From a5f16ddf0fd59dae4976de7918afc4c642a27e8a Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Wed, 18 Jan 2023 12:56:31 +0100
Subject: [PATCH] SSDM-13329 Removed eu_agronomics, eu_basynthec, eu_basysbio
projects. Changed build configs to remove these projects
---
build_resources/gradle/build_openbis.sh | 3 -
eu_agronomics/.classpath | 13 -
eu_agronomics/.gitignore | 4 -
eu_agronomics/.project | 28 -
.../source/java/SampleWithProperties.java | 57 -
eu_agronomics/source/java/Tsv2openBIS.java | 219 -
eu_agronomics/source/java/Tsv2upload.java | 153 -
eu_agronomics/source/java/TsvMangler.java | 485 --
eu_agronomics/source/java/TsvUploader.java | 398 --
.../ethz/bsse/cisd/dss/agronomics/.gitignore | 0
eu_agronomics/source/java/columnMapper.java | 156 -
eu_agronomics/source/java/headerReplacer.java | 199 -
eu_agronomics/source/java/mapColumns.java | 88 -
eu_agronomics/source/java/replaceHeader.java | 78 -
eu_agronomics/targets/.gitignore | 0
eu_basynthec/.classpath | 25 -
eu_basynthec/.gitignore | 5 -
eu_basynthec/.project | 34 -
eu_basynthec/.pydevproject | 7 -
eu_basynthec/build/antrun.sh | 6 -
eu_basynthec/build/build.xml | 47 -
eu_basynthec/dist/etc/data-set-handler.py | 5 -
eu_basynthec/dist/etc/data-set-validator.py | 4 -
.../etc/growth-profiles/data-set-handler.py | 139 -
.../etc/growth-profiles/data-set-validator.py | 60 -
eu_basynthec/dist/etc/log.xml | 55 -
.../dist/etc/metabolomics/data-set-handler.py | 82 -
.../etc/metabolomics/data-set-validator.py | 67 -
.../etc/metabolomics2/data-set-handler.py | 188 -
.../etc/metabolomics2/data-set-validator.py | 86 -
.../dist/etc/proteomics/data-set-handler.py | 94 -
.../dist/etc/proteomics/data-set-validator.py | 74 -
eu_basynthec/dist/etc/service.properties | 180 -
.../dist/etc/shared/shared-classes.py | 210 -
.../etc/transcriptomics/data-set-handler.py | 208 -
.../etc/transcriptomics/data-set-validator.py | 81 -
eu_basynthec/etc/log.xml | 19 -
eu_basynthec/etc/service.properties | 194 -
eu_basynthec/etc/setup.textile | 39 -
.../resource/db/basynthec_metadata.sql | 362 --
.../resource/db/db_initialize_basynthec.sh | 3 -
.../resource/dependency-structure.ddf | 16 -
.../basynthec/browser/basynthec-browser.js | 1641 -------
.../basynthec/browser/basynthec-style.css | 218 -
.../1/as/webapps/basynthec/browser/button.css | 52 -
.../as/webapps/basynthec/browser/d3-test.html | 87 -
.../1/as/webapps/basynthec/browser/d3.js | 4013 -----------------
.../as/webapps/basynthec/browser/d3.layout.js | 1865 --------
.../1/as/webapps/basynthec/browser/d3.time.js | 692 ---
.../1/as/webapps/basynthec/browser/d3.tsv.js | 101 -
.../basynthec/browser/dendrogram-filter.js | 55 -
.../basynthec/browser/images/openBIS_Logo.png | Bin 7229 -> 0 bytes
.../basynthec/browser/images/openBIS_Logo.svg | 68 -
.../1/as/webapps/basynthec/browser/index.htm | 10 -
.../1/as/webapps/basynthec/browser/index.html | 128 -
.../basynthec/browser/lib/colorbrewer/LICENSE | 38 -
.../browser/lib/colorbrewer/colorbrewer.css | 1327 ------
.../browser/lib/colorbrewer/colorbrewer.js | 32 -
.../basynthec/browser/openbis-basynthec.js | 83 -
.../1/as/webapps/basynthec/plugin.properties | 3 -
.../chicago/data-from-server.csv | 518 ---
.../load-data-from-file-and-put-to-table.py | 78 -
.../load-data-from-server-and-save-in-file.py | 58 -
.../chicago/original-data-from-server.json | 1 -
.../chicago/plugin.properties | 3 -
.../examples/AbstractBaSynthecClient.java | 63 -
.../cisd/client/examples/BaSynthecClient.java | 146 -
.../cisd/client/examples/DataSetSearch.java | 294 --
.../client/examples/ExperimentLister.java | 218 -
.../cisd/dss/TimeSeriesDataExcel.java | 149 -
.../basynthec/cisd/dss/ValidationHelper.java | 53 -
eu_basynthec/source/python/master-data.py | 763 ----
.../examples/Metabolomics-BadData.xlsx | Bin 11000 -> 0 bytes
.../examples/Metabolomics-Example.xlsx | Bin 11073 -> 0 bytes
.../examples/Metabolomics-GarbageData.xlsx | Bin 11002 -> 0 bytes
.../examples/Metabolomics-Template.xlsx | Bin 10586 -> 0 bytes
.../examples/Metabolomics1-BadData.xlsx | Bin 10131 -> 0 bytes
.../examples/Metabolomics1-Example.xlsx | Bin 10401 -> 0 bytes
.../examples/Metabolomics1-Template.xlsx | Bin 9568 -> 0 bytes
.../sourceTest/examples/OD600-BadData.xlsx | Bin 10098 -> 0 bytes
.../sourceTest/examples/OD600-Example.xlsx | Bin 10672 -> 0 bytes
.../sourceTest/examples/OD600-Template.xlsx | Bin 9254 -> 0 bytes
.../examples/Proteomics-BadHeader.xlsx | Bin 9891 -> 0 bytes
.../examples/Proteomics-Example.xlsx | Bin 10071 -> 0 bytes
.../examples/Proteomics-Template.xlsx | Bin 9751 -> 0 bytes
.../examples/Transcriptomics-Example.xlsx | Bin 11590 -> 0 bytes
.../examples/Transcriptomics-Template.xlsx | Bin 9872 -> 0 bytes
...stractBaSynthecDataSetRegistratorTest.java | 212 -
.../cisd/dss/TimeSeriesDataExcelTest.java | 132 -
.../OD600DataSetRegistratorTest.java | 110 -
.../growthprofiles/OD600ValidatorTest.java | 72 -
.../MetabolomicsDataSetRegistrator2Test.java | 86 -
.../MetabolomicsDataSetRegistratorTest.java | 80 -
.../MetabolomicsValidator2Test.java | 77 -
.../MetabolomicsValidatorTest.java | 65 -
.../ProteomicsDataSetRegistratorTest.java | 82 -
.../proteomics/ProteomicsValidatorTest.java | 65 -
...TranscriptomicsDataSetRegistratorTest.java | 140 -
.../TranscriptomicsValidatorTest.java | 56 -
eu_basynthec/sourceTest/java/tests.xml | 14 -
eu_basysbio/.classpath | 22 -
eu_basysbio/.gitignore | 8 -
eu_basysbio/.project | 28 -
eu_basysbio/build/antrun.sh | 6 -
eu_basysbio/build/build.xml | 47 -
eu_basysbio/dist/etc/log.xml | 56 -
eu_basysbio/dist/etc/service.properties | 205 -
eu_basysbio/etc/log.xml | 19 -
eu_basysbio/etc/service.properties | 487 --
eu_basysbio/resource/dependency-structure.ddf | 16 -
eu_basysbio/resource/openBIS-script.txt | 75 -
.../source/bash/create-data-set-type.txt | 18 -
.../source/bash/create-data-set-types.sh | 46 -
.../cisd/dss/AbstractColumnInjection.java | 45 -
.../cisd/dss/AbstractDataSetUploader.java | 159 -
.../basysbio/cisd/dss/AbstractDataValue.java | 72 -
.../basysbio/cisd/dss/AbstractSQLArray.java | 114 -
.../eu/basysbio/cisd/dss/ChipChipData.java | 223 -
.../cisd/dss/ChipChipInjectionFactory.java | 192 -
.../java/eu/basysbio/cisd/dss/DBUtils.java | 103 -
.../basysbio/cisd/dss/DataColumnHeader.java | 290 --
.../cisd/dss/DataColumnHeaderValidator.java | 241 -
.../basysbio/cisd/dss/DataHeaderProperty.java | 145 -
.../eu/basysbio/cisd/dss/DataSetHandler.java | 130 -
.../cisd/dss/DataSetInfoExtractor.java | 89 -
.../cisd/dss/DataSetPropertiesExtractor.java | 50 -
.../cisd/dss/DataSetPropertiesValidator.java | 151 -
.../cisd/dss/DataSetTypeTranslator.java | 77 -
.../cisd/dss/DataSetUploaderFactory.java | 83 -
.../eu/basysbio/cisd/dss/DatabaseFeeder.java | 335 --
.../eu/basysbio/cisd/dss/HeaderUtils.java | 415 --
.../basysbio/cisd/dss/IColumnInjection.java | 26 -
.../cisd/dss/IDataSetPropertiesExtractor.java | 31 -
.../basysbio/cisd/dss/IDataSetUploader.java | 35 -
.../cisd/dss/IDataSetUploaderFactory.java | 34 -
.../eu/basysbio/cisd/dss/IDatabaseFeeder.java | 43 -
.../eu/basysbio/cisd/dss/IFileManager.java | 32 -
.../basysbio/cisd/dss/IInjectionFactory.java | 26 -
.../eu/basysbio/cisd/dss/ITimeSeriesDAO.java | 107 -
.../dss/LcaMicDataSetPropertiesExtractor.java | 59 -
.../cisd/dss/LcaMicDataSetUploader.java | 190 -
.../PostRegistrationDatabaseUploadTask.java | 217 -
.../cisd/dss/SimpleSQLStringArray.java | 100 -
.../basysbio/cisd/dss/StorageProcessor.java | 158 -
.../basysbio/cisd/dss/StringArrayMapper.java | 57 -
.../eu/basysbio/cisd/dss/TSVOutputWriter.java | 98 -
.../cisd/dss/TimePointPropertyType.java | 116 -
.../TimeSeriesAndTimePointDataSetHandler.java | 251 --
.../cisd/dss/TimeSeriesColumnDescriptor.java | 133 -
.../cisd/dss/TimeSeriesDataSetUploader.java | 89 -
.../TimeSeriesDataSetUploaderParameters.java | 70 -
.../cisd/dss/TimeSeriesInjectionFactory.java | 151 -
.../TimeSeriesPropertiesReportingPlugin.java | 90 -
...eriesPropertiesUpdateProcessingPlugin.java | 81 -
.../cisd/dss/TimeSeriesPropertyType.java | 98 -
.../eu/basysbio/cisd/dss/TimeSeriesValue.java | 136 -
.../eu/basysbio/cisd/dss/TypeExtractor.java | 97 -
.../java/eu/basysbio/cisd/dss/Util.java | 77 -
.../cisd/dss/ValueGroupDescriptor.java | 192 -
.../cisd/dss/ValueGroupIdGenerator.java | 48 -
.../source/sql/postgresql/001/schema-001.pdf | Bin 23163 -> 0 bytes
.../source/sql/postgresql/001/schema-001.png | Bin 35940 -> 0 bytes
.../source/sql/postgresql/001/schema-001.sql | 168 -
.../source/sql/postgresql/002/grants-002.sql | 33 -
.../source/sql/postgresql/002/schema-002.pdf | Bin 23163 -> 0 bytes
.../source/sql/postgresql/002/schema-002.png | Bin 35940 -> 0 bytes
.../source/sql/postgresql/002/schema-002.sql | 168 -
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.../source/sql/postgresql/003/schema-003.sql | 168 -
.../source/sql/postgresql/004/grants-004.sql | 33 -
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.../source/sql/postgresql/004/schema-004.sql | 170 -
.../source/sql/postgresql/005/grants-005.sql | 33 -
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.../source/sql/postgresql/005/schema-005.sql | 170 -
.../source/sql/postgresql/006/schema-006.dez | 2426 ----------
.../source/sql/postgresql/006/schema-006.png | Bin 44451 -> 0 bytes
.../source/sql/postgresql/006/schema-006.sql | 153 -
.../source/sql/postgresql/007/grants-007.sql | 19 -
.../source/sql/postgresql/007/schema-007.dez | 2426 ----------
.../source/sql/postgresql/007/schema-007.png | Bin 44451 -> 0 bytes
.../source/sql/postgresql/007/schema-007.sql | 153 -
.../source/sql/postgresql/008/grants-008.sql | 19 -
.../source/sql/postgresql/008/schema-008.dez | 2356 ----------
.../source/sql/postgresql/008/schema-008.png | Bin 48589 -> 0 bytes
.../source/sql/postgresql/008/schema-008.sql | 150 -
.../migration/migration-001-002.sql | 33 -
.../migration/migration-002-003.sql | 1 -
.../migration/migration-003-004.sql | 4 -
.../migration/migration-004-005.sql | 18 -
.../migration/migration-006-007.sql | 19 -
.../migration/migration-007-008.sql | 10 -
.../dss/DataColumnHeaderValidatorTest.java | 222 -
.../basysbio/cisd/dss/DataSetHandlerTest.java | 390 --
.../cisd/dss/DataSetTypeTranslatorTest.java | 65 -
.../eu/basysbio/cisd/dss/HeaderUtilsTest.java | 57 -
.../LcaMicDataSetPropertiesExtractorTest.java | 75 -
.../cisd/dss/LcaMicDataSetUploaderTest.java | 207 -
.../cisd/dss/TSVOutputWriterTest.java | 69 -
...eSeriesAndTimePointDataSetHandlerTest.java | 215 -
.../dss/TimeSeriesDataSetUploaderTest.java | 361 --
.../cisd/dss/TimeSeriesHeaderUtilsTest.java | 369 --
...meSeriesPropertiesReportingPluginTest.java | 91 -
.../cisd/dss/TimeSeriesPropertyTypeTest.java | 34 -
.../basysbio/cisd/dss/TypeExtractorTest.java | 99 -
.../basysbio/cisd/dss/UploaderTestCase.java | 70 -
eu_basysbio/sourceTest/java/tests.xml | 14 -
openbis_all/build/build.xml | 14 -
209 files changed, 36023 deletions(-)
delete mode 100644 eu_agronomics/.classpath
delete mode 100644 eu_agronomics/.gitignore
delete mode 100644 eu_agronomics/.project
delete mode 100644 eu_agronomics/source/java/SampleWithProperties.java
delete mode 100644 eu_agronomics/source/java/Tsv2openBIS.java
delete mode 100644 eu_agronomics/source/java/Tsv2upload.java
delete mode 100644 eu_agronomics/source/java/TsvMangler.java
delete mode 100644 eu_agronomics/source/java/TsvUploader.java
delete mode 100644 eu_agronomics/source/java/ch/ethz/bsse/cisd/dss/agronomics/.gitignore
delete mode 100644 eu_agronomics/source/java/columnMapper.java
delete mode 100644 eu_agronomics/source/java/headerReplacer.java
delete mode 100644 eu_agronomics/source/java/mapColumns.java
delete mode 100644 eu_agronomics/source/java/replaceHeader.java
delete mode 100644 eu_agronomics/targets/.gitignore
delete mode 100644 eu_basynthec/.classpath
delete mode 100644 eu_basynthec/.gitignore
delete mode 100644 eu_basynthec/.project
delete mode 100644 eu_basynthec/.pydevproject
delete mode 100755 eu_basynthec/build/antrun.sh
delete mode 100644 eu_basynthec/build/build.xml
delete mode 100644 eu_basynthec/dist/etc/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/data-set-validator.py
delete mode 100644 eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/growth-profiles/data-set-validator.py
delete mode 100644 eu_basynthec/dist/etc/log.xml
delete mode 100644 eu_basynthec/dist/etc/metabolomics/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/metabolomics/data-set-validator.py
delete mode 100644 eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/metabolomics2/data-set-validator.py
delete mode 100644 eu_basynthec/dist/etc/proteomics/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/proteomics/data-set-validator.py
delete mode 100644 eu_basynthec/dist/etc/service.properties
delete mode 100644 eu_basynthec/dist/etc/shared/shared-classes.py
delete mode 100644 eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
delete mode 100644 eu_basynthec/dist/etc/transcriptomics/data-set-validator.py
delete mode 100644 eu_basynthec/etc/log.xml
delete mode 100644 eu_basynthec/etc/service.properties
delete mode 100644 eu_basynthec/etc/setup.textile
delete mode 100644 eu_basynthec/resource/db/basynthec_metadata.sql
delete mode 100644 eu_basynthec/resource/db/db_initialize_basynthec.sh
delete mode 100644 eu_basynthec/resource/dependency-structure.ddf
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-style.css
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/button.css
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3-test.html
delete mode 100755 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.js
delete mode 100755 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.layout.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.time.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.tsv.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/dendrogram-filter.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/images/openBIS_Logo.png
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/images/openBIS_Logo.svg
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.htm
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.html
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/LICENSE
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.css
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delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/openbis-basynthec.js
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/plugin.properties
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/original-data-from-server.json
delete mode 100644 eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/client/examples/AbstractBaSynthecClient.java
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/dss/TimeSeriesDataExcel.java
delete mode 100644 eu_basynthec/source/java/eu/basynthec/cisd/dss/ValidationHelper.java
delete mode 100644 eu_basynthec/source/python/master-data.py
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics-BadData.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics-Example.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics-GarbageData.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics-Template.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics1-BadData.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics1-Example.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Metabolomics1-Template.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/OD600-BadData.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/OD600-Example.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/OD600-Template.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Proteomics-BadHeader.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Proteomics-Example.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Proteomics-Template.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Transcriptomics-Example.xlsx
delete mode 100644 eu_basynthec/sourceTest/examples/Transcriptomics-Template.xlsx
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/TimeSeriesDataExcelTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600ValidatorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidatorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsValidatorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsValidatorTest.java
delete mode 100644 eu_basynthec/sourceTest/java/tests.xml
delete mode 100644 eu_basysbio/.classpath
delete mode 100644 eu_basysbio/.gitignore
delete mode 100644 eu_basysbio/.project
delete mode 100755 eu_basysbio/build/antrun.sh
delete mode 100644 eu_basysbio/build/build.xml
delete mode 100644 eu_basysbio/dist/etc/log.xml
delete mode 100644 eu_basysbio/dist/etc/service.properties
delete mode 100644 eu_basysbio/etc/log.xml
delete mode 100644 eu_basysbio/etc/service.properties
delete mode 100644 eu_basysbio/resource/dependency-structure.ddf
delete mode 100644 eu_basysbio/resource/openBIS-script.txt
delete mode 100644 eu_basysbio/source/bash/create-data-set-type.txt
delete mode 100755 eu_basysbio/source/bash/create-data-set-types.sh
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractColumnInjection.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataSetUploader.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataValue.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractSQLArray.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipData.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipInjectionFactory.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DBUtils.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeader.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeaderValidator.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataHeaderProperty.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetHandler.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetInfoExtractor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesExtractor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesValidator.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetTypeTranslator.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetUploaderFactory.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/DatabaseFeeder.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/HeaderUtils.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IColumnInjection.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetPropertiesExtractor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploaderFactory.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IDatabaseFeeder.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IFileManager.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/IInjectionFactory.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/ITimeSeriesDAO.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/PostRegistrationDatabaseUploadTask.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/SimpleSQLStringArray.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/StorageProcessor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/StringArrayMapper.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TSVOutputWriter.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimePointPropertyType.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesColumnDescriptor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploader.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderParameters.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesInjectionFactory.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPlugin.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesUpdateProcessingPlugin.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertyType.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesValue.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/TypeExtractor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/Util.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupDescriptor.java
delete mode 100644 eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupIdGenerator.java
delete mode 100755 eu_basysbio/source/sql/postgresql/001/schema-001.pdf
delete mode 100755 eu_basysbio/source/sql/postgresql/001/schema-001.png
delete mode 100755 eu_basysbio/source/sql/postgresql/001/schema-001.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/002/grants-002.sql
delete mode 100755 eu_basysbio/source/sql/postgresql/002/schema-002.pdf
delete mode 100755 eu_basysbio/source/sql/postgresql/002/schema-002.png
delete mode 100755 eu_basysbio/source/sql/postgresql/002/schema-002.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/003/grants-003.sql
delete mode 100755 eu_basysbio/source/sql/postgresql/003/schema-003.png
delete mode 100755 eu_basysbio/source/sql/postgresql/003/schema-003.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/004/grants-004.sql
delete mode 100755 eu_basysbio/source/sql/postgresql/004/schema-004.png
delete mode 100755 eu_basysbio/source/sql/postgresql/004/schema-004.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/005/grants-005.sql
delete mode 100755 eu_basysbio/source/sql/postgresql/005/schema-005.png
delete mode 100755 eu_basysbio/source/sql/postgresql/005/schema-005.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/006/schema-006.dez
delete mode 100644 eu_basysbio/source/sql/postgresql/006/schema-006.png
delete mode 100644 eu_basysbio/source/sql/postgresql/006/schema-006.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/007/grants-007.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/007/schema-007.dez
delete mode 100644 eu_basysbio/source/sql/postgresql/007/schema-007.png
delete mode 100644 eu_basysbio/source/sql/postgresql/007/schema-007.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/008/grants-008.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/008/schema-008.dez
delete mode 100644 eu_basysbio/source/sql/postgresql/008/schema-008.png
delete mode 100644 eu_basysbio/source/sql/postgresql/008/schema-008.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-001-002.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-002-003.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-003-004.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-004-005.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-006-007.sql
delete mode 100644 eu_basysbio/source/sql/postgresql/migration/migration-007-008.sql
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataColumnHeaderValidatorTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetHandlerTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetTypeTranslatorTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/HeaderUtilsTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TSVOutputWriterTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesHeaderUtilsTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPluginTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertyTypeTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TypeExtractorTest.java
delete mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/UploaderTestCase.java
delete mode 100644 eu_basysbio/sourceTest/java/tests.xml
diff --git a/build_resources/gradle/build_openbis.sh b/build_resources/gradle/build_openbis.sh
index 6a3dcffe313..200f219e781 100755
--- a/build_resources/gradle/build_openbis.sh
+++ b/build_resources/gradle/build_openbis.sh
@@ -12,9 +12,6 @@ datamover \
datastore_server \
dbmigration \
deep_sequencing_unit \
-eu_agronomics \
-eu_basynthec \
-eu_basysbio \
image_readers \
installation \
integration-tests \
diff --git a/eu_agronomics/.classpath b/eu_agronomics/.classpath
deleted file mode 100644
index 27906142d82..00000000000
--- a/eu_agronomics/.classpath
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
- <classpathentry combineaccessrules="false" kind="src" path="/common"/>
- <classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
- <classpathentry kind="lib" path="/libraries/spring/spring-core.jar"/>
- <classpathentry combineaccessrules="false" kind="src" path="/openbis-common"/>
- <classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
- <classpathentry kind="lib" path="/libraries/cisd-args4j/cisd-args4j.jar" sourcepath="/libraries/cisd-args4j/cisd-args4j-src.zip"/>
- <classpathentry kind="output" path="targets/classes"/>
-</classpath>
diff --git a/eu_agronomics/.gitignore b/eu_agronomics/.gitignore
deleted file mode 100644
index e761d9e3013..00000000000
--- a/eu_agronomics/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-targets
-/.idea/
-*.iml
-*.eml
\ No newline at end of file
diff --git a/eu_agronomics/.project b/eu_agronomics/.project
deleted file mode 100644
index 28237daf843..00000000000
--- a/eu_agronomics/.project
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu_agronomics</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
- <filteredResources>
- <filter>
- <id>1332321366607</id>
- <name></name>
- <type>26</type>
- <matcher>
- <id>org.eclipse.ui.ide.multiFilter</id>
- <arguments>1.0-name-matches-true-false-.git</arguments>
- </matcher>
- </filter>
- </filteredResources>
-</projectDescription>
diff --git a/eu_agronomics/source/java/SampleWithProperties.java b/eu_agronomics/source/java/SampleWithProperties.java
deleted file mode 100644
index f0ff6489ea1..00000000000
--- a/eu_agronomics/source/java/SampleWithProperties.java
+++ /dev/null
@@ -1,57 +0,0 @@
-import java.util.Collection;
-import java.util.Set;
-import java.util.TreeMap;
-
-/*
- * 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.
- */
-
-/**
- * @author walshs
- */
-public class SampleWithProperties
-{
-
- String sname = new String(); // sample name
-
- TreeMap<String, String> pvs = new TreeMap<String, String>();
-
- public SampleWithProperties(String s)
- {
- sname = s;
- }
-
- public void addProperty(String k, String v)
- {
- pvs.put(k, v);
- }
-
- public String getName()
- {
- return sname;
- }
-
- public Set<String> getPropertyTypes()
- {
- return pvs.keySet();
-
- }
-
- public Collection<String> getPropertyValues()
- {
- return pvs.values();
- }
-
-}
diff --git a/eu_agronomics/source/java/Tsv2openBIS.java b/eu_agronomics/source/java/Tsv2openBIS.java
deleted file mode 100644
index e3a55f3ab7f..00000000000
--- a/eu_agronomics/source/java/Tsv2openBIS.java
+++ /dev/null
@@ -1,219 +0,0 @@
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-
-/**
- * @author walshs
- */
-
-// to add
-// - ignore blank lines - unresolved problem
-// - list DataSet properties
-// - use log4j
-// - use args4j
-// -
-//
-
-class Tsv2openBIS
-{
-
- public static void main(String args[])
- {
-
- File d = new File(".");
- try
- {
- String pwd = d.getCanonicalPath();
- System.out.println("Working dir : " + pwd);
- } catch (IOException ioe)
- {
-
- System.err.println(ioe.getMessage());
- }
-
- TsvMangler mangler = null;
-
- try
- {
-
- mangler = getTsvMangler(args);
- mangler.writeDataForDssUploadOneDirPerRowStyle();
-
- mangler.writeSamplesFile();
- mangler.writeServiceDotProperties();
- mangler.writeDssMkdir();
- mangler.writeSamplePropertyLoader();
- mangler.writeDataSetPropertyLoader();
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println(ex.getMessage());
- System.out.println("Usage follows.....\n\n");
- printUsage();
- }
- System.out.println("Done.\n");
- }
-
- public static void printArgs(String args[])
- {
- for (String s : args)
- {
- System.out.println(s);
- }
- }
-
- public static String stripValue(String s)
- {
- String[] s1 = s.split("=");
- // System.out.println("value is " + s1[1]);
- return s1[1];
- }
-
- public static TsvMangler getTsvMangler(String args[]) throws Exception
- {
-
- Integer head = null;
- String file = null;
- String dsn = null;
- String expt = null;
- String project = null;
- ArrayList<Integer> igal = new ArrayList<Integer>(); // ignore ArrayList
- ArrayList<Integer> kcal = new ArrayList<Integer>(); // key columns ArrayList
- HashMap<Integer, String> dspts = new HashMap<Integer, String>(); // DataSet Property Types
- HashMap<Integer, String> spts = new HashMap<Integer, String>(); // Sample Property Types
-
- for (String s : args)
- {
- if (s.matches("head=\\d{1}"))
- {
- head = Integer.parseInt(stripValue(s));
-
- } else if (s.matches("ignore=[\\d|,]*"))
- {
- String[] igs = (stripValue(s)).split(",");
-
- for (String i : igs)
- {
- igal.add(Integer.parseInt(i));
- }
-
- } else if (s.matches("file=.*"))
- {
- file = stripValue(s);
-
- } else if (s.matches("project=.*"))
- {
- project = stripValue(s);
- }
- else if (s.matches("dataSetName=.*"))
- {
- dsn = stripValue(s);
-
- } else if (s.matches("expt=\\w+"))
- {
- expt = stripValue(s);
- } else if (s.matches("keyCols=[\\d|,]+"))
- {
-
- String[] kcs = (stripValue(s)).split(",");
-
- for (String i : kcs)
- {
- kcal.add(Integer.parseInt(i));
- }
-
- } else if (s.matches("dataSetPropCols=\\S+"))
- {
-
- String[] foo = (stripValue(s)).split(",");
-
- for (String i : foo)
- {
- String[] bits = i.split(":");
- dspts.put(Integer.parseInt(bits[0]), bits[1]);
- }
- // System.out.println(dspts.toString());
- }
- else if (s.matches("samplePropCols=\\S+"))
- {
-
- String[] foo = (stripValue(s)).split(",");
-
- for (String i : foo)
- {
- String[] bits = i.split(":");
- spts.put(Integer.parseInt(bits[0]), bits[1]);
- }
- // System.out.println(dspts.toString());
- }
- else
- {
- // Exception for unrecognised arguments
- throw new Exception("Can't parse args");
- }
- }
-
- if (head == null)
- {
- throw new Exception("<head> not set");
- }
- if (dsn == null)
- {
- throw new Exception("<dataSetName> not set");
- }
- if (file == null)
- {
- throw new Exception("<file> not set");
- }
- if (expt == null)
- {
- throw new Exception("<expt> not set");
- }
- if (project == null)
- {
- throw new Exception("<project> not set");
- }
-
- TsvMangler mangler = new TsvMangler(head, igal, file, kcal, expt, dspts, dsn, spts, project);
-
- return mangler;
- }
-
- public static void printUsage()
- {
-
- System.out
- .println("------------------------------------------------------------------------------------------------------------------------------------\n"
- + "Description : Program to convert TSV file into a file and directory struture suitable for upload by OpenBIS Data Store Server (DSS).\n"
- + " It also writes DSS upload thread configuration suitable for this TSV for inclusion in service-properties\n"
- + "\n"
- + "Usage :\n"
- + "\n"
- + "\te.g. Tsv2openBIS head=1 ignore=2,3 keyCols=2,4,5 project=AGRON-OMICS samplePropCols=4:USER.AGRON-OMICS_ECOTYPE dataSetName=PHENOTYPE_FEATURE_SET dataSetPropCols=1:USER.PROTOCOL,5:USER.SOWING_DATE file=/tmp/my.tsv expt=PILOT_COMAPARTIVE_EXPERIMENT\n"
- + "\n"
- + "<head> is the row to use for results.txt headings. i.e. 1 means the first row\n"
- + "\n"
- + "<keyCols> is a comma separated list of columns from which construct the OpenBIS sampe key\n"
- + "\n"
- + "<file> file is the name of the TSV file \n"
- + "\n"
- + "<expt> A string representing the experiment which is only used as part of the path for output files at the top level\n"
- + "\n"
- + "<project> A string representing the project. It is used as part of the sample prefix i.e. CISD:/<project>/SAMPLE_1\n"
- + "\n"
- + "All of <head>,<ignore>,<file>,<expt>,<project> are mandatory arguments. The following list of arguments are optional :\n"
- + "\n"
- + "<ignore> can be set to nothing (i.e. ignore='') in the case that all lines are either a heading or data to be processed\n"
- + "\n"
- + "<dataSetPropCols> is a comma separated list of key-value pairs which give configuration to write DataSet Property Types\n"
- + " e.g. 5:USER.SOWING_DATE means use column number 5 values for the USER.SOWING_DATE DataSet Property\n"
- + " clearly, column number 1 means the first column in the spreadsheet\n"
- + ""
- + "<samplePropCols> is a comma separated list of key-value pairs which give configuration to write Sample Property Types\n"
- + " e.g. 4:USER.AGRON-OMICS_ECOTYPE means use column number 4 values for the USER.AGRON-OMICS_ECOTYPE DataSet Property\n"
- + " clearly, column number 1 means the first column in the spreadsheet\n");
- }
-
-}
diff --git a/eu_agronomics/source/java/Tsv2upload.java b/eu_agronomics/source/java/Tsv2upload.java
deleted file mode 100644
index 826810fd4f2..00000000000
--- a/eu_agronomics/source/java/Tsv2upload.java
+++ /dev/null
@@ -1,153 +0,0 @@
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-
-/**
- * @author walshs
- */
-
-// to add
-// 1. ignore blank lines - unresolved problem
-// 4. list DataSet properties
-
-// use log4j
-// use args4j
-
-class Tsv2upload
-{
-
- public static void main(String args[])
- {
-
- File d = new File(".");
- try
- {
- String pwd = d.getCanonicalPath();
- System.out.println("Working dir : " + pwd);
- } catch (IOException ioe)
- {
-
- System.err.println(ioe.getMessage());
- }
-
- TsvUploader up = null;
-
- try
- {
-
- up = getUploader(args);
- up.writeDataForDssUpload();
- up.writeSamplesFile();
- up.writeServiceDotProperties();
- up.writeDssMkdir();
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println(ex.getMessage());
- System.out.println("Usage follows.....\n\n");
- printUsage();
- }
- }
-
- public static void printArgs(String args[])
- {
- for (String s : args)
- {
- System.out.println(s);
- }
- }
-
- public static String stripValue(String s)
- {
- String[] s1 = s.split("=");
- // System.out.println("value is " + s1[1]);
- return s1[1];
- }
-
- public static TsvUploader getUploader(String args[]) throws Exception
- {
-
- Integer head = null;
- String file = null;
- String tag = null;
- ArrayList<Integer> igal = new ArrayList<Integer>(); // ignore ArrayList
- ArrayList<Integer> kcal = new ArrayList<Integer>(); // key columns ArrayList
-
- for (String s : args)
- {
- if (s.matches("head=\\d{1}"))
- {
- head = Integer.parseInt(stripValue(s));
-
- } else if (s.matches("ignore=[\\d|,]*"))
- {
- String[] igs = (stripValue(s)).split(",");
-
- for (String i : igs)
- {
- igal.add(Integer.parseInt(i));
- }
-
- } else if (s.matches("file=.*"))
- {
- file = stripValue(s);
-
- } else if (s.matches("tag=\\w+"))
- {
- tag = stripValue(s);
- }
- else if (s.matches("keyCols=[\\d|,]+"))
- {
-
- String[] kcs = (stripValue(s)).split(",");
-
- for (String i : kcs)
- {
- kcal.add(Integer.parseInt(i));
- }
-
- } else
- {
- // Exception for unrecognised arguments
- throw new Exception("Can't parse args");
- }
- }
-
- if (head == null)
- {
- throw new Exception("<head> not set");
- }
- if (file == null)
- {
- throw new Exception("<file> not set");
- }
- if (tag == null)
- {
- throw new Exception("<tag> not set");
- }
-
- TsvUploader up = new TsvUploader(head, igal, file, kcal, tag);
-
- return up;
- }
-
- public static void printUsage()
- {
-
- System.out
- .println("------------------------------------------------------------------------------------------------------------------------------------\n"
- + "Description : Program to convert TSV file into a file and directory struture suitable for upload by OpenBIS Data Store Server (DSS).\n"
- + " It also writes DSS upload thread configuration suitable for this TSV for inclusion in service-properties\n\n"
- + "Usage :\n\n"
- + "\te.g. Tsv2upload head=1 ignore=2,3 keyCols=2,4,5 file=/tmp/my.tsv tag=PCE_SHARED\n\n"
- + "<head> is the row to use for data-set-property. i.e. 1 means the first row\n"
- + "<keyCols> is a comma separated list of columns from which construct the OpenBIS sampe key\n"
- + "<file> file is the name of the TSV file \n\n"
- + "<tag> a user defined tag which is used as part of the path for output files"
- + "All of <head>,<ignore>,<file> are mandatory arguments.\n"
- + "<ignore> can be set to nothing (i.e. ignore='') in the case that all lines are either a heading or data to be processed\n");
-
- }
-
-}
diff --git a/eu_agronomics/source/java/TsvMangler.java b/eu_agronomics/source/java/TsvMangler.java
deleted file mode 100644
index 4a9e2d02f8c..00000000000
--- a/eu_agronomics/source/java/TsvMangler.java
+++ /dev/null
@@ -1,485 +0,0 @@
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Scanner;
-
-import org.apache.commons.lang.StringUtils;
-
-/**
- * @author walshs
- */
-
-class TsvMangler
-{
-
- // The names of these files correspond to functions available in the openBIS
- // interface which are used to add Samples with properties and to attach
- // samples to experiment
- private final String sampleRegisterFile = "SAMPLES_register_from_a_file_and_attach.txt";
-
- private final String sampleListFile = "SAMPLES_specify_the_list_of_existing_samples.txt";
-
- // The Data Store Server default incoming directory is needed to
- // write a portion of it's service.properties
- // Assumes login is openBis
- private final String incomingDir = new String("~/sprint/datastore_server/data/incoming");
-
- // An integer specification the row which contains column headings
- private final int headRow;
-
- // The column headings specified by headRow are stored in header
- private ArrayList<String> header;
-
- // Rows to ignore
- private final ArrayList<Integer> ignoreRow;
-
- // The columns which define a unique Sample key
- private final ArrayList<Integer> keyCols = new ArrayList<Integer>();
-
- // List of Samples with Properties
- private final ArrayList<SampleWithProperties> swp = new ArrayList<SampleWithProperties>();
-
- // The file to parse
- private final String inFile;
-
- // The name of the DataSet used by the Date Set Server
- private final String dataSetName;
-
- // The name of the experiment
- private final String expt;
-
- // The project name
- private final String project;
-
- // The TSV is stored as an ArrayList of ArrayLists (of Strings)
- private final ArrayList<ArrayList<String>> data = new ArrayList<ArrayList<String>>();
-
- // directory for writing output files
- private String topLevel = new String();
-
- // Data Set Property Types column config
- private HashMap<Integer, String> dspts = new HashMap<Integer, String>();
-
- // Sample Property Types column config
- private final HashMap<Integer, String> spts = new HashMap<Integer, String>();
-
- // CONSTRUCTER
- public TsvMangler(int h, ArrayList<Integer> i, String in, ArrayList<Integer> k, String e,
- HashMap<Integer, String> d, String dsn, HashMap<Integer, String> s, String p)
- {
- headRow = h;
- ignoreRow = i;
- inFile = in;
- expt = e;
- dspts = d;
- dataSetName = dsn;
- project = p;
-
- // Change column specs from 1 based references to 0 based refs
- // for Sample key columns
- Iterator<Integer> iterator = k.iterator();
- while (iterator.hasNext())
- {
- Integer j = new Integer(iterator.next());
- j--;
- keyCols.add(j);
-
- }
-
- // Change column specs from 1 based references to 0 based refs
- // for Sample Property Types
- for (Integer foo : s.keySet())
- {
- Integer bar = foo;
- bar--;
- spts.put(bar, s.get(foo));
- }
-
- loadTsvFile();
-
- System.out.println("header is size ; " + header.size());
-
- generateSampleKeys();
-
- topLevel =
- ("/tmp/Tsv2openBIS/" + expt + '/' + System.getProperty("user.name") + "/"
- + System.currentTimeMillis() + "/");
-
- File top = new File(topLevel);
- top.mkdirs();
-
- System.out.println("Writing files to " + topLevel);
-
- }
-
- private void loadTsvFile()
- {
- // loads the tsv to memory
- // splits the data and header into seperate structures
- try
- {
- BufferedReader input = new BufferedReader(new FileReader(inFile));
- try
- {
- String line = null;
-
- Integer lineNum = 0;
-
- while ((line = input.readLine()) != null)
- {
-
- lineNum++;
- if (line.matches("^\\s+$"))
- {
- System.err.println("Skipping line " + lineNum + " as it contains no data");
- // Weird bug with TSV generated by excel
- // This line.match skips some empty lines because the println runs
- // However, it doesn't match all empty lines as some get put into the "data"
- // ArrayList
- // Can see this when using the debugger
- // It's difficult to inspect because the Mac command line tools such as tail
- // and less
- // don't recognise /r as a newline break. They display as ^M.
- // However, the java readLine doesn't have a problem.
- // Easy quick work around was to go into Excel and delete the blank row of
- // cells
- // so that they are truly empty
-
- } else
- {
-
- ArrayList<String> dataLine = new ArrayList<String>();
-
- Scanner tokenize = new Scanner(line).useDelimiter("\t");
- while (tokenize.hasNext())
- {
- dataLine.add(tokenize.next());
- }
- if (lineNum == headRow)
- {
- header = dataLine;
-
- } else if (ignoreRow.contains(lineNum))
- {
- // do nothing
- } else
- {
- data.add(dataLine);
- }
- }
-
- }
- } finally
- {
- input.close();
- }
- } catch (IOException ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void generateSampleKeys()
- {
-
- // Generate openBIS SAMPLE IDs
- Iterator<ArrayList<String>> di = data.iterator();
- String key2;
-
- while (di.hasNext())
- {
- ArrayList<String> row = di.next();
-
- Iterator<Integer> kci = keyCols.iterator();
- StringBuffer buf = new StringBuffer();
- while (kci.hasNext())
- {
- Integer i = kci.next();
- String value = row.get(i);
- buf.append(value + '_');
- }
- key2 = new String(StringUtils.chop(buf.toString()));
- key2 = key2.toUpperCase();
-
- SampleWithProperties s = new SampleWithProperties(key2);
-
- // now have to add properties
- Iterator<Integer> pi = spts.keySet().iterator();
- while (pi.hasNext())
- {
- Integer key3 = pi.next();
- String val = row.get(key3);
- val = val.toUpperCase();
- s.addProperty(spts.get(key3), val);
- }
- swp.add(s);
- }
- }
-
- private String getDataSetPropertiesAsText()
- {
-
- return StringUtils.join(dspts.values().toArray(), "\n");
- }
-
- public void writeDataSetPropertyLoader()
- {
-
- File f = new File(topLevel + "DataSetProperties.txt");
-
- String txt =
- "This file simply lists DataSet properties to be registerd for the DataSet "
- + dataSetName
- + "\n"
- + "When the HTTPInvoker API is available this method could write a script to automate\n"
- + "the registration process\n" + "Anyhow, for now we just list : \n\n"
- + getDataSetPropertiesAsText();
-
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(txt);
- fOut.close();
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- public void writeSamplePropertyLoader()
- {
-
- File f = new File(topLevel + "SampleProperties.txt");
-
- String txt =
- "This file simply lists Sample properties to be registerd for the sample.\n"
- + "When the HTTPInvoker API is available this method could write a script to automate\n"
- + "the registration process\n" + "Anyhow, for now we just list : \n\n"
- + getSamplePropertiesAsText();
-
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(txt);
- fOut.close();
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- private Object[] getSamplePropertiesAsArray()
- {
-
- // Uses the first Samples With Properties object
- // All these object have the same Property Types
- return (swp.get(0)).getPropertyTypes().toArray();
-
- }
-
- private String getSamplePropertiesAsText()
- {
-
- return StringUtils.join(getSamplePropertiesAsArray(), "\n");
- }
-
- public void writeSamplesFile()
- {
-
- Iterator<SampleWithProperties> swpi = swp.iterator();
- String head =
- ("identifier\t" + StringUtils.join(getSamplePropertiesAsArray(), "\t") + "\n");
- StringBuffer body = new StringBuffer("");
- StringBuffer sl = new StringBuffer("");
-
- while (swpi.hasNext())
- {
- SampleWithProperties sample = swpi.next();
-
- body.append("CISD:/" + project + "/" + sample.getName() + "\t"
- + StringUtils.join(sample.getPropertyValues().toArray(), "\t") + "\n");
- sl.append(sample.getName() + "\n");
- }
-
- File f = new File(topLevel + sampleRegisterFile);
- File f2 = new File(topLevel + sampleListFile);
-
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(head.toString());
- fOut.write(body.toString());
- fOut.close();
-
- BufferedWriter fOut2 = new BufferedWriter(new FileWriter(f2));
- fOut2.write(sl.toString());
- fOut2.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- private String getConfigFromTemplate(String t)
- {
-
- StringBuffer sb = new StringBuffer();
- sb.append("\n");
- sb
- .append("# ---------------------------------------------------------------------------\n");
- sb.append("# " + t + " thread configuration\n");
- sb
- .append("# ---------------------------------------------------------------------------\n");
- sb.append("# The directory to watch for incoming data.\n");
- sb.append(t + ".incoming-dir = data/incoming/" + t + "\n");
- sb.append(t + ".incoming-data-completeness-condition = auto-detection\n");
- sb.append(t + ".space-code = " + project + "\n");
- sb.append("# ---------------- Plugin properties\n");
- sb
- .append(t
- + ".data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor\n");
- sb.append("# following should be set to $ further up the file \n");
- sb
- .append(t
- + ".data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}\n");
- sb.append(t + ".data-set-info-extractor.space-code = " + project + "\n");
- sb
- .append(t
- + ".data-set-info-extractor.data-set-properties-file-name = data-set-properties.tsv\n");
- sb.append(t + ".type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor\n");
- sb.append(t + ".type-extractor.file-format-type = TSV\n");
- sb.append(t + ".type-extractor.locator-type = RELATIVE_LOCATION\n");
- sb.append(t + ".type-extractor.data-set-type = " + t + "\n");
- sb.append(t + ".storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor\n");
- return sb.toString();
- }
-
- public void writeDssMkdir()
- {
-
- StringBuffer mkdir = new StringBuffer("#!/bin/bash\n" + "mkdir -v ");
- mkdir.append(incomingDir + "/" + dataSetName + "\n");
- File f = new File(topLevel + "make_incoming_dirs.sh");
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(mkdir.toString());
- fOut.close();
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- public void writeServiceDotProperties()
- {
-
- String inputsLine = new String("inputs=" + dataSetName);
- StringBuffer config = new StringBuffer();
- String t = getConfigFromTemplate(dataSetName);
- config.append(t);
-
- String sptext = new String(inputsLine + "\n\n" + config.toString() + "\n\n");
-
- File f = new File(topLevel + "thread_config_service_properties.txt");
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(sptext);
- fOut.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
- }
-
- public void writeDataForDssUploadOneDirPerRowStyle()
- {
-
- Iterator<ArrayList<String>> di = data.iterator();
- Iterator<SampleWithProperties> swpi = swp.iterator();
- // each row of data
- while (di.hasNext())
- {
- ArrayList<String> row = di.next();
- String sample = swpi.next().getName();
- // a cell of data
- Iterator<String> ci = row.iterator();
- Iterator<String> hi = header.iterator();
-
- File path = new File(topLevel + "/DataSet/" + dataSetName + "/" + sample + "/");
- File ftsv = new File(path + "/data-set-properties.tsv");
- File fres = new File(path + "/result.txt");
- try
- {
- path.mkdirs();
- BufferedWriter ftsvOut = new BufferedWriter(new FileWriter(ftsv)); // TSV
- BufferedWriter fresOut = new BufferedWriter(new FileWriter(fres)); // RESULT
-
- // write the first line of the result file
- while (hi.hasNext())
- {
- String head = hi.next().toUpperCase();
- fresOut.write("'" + head + "'" + "\t");
- }
- fresOut.write("\n");
-
- // write the first line of the data-set-properties file
- ftsvOut.write("property\tvalue\n");
-
- // write the data and meta-data
- Integer j = 0;
- while (ci.hasNext())
- {
- j++;
- // String cell = ci.next().toUpperCase();
- String cell = ci.next();
- if (dspts.containsKey(j))
- {
- if (cell.equals(""))
- {
- System.err.println(dspts.get(j) + " is `" + cell + "` for sample "
- + sample);
- } else
- {
- ftsvOut.write(dspts.get(j) + "\t" + cell + "\n");
- }
- }
- fresOut.write("'" + cell + "'" + "\t");
-
- }
-
- System.out.println("printed " + j + " cells for sample " + sample + "\n");
- Integer blankCells = header.size() - j;
- System.out.println("need to print " + blankCells + " blank cells\n");
-
- while (blankCells > 0)
- {
- fresOut.write("''" + "\t");
- blankCells--;
- }
-
- fresOut.write("\n");
-
- ftsvOut.close();
- fresOut.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
- }
- }
-}
\ No newline at end of file
diff --git a/eu_agronomics/source/java/TsvUploader.java b/eu_agronomics/source/java/TsvUploader.java
deleted file mode 100644
index 06f05c35f50..00000000000
--- a/eu_agronomics/source/java/TsvUploader.java
+++ /dev/null
@@ -1,398 +0,0 @@
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Scanner;
-
-import org.apache.commons.lang.StringUtils;
-
-/**
- * @author walshs
- */
-
-class TsvUploader
-{
-
- private final String incomingDir =
- new String("/localhome/openbis/sprint/datastore_server/data/incoming");
-
- private final int headRow;
-
- private final ArrayList<Integer> ignoreRow;
-
- private final ArrayList<Integer> keyCols = new ArrayList<Integer>();
-
- // SampleKeys are generated according to numeric specification supplied in keyCols
- private ArrayList<String> sampleKeys = new ArrayList<String>();
-
- private final String inFile;
-
- private final String tag;
-
- private final ArrayList<ArrayList<String>> data = new ArrayList<ArrayList<String>>();
-
- private ArrayList<String> header;
-
- // directory for writing output files
- private String topLevel = new String();
-
- // CONSTRUCTER
- public TsvUploader(int h, ArrayList<Integer> i, String in, ArrayList<Integer> k, String t)
- {
- headRow = h;
- ignoreRow = i;
- inFile = in;
- tag = t;
-
- // change column specs from 1 based references to 0 based refs
- Iterator<Integer> iterator = k.iterator();
- while (iterator.hasNext())
- {
- Integer j = new Integer(iterator.next());
- j--;
- keyCols.add(j);
- }
-
- loadTsvFile();
-
- generateSampleKeys();
-
- topLevel =
- ("/tmp/Tsv2upload/" + tag + '/' + System.getProperty("user.name") + "/"
- + System.currentTimeMillis() + "/");
-
- File top = new File(topLevel);
- top.mkdirs();
-
- System.out.println("Writing files to " + topLevel);
-
- }
-
- private void loadTsvFile()
- {
- // loads the tsv to memory
- // splits the data and header into seperate structures
- try
- {
- BufferedReader input = new BufferedReader(new FileReader(inFile));
- try
- {
- String line = null;
-
- Integer lineNum = 0;
-
- while ((line = input.readLine()) != null)
- {
-
- lineNum++;
- if (line.matches("^\\s+$"))
- {
- System.err.println("Skipping line " + lineNum + " as it contains no data");
- // Weird bug with TSV generated by excel
- // This line.match skips some empty lines because the println runs
- // However, it doesn't match all empty lines as some get put into the "data"
- // ArrayList
- // Can see this when using the debugger
- // It's difficult to inspect because the Mac command line tools such as tail
- // and less
- // don't recognise /r as a newline break. They display as ^M.
- // However, the java readLine doesn't have a problem.
- // Easy quick work around was to go into Excel and delete the blank row of
- // cells
- // so that they are truly empty
-
- } else
- {
-
- ArrayList<String> dataLine = new ArrayList<String>();
-
- Scanner tokenize = new Scanner(line).useDelimiter("\t");
- while (tokenize.hasNext())
- {
- dataLine.add(tokenize.next());
- }
- if (lineNum == headRow)
- {
- header = dataLine;
-
- } else if (ignoreRow.contains(lineNum))
- {
- // do nothing
- } else
- {
- data.add(dataLine);
- }
- }
-
- }
- } finally
- {
- input.close();
- }
- } catch (IOException ex)
- {
- ex.printStackTrace();
- }
- }
-
- public String listSampleKeyColumns()
- {
- Iterator<Integer> iterator = keyCols.iterator();
- StringBuffer skcols = new StringBuffer();
- while (iterator.hasNext())
- {
- skcols.append("Key Col :" + header.get(iterator.next()) + "\n");
- }
- return skcols.toString();
- }
-
- // private void writeTopLevelDirs()
- // {
- //
- // Iterator<String> hid = header.iterator();
- // while (hid.hasNext())
- // {
- // String topDir = topLevel.concat(hid.next());
- // // System.out.println(topDir);
- // try
- // {
- // File d = new File(topDir);
- // boolean success = d.mkdirs();
- // if (success)
- // {
- // // System.out.println("Directory: " + topDir + " created");
- // } else
- // {
- // System.out.println("failed to make " + topDir);
- // }
- // } catch (SecurityException se)
- // {
- // System.err.println("Error: " + se.getMessage());
- // }
- // }
- // }
-
- private void generateSampleKeys()
- {
-
- // generate openBIS SAMPLE IDs
- Iterator<ArrayList<String>> di = data.iterator();
- String key2;
- ArrayList<String> sks = new ArrayList<String>();
- while (di.hasNext())
- {
- ArrayList<String> row = di.next();
-
- Iterator<Integer> kci = keyCols.iterator();
- StringBuffer key = new StringBuffer();
- while (kci.hasNext())
- {
- String value = row.get(kci.next());
- key.append(value + '_');
- }
- key2 = new String(StringUtils.chop(key.toString()));
- key2 = key2.toUpperCase();
- sks.add(key2);
- }
-
- sampleKeys = sks;
- }
-
- public String sampleKeysAsString()
- {
- return sampleKeys.toString();
- }
-
- public void writeSamplesFile()
- {
-
- // Batch upload of samples requires a knowledge of Sample type
- // property types
- //
- // It would be possible to supply arguments so that the file for
- // batch upload of Samples could be written
- // This would need a sample prefix
- //
- // i.e. sample_prefix = CISD:/AGRON-OMICS/
- //
- // and a structure to specify which columns of the data are sample
- // meta-data
- //
- // e.g. sample_meta=[user.ecotype@1,user.color@4]
- //
- // for now I avoid this
-
- Iterator<String> si = sampleKeys.iterator();
- StringBuffer s = new StringBuffer("identifier\n");
- StringBuffer sl = new StringBuffer("");
- while (si.hasNext())
- {
- String sample = si.next();
- s.append("CISD:/AGRON-OMICS/" + sample + "\n");
- sl.append(sample + "\n");
- }
-
- File f = new File(topLevel + "SAMPLES_register_from_a_file_and_attach.txt");
- File f2 = new File(topLevel + "SAMPLES_specify_the_list_of_existing_samples.txt");
-
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(s.toString());
- fOut.close();
-
- BufferedWriter fOut2 = new BufferedWriter(new FileWriter(f2));
- fOut2.write(sl.toString());
- fOut2.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- private String getConfigFromTemplate(String t)
- {
-
- StringBuffer sb = new StringBuffer();
- sb.append("\n");
- sb
- .append("# ---------------------------------------------------------------------------\n");
- sb.append("# " + t + " thread configuration\n");
- sb
- .append("# ---------------------------------------------------------------------------\n");
- sb.append("# The directory to watch for incoming data.\n");
- sb.append(t + ".incoming-dir = data/incoming/" + t + "\n");
- sb.append(t + ".incoming-data-completeness-condition = auto-detection\n");
- sb.append(t + ".space-code = 'AGRON-OMICS'\n");
- sb.append("# ---------------- Plugin properties\n");
- sb
- .append(t
- + ".data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor\n");
- sb.append("# following should be set to $ further up the file \n");
- sb
- .append(t
- + ".data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}\n");
- sb.append(t + ".data-set-info-extractor.space-code = AGRON-OMICS\n");
- sb
- .append(t
- + ".data-set-info-extractor.data-set-properties-file-name = data-set-properties.tsv\n");
- sb.append(t + ".type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor\n");
- sb.append(t + ".type-extractor.file-format-type = TSV\n");
- sb.append(t + ".type-extractor.locator-type = RELATIVE_LOCATION\n");
- sb.append(t + ".type-extractor.data-set-type = " + t + "\n");
- sb.append(t + ".storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor\n");
- return sb.toString();
- }
-
- public void writeDssMkdir()
- {
-
- StringBuffer mkdir = new StringBuffer("#!/bin/bash\n" + "mkdir -v ");
-
- Iterator<String> hid = header.iterator();
- while (hid.hasNext())
- {
- String head = hid.next();
- mkdir.append(incomingDir + "/" + head + " ");
- }
- mkdir.append("\n");
- File f = new File(topLevel + "make_incoming_dirs.sh");
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(mkdir.toString());
- fOut.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
-
- }
-
- public void writeServiceDotProperties()
- {
-
- StringBuffer inputsLine = new StringBuffer("inputs=");
- StringBuffer config = new StringBuffer();
- Iterator<String> hid = header.iterator();
- while (hid.hasNext())
- {
- String head = hid.next();
- String t = getConfigFromTemplate(head);
- config.append(t);
- inputsLine.append(head + ",");
- }
- String sptext =
- new String(StringUtils.chop(inputsLine.toString()) + "\n\n" + config.toString()
- + "\n\n");
-
- File f = new File(topLevel + "thread_config_service_properties.txt");
- try
- {
- BufferedWriter fOut = new BufferedWriter(new FileWriter(f));
- fOut.write(sptext);
- fOut.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
- }
-
- public void writeDataForDssUpload()
- {
-
- // writeTopLevelDirs();
-
- Iterator<ArrayList<String>> di = data.iterator();
- Iterator<String> sKey = sampleKeys.iterator();
- // each row of data
- System.err.println("Writing Files");
- while (di.hasNext())
- {
- System.err.print(".");
- ArrayList<String> row = di.next();
- String sample = sKey.next();
- // a cell of data
- Iterator<String> ci = row.iterator();
- Iterator<String> hi = header.iterator();
- while (ci.hasNext())
- {
- String cell = ci.next().toUpperCase();
- String head = hi.next();
-
- File path = new File(topLevel + "/DataSet/" + head + "/" + sample + "/");
- File ftsv = new File(path + "/data-set-properties.tsv");
- File fres = new File(path + "/result.txt");
- try
- {
- path.mkdirs();
- BufferedWriter ftsvOut = new BufferedWriter(new FileWriter(ftsv));
- ftsvOut.write("property\tvalue\n");
- if (cell.matches("\\S+"))
- {
- ftsvOut.write("USER." + head + "\t" + cell + "\n");
- }
- ftsvOut.close();
-
- BufferedWriter fresOut = new BufferedWriter(new FileWriter(fres));
- fresOut.write(cell + "\n");
- fresOut.close();
-
- } catch (Exception e)
- {
- System.err.println("Error: " + e.getMessage());
- }
- }
- }
- System.err.println("\nDone Writing Files.");
-
- }
-}
\ No newline at end of file
diff --git a/eu_agronomics/source/java/ch/ethz/bsse/cisd/dss/agronomics/.gitignore b/eu_agronomics/source/java/ch/ethz/bsse/cisd/dss/agronomics/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/eu_agronomics/source/java/columnMapper.java b/eu_agronomics/source/java/columnMapper.java
deleted file mode 100644
index ce54edae391..00000000000
--- a/eu_agronomics/source/java/columnMapper.java
+++ /dev/null
@@ -1,156 +0,0 @@
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Scanner;
-
-import org.apache.commons.lang.StringUtils;
-
-/*
- * 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.
- */
-
-/**
- * @author walshs
- */
-public class columnMapper
-{
-
- // column headings index
- Integer inIndex;
-
- // in filename
- String inFile;
-
- // incoming Mapping File
- String inMapFile;
-
- // quick mapper specification
- String quickMapper;
-
- // hash Map of things to replace
- HashMap<String, String> hm = new HashMap<String, String>();
-
- // Common units
- Boolean commonUnits;
-
- // User supplied units
- String userUnits;
-
- // Upper case the heading
- Boolean upperCase;
-
- public columnMapper(int index, String infile, String q, Boolean c, String u, Boolean uc)
- {
- inIndex = index;
- inFile = infile;
- quickMapper = q;
- commonUnits = c;
- userUnits = u;
- upperCase = uc;
-
- createMapStruct();
- createMapStub();
- }
-
- private void createMapStruct()
- {
-
- if (quickMapper == null)
- {
- // do nothing
- } else
- {
-
- Scanner pairs = new Scanner(quickMapper).useDelimiter(",");
- while (pairs.hasNext())
- {
- String pair = pairs.next();
- String[] kv = StringUtils.split(pair, "=");
- hm.put(kv[0], kv[1]);
- }
-
- }
-
- }
-
- private void createMapStub()
- {
- try
- {
- BufferedReader input = new BufferedReader(new FileReader(inFile));
- String line = null;
- Integer lineNum = 0;
- StringBuffer units = new StringBuffer(" (");
- Boolean haveUnits = false;
- if (commonUnits)
- {
- units.append("mm^2 g µm^2 ");
- haveUnits = true;
- }
-
- if (userUnits == null)
- {
- // nothing to do
- } else
- {
- units.append(userUnits);
- haveUnits = true;
- }
- units.append(")");
-
- while ((line = input.readLine()) != null)
- {
- lineNum++;
- if (lineNum == inIndex)
- {
- Scanner tokenize = new Scanner(line).useDelimiter("\t");
- while (tokenize.hasNext())
- {
-
- String toke = tokenize.next();
-
- String toke2 = new String(toke);
- if (upperCase)
- {
- toke2 = StringUtils.upperCase(toke2);
- }
-
- toke2 = toke2.replace(" ", "_");
- for (String s : hm.keySet())
- {
- toke2 = toke2.replace(s, hm.get(s));
- }
-
- System.out.print(toke + "\t" + toke2);
-
- if (haveUnits)
- {
- System.out.print(units.toString());
- }
- System.out.print("\n");
-
- }
-
- }
- }
- input.close();
-
- } catch (IOException ex)
- {
- ex.printStackTrace();
- }
- }
-}
diff --git a/eu_agronomics/source/java/headerReplacer.java b/eu_agronomics/source/java/headerReplacer.java
deleted file mode 100644
index 24e4636f02c..00000000000
--- a/eu_agronomics/source/java/headerReplacer.java
+++ /dev/null
@@ -1,199 +0,0 @@
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Scanner;
-
-import org.apache.commons.lang.StringUtils;
-
-/*
- * 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.
- */
-
-/**
- * @author walshs
- */
-public class headerReplacer
-{
-
- String inFile;
-
- Integer headerIndex;
-
- String mapFile;
-
- String outFile;
-
- HashMap<String, String> hm = new HashMap<String, String>();
-
- public headerReplacer(String file, Integer i, String m, String o)
- {
-
- inFile = file;
- headerIndex = i;
- mapFile = m;
- outFile = o;
-
- try
- {
- createHashMap();
- } catch (Exception ex)
- {
- System.err.println(ex.getMessage());
- ex.printStackTrace();
- System.exit(0);
- }
-
- try
- {
- createOutFile();
- } catch (Exception ex)
- {
- System.err.println(ex.getMessage());
- }
- }
-
- private void createHashMap() throws Exception
- {
-
- BufferedReader input = null;
- try
- {
- input = new BufferedReader(new FileReader(mapFile));
- String line = null;
-
- int lineNum = 0;
- while ((line = input.readLine()) != null)
- {
- lineNum++;
- String[] j = line.split("\t");
- if (j.length != 2)
- {
- throw new Exception(
- "Expecting just 2 values separated by a tab-character in "
- + mapFile
- + " at line "
- + lineNum
- + "\nLine is : \""
- + line
- + "\"\nLine contains "
- + j.length
- + " value(s) some of which may be empty strings or hiddden characters\n");
- } else
- {
- if (hm.containsKey(j[0]))
- {
- throw new Exception("Duplicate key " + j[0] + " in map file " + mapFile);
- } else
- {
- hm.put(j[0], j[1]);
- }
- }
-
- }
- input.close();
-
- } catch (IOException ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (input != null)
- {
- input.close();
- }
- }
-
- }
-
- private void createOutFile() throws Exception
- {
- BufferedReader input;
- BufferedWriter fOut = null;
- try
- {
- input = new BufferedReader(new FileReader(inFile));
- String line = null;
- Integer lineNum = 0;
- File f = new File("./" + outFile);
- System.out.println("Attempting to write the file " + f.toString());
- // f.mkdirs();
- if (f.exists())
- {
- System.out.println("File exists " + f.toString());
- input.close();
- throw new Exception("Output file already exists on the file system. Delete the existing file and re-run. File is :\n" + f.toString());
- }
- f.createNewFile();
-
- try
- {
- fOut = new BufferedWriter(new FileWriter(f));
-
- while ((line = input.readLine()) != null)
- {
- lineNum++;
- if (lineNum == headerIndex)
- {
- Scanner tokenize = new Scanner(line).useDelimiter("\t");
-
- ArrayList<String> headings = new ArrayList<String>();
- while (tokenize.hasNext())
- {
-
- String toke = tokenize.next();
-
- if (hm.containsKey(toke))
- {
- headings.add(hm.get(toke));
- } else
- {
- throw new Exception("The column heading \"" + toke + "\" in " + inFile
- + " does not exist in mapFile " + mapFile);
- }
-
- }
- String headrow = StringUtils.join(headings.toArray(), "\t") + "\n";
- fOut.write(headrow);
-
- } else
- {
- fOut.write(line + "\n");
- }
- }
- input.close();
- fOut.close();
- } finally
- {
- input.close();
- if (fOut != null)
- {
- fOut.close();
- }
- }
- System.out.println("Done writing.");
-
- } catch (IOException ex)
- {
- ex.printStackTrace();
- }
-
- }
-
-}
diff --git a/eu_agronomics/source/java/mapColumns.java b/eu_agronomics/source/java/mapColumns.java
deleted file mode 100644
index 594311a11b0..00000000000
--- a/eu_agronomics/source/java/mapColumns.java
+++ /dev/null
@@ -1,88 +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.
- */
-
-import org.apache.commons.lang.StringUtils;
-import ch.systemsx.cisd.args4j.CmdLineParser;
-import ch.systemsx.cisd.args4j.Option;
-import ch.systemsx.cisd.args4j.CmdLineException;
-
-/**
- * @author walshs
- */
-
-public class mapColumns
-{
-
- @Option(name = "-f", longName = "tsvFile", metaVar = "TSV File ",
- usage = "The Tab Separated Value file to manipulate", required = true)
- private static String file = null;
-
- @Option(name = "-i", longName = "headingsIndex", metaVar = "Row number",
- usage = "Row number of the column headings. 1 is the first.", required = true)
- private static Integer i = -1;
-
- @Option(name = "-uc", longName = "upperCase", metaVar = "Upper case the headings",
- usage = "By default headings are upper-cased", required = false)
- private static Boolean uc = true;
-
- @Option(name = "-q", longName = "quickMapper", metaVar = "Replace characters",
- usage = "Quick mappers specify what to replace as key value pairs", required = false)
- private static String q = "";
-
- @Option(name = "-c", longName = "commonUnits", metaVar = "Include some common units for editing",
- usage = "", required = true)
- private static Boolean c;
-
- @Option(name = "-u", longName = "userUnits", metaVar = "User supplied units",
- usage = "User supplied units are added verbatamin", required = false)
- private static String u;
-
- public void doArgs(String[] args)
- {
- CmdLineParser parser = new CmdLineParser(this);
- parser.setUsageWidth(150);
- try
- {
-
- parser.parseArgument(args);
- // some checking
- if (i < 0)
- {
- throw new CmdLineException("Problem with headings index which was set to " + i);
- }
-
- } catch (CmdLineException e)
- {
-
- System.err.println(e.getMessage());
- System.err.println("Options were \"" + StringUtils.join(args, " ") + "\"\n");
- System.out.println("Usage is :\n\njava mapColumns [ options...]" + "\n");
- parser.printUsage(System.out);
- System.out.println();
-
- return;
- }
- }
-
- public static void main(String[] args)
- {
- new mapColumns().doArgs(args);
-
- new columnMapper(i, file, q, c, u, uc);
-
- }
-
-}
diff --git a/eu_agronomics/source/java/replaceHeader.java b/eu_agronomics/source/java/replaceHeader.java
deleted file mode 100644
index c4ed2581468..00000000000
--- a/eu_agronomics/source/java/replaceHeader.java
+++ /dev/null
@@ -1,78 +0,0 @@
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.args4j.CmdLineException;
-import ch.systemsx.cisd.args4j.CmdLineParser;
-import ch.systemsx.cisd.args4j.Option;
-
-/*
- * 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.
- */
-
-/**
- * @author walshs
- */
-public class replaceHeader
-{
- @Option(name = "-f", longName = "tsvFile", metaVar = "TSV File ",
- usage = "The Tab Separated Value file to manipulate", required = true)
- private static String file = null;
-
- @Option(name = "-i", longName = "headingsIndex", metaVar = "Row number",
- usage = "Row number of the column headings. 1 is the first.", required = true)
- private static Integer i = -1;
-
- @Option(name = "-m", longName = "mappingsFile", metaVar = "The mappings file",
- usage = "The TSV file of mappings from the current header names to the new ones", required = true)
- private static String m = "";
-
- @Option(name = "-o", longName = "outputFile", metaVar = "The output file",
- usage = "The name and path of the output file", required = true)
- private static String o;
-
- public void doArgs(String[] args)
- {
- CmdLineParser parser = new CmdLineParser(this);
- parser.setUsageWidth(150);
- try
- {
-
- parser.parseArgument(args);
- // some checking
- if (i < 0)
- {
- throw new CmdLineException("Problem with headings index which was set to " + i);
- }
-
- } catch (CmdLineException e)
- {
-
- System.err.println(e.getMessage());
- System.err.println("Options were \"" + StringUtils.join(args, " ") + "\"\n");
- System.out.println("Usage is :\n\njava replaceHeader [ options...]" + "\n");
- parser.printUsage(System.out);
- System.out.println();
-
- return;
- }
- }
-
- public static void main(String[] args)
- {
- new replaceHeader().doArgs(args);
-
- new headerReplacer(file, i, m, o);
- }
-
-}
diff --git a/eu_agronomics/targets/.gitignore b/eu_agronomics/targets/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/eu_basynthec/.classpath b/eu_basynthec/.classpath
deleted file mode 100644
index 12257a3b00a..00000000000
--- a/eu_basynthec/.classpath
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
- <classpathentry combineaccessrules="false" kind="src" path="/common"/>
- <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
- <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
- <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
- <classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
- <classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
- <classpathentry kind="lib" path="/libraries/jaxb/jaxb-api.jar" sourcepath="/libraries/jaxb/jaxb-api-src.zip"/>
- <classpathentry kind="lib" path="/libraries/jaxb/jsr173_1.0_api.jar"/>
- <classpathentry kind="lib" path="/libraries/cisd-args4j/cisd-args4j.jar" sourcepath="/libraries/cisd-args4j/cisd-args4j-src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
- <classpathentry kind="lib" path="/libraries/spring/spring-core.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="/libraries/poi/poi.jar"/>
- <classpathentry kind="output" path="targets/classes"/>
-</classpath>
diff --git a/eu_basynthec/.gitignore b/eu_basynthec/.gitignore
deleted file mode 100644
index e5578c439b0..00000000000
--- a/eu_basynthec/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-/targets
-/test-output
-\.shredder
-\.updater
-/log-registrations
diff --git a/eu_basynthec/.project b/eu_basynthec/.project
deleted file mode 100644
index 5c1634e8166..00000000000
--- a/eu_basynthec/.project
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu_basynthec</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.python.pydev.PyDevBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.python.pydev.pythonNature</nature>
- </natures>
- <filteredResources>
- <filter>
- <id>1332321366607</id>
- <name></name>
- <type>26</type>
- <matcher>
- <id>org.eclipse.ui.ide.multiFilter</id>
- <arguments>1.0-name-matches-true-false-.git</arguments>
- </matcher>
- </filter>
- </filteredResources>
-</projectDescription>
diff --git a/eu_basynthec/.pydevproject b/eu_basynthec/.pydevproject
deleted file mode 100644
index a9cca037b33..00000000000
--- a/eu_basynthec/.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/eu_basynthec/build/antrun.sh b/eu_basynthec/build/antrun.sh
deleted file mode 100755
index 5ff1a62b259..00000000000
--- a/eu_basynthec/build/antrun.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#! /bin/bash
-
-ME="$0"
-MYDIR=${ME%/*}
-cd $MYDIR
-ant -lib ../../build_resources/lib/ecj.jar "$@"
diff --git a/eu_basynthec/build/build.xml b/eu_basynthec/build/build.xml
deleted file mode 100644
index 0868f083e80..00000000000
--- a/eu_basynthec/build/build.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<project name="eu_basynthec" default="ci" basedir="..">
- <import file="../../datastore_server/build/build.xml" />
- <import file="../../openbis/build/build.xml" />
- <project-classpath name="ecp" classes="${classes}" />
-
- <property name="variant" value="-basynthec" />
- <property name="original.dist" value="dist" />
- <property name="mainfolder" value="eu_basynthec" />
-
- <target name="compile" depends="build-common.compile, clean" />
-
- <target name="run-tests">
- <antcall target="build-common.run-tests">
- <param name="test.suite" value="tests.xml" />
- </antcall>
- </target>
-
- <target name="jar" depends="compile">
- <mkdir dir="${dist}" />
- <build-info revision="revision.number" version="version.number" clean="clean.flag" />
- <echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
- <jar destfile="${plugin-jar.file}">
- <fileset dir="${classes}">
- <include name="eu/**/*.class" />
- <include name="${build.info.filename}" />
- </fileset>
- <fileset dir="source">
- <include name="**/*.sql" />
- </fileset>
- <manifest>
- <attribute name="Version" value="${version.number}" />
- <attribute name="Build-Number"
- value="${version.number} (r${revision.number},${clean.flag})" />
- </manifest>
- </jar>
- </target>
- <!--
- // Task for creating distributions
- -->
- <target name="dist" depends="jar, datastore_server.make-plugin-dist" />
-
- <!--
- // Task for continuous integration server.
- -->
- <target name="ci" depends="build-common.ci, dist, check-dependencies" />
-
-</project>
\ No newline at end of file
diff --git a/eu_basynthec/dist/etc/data-set-handler.py b/eu_basynthec/dist/etc/data-set-handler.py
deleted file mode 100644
index 40ef48acbb2..00000000000
--- a/eu_basynthec/dist/etc/data-set-handler.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""Just import the data into openbis"""
-tr = service.transaction(incoming)
-dataSet = tr.createNewDataSet()
-tr.moveFile(incoming.getAbsolutePath(), dataSet)
-
diff --git a/eu_basynthec/dist/etc/data-set-validator.py b/eu_basynthec/dist/etc/data-set-validator.py
deleted file mode 100644
index 567cb2e9fad..00000000000
--- a/eu_basynthec/dist/etc/data-set-validator.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-def validate_data_set_file(file):
- errors = []
- return errors
diff --git a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py b/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
deleted file mode 100644
index 8bdccd87bb3..00000000000
--- a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
+++ /dev/null
@@ -1,139 +0,0 @@
-from datetime import datetime
-from eu.basynthec.cisd.dss import TimeSeriesDataExcel
-
-def set_data_type(data_set):
- data_set.setPropertyValue("DATA_TYPE", "OD600")
-
-def retrieve_experiment(tr, exp_id):
- """Get the specified experiment form the server. Return the experiment."""
- if exp_id is None:
- exp = None
- else:
- exp = tr.getExperiment(exp_id)
- return exp
-
-def extract_strains():
- """Extract the strains from the data sheet"""
- strains = []
- lines = timeSeriesData.getRawDataLines()
- for i in range(1, len(lines)):
- line = lines[i]
- strains.append(line[0].upper())
- return ",".join(strains)
-
-def strain_canonical(strainId):
- """Return the canonical form of the strainId"""
- if strainId.lower().startswith('jjs-din'):
- return "JJS-DIn" + strainId[7:]
- else:
- return strainId.upper()
-
-def assign_properties(dataset, metadata):
- """Assign properties to the data set from information in the data."""
- propertyNameMap = {
- "STRAIN_NAMES": "STRAIN_NAMES",
- "TIMEPOINT TYPE": "TIMEPOINT_TYPE",
- "CELL LOCATION": "CELL_LOCATION",
- "VALUE TYPE": "VALUE_TYPE",
- "VALUE UNIT": "VALUE_UNIT",
- "SCALE": "SCALE"
- }
-
- for prop in metadata.keySet():
- key = propertyNameMap.get(prop)
- if key is not None:
- value = metadata.get(prop)
- if (key == "STRAIN"):
- value = value + " (STRAIN)"
- dataset.setPropertyValue(key, strain_canonical(value))
-
-def convert_data_to_tsv(tr, dataset, location):
- """Create a tsv file containing the data and add it to the data set."""
- tr.createNewDirectory(dataset, location)
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
- tsv = open(tsvFileName, 'w')
- for line in timeSeriesData.getRawDataLines():
- for i in range(0, len(line) - 1):
- tsv.write(line[i])
- tsv.write("\t")
- tsv.write(line[len(line) - 1])
- tsv.write("\n")
- tsv.close()
-
-def convert_data_to_split_tsv(tr, dataset, location):
- """Create one tsv file per strain in the original data."""
- raw_data_lines = timeSeriesData.getRawDataLines()
-
- # Extract the header -- this is shared by all files
- header_line = raw_data_lines[0]
- # In the header we don't need the strain, but we start with a run number
- header = 'RunNumber\t' + '\t'.join(header_line[1:len(header_line)])
-
- tr.createNewDirectory(dataset, location)
-
- # Keep track of the strains, since a strain can be measured multiple times
- data_per_strain = {}
-
- lines_len = len(raw_data_lines)
- for i in range(1, len(raw_data_lines)):
- line = raw_data_lines[i]
- strain_name = line[0]
- strain_data = data_per_strain.setdefault(strain_name, [])
- # Append the line -- this is run number + the data
- strain_data.append(str(len(strain_data)) + '\t' + '\t'.join(line[1:len(line)]))
-
- # Create the files
- for strain in data_per_strain.iterkeys():
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + "_" + strain + ".tsv")
- tsv = open(tsvFileName, 'w')
- tsv.write(header)
-
- strain_data = data_per_strain[strain]
- for line in strain_data:
- tsv.write("\n")
- tsv.write(line)
- tsv.close()
-
-def store_original_data(tr, dataset, location):
- """Put the original data into the data set."""
- tr.createNewDirectory(dataset, location)
- tr.moveFile(incoming.getAbsolutePath(), dataset, location + "/" + incoming.getName())
-
-
-tr = service.transaction(incoming)
-timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsolutePath())
-
-# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("OD600")
-metadata = timeSeriesData.getMetadataMap()
-# Strains are not in the metadata, but in the data, so extract them
-metadata["STRAIN_NAMES"] = extract_strains()
-assign_properties(dataset, metadata)
-
-# Store the original and tsv data in data sets
-original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
-set_data_type(original_dataset)
-store_original_data(tr, original_dataset, "xls")
-
-tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
-set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, tsv_dataset, "tsv-multi")
-
-tsv_split_dataset = tr.createNewDataSet("TSV_EXPORT")
-set_data_type(tsv_split_dataset)
-convert_data_to_split_tsv(tr, tsv_split_dataset, "tsv")
-
-# Make the original contain these
-contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode(), tsv_split_dataset.getDataSetCode()]
-dataset.setContainedDataSetCodes(contained_codes)
-
-
-# If no experiment has been set, then get the experiment from the excel file
-if dataset.getExperiment() is None:
- exp_id = metadata.get("EXPERIMENT")
- exp = retrieve_experiment(tr, exp_id)
- if exp is not None:
- dataset.setExperiment(exp)
- original_dataset.setExperiment(exp)
- tsv_dataset.setExperiment(exp)
- tsv_split_dataset.setExperiment(exp)
diff --git a/eu_basynthec/dist/etc/growth-profiles/data-set-validator.py b/eu_basynthec/dist/etc/growth-profiles/data-set-validator.py
deleted file mode 100644
index 2931bd16e6c..00000000000
--- a/eu_basynthec/dist/etc/growth-profiles/data-set-validator.py
+++ /dev/null
@@ -1,60 +0,0 @@
-def validate_data(timeSeriesData, errors):
- dataLines = timeSeriesData.getRawDataLines()
- lineCount = 0
- for line in dataLines:
- # The header needs to be Abs
- if lineCount is 0:
- if line[0] != "Strain":
- errors.append(createFileValidationError("The first data column must be 'Strain'"))
- break
- lineCount = lineCount + 1
- continue
-
- # The compound id should be one of these forms
- strain = line[0].upper()
- if not isStrainIdValid(strain):
- errors.append(createFileValidationError("Line " + str(lineCount + 1) + ", column 1 " + strainValidationErrorMessageFragment(strain)))
- lineCount = lineCount + 1
-
-def validate_metadata(time_series_data, errors):
- metadata = time_series_data.getMetadataMap()
- validationHelper = ValidationHelper(metadata, errors)
-
- # validate the header format
- validationHelper.validateDefaultHeaderFormat()
-
- # validate the timepoint type
- validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE",
- "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")
-
- # validate the cell location
- validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
- "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")
-
- # validate the value type
- validationHelper.validateControlledVocabularyProperty("VALUE TYPE",
- "value type", ['VALUE', 'MEAN', 'MEDIAN', 'STD', 'VAR', 'ERROR', 'IQR'],
- "'Value', 'Mean', 'Median', 'Std', 'Var', 'Error', 'Iqr'")
-
- # validate the value unit
- validationHelper.validateControlledVocabularyProperty("VALUE UNIT",
- "value unit", ['DIMENSIONLESS'], "'DIMENSIONLESS'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
- ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")
-
-def validate_data_set_file(file):
- errors = []
- time_series_data = create_time_series_excel(file.getAbsolutePath())
- if time_series_data is None:
- errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
- return errors
-
- # validate the metadata
- validate_metadata(time_series_data, errors)
-
- # validate the data
- validate_data(time_series_data, errors)
-
- return errors
diff --git a/eu_basynthec/dist/etc/log.xml b/eu_basynthec/dist/etc/log.xml
deleted file mode 100644
index 7a54e2382cb..00000000000
--- a/eu_basynthec/dist/etc/log.xml
+++ /dev/null
@@ -1,55 +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="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender">
-
- <param name="File" value="log/datastore_server_log.txt"/>
- <param name="DatePattern" value="'.'yyyy-MM-dd"/>
-
- <layout class="org.apache.log4j.PatternLayout">
- <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
- </layout>
-
- </appender>
-
- <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" />
-
- <appender name="EMAIL" class="org.apache.log4j.net.SMTPAppender">
-
- <param name="BufferSize" value="512" />
- <param name="SMTPHost" value="localhost" />
- <param name="From" value="datastore_server@localhost" />
- <param name="To" value="root@localhost" />
- <param name="Subject" value="ATTENTION: etl server" />
- <param name="EvaluatorClass" value="ch.systemsx.cisd.common.logging.AlwaysTrueTriggeringEventEvaluator" />
-
- <layout class="org.apache.log4j.PatternLayout">
- <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
- </layout>
-
- <!--filter class="org.apache.log4j.varia.LevelRangeFilter">
- <param name="LevelMin" value="ERROR"/>
- <param name="LevelMax" value="FATAL"/>
- </filter-->
-
- </appender>
-
- <category name="NOTIFY">
- <priority value="info" />
- <appender-ref ref="EMAIL" />
- </category>
-
- <root>
- <priority value="info" />
- <appender-ref ref="DEFAULT" />
- </root>
-
-</log4j:configuration>
diff --git a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
deleted file mode 100644
index eee034223fc..00000000000
--- a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
+++ /dev/null
@@ -1,82 +0,0 @@
-from datetime import datetime
-from eu.basynthec.cisd.dss import TimeSeriesDataExcel
-
-def set_data_type(data_set):
- data_set.setPropertyValue("DATA_TYPE", "METABOLITE_INTENSITIES")
-
-def retrieve_experiment(tr, exp_id):
- """Get the specified experiment form the server. Return the experiment."""
- if exp_id is None:
- exp = None
- else:
- exp = tr.getExperiment(exp_id)
- return exp
-
-def assign_properties(dataset, metadata):
- """Assign properties to the data set from information in the data."""
- propertyNameMap = {
- "STRAIN":"STRAIN_NAMES",
- "TIMEPOINT TYPE": "TIMEPOINT_TYPE",
- "CELL LOCATION": "CELL_LOCATION",
- "VALUE TYPE": "VALUE_TYPE",
- "VALUE UNIT": "VALUE_UNIT",
- "SCALE": "SCALE"
- }
-
- for prop in metadata.keySet():
- key = propertyNameMap.get(prop)
- if key is not None:
- value = metadata.get(prop)
- dataset.setPropertyValue(key, value.upper())
-
-def convert_data_to_tsv(tr, dataset, location):
- """Create a tsv file containing the data and add it to the data set."""
- tr.createNewDirectory(dataset, location)
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
- tsv = open(tsvFileName, 'w')
- for line in timeSeriesData.getRawDataLines():
- for i in range(0, len(line) - 1):
- tsv.write(line[i])
- tsv.write("\t")
- tsv.write(line[len(line) - 1])
- tsv.write("\n")
- tsv.close()
-
-def store_original_data(tr, dataset, location):
- """Put the original data into the data set."""
- tr.createNewDirectory(dataset, location)
- tr.moveFile(incoming.getAbsolutePath(), dataset, location + "/" + incoming.getName())
-
-
-tr = service.transaction(incoming)
-timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsolutePath())
-
-# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("METABOLITE_INTENSITIES")
-metadata = timeSeriesData.getMetadataMap()
-assign_properties(dataset, metadata)
-
-# Store the original and tsv data in data sets
-original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
-set_data_type(original_dataset)
-store_original_data(tr, original_dataset, "xls")
-
-tsv_dataset = tr.createNewDataSet("TSV_EXPORT")
-set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, tsv_dataset, "tsv")
-
-# Make the original contain these
-contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode()]
-dataset.setContainedDataSetCodes(contained_codes)
-
-
-# If no experiment has been set, then get the experiment from the excel file
-if dataset.getExperiment() is None:
- exp_id = metadata.get("EXPERIMENT")
- exp = retrieve_experiment(tr, exp_id)
- if exp is not None:
- dataset.setExperiment(exp)
- original_dataset.setExperiment(exp)
- tsv_dataset.setExperiment(exp)
-
-
diff --git a/eu_basynthec/dist/etc/metabolomics/data-set-validator.py b/eu_basynthec/dist/etc/metabolomics/data-set-validator.py
deleted file mode 100644
index 0e77b3af1eb..00000000000
--- a/eu_basynthec/dist/etc/metabolomics/data-set-validator.py
+++ /dev/null
@@ -1,67 +0,0 @@
-
-def validate_data(time_series_data, errors):
- chebiRegex = re.compile("^CHEBI:[0-9]+")
- bsbmeRegex = re.compile("^BSBME:[0-9]+")
- dataLines = time_series_data.getRawDataLines()
- lineCount = 0
- for line in dataLines:
- # The header needs to be CompoundID
- if lineCount is 0:
- if line[0] != "CompoundID":
- errors.append(createFileValidationError("The first data column must be 'CompoundID'"))
- break
- lineCount = lineCount + 1
- continue
-
- # The compound id should be one of these forms
- compoundId = line[0]
- if not chebiRegex.match(compoundId):
- if not bsbmeRegex.match(compoundId):
- errors.append(createFileValidationError("Line " + str(lineCount + 1) + ", column 1 must be of the format 'CHEBI:#' or 'BSBME:#' (instead of " + compoundId + ")."))
- lineCount = lineCount + 1
-
-def validate_metadata(time_series_data, errors):
- metadata = time_series_data.getMetadataMap()
- validationHelper = ValidationHelper(metadata, errors)
-
- # validate the strain
- validationHelper.validateStrain()
-
- # validate the header format
- validationHelper.validateDefaultHeaderFormat()
-
- # validate the timepoint type
- validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE",
- "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")
-
- # validate the cell location
- validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
- "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")
-
- # validate the value type
- validationHelper.validateControlledVocabularyProperty("VALUE TYPE",
- "value type", ['VALUE', 'MEAN', 'MEDIAN', 'STD', 'VAR', 'ERROR', 'IQR'],
- "'Value', 'Mean', 'Median', 'Std', 'Var', 'Error', 'Iqr'")
-
- # validate the value unit
- validationHelper.validateControlledVocabularyProperty("VALUE UNIT",
- "value unit", ['MM', 'UM', 'RATIOT1', 'RATIOCS'], "'mM', 'uM', 'RatioT1', 'RatioCs'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
- ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")
-
-def validate_data_set_file(file):
- errors = []
- time_series_data = create_time_series_excel(file.getAbsolutePath())
- if time_series_data is None:
- errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
- return errors
-
- # validate the metadata
- validate_metadata(time_series_data, errors)
-
- # validate the data
- validate_data(time_series_data, errors)
-
- return errors
diff --git a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
deleted file mode 100644
index 01d1a47bd7c..00000000000
--- a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
+++ /dev/null
@@ -1,188 +0,0 @@
-from datetime import datetime
-from eu.basynthec.cisd.dss import TimeSeriesDataExcel
-
-def set_data_type(data_set):
- data_set.setPropertyValue("DATA_TYPE", "METABOLITE_INTENSITIES")
-
-def getInitialDataRowAndCol(metadata):
- """Extract the initial row and column as specified in the metadata. Returns an array with [row, col]."""
- # get the raw value from the map
- first_data_row = metadata.get("START DATA ROW")
- first_data_col = metadata.get("START DATA COL")
-
- # convert the row numeric string to an int
- if first_data_row is None:
- first_data_row = 0
- else:
- first_data_row = int(float(first_data_row)) - 1
-
- # convert the column spreadsheet value to an int
- if first_data_col is None:
- first_data_col = 0
- else:
- # columns start at A
- first_data_col = ord(first_data_col) - ord('A')
- return [first_data_row, first_data_col]
-
-def retrieve_experiment(tr, exp_id):
- """Get the specified experiment form the server. Return the experiment."""
- if exp_id is None:
- exp = None
- else:
- exp = tr.getExperiment(exp_id)
- return exp
-
-def assign_properties(dataset, metadata):
- """Assign properties to the data set from information in the data."""
- propertyNameMap = {
- "STRAIN_NAMES":"STRAIN_NAMES",
- "TIMEPOINT TYPE": "TIMEPOINT_TYPE",
- "CELL LOCATION": "CELL_LOCATION",
- "VALUE_TYPES": "VALUE_TYPES",
- "VALUE UNIT": "VALUE_UNIT",
- "SCALE": "SCALE"
- }
-
- for prop in metadata.keySet():
- key = propertyNameMap.get(prop)
- if key is not None:
- value = metadata.get(prop)
- dataset.setPropertyValue(key, value.upper())
-
-def convert_data_to_tsv(tr, dataset, location):
- """Create a tsv file containing the data and add it to the data set."""
- tr.createNewDirectory(dataset, location)
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
- tsv = open(tsvFileName, 'w')
- for line in timeSeriesData.getRawDataLines():
- for i in range(0, len(line) - 1):
- field = line[i]
- if field is None:
- field = ""
- tsv.write(field)
- tsv.write("\t")
- tsv.write(line[len(line) - 1])
- tsv.write("\n")
- tsv.close()
-
-class SplitColumnInfo:
- """
- A class that stores, for each column in the file, the column number, the strain name,
- the biological replicate, the hybridization number, and the column offset in the resulting file
- """
- def __init__(self, column, strain_name, value_type, value_unit, output_col):
- self.column = column
- self.strain_name = strain_name
- self.value_type = value_type
- self.value_unit = value_unit
- self.output_col = output_col
-
- tsv = None
-
-def convert_data_to_split_tsv(tr, start_row, start_col, dataset, location):
- """Create one tsv file per strain in the original data."""
- raw_data = timeSeriesData.getRawDataLines()
-
- # Keep track of the mapping from columns to strains and strains to columns
- column_infos = []
- strain_column_info = {}
-
- # Extract the column / strain mapping
- header_line = raw_data[start_row]
- header_regex = re.compile("^(MGP[0-9]{1,3})-([0-9]) ([0-9]+)")
- for i in range(start_col, len(header_line)):
- match = header_regex.match(header_line[i])
- strain_name = match.group(1)
- strain_cols = strain_column_info.setdefault(strain_name, [])
- column_info = SplitColumnInfo(i, strain_name, match.group(2), match.group(3), len(strain_cols))
- strain_cols.append(column_info)
- column_infos.append(column_info)
-
- # create the files
- tr.createNewDirectory(dataset, location)
- for strain in strain_column_info.iterkeys():
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + "_" + strain + ".tsv")
- tsv = open(tsvFileName, 'w')
- for column_info in strain_column_info[strain]:
- column_info.tsv = tsv
-
- # Write the header
- line = raw_data[start_row]
- tag = line[0]
- # write the first column to each file
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.write(tag)
-
- for column_info in column_infos:
- column_info.tsv.write('\t')
- column_info.tsv.write(column_info.bio_replicate)
- column_info.tsv.write(' ')
- column_info.tsv.write(column_info.hybrid_number)
-
- # Write the data to the files
- for i in range(start_row + 1, len(raw_data)):
- line = raw_data[i]
- tag = line[0]
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.write('\n')
- # write the first column to each file
- strain_column_info[strain][0].tsv.write(tag)
- # Write the remaining data to each file
- for column_info in column_infos:
- column_info.tsv.write('\t')
- column_info.tsv.write(line[column_info.column])
-
- # Close each file
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.close()
-
-def store_original_data(tr, dataset, location):
- """Put the original data into the data set."""
- tr.createNewDirectory(dataset, location)
- tr.moveFile(incoming.getAbsolutePath(), dataset, location + "/" + incoming.getName())
-
-def extract_strains(start_row, start_col):
- """Extract the strain names from the header."""
- strains = []
- line = timeSeriesData.getRawDataLines()[0]
- for i in range(start_col, len(line)):
- strain = line[i]
- if (strain not in strains):
- strains.append(strain)
- return ",".join(strains)
-
-
-tr = service.transaction(incoming)
-timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsolutePath())
-dataStart = getInitialDataRowAndCol(timeSeriesData.getMetadataMap())
-
-# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("METABOLITE_INTENSITIES")
-metadata = timeSeriesData.getMetadataMap()
-metadata["STRAIN_NAMES"] = extract_strains(dataStart[0], dataStart[1])
-assign_properties(dataset, metadata)
-
-# Store the original and tsv data in data sets
-original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
-set_data_type(original_dataset)
-store_original_data(tr, original_dataset, "xls")
-
-tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
-set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, tsv_dataset, "tsv-multi")
-
-# Make the original contain these
-contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode()]
-dataset.setContainedDataSetCodes(contained_codes)
-
-
-# If no experiment has been set, then get the experiment from the excel file
-if dataset.getExperiment() is None:
- exp_id = metadata.get("EXPERIMENT")
- exp = retrieve_experiment(tr, exp_id)
- if exp is not None:
- dataset.setExperiment(exp)
- original_dataset.setExperiment(exp)
- tsv_dataset.setExperiment(exp)
-
-
diff --git a/eu_basynthec/dist/etc/metabolomics2/data-set-validator.py b/eu_basynthec/dist/etc/metabolomics2/data-set-validator.py
deleted file mode 100644
index dccab2fa405..00000000000
--- a/eu_basynthec/dist/etc/metabolomics2/data-set-validator.py
+++ /dev/null
@@ -1,86 +0,0 @@
-# validate the header -- row 1 contains a strainid, row 2 a value type
-def validate_header_line(row, first_data_col, line, errors):
- # validate the strain
- if row is 0:
- for i in range(first_data_col, len(line)):
- strain = line[i]
- if not isStrainIdValid(strain):
- errors.append(createFileValidationError("Strain in col " + str(i + 1) + " " + strainValidationErrorMessageFragment(strain)))
- # validate the value type
- else:
- for i in range(first_data_col, len(line)):
- isControlledVocabularyPropertyValid(line[i],
- "value type", ['VALUE', 'MEAN', 'MEDIAN', 'STD', 'VAR', 'ERROR', 'IQR'],
- "'Value', 'Mean', 'Median', 'Std', 'Var', 'Error', 'Iqr'",
- errors)
-
-def validate_data(time_series_data, first_data_row, first_data_col, errors):
- chebiRegex = re.compile("^CHEBI:[0-9]+")
- bsbmeRegex = re.compile("^BSBME:[0-9]+")
- dataLines = time_series_data.getRawDataLines()
- lineCount = 0
- for line in dataLines:
- # Dispatch to another function to validate the header
- if lineCount < first_data_row:
- validate_header_line(lineCount, first_data_col, line, errors)
- lineCount = lineCount + 1
- continue
-
- # The header needs to be CompoundID
- if lineCount is first_data_row:
- if line[0] != "CompoundID":
- errors.append(createFileValidationError("The first data column must be 'CompoundID'"))
- break
- lineCount = lineCount + 1
- continue
-
- # The compound id should be one of these forms
- compoundId = line[0]
- if not chebiRegex.match(compoundId):
- if not bsbmeRegex.match(compoundId):
- errors.append(createFileValidationError("Line " + str(lineCount + 1) + ", column 1 must be of the format 'CHEBI:#' or 'BSBME:#' (instead of " + compoundId + ")."))
- lineCount = lineCount + 1
-
-def validate_metadata(time_series_data, errors):
- metadata = time_series_data.getMetadataMap()
- validationHelper = ValidationHelper(metadata, errors)
-
- # validate the header format
- validationHelper.validateExplicitHeaderFormat("METABOL HYBRID")
-
- # validate the timepoint type
- validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE",
- "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")
-
- # validate the cell location
- validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
- "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
- ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("VALUE UNIT", "value unit",
- ['MM', 'UM', 'RATIOT1', 'RATIOCS'], "'mM', 'uM', 'RatioT1', 'RatioCs'",)
-
- # validate the data position specification
- validationHelper.validateStartDataRowCol()
-
-
-def validate_data_set_file(file):
- errors = []
- time_series_data = create_time_series_excel(file.getAbsolutePath())
- if time_series_data is None:
- errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
- return errors
-
- # validate the metadata
- validate_metadata(time_series_data, errors)
-
- data_start = getInitialDataRowAndCol(time_series_data.getMetadataMap())
-
- # validate the data
- validate_data(time_series_data, data_start[0], data_start[1], errors)
-
- return errors
diff --git a/eu_basynthec/dist/etc/proteomics/data-set-handler.py b/eu_basynthec/dist/etc/proteomics/data-set-handler.py
deleted file mode 100644
index 8851788856b..00000000000
--- a/eu_basynthec/dist/etc/proteomics/data-set-handler.py
+++ /dev/null
@@ -1,94 +0,0 @@
-from datetime import datetime
-from eu.basynthec.cisd.dss import TimeSeriesDataExcel
-
-def set_data_type(data_set):
- data_set.setPropertyValue("DATA_TYPE", "PROTEIN_QUANTIFICATIONS")
-
-def retrieve_experiment(tr, exp_id):
- """Get the specified experiment form the server. Return the experiment."""
- if exp_id is None:
- exp = None
- else:
- exp = tr.getExperiment(exp_id)
- return exp
-
-def strain_canonical(strainId):
- """Return the canonical form of the strainId"""
- if strainId.lower().startswith('jjs-din'):
- return "JJS-DIn" + strainId[7:]
- else:
- return strainId.upper()
-
-def assign_properties(dataset, metadata):
- """Assign properties to the data set from information in the data."""
- propertyNameMap = {
- "STRAIN":"STRAIN_NAMES",
- "TIMEPOINT TYPE": "TIMEPOINT_TYPE",
- "CELL LOCATION": "CELL_LOCATION",
- "VALUE UNIT": "VALUE_UNIT",
- "SCALE": "SCALE"
- }
-
- for prop in metadata.keySet():
- key = propertyNameMap.get(prop)
- if key is not None:
- value = metadata.get(prop)
- if (key == "STRAIN"):
- value = value + " (STRAIN)"
- if (key == "VALUE_UNIT" and value == "fmol/ug"):
- value = "FMOL_UG"
- dataset.setPropertyValue(key, strain_canonical(value))
-
-def convert_data_to_tsv(tr, dataset, location):
- """Create a tsv file containing the data and add it to the data set."""
- tr.createNewDirectory(dataset, location)
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
- tsv = open(tsvFileName, 'w')
- for line in timeSeriesData.getRawDataLines():
- for i in range(0, len(line) - 1):
- if (line[i]):
- tsv.write(line[i])
- tsv.write("\t")
- if (line[len(line) - 1]):
- tsv.write(line[len(line) - 1])
- tsv.write("\n")
- tsv.close()
-
-def store_original_data(tr, dataset, location):
- """Put the original data into the data set."""
- tr.createNewDirectory(dataset, location)
- tr.moveFile(incoming.getAbsolutePath(), dataset, location + "/" + incoming.getName())
-
-
-tr = service.transaction(incoming)
-timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsolutePath())
-
-# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("PROTEIN_QUANTIFICATIONS")
-metadata = timeSeriesData.getMetadataMap()
-assign_properties(dataset, metadata)
-
-# Store the original and tsv data in data sets
-original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
-set_data_type(original_dataset)
-store_original_data(tr, original_dataset, "xls")
-
-tsv_dataset = tr.createNewDataSet("TSV_EXPORT")
-set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, tsv_dataset, "tsv")
-
-# Make the original contain these
-contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode()]
-dataset.setContainedDataSetCodes(contained_codes)
-
-
-# If no experiment has been set, then get the experiment from the excel file
-if dataset.getExperiment() is None:
- exp_id = metadata.get("EXPERIMENT")
- exp = retrieve_experiment(tr, exp_id)
- if exp is not None:
- dataset.setExperiment(exp)
- original_dataset.setExperiment(exp)
- tsv_dataset.setExperiment(exp)
-
-
diff --git a/eu_basynthec/dist/etc/proteomics/data-set-validator.py b/eu_basynthec/dist/etc/proteomics/data-set-validator.py
deleted file mode 100644
index 41895f33cf2..00000000000
--- a/eu_basynthec/dist/etc/proteomics/data-set-validator.py
+++ /dev/null
@@ -1,74 +0,0 @@
-def validate_data(time_series_data, errors):
- gene_locus_regex = re.compile("^BSU[0-9]+|^BSU_misc_RNA_[0-9]+|^VMG_[0-9]+_[0-9]+(_c)?")
- # Column headers encode timepoint, value type, biological replicates, technical replicates
- column_header_regex = re.compile("^(\+|-)?[0-9]+::(value|mean|median|std|var|error|iqr)::b.+::t.+")
- dataLines = time_series_data.getRawDataLines()
- lineCount = 0
- for line in dataLines:
- # The fist header needs to be GeneLocus or Spot-ID
- if lineCount is 0:
- first_col = line[0]
- is_gene_locus = first_col == "GeneLocus"
- is_spot_id = first_col == "Spot-ID"
- if not (is_gene_locus or is_spot_id):
- errors.append(createFileValidationError("The first data column must be 'GeneLocus'"))
- break
- lineCount = lineCount + 1
- has_human_readable = line[1] == "HumanReadable"
-
- if has_human_readable:
- range_start = 2
- else:
- range_start = 1
- for i in range(range_start, len(line)):
- if not column_header_regex.match(line[i].lower()):
- errors.append(createFileValidationError("Column " + str(i) + " header must be of the format Timepoint::(value|mean|median|std|var|error|iqr)::Biological Replicates::Technical Replicates, (instead of " + line[i] + ")."))
- continue
-
- # The compound id should be one of these forms
- if is_gene_locus:
- gene_locus = line[0]
- if not gene_locus_regex.match(gene_locus):
- errors.append(createFileValidationError("Line " + str(lineCount + 1) + ", column 1 must be of the format 'BSU#', 'BSU_misc_RNA_#', 'VMG_#_#', or 'VMG_#_#_c' (instead of " + gene_locus + ")."))
- lineCount = lineCount + 1
-
-def validate_metadata(time_series_data, errors):
- metadata = time_series_data.getMetadataMap()
- validationHelper = ValidationHelper(metadata, errors)
-
- # validate the strain
- validationHelper.validateStrain()
-
- # validate the header format
- validationHelper.validateExplicitHeaderFormat("TIME::VALUE_TYPE")
-
- # validate the timepoint type
- validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE",
- "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")
-
- # validate the cell location
- validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
- "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")
-
- # validate the value unit
- validationHelper.validateControlledVocabularyProperty("VALUE UNIT",
- "value unit", ['MM', 'UM', 'PERCENT', 'RATIOT1', 'RATIOCS', 'AU', 'DIMENSIONLESS', 'FMOL/UG'], "'mM', 'uM', 'Percent', 'RatioT1', 'RatioCs', 'AU', 'Dimensionless', 'fmol/ug'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
- ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")
-
-def validate_data_set_file(file):
- errors = []
- time_series_data = create_time_series_excel(file.getAbsolutePath())
- if time_series_data is None:
- errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
- return errors
-
- # validate the metadata
- validate_metadata(time_series_data, errors)
-
- # validate the data
- validate_data(time_series_data, errors)
-
- return errors
diff --git a/eu_basynthec/dist/etc/service.properties b/eu_basynthec/dist/etc/service.properties
deleted file mode 100644
index 0519e9f5cf1..00000000000
--- a/eu_basynthec/dist/etc/service.properties
+++ /dev/null
@@ -1,180 +0,0 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = BASYNTHEC
-
-# The root directory of the data store
-storeroot-dir = ${data-folder}/store
-
-# 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 = 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 = 60
-
-# 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
-
-# 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
-
-# The URL of the openBIS server
-server-url = https://localhost:8443
-
-# 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 = https://localhost:8444
-
-# SMTP properties (must start with 'mail' to be considered).
-# mail.smtp.host = localhost
-# 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
-
-# ---------------------------------------------------------------------------
-# INTERNAL CONFIGURATION,
-# Do not change this part unless you are developing openBIS extensions.
-# ---------------------------------------------------------------------------
-
-# ---------------------------------------------------------------------------
-# reporting and processing plugins configuration
-# ---------------------------------------------------------------------------
-
-# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
-reporting-plugins = tsv-viewer
-
-tsv-viewer.label = Time Series
-tsv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA
-tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
-
-# ---------------------------------------------------------------------------
-# BEGIN DROPBOXES
-# ---------------------------------------------------------------------------
-
-# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
-# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs = main-thread, metabolomics, growth-profiles, transcriptomics, proteomics
-
-# ---------------------------------------------------------------------------
-# main thread configuration
-# ---------------------------------------------------------------------------
-main-thread.incoming-dir = ${root}/incoming
-
-# 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'.
-main-thread.incoming-data-completeness-condition = auto-detection
-main-thread.delete-unidentified = true
-
-main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.script-path = /local0/openbis/jython_scripts/data-set-handler.py
-main-thread.validation-script-path = /local0/openbis/jython_scripts/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# metabolomics thread configuration
-# ---------------------------------------------------------------------------
-metabolomics.incoming-dir = ${root}/incoming-metabolomics
-metabolomics.incoming-data-completeness-condition = auto-detection
-metabolomics.delete-unidentified = true
-metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-metabolomics.script-path = /local0/openbis/jython_scripts/metabolomics/data-set-handler.py
-metabolomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/metabolomics/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# growth-profiles thread configuration
-# ---------------------------------------------------------------------------
-growth-profiles.incoming-dir = ${root}/incoming-od600
-growth-profiles.incoming-data-completeness-condition = auto-detection
-growth-profiles.delete-unidentified = true
-growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-growth-profiles.script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/growth-profiles/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# transcriptomics thread configuration
-# ---------------------------------------------------------------------------
-transcriptomics.incoming-dir = ${root}/incoming-transcriptomics
-transcriptomics.incoming-data-completeness-condition = auto-detection
-transcriptomics.delete-unidentified = true
-transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-transcriptomics.script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/transcriptomics/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# proteomics thread configuration
-# ---------------------------------------------------------------------------
-proteomics.incoming-dir = ${root}/incoming-proteomics
-proteomics.incoming-data-completeness-condition = auto-detection
-proteomics.delete-unidentified = true
-proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-proteomics.script-path = /local0/openbis/jython_scripts/proteomics/data-set-handler.py
-proteomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/proteomics/data-set-validator.py
-
-
-#
-# The dss-rpc section configures the RPC put functionality by providing a mapping between data
-# set type and input thread parameters.
-#
-# The default input thread is specified by the put-default key. If not specified, the first input
-# thread will be used.
-#
-# Mappings are specified by dss-rpc.<data-set-code> = <thread-name>
-#
-# If this section is empty, then the first input thread will be used.
-#
-dss-rpc.put-default = main-thread
-dss-rpc.put.METABOLITE_INTENSITIES = metabolomics
-dss-rpc.put.OD600 = growth-profiles
-dss-rpc.put.TRANSCRIPTOMICS = transcriptomics
-dss-rpc.put.PROTEIN_QUANTIFICATIONS = proteomics
-
diff --git a/eu_basynthec/dist/etc/shared/shared-classes.py b/eu_basynthec/dist/etc/shared/shared-classes.py
deleted file mode 100644
index 054c4992814..00000000000
--- a/eu_basynthec/dist/etc/shared/shared-classes.py
+++ /dev/null
@@ -1,210 +0,0 @@
-"""
-Code that is shared between the handlers and validators for different data set types.
-
-Includes a class for reading time series data from Excel, and code for validating BaSynthec data, in particular strains.
-"""
-import os
-import re
-import sys
-import java.io.File
-from java.io import IOException
-from java.lang import IllegalArgumentException
-from ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation import ValidationError, ValidationScriptRunner
-from ch.systemsx.cisd.openbis.dss.generic.shared.utils import ExcelFileReader
-from ch.systemsx.cisd.common.logging import LogFactory, LogCategory
-
-operationLog = LogFactory.getLogger(LogCategory.OPERATION, ValidationScriptRunner)
-OPENBIS_METADATA_SHEET_NAME = "openbis-metadata"
-OPENBIS_DATA_SHEET_NAME = "openbis-data"
-
-class TimeSeriesDataExcel:
- """
- An abstraction for accessing time series data following the BaSynthec conventions
- from an Excel file. This class ported from Java, thus the camelCase naming.
- """
- def __init__(self, file, fileReader):
- self.file = file
- self.fileReader = fileReader
-
- def getRawMetadataLines(self):
- """Get the raw lines of the metadata sheet."""
- try:
- return self.fileReader.readLines(OPENBIS_METADATA_SHEET_NAME);
- except IOException, ex:
- operationLog.error("Could not read data from [file: " + self.file.getPath() + ", sheet: "
- + OPENBIS_METADATA_SHEET_NAME + "]", ex)
- return []
-
- def getRawDataLines(self):
- """Get the raw lines of the data sheet."""
- try:
- return self.fileReader.readLines(OPENBIS_DATA_SHEET_NAME)
- except IOException, ex:
- operationLog.error("Could not read data from [file: " + file.getPath() + ", sheet: "
- + OPENBIS_DATA_SHEET_NAME + "]", ex)
- return []
-
- def getMetadataMap(self):
- """
- Return the metadata has a hashmap, with all keys uppercased.
-
- Assumes the metadata sheet corresponds to the following format: [Property] [Value] [... stuff
- that can be ignored], that is the property name is in column 1 and property value is in
- column 2, and everything else can be ignored.
- """
- metadataMap = {}
- metadataLines = self.getRawMetadataLines()
-
- # Skip the first line, this is just the header
- for i in range(1, metadataLines.size()):
- line = metadataLines.get(i)
- value = line[1];
- if "BLANK" == value:
- value = None
- if line[0] is not None:
- metadataMap[line[0].upper()] = value
- return metadataMap
-
-def create_time_series_excel(fileName):
- """Factory method for the TimeSeriesData object. Returns None if it cannot be created."""
- file = java.io.File(fileName)
- try:
- workbook = ExcelFileReader.getExcelWorkbook(file)
- fileReader = ExcelFileReader(workbook, True)
- return TimeSeriesDataExcel(file, fileReader)
- except IllegalArgumentException, ex:
- operationLog.error("Could not open file [" + fileName + "] as Excel data.", ex)
- except IOException, ex:
- operationLog.error("Could not open file [" + fileName + "] as Excel data.", ex)
- return None
-
-
-
-class ValidationHelper:
- """
- Methods for simplifying validation in BaSynthec.
- This class is ported from Java, thus the camelCase naming.
- """
- def __init__(self, metadataMap, errors):
- self.metadataMap = metadataMap
- self.errors = errors
-
- def checkIsSpecified(self, property, displayName):
- """Verify that a property is specified; if not, add a validation error to the list."""
- if self.metadataMap.get(property) is None:
- self.errors.append(ValidationError.createFileValidationError("A " + displayName
- + " must be specified."))
- return False
- return True
-
- def validateStrain(self):
- """Verify that the strain is specified and of the correct format"""
- if not self.checkIsSpecified("STRAIN", "strain"):
- return
- strain = self.metadataMap.get("STRAIN")
- if not isStrainIdValid(strain):
- self.errors.append(createFileValidationError("Strain " + strainValidationErrorMessageFragment(strain)))
-
- def validateDefaultHeaderFormat(self):
- """Validate that header format is either not specified or matches default (TIME)"""
- if self.metadataMap.get("HEADER FORMAT") is None:
- return
- format = self.metadataMap.get("HEADER FORMAT")
- expected_format = "TIME"
- if expected_format != format:
- self.errors.append(createFileValidationError("Header format must be " + expected_format + " (not " + format + ")."))
-
- def validateExplicitHeaderFormat(self, expected_format):
- """Validate that header format is specified and matches the expected_format argument"""
- if not self.checkIsSpecified("HEADER FORMAT", "header format"):
- return
- format = self.metadataMap.get("HEADER FORMAT")
- if expected_format != format:
- self.errors.append(createFileValidationError("Header format must be " + expected_format + " (not " + format + ")."))
-
- def validateControlledVocabularyProperty(self, property, displayName, allowedValues, allowedValuesDisplay):
- """Validate that the property is specified and in the list of allowed values"""
- value = self.metadataMap.get(property)
- isControlledVocabularyPropertyValid(value, displayName, allowedValues, allowedValuesDisplay, self.errors)
-
- def validateStartDataRowCol(self):
- if self.checkIsSpecified("START DATA ROW", "Start Data Row"):
- value = self.metadataMap.get("START DATA ROW")
- match = re.match("[0-9]+", value)
- if match is None:
- self.errors.append(createFileValidationError("The Start Data Row must be a number (not " + value + ")."))
- if self.checkIsSpecified("START DATA COL", "Start Data Col"):
- value = self.metadataMap.get("START DATA COL")
- match = re.match("[A-Z]", value)
- if match is None:
- self.errors.append(createFileValidationError("The Start Data Col must be a letter between A and Z (not " + value + ")."))
-
-#
-# Strain validation stuff
-#
-strainIdRegexMin = re.compile("^ms|chassis\s*[1-3]|wt 168 trp\+|jjs-mgp254")
-strainIdRegexFull = re.compile("^jjs-mgp[0-9]{1,3}|^jjs-din[0-9]{1,3}|^ms|chassis\s*[1-3]|wt 168 trp\+")
-strainIds = {}
-home_dir = os.environ.get('HOME', '')
-if os.path.exists(home_dir + '/var/strainids.txt'):
- for sid in open(home_dir + '/var/strainids.txt').readlines():
- strainIds[sid.strip().lower()] = 1
-
-def _match(regex, strainId):
- match = regex.match(strainId)
- if match is None:
- return False
- return len(match.group(0)) == len(strainId)
-
-def isStrainIdValid(strainId):
- """Return true if the strain id passes validation (has the form specified in the regex and is in Chris' strain db)"""
- strainIdLower = strainId.lower()
- if len(strainIds) > 0:
- return strainIds.has_key(strainIdLower) or _match(strainIdRegexMin, strainIdLower)
- else:
- return _match(strainIdRegexFull, strainIdLower)
-
-def strainValidationErrorMessageFragment(strain):
- """Return a sentence fragment describing the strain validation error."""
- return "must be either JJS-MGP[0-999], JJS-DIN[0-999], MS, CHASSIS [1-3], or WT 168 TRP+ (instead of " + strain + ")."
-
-def isControlledVocabularyPropertyValid(value, displayName, allowedValues, allowedValuesDisplay, errors):
- """Validate that the property is specified and in the list of allowed values"""
- if value is None:
- errors.append(ValidationError.createFileValidationError("A " + displayName + " must be specified."))
- return False
- value = value.upper()
- if value not in allowedValues:
- if len(allowedValues) > 1:
- errors.append(createFileValidationError("The " + displayName + " must be one of " + allowedValuesDisplay + " (not " + value + ")."))
- return False
- else:
- errors.append(createFileValidationError("The " + displayName + " must be " + allowedValuesDisplay + " (not " + value + ")."))
- return False
- return True
-
-def getInitialDataRowAndCol(metadata):
- """Extract the initial row and column as specified in the metadata. Returns an array with [row, col]."""
- # get the raw value from the map
- first_data_row = metadata.get("START DATA ROW")
- first_data_col = metadata.get("START DATA COL")
-
- # convert the row numeric string to an int
- if first_data_row is None:
- first_data_row = 0
- else:
- try:
- first_data_row = int(float(first_data_row)) - 1
- except:
- first_data_row = 0
-
- # convert the column spreadsheet value to an int
- if first_data_col is None:
- first_data_col = 0
- else:
- # columns start at A
- try:
- first_data_col = ord(first_data_col) - ord('A')
- except:
- first_data_cal = 0
- return [first_data_row, first_data_col]
diff --git a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
deleted file mode 100644
index dde79f935c0..00000000000
--- a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
+++ /dev/null
@@ -1,208 +0,0 @@
-from datetime import datetime
-from eu.basynthec.cisd.dss import TimeSeriesDataExcel
-import re
-
-# A Regex for matching the column headers
-header_regex = re.compile("^(.+)-(.*) ([0-9]+)")
-
-def set_data_type(data_set):
- data_set.setPropertyValue("DATA_TYPE", "TRANSCRIPTOMICS")
-
-def getInitialDataRowAndCol(metadata):
- """Extract the initial row and column as specified in the metadata. Returns an array with [row, col]."""
- # get the raw value from the map
- first_data_row = metadata.get("START DATA ROW")
- first_data_col = metadata.get("START DATA COL")
-
- # convert the row numeric string to an int
- if first_data_row is None:
- first_data_row = 0
- else:
- first_data_row = int(float(first_data_row)) - 1
-
- # convert the column spreadsheet value to an int
- if first_data_col is None:
- first_data_col = 0
- else:
- # columns start at A
- first_data_col = ord(first_data_col) - ord('A')
- return [first_data_row, first_data_col]
-
-
-def retrieve_experiment(tr, exp_id):
- """Get the specified experiment form the server. Return the experiment."""
- if exp_id is None:
- exp = None
- else:
- exp = tr.getExperiment(exp_id)
- return exp
-
-def strain_canonical(strainId):
- """Return the canonical form of the strainId"""
- if strainId.lower().startswith('jjs-din'):
- return "JJS-DIn" + strainId[7:]
- else:
- return strainId.upper()
-
-def assign_properties(dataset, metadata):
- """Assign properties to the data set from information in the data."""
- propertyNameMap = {
- "STRAIN_NAMES": "STRAIN_NAMES",
- "TIMEPOINT TYPE": "TIMEPOINT_TYPE",
- "CELL LOCATION": "CELL_LOCATION",
- "VALUE TYPE": "VALUE_TYPE",
- "VALUE UNIT": "VALUE_UNIT",
- "SCALE": "SCALE"
- }
-
- for prop in metadata.keySet():
- key = propertyNameMap.get(prop)
- if key is not None:
- value = metadata.get(prop)
- if (key == "STRAIN"):
- value = value + " (STRAIN)"
- dataset.setPropertyValue(key, strain_canonical(value))
-
-def convert_data_to_tsv(tr, start_row, start_col, dataset, location):
- """Create a tsv file containing the data and add it to the data set."""
- tr.createNewDirectory(dataset, location)
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
- tsv = open(tsvFileName, 'w')
- raw_data = timeSeriesData.getRawDataLines()
- for i in range(start_row, len(raw_data)):
- line = raw_data[i]
- # write the metabolite id
- tsv.write(line[0])
- tsv.write("\t")
- for j in range(start_col, len(line) - 1):
- tsv.write(line[j])
- tsv.write("\t")
- tsv.write(line[len(line) - 1])
- tsv.write("\n")
- tsv.close()
-
-class SplitColumnInfo:
- """
- A class that stores, for each column in the file, the column number, the strain name,
- the biological replicate, the hybridization number, and the column offset in the resulting file
- """
- def __init__(self, column, strain_name, bio_replicate, hybrid_number, output_col):
- self.column = column
- self.strain_name = strain_name
- self.bio_replicate = bio_replicate
- self.hybrid_number = hybrid_number
- self.output_col = output_col
-
- tsv = None
-
-
-def convert_data_to_split_tsv(tr, start_row, start_col, dataset, location):
- """Create one tsv file per strain in the original data."""
- raw_data = timeSeriesData.getRawDataLines()
-
- # Keep track of the mapping from columns to strains and strains to columns
- column_infos = []
- strain_column_info = {}
-
- # Extract the column / strain mapping
- header_line = raw_data[start_row]
- for i in range(start_col, len(header_line)):
- match = header_regex.match(header_line[i])
- strain_name = match.group(1)
- strain_cols = strain_column_info.setdefault(strain_name, [])
- column_info = SplitColumnInfo(i, strain_name, match.group(2), match.group(3), len(strain_cols))
- strain_cols.append(column_info)
- column_infos.append(column_info)
-
- # create the files
- tr.createNewDirectory(dataset, location)
- for strain in strain_column_info.iterkeys():
- tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + "_" + strain + ".tsv")
- tsv = open(tsvFileName, 'w')
- for column_info in strain_column_info[strain]:
- column_info.tsv = tsv
-
- # Write the header
- line = raw_data[start_row]
- tag = line[0]
- # write the first column to each file
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.write(tag)
-
- for column_info in column_infos:
- column_info.tsv.write('\t')
- column_info.tsv.write(column_info.bio_replicate)
- column_info.tsv.write(' ')
- column_info.tsv.write(column_info.hybrid_number)
-
- # Write the data to the files
- for i in range(start_row + 1, len(raw_data)):
- line = raw_data[i]
- tag = line[0]
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.write('\n')
- # write the first column to each file
- strain_column_info[strain][0].tsv.write(tag)
- # Write the remaining data to each file
- for column_info in column_infos:
- column_info.tsv.write('\t')
- column_info.tsv.write(line[column_info.column])
-
- # Close each file
- for strain in strain_column_info.iterkeys():
- strain_column_info[strain][0].tsv.close()
-
-def store_original_data(tr, dataset, location):
- """Put the original data into the data set."""
- tr.createNewDirectory(dataset, location)
- tr.moveFile(incoming.getAbsolutePath(), dataset, location + "/" + incoming.getName())
-
-def extract_strains(start_row, start_col):
- """Extract the strain names from the header. These have already been validated by the validator."""
- strains = []
- line = timeSeriesData.getRawDataLines()[start_row]
- for i in range(start_col, len(line)):
- match = header_regex.match(line[i])
- strains.append(match.group(1))
- return ",".join(strains)
-
-
-
-tr = service.transaction(incoming)
-timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsolutePath())
-dataStart = getInitialDataRowAndCol(timeSeriesData.getMetadataMap())
-
-# create the data set and assign the metadata from the file
-dataset = tr.createNewDataSet("TRANSCRIPTOMICS")
-metadata = timeSeriesData.getMetadataMap()
-metadata["STRAIN_NAMES"] = extract_strains(dataStart[0], dataStart[1])
-assign_properties(dataset, metadata)
-
-# Store the original and tsv data in data sets
-original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL")
-set_data_type(original_dataset)
-store_original_data(tr, original_dataset, "xls")
-
-tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
-set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, dataStart[0], dataStart[1], tsv_dataset, "tsv-multi")
-
-tsv_split_dataset = tr.createNewDataSet("TSV_EXPORT")
-set_data_type(tsv_split_dataset)
-convert_data_to_split_tsv(tr, dataStart[0], dataStart[1], tsv_split_dataset, "tsv")
-
-# Make the original contain these
-contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode(), tsv_split_dataset.getDataSetCode()]
-dataset.setContainedDataSetCodes(contained_codes)
-
-
-# If no experiment has been set, then get the experiment from the excel file
-if dataset.getExperiment() is None:
- exp_id = metadata.get("EXPERIMENT")
- exp = retrieve_experiment(tr, exp_id)
- if exp is not None:
- dataset.setExperiment(exp)
- original_dataset.setExperiment(exp)
- tsv_dataset.setExperiment(exp)
- tsv_split_dataset.setExperiment(exp)
-
diff --git a/eu_basynthec/dist/etc/transcriptomics/data-set-validator.py b/eu_basynthec/dist/etc/transcriptomics/data-set-validator.py
deleted file mode 100644
index 71c191ff26e..00000000000
--- a/eu_basynthec/dist/etc/transcriptomics/data-set-validator.py
+++ /dev/null
@@ -1,81 +0,0 @@
-def validate_header(line, first_data_col, errors):
- """Validate the header, returning False if there is no point in continuing validation"""
- if line[0] != "Locustag":
- errors.append(createFileValidationError("The first data column must be 'Locustag' (not " + line[0] + ")."))
- return False
- header_regex = re.compile("^(.+)-(.*) ([0-9]+)")
- for i in range(first_data_col, len(line)):
- match = header_regex.match(line[i])
- if match is None:
- errors.append(createFileValidationError("The column header + " + str(i) + " must be of the form [STRAIN]-[BIOLOGICAL REPLICATE] [HYBRIDIZATION NUMBER]. " + line[i] + " is not."))
- continue
- strainName = match.group(1)
- if isStrainIdValid(strainName) is False:
- errors.append(createFileValidationError("The column header + " + str(i) + " must be of the form [STRAIN]-[BIOLOGICAL REPLICATE] [HYBRIDIZATION NUMBER]. " + strainName + " is not a recognized strain."))
- continue
-
-
-
-def validate_data(time_series_data, first_data_row, first_data_col, errors):
- gene_locus_regex = re.compile("^BSU[0-9]+|^BSU_misc_RNA_[0-9]+|^VMG_[0-9]+_[0-9]+(_c)?")
- dataLines = time_series_data.getRawDataLines()
- for i in range(first_data_row, len(dataLines)):
- line = dataLines[i]
- # The header needs to be CompoundID
- if i is first_data_row:
- if not validate_header(line, first_data_col, errors):
- break
- continue
-
- # The compound id should be one of these forms
- gene_locus = line[0]
- if not gene_locus_regex.match(gene_locus):
- errors.append(createFileValidationError("Line " + str(i + 1) + ", column 1 must be of the format 'BSU#', 'BSU_misc_RNA_#', 'VMG_#_#', or 'VMG_#_#_c' (instead of " + gene_locus + ")."))
-
-def validate_metadata(time_series_data, errors):
- metadata = time_series_data.getMetadataMap()
- validationHelper = ValidationHelper(metadata, errors)
-
- # validate the header format
- validationHelper.validateExplicitHeaderFormat("STRAIN-BIOREP HYBRID")
-
- # validate the timepoint type
- validationHelper.validateControlledVocabularyProperty("TIMEPOINT TYPE",
- "time point type", ['EX', 'IN', 'SI'], "'EX', 'IN', 'SI'")
-
- # validate the cell location
- validationHelper.validateControlledVocabularyProperty("CELL LOCATION",
- "cell location", ['CE', 'ES', 'ME', 'CY', 'NC'], "'CE', 'ES', 'ME', 'CY', 'NC'")
-
- # validate the value type
- validationHelper.validateControlledVocabularyProperty("VALUE TYPE",
- "value type", ['VALUE', 'MEAN', 'MEDIAN', 'STD', 'VAR', 'ERROR', 'IQR'],
- "'Value', 'Mean', 'Median', 'Std', 'Var', 'Error', 'Iqr'")
-
- # validate the value unit
- validationHelper.validateControlledVocabularyProperty("VALUE UNIT",
- "value unit", ['MM', 'UM', 'PERCENT', 'RATIOT1', 'RATIOCS', 'AU', 'DIMENSIONLESS'], "'mM', 'uM', 'Percent', 'RatioT1', 'RatioCs', 'AU', 'Dimensionless'")
-
- # validate the scale
- validationHelper.validateControlledVocabularyProperty("SCALE", "scale",
- ['LIN', 'LOG2', 'LOG10', 'LN'], "'lin', 'log2', 'log10', 'ln'")
-
- # validate the data position specification
- validationHelper.validateStartDataRowCol()
-
-def validate_data_set_file(file):
- errors = []
- time_series_data = create_time_series_excel(file.getAbsolutePath())
- if time_series_data is None:
- errors.append(createFileValidationError(file.getName() + " is not an Excel file."))
- return errors
-
- # validate the metadata
- validate_metadata(time_series_data, errors)
-
- data_start = getInitialDataRowAndCol(time_series_data.getMetadataMap())
-
- # validate the data
- validate_data(time_series_data, data_start[0], data_start[1], errors)
-
- return errors
diff --git a/eu_basynthec/etc/log.xml b/eu_basynthec/etc/log.xml
deleted file mode 100644
index 5cee0a68436..00000000000
--- a/eu_basynthec/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/eu_basynthec/etc/service.properties b/eu_basynthec/etc/service.properties
deleted file mode 100644
index 2bd62a7a9ae..00000000000
--- a/eu_basynthec/etc/service.properties
+++ /dev/null
@@ -1,194 +0,0 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS1
-
-data-folder = ../eu_basynthec/targets/data
-
-# The root directory of the data store
-storeroot-dir = ${data-folder}/store
-
-# The directory for incoming files over rpc
-rpc-incoming-dir = ${data-folder}/incoming
-
-# 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
-
-# Set to 'false' for development/testing without deployed server. In this mode datastore will not use
-# SSL when connecting to openbis. Otherwise all 'keystore' properties need to be set for SSL connection
-# (default when use-ssl property is not set so there is no need to specify it on production servers).
-use-ssl = false
-
-# 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 = 10
-
-# 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
-
-# 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
-
-# The URL of the openBIS server
-server-url = http://localhost:8888
-
-# The username to use when contacting the openBIS server
-username = etlserver-basynthec
-
-# The password to use when contacting the openBIS server
-password = etlserver
-
-# The base URL for Web client access.
-download-url = http://localhost:${port}
-
-# SMTP properties (must start with 'mail' to be considered).
-# mail.smtp.host = localhost
-# mail.from = datastore_server@localhost
-mail.smtp.host = file://targets/playground/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
-
-# ---------------------------------------------------------------------------
-# INTERNAL CONFIGURATION,
-# Do not change this part unless you are developing openBIS extensions.
-# ---------------------------------------------------------------------------
-
-# ---------------------------------------------------------------------------
-# reporting and processing plugins configuration
-# ---------------------------------------------------------------------------
-
-# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
-reporting-plugins = tsv-viewer
-
-tsv-viewer.label = Time Series
-tsv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA
-tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
-
-# ---------------------------------------------------------------------------
-# BEGIN DROPBOXES
-# ---------------------------------------------------------------------------
-
-# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
-# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs = main-thread, metabolomics, growth-profiles, transcriptomics, proteomics
-
-incoming-dir-create = true
-
-# ---------------------------------------------------------------------------
-# main thread configuration
-# ---------------------------------------------------------------------------
-main-thread.incoming-dir = ${data-folder}/incoming
-
-# 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'.
-main-thread.incoming-data-completeness-condition = auto-detection
-main-thread.delete-unidentified = true
-
-main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.script-path = ../eu_basynthec/dist/etc/data-set-handler.py
-main-thread.validation-script-path = ../eu_basynthec/dist/etc/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# metabolomics thread configuration
-# ---------------------------------------------------------------------------
-metabolomics.incoming-dir = ${data-folder}/incoming-metabolomics
-metabolomics.incoming-data-completeness-condition = auto-detection
-metabolomics.delete-unidentified = true
-metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-metabolomics.script-path = ../eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
-metabolomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/metabolomics2/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# growth-profiles thread configuration
-# ---------------------------------------------------------------------------
-growth-profiles.incoming-dir = ${data-folder}/incoming-od600
-growth-profiles.incoming-data-completeness-condition = auto-detection
-growth-profiles.delete-unidentified = true
-growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-growth-profiles.script-path = ../eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/growth-profiles/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# transcriptomics thread configuration
-# ---------------------------------------------------------------------------
-transcriptomics.incoming-dir = ${data-folder}/incoming-transcriptomics
-transcriptomics.incoming-data-completeness-condition = auto-detection
-transcriptomics.delete-unidentified = true
-transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-transcriptomics.script-path = ../eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/transcriptomics/data-set-validator.py
-
-# ---------------------------------------------------------------------------
-# proteomics thread configuration
-# ---------------------------------------------------------------------------
-proteomics.incoming-dir = ${data-folder}/incoming-proteomics
-proteomics.incoming-data-completeness-condition = auto-detection
-proteomics.delete-unidentified = true
-proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
-proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-proteomics.script-path = ../eu_basynthec/dist/etc/proteomics/data-set-handler.py
-proteomics.validation-script-path = ../eu_basynthec/dist/etc/shared/shared-classes.py,../eu_basynthec/dist/etc/proteomics/data-set-validator.py
-
-
-#
-# The dss-rpc section configures the RPC put functionality by providing a mapping between data
-# set type and input thread parameters.
-#
-# The default input thread is specified by the put-default key. If not specified, the first input
-# thread will be used.
-#
-# Mappings are specified by dss-rpc.<data-set-code> = <thread-name>
-#
-# If this section is empty, then the first input thread will be used.
-#
-dss-rpc.put-default = main-thread
-dss-rpc.put.METABOLITE_INTENSITIES = metabolomics
-dss-rpc.put.OD600 = growth-profiles
-dss-rpc.put.TRANSCRIPTOMICS = transcriptomics
-dss-rpc.put.PROTEIN_QUANTIFICATIONS = proteomics
-
diff --git a/eu_basynthec/etc/setup.textile b/eu_basynthec/etc/setup.textile
deleted file mode 100644
index 45cefb32733..00000000000
--- a/eu_basynthec/etc/setup.textile
+++ /dev/null
@@ -1,39 +0,0 @@
-h1. Introduction
-
-The CINA project uses the data store server not just for storing data sets, but for registering experiments and samples as well. Folders representing experiments, samples, and data sets are identified by special files in the top level: *experiment.properties*, *sample.properties*, and *dataset.properties* respectively.
-
-The data store server, upon recognizing one of the special files, registers an experiment, a sample, or a data set (_note: data sets not yet implemented_) in the database using the information specified in the properties file, and it also creates a data set containing the contents of the folder and associates this data set to the entity.
-
-h1. Configuration
-
-h3. Data Sets Types
-
-* Add a data set type with the code CINA_EXP_PREP — this is the data set for preparation information for an experiment
-* Add a data set type with code CINA_SAMPLE_PREP — this is the data set for preparation information for a sample
-
-h3. Sample Types
-
-* Add a sample type with the code CINA_SAMPLE_TYPE — this is the sample type for all CINA samples
-
-h3. Experiment Types
-
-* Add an experiment type with the code CINA_EXP_TYPE — this is the experiment type for all CINA experiments
-
-h1. Use
-
-h2. Registering an Experiment
-
-To register an experiment using this mechanism, it is necessary to create an experiment.properties file. This file needs to have three keys: *project.identifier*, *experiment.code-prefix*, and *experiment.owner-email*. Here is an example:
-<pre>
- project.identifier = /CINA/CINA1
- experiment.code-prefix = EXP
- experiment.owner-email = no-one@nowhere.ch
-</pre>
-
-h2. Register a Sample
-
-When an experiment has been registered this way, it will send an email to the experiment owner with a properties file that can be used to register samples. Use this properties file to register samples.
-
-h2. Register a Data Set
-
-This not yet implemented.
\ No newline at end of file
diff --git a/eu_basynthec/resource/db/basynthec_metadata.sql b/eu_basynthec/resource/db/basynthec_metadata.sql
deleted file mode 100644
index 2321b9704a5..00000000000
--- a/eu_basynthec/resource/db/basynthec_metadata.sql
+++ /dev/null
@@ -1,362 +0,0 @@
---
--- PostgreSQL database dump
---
-
--- Dumped from database version 9.0.4
--- Dumped by pg_dump version 9.0.4
--- Started on 2011-07-13 14:18:14 CEST
-
-SET statement_timeout = 0;
-SET client_encoding = 'UTF8';
-SET standard_conforming_strings = off;
-SET check_function_bodies = false;
-SET client_min_messages = warning;
-SET escape_string_warning = off;
-
-SET search_path = public, pg_catalog;
-
---
--- TOC entry 2213 (class 0 OID 0)
--- Dependencies: 1751
--- Name: controlled_vocabulary_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('controlled_vocabulary_id_seq', 10, true);
-
-
---
--- TOC entry 2214 (class 0 OID 0)
--- Dependencies: 1752
--- Name: cvte_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('cvte_id_seq', 40, true);
-
-
---
--- TOC entry 2215 (class 0 OID 0)
--- Dependencies: 1773
--- Name: data_set_type_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('data_set_type_id_seq', 9, true);
-
-
---
--- TOC entry 2216 (class 0 OID 0)
--- Dependencies: 1783
--- Name: dstpt_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('dstpt_id_seq', 35, true);
-
-
---
--- TOC entry 2217 (class 0 OID 0)
--- Dependencies: 1759
--- Name: etpt_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('etpt_id_seq', 9, true);
-
-
---
--- TOC entry 2218 (class 0 OID 0)
--- Dependencies: 1765
--- Name: experiment_type_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('experiment_type_id_seq', 1, true);
-
-
---
--- TOC entry 2219 (class 0 OID 0)
--- Dependencies: 1769
--- Name: material_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('material_id_seq', 1, true);
-
-
---
--- TOC entry 2220 (class 0 OID 0)
--- Dependencies: 1770
--- Name: material_property_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('material_property_id_seq', 27, true);
-
-
---
--- TOC entry 2221 (class 0 OID 0)
--- Dependencies: 1771
--- Name: material_type_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('material_type_id_seq', 1, true);
-
-
---
--- TOC entry 2222 (class 0 OID 0)
--- Dependencies: 1772
--- Name: mtpt_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('mtpt_id_seq', 1, false);
-
-
---
--- TOC entry 2223 (class 0 OID 0)
--- Dependencies: 1776
--- Name: property_type_id_seq; Type: SEQUENCE SET; Schema: public; Owner: cramakri
---
-
-SELECT pg_catalog.setval('property_type_id_seq', 23, true);
-
-
---
--- TOC entry 2200 (class 0 OID 574065)
--- Dependencies: 1707
--- Data for Name: controlled_vocabularies; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY controlled_vocabularies (id, code, description, registration_timestamp, pers_id_registerer, is_managed_internally, is_internal_namespace, dbin_id, modification_timestamp, is_chosen_from_list, source_uri) FROM stdin;
-1 STORAGE_FORMAT The on-disk storage format of a data set 2011-07-07 17:48:22.649816+02 1 t t 1 2011-07-07 17:48:22.649816+02 t \N
-2 GROWTH_MEDIA Growth media for B. Subtilis. 2011-06-01 14:21:40.40244+02 2 f f 1 2011-06-01 14:21:40.415+02 t \N
-3 TEMPERATURE Temperature the experiment was conducted under 2011-06-01 14:22:36.240178+02 2 f f 1 2011-06-01 14:22:36.241+02 t \N
-4 CONTAINER Container in which the experiment was performed. 2011-06-01 14:23:09.455946+02 2 f f 1 2011-06-01 14:23:09.458+02 t \N
-5 TECHNOLOGY Technologies used in BaSynthec 2011-06-01 14:32:54.940133+02 2 f f 1 2011-06-01 14:32:54.941+02 t \N
-6 DEVICE Devices used to produce measurements. 2011-06-01 14:33:26.888983+02 2 f f 1 2011-06-01 14:33:26.89+02 t \N
-7 TIMEPOINT_TYPE Timepoint Type 2011-06-01 14:59:35.528305+02 2 f f 1 2011-06-01 14:59:35.529+02 t \N
-8 CELL_LOCATION Cell Location 2011-06-01 14:59:51.638904+02 2 f f 1 2011-06-01 14:59:51.639+02 t \N
-9 VALUE_TYPE Value Type 2011-06-01 15:07:15.850051+02 2 f f 1 2011-06-01 15:07:15.85+02 t \N
-11 SCALE Scale 2011-06-01 15:08:55.973041+02 2 f f 1 2011-06-01 15:08:55.973+02 t \N
-10 VALUE_UNIT Value Unit 2011-06-01 15:07:40.656819+02 2 f f 1 2011-06-07 11:06:21.669+02 t \N
-\.
-
-
---
--- TOC entry 2201 (class 0 OID 574076)
--- Dependencies: 1708 2200
--- Data for Name: controlled_vocabulary_terms; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY controlled_vocabulary_terms (id, code, registration_timestamp, covo_id, pers_id_registerer, label, description, ordinal, is_official) FROM stdin;
-1 PROPRIETARY 2011-07-07 17:48:22.649816+02 1 1 \N \N 1 t
-2 BDS_DIRECTORY 2011-07-07 17:48:22.649816+02 1 1 \N \N 2 t
-3 MALATE 2011-06-01 14:21:40.40244+02 2 2 \N \N 1 t
-4 GLUCOSE 2011-06-01 14:21:40.40244+02 2 2 \N \N 2 t
-5 20 2011-06-01 14:22:36.240178+02 3 2 \N \N 1 t
-6 30 2011-06-01 14:22:36.240178+02 3 2 \N \N 2 t
-7 40 2011-06-01 14:22:36.240178+02 3 2 \N \N 3 t
-8 FLASK 2011-06-01 14:23:09.455946+02 4 2 \N \N 1 t
-9 METABOLOMICS 2011-06-01 14:32:54.940133+02 5 2 \N \N 1 t
-10 PHYSIOLOGY 2011-06-01 14:32:54.940133+02 5 2 \N \N 2 t
-11 PROTEOMICS 2011-06-01 14:32:54.940133+02 5 2 \N \N 3 t
-12 TRANSCRIPTOMICS 2011-06-01 14:32:54.940133+02 5 2 \N \N 4 t
-13 ORBITRAP 2011-06-01 14:33:26.888983+02 2 2 \N \N 1 t
-14 EX 2011-06-01 14:59:35.528305+02 7 2 \N \N 1 t
-15 IN 2011-06-01 14:59:35.528305+02 7 2 \N \N 2 t
-16 SI 2011-06-01 14:59:35.528305+02 7 2 \N \N 3 t
-17 CE 2011-06-01 14:59:51.638904+02 8 2 \N \N 1 t
-18 ES 2011-06-01 14:59:51.638904+02 8 2 \N \N 2 t
-19 ME 2011-06-01 14:59:51.638904+02 8 2 \N \N 3 t
-20 CY 2011-06-01 14:59:51.638904+02 8 2 \N \N 4 t
-21 NC 2011-06-01 14:59:51.638904+02 8 2 \N \N 5 t
-22 VALUE 2011-06-01 15:07:15.850051+02 9 2 \N \N 1 t
-23 MEAN 2011-06-01 15:07:15.850051+02 9 2 \N \N 2 t
-24 MEDIAN 2011-06-01 15:07:15.850051+02 9 2 \N \N 3 t
-25 STD 2011-06-01 15:07:15.850051+02 9 2 \N \N 4 t
-26 VAR 2011-06-01 15:07:15.850051+02 9 2 \N \N 5 t
-27 ERROR 2011-06-01 15:07:15.850051+02 9 2 \N \N 6 t
-28 IQR 2011-06-01 15:07:15.850051+02 9 2 \N \N 7 t
-29 MM 2011-06-01 15:07:40.656819+02 10 2 \N \N 1 t
-30 UM 2011-06-01 15:07:40.656819+02 10 2 \N \N 2 t
-34 LIN 2011-06-01 15:08:55.973041+02 11 2 \N \N 1 t
-35 LOG2 2011-06-01 15:08:55.973041+02 11 2 \N \N 2 t
-36 LOG10 2011-06-01 15:08:55.973041+02 11 2 \N \N 3 t
-37 LN 2011-06-01 15:08:55.973041+02 11 2 \N \N 4 t
-31 RATIOT1 2011-06-01 15:07:40.656819+02 10 2 \N \N 4 t
-33 RATIOCS 2011-06-01 15:08:14.224243+02 10 2 \N \N 5 t
-38 PERCENT 2011-06-07 09:25:59.284385+02 10 2 \N \N 3 t
-39 AU 2011-06-07 09:26:07.523864+02 10 2 \N \N 6 t
-40 DIMENSIONLESS 2011-06-07 11:06:21.616952+02 10 2 \N \N 7 t
-\.
-
-
---
--- TOC entry 2208 (class 0 OID 574259)
--- Dependencies: 1733
--- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path, is_container) FROM stdin;
-1 UNKNOWN Unknown 1 2011-07-07 17:48:22.649816+02 \N \N f
-2 RAW Raw data 1 2011-06-01 14:35:43.248544+02 \N \N f
-7 EXCEL_ORIGINAL Excel data 1 2011-07-07 14:24:59.205768+02 \N \N f
-8 TSV_EXPORT An export of the data containing one strain per file. 1 2011-07-07 14:25:32.331964+02 \N \N f
-9 TSV_MULTISTRAIN_EXPORT An export of the data containing multiple strains per file. 1 2011-07-07 14:26:06.13375+02 \N \N f
-5 TRANSCRIPTOMICS Transcriptomics data 1 2011-06-07 09:43:30.916419+02 \N \N t
-3 METABOLITE_INTENSITIES Metabolite intensities 1 2011-06-01 15:09:15.822214+02 \N \N t
-4 OD600 Growth profiles 1 2011-06-07 09:40:07.551324+02 \N \N t
-6 PROTEIN_QUANTIFICATIONS Protein quantifications 1 2011-06-07 09:44:55.591374+02 \N \N t
-\.
-
-
---
--- TOC entry 2206 (class 0 OID 574243)
--- Dependencies: 1731
--- Data for Name: material_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY material_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
-1 STRAIN Strain 1 2011-06-01 14:48:39.161056+02
-\.
-
-
---
--- TOC entry 2209 (class 0 OID 574282)
--- Dependencies: 1736 2200 2206
--- Data for Name: property_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY property_types (id, code, description, label, daty_id, registration_timestamp, pers_id_registerer, covo_id, is_managed_internally, is_internal_namespace, dbin_id, maty_prop_id, schema, transformation) FROM stdin;
-1 DESCRIPTION A Description Description 1 2011-07-07 17:48:22.649816+02 1 \N f f 1 \N \N \N
-2 MEDIUM The growth medium for the experiment Medium 7 2011-06-01 14:23:50.820065+02 2 2 f f 1 \N \N \N
-4 CONTAINER The type of container in which the experiment was carried out. Container 7 2011-06-01 14:24:40.461839+02 2 4 f f 1 \N \N \N
-5 CONTAINER_VOLUME The volume of the container. Container Volume 1 2011-06-01 14:25:42.437944+02 2 \N f f 1 \N \N \N
-6 MISC_GROWTH_CONDITIONS Miscellaneous growth conditions. Growth Conditions 2 2011-06-01 14:26:20.93953+02 2 \N f f 1 \N \N \N
-7 SHAKER_RPM The RPMs of the shaker used to prepare the experiment. Shaker RPM 3 2011-06-01 14:26:51.368174+02 2 \N f f 1 \N \N \N
-8 COMMENTS Miscellaneous comments. Comments 2 2011-06-01 14:27:17.239486+02 2 \N f f 1 \N \N \N
-9 TECHNOLOGY The technology used for a measurement. Technology 7 2011-06-01 14:34:38.569805+02 2 5 f f 1 \N \N \N
-10 DEVICE The device used for a measurement. Device 7 2011-06-01 14:35:02.06542+02 2 6 f f 1 \N \N \N
-11 OPERATOR The operator of a device. Operator 1 2011-06-01 14:35:20.308799+02 2 \N f f 1 \N \N \N
-12 STRAIN_NAME The name of the strain. Name 1 2011-06-01 14:49:27.382572+02 2 \N f f 1 \N \N \N
-13 STRAIN The strain of B. Subtilis. Strain 8 2011-06-01 14:52:49.555029+02 2 \N f f 1 1 \N \N
-14 TIMEPOINT_TYPE Timepoint Type Timepoint Type 7 2011-06-01 15:10:26.249761+02 2 7 f f 1 \N \N \N
-15 CELL_LOCATION Cell Location Cell Location 7 2011-06-01 15:10:41.349422+02 2 8 f f 1 \N \N \N
-16 VALUE_TYPE Value Type Value Type 7 2011-06-01 15:11:00.652368+02 2 9 f f 1 \N \N \N
-17 VALUE_UNIT Value Unit Value Unit 7 2011-06-01 15:11:20.926301+02 2 10 f f 1 \N \N \N
-18 SCALE Scale Scale 7 2011-06-01 15:11:36.989897+02 2 11 f f 1 \N \N \N
-19 TEMPERATURE The temperature under which the experiment was carried out. Temperature 4 2011-06-15 09:55:42.66193+02 2 \N f f 1 \N \N \N
-20 STRAIN_NAMES Strain Names Strain Names 1 2011-06-29 15:53:03.26604+02 2 \N f f 1 \N \N \N
-21 REFERENCE_STRAIN Reference Strain Reference Strain 8 2011-06-29 15:53:42.397136+02 2 \N f f 1 1 \N \N
-22 EXPERIMENT_DATE Experiment Date Experiment Date 6 2011-06-29 15:54:09.331516+02 2 \N f f 1 \N \N \N
-23 DATA_TYPE Data Type Data Type 1 2011-07-11 14:51:57.899818+02 2 \N f f 1 \N \N \N
-\.
-
-
---
--- TOC entry 2210 (class 0 OID 574345)
--- Dependencies: 1743 2208 2209
--- Data for Name: data_set_type_property_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, ordinal, section, script_id) FROM stdin;
-1 2 9 t f 2 2011-06-01 14:44:56.126417+02 2 \N \N
-2 2 10 f f 2 2011-06-01 14:45:10.671022+02 3 \N \N
-3 2 11 f f 2 2011-06-01 14:45:20.412582+02 4 \N \N
-4 2 13 t f 2 2011-06-01 14:55:14.000965+02 1 \N \N
-5 3 13 f f 2 2011-06-01 15:09:45.526152+02 1 \N \N
-11 4 13 f f 2 2011-06-07 09:41:19.577666+02 1 \N \N
-17 5 13 f f 2 2011-06-07 09:45:57.381638+02 1 \N \N
-23 6 13 f f 2 2011-06-07 10:26:20.876194+02 1 \N \N
-12 4 14 f f 2 2011-06-07 09:41:39.189056+02 3 \N \N
-13 4 15 f f 2 2011-06-07 09:42:00.464051+02 4 \N \N
-14 4 16 f f 2 2011-06-07 09:42:14.906524+02 5 \N \N
-15 4 17 f f 2 2011-06-07 09:42:30.293596+02 6 \N \N
-16 4 18 f f 2 2011-06-07 09:42:36.606913+02 7 \N \N
-29 4 20 f f 2 2011-06-29 15:56:25.578782+02 2 \N \N
-24 6 14 f f 2 2011-06-07 10:26:37.439939+02 3 \N \N
-25 6 15 f f 2 2011-06-07 10:27:03.19151+02 4 \N \N
-27 6 17 f f 2 2011-06-07 10:27:23.191867+02 6 \N \N
-28 6 18 f f 2 2011-06-07 10:27:33.149813+02 7 \N \N
-30 6 20 f f 2 2011-06-29 15:56:36.804424+02 2 \N \N
-18 5 14 f f 2 2011-06-07 09:46:07.477336+02 3 \N \N
-19 5 15 f f 2 2011-06-07 09:46:23.775868+02 4 \N \N
-20 5 16 f f 2 2011-06-07 09:46:34.150697+02 5 \N \N
-21 5 17 f f 2 2011-06-07 09:46:42.908173+02 6 \N \N
-22 5 18 f f 2 2011-06-07 09:46:49.641018+02 7 \N \N
-31 5 20 f f 2 2011-06-29 15:56:49.612258+02 2 \N \N
-32 6 21 f f 2 2011-06-29 15:59:14.016583+02 8 \N \N
-6 3 14 f f 2 2011-06-01 15:11:51.457314+02 3 \N \N
-7 3 15 f f 2 2011-06-01 15:12:06.094358+02 4 \N \N
-8 3 16 f f 2 2011-06-01 15:12:17.388726+02 5 \N \N
-9 3 17 f f 2 2011-06-01 15:12:25.79652+02 6 \N \N
-10 3 18 f f 2 2011-06-01 15:12:35.809392+02 7 \N \N
-26 3 20 f f 2 2011-06-29 15:55:28.052352+02 2 \N \N
-33 7 23 f f 2 2011-07-11 14:52:15.733339+02 1 \N \N
-34 8 23 f f 2 2011-07-11 14:52:25.133573+02 1 \N \N
-35 9 23 f f 2 2011-07-11 14:52:33.108668+02 1 \N \N
-\.
-
-
---
--- TOC entry 2202 (class 0 OID 574167)
--- Dependencies: 1721
--- Data for Name: experiment_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY experiment_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
-1 BASYNTHEC The BaSynthec experiment type. 1 2011-06-01 14:08:24.183425+02
-\.
-
-
---
--- TOC entry 2203 (class 0 OID 574174)
--- Dependencies: 1722 2202 2209
--- Data for Name: experiment_type_property_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY experiment_type_property_types (id, exty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, ordinal, section, script_id) FROM stdin;
-1 1 1 f f 2 2011-06-01 14:11:11.407487+02 1 \N \N
-2 1 2 f f 2 2011-06-01 14:30:06.812876+02 2 \N \N
-4 1 4 f f 2 2011-06-01 14:30:23.277699+02 5 \N \N
-5 1 5 f f 2 2011-06-01 14:30:28.637025+02 6 \N \N
-6 1 6 f f 2 2011-06-01 14:30:43.373831+02 7 \N \N
-7 1 7 f f 2 2011-06-01 14:30:54.766288+02 8 \N \N
-8 1 8 f f 2 2011-06-01 14:31:02.906052+02 9 \N \N
-3 1 19 f f 2 2011-06-15 10:01:30.732512+02 3 \N \N
-9 1 22 f f 2 2011-06-29 15:59:28.462793+02 10 \N \N
-\.
-
-
---
--- TOC entry 2207 (class 0 OID 574250)
--- Dependencies: 1732 2206 2209
--- Data for Name: material_type_property_types; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY material_type_property_types (id, maty_id, prty_id, is_mandatory, is_managed_internally, registration_timestamp, pers_id_registerer, ordinal, section, script_id) FROM stdin;
-1 1 12 t f 2011-06-01 14:50:16.872011+02 2 1 \N \N
-\.
-
-
---
--- TOC entry 2204 (class 0 OID 574227)
--- Dependencies: 1729 2206
--- Data for Name: materials; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY materials (id, code, maty_id, pers_id_registerer, registration_timestamp, modification_timestamp, dbin_id) FROM stdin;
-1 STRAIN1 1 2 2011-06-01 14:51:19.288314+02 2011-06-01 14:51:19.647+02 1
-\.
-
-
---
--- TOC entry 2205 (class 0 OID 574235)
--- Dependencies: 1730 2201 2204 2204 2207
--- Data for Name: material_properties; Type: TABLE DATA; Schema: public; Owner: cramakri
---
-
-COPY material_properties (id, mate_id, mtpt_id, value, registration_timestamp, modification_timestamp, pers_id_registerer, cvte_id, mate_prop_id) FROM stdin;
-1 1 1 Strain 1 2011-06-01 14:51:19.288314+02 2011-06-01 14:51:19.65+02 2 \N \N
-\.
-
-
--- Completed on 2011-07-13 14:18:15 CEST
-
---
--- PostgreSQL database dump complete
---
-
diff --git a/eu_basynthec/resource/db/db_initialize_basynthec.sh b/eu_basynthec/resource/db/db_initialize_basynthec.sh
deleted file mode 100644
index 1e51ee70a5e..00000000000
--- a/eu_basynthec/resource/db/db_initialize_basynthec.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-DB=openbis_basynthec
-psql -U $USER -h localhost -p 5432 -d $DB -f basynthec_metadata.sql
diff --git a/eu_basynthec/resource/dependency-structure.ddf b/eu_basynthec/resource/dependency-structure.ddf
deleted file mode 100644
index 2146ec57497..00000000000
--- a/eu_basynthec/resource/dependency-structure.ddf
+++ /dev/null
@@ -1,16 +0,0 @@
-#show allResults
-
-{root} = eu.basynthec.cisd
-{dss} = ${root}.dss
-{openbis} = ch.systemsx.cisd.openbis
-
-######################################################################
-# Check dependencies to openbis
-
-[dss] = ${dss}.*
-[private_openbis] = ${openbis}.* excluding [dss] ${openbis}.dss.generic.shared.* ${openbis}.generic.shared.* ${openbis}.dss.etl.* ${openbis}.common.*
-
-check sets [dss]
-
-check [dss] independentOf [private_openbis]
-
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
deleted file mode 100644
index b83cd5a0e83..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js
+++ /dev/null
@@ -1,1641 +0,0 @@
-// The width of the visualization
-var w = 500;
-
-var curveColors = d3.scale.category10().domain([0, 9]);
-
-/**
- * Abstract superclass for the wrapper classes.
- * @constructor
- */
-function AbstractThingWrapper() {
- this.isDataSet = function() { return false; }
- this.isStrain = function() { return false; }
-}
-
-/**
- * Create a wrapper on a data set designed to be displayed as a data set.
- *
- * @constructor
- */
-function DataSetWrapper(dataSet) {
- var strainNames;
- if (dataSet.properties[STRAIN_PROP_NAME] != null)
- strainNames = dataSet.properties[STRAIN_PROP_NAME].split(",");
- else
- strainNames = [dataSet.properties["STRAIN_NAME"]];
-
- this.strainNames = strainNames;
- this.dataSet = dataSet;
- this.dateString = timeformat(new Date(dataSet.registrationDetails.registrationDate));
- this.strainString =
- (strainNames.length < 3) ?
- strainNames.join(" ") :
- "" + strainNames.length + " strain(s)";
- this.userEmail = dataSet.registrationDetails.userEmail;
- this.name = dataSet.code;
-}
-
-DataSetWrapper.prototype = new AbstractThingWrapper();
-DataSetWrapper.prototype.constructor = DataSetWrapper;
-DataSetWrapper.prototype.isDataSet = function() { return true; }
-
-/**
- * Create a wrapper that represents a strain to be displayed
- *
- * @constructor
- */
-function StrainWrapper(strainName)
-{
- this.strainName = strainName;
- this.dataSets = [];
-}
-
-StrainWrapper.prototype = new AbstractThingWrapper();
-StrainWrapper.prototype.constructor = StrainWrapper;
-StrainWrapper.prototype.isStrain = function() { return true; }
-
-var presenterModeTypeDataSet = "DATA_SET", presenterModeTypeStrain = "STRAIN";
-
-/**
- * An object responsible for managing the view
- */
-function AppPresenter() {
- this.didCreateVis = false;
- this.presenterMode = presenterModeTypeDataSet;
- this.visualizationContainers = [];
-}
-
-/** Hides the explanation and shows the element to display the explanation again */
-AppPresenter.prototype.hideExplanation = function() {
- $('#explanation').hide();
- $('#explanation-show').show();
-}
-
-/** Display the explanation again */
-AppPresenter.prototype.showExplanation = function() {
- $('#explanation-show').hide();
- $('#explanation').show();
-}
-
-/** Show the data sets grouped by type */
-AppPresenter.prototype.switchToDataSetTypeView = function()
-{
- this.presenterMode = presenterModeTypeDataSet;
- this.hideExplanation();
- this.toggleDisplayedVisualizations(dataSetTypeVis);
- od600InspectorView.removeAll(250);
- dataSetInspectorView.updateView();
-}
-
-/** Show the data sets by strain*/
-AppPresenter.prototype.switchToStrainView = function()
-{
- this.presenterMode = presenterModeTypeDataSet;
- this.hideExplanation();
- this.toggleDisplayedVisualizations(strainVis);
- od600InspectorView.removeAll(250);
- dataSetInspectorView.updateView();
-}
-
-/** Show the data sets by strains with OD600 data*/
-AppPresenter.prototype.switchToOD600View = function()
-{
- this.presenterMode = presenterModeTypeStrain;
- this.hideExplanation();
- this.toggleDisplayedVisualizations(od600StrainVis);
- dataSetInspectorView.removeAll(250);
- od600InspectorView.updateView();
-}
-
-/** This view is very similar to the OD600 view, but the data is also divided into two main groups:
- * - strains for which there are phenotypes, predictions, and data in the openBIS database
- * - strains for which there are phenotypes or predictions, but no data in the openBIS database
- * (in this group strains with phenotypes and predictions should be marked green; strains with
- * phenotypes only should be marked blue; strains with predictions only should be yellow)
- * Information about the phenotypes and predictions is retrieved from UChicago strain database
- * (http://pubseed.theseed.org/model-prod/StrainServer.cgi) and cached at the server-side in OpenBIS.
- */
-AppPresenter.prototype.switchToOD600WithPhenotypesAndPredictionsView = function()
-{
- this.presenterMode = presenterModeTypeStrain;
- this.hideExplanation();
- this.toggleDisplayedVisualizations(od600StrainWithPhenotypesAndPredictionsVis);
- dataSetInspectorView.removeAll(250);
- od600InspectorView.updateView();
-}
-
-/** Utility function to gracefully switch from one visualization to another */
-AppPresenter.prototype.toggleDisplayedVisualizations = function(visToShow)
-{
- this.visualizationContainers.forEach(function(vis) {
- if (vis == visToShow) {
- if (od600StrainVis == vis || od600StrainWithPhenotypesAndPredictionsVis == vis) {
- // So that scrolling works
- vis.style("display", "block");
- } else {
- vis.style("display", "inline");
- }
- vis
- .transition()
- .duration(1000)
- .style("opacity", 1);
- } else {
- // change to "inline" element to eliminate jumping of two "block" elements during transition
- vis.style("display","inline");
- vis
- .transition()
- .duration(1000)
- .style("opacity", 0)
- .style("display", "none")
- }
- });
-}
-
-/**
- * Shows the list of data sets retrieved from the openBIS server.
- */
-AppPresenter.prototype.showDataSets = function(bisDataSets) {
- if (null == bisDataSets) return;
-
- basynthec.dataSetList = bisDataSets.filter(function(dataSet) {
- return IGNORED_DATASET_TYPES.indexOf(dataSet.dataSetTypeCode) == -1;
- });
-
- // sort data sets
- var sortByTypeAndRegistration = function(a, b) {
- if (a.dataSetTypeCode == b.dataSetTypeCode) {
- return b.registrationDetails.registrationDate - a.registrationDetails.registrationDate;
- }
- return (a.dataSetTypeCode < b.dataSetTypeCode) ? -1 : 1;
- };
-
- basynthec.dataSetList.sort(sortByTypeAndRegistration);
-
- model.initialize(function(){
- presenter.refreshDataSetTypeTables();
- presenter.refreshStrainTables();
- presenter.refreshOd600StrainTables();
- presenter.refreshOd600StrainWithPhenotypesAndPredictionsTables();
- });
-}
-
-AppPresenter.prototype.refreshStrainTables = function() {
- this.createVis();
- strainView.updateView(1000);
-}
-
-AppPresenter.prototype.refreshDataSetTypeTables = function() {
- this.createVis();
-
- od600View.updateView();
- metabolomicsView.updateView();
- transcriptomicsView.updateView();
- proteomicsView.updateView();
- sequencesCm5View.updateView();
- sequencesGenbankView.updateView();
- intervalAnnotationsView.updateView();
- metabolicModelView.updateView();
-}
-
-AppPresenter.prototype.refreshOd600StrainTables = function() {
- this.createVis();
- od600StrainView.updateView(1000);
-}
-
-AppPresenter.prototype.refreshOd600StrainWithPhenotypesAndPredictionsTables = function() {
- this.createVis();
- od600StrainWithPhenotypesAndPredictionsView.updateView(1000);
-}
-
-
-AppPresenter.prototype.createVis = function()
-{
- if (this.didCreateVis) return;
-
- var top = d3.select("#main");
- var tableRoot = top.append("div").attr("id", "table-root").style("width", w + 5 + "px").style("float", "left");
-
-
- // An element for the inspectors.
- inspectors = top.append("span")
- .style("width", "500px")
- .style("position", "relative")
- .style("overflow", "auto")
- .style("float", "left")
- .style("left", "20px");
-
- // Create the dataSetType visualization
- dataSetTypeVis = tableRoot.append("div");
- dataSetTypeVis.style("width", w + "px");
- od600View = new DataSummaryView(dataSetTypeVis, "OD600", "od600", "OD600");
- metabolomicsView = new DataSummaryView(dataSetTypeVis, "Metabolomics", "metabolomics", "METABOLITE_INTENSITIES");
- transcriptomicsView = new DataSummaryView(dataSetTypeVis, "Transcriptomics", "transcriptomics", "TRANSCRIPTOMICS");
- proteomicsView = new DataSummaryView(dataSetTypeVis, "Proteomics", "proteomics", "PROTEIN_QUANTIFICATIONS");
- sequencesCm5View = new DataSummaryView(dataSetTypeVis, "Sequences (CM5)", "sequencesCm5", "SEQUENCE_CM5");
- sequencesGenbankView = new DataSummaryView(dataSetTypeVis, "Sequences (Genbank)", "sequencesGenbank", "SEQUENCE_GENBANK");
- intervalAnnotationsView = new DataSummaryView(dataSetTypeVis, "Interval Annotations", "intervalAnnotations", "INTERVAL_ANNOTATIONS");
- metabolicModelView = new DataSummaryView(dataSetTypeVis, "Metabolic Model", "metabolicModel", "METABOLIC_MODEL");
-
- // Initially hide the strain view -- it is activated by the radio button
- strainVis = tableRoot.append("div").style("display", "none");
- strainVis.style("width", w + "px");
- strainVis.style("opacity", "0");
- strainView = new StrainView();
-
- od600StrainVis = tableRoot.append("div").style("display", "none");
- od600StrainVis.style("width", w + "px");
- od600StrainVis.style("height",w + "px");
- od600StrainVis.style("overflow-y", "scroll");
- od600StrainVis.style("opacity", "0");
- od600StrainView = new Od600StrainView();
-
- od600StrainWithPhenotypesAndPredictionsVis = tableRoot.append("div").style("display", "none");
- od600StrainWithPhenotypesAndPredictionsVis.style("width", w + "px");
- od600StrainWithPhenotypesAndPredictionsVis.style("opacity", "0");
-
- od600StrainWithPhenotypesAndPredictionsVisScroll = od600StrainWithPhenotypesAndPredictionsVis.append("div");
- od600StrainWithPhenotypesAndPredictionsVisScroll.style("height", ($(window).height() - 250) + "px");
- od600StrainWithPhenotypesAndPredictionsVisScroll.style("overflow-y", "scroll");
-
- od600StrainWithPhenotypesAndPredictionsVisLegend = od600StrainWithPhenotypesAndPredictionsVis.append("div");
-
- od600StrainWithPhenotypesAndPredictionsView = new Od600StrainWithPhenotypesAndPredictionsView();
-
- this.visualizationContainers = [dataSetTypeVis, strainVis, od600StrainVis, od600StrainWithPhenotypesAndPredictionsVis];
-
- dataSetInspectorView = new DataSetInspectorView();
- od600InspectorView = new Od600InspectorView();
-
- this.didCreateVis = true;
-}
-
-AppPresenter.prototype.updateInspectors = function(duration)
-{
- if (this.presenterMode == presenterModeTypeDataSet)
- {
- dataSetInspectorView.updateView(duration);
- } else {
- od600InspectorView.updateView(duration);
- }
-}
-
-/** Download a file referenced in a table. */
-AppPresenter.prototype.downloadTableFile = function(d)
-{
- // If there is no dataset, this is just a marker for loading
- if (!d.dataset) return;
-
- var action = function(data) {
- try {
- document.location.href = data.result
- } catch (err) {
- // just ignore errors
- }
- };
- basynthec.server.getDownloadUrlForFileForDataSet(d.dataset.bis.code, d.pathInDataSet, action);
-}
-
-AppPresenter.prototype.toggleInspected = function(d, connectedNode) {
- this.hideExplanation();
-
- var lexicalParent = this;
-
- function retrieveFilesForDataSets(dataSets) {
- dataSets.forEach(function(ds) { lexicalParent.retrieveFilesForDataSet(ds); });
- }
-
- function classForNode(d) { return (d.inspected) ? "inspected" : "" };
-
- if (d.inspected) {
- var index = inspected.indexOf(d)
- if (index > -1) inspected.splice(index, 1);
- d.inspected = false;
- } else {
- d.inspected = true;
- d.connectedNode = connectedNode;
- inspected.push(d);
- if (d instanceof DataSetWrapper) {
- d.dataSets = [{ bis : d.dataSet }];
- retrieveFilesForDataSets(d.dataSets);
- } else if (!d.dataSets) {
- d.dataSets = model.dataSetsByStrain[d.name].dataSets.map(function(ds){ return {bis : ds} });
- retrieveFilesForDataSets(d.dataSets);
- }
- }
-
- d3.select(d.connectedNode).attr("class", classForNode(d))
- this.updateInspectors(500);
-}
-
-AppPresenter.prototype.toggleOd600Inspected = function(d) {
- this.hideExplanation();
-
- var lexicalParent = this;
-
- function retrieveFilesForDataSets(dataSets) {
- dataSets.forEach(function(ds) { lexicalParent.retrieveFilesForDataSet(ds); });
- }
-
- function classForNode(d) { return (d.od600Inspected) ? "inspected" : "" };
-
- var inspectedItem = null;
- var inspectedIndex = null;
-
- $.each(od600Inspected, function(index, item){
- if(item.name == d.name){
- inspectedItem = item;
- inspectedIndex = index;
- return false;
- }
- });
-
- if (inspectedItem) {
- od600Inspected.splice(inspectedIndex, 1);
- } else {
- od600Inspected.push(d);
- if (d instanceof DataSetWrapper) {
- d.dataSets = [{ bis : d.dataSet }];
- retrieveFilesForDataSets(d.dataSets);
- } else if (!d.dataSets && d.data.isKnown) {
- d.dataSets = model.dataSetsByStrain[d.name].dataSets.map(function(ds){ return {bis : ds} });
- retrieveFilesForDataSets(d.dataSets);
- }
- }
-
- this.updateInspectors(500);
- od600StrainView.updateView(1);
- od600StrainWithPhenotypesAndPredictionsView.updateView(1);
-}
-
-AppPresenter.prototype.retrieveFilesForDataSet = function(ds)
-{
- if (ds.files) {
- // already retrieved
- return;
- }
-
- ds.loadingFiles = true;
- ds.files = [];
-
- var lexicalParent = this;
-
- basynthec.server.listFilesForDataSet(ds.bis.code, "/", true, function(data) {
- if (!data.result) {
- return;
- }
- data.result.forEach(function (file) { file.dataset = ds });
- ds.files = ds.files.concat(data.result);
-
- ds.loadingFiles = false;
- presenter.updateInspectors(500);
-
- if (isOd600DataSet(ds)) {
- lexicalParent.retrieveOd600DataForDataSet(ds)
- }
-
- });
-}
-
-/** Load the OD600 data from the server. This function assumes that the files are already known. */
-AppPresenter.prototype.retrieveOd600DataForDataSet = function(ds)
-{
- if (ds.od600Rows) {
- // already retrieved
- return;
- }
-
- ds.loadingOd600 = true;
- ds.od600Rows = [];
-
- // Figure out the path to the multistrain TSV file -- this path ends with "xls.tsv".
- var tsvPathInDataSet = "";
- ds.files.forEach(function (file) { if (endsWith(file.pathInDataSet, "xls.tsv")) tsvPathInDataSet = file.pathInDataSet});
-
- var tsvUrl = dssUrl + "/" + ds.bis.code + "/" + tsvPathInDataSet + "?sessionID=" + basynthec.server.sessionToken;
-
- var lexicalParent = this;
-
- d3.text(tsvUrl, "text/tsv", function(text) {
- var rows = d3.tsv.parseRows(text, "\t");
- ds.od600Rows = rows;
- lexicalParent.initializeOd600Map(ds);
- ds.loadingOd600 = false;
- presenter.updateInspectors(500);
- });
-}
-
-/**
- * Initialize a map of the OD600 data, where the key is the strain and the value is an array
- *
- * Assumes that ds.od600Rows has already been set
- */
-AppPresenter.prototype.initializeOd600Map = function(ds)
-{
- ds.od600Map = {};
- // The first line of data contains the timepoints
- ds.od600Timepoints = ds.od600Rows[0].slice(2);
- var i;
- for (i = 1; i < ds.od600Rows.length; ++i) {
- var line = ds.od600Rows[i];
- var strain = line[0].toUpperCase();
- var data = line.slice(2).map(function(str) { return parseFloat(str)});
- if (null == ds.od600Map[strain]) ds.od600Map[strain] = [];
- ds.od600Map[strain].push(data);
- }
-}
-
-
-/**
- * An object responsible for managing the data to show
- */
-function AppModel() {
- // a map holding data sets by strain
- this.dataSetsByStrain = { };
-
- // Groups of strains to be displayed
- this.strainGroups = [];
-
- // A map holding data sets by type
- this.dataSetsByType = { };
-
- // A set of all known growth media
- this.growthMediaSet = {};
-}
-
-AppModel.prototype.initialize = function(callback) {
- this.initializeDataSetsByType();
- this.initializeDataSetsByStrain();
- this.initializeStrainGroups();
- this.initializeOd600Model();
- this.initializeOd600WithPhenotypesAndPredictionsModel(callback);
-}
-
-AppModel.prototype.addGrowthMedium = function(medium, strain) {
- var mediumList = this.growthMediaSet[medium];
- if (null == mediumList) {
- mediumList = [];
- this.growthMediaSet[medium] = mediumList;
- }
- mediumList.push(strain);
-}
-
-/** Compute the dataSetsByType variable */
-AppModel.prototype.initializeDataSetsByType = function() {
- // Group data sets by type
- this.dataSetsByType = basynthec.dataSetList.reduce(
- function(result, dataSet) {
- var listForType = result[dataSet.dataSetTypeCode];
- if (listForType == null) {
- listForType = [];
- result[dataSet.dataSetTypeCode] = