty("greetings", "hello");
-
- try
- {
- Util.getAndCheckProperties(properties, entityType);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("The following mandatory properties are missed: [answer]", ex.getMessage());
- }
- }
-
- private SampleTypePropertyType createETPT(String code, boolean mandatory)
- {
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(code);
- SampleTypePropertyType etpt = new SampleTypePropertyType();
- etpt.setPropertyType(propertyType);
- etpt.setMandatory(mandatory);
- return etpt;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/DependencyCheckingTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/DependencyCheckingTest.java
deleted file mode 100644
index c5d317bd38f..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/DependencyCheckingTest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics;
-
-import ch.systemsx.cisd.common.test.AbstractDependencyCheckingTestCase;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DependencyCheckingTest extends AbstractDependencyCheckingTestCase
-{
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacadeTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacadeTest.java
deleted file mode 100644
index 82048aff03a..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/api/v1/ProteomicsDataApiFacadeTest.java
+++ /dev/null
@@ -1,223 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.api.v1;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Set;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteomicsDataApiFacadeTest extends AssertJUnit
-{
- private static final String SESSION_TOKEN = "Session-42";
-
- private Mockery context;
-
- private IProteomicsDataService proteomicsDataService;
-
- private IGeneralInformationService generalInfoService;
-
- private IProteomicsDataApiFacade facade;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- proteomicsDataService = context.mock(IProteomicsDataService.class);
- generalInfoService = context.mock(IGeneralInformationService.class);
- facade = new ProteomicsDataApiFacade(proteomicsDataService, generalInfoService, SESSION_TOKEN);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetSessionToken()
- {
- assertEquals(SESSION_TOKEN, facade.getSessionToken());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLogout()
- {
- context.checking(new Expectations()
- {
- {
- one(generalInfoService).logout(SESSION_TOKEN);
- }
- });
-
- facade.logout();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListDataStoreServerProcessingPluginInfos()
- {
- final List<DataStoreServerProcessingPluginInfo> result =
- new LinkedList<DataStoreServerProcessingPluginInfo>();
- context.checking(new Expectations()
- {
- {
- one(proteomicsDataService).listDataStoreServerProcessingPluginInfos(SESSION_TOKEN);
- will(returnValue(result));
- }
- });
-
- assertSame(result, facade.listDataStoreServerProcessingPluginInfos());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamples()
- {
- final List<MsInjectionDataInfo> result = new LinkedList<MsInjectionDataInfo>();
- context.checking(new Expectations()
- {
- {
- one(proteomicsDataService).listRawDataSamples(SESSION_TOKEN, "user1");
- will(returnValue(result));
- }
- });
-
- assertSame(result, facade.listRawDataSamples("user1"));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListAllRawDataSamples()
- {
- final List<MsInjectionDataInfo> result = new LinkedList<MsInjectionDataInfo>();
- context.checking(new Expectations()
- {
- {
- one(proteomicsDataService).listAllRawDataSamples(SESSION_TOKEN, "user1");
- will(returnValue(result));
- }
- });
-
- assertSame(result, facade.listAllRawDataSamples("user1"));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessDataSets()
- {
- context.checking(new Expectations()
- {
- {
- one(proteomicsDataService).processDataSets(SESSION_TOKEN, "user1", "key",
- Arrays.asList("ds1", "ds2"));
- }
- });
-
- facade.processDataSets("user1", "key", Arrays.asList("ds1", "ds2"));
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListProjectsButNoUserRoles()
- {
- context.checking(new Expectations()
- {
- {
- one(generalInfoService).listNamedRoleSets(SESSION_TOKEN);
- will(returnValue(new HashMap<String, Set<Role>>()));
- }
- });
-
- try
- {
- facade.listProjects("user1");
- fail("IllegalStateException expected");
- } catch (IllegalStateException ex)
- {
- assertEquals("Role set SPACE_USER not known.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListProjects()
- {
- context.checking(new Expectations()
- {
- {
- one(generalInfoService).listNamedRoleSets(SESSION_TOKEN);
- HashMap<String, Set<Role>> sets = new HashMap<String, Set<Role>>();
- HashSet<Role> set = new HashSet<Role>();
- set.add(new Role("R1", true));
- set.add(new Role("R2", false));
- sets.put("SPACE_USER", set);
- will(returnValue(sets));
-
- one(generalInfoService).listSpacesWithProjectsAndRoleAssignments(SESSION_TOKEN, null);
- SpaceWithProjectsAndRoleAssignments a = createSpace("A", "alpha", "beta");
- a.add("user1", new Role("R1", true));
- a.add("user1", new Role("R3", false));
- SpaceWithProjectsAndRoleAssignments b = createSpace("B", "gamma");
- b.add("user1", new Role("R2", true));
- will(returnValue(Arrays.asList(a, b)));
- }
- });
-
- List<Project> projects = facade.listProjects("user1");
-
- assertEquals("[/A/alpha, /A/beta]", projects.toString());
- context.assertIsSatisfied();
- }
-
- private SpaceWithProjectsAndRoleAssignments createSpace(String spaceCode, String... projects)
- {
- SpaceWithProjectsAndRoleAssignments space = new SpaceWithProjectsAndRoleAssignments(spaceCode);
- long id = 1;
- for (String project : projects)
- {
- space.add(new Project(id, Long.toString(id), spaceCode, project, null));
- ++id;
- }
- return space;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderersTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderersTest.java
deleted file mode 100644
index 9676c640cba..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinRenderersTest.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application;
-
-import java.util.Arrays;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.application.ProteinRenderers;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Peptide;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.PeptideModification;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinRenderersTest extends AssertJUnit
-{
- @Test
- public void testRenderAminoAcidSymbol()
- {
- assertEquals("<font style='text-decoration:underline; cursor:pointer' "
- + "color='blue' title='mass=4.5'>A</font>",
- ProteinRenderers.renderAminoAcidSymbol('A', null, 4.5));
- assertEquals("<font style='text-decoration:underline; cursor:pointer' "
- + "color='blue' title='position=42, mass=4.5'>A</font>",
- ProteinRenderers.renderAminoAcidSymbol('A', 42, 4.5));
- }
-
- @Test
- public void testMarkOccurrencesWithHtml()
- {
- Peptide p1 = peptide("defgh:2=4.25");
- Peptide p2 = peptide("ijk:1=-2.75");
- Peptide p3 = peptide("jko");
- Peptide p4 = peptide("jjab");
- String e = ProteinRenderers.renderAminoAcidSymbol('e', 5, 4.25);
- String i1 = ProteinRenderers.renderAminoAcidSymbol('i', 9, -2.75);
- String i2 = ProteinRenderers.renderAminoAcidSymbol('i', 15, -2.75);
- assertEquals(
- "abc<font color='red'>d" + e + " fgh" + i1 + "j k</font>lmn<font color='red'>"
- + i2 + " jko</font>pq rstu",
- ProteinRenderers.markOccurrencesWithHtml("abcdefghijklmnijkopqrstu",
- Arrays.asList(p1, p2, p3, p4), 5));
- }
-
- private Peptide peptide(String description)
- {
- Peptide peptide = new Peptide();
- int indexOfColon = description.indexOf(':');
- if (indexOfColon < 0)
- {
- peptide.setSequence(description);
- return peptide;
- }
- peptide.setSequence(description.substring(0, indexOfColon));
- String[] modificationDescriptions = description.substring(indexOfColon + 1).split(",");
- for (String modificationDescription : modificationDescriptions)
- {
- String[] posAndMass = modificationDescription.split("=");
- PeptideModification peptideModification = new PeptideModification();
- peptideModification.setPosition(Integer.parseInt(posAndMass[0]));
- peptideModification.setMass(Double.parseDouble(posAndMass[1]));
- peptide.getModifications().add(peptideModification);
- }
- return peptide;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/.gitignore b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceTest.java
deleted file mode 100644
index 6eee125b577..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientServiceTest.java
+++ /dev/null
@@ -1,302 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
-import ch.systemsx.cisd.common.utilities.MockTimeProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GridRowModels;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSetFetchConfig;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.DefaultResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IResultSetManager;
-import ch.systemsx.cisd.openbis.generic.shared.WebClientConfigurationProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.SessionConstants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
-import ch.systemsx.cisd.openbis.generic.shared.util.CacheManager;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.Constants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.PhosphoNetXClientService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = { AbstractClientService.class, PhosphoNetXClientService.class, CacheManager.class })
-public class PhosphoNetXClientServiceTest extends AbstractFileSystemTestCase
-{
- private static final String SESSION_TOKEN = "session-token";
-
- private static final class SimpleResultSetManager<K> implements IResultSetManager<K>
- {
-
- @Override
- public <T> IResultSet<K, T> getResultSet(String sessionToken,
- IResultSetConfig<K, T> resultConfig, IOriginalDataProvider<T> dataProvider)
- throws UserFailureException
- {
- List<TableModelColumnHeader> headers = dataProvider.getHeaders();
- List<T> originalData = dataProvider.getOriginalData(Integer.MAX_VALUE);
- List<GridRowModel<T>> rows = new ArrayList<GridRowModel<T>>();
- for (int i = 0; i < originalData.size(); i++)
- {
- T rowData = originalData.get(i);
- rows.add(new GridRowModel<T>(rowData, null));
- }
- return new DefaultResultSet<K, T>(resultConfig.getCacheConfig().tryGetResultSetKey(),
- new GridRowModels<T>(rows, headers, null, null), rows.size(), false);
- }
-
- @Override
- public void removeResultSet(K resultSetKey) throws UserFailureException
- {
- }
-
- @Override
- public void lockResultSet(K resultSetKey)
- {
- }
-
- }
-
- private Mockery context;
-
- private IPhosphoNetXServer server;
-
- private PhosphoNetXClientService clientService;
-
- private IRequestContextProvider requestContextProvider;
-
- private HttpServletRequest request;
-
- private HttpSession httpSession;
-
- private File cacheFolder;
-
- @BeforeMethod
- public final void beforeMethod() throws Exception
- {
- context = new Mockery();
- server = context.mock(IPhosphoNetXServer.class);
- requestContextProvider = context.mock(IRequestContextProvider.class);
- request = context.mock(HttpServletRequest.class);
- httpSession = context.mock(HttpSession.class);
- clientService = new PhosphoNetXClientService();
- clientService.server = server;
- clientService.requestContextProvider = requestContextProvider;
- context.checking(new Expectations()
- {
- {
- allowing(requestContextProvider).getHttpServletRequest();
- will(returnValue(request));
-
- allowing(request).getSession(false);
- will(returnValue(httpSession));
-
- allowing(httpSession).getAttribute("openbis-session-token");
- will(returnValue(SESSION_TOKEN));
-
- allowing(httpSession).getAttribute(SessionConstants.OPENBIS_RESULT_SET_MANAGER);
- will(returnValue(new SimpleResultSetManager<String>()));
- }
- });
- Properties properties = new Properties();
- cacheFolder = new File(workingDirectory, "cache");
- if (cacheFolder.exists())
- {
- assertTrue(FileUtilities.deleteRecursively(cacheFolder));
- }
- properties.setProperty("technologies", Constants.TECHNOLOGY_NAME);
- properties.setProperty(Constants.TECHNOLOGY_NAME + "." + CacheManager.CACHE_FOLDER_KEY,
- cacheFolder.getPath());
- clientService.webClientConfigurationProvider =
- new WebClientConfigurationProvider(properties);
- clientService.timeProvider = new MockTimeProvider();
- clientService.afterPropertiesSet();
- }
-
- @AfterMethod
- public final void afterMethod()
- {
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetAbundanceColumnDefinitionsForProteinByExperiment()
- {
- final TechId experimentID = new TechId(41L);
- final AbundanceColumnDefinition colDef = new AbundanceColumnDefinition();
- colDef.setSampleCode("S1");
- Treatment treatment = new Treatment();
- treatment.setType("type1");
- treatment.setTypeCode("code");
- colDef.setTreatments(Arrays.asList(treatment));
- context.checking(new Expectations()
- {
- {
- one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
- experimentID, null);
- will(returnValue(Arrays.asList(colDef)));
- }
- });
-
- List<AbundanceColumnDefinition> colDefs =
- clientService.getAbundanceColumnDefinitionsForProteinByExperiment(experimentID,
- null);
- colDefs =
- clientService.getAbundanceColumnDefinitionsForProteinByExperiment(experimentID,
- null);
- assertEquals(colDef.getSampleCode(), colDefs.get(0).getSampleCode());
- assertEquals(treatment.getType(), colDefs.get(0).getTreatments().get(0).getType());
- assertEquals(1, colDefs.size());
- assertEquals(3, cacheFolder.listFiles().length);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListProteinsByExperiment()
- {
- final TechId experimentID1 = new TechId(42L);
- final TechId experimentID2 = new TechId(4711L);
- final AbundanceColumnDefinition colDef = new AbundanceColumnDefinition();
- colDef.setSampleCode("S1");
- Treatment treatment = new Treatment();
- treatment.setType("type1");
- treatment.setTypeCode("code");
- colDef.setTreatments(Arrays.asList(treatment));
- final double fdr1 = 0.125;
- final double fdr2 = 0.25;
- final AggregateFunction f1 = AggregateFunction.MAX;
- final AggregateFunction f2 = AggregateFunction.MIN;
- final String treatment1 = "t1";
- final String treatment2 = "t2";
- final ProteinInfo p1 = createProtein(1);
- final ProteinInfo p2 = createProtein(2);
- final ProteinInfo p3 = createProtein(3);
- final ProteinInfo p4 = createProtein(4);
- final ProteinInfo p5 = createProtein(5);
- final ProteinInfo p6 = createProtein(6);
- context.checking(new Expectations()
- {
- {
- one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
- experimentID1, treatment1);
- will(returnValue(Arrays.asList(colDef)));
- one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
- experimentID1, treatment2);
- will(returnValue(Arrays.asList(colDef)));
- one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
- experimentID2, treatment1);
- will(returnValue(Arrays.asList(colDef)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr1, f1,
- treatment1, false);
- will(returnValue(Arrays.asList(p1)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID2, fdr1, f1,
- treatment1, false);
- will(returnValue(Arrays.asList(p2)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr2, f1,
- treatment1, false);
- will(returnValue(Arrays.asList(p3)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr1, f2,
- treatment1, false);
- will(returnValue(Arrays.asList(p4)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr1, f1,
- treatment2, false);
- will(returnValue(Arrays.asList(p5)));
- one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr1, f1,
- treatment1, true);
- will(returnValue(Arrays.asList(p6)));
-
- }
- });
-
- listAndCheckProteins(p1, experimentID1, fdr1, f1, treatment1, false);
- listAndCheckProteins(p2, experimentID2, fdr1, f1, treatment1, false);
- listAndCheckProteins(p3, experimentID1, fdr2, f1, treatment1, false);
- listAndCheckProteins(p4, experimentID1, fdr1, f2, treatment1, false);
- listAndCheckProteins(p5, experimentID1, fdr1, f1, treatment2, false);
- listAndCheckProteins(p6, experimentID1, fdr1, f1, treatment1, true);
- listAndCheckProteins(p1, experimentID1, fdr1, f1, treatment1, false);
- listAndCheckProteins(p2, experimentID2, fdr1, f1, treatment1, false);
- listAndCheckProteins(p3, experimentID1, fdr2, f1, treatment1, false);
- listAndCheckProteins(p4, experimentID1, fdr1, f2, treatment1, false);
- listAndCheckProteins(p5, experimentID1, fdr1, f1, treatment2, false);
- listAndCheckProteins(p6, experimentID1, fdr1, f1, treatment1, true);
- assertEquals("Unexpectd number of files: " + Arrays.asList(cacheFolder.listFiles()), 19,
- cacheFolder.listFiles().length);
-
- context.assertIsSatisfied();
- }
-
- private void listAndCheckProteins(ProteinInfo protein, TechId experimentId,
- double falseDiscoveryRate, AggregateFunction function, String treatmentTypeCode,
- boolean aggregateOnOriginal)
- {
- ListProteinByExperimentCriteria criteria = new ListProteinByExperimentCriteria();
- criteria.setCacheConfig(ResultSetFetchConfig.createFetchFromCache("key"));
- criteria.setExperimentID(experimentId);
- criteria.setFalseDiscoveryRate(falseDiscoveryRate);
- criteria.setAggregateFunction(function);
- criteria.setTreatmentTypeCode(treatmentTypeCode);
- criteria.setAggregateOriginal(aggregateOnOriginal);
- TypedTableResultSet<ProteinInfo> rs = clientService.listProteinsByExperiment(criteria);
- ProteinInfo actualProtein = rs.getResultSet().getList().get(0).getOriginalObject().getObjectOrNull();
- assertEquals(protein.getId(), actualProtein.getId());
- assertEquals(protein.getDescription(), actualProtein.getDescription());
- assertEquals(1, rs.getResultSet().getTotalLength());
- }
-
- private ProteinInfo createProtein(long id)
- {
- ProteinInfo protein = new ProteinInfo();
- protein.setId(new TechId(id));
- protein.setDescription("Protein " + id);
- protein.setAbundances(new HashMap<Long, Double>());
- return protein;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProviderTest.java
deleted file mode 100644
index 8cac244ce94..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/RawDataSampleProviderTest.java
+++ /dev/null
@@ -1,231 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.CODE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.PARENT;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.RawDataSampleGridIDs.REGISTRATION_DATE;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.RawDataSampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = RawDataSampleProvider.class)
-public class RawDataSampleProviderTest extends AbstractServerTestCase
-{
- private IProteomicsDataServiceInternal service;
-
- private RawDataSampleProvider provider;
-
- @Override
- @BeforeMethod
- public final void setUp()
- {
- super.setUp();
- service = context.mock(IProteomicsDataServiceInternal.class);
- provider = new RawDataSampleProvider(service, SESSION_TOKEN);
- }
-
- @Test
- public void testGetHeadersForNoData()
- {
- prepareListRawDataSamples();
-
- List<TableModelColumnHeader> headers = provider.getTableModel(Integer.MAX_VALUE).getHeader();
-
- assertFixedColumns(headers);
- assertEquals(4, headers.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetHeaders()
- {
- Sample ms1 = sample("MS1", sample("ABC", "alpha", "beta"), "one");
- Sample ms2 = sample("MS2", sample("DE", "gamma", "beta"), "one");
- Sample ms3 = sample("MS3", sample("DE", "gamma", "alpha"), "two");
- prepareListRawDataSamples(ms1, ms2, ms3);
-
- List<TableModelColumnHeader> headers = provider.getTableModel(Integer.MAX_VALUE).getHeader();
-
- assertFixedColumns(headers);
- assertPropertyHeader("one", "USER-ONE", 4, headers);
- assertPropertyHeader("two", "USER-TWO", 5, headers);
- assertPropertyHeader("alpha", "BIO_USER-ALPHA", 6, headers);
- assertPropertyHeader("beta", "BIO_USER-BETA", 7, headers);
- assertPropertyHeader("gamma", "BIO_USER-GAMMA", 8, headers);
- assertEquals(9, headers.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetOriginalDataForNoData()
- {
- prepareListRawDataSamples();
-
- List<TableModelRowWithObject<Sample>> data = provider.getTableModel(Integer.MAX_VALUE).getRows();
-
- assertEquals(0, data.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetOriginalData()
- {
- Sample ms1 = sample("MS1", sample("ABC", "beta", "alpha"), "one");
- Sample ms2 = sample("MS2", sample("DE", "gamma", "beta"), "one");
- Sample parent = sample("FG", "alpha", "gamma");
- Experiment experiment = new Experiment();
- experiment.setIdentifier("/G/P/E1");
- parent.setExperiment(experiment);
- Sample ms3 = sample("MS3", parent, "2");
- prepareListRawDataSamples(ms1, ms2, ms3);
-
- TypedTableModel<Sample> tableModel = provider.getTableModel(Integer.MAX_VALUE);
- List<TableModelRowWithObject<Sample>> data = tableModel.getRows();
-
- assertEquals(3, data.size());
- assertEquals("[null, null, null, null, 2, one, alpha, beta, gamma]", tableModel.getHeader().toString());
- assertRow("MS1, Mon Mar 30 17:18:20 CET 1970, /G/ABC, , , 3, 6, 4, ", data.get(0));
- assertRow("MS2, Mon Mar 30 17:20:00 CET 1970, /G/DE, , , 3, , 5, 5", data.get(1));
- assertRow("MS3, Mon Mar 30 17:21:40 CET 1970, /G/FG, /G/P/E1, 1, , 5, , 6", data.get(2));
- context.assertIsSatisfied();
- }
-
- private void assertRow(String expectedRow, TableModelRow row)
- {
- StringBuilder builder = new StringBuilder();
- int length = expectedRow.split(",").length;
- for (int i = 0; i < length; i++)
- {
- if (builder.length() > 0)
- {
- builder.append(", ");
- }
- builder.append(row.getValues().get(i));
- }
- assertEquals(expectedRow, builder.toString());
- }
-
- private void assertFixedColumns(List<TableModelColumnHeader> headers)
- {
- assertUntitledHeader(CODE, 0, DataTypeCode.VARCHAR, headers.get(0));
- assertUntitledHeader(REGISTRATION_DATE, 1, DataTypeCode.TIMESTAMP, headers.get(1));
- assertUntitledHeader(PARENT, 2, DataTypeCode.VARCHAR, headers.get(2));
- }
-
- private void assertUntitledHeader(String expectedCode, int expectedIndex,
- DataTypeCode expectedType, TableModelColumnHeader header)
- {
- assertHeader(null, expectedCode, expectedIndex, expectedType, header);
- }
-
- private void assertPropertyHeader(String expectedLabel, String expectedCode, int index, List<TableModelColumnHeader> headers)
- {
- TableModelColumnHeader header = headers.get(index);
- assertHeader(expectedLabel, expectedCode, index, DataTypeCode.INTEGER, header);
- }
-
- private void assertHeader(String expectedTitle, String expectedCode, int expectedIndex,
- DataTypeCode expectedType, TableModelColumnHeader header)
- {
- assertEquals(expectedTitle, header.getTitle());
- assertEquals(expectedCode, header.getId());
- assertEquals(expectedIndex, header.getIndex());
- assertEquals(expectedType, header.getDataType());
- }
-
- private Sample sample(String code, Sample parent, String... properties)
- {
- Sample sample = sample(code, properties);
- sample.setGeneratedFrom(parent);
- return sample;
- }
-
- private Sample sample(String code, String... properties)
- {
- Sample sample = new Sample();
- sample.setCode(code);
- sample.setIdentifier("/G/" + code);
- sample.setId((long) code.hashCode());
- sample.setRegistrationDate(new Date(code.hashCode() * 100000L));
- sample.setProperties(createProperties(properties));
- return sample;
- }
-
- private List<IEntityProperty> createProperties(String... labels)
- {
- ArrayList<IEntityProperty> properties = new ArrayList<IEntityProperty>();
- for (String label : labels)
- {
- GenericEntityProperty property = new GenericEntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setLabel(label);
- propertyType.setCode(propertyType.getLabel().toUpperCase());
- propertyType.setSimpleCode(propertyType.getCode());
- DataType dataType = new DataType();
- dataType.setCode(DataTypeCode.INTEGER);
- propertyType.setDataType(dataType);
- property.setPropertyType(propertyType);
- property.setValue(Integer.toString(label.length() + properties.size()));
- properties.add(property);
- }
- return properties;
- }
-
- private void prepareListRawDataSamples(final Sample... samples)
- {
- context.checking(new Expectations()
- {
- {
- one(service).listRawDataSamples(SESSION_TOKEN);
- List<MsInjectionSample> list = new ArrayList<MsInjectionSample>();
- for (Sample sample : samples)
- {
- list.add(new MsInjectionSample(sample, Arrays.<AbstractExternalData> asList()));
- }
- will(returnValue(list));
- }
- });
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java
deleted file mode 100644
index 01b17862c6c..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import java.util.Arrays;
-
-import org.jmock.Expectations;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractProviderTest;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinSequenceProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequence;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSequenceProviderTest extends AbstractProviderTest
-{
- @Test
- public void test()
- {
- final ProteinSequence ps = new ProteinSequence();
- ps.setShortName("short-name");
- ps.setDatabaseNameAndVersion("db-version");
- ps.setSequence("ABC");
- final IPhosphoNetXServer phosphonetxServer = context.mock(IPhosphoNetXServer.class);
- context.checking(new Expectations()
- {
- {
- one(phosphonetxServer).listProteinSequencesByProteinReference(SESSION_TOKEN, new TechId(42), new TechId(43));
- will(returnValue(Arrays.asList(ps)));
- }
- });
- ProteinSequenceProvider provider =
- new ProteinSequenceProvider(phosphonetxServer, SESSION_TOKEN, new TechId(42), new TechId(43));
-
- TypedTableModel<ProteinSequence> model = provider.createTableModel();
-
- assertEquals("[SEQUENCE_SHORT_NAME, DATABASE_NAME_AND_VERSION, SEQUENCE]", getHeaderIDs(model).toString());
- assertEquals("[VARCHAR, VARCHAR, VARCHAR]", getHeaderDataTypes(model).toString());
- assertEquals("[null, null, null]", getHeaderEntityKinds(model).toString());
- assertSame(ps, model.getRows().get(0).getObjectOrNull());
- assertEquals("[short-name, db-version, ABC]", model.getRows().get(0).getValues().toString());
- assertEquals(1, model.getRows().size());
- context.assertIsSatisfied();
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProviderTest.java
deleted file mode 100644
index bcd305c7221..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSummaryProviderTest.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset;
-
-import java.util.Arrays;
-
-import org.jmock.Expectations;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractProviderTest;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
-import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.server.resultset.ProteinSummaryProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSummaryProviderTest extends AbstractProviderTest
-{
- @Test
- public void test()
- {
- final ProteinSummary ps = new ProteinSummary();
- ps.setFDR(0.125);
- ps.setProteinCount(42);
- ps.setPeptideCount(4711);
- ps.setDecoyProteinCount(2);
- ps.setDecoyPeptideCount(5);
- final IPhosphoNetXServer phosphonetxServer = context.mock(IPhosphoNetXServer.class);
- context.checking(new Expectations()
- {
- {
- one(phosphonetxServer).listProteinSummariesByExperiment(SESSION_TOKEN,
- new TechId(12));
- will(returnValue(Arrays.asList(ps)));
- }
- });
- ProteinSummaryProvider provider =
- new ProteinSummaryProvider(phosphonetxServer, SESSION_TOKEN, new TechId(12));
-
- TypedTableModel<ProteinSummary> model = provider.createTableModel();
-
- assertEquals(
- "[FDR, PROTEIN_COUNT, PEPTIDE_COUNT, DECOY_PROTEIN_COUNT, DECOY_PEPTIDE_COUNT]",
- getHeaderIDs(model).toString());
- assertEquals("[REAL, INTEGER, INTEGER, INTEGER, INTEGER]", getHeaderDataTypes(model)
- .toString());
- assertEquals("[null, null, null, null, null]", getHeaderEntityKinds(model).toString());
- assertSame(ps, model.getRows().get(0).getObjectOrNull());
- assertEquals("[0.125, 42, 4711, 2, 5]", model.getRows().get(0).getValues().toString());
- assertEquals(1, model.getRows().size());
- context.assertIsSatisfied();
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java
deleted file mode 100644
index 7c0980fc7ab..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java
+++ /dev/null
@@ -1,188 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
-import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IAbundanceColumnDefinitionTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinDetailsBO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IProteinRelatedSampleTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinDetails;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = PhosphoNetXServer.class)
-public class PhosphoNetXServerTest extends AbstractServerTestCase
-{
- private static final TechId EXPERIMENT_ID = new TechId(42L);
-
- private static final String EXPERIMENT_PERM_ID = "e123-45";
-
- private static final String SAMPLE_PERM_ID = "s34-56";
-
- private IPhosphoNetXDAOFactory phosphoNetXDAOFactory;
-
- private IBusinessObjectFactory boFactory;
-
- private ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin;
-
- private IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin;
-
- private IProteinQueryDAO proteinDAO;
-
- private PhosphoNetXServer server;
-
- private IAbundanceColumnDefinitionTable abundanceColumnDefinitionTable;
-
- private ISampleProvider sampleProvider;
-
- private IProteinDetailsBO proteinDetailsBO;
-
- private IProteinRelatedSampleTable proteinRelatedSampleTable;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- phosphoNetXDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
- boFactory = context.mock(IBusinessObjectFactory.class);
- sampleTypeSlaveServerPlugin = context.mock(ISampleTypeSlaveServerPlugin.class);
- dataSetTypeSlaveServerPlugin = context.mock(IDataSetTypeSlaveServerPlugin.class);
- proteinDAO = context.mock(IProteinQueryDAO.class);
- abundanceColumnDefinitionTable = context.mock(IAbundanceColumnDefinitionTable.class);
- proteinDetailsBO = context.mock(IProteinDetailsBO.class);
- proteinRelatedSampleTable = context.mock(IProteinRelatedSampleTable.class);
- sampleProvider = context.mock(ISampleProvider.class);
- server =
- new PhosphoNetXServer(sessionManager, daoFactory, propertiesBatchManager,
- phosphoNetXDAOFactory, boFactory, sampleTypeSlaveServerPlugin,
- dataSetTypeSlaveServerPlugin);
- context.checking(new Expectations()
- {
- {
- allowing(boFactory).createProteinDetailsBO(session);
- will(returnValue(proteinDetailsBO));
-
- allowing(boFactory).createProteinRelatedSampleTable(session);
- will(returnValue(proteinRelatedSampleTable));
- }
- });
- }
-
- @Test
- public void testGetAbundanceColumnDefinitionsForProteinByExperiment()
- {
- prepareGetSession();
- final MockDataSet<String> mockDataSet = new MockDataSet<String>();
- mockDataSet.add(SAMPLE_PERM_ID);
- final List<AbundanceColumnDefinition> result = Arrays.asList();
- context.checking(new Expectations()
- {
- {
- one(experimentDAO).getByTechId(EXPERIMENT_ID);
- ExperimentPE experimentPE = new ExperimentPE();
- experimentPE.setPermId(EXPERIMENT_PERM_ID);
- will(returnValue(experimentPE));
-
- allowing(phosphoNetXDAOFactory).getProteinQueryDAO(EXPERIMENT_ID);
- will(returnValue(proteinDAO));
-
- one(proteinDAO).listAbundanceRelatedSamplePermIDsByExperiment(EXPERIMENT_PERM_ID);
- will(returnValue(mockDataSet));
-
- one(boFactory).createAbundanceColumnDefinitionTable(session);
- will(returnValue(abundanceColumnDefinitionTable));
-
- one(boFactory).createSampleProvider(session);
- will(returnValue(sampleProvider));
-
- one(sampleProvider).loadByExperimentID(EXPERIMENT_ID);
-
- one(sampleProvider).getSample(SAMPLE_PERM_ID);
- Sample sample = new Sample();
- sample.setPermId(SAMPLE_PERM_ID);
- will(returnValue(sample));
-
- one(abundanceColumnDefinitionTable).add(sample);
-
- one(abundanceColumnDefinitionTable).getSortedAndAggregatedDefinitions("PH");
- will(returnValue(result));
- }
- });
-
- List<AbundanceColumnDefinition> definitions =
- server.getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
- EXPERIMENT_ID, "PH");
- assertSame(result, definitions);
- assertEquals(true, mockDataSet.hasCloseBeenInvoked());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListProteinRelatedSamplesByProtein()
- {
- prepareGetSession();
- final TechId experimentID = new TechId(42);
- final TechId proteinReferenceID = new TechId(4711);
- final List<Object> result = Arrays.asList();
- context.checking(new Expectations()
- {
- {
- one(proteinDetailsBO).loadByExperimentAndReference(experimentID,
- proteinReferenceID);
- one(proteinDetailsBO).getDetailsOrNull();
- ProteinDetails details = new ProteinDetails();
- String sequence = "abcdefabcab";
- details.setSequence(sequence);
- will(returnValue(details));
-
- one(proteinRelatedSampleTable).load(session, experimentID, proteinReferenceID, sequence);
- one(proteinRelatedSampleTable).getSamples();
- will(returnValue(result));
- }
- });
-
- List<ProteinRelatedSample> list =
- server.listProteinRelatedSamplesByProtein(SESSION_TOKEN, experimentID,
- proteinReferenceID);
-
- assertSame(result, list);
- context.assertIsSatisfied();
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalTest.java
deleted file mode 100644
index 7d4729d7446..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternalTest.java
+++ /dev/null
@@ -1,449 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.PROCESSING;
-import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.QUERIES;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.openbis.generic.server.TestJythonEvaluatorPool;
-import ch.systemsx.cisd.openbis.generic.server.authorization.TestAuthorizationConfig;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.ManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleLoader;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = ProteomicsDataServiceInternal.class)
-public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
-{
- private static final String GROUP_CODE = "g";
-
- private static final String COPY_PROCESSING_KEY = "copy-data-sets";
-
- private static final String EXPERIMENT_TYPE = "EXPE";
-
- private IProteomicsDataServiceInternal service;
-
- private ICommonBusinessObjectFactory commonBoFactory;
-
- private ExperimentTypePE experimentType;
-
- private IBusinessObjectFactory boFactory;
-
- private ISampleLoader sampleLoader;
-
- @Override
- @BeforeMethod
- public final void setUp()
- {
- super.setUp();
- commonBoFactory = context.mock(ICommonBusinessObjectFactory.class);
- boFactory = context.mock(IBusinessObjectFactory.class);
- sampleLoader = context.mock(ISampleLoader.class);
- service =
- new ProteomicsDataServiceInternal(sessionManager, daoFactory,
- propertiesBatchManager, commonBoFactory, boFactory,
- new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool()));
- experimentType = new ExperimentTypePE();
- experimentType.setCode(EXPERIMENT_TYPE);
- PersonPE person = new PersonPE();
- RoleAssignmentPE roleAssignment = new RoleAssignmentPE();
- roleAssignment.setRole(RoleCode.ADMIN);
- SpacePE group = new SpacePE();
- group.setCode("Space-0");
- roleAssignment.setSpace(group);
- person.setRoleAssignments(Collections.singleton(roleAssignment));
- session.setPerson(person);
- }
-
- @Test
- public void testListRawDataSamples()
- {
- prepareGetSession();
- prepareListRawDataSamples(42L);
-
- List<MsInjectionSample> samples = service.listRawDataSamples(SESSION_TOKEN);
-
- assertEquals(42L, samples.get(0).getSample().getId().longValue());
- assertEquals(1, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessDataSets()
- {
- prepareGetSession();
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- prepareProcessDataSets(session, parameterBindings, "ds1", "ds2");
-
- service.processDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, Arrays.asList("ds1", "ds2"));
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListExperiments()
- {
- prepareGetSession();
- final ExperimentPE e1 = experiment(1);
- final ExperimentPE e2 = experiment(2, "a");
- prepareListExperiments(e1, e2);
-
- List<Experiment> list = service.listExperiments(SESSION_TOKEN, EXPERIMENT_TYPE);
-
- assertEquals("/G/P/e1", list.get(0).getIdentifier());
- assertEquals(1, list.get(0).getRegistrationDate().getTime());
- assertEquals(0, list.get(0).getProperties().size());
- assertEquals("/G/P/e2", list.get(1).getIdentifier());
- assertEquals(4, list.get(1).getRegistrationDate().getTime());
- assertEquals("A", list.get(1).getProperties().get(0).getPropertyType().getCode());
- assertEquals("a-value", list.get(1).getProperties().get(0).getValue());
- assertEquals(1, list.get(1).getProperties().size());
- assertEquals(2, list.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessSearchData()
- {
- final Session testSession = createSessionAndPrepareGetSession(GROUP_CODE);
- final ExperimentPE e1 = experiment(1);
- final ExperimentPE e2 = experiment(2, "a");
- context.checking(new Expectations()
- {
- {
- one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
- will(returnValue(e1));
-
- one(dataSetDAO).listDataSets(e1);
- ExternalDataPE ds1 = new ExternalDataPE();
- ds1.setCode("ds1");
- will(returnValue(Arrays.asList(ds1)));
-
- one(experimentDAO).tryGetByTechId(new TechId(e2.getId()));
- will(returnValue(e2));
-
- one(dataSetDAO).listDataSets(e2);
- ExternalDataPE ds2 = new ExternalDataPE();
- ds2.setCode("ds2");
- will(returnValue(Arrays.asList(ds2)));
- }
- });
- prepareProcessDataSets(testSession, new HashMap<String, String>(), "ds1", "ds2");
-
- service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
- new long[] { e1.getId(), e2.getId() });
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessSearchDataFilteredByValidator()
- {
- Session testSession = createSessionAndPrepareGetSession(GROUP_CODE + 2);
- final ExperimentPE e1 = experiment(1);
- final ExperimentPE e2 = experiment(2, "a");
-
- context.checking(new Expectations()
- {
- {
- allowing(daoFactory).getAuthorizationConfig();
- will(returnValue(new TestAuthorizationConfig(false, false)));
-
- one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
- will(returnValue(e1));
-
- one(experimentDAO).tryGetByTechId(new TechId(e2.getId()));
- will(returnValue(e2));
- }
- });
- prepareProcessDataSets(testSession, new HashMap<String, String>());
-
- service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
- new long[] { e1.getId(), e2.getId() });
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessSearchDataFilteredByIds()
- {
- Session testSession = createSessionAndPrepareGetSession(GROUP_CODE);
- final ExperimentPE e1 = experiment(1);
- context.checking(new Expectations()
- {
- {
- one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
- will(returnValue(e1));
-
- one(dataSetDAO).listDataSets(e1);
- ExternalDataPE ds1 = new ExternalDataPE();
- ds1.setCode("ds1");
- will(returnValue(Arrays.asList(ds1)));
- }
- });
- prepareProcessDataSets(testSession, new HashMap<String, String>(), "ds1");
-
- service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
- new long[] { e1.getId() });
-
- context.assertIsSatisfied();
- }
-
- private Session createSessionAndPrepareGetSession(String spaceCode)
- {
- final Session testSession =
- new Session(CommonTestUtils.USER_ID, SESSION_TOKEN, PRINCIPAL, "remote-host", 1);
- PersonPE person = new PersonPE();
- RoleAssignmentPE roleAssignmentPE = new RoleAssignmentPE();
- SpacePE group = new SpacePE();
- group.setCode(spaceCode);
- roleAssignmentPE.setRole(RoleCode.ADMIN);
- roleAssignmentPE.setSpace(group);
- person.setRoleAssignments(new HashSet<RoleAssignmentPE>(Arrays.asList(roleAssignmentPE)));
- testSession.setPerson(person);
- context.checking(new Expectations()
- {
- {
- allowing(sessionManager).getSession(SESSION_TOKEN);
- will(returnValue(testSession));
- }
- });
- return testSession;
- }
-
- private void prepareListExperiments(final ExperimentPE... experiments)
- {
- context.checking(new Expectations()
- {
- {
- one(daoFactory).getEntityTypeDAO(EntityKind.EXPERIMENT);
- will(returnValue(entityTypeDAO));
-
- one(entityTypeDAO).tryToFindEntityTypeByCode(EXPERIMENT_TYPE);
- will(returnValue(experimentType));
-
- one(experimentDAO).listExperimentsWithProperties(experimentType, null, null);
- will(returnValue(Arrays.asList(experiments)));
-
- one(metaprojectDAO).listMetaprojectAssignmentsForEntities(
- session.tryGetPerson(), Arrays.asList(experiments),
- EntityKind.EXPERIMENT);
- }
- });
- }
-
- private void prepareProcessDataSets(final Session testSession,
- final Map<String, String> parameterBindings, final String... dataSetCodes)
- {
- context.checking(new Expectations()
- {
- {
- one(dataStoreDAO).listDataStores();
- DataStorePE s1 =
- store("s1", service("a", PROCESSING),
- service(COPY_PROCESSING_KEY, QUERIES));
- DataStorePE s2 = store("s2", service(COPY_PROCESSING_KEY, PROCESSING));
- will(returnValue(Arrays.asList(s1, s2)));
-
- one(commonBoFactory).createDataSetTable(testSession);
- will(returnValue(dataSetTable));
-
- one(dataSetTable).processDatasets(COPY_PROCESSING_KEY, "s2",
- Arrays.asList(dataSetCodes), parameterBindings);
- }
-
- });
- }
-
- private void prepareListRawDataSamples(final Long... sampleIDs)
- {
- final List<Sample> samples = new ArrayList<Sample>();
- final LinkedHashSet<Long> experimentIds = new LinkedHashSet<Long>();
- final List<ExperimentPE> bioExperiments = new ArrayList<ExperimentPE>();
- for (Long id : sampleIDs)
- {
- Sample sample = new Sample();
- sample.setId(id);
- sample.setCode("s-" + id);
- sample.setIdentifier("S" + id);
- Experiment experiment = new Experiment();
- experiment.setId(id * 10);
- sample.setExperiment(experiment);
- Sample parent = new Sample();
- parent.setId(id * 100);
- Space space = new Space();
- space.setCode("Space-" + id % 2);
- parent.setSpace(space);
- Experiment parentExperiment = new Experiment();
- parentExperiment.setId(id * 20);
- parent.setExperiment(parentExperiment);
- sample.setGeneratedFrom(parent);
- samples.add(sample);
- if (id % 2 == 0)
- {
- ExperimentPE bioExperiment =
- createExperiment("e-type", "exp-" + id, space.getCode());
- bioExperiment.setId(parentExperiment.getId());
- bioExperiments.add(bioExperiment);
- experimentIds.add(bioExperiment.getId());
- }
- }
- context.checking(new Expectations()
- {
- {
- one(boFactory).createSampleLoader(session);
- will(returnValue(sampleLoader));
-
- one(sampleLoader).listSamplesWithParentsByTypeAndSpace(
- CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE,
- CommonConstants.MS_DATA_SPACE);
- will(returnValue(samples));
-
- one(experimentDAO).listExperimentsWithProperties(experimentIds);
- will(returnValue(bioExperiments));
-
- List<Sample> filteredSamples = new ArrayList<Sample>();
- Map<Sample, List<PhysicalDataSet>> dataSetsBySamples =
- new HashMap<Sample, List<PhysicalDataSet>>();
- for (Sample sample : samples)
- {
- if ("Space-0".equals(sample.getGeneratedFrom().getSpace().getCode()))
- {
- Long id = sample.getId();
- String dataSetType = "dt-" + id % 2;
- long ds1Id = id * 1000;
- PhysicalDataSet ds1 =
- new DataSetBuilder(ds1Id).code("ds-" + id)
- .registrationDate(new Date(ds1Id)).sample(sample)
- .type(dataSetType).getDataSet();
-
- long ds2Id = (id + 1) * 1001;
- PhysicalDataSet ds2 =
- new DataSetBuilder(ds2Id).code("ds-" + id + 1)
- .registrationDate(new Date(ds2Id)).sample(sample)
- .type(dataSetType).getDataSet();
-
- long ds2ChildId = ds2.getId() + 1;
- PhysicalDataSet ds2Child =
- new DataSetBuilder(ds2ChildId).code(ds2.getCode() + "-child")
- .registrationDate(new Date(ds2ChildId)).sample(sample)
- .type(dataSetType).getDataSet();
-
- ds2.setChildren(Arrays.<AbstractExternalData> asList(ds2Child));
- dataSetsBySamples.put(sample, Arrays.asList(ds1, ds2));
-
- filteredSamples.add(sample);
- }
- }
-
- one(commonBoFactory).createDatasetLister(session);
- will(returnValue(datasetLister));
-
- one(datasetLister).listAllDataSetsFor(filteredSamples);
- will(returnValue(dataSetsBySamples));
-
- }
- });
- }
-
- private ExperimentPE experiment(long id, String... properties)
- {
- ExperimentPE experiment = new ExperimentPE();
- experiment.setExperimentType(experimentType);
- experiment.setId(id);
- experiment.setCode("e" + id);
- ProjectPE project = new ProjectPE();
- project.setCode("p");
- SpacePE group =
- CommonTestUtils.createSpace(GROUP_CODE);
- project.setSpace(group);
- experiment.setProject(project);
- experiment.setRegistrationDate(new Date(id * id));
- if (properties.length > 0)
- {
- LinkedHashSet<EntityPropertyPE> props = new LinkedHashSet<EntityPropertyPE>();
- for (String property : properties)
- {
- props.add(CommonTestUtils.createExperimentPropertyPE(property, EXPERIMENT_TYPE,
- DataTypeCode.VARCHAR, property + "-value"));
- }
- experiment.setProperties(props);
- }
- return experiment;
- }
-
- private DataStorePE store(String code, DataStoreServicePE... services)
- {
- DataStorePE store = new DataStorePE();
- store.setCode(code);
- store.setServices(new LinkedHashSet<DataStoreServicePE>(Arrays.asList(services)));
- return store;
- }
-
- private DataStoreServicePE service(String key, DataStoreServiceKind kind)
- {
- DataStoreServicePE dataStoreService = new DataStoreServicePE();
- dataStoreService.setKey(key);
- dataStoreService.setKind(kind);
- return dataStoreService;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ServerInterfaceRegressionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ServerInterfaceRegressionTest.java
deleted file mode 100644
index e00a088a3c2..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ServerInterfaceRegressionTest.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.server.util.AnnotationAppliedTestCase;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ServerInterfaceRegressionTest extends AnnotationAppliedTestCase
-{
- @Test
- public void testServerAnnotations()
- {
- assertMandatoryMethodAnnotations(IPhosphoNetXServer.class, PhosphoNetXServer.class, null);
- }
-
- @Test
- public void testDataServiceInternalAnnotations()
- {
- assertMandatoryMethodAnnotations(IProteomicsDataServiceInternal.class,
- ProteomicsDataServiceInternal.class, null);
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceTest.java
deleted file mode 100644
index 6d981e82a83..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ProteomicsDataServiceTest.java
+++ /dev/null
@@ -1,426 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.PropertyKey;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteomicsDataServiceTest extends AbstractServerTestCase
-{
- private static final String MS_SEARCH = "MS_SEARCH";
-
- private static final String RAW_DATA = "RAW_DATA";
-
- private static final String MZXML_DATA = "MZXML_DATA";
-
- private IProteomicsDataServiceInternal internalService;
-
- private IProteomicsDataService service;
-
- private SessionContextDTO session2;
-
- @Override
- @BeforeMethod
- public final void setUp()
- {
- super.setUp();
- internalService = context.mock(IProteomicsDataServiceInternal.class);
- service =
- new ProteomicsDataService(sessionManager, daoFactory, propertiesBatchManager,
- internalService);
- session2 = new SessionContextDTO();
- session2.setSessionToken(SESSION_TOKEN + "2");
- }
-
- @Test
- public void testListDataStoreServerProcessingPluginInfos()
- {
- prepareGetSession();
- DataStoreServicePE s1 = new DataStoreServicePE();
- s1.setKind(DataStoreServiceKind.QUERIES);
- DataStoreServicePE s2 = new DataStoreServicePE();
- s2.setKind(DataStoreServiceKind.PROCESSING);
- s2.setKey("my-key");
- s2.setLabel("my label");
- DataSetTypePE dataSetType = new DataSetTypePE();
- dataSetType.setCode("my type");
- s2.setDatasetTypes(Collections.singleton(dataSetType));
- final DataStorePE store = new DataStorePE();
- store.setServices(new HashSet<DataStoreServicePE>(Arrays.asList(s1, s2)));
- context.checking(new Expectations()
- {
- {
- one(dataStoreDAO).listDataStores();
- will(returnValue(Arrays.asList(store)));
- }
- });
-
- List<DataStoreServerProcessingPluginInfo> infos =
- service.listDataStoreServerProcessingPluginInfos(SESSION_TOKEN);
-
- assertEquals(s2.getKey(), infos.get(0).getKey());
- assertEquals(s2.getLabel(), infos.get(0).getLabel());
- assertEquals(Arrays.asList(dataSetType.getCode()), infos.get(0).getDatasetTypeCodes());
- assertEquals(1, infos.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUnknownUser()
- {
- prepareGetSession();
- prepareLoginLogout(null);
-
- try
- {
- service.listRawDataSamples(SESSION_TOKEN, "abc");
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Unknown user ID: abc", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamples()
- {
- prepareGetSession();
- prepareLoginLogout(session2);
- final Sample sample = new Sample();
- sample.setId(4711L);
- sample.setCode("ms-inj-42");
- sample.setRegistrationDate(new Date(4711));
- IEntityProperty p1 = property("integer", DataTypeCode.INTEGER, "123456");
- IEntityProperty p2 = property("real", DataTypeCode.REAL, "1.25");
- IEntityProperty p3 = property("string", DataTypeCode.VARCHAR, "hello");
- sample.setProperties(Arrays.asList(p1, p2, p3));
- Sample parent = new Sample();
- parent.setId(4710L);
- parent.setIdentifier("parent");
- IEntityProperty p4 = property("boolean", DataTypeCode.BOOLEAN, "true");
- IEntityProperty p5 = property("link", DataTypeCode.HYPERLINK, "link");
- parent.setProperties(Arrays.asList(p4, p5));
- Experiment experiment = new Experiment();
- experiment.setId(4747L);
- experiment.setCode("exp1");
- Project project = new Project();
- project.setCode("project1");
- Space space = new Space();
- space.setCode("space1");
- project.setSpace(space);
- experiment.setProject(project);
- experiment.setRegistrationDate(new Date(1234567));
- IEntityProperty p6 = property("ex", DataTypeCode.VARCHAR, "exp");
- experiment.setProperties(Arrays.<IEntityProperty> asList(p6));
- parent.setExperiment(experiment);
- sample.setGeneratedFrom(parent);
- final AbstractExternalData ds1 = createDataSet(RAW_DATA, 10);
- final AbstractExternalData ds2 = createDataSet(MZXML_DATA, 20);
- AbstractExternalData ds3 = createDataSet(MZXML_DATA, 15);
- AbstractExternalData ds4 = createDataSet(RAW_DATA, 30);
- ds2.setChildren(Arrays.asList(ds3));
- ds3.setChildren(Arrays.asList(ds4));
- context.checking(new Expectations()
- {
- {
- one(internalService).listRawDataSamples(session2.getSessionToken());
- MsInjectionSample msInjectionSample = new MsInjectionSample(sample, Arrays.asList(ds1, ds2));
- will(returnValue(Arrays.asList(msInjectionSample)));
- }
- });
-
- List<MsInjectionDataInfo> infos = service.listRawDataSamples(SESSION_TOKEN, "abc");
-
- MsInjectionDataInfo info = infos.get(0);
- assertEquals(sample.getId().longValue(), info.getMsInjectionSampleID());
- assertEquals(sample.getCode(), info.getMsInjectionSampleCode());
- assertEquals(sample.getRegistrationDate(), info.getMsInjectionSampleRegistrationDate());
- checkProperties(info.getMsInjectionSampleProperties(), p1, p2, p3);
- assertEquals(parent.getId().longValue(), info.getBiologicalSampleID());
- assertEquals(parent.getIdentifier(), info.getBiologicalSampleIdentifier());
- checkProperties(info.getBiologicalSampleProperties(), p4, p5);
- assertEquals("4747:space1/project1/exp1 date:1234567 {ex[EX]=exp}",
- renderExperiment(info.getBiologicalExperiment()));
- checkProperties(info.getBiologicalExperiment().getProperties(), p6);
- List<DataSet> dataSets = new ArrayList<DataSet>(info.getDataSets());
- Collections.sort(dataSets, new Comparator<DataSet>()
- {
- @Override
- public int compare(DataSet d1, DataSet d2)
- {
- return d1.getCode().compareTo(d2.getCode());
- }
- });
- assertEquals("20:MZXML_DATA-20 [MZXML_DATA date:20] {n[N]=2.5}, children:15",
- renderDataSet(dataSets.get(0)));
- assertEquals("10:RAW_DATA-10 [RAW_DATA date:10] {n[N]=2.5}", renderDataSet(dataSets.get(1)));
- assertEquals("15:MZXML_DATA-15 [MZXML_DATA date:15] {n[N]=2.5}, parent:20 , children:30",
- renderDataSet(dataSets.get(0).getChildren().iterator().next()));
- assertEquals("30:RAW_DATA-30 [RAW_DATA date:30] {n[N]=2.5}, parent:15",
- renderDataSet(dataSets.get(0).getChildren().iterator().next().getChildren()
- .iterator().next()));
- assertEquals(2, dataSets.size());
- Map<String, Date> dates = info.getLatestDataSetRegistrationDates();
- assertEquals(30, dates.get(RAW_DATA).getTime());
- assertEquals(20, dates.get(MZXML_DATA).getTime());
- assertEquals(2, dates.size());
- assertEquals(1, infos.size());
- context.assertIsSatisfied();
- }
-
- private String renderExperiment(ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment experiment)
- {
- StringBuilder builder = new StringBuilder();
- builder.append(experiment.getId()).append(":").append(experiment.getSpaceCode());
- builder.append('/').append(experiment.getProjectCode());
- builder.append('/').append(experiment.getCode());
- builder.append(" date:").append(experiment.getRegistrationDate().getTime());
- builder.append(' ').append(experiment.getProperties());
- return builder.toString();
- }
-
- private String renderDataSet(DataSet dataSet)
- {
- StringBuilder builder = new StringBuilder();
- builder.append(dataSet.getId()).append(":").append(dataSet.getCode());
- builder.append(" [").append(dataSet.getType()).append(" date:");
- builder.append(dataSet.getRegistrationDate().getTime()).append("] ");
- builder.append(dataSet.getProperties());
- Set<DataSet> parents = dataSet.getParents();
- if (parents != null && parents.isEmpty() == false)
- {
- builder.append(", parent:");
- for (DataSet parent : parents)
- {
- builder.append(parent.getId()).append(' ');
- }
- }
- Set<DataSet> children = dataSet.getChildren();
- if (children != null && children.isEmpty() == false)
- {
- builder.append(", children:");
- for (DataSet child : children)
- {
- builder.append(child.getId()).append(' ');
- }
- }
- return builder.toString().trim();
- }
-
- @Test
- public void testProcessDataSetsForUnknownUser()
- {
- prepareGetSession();
- prepareLoginLogout(null);
-
- try
- {
- service.processDataSets(SESSION_TOKEN, "abc", null, Arrays.asList("ds1"));
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Unknown user ID: abc", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessDataSets()
- {
- prepareGetSession();
- prepareLoginLogout(session2);
- context.checking(new Expectations()
- {
- {
- one(internalService).processDataSets(session2.getSessionToken(), "dsp1", Arrays.asList("ds1"));
- }
- });
-
- service.processDataSets(SESSION_TOKEN, "abc", "dsp1", Arrays.asList("ds1"));
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListExperiments()
- {
- prepareGetSession();
- prepareLoginLogout(session2);
- final Experiment e = new Experiment();
- e.setId(42L);
- e.setCode("E42");
- Project project = new Project();
- project.setCode("p");
- Space space = new Space();
- space.setCode("s");
- project.setSpace(space);
- e.setProject(project);
- e.setRegistrationDate(new Date(4711));
- EntityProperty p1 = new EntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode("ANSWER");
- propertyType.setLabel("answer");
- propertyType.setDataType(new DataType(DataTypeCode.INTEGER));
- p1.setPropertyType(propertyType);
- p1.setValue("42");
- e.setProperties(Arrays.<IEntityProperty> asList(p1));
- context.checking(new Expectations()
- {
- {
- one(internalService).listExperiments(session2.getSessionToken(), MS_SEARCH);
- will(returnValue(Arrays.asList(e)));
- }
- });
-
- List<ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.Experiment> experiments =
- service.listExperiments(SESSION_TOKEN, "abc", MS_SEARCH);
-
- assertEquals(e.getId().longValue(), experiments.get(0).getId());
- assertEquals(e.getCode(), experiments.get(0).getCode());
- assertEquals(e.getProject().getCode(), experiments.get(0).getProjectCode());
- assertEquals(e.getProject().getSpace().getCode(), experiments.get(0).getSpaceCode());
- assertEquals(e.getRegistrationDate(), experiments.get(0).getRegistrationDate());
- Map<PropertyKey, Serializable> properties = experiments.get(0).getProperties();
- Set<Entry<PropertyKey, Serializable>> entrySet = properties.entrySet();
- List<Entry<PropertyKey, Serializable>> list = new ArrayList<Entry<PropertyKey, Serializable>>(entrySet);
- assertEquals(e.getProperties().get(0).getPropertyType().getCode(), list.get(0).getKey().getId());
- assertEquals(e.getProperties().get(0).getPropertyType().getLabel(), list.get(0).getKey().getLabel());
- Serializable value = list.get(0).getValue();
- assertEquals(Long.class, value.getClass());
- assertEquals(e.getProperties().get(0).getValue(), value.toString());
- assertEquals(1, properties.size());
- assertEquals(1, experiments.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testProcessSearchData()
- {
- prepareGetSession();
- prepareLoginLogout(session2);
- final long[] ids = new long[] { 42 };
- context.checking(new Expectations()
- {
- {
- one(internalService).processProteinResultDataSets(session2.getSessionToken(),
- "dsp1", MS_SEARCH, ids);
- }
- });
-
- service.processProteinResultDataSets(SESSION_TOKEN, "abc", "dsp1", MS_SEARCH, ids);
-
- context.assertIsSatisfied();
- }
-
- private void prepareLoginLogout(final SessionContextDTO mySession)
- {
- context.checking(new Expectations()
- {
- {
- one(internalService).tryAuthenticate("abc", "dummy-password");
- will(returnValue(mySession));
-
- if (mySession != null)
- {
- one(internalService).logout(mySession.getSessionToken());
- }
- }
- });
- }
-
- private void checkProperties(Map<PropertyKey, Serializable> properties, IEntityProperty... expectedProperties)
- {
- for (IEntityProperty expectedProperty : expectedProperties)
- {
- PropertyType propertyType = expectedProperty.getPropertyType();
- PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
- Serializable v = properties.get(key);
- assertNotNull("Missing property: " + key, v);
- assertEquals("Property " + propertyType, expectedProperty.tryGetAsString(), String.valueOf(v));
- }
- assertEquals(expectedProperties.length, properties.size());
- }
-
- private IEntityProperty property(String code, DataTypeCode dataTypeCode, String value)
- {
- EntityProperty property = new EntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(code.toUpperCase());
- propertyType.setLabel(code);
- propertyType.setDataType(new DataType(dataTypeCode));
- property.setPropertyType(propertyType);
- property.setValue(value);
- return property;
- }
-
- private AbstractExternalData createDataSet(String type, long date)
- {
- AbstractExternalData dataSet = new ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet();
- dataSet.setId(date);
- dataSet.setCode(type + "-" + date);
- dataSet.setDataSetType(new DataSetType(type));
- dataSet.setRegistrationDate(new Date(date));
- dataSet.setDataSetProperties(Arrays.asList(property("n", DataTypeCode.REAL, "2.5")));
- return dataSet;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ServerInterfaceRegressionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ServerInterfaceRegressionTest.java
deleted file mode 100644
index 78a756dd9d2..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/api/v1/ServerInterfaceRegressionTest.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.server.util.AnnotationAppliedTestCase;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ServerInterfaceRegressionTest extends AnnotationAppliedTestCase
-{
- @Test
- public void testServerAnnotations()
- {
- assertMandatoryMethodAnnotations(IProteomicsDataService.class, ProteomicsDataService.class,
- "logout: RolesAllowed\n" + "tryToAuthenticateAtRawDataServer: RolesAllowed\n", null);
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidatorTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidatorTest.java
deleted file mode 100644
index 1252d2eb5b7..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/authorization/validator/RawDataSampleValidatorTest.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator;
-
-import java.util.Arrays;
-import java.util.LinkedHashSet;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationDataProvider;
-import ch.systemsx.cisd.openbis.generic.server.authorization.TestAuthorizationConfig;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class RawDataSampleValidatorTest extends AssertJUnit
-{
-
- private static final MsInjectionSample NO_PARENT = create("no-parent", null);
-
- private static final MsInjectionSample WITH_INSTANCE_PARENT = create("with-instance-parent", "/parent");
-
- private static final MsInjectionSample WITH_PARENT_IN_G1 = create("with-parent-in-g1", "/g1/parent");
-
- private static final MsInjectionSample WITH_PARENT_IN_G2 = create("with-parent-in-g2", "/g2/parent");
-
- private Mockery context;
-
- private RawDataSampleValidator validator;
-
- private IDAOFactory daoFactory;
-
- @BeforeMethod
- protected void beforeMethod()
- {
- context = new Mockery();
- daoFactory = context.mock(IDAOFactory.class);
- validator = new RawDataSampleValidator();
- validator.init(new AuthorizationDataProvider(daoFactory));
- }
-
- @AfterMethod
- protected void afterMethod()
- {
- context.assertIsSatisfied();
- }
-
- private static MsInjectionSample create(String sampleCode, String parentSampleIdentifierOrNull)
- {
- Sample sample = new Sample();
- sample.setCode(sampleCode);
- if (parentSampleIdentifierOrNull != null)
- {
- Sample parent = new Sample();
- parent.setIdentifier(parentSampleIdentifierOrNull);
- SampleIdentifier identifier =
- SampleIdentifierFactory.parse(parentSampleIdentifierOrNull);
- parent.setCode(identifier.getSampleCode());
- SpaceIdentifier spaceLevel = identifier.getSpaceLevel();
- if (spaceLevel != null)
- {
- Space space = new Space();
- space.setCode(spaceLevel.getSpaceCode());
- parent.setSpace(space);
- }
- sample.setGeneratedFrom(parent);
- }
- return new MsInjectionSample(sample, Arrays.<AbstractExternalData> asList());
- }
-
- @Test
- public void testUserWithNoRights()
- {
- context.checking(new Expectations()
- {
- {
- allowing(daoFactory).getAuthorizationConfig();
- will(returnValue(new TestAuthorizationConfig(false, false)));
- }
- });
-
- PersonPE person = createPersonWithRoles();
-
- assertEquals(false, validator.isValid(person, NO_PARENT));
- assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
- assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G1));
- assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
- }
-
- @Test
- public void testUserWithRightsForGroupG1()
- {
- context.checking(new Expectations()
- {
- {
- allowing(daoFactory).getAuthorizationConfig();
- will(returnValue(new TestAuthorizationConfig(false, false)));
- }
- });
-
- PersonPE person = createPersonWithRoles(createRole("G1"));
-
- assertEquals(false, validator.isValid(person, NO_PARENT));
- assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
- assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
- assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
- }
-
- @Test
- public void testUserWithRightsForGroupG1AndG2()
- {
- PersonPE person = createPersonWithRoles(createRole("G1"), createRole("G2"));
-
- assertEquals(false, validator.isValid(person, NO_PARENT));
- assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
- assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
- assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G2));
- }
-
- @Test
- public void testUserWithRightsForForInstanceT()
- {
- PersonPE person = createPersonWithRoles(createRole(null));
-
- assertEquals(false, validator.isValid(person, NO_PARENT));
- assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
- assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
- assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G2));
- }
-
- private PersonPE createPersonWithRoles(RoleAssignmentPE... roles)
- {
- PersonPE person = new PersonPE();
- person.setRoleAssignments(new LinkedHashSet<RoleAssignmentPE>(Arrays.asList(roles)));
- return person;
- }
-
- private RoleAssignmentPE createRole(String groupCodeOrNull)
- {
- RoleAssignmentPE role = new RoleAssignmentPE();
- role.setRole(RoleCode.ADMIN);
-
- if (groupCodeOrNull != null)
- {
- SpacePE group = new SpacePE();
- group.setCode(groupCodeOrNull);
- role.setSpace(group);
- }
- return role;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java
deleted file mode 100644
index df0bba52ee2..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import org.testng.annotations.BeforeMethod;
-
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractBOTestCase extends AbstractServerTestCase
-{
- protected IPhosphoNetXDAOFactory specificDAOFactory;
-
- protected IProteinQueryDAO proteinDAO;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
- proteinDAO = context.mock(IProteinQueryDAO.class);
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractLoaderTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractLoaderTestCase.java
deleted file mode 100644
index b8ea7079891..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractLoaderTestCase.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.authentication.Principal;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOWithoutContextTest;
-import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-
-/**
- * @author Franz-Josef Elmer
- */
-@ContextConfiguration(locations = "classpath:proteomics-applicationContext.xml")
-// In 'commonContext.xml', our transaction manager is called 'transaction-manager' (by default
-// Spring looks for 'transactionManager').
-@Transactional(transactionManager = "transaction-manager")
-@Rollback
-public abstract class AbstractLoaderTestCase extends AbstractDAOWithoutContextTest
-{
- private static final Principal PRINCIPAL = new Principal(CommonTestUtils.USER_ID, "john",
- "doe", "j@d");
-
- private static final String SESSION_TOKEN = "session-token";
-
- protected ICommonBusinessObjectFactory boFactory;
-
- @Autowired
- public final void setBoFactory(final ICommonBusinessObjectFactory boFactory)
- {
- this.boFactory = boFactory;
- }
-
- protected Session session()
- {
- return new Session(CommonTestUtils.USER_ID, SESSION_TOKEN,
- PRINCIPAL, "remote-host", 1);
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTableTest.java
deleted file mode 100644
index eb09955054b..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceColumnDefinitionTableTest.java
+++ /dev/null
@@ -1,169 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.server.business.TreatmentFinder.TREATMENT_TYPE_CODE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.server.business.TreatmentFinder.TREATMENT_VALUE_CODE;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.AbundanceColumnDefinitionTable;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AbundanceColumnDefinitionTableTest extends AbstractServerTestCase
-{
- private IPhosphoNetXDAOFactory phosphoNetXDAOFactory;
-
- private AbundanceColumnDefinitionTable table;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- phosphoNetXDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
- table = new AbundanceColumnDefinitionTable(daoFactory, phosphoNetXDAOFactory, session);
- }
-
- @Test
- public void testNoAbundanceColumns()
- {
- List<AbundanceColumnDefinition> definitions = table.getSortedAndAggregatedDefinitions(null);
-
- assertEquals(0, definitions.size());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testOneAbundanceColumnWithoutTreatment()
- {
- Sample s1 = createSample(42);
-
- table.add(s1);
- List<AbundanceColumnDefinition> definitions = table.getSortedAndAggregatedDefinitions(null);
-
- assertEquals(1, definitions.size());
- assertEquals(42l, definitions.get(0).getID());
- assertEquals("code-42", definitions.get(0).getSampleCode());
- assertEquals(0, definitions.get(0).getTreatments().size());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testOneAbundanceColumnWithOneTreatment()
- {
- Sample s1 = createSample(42);
- addTreatment(s1, "", "abc");
-
- table.add(s1);
- List<AbundanceColumnDefinition> definitions = table.getSortedAndAggregatedDefinitions(null);
-
- assertEquals(1, definitions.size());
- assertEquals(42l, definitions.get(0).getID());
- assertEquals("code-42", definitions.get(0).getSampleCode());
- assertEquals(1, definitions.get(0).getTreatments().size());
- assertEquals("pH", definitions.get(0).getTreatments().get(0).getType());
- assertEquals("PH", definitions.get(0).getTreatments().get(0).getTypeCode());
- assertEquals("abc", definitions.get(0).getTreatments().get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAbundanceColumnsForTwoSamplesWithSameParent()
- {
- Sample s1 = createSample(42);
- Sample s2 = createSample(43);
- Sample parent = createSample(4711);
- s1.setGeneratedFrom(parent);
- s2.setGeneratedFrom(parent);
- addTreatment(parent, "", "abc");
-
- table.add(s1);
- table.add(s2);
- List<AbundanceColumnDefinition> definitions = table.getSortedAndAggregatedDefinitions(null);
-
- assertEquals(1, definitions.size());
- assertEquals(4711l, definitions.get(0).getID());
- assertEquals("code-4711", definitions.get(0).getSampleCode());
- assertEquals(1, definitions.get(0).getTreatments().size());
- assertEquals("pH", definitions.get(0).getTreatments().get(0).getType());
- assertEquals("PH", definitions.get(0).getTreatments().get(0).getTypeCode());
- assertEquals("abc", definitions.get(0).getTreatments().get(0).getValue());
-
- context.assertIsSatisfied();
- }
-
- private Sample createSample(long sampleID)
- {
- Sample sample = new Sample();
- sample.setId(sampleID);
- sample.setCode("code-" + sampleID);
- sample.setPermId("abc-" + sampleID);
- sample.setProperties(Collections.<IEntityProperty> emptyList());
- return sample;
- }
-
- private void addTreatment(Sample sample, String type, String value)
- {
- List<IEntityProperty> properties = new ArrayList<IEntityProperty>();
- EntityProperty sampleProperty = new EntityProperty();
- sampleProperty.setPropertyType(createPropertyType(TREATMENT_TYPE_CODE + type));
- VocabularyTerm term = new VocabularyTerm();
- term.setCode("PH");
- term.setLabel("pH");
- sampleProperty.setVocabularyTerm(term);
- properties.add(sampleProperty);
-
- sampleProperty = new EntityProperty();
- sampleProperty.setPropertyType(createPropertyType(TREATMENT_VALUE_CODE + type));
- sampleProperty.setValue(value);
- properties.add(sampleProperty);
-
- sample.setProperties(properties);
- }
-
- private PropertyType createPropertyType(String code)
- {
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(code);
- DataType dataType = new DataType();
- dataType.setCode(DataTypeCode.VARCHAR);
- propertyType.setDataType(dataType);
- return propertyType;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManagerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManagerTest.java
deleted file mode 100644
index 34fe966b910..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbundanceManagerTest.java
+++ /dev/null
@@ -1,170 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Iterator;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.AbundanceManager;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinWithAbundances;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AbundanceManagerTest extends AbstractServerTestCase
-{
- private static final String PERM_ID1 = "s101";
-
- private static final String PERM_ID2 = "s102";
-
- private static final long SAMPLE_ID_A = 42;
-
- private static final long SAMPLE_ID_B = 4711;
-
- private AbundanceManager abundanceManager;
-
- private ISampleProvider sampleProvider;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
-
- sampleProvider = context.mock(ISampleProvider.class);
- abundanceManager = new AbundanceManager(sampleProvider);
- }
-
- @Test
- public void testNoProteinReferenceHandled()
- {
- assertEquals(0, abundanceManager.getSampleIDs().size());
- assertEquals(0, abundanceManager.getProteinsWithAbundances().size());
- }
-
- @Test
- public void testHandleTwoProteinReferencesButOnlyOneHasAnAbundance()
- {
- prepareSampleIDProvider();
- ProteinReferenceWithProtein protein1 = new ProteinReferenceWithProtein();
- protein1.setId(1);
- protein1.setAccessionNumber("abc1");
- protein1.setDescription("abc one");
- ProteinAbundance proteinAbundance = new ProteinAbundance();
- proteinAbundance.setSampleID(PERM_ID1);
- proteinAbundance.setAbundance(1.5);
- abundanceManager.handle(protein1, Collections.singletonList(proteinAbundance));
- ProteinReferenceWithProtein protein2 = new ProteinReferenceWithProtein();
- protein2.setId(2);
- protein2.setAccessionNumber("abc2");
- protein2.setDescription("abc two");
- abundanceManager.handle(protein2, null);
-
- assertEquals(1, abundanceManager.getSampleIDs().size());
- Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
- assertEquals(2, proteinsWithAbundances.size());
- Iterator<ProteinWithAbundances> iterator = proteinsWithAbundances.iterator();
- ProteinWithAbundances p1 = iterator.next();
- assertEquals(1, p1.getId());
- assertEquals("abc one", p1.getDescription());
- assertEquals("abc1", p1.getAccessionNumber());
- assertEquals(1, p1.getSampleIDs().size());
- assertEquals(SAMPLE_ID_A, p1.getSampleIDs().iterator().next().longValue());
- assertEquals(0, p1.getAbundancesForSample(12345678).length);
- assertEquals(1, p1.getAbundancesForSample(SAMPLE_ID_A).length);
- assertEquals(1.5, p1.getAbundancesForSample(SAMPLE_ID_A)[0]);
- ProteinWithAbundances p2 = iterator.next();
- assertEquals(2, p2.getId());
- assertEquals("abc two", p2.getDescription());
- assertEquals("abc2", p2.getAccessionNumber());
- assertEquals(0, p2.getSampleIDs().size());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testHandleProteinReferencesWithManyAbundancesForTwoSamples()
- {
- prepareSampleIDProvider();
- ProteinReferenceWithProtein protein1 = new ProteinReferenceWithProtein();
- protein1.setId(1);
- protein1.setAccessionNumber("abc1");
- protein1.setDescription("abc one");
-
- abundanceManager.handle(protein1, Arrays.asList(a(PERM_ID1, 1.5), a(PERM_ID1, 2.25), a(
- PERM_ID2, 42), a(PERM_ID2, 4.75), a(PERM_ID2, 7.5)));
-
- assertEquals(2, abundanceManager.getSampleIDs().size());
- Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
- assertEquals(1, proteinsWithAbundances.size());
- ProteinWithAbundances protein = proteinsWithAbundances.iterator().next();
- assertEquals(1, protein.getId());
- assertEquals("abc one", protein.getDescription());
- assertEquals("abc1", protein.getAccessionNumber());
- assertEquals(2, protein.getSampleIDs().size());
- Iterator<Long> iterator = protein.getSampleIDs().iterator();
- assertEquals(SAMPLE_ID_A, iterator.next().longValue());
- assertEquals(SAMPLE_ID_B, iterator.next().longValue());
- assertEquals(2, protein.getAbundancesForSample(SAMPLE_ID_A).length);
- assertEquals(1.5, protein.getAbundancesForSample(SAMPLE_ID_A)[0]);
- assertEquals(2.25, protein.getAbundancesForSample(SAMPLE_ID_A)[1]);
- assertEquals(3, protein.getAbundancesForSample(SAMPLE_ID_B).length);
- assertEquals(42.0, protein.getAbundancesForSample(SAMPLE_ID_B)[0]);
- assertEquals(4.75, protein.getAbundancesForSample(SAMPLE_ID_B)[1]);
- assertEquals(7.5, protein.getAbundancesForSample(SAMPLE_ID_B)[2]);
-
- context.assertIsSatisfied();
- }
-
- private void prepareSampleIDProvider()
- {
- context.checking(new Expectations()
- {
- {
- allowing(sampleProvider).getSample(PERM_ID1);
- Sample s1 = new Sample();
- s1.setId(SAMPLE_ID_A);
- will(returnValue(s1));
- allowing(sampleProvider).getSample(PERM_ID2);
- Sample s2 = new Sample();
- Sample parent = new Sample();
- parent.setId(SAMPLE_ID_B);
- s2.setGeneratedFrom(parent);
- will(returnValue(s2));
- }
- });
- }
-
- private ProteinAbundance a(String samplePermID, double abundance)
- {
- ProteinAbundance protein = new ProteinAbundance();
- protein.setSampleID(samplePermID);
- protein.setAbundance(abundance);
- return protein;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilderTest.java
deleted file mode 100644
index 4a881fe08b1..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AccessionNumberBuilderTest.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.AccessionNumberBuilder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AccessionNumberBuilderTest extends AssertJUnit
-{
- @Test
- public void test()
- {
- check(null, "", "");
- check(null, "abc", "abc");
- check(null, "DECOY_abc", "DECOY_abc");
- check("", "abc", "|abc");
- check("", "DECOY_abc", "DECOY_|abc");
- check("", "ab", "|ab|c");
- check("a", "b", "a|b");
- check("a", "DECOY_b", "DECOY_a|b");
- check("a", "DECOY_b", "DECOY_a|DECOY_b");
- check("a", "b", "a|b|c");
- check("a", "DECOY_b", "DECOY_a|b|c");
- check("a", "DECOY_b", "DECOY_a|DECOY_b|c");
- check("a", "", "a||c");
- check("a", "DECOY_", "DECOY_a||c");
- check("", "", "||c");
- check("", "", "||");
- check("", "", "|");
- }
-
- private void check(String expectedType, String expectedAccessionNumber, String fullAccessionNumber)
- {
- AccessionNumberBuilder builder = new AccessionNumberBuilder(fullAccessionNumber);
- assertEquals(expectedType, builder.getTypeOrNull());
- assertEquals(expectedAccessionNumber, builder.getAccessionNumber());
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java
deleted file mode 100644
index 394afd559d3..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ErrorModelTest extends AssertJUnit
-{
- private static final double TOL = 1e-6;
-
- private static final long DATA_SET1_ID = 42;
-
- private static final long DATA_SET2_ID = 43;
-
- private static final long DATA_SET3_ID = 44;
-
- private Mockery context;
-
- private IProteinQueryDAO proteinQueryDAO;
-
- private ErrorModel errorModel;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- proteinQueryDAO = context.mock(IProteinQueryDAO.class);
- errorModel = new ErrorModel(proteinQueryDAO);
- context.checking(new Expectations()
- {
- {
-
- atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET1_ID);
- MockDataSet<ProbabilityFDRMapping> dataSet1 = new MockDataSet<ProbabilityFDRMapping>();
- createEntry(dataSet1, 0.4, 0.9);
- createEntry(dataSet1, 0.5, 0.95);
- will(returnValue(dataSet1));
-
- atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET2_ID);
- MockDataSet<ProbabilityFDRMapping> dataSet2 = new MockDataSet<ProbabilityFDRMapping>();
- createEntry(dataSet2, 1, 1);
- createEntry(dataSet2, 0.4, 0.9);
- createEntry(dataSet2, 0.1, 0.7);
- createEntry(dataSet2, 0.0, 0.6);
- will(returnValue(dataSet2));
-
- atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET3_ID);
- MockDataSet<ProbabilityFDRMapping> dataSet3 = new MockDataSet<ProbabilityFDRMapping>();
- will(returnValue(dataSet3));
- }
- });
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExact()
- {
- IdentifiedProtein protein = create(DATA_SET1_ID, 0.4);
- errorModel.setFalseDiscoveryRateFor(protein);
-
- assertEquals(0.9, protein.getFalseDiscoveryRate(), TOL);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testInterpolation()
- {
- IdentifiedProtein protein = create(DATA_SET1_ID, 0.42);
- errorModel.setFalseDiscoveryRateFor(protein);
-
- assertEquals(0.91, protein.getFalseDiscoveryRate(), TOL);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCachedMapping()
- {
- IdentifiedProtein protein = create(DATA_SET1_ID, 0.42);
- errorModel.setFalseDiscoveryRateFor(protein);
-
- assertEquals(0.91, protein.getFalseDiscoveryRate(), TOL);
-
- protein = create(DATA_SET2_ID, 0.25);
- errorModel.setFalseDiscoveryRateFor(protein);
-
- assertEquals(0.8, protein.getFalseDiscoveryRate(), TOL);
-
- protein = create(DATA_SET1_ID, 0.5);
- errorModel.setFalseDiscoveryRateFor(protein);
-
- assertEquals(0.95, protein.getFalseDiscoveryRate(), TOL);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNoMappings()
- {
- IdentifiedProtein protein = create(DATA_SET3_ID, 0.2);
-
- errorModel.setFalseDiscoveryRateFor(protein);
-
- double falseDiscoveryRate = protein.getFalseDiscoveryRate();
- assertTrue("unexpected FDR: " + falseDiscoveryRate, Double.isNaN(falseDiscoveryRate));
- }
-
- private IdentifiedProtein create(long dataSetID, double probability)
- {
- IdentifiedProtein protein = new IdentifiedProtein();
- protein.setDataSetID(dataSetID);
- protein.setProbability(probability);
- return protein;
- }
-
- private void createEntry(MockDataSet<ProbabilityFDRMapping> dataSet, double propability,
- double falseDiscoveryRate)
- {
- ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
- mapping.setProbability(propability);
- mapping.setFalseDiscoveryRate(falseDiscoveryRate);
- dataSet.add(mapping);
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java
deleted file mode 100644
index 3f7b6ad9887..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.server.TestJythonEvaluatorPool;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.ManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Test(groups = "db")
-public class ExperimentLoaderTest extends AbstractLoaderTestCase
-{
- @Test
- public void test()
- {
- ExperimentLoader loader =
- new ExperimentLoader(daoFactory, new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool()));
- List<Sample> samples = loadSamples(980L, 981L, 986L);
-
- loader.enrichWithExperiments(session(), samples);
-
- StringBuilder builder = new StringBuilder();
- for (Sample sample : samples)
- {
- builder.append(sample.getId()).append(' ').append(sample.getCode());
- Experiment experiment = sample.getExperiment();
- if (experiment != null)
- {
- builder.append(": ").append(experiment.getCode()).append(' ');
- builder.append(getSortedProperties(experiment));
- }
- builder.append('\n');
- }
- assertEquals("980 3V-126\n" + "981 DP\n"
- + "986 3VCP5: EXP10 [DESCRIPTION: A simple experiment, GENDER: MALE]\n",
- builder.toString());
- }
-
- private List<Sample> loadSamples(Long... ids)
- {
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
- List<Sample> list = new ArrayList<Sample>();
- for (Long id : ids)
- {
- list.add(SampleTranslator.translate(sampleDAO.tryGetByTechId(new TechId(id)), "", null,
- new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool()), null));
-
- }
- return list;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java
deleted file mode 100644
index 3c2741cf5b6..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java
+++ /dev/null
@@ -1,302 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import it.unimi.dsi.fastutil.longs.LongArraySet;
-import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Map;
-
-import net.lemnik.eodsql.DataSet;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinInfo;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProtein;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinInfoTableTest extends AbstractBOTestCase
-{
- private static final double COVERAGE = 0.5;
-
- private static final String PERM_ID_PREFIX = "abc-";
-
- private static final long SAMPLE_ID_3 = 211L;
-
- private static final long SAMPLE_ID_2 = 102L;
-
- private static final long SAMPLE_ID_1 = 101L;
-
- private static final Double ABUNDANCE = new Double(47.11);
-
- private static final long PROTEIN_ID = 4141L;
-
- private static final long PROTEIN_REFERENCE_ID = 41L;
-
- private static final String SAMPLE_PERM_ID = "s47-11";
-
- private static final long SAMPLE_ID = 4711;
-
- private static final long DATA_SET_ID = 42L;
-
- private static final TechId EXPERIMENT_ID = new TechId(234L);
-
- private static final String EXPERIMENT_PERM_ID = "abc-234";
-
- private static final double FALSE_DISCOVERY_RATE = 0.25;
-
- private static final String ACCESSION_NUMBER = "ABC123";
-
- private ProteinInfoTable table;
-
- private ArrayList<AbundanceColumnDefinition> definitions;
-
- private ISampleProvider sampleProvider;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- sampleProvider = context.mock(ISampleProvider.class);
- table = new ProteinInfoTable(daoFactory, specificDAOFactory, session, sampleProvider);
- definitions = new ArrayList<AbundanceColumnDefinition>();
- definitions.add(create(SAMPLE_ID_1, SAMPLE_ID_2));
- definitions.add(create(SAMPLE_ID_3));
- }
-
- private AbundanceColumnDefinition create(long... ids)
- {
- AbundanceColumnDefinition definition = new AbundanceColumnDefinition();
- for (long id : ids)
- {
- definition.addSampleID(id);
- }
- return definition;
- }
-
- @Test
- public void testLoadLeadingToAnEmptyTable()
- {
- prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
- MockDataSet<ProteinReferenceWithProtein> proteinReferences = new MockDataSet<ProteinReferenceWithProtein>();
- MockDataSet<ProteinAbundance> proteinAbundances = new MockDataSet<ProteinAbundance>();
- prepareLoadDataSet(proteinReferences, proteinAbundances);
-
- table.load(Arrays.<AbundanceColumnDefinition> asList(), EXPERIMENT_ID,
- FALSE_DISCOVERY_RATE, AggregateFunction.MEAN, false);
-
- assertEquals(0, table.getProteinInfos().size());
-
- assertEquals(true, proteinReferences.hasCloseBeenInvoked());
- assertEquals(true, proteinAbundances.hasCloseBeenInvoked());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testSimpleLoad()
- {
- prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
- MockDataSet<ProteinReferenceWithProtein> proteinReferences =
- new MockDataSet<ProteinReferenceWithProtein>();
- MockDataSet<ProteinAbundance> abundances = new MockDataSet<ProteinAbundance>();
- ProteinReferenceWithProtein proteinReference = new ProteinReferenceWithProtein();
- proteinReference.setDataSetID(DATA_SET_ID);
- proteinReference.setProteinID(PROTEIN_ID);
- proteinReference.setAccessionNumber(ACCESSION_NUMBER);
- proteinReference.setId(PROTEIN_REFERENCE_ID);
- proteinReferences.add(proteinReference);
- ProteinAbundance proteinAbundance = new ProteinAbundance();
- proteinAbundance.setId(PROTEIN_ID);
- proteinAbundance.setAbundance(ABUNDANCE);
- proteinAbundance.setSampleID(SAMPLE_PERM_ID);
- abundances.add(proteinAbundance);
- proteinReference = new ProteinReferenceWithProtein();
- proteinReference.setProteinID(PROTEIN_ID);
- proteinReference.setId(PROTEIN_REFERENCE_ID);
- proteinReference.setProbability(1);
- proteinReference.setDataSetID(DATA_SET_ID);
- proteinReferences.add(proteinReference);
- final MockDataSet<ProbabilityFDRMapping> mappings = new MockDataSet<ProbabilityFDRMapping>();
- mappings.add(new ProbabilityFDRMapping());
- ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
- mapping.setProbability(1);
- mapping.setFalseDiscoveryRate(1);
- mappings.add(mapping);
- prepareLoadDataSet(proteinReferences, abundances);
- context.checking(new Expectations()
- {
- {
- one(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
- will(returnValue(mappings));
-
- one(sampleProvider).getSample(SAMPLE_PERM_ID);
- Sample sample = new Sample();
- Sample parent = new Sample();
- parent.setId(SAMPLE_ID);
- sample.setGeneratedFrom(parent);
- will(returnValue(sample));
- }
- });
-
- table.load(Arrays.<AbundanceColumnDefinition> asList(), EXPERIMENT_ID,
- FALSE_DISCOVERY_RATE, AggregateFunction.MEAN, false);
-
- Collection<ProteinInfo> proteins = table.getProteinInfos();
- assertEquals(1, proteins.size());
- ProteinInfo protein = proteins.iterator().next();
- assertEquals(PROTEIN_REFERENCE_ID, protein.getId().getId().longValue());
- assertEquals(ACCESSION_NUMBER, protein.getAccessionNumber());
-
- assertEquals(true, proteinReferences.hasCloseBeenInvoked());
- assertEquals(true, mappings.hasCloseBeenInvoked());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLoadWithAggregationOnOriginal()
- {
- checkAggregationType(2.0, true);
- }
-
- @Test
- public void testLoadWithAggregationOnAggregation()
- {
- checkAggregationType(2.25, false);
- }
-
- private void checkAggregationType(double expectedAbundance, boolean aggregateOriginal)
- {
- prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
- final MockDataSet<ProteinReferenceWithProtein> proteinReferences =
- new MockDataSet<ProteinReferenceWithProtein>();
- ProteinReferenceWithProtein proteinReference = new ProteinReferenceWithProtein();
- proteinReference.setProteinID(PROTEIN_ID);
- proteinReference.setDataSetID(DATA_SET_ID);
- proteinReference.setAccessionNumber(ACCESSION_NUMBER);
- proteinReference.setId(PROTEIN_REFERENCE_ID);
- proteinReference.setCoverage(COVERAGE);
- proteinReferences.add(proteinReference);
- MockDataSet<ProteinAbundance> proteinAbundances = new MockDataSet<ProteinAbundance>();
- proteinAbundances.add(createProteinAbundance(SAMPLE_ID_1, 1));
- proteinAbundances.add(createProteinAbundance(SAMPLE_ID_1, 2));
- proteinAbundances.add(createProteinAbundance(SAMPLE_ID_2, 3));
- proteinAbundances.add(createProteinAbundance(SAMPLE_ID_3, 20));
- final MockDataSet<ProbabilityFDRMapping> mappings = new MockDataSet<ProbabilityFDRMapping>();
- mappings.add(new ProbabilityFDRMapping());
- ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
- mapping.setProbability(1);
- mapping.setFalseDiscoveryRate(1);
- mappings.add(mapping);
- prepareLoadDataSet(proteinReferences, proteinAbundances);
- context.checking(new Expectations()
- {
- {
- one(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
- will(returnValue(mappings));
-
- for (long id : new long[] { SAMPLE_ID_1, SAMPLE_ID_2, SAMPLE_ID_3 })
- {
- atLeast(1).of(sampleProvider).getSample(PERM_ID_PREFIX + id);
- Sample sample = new Sample();
- sample.setId(id);
- will(returnValue(sample));
- }
- }
- });
-
- table.load(definitions, EXPERIMENT_ID,
- FALSE_DISCOVERY_RATE, AggregateFunction.MEAN, aggregateOriginal);
-
- Collection<ProteinInfo> proteins = table.getProteinInfos();
- assertEquals(1, proteins.size());
- ProteinInfo protein = proteins.iterator().next();
- assertEquals(PROTEIN_REFERENCE_ID, protein.getId().getId().longValue());
- assertEquals(ACCESSION_NUMBER, protein.getAccessionNumber());
- Map<Long, Double> abundances = protein.getAbundances();
- assertEquals(2, abundances.size());
- assertEquals(expectedAbundance, abundances.get(SAMPLE_ID_1 * 37 + SAMPLE_ID_2).doubleValue());
- assertEquals(20.0, abundances.get(SAMPLE_ID_3).doubleValue());
- assertEquals(100 * COVERAGE, protein.getCoverage());
-
- assertEquals(true, proteinReferences.hasCloseBeenInvoked());
- assertEquals(true, mappings.hasCloseBeenInvoked());
- context.assertIsSatisfied();
- }
-
- private void prepareGetProteinQueryDAO(final String experimentPermID)
- {
- context.checking(new Expectations()
- {
- {
- one(specificDAOFactory).getProteinQueryDAO(experimentPermID);
- will(returnValue(proteinDAO));
- }
- });
- }
-
- private void prepareLoadDataSet(
- final MockDataSet<ProteinReferenceWithProtein> proteinReferences,
- final DataSet<ProteinAbundance> proteinAbundances)
- {
- context.checking(new Expectations()
- {
- {
- one(experimentDAO).getByTechId(EXPERIMENT_ID);
- ExperimentPE experimentPE = new ExperimentPE();
- experimentPE.setPermId(EXPERIMENT_PERM_ID);
- will(returnValue(experimentPE));
-
- one(proteinDAO).listProteinReferencesByExperiment(EXPERIMENT_PERM_ID);
- will(returnValue(proteinReferences));
-
- LongSet proteinIDs = new LongArraySet();
- for (ProteinReferenceWithProtein p : proteinReferences)
- {
- proteinIDs.add(p.getProteinID());
- }
- one(proteinDAO).listProteinWithAbundanceByExperiment(proteinIDs);
- will(returnValue(proteinAbundances));
- }
- });
- }
-
- private ProteinAbundance createProteinAbundance(long sampleID, double abundance)
- {
- ProteinAbundance proteinAbundance = new ProteinAbundance();
- proteinAbundance.setSampleID(PERM_ID_PREFIX + sampleID);
- proteinAbundance.setId(PROTEIN_ID);
- proteinAbundance.setAbundance(abundance);
- return proteinAbundance;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java
deleted file mode 100644
index 66e5a0a788e..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.List;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.generic.server.TestJythonEvaluatorPool;
-import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.EntityTypePropertyTypePEBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.SamplePEBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.SampleTypePEBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.SpacePEBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.ManagedPropertyEvaluatorFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinRelatedSample;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SampleAbundance;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.SamplePeptideModification;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinRelatedSampleTableTest extends AbstractBOTestCase
-{
- private ProteinRelatedSampleTable table;
-
- private SamplePE sample1;
-
- private SamplePE sample2;
-
- private SamplePE sample3;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- table =
- new ProteinRelatedSampleTable(daoFactory, specificDAOFactory,
- new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool()));
-
- SpacePE space =
- new SpacePEBuilder()
- .code("s")
- .getSpace();
- SampleTypePEBuilder sampleTypeBuilder = new SampleTypePEBuilder().code("my-type");
- PropertyTypePE propertyType =
- CommonTestUtils.createPropertyType("A", DataTypeCode.VARCHAR, null, null);
- EntityTypePropertyTypePEBuilder e = sampleTypeBuilder.assign(propertyType);
- EntityTypePropertyTypePE etpt = e.getEntityTypePropertyType();
- SampleTypePE sampleType = sampleTypeBuilder.getSampleType();
- sample1 =
- new SamplePEBuilder(1).space(space).code("S1").permID("s-1").type(sampleType)
- .property(etpt, "hello").getSample();
- sample2 =
- new SamplePEBuilder(2).space(space).code("S2").permID("s-2").type(sampleType)
- .getSample();
- sample3 =
- new SamplePEBuilder(3).space(space).code("S3").permID("s-3").type(sampleType)
- .getSample();
- }
-
- @Test
- public void test()
- {
- final TechId experimentID = new TechId(42);
- final TechId proteinReferenceID = new TechId(43);
- context.checking(new Expectations()
- {
- {
- one(specificDAOFactory).getProteinQueryDAO(experimentID);
- will(returnValue(proteinDAO));
-
- one(experimentDAO).getByTechId(experimentID);
- ExperimentPE experiment = new ExperimentPE();
- experiment.setPermId("exp-1");
- will(returnValue(experiment));
-
- one(proteinDAO).listSampleAbundanceByProtein(experiment.getPermId(),
- proteinReferenceID.getId());
- MockDataSet<SampleAbundance> sampleAbundances =
- new MockDataSet<SampleAbundance>();
- sampleAbundances.add(sampleAbundance("s-1", 0.25));
- sampleAbundances.add(sampleAbundance("s-2", 0.75));
- will(returnValue(sampleAbundances));
-
- one(proteinDAO).listSamplePeptideModificatioByProtein(experiment.getPermId(),
- proteinReferenceID.getId());
- MockDataSet<SamplePeptideModification> modifications =
- new MockDataSet<SamplePeptideModification>();
- modifications.add(modification("s-2", "ab", 1, 21.5, 0.25));
- modifications.add(modification("s-3", "def", 1, 12.375, 0.5));
- modifications.add(modification("s-3", "def", 3, -1.5, 0.75));
- will(returnValue(modifications));
-
- one(sampleDAO).tryToFindByPermID("s-1");
- will(returnValue(sample1));
-
- one(sampleDAO).tryToFindByPermID("s-2");
- will(returnValue(sample2));
-
- one(sampleDAO).tryToFindByPermID("s-3");
- will(returnValue(sample3));
- }
- });
-
- table.load(session, experimentID, proteinReferenceID, "abcdefabcab");
-
- List<ProteinRelatedSample> samples = table.getSamples();
- assertEquals("1:s-1:S1:/s/S1:SAMPLE:my-type:[A: hello]:0.25::null:null:null",
- render(samples.get(0)));
- assertEquals("2:s-2:S2:/s/S2:SAMPLE:my-type:[]:0.75:a:1:21.5:0.25",
- render(samples.get(1)));
- assertEquals("2:s-2:S2:/s/S2:SAMPLE:my-type:[]:0.75:a:7:21.5:0.25",
- render(samples.get(2)));
- assertEquals("2:s-2:S2:/s/S2:SAMPLE:my-type:[]:0.75:a:10:21.5:0.25",
- render(samples.get(3)));
- assertEquals("3:s-3:S3:/s/S3:SAMPLE:my-type:[]:null:d:4:12.375:0.5",
- render(samples.get(4)));
- assertEquals("3:s-3:S3:/s/S3:SAMPLE:my-type:[]:null:f:6:-1.5:0.75",
- render(samples.get(5)));
- assertEquals(6, samples.size());
- context.assertIsSatisfied();
- }
-
- private String render(ProteinRelatedSample sample)
- {
- char modifiedAminoAcid = sample.getModifiedAminoAcid();
- return sample.getId() + ":" + sample.getPermId() + ":" + sample.getCode() + ":"
- + sample.getIdentifier() + ":" + sample.getEntityKind() + ":"
- + sample.getEntityType() + ":" + sample.getProperties() + ":"
- + sample.getAbundance() + ":"
- + (modifiedAminoAcid == 0 ? "" : Character.toString(modifiedAminoAcid)) + ":"
- + sample.getModificationPosition() + ":" + sample.getModificationMass() + ":"
- + sample.getModificationFraction();
- }
-
- private SampleAbundance sampleAbundance(String permID, double abundance)
- {
- SampleAbundance sampleAbundance = new SampleAbundance();
- sampleAbundance.setSamplePermID(permID);
- sampleAbundance.setAbundance(abundance);
- return sampleAbundance;
- }
-
- private SamplePeptideModification modification(String permID, String sequence, int position,
- double mass, double fraction)
- {
- SamplePeptideModification modification = new SamplePeptideModification();
- modification.setSamplePermID(permID);
- modification.setSequence(sequence);
- modification.setPosition(position);
- modification.setMass(mass);
- modification.setFraction(fraction);
- return modification;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java
deleted file mode 100644
index 119088608ed..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java
+++ /dev/null
@@ -1,206 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ProteinSummaryTable.FDR_LEVELS;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSummary;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ProteinSummaryTableTest extends AbstractServerTestCase
-{
- private static final TechId EXPERIMENT_ID = new TechId(234L);
-
- private static final String EXPERIMENT_PERM_ID = "abc-234";
-
- private static final long DATA_SET_ID = 42L;
-
- private IPhosphoNetXDAOFactory specificDAOFactory;
-
- private IProteinQueryDAO proteinDAO;
-
- private ProteinSummaryTable table;
-
- @Override
- @BeforeMethod
- public void setUp()
- {
- super.setUp();
- specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
- proteinDAO = context.mock(IProteinQueryDAO.class);
- table = new ProteinSummaryTable(daoFactory, specificDAOFactory, session);
- }
-
- @Test
- public void testLoadEmptyData()
- {
- prepare();
-
- table.load(EXPERIMENT_ID);
-
- List<ProteinSummary> summaries = table.getProteinSummaries();
- for (ProteinSummary proteinSummary : summaries)
- {
- assertEquals(0, proteinSummary.getProteinCount());
- assertEquals(0, proteinSummary.getPeptideCount());
- }
- assertEquals(FDR_LEVELS.length, summaries.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLoadData()
- {
- ProteinReferenceWithProbabilityAndPeptide i1 = createItem("A", 0.5, 123, "ABCD");
- ProteinReferenceWithProbabilityAndPeptide i2 = createItem("B", 0.5, 123, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i3 = createItem("C", 0.75, 123, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i4 = createItem("D", 0.75, 456, "ABC");
- ProteinReferenceWithProbabilityAndPeptide i5 = createItem("E", 1, 456, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i6 = createItem("F", 1, 456, "XYZ");
- ProteinReferenceWithProbabilityAndPeptide i7 = createItem("DECOY_F", 0.75, 456, "XYZ");
- prepare(i1, i2, i3, i4, i5, i6, i7);
- context.checking(new Expectations()
- {
- {
- allowing(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
- MockDataSet<ProbabilityFDRMapping> dataSet =
- new MockDataSet<ProbabilityFDRMapping>();
- dataSet.add(createMappingItem(0.5, FDR_LEVELS[3]));
- dataSet.add(createMappingItem(0.75, FDR_LEVELS[2]));
- dataSet.add(createMappingItem(1, FDR_LEVELS[0]));
- will(returnValue(dataSet));
- }
-
- });
- table.load(EXPERIMENT_ID);
-
- List<ProteinSummary> summaries = table.getProteinSummaries();
- assertSummary(0, 1, 2, 0, 0, summaries);
- assertSummary(1, 1, 2, 0, 0, summaries);
- assertSummary(2, 2, 3, 1, 1, summaries);
- assertSummary(3, 2, 4, 1, 1, summaries);
- assertSummary(4, 2, 4, 1, 1, summaries);
- assertEquals(FDR_LEVELS.length, summaries.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLoadDataWithNoFDRMapping()
- {
- ProteinReferenceWithProbabilityAndPeptide i1 = createItem("A", 0.5, 123, "ABCD");
- ProteinReferenceWithProbabilityAndPeptide i2 = createItem("B", 0.5, 123, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i3 = createItem("C", 0.75, 123, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i4 = createItem("D", 0.75, 456, "ABC");
- ProteinReferenceWithProbabilityAndPeptide i5 = createItem("E", 1, 456, "DEF");
- ProteinReferenceWithProbabilityAndPeptide i6 = createItem("F", 1, 456, "XYZ");
- ProteinReferenceWithProbabilityAndPeptide i7 = createItem("DECOY_F", 0.75, 456, "XYZ");
- prepare(i1, i2, i3, i4, i5, i6, i7);
- context.checking(new Expectations()
- {
- {
- allowing(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
- MockDataSet<ProbabilityFDRMapping> dataSet =
- new MockDataSet<ProbabilityFDRMapping>();
- will(returnValue(dataSet));
- }
- });
- table.load(EXPERIMENT_ID);
-
- List<ProteinSummary> summaries = table.getProteinSummaries();
- assertSummary(0, 2, 4, 1, 1, summaries);
- assertSummary(1, 2, 4, 1, 1, summaries);
- assertSummary(2, 2, 4, 1, 1, summaries);
- assertSummary(3, 2, 4, 1, 1, summaries);
- assertSummary(4, 2, 4, 1, 1, summaries);
- assertEquals(FDR_LEVELS.length, summaries.size());
- context.assertIsSatisfied();
- }
-
- private void assertSummary(int index, int expectedProteinCount, int expectedPeptideCount,
- int expectedDecoyProteinCount, int expectedDecoyPeptideCount,
- List<ProteinSummary> summaries)
- {
- ProteinSummary proteinSummary = summaries.get(index);
- assertEquals(FDR_LEVELS[index], proteinSummary.getFDR(), 1e-6);
- assertEquals(expectedProteinCount, proteinSummary.getProteinCount());
- assertEquals(expectedPeptideCount, proteinSummary.getPeptideCount());
- assertEquals(expectedDecoyProteinCount, proteinSummary.getDecoyProteinCount());
- assertEquals(expectedDecoyPeptideCount, proteinSummary.getDecoyPeptideCount());
- }
-
- private ProbabilityFDRMapping createMappingItem(double probability, double falseDiscoveryRate)
- {
- ProbabilityFDRMapping m1 = new ProbabilityFDRMapping();
- m1.setProbability(probability);
- m1.setFalseDiscoveryRate(falseDiscoveryRate);
- return m1;
- }
-
- private void prepare(final ProteinReferenceWithProbabilityAndPeptide... items)
- {
- context.checking(new Expectations()
- {
- {
- allowing(specificDAOFactory).getProteinQueryDAO(EXPERIMENT_ID);
- will(returnValue(proteinDAO));
-
- one(experimentDAO).getByTechId(EXPERIMENT_ID);
- ExperimentPE experimentPE = new ExperimentPE();
- experimentPE.setPermId(EXPERIMENT_PERM_ID);
- will(returnValue(experimentPE));
-
- one(proteinDAO).listProteinsWithProbabilityAndPeptidesByExperiment(
- EXPERIMENT_PERM_ID);
- MockDataSet<ProteinReferenceWithProbabilityAndPeptide> dataSet =
- new MockDataSet<ProteinReferenceWithProbabilityAndPeptide>();
- dataSet.addAll(Arrays.asList(items));
- will(returnValue(dataSet));
- }
- });
- }
-
- private ProteinReferenceWithProbabilityAndPeptide createItem(String accessionNumber, double probability,
- long id, String peptideSequence)
- {
- ProteinReferenceWithProbabilityAndPeptide item =
- new ProteinReferenceWithProbabilityAndPeptide();
- item.setDataSetID(DATA_SET_ID);
- item.setProbability(probability);
- item.setId(id);
- item.setPeptideSequence(peptideSequence);
- item.setAccessionNumber(accessionNumber);
- return item;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProviderTest.java
deleted file mode 100644
index 0196a241d72..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleIDProviderTest.java
+++ /dev/null
@@ -1,122 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.RelationshipTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SampleIDProviderTest extends AbstractServerTestCase
-{
- private static final String PERM_ID = "abc-1";
-
- private static final Long ID = 42L;
-
- private SampleIDProvider sampleIDProvider;
-
- @BeforeMethod
- @Override
- public void setUp()
- {
- super.setUp();
- sampleIDProvider = new SampleIDProvider(sampleDAO);
- }
-
- @Test
- public void testGetUnkownSample()
- {
- context.checking(new Expectations()
- {
- {
- one(sampleDAO).tryToFindByPermID(PERM_ID);
- will(returnValue(null));
- }
- });
-
- try
- {
- sampleIDProvider.getSampleIDOrParentSampleID(PERM_ID);
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
- {
- assertEquals("No sample found for permID " + PERM_ID, e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetSampleIDTwice()
- {
- context.checking(new Expectations()
- {
- {
- one(sampleDAO).tryToFindByPermID(PERM_ID);
- SamplePE sample = new SamplePE();
- sample.setId(ID);
- will(returnValue(sample));
- }
- });
-
- long s1 = sampleIDProvider.getSampleIDOrParentSampleID(PERM_ID);
- long s2 = sampleIDProvider.getSampleIDOrParentSampleID(PERM_ID);
- assertEquals(ID.longValue(), s1);
- assertEquals(ID.longValue(), s2);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetParentSampleIDTwice()
- {
- context.checking(new Expectations()
- {
- {
- one(sampleDAO).tryToFindByPermID(PERM_ID);
- SamplePE parentSample = new SamplePE();
- parentSample.setCode("s1");
- parentSample.setId(ID);
- SamplePE sample = new SamplePE();
- sample.setCode("s1");
- sample.setId(2 * ID);
- RelationshipTypePE relationship = new RelationshipTypePE();
- relationship.setCode(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
- sample.addParentRelationship(new SampleRelationshipPE(parentSample, sample,
- relationship, new PersonPE()));
- will(returnValue(sample));
- }
- });
-
- long s1 = sampleIDProvider.getSampleIDOrParentSampleID(PERM_ID);
- long s2 = sampleIDProvider.getSampleIDOrParentSampleID(PERM_ID);
- assertEquals(ID.longValue(), s1);
- assertEquals(ID.longValue(), s2);
-
- context.assertIsSatisfied();
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoaderTest.java
deleted file mode 100644
index 73196040ee2..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleLoaderTest.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Test(groups = "db")
-public class SampleLoaderTest extends AbstractLoaderTestCase
-{
-
- @Test
- public void test()
- {
- Session session = session();
- session.setPerson(new PersonPE());
- SampleLoader loader = new SampleLoader(session, daoFactory, boFactory);
- List<Sample> samples = loader.listSamplesWithParentsByTypeAndSpace("CELL_PLATE", "CISD");
- Collections.sort(samples, new Comparator<Sample>()
- {
- @Override
- public int compare(Sample s1, Sample s2)
- {
- return s1.getCode().compareTo(s2.getCode());
- }
- });
- StringBuilder builder = new StringBuilder();
- for (Sample sample : samples)
- {
- Sample parent = sample.getGeneratedFrom();
- builder.append(sample.getCode()).append(" ").append(getSortedProperties(sample));
- builder.append(" <- ").append(parent.getCode()).append(" ");
- builder.append(getSortedProperties(parent)).append('\n');
- }
- assertEquals("3VCP5 [] <- 3V-125 [OFFSET: 49]\n"
- + "3VCP7 [COMMENT: test comment, ORGANISM: RAT, SIZE: 4711] <- 3V-125 [OFFSET: 49]\n"
- + "3VCP8 [] <- 3V-125 [OFFSET: 49]\n"
- + "CP-TEST-1 [ANY_MATERIAL: 1 (GENE), BACTERIUM: BACTERIUM-X (BACTERIUM), "
- + "COMMENT: very advanced stuff, ORGANISM: HUMAN, SIZE: 123] "
- + "<- CP-TEST-2 [ANY_MATERIAL: 2 (GENE), BACTERIUM: BACTERIUM-Y (BACTERIUM), "
- + "COMMENT: extremely simple stuff, ORGANISM: GORILLA, SIZE: 321]\n"
- + "CP1-A1 [] <- DP1-A [OFFSET: 42]\n"
- + "CP1-A2 [] <- DP1-A [OFFSET: 42]\n"
- + "CP1-B1 [] <- DP1-B [OFFSET: 42]\n"
- + "CP2-A1 [] <- DP2-A [OFFSET: 42]\n", builder.toString());
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProviderTest.java
deleted file mode 100644
index a9f632f812e..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleProviderTest.java
+++ /dev/null
@@ -1,180 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.authentication.Principal;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.IBusinessObjectFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ISampleProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.SampleProvider;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class SampleProviderTest extends AssertJUnit
-{
- private static final class MatcherOfSampleCriteriaByChildrenIDs extends
- BaseMatcher<ListOrSearchSampleCriteria>
- {
- private final Collection<Long> childrenIDs;
-
- private MatcherOfSampleCriteriaByChildrenIDs(Collection<Long> childrenIDs)
- {
- this.childrenIDs = childrenIDs;
- }
-
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof ListOrSearchSampleCriteria)
- {
- ListOrSearchSampleCriteria criteria = (ListOrSearchSampleCriteria) item;
- assertEquals(true, criteria.isEnrichDependentSamplesWithProperties());
- assertEquals(childrenIDs.toString(), criteria.getChildrenSampleIds().toString());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- }
- }
-
- private static final Principal PRINCIPAL =
- new Principal(CommonTestUtils.USER_ID, "john", "doe", "j@d");
-
- private static final String SESSION_TOKEN = "session-token";
-
- private static final Session SESSION =
- new Session(CommonTestUtils.USER_ID, SESSION_TOKEN, PRINCIPAL, "remote-host", 1);
-
- private static final TechId EXPERIMENT_ID = new TechId(4711);
-
- private Mockery context;
-
- private IBusinessObjectFactory boFactory;
-
- private ISampleProvider sampleProvider;
-
- private ISampleLister sampleLister;
-
- @BeforeMethod
- public void setUp()
- {
- context = new Mockery();
- boFactory = context.mock(IBusinessObjectFactory.class);
- sampleLister = context.mock(ISampleLister.class);
- sampleProvider = new SampleProvider(SESSION, boFactory);
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void test()
- {
- final Sample s1 = createSample("abc");
- final Sample s2 = createSample("123");
- final Sample s3 = createSample("parent-of-123");
- context.checking(new Expectations()
- {
- {
- one(boFactory).createSampleLister(SESSION);
- will(returnValue(sampleLister));
-
- one(sampleLister).list(with(new BaseMatcher<ListOrSearchSampleCriteria>()
- {
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof ListOrSearchSampleCriteria)
- {
- ListOrSearchSampleCriteria criteria = (ListOrSearchSampleCriteria) item;
- assertEquals(true, criteria.isEnrichDependentSamplesWithProperties());
- assertEquals(EXPERIMENT_ID, criteria.getExperimentId());
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- }
- }));
- will(returnValue(Arrays.asList(s1, s2)));
-
- one(sampleLister).list(
- with(new MatcherOfSampleCriteriaByChildrenIDs(Arrays.asList(s1.getId(),
- s2.getId()))));
- will(returnValue(Arrays.asList(s3)));
-
- one(sampleLister).list(
- with(new MatcherOfSampleCriteriaByChildrenIDs(Arrays.asList(s3.getId()))));
- will(returnValue(Arrays.asList()));
- }
- });
-
- sampleProvider.loadByExperimentID(EXPERIMENT_ID);
- assertSame(s1, sampleProvider.getSample(s1.getPermId()));
- assertSame(s2, sampleProvider.getSample(s2.getPermId()));
- assertSame(s3, sampleProvider.getSample(s3.getPermId()));
- try
- {
- sampleProvider.getSample("42");
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("No sample with following perm ID registered in openBIS: 42", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private Sample createSample(String samplePermID)
- {
- Sample sample = new Sample();
- sample.setId((long) samplePermID.hashCode());
- sample.setPermId(samplePermID);
- return sample;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinderTest.java
deleted file mode 100644
index 00ee7155f25..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/TreatmentFinderTest.java
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-
-import static ch.systemsx.cisd.openbis.plugin.proteomics.server.business.TreatmentFinder.TREATMENT_TYPE_CODE;
-import static ch.systemsx.cisd.openbis.plugin.proteomics.server.business.TreatmentFinder.TREATMENT_VALUE_CODE;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.TreatmentFinder;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TreatmentFinderTest extends AssertJUnit
-{
- @Test
- public void testFindingTreatmentsInSample()
- {
- Sample sample = createSample();
- sample.getProperties().add(create("BLABLA", "blub", DataTypeCode.MULTILINE_VARCHAR));
- addTreatment(sample, "", "pH", "7");
- addTreatment(sample, "1", "PLASMA", "20");
- addTreatment(sample, "2", "VIRUS", "HIV", DataTypeCode.MATERIAL);
-
- List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
-
- assertEquals(3, treatments.size());
- assertTreatment("7", "pH", treatments.get(0));
- assertTreatment("20", "PLASMA", treatments.get(1));
- assertTreatment("HIV", "VIRUS", DataTypeCode.MATERIAL, treatments.get(2));
- }
-
- @Test
- public void testFindingTreatmentsInAncestorsOverriddenInDescendants()
- {
- Sample sample = createSample();
- Sample parentSample = createSample();
- sample.setGeneratedFrom(parentSample);
- Sample grandParentSample = createSample();
- parentSample.setGeneratedFrom(grandParentSample);
- addTreatment(grandParentSample, "1", "PLASMA", "35");
- parentSample.getProperties().add(create("BLABLA", "blub", DataTypeCode.MULTILINE_VARCHAR));
- addTreatment(parentSample, "", "pH", "7");
- addTreatment(sample, "", "PLASMA", "20");
-
- List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
-
- assertEquals(2, treatments.size());
- assertTreatment("7", "pH", treatments.get(0));
- assertTreatment("20", "PLASMA", treatments.get(1));
- }
-
- @Test
- public void testFindingTreatmentsWhereTreatmentTypeIsNotAVocabulary()
- {
- Sample sample = createSample();
- sample.getProperties().add(create(TREATMENT_TYPE_CODE, "pH", DataTypeCode.VARCHAR));
-
- try
- {
- new TreatmentFinder().findTreatmentsOf(sample);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Data type of property type '" + TREATMENT_TYPE_CODE
- + "' must be a vocabulary.", e.getMessage());
- }
- }
-
- @Test
- public void testFindingTreatmentsWhereOnlyTreatmentTypeIsDefined()
- {
- Sample sample = createSample();
- sample.getProperties().add(create(TREATMENT_TYPE_CODE, "pH", DataTypeCode.CONTROLLEDVOCABULARY));
-
- List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
-
- assertEquals(1, treatments.size());
- assertTreatment("", "pH", treatments.get(0));
- }
-
- @Test
- public void testFindingTreatmentsWhereOnlyTreatmentValueIsDefined()
- {
- Sample sample = createSample();
- sample.getProperties().add(create(TREATMENT_VALUE_CODE, "HIV", DataTypeCode.MATERIAL));
-
- List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
-
- assertEquals(1, treatments.size());
- assertTreatment("HIV", "", DataTypeCode.MATERIAL, treatments.get(0));
- }
-
- private void assertTreatment(String expectedValue, String expectedType, Treatment treatment)
- {
- assertTreatment(expectedValue, expectedType, DataTypeCode.VARCHAR, treatment);
- }
-
- private void assertTreatment(String expectedValue, String expectedType,
- DataTypeCode expectedDataType, Treatment treatment)
- {
- assertEquals("Actual treatment: " + treatment, expectedValue, treatment.getValue());
- assertEquals("Actual treatment: " + treatment, expectedDataType.toString(), treatment
- .getValueType());
- assertEquals("Actual treatment: " + treatment, expectedType, treatment.getType());
- assertEquals("Actual treatment: " + treatment, expectedValue + " " + expectedType,
- treatment.getLabel());
- }
-
- private void addTreatment(Sample sample, String treatmentCodePostfix, String treatmentType,
- String treatmentValue)
- {
- addTreatment(sample, treatmentCodePostfix, treatmentType, treatmentValue,
- DataTypeCode.VARCHAR);
- }
-
- private void addTreatment(Sample sample, String treatmentCodePostfix, String treatmentType,
- String treatmentValue, DataTypeCode valueType)
- {
- List<IEntityProperty> properties = sample.getProperties();
- properties.add(create(TREATMENT_TYPE_CODE + treatmentCodePostfix, treatmentType,
- DataTypeCode.CONTROLLEDVOCABULARY));
- properties.add(create(TREATMENT_VALUE_CODE + treatmentCodePostfix, treatmentValue,
- valueType));
- }
-
- private IEntityProperty create(String code, String value, DataTypeCode type)
- {
- EntityProperty sampleProperty = new EntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(code);
- DataType dataType = new DataType();
- dataType.setCode(type);
- propertyType.setDataType(dataType);
- sampleProperty.setPropertyType(propertyType);
- switch (type)
- {
- case CONTROLLEDVOCABULARY:
- VocabularyTerm term = new VocabularyTerm();
- if (Character.isUpperCase(value.charAt(0)))
- {
- term.setCode(value);
- } else
- {
- term.setCode(value.toUpperCase());
- term.setLabel(value);
- }
- sampleProperty.setVocabularyTerm(term);
- break;
- case MATERIAL:
- Material material = new Material();
- material.setCode(value);
- sampleProperty.setMaterial(material);
- break;
- default:
- sampleProperty.setValue(value);
- }
- return sampleProperty;
- }
-
- private Sample createSample()
- {
- Sample sample = new Sample();
- sample.setProperties(new ArrayList<IEntityProperty>());
- return sample;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinitionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinitionTest.java
deleted file mode 100644
index 0ba2429877e..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AbundanceColumnDefinitionTest.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.util.Arrays;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.Treatment;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AbundanceColumnDefinitionTest extends AssertJUnit
-{
- @Test
- public void testCompareTwoDefinitonsWithoutTreatmentsAndSampleCodes()
- {
- AbundanceColumnDefinition d1 = new AbundanceColumnDefinition();
- AbundanceColumnDefinition d2 = create(null);
-
- assertEquals(0, d1.compareTo(d2));
-
- d1.setSampleCode("bla");
-
- assertEquals(0, d1.compareTo(d2));
- }
-
- @Test
- public void testCompareTwoDefinitonsWithoutTreatmentsButSampleCodes()
- {
- AbundanceColumnDefinition d1 = create("abc");
- AbundanceColumnDefinition d2 = create("abc");
-
- assertEquals(0, d1.compareTo(d2));
-
- d2.setSampleCode("def");
-
- assertEquals(true, d1.compareTo(d2) < 0);
- }
-
- @Test
- public void testCompareTwoDefinitonsWithDifferentNumberOfTreatments()
- {
- AbundanceColumnDefinition d1 = create("abc");
- d1.setSampleCode("abc");
- AbundanceColumnDefinition d2 = create("abc", new Treatment());
- d2.setSampleCode("abc");
-
- assertEquals(true, d1.compareTo(d2) < 0);
- }
-
- @Test
- public void testCompareTwoDefinitonsWithOneNonNumericalTreatment()
- {
- AbundanceColumnDefinition d1 = create("abc", treatment("light", "red"));
- AbundanceColumnDefinition d2 = create("abc", treatment("light", "blue"));
-
- assertEquals(true, d1.compareTo(d2) > 0);
- }
-
- @Test
- public void testCompareTwoDefinitonsWithOneNumericalTreatment()
- {
- AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.5"), treatment("T", "yes"));
- AbundanceColumnDefinition d2 = create("abc", treatment("pH", "9e-1"));
-
- assertEquals(true, d1.compareTo(d2) > 0);
- }
-
- @Test
- public void testCompareTwoDefinitonsWithOneNumericalTreatmentButDifferentTypes()
- {
- AbundanceColumnDefinition d1 = create("abc", treatment("K", "7.5"));
- AbundanceColumnDefinition d2 = create("abc", treatment("pH", "9e-1"));
-
- assertEquals(true, d1.compareTo(d2) < 0);
- }
-
- @Test
- public void testCompareTwoDefinitonsWithTwoNumericalTreatment()
- {
- AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.50"), treatment("T", "13"));
- AbundanceColumnDefinition d2 = create("abc", treatment("pH", "0.75e1"), treatment("T", "8"));
-
- assertEquals(true, d1.compareTo(d2) > 0);
- }
-
- private AbundanceColumnDefinition create(String sampleCode, Treatment... treatments)
- {
- AbundanceColumnDefinition definition = new AbundanceColumnDefinition();
- definition.setSampleCode(sampleCode);
- definition.setTreatments(Arrays.asList(treatments));
- return definition;
- }
-
- private Treatment treatment(String type, String value)
- {
- Treatment treatment = new Treatment();
- treatment.setType(type);
- treatment.setValue(value);
- return treatment;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunctionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunctionTest.java
deleted file mode 100644
index 51ef5b19421..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/AggregateFunctionTest.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.AggregateFunction;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregateFunctionTest extends AssertJUnit
-{
- @Test
- public void testMean()
- {
- assertEquals(42.0, AggregateFunction.MEAN.aggregate(new double[] { 42 }));
- assertEquals(42.5, AggregateFunction.MEAN.aggregate(new double[] { 42, 43 }));
- assertEquals(44.0, AggregateFunction.MEAN.aggregate(new double[] { 42, 42, 48 }));
- }
-
- @Test
- public void testMedian()
- {
- assertEquals(42.0, AggregateFunction.MEDIAN.aggregate(new double[] { 42 }));
- assertEquals(42.5, AggregateFunction.MEDIAN.aggregate(new double[] { 42, 43 }));
- assertEquals(43.0, AggregateFunction.MEDIAN.aggregate(new double[] { 42, 43, 50 }));
- assertEquals(46.5, AggregateFunction.MEDIAN.aggregate(new double[] { 42, 43, 50, 59 }));
- }
-
- @Test
- public void testSum()
- {
- assertEquals(42.0, AggregateFunction.SUM.aggregate(new double[] { 42 }));
- assertEquals(85.0, AggregateFunction.SUM.aggregate(new double[] { 42, 43 }));
- }
-
- @Test
- public void testMin()
- {
- assertEquals(42.0, AggregateFunction.MIN.aggregate(new double[] { 42 }));
- assertEquals(42.0, AggregateFunction.MIN.aggregate(new double[] { 42, 43 }));
- }
-
- @Test
- public void testMax()
- {
- assertEquals(42.0, AggregateFunction.MAX.aggregate(new double[] { 42 }));
- assertEquals(43.0, AggregateFunction.MAX.aggregate(new double[] { 42, 43 }));
- }
-
- @Test
- public void testCount()
- {
- assertEquals(1.0, AggregateFunction.COUNT.aggregate(new double[] { 42 }));
- assertEquals(2.0, AggregateFunction.COUNT.aggregate(new double[] { 42, 43 }));
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtilTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtilTest.java
deleted file mode 100644
index 248567447e0..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/basic/dto/OccurrenceUtilTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto;
-
-import java.util.Arrays;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.OccurrenceUtil;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class OccurrenceUtilTest extends AssertJUnit
-{
- @Test
- public void testNoCoverage()
- {
- check("[]", "");
- check("[]", "abc", "xx");
- check("[]", "xx");
- check("[]", "abc");
- }
-
- @Test
- public void testFullCoverage()
- {
- check("[[abc@0]]", "abc", "abc");
- }
-
- @Test
- public void testPartialAndOverlappingCoverage()
- {
- check("[[ab@0], [abcd@4], [ab@13]]", "abc abcde hahab", "ab", "bcd");
- check("[[ab@0], [abcd@4], [ab@13]]", "abc abcde hahab", "ab", "cd");
- check("[[abc@0], [abc@4], [ab@13]]", "abc abcde hahab", "ab", "b", "c");
- check("[[abc@0], [abc@4], [b@14]]", "abc abcde hahab", "abc", "b");
- check("[[abcde@0]]", "abcdef", "abcd", "b", "de");
- check("[[haha@10]]", "abc abcde hahab", "haha", "h");
- }
-
- private void check(String expectedList, String sequence, String... words)
- {
- assertEquals(expectedList, OccurrenceUtil.getCoverage(sequence, Arrays.asList(words)).toString());
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/AbstractProteomicsSystemTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/AbstractProteomicsSystemTestCase.java
deleted file mode 100644
index a1d2981b429..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/AbstractProteomicsSystemTestCase.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests;
-
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.SystemTestCase;
-import ch.systemsx.cisd.openbis.generic.server.ICommonServerForInternalUse;
-import ch.systemsx.cisd.openbis.generic.shared.IServiceForDataStoreServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Grantee;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.api.v1.Constants;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.IProteomicsDataService;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractProteomicsSystemTestCase extends SystemTestCase
-{
-
- /**
- *
- *
- */
- public AbstractProteomicsSystemTestCase()
- {
- super();
- }
-
- @Override
- protected String getApplicationContextLocation()
- {
- return "classpath:proteomics-applicationContext.xml";
- }
-
- protected String registerPerson(String userID)
- {
- ICommonServerForInternalUse commonServer = getCommonServer();
- String systemSessionToken = commonServer.tryToAuthenticateAsSystem().getSessionToken();
- commonServer.registerPerson(systemSessionToken, userID);
- return userID;
- }
-
- protected void assignInstanceRole(String userID, RoleCode roleCode)
- {
- ICommonServerForInternalUse commonServer = getCommonServer();
- String systemSessionToken = commonServer.tryToAuthenticateAsSystem().getSessionToken();
- commonServer.registerInstanceRole(systemSessionToken, roleCode,
- Grantee.createPerson(userID));
- }
-
- protected void assignSpaceRole(String userID, RoleCode roleCode, SpaceIdentifier spaceIdentifier)
- {
- ICommonServerForInternalUse commonServer = getCommonServer();
- String systemSessionToken = commonServer.tryToAuthenticateAsSystem().getSessionToken();
- commonServer.registerSpaceRole(systemSessionToken, roleCode, spaceIdentifier,
- Grantee.createPerson(userID));
- }
-
- protected String authenticateAs(String user)
- {
- return getCommonServer().tryAuthenticate(user, "password").getSessionToken();
- }
-
- protected ICommonServerForInternalUse getCommonServer()
- {
- return getBean(ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER);
- }
-
- protected IGenericServer getGenericServer()
- {
- return getBean(ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER);
- }
-
- protected IServiceForDataStoreServer getServiceForDSS()
- {
- return getBean(ch.systemsx.cisd.openbis.generic.shared.ResourceNames.ETL_SERVICE);
- }
-
- protected IProteomicsDataServiceInternal getDataServiceInternal()
- {
- return getBean(Constants.PROTEOMICS_DATA_SERVICE_INTERNAL);
- }
-
- protected IProteomicsDataService getDataService()
- {
- return getBean(Constants.PROTEOMICS_DATA_SERVICE);
- }
-
- protected IPhosphoNetXServer getServer()
- {
- return getBean(ResourceNames.PROTEOMICS_PLUGIN_SERVER);
- }
-
-}
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ProteomicsDataServiceTest.java
deleted file mode 100644
index 22c5f68a15f..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ProteomicsDataServiceTest.java
+++ /dev/null
@@ -1,201 +0,0 @@
-/*
- * Copyright 2016 ETH Zuerich, SIS
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.collection.SimpleComparator;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.shared.basic.string.CommaSeparatedListBuilder;
-import ch.systemsx.cisd.common.test.AssertionUtil;
-import ch.systemsx.cisd.openbis.generic.shared.IServiceForDataStoreServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetTypeBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleTypeBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.api.v1.dto.MsInjectionDataInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Test(groups = { "slow", "systemtest" })
-public class ProteomicsDataServiceTest extends AbstractProteomicsSystemTestCase
-{
- private static final String EXPERIMENT_IDENTIFIER = "/MS_DATA/A/E";
-
- private String sessionToken;
-
- private Long experimentId;
-
- private long[] sampleIds;
-
- @BeforeTest
- public void setUpExamples()
- {
- sessionToken = authenticateAs("test");
- getCommonServer().registerSpace(sessionToken, "MS_DATA", null);
- getCommonServer().registerProject(sessionToken, ProjectIdentifierFactory.parse("/MS_DATA/A"),
- null, null, Arrays.<NewAttachment> asList());
- NewExperiment experiment = new NewExperiment();
- experiment.setExperimentTypeCode("MS_SEARCH");
- experiment.setIdentifier(EXPERIMENT_IDENTIFIER);
- experimentId = getGenericServer().registerExperiment(sessionToken, experiment, Arrays.<NewAttachment> asList()).getId();
- NewSamplesWithTypes samples = new NewSamplesWithTypes();
- SampleType sampleType = new SampleTypeBuilder().code("MS_INJECTION").getSampleType();
- samples.setEntityType(sampleType);
- List<NewSample> msInjectionSamples = createMsInjectionSamples("/TEST-SPACE/CP-TEST-4", null, "/CISD/3VCP5");
- samples.setNewEntities(msInjectionSamples);
- getGenericServer().registerSamples(sessionToken, Arrays.asList(samples));
- IServiceForDataStoreServer serviceForDSS = getServiceForDSS();
- for (int i = 0; i < msInjectionSamples.size(); i++)
- {
- NewSample sample = msInjectionSamples.get(i);
- NewExternalData dataSet = new NewExternalData();
- dataSet.setDataSetType(new DataSetTypeBuilder().code("UNKNOWN").getDataSetType());
- dataSet.setDataSetKind(DataSetKind.PHYSICAL);
- dataSet.setCode("DS-" + i);
- dataSet.setFileFormatType(new FileFormatType("XML"));
- dataSet.setDataStoreCode("STANDARD");
- dataSet.setLocation("a/b/c/" + dataSet.getCode());
- dataSet.setLocatorType(new LocatorType("RELATIVE_LOCATION"));
- dataSet.setStorageFormat(StorageFormat.PROPRIETARY);
- serviceForDSS.registerDataSet(sessionToken, SampleIdentifierFactory.parse(sample),
- dataSet);
- }
- ListSampleCriteria criteria = ListSampleCriteria.createForExperiment(new TechId(experimentId));
- List<Sample> samples2 = getCommonServer().listSamples(sessionToken, criteria);
- sampleIds = new long[samples2.size()];
- for (int i = 0; i < sampleIds.length; i++)
- {
- sampleIds[i] = samples2.get(i).getId();
- }
- Arrays.sort(sampleIds);
- }
-
- @Test
- public void testListRawDataSamplesForAdminUser()
- {
- List<MsInjectionDataInfo> samples = getDataService().listRawDataSamples(sessionToken, "test");
-
- assertEquals("MSI-0:/TEST-SPACE/CP-TEST-4:/TEST-SPACE/NOE/EXP-TEST-2, "
- + "MSI-2:/CISD/3VCP5:/CISD/NEMO/EXP10", renderMsInjectionDataInfos(samples));
- }
-
- @Test
- public void testListRawDataSamplesForSpaceUser()
- {
- List<MsInjectionDataInfo> samples = getDataService().listRawDataSamples(sessionToken, "test_role");
-
- assertEquals("MSI-2:/CISD/3VCP5:/CISD/NEMO/EXP10", renderMsInjectionDataInfos(samples));
- }
-
- @Test
- public void testListAllRawDataSamplesForAdminUser()
- {
- List<MsInjectionDataInfo> samples = getDataService().listAllRawDataSamples(sessionToken, "test");
-
- assertEquals("MSI-0:/TEST-SPACE/CP-TEST-4:/TEST-SPACE/NOE/EXP-TEST-2, "
- + "MSI-2:/CISD/3VCP5:/CISD/NEMO/EXP10", renderMsInjectionDataInfos(samples));
- }
-
- @Test
- public void testListAllRawDataSamplesForSpaceUser()
- {
- List<MsInjectionDataInfo> samples = getDataService().listAllRawDataSamples(sessionToken, "test_role");
-
- assertEquals("MSI-0:null:null, "
- + "MSI-2:/CISD/3VCP5:/CISD/NEMO/EXP10", renderMsInjectionDataInfos(samples));
- }
-
- @Test
- public void testProcessingRawDataForAdminUser()
- {
- try
- {
- getDataService().processingRawData(sessionToken, "test", "test-processing", sampleIds, "UNKNOWN");
- } catch (EnvironmentFailureException ex)
- {
- AssertionUtil.assertContains("[DS-0, DS-2]", ex.getMessage());
- }
- }
-
- @Test
- public void testProcessingRawDataForSpaceUser()
- {
- try
- {
- getDataService().processingRawData(sessionToken, "test_role", "test-processing", sampleIds, "UNKNOWN");
- } catch (EnvironmentFailureException ex)
- {
- AssertionUtil.assertContains("[DS-2]", ex.getMessage());
- }
- }
-
- private String renderMsInjectionDataInfos(List<MsInjectionDataInfo> infos)
- {
- Collections.sort(infos, new SimpleComparator<MsInjectionDataInfo, String>()
- {
- @Override
- public String evaluate(MsInjectionDataInfo item)
- {
- return item.getMsInjectionSampleCode();
- }
- });
- CommaSeparatedListBuilder builder = new CommaSeparatedListBuilder();
- for (MsInjectionDataInfo info : infos)
- {
- builder.append(info.getMsInjectionSampleCode() + ":" + info.getBiologicalSampleIdentifier() + ":"
- + info.getBiologicalExperimentIdentifier());
- }
- return builder.toString();
- }
-
- private List<NewSample> createMsInjectionSamples(String... parentIdentifiers)
- {
- List<NewSample> samples = new ArrayList<NewSample>();
- SampleType sampleType = new SampleTypeBuilder().code("MS_INJECTION").getSampleType();
- for (int i = 0; i < parentIdentifiers.length; i++)
- {
- NewSample sample = new NewSample();
- sample.setParentIdentifier(parentIdentifiers[i]);
- sample.setIdentifier("/MS_DATA/MSI-" + i);
- sample.setSampleType(sampleType);
- sample.setExperimentIdentifier(EXPERIMENT_IDENTIFIER);
- samples.add(sample);
- }
- return samples;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ServerAuthorizationTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ServerAuthorizationTest.java
deleted file mode 100644
index 1211b9ac241..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/ServerAuthorizationTest.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.IProteomicsDataServiceInternal;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Test(groups = { "slow", "systemtest" })
-public class ServerAuthorizationTest extends AbstractProteomicsSystemTestCase
-{
- private static final String USER_A = "USER_A";
-
- private static final String USER_INSTANCE_OBSERVER = "USER_B";
-
- private static final SpaceIdentifier SPACE_A = new SpaceIdentifier("CISD");
-
- @BeforeClass
- public void createTestUsers()
- {
- assignSpaceRole(registerPerson(USER_A), RoleCode.ETL_SERVER, SPACE_A);
- assignInstanceRole(registerPerson(USER_INSTANCE_OBSERVER), RoleCode.OBSERVER);
- }
-
- @Test(expectedExceptions = AuthorizationFailureException.class)
- public void testForServerSetSessionUserFailedBecauseOfAuthorization()
- {
- String sessionToken = authenticateAs(USER_A);
- getServer().setSessionUser(sessionToken, "abc");
- }
-
- @Test(expectedExceptions = AuthorizationFailureException.class)
- public void testListProteinSummariesByExperimentFailedBecauseOfAuthorization()
- {
- String sessionToken = authenticateAs(USER_A);
- getServer().listProteinSummariesByExperiment(sessionToken, new TechId(42));
- }
-
- @Test(expectedExceptions = AuthorizationFailureException.class)
- public void testForDataServiceInternalSetSessionUserFailedBecauseOfAuthorization()
- {
- IProteomicsDataServiceInternal dataServiceInternal = getDataServiceInternal();
- String sessionToken = dataServiceInternal.tryAuthenticate(USER_A, "abc").getSessionToken();
- dataServiceInternal.setSessionUser(sessionToken, "abc");
- }
-
- @Test(expectedExceptions = AuthorizationFailureException.class)
- public void testForDataServiceInternalListExperimentsFailedBecauseOfAuthorization()
- {
- IProteomicsDataServiceInternal dataServiceInternal = getDataServiceInternal();
- String sessionToken = dataServiceInternal.tryAuthenticate(USER_A, "abc").getSessionToken();
- dataServiceInternal.listExperiments(sessionToken, "MS_SEARCH");
- }
-
- @Test
- public void testForDataServiceListExperimentsFailedBecauseOfAuthorization()
- {
- String sessionToken = authenticateAs(USER_A);
- try
- {
- getDataService().listExperiments(sessionToken, USER_A, "MS_SEARCH");
- fail("AuthorizationFailureException expected");
- } catch (AuthorizationFailureException ex)
- {
- assertEquals("Authorization failure: ERROR: \"None of method roles "
- + "'[INSTANCE_OBSERVER, INSTANCE_ADMIN]' "
- + "could be found in roles of user 'USER_A'.\".", ex.getMessage());
- }
- }
-
- @Test
- public void testForDataServiceListExperimentsFailedBecauseOfAuthorizationOnSecondLevel()
- {
- String sessionToken = authenticateAs(USER_INSTANCE_OBSERVER);
- try
- {
- getDataService().listExperiments(sessionToken, USER_A, "MS_SEARCH");
- fail("AuthorizationFailureException expected");
- } catch (AuthorizationFailureException ex)
- {
- assertEquals("Authorization failure: ERROR: \"None of method roles "
- + "'[PROJECT_USER, PROJECT_POWER_USER, PROJECT_ADMIN, SPACE_ADMIN, INSTANCE_ADMIN, SPACE_POWER_USER, SPACE_USER]' "
- + "could be found in roles of user 'USER_A'.\".", ex.getMessage());
- }
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/CommonValidatorProteomicsSystemTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/CommonValidatorProteomicsSystemTest.java
deleted file mode 100644
index 109f75aea32..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/CommonValidatorProteomicsSystemTest.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2017 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator;
-
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.validator.CommonValidatorSystemTest;
-
-/**
- * @author pkupczyk
- */
-public abstract class CommonValidatorProteomicsSystemTest<O> extends CommonValidatorSystemTest<O>
-{
-
- @Override
- protected String getApplicationContextLocation()
- {
- return "classpath:proteomics-applicationContext.xml";
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/ParentSampleValidatorSystemTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/ParentSampleValidatorSystemTest.java
deleted file mode 100644
index 09d22f285ec..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/ParentSampleValidatorSystemTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2017 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.sample;
-
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.ProjectAuthorizationUser;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.common.SampleUtil;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.validator.CommonValidatorSystemTestAssertions;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.validator.CommonValidatorSystemTestSampleAssertions;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.CommonValidatorProteomicsSystemTest;
-
-/**
- * @author pkupczyk
- */
-public class ParentSampleValidatorSystemTest extends CommonValidatorProteomicsSystemTest<Sample>
-{
-
- @Override
- public Object[] getParams()
- {
- return getSampleKinds(SampleKind.SHARED_READ);
- }
-
- @Override
- protected Sample createObject(SpacePE spacePE, ProjectPE projectPE, Object param)
- {
- Sample parent = SampleUtil.createObject(this, spacePE, projectPE, param);
- Sample sample = new Sample();
- sample.addParent(parent);
- return sample;
- }
-
- @Override
- protected Sample validateObject(ProjectAuthorizationUser user, Sample object, Object param)
- {
- return getBean(SampleValidatorProteomicsTestService.class).testParentSampleValidator(user.getSessionProvider(), object);
- }
-
- @Override
- protected CommonValidatorSystemTestAssertions<Sample> getAssertions()
- {
- return new CommonValidatorSystemTestSampleAssertions<>(super.getAssertions());
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/RawDataSampleValidatorSystemTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/RawDataSampleValidatorSystemTest.java
deleted file mode 100644
index 9a06c6a653e..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/RawDataSampleValidatorSystemTest.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright 2017 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.sample;
-
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.ProjectAuthorizationUser;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.common.SampleUtil;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.validator.CommonValidatorSystemTestAssertions;
-import ch.systemsx.cisd.openbis.datastoreserver.systemtests.authorization.validator.CommonValidatorSystemTestSampleAssertions;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-import ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.CommonValidatorProteomicsSystemTest;
-
-/**
- * @author pkupczyk
- */
-public class RawDataSampleValidatorSystemTest extends CommonValidatorProteomicsSystemTest<MsInjectionSample>
-{
-
- @Override
- public Object[] getParams()
- {
- return getSampleKinds(SampleKind.SHARED_READ);
- }
-
- @Override
- protected MsInjectionSample createObject(SpacePE spacePE, ProjectPE projectPE, Object param)
- {
- Sample parent = SampleUtil.createObject(this, spacePE, projectPE, param);
- Sample sample = new Sample();
- sample.addParent(parent);
- return new MsInjectionSample(sample, null);
- }
-
- @Override
- protected MsInjectionSample validateObject(ProjectAuthorizationUser user, MsInjectionSample object, Object param)
- {
- return getBean(SampleValidatorProteomicsTestService.class).testRawDataSampleValidator(user.getSessionProvider(), object);
- }
-
- @Override
- protected CommonValidatorSystemTestAssertions<MsInjectionSample> getAssertions()
- {
- return new CommonValidatorSystemTestSampleAssertions<>(super.getAssertions());
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/SampleValidatorProteomicsTestService.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/SampleValidatorProteomicsTestService.java
deleted file mode 100644
index 4b988f35884..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/proteomics/systemtests/authorization/validator/sample/SampleValidatorProteomicsTestService.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2017 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.sample;
-
-import org.springframework.stereotype.Component;
-import org.springframework.transaction.annotation.Transactional;
-
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSessionProvider;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.ParentSampleValidator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.RawDataSampleValidator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.MsInjectionSample;
-
-/**
- * @author pkupczyk
- */
-@Component
-public class SampleValidatorProteomicsTestService
-{
-
- @Transactional
- @RolesAllowed(value = { RoleWithHierarchy.PROJECT_OBSERVER })
- @ReturnValueFilter(validatorClass = ParentSampleValidator.class)
- public Sample testParentSampleValidator(IAuthSessionProvider sessionProvider, Sample sample)
- {
- return sample;
- }
-
- @Transactional
- @RolesAllowed(value = { RoleWithHierarchy.PROJECT_OBSERVER })
- @ReturnValueFilter(validatorClass = RawDataSampleValidator.class)
- public MsInjectionSample testRawDataSampleValidator(IAuthSessionProvider sessionProvider, MsInjectionSample sample)
- {
- return sample;
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/tests.xml b/rtd_phosphonetx/sourceTest/java/tests.xml
deleted file mode 100644
index 34383147e47..00000000000
--- a/rtd_phosphonetx/sourceTest/java/tests.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<suite name="All" verbose="2" >
- <test name="All" annotations="JDK">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="ch.systemsx.cisd.openbis.etlserver.proteomics.*" />
- <package name="ch.systemsx.cisd.openbis.dss.proteomics.*" />
- <package name="ch.systemsx.cisd.openbis.plugin.proteomics.*" />
- </packages>
- </test>
-</suite>
diff --git a/rtd_phosphonetx/sourceTest/java/tests_project_authorization.xml b/rtd_phosphonetx/sourceTest/java/tests_project_authorization.xml
deleted file mode 100644
index 22211d608c9..00000000000
--- a/rtd_phosphonetx/sourceTest/java/tests_project_authorization.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<suite name="projectAuthorization" verbose="2">
- <test name="unit" annotations="JDK">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="ch.systemsx.cisd.openbis.proteomics.systemtests.authorization.validator.*" />
- </packages>
- </test>
-</suite>
diff --git a/rtd_phosphonetx/sourceTest/java/tests_system.xml b/rtd_phosphonetx/sourceTest/java/tests_system.xml
deleted file mode 100644
index f5f68092a5b..00000000000
--- a/rtd_phosphonetx/sourceTest/java/tests_system.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<suite name="SystemTests" verbose="2" >
- <test name="SystemTests" annotations="JDK">
- <packages>
- <package name="ch.systemsx.cisd.openbis.proteomics.systemtests.*" />
- </packages>
- </test>
-</suite>
--
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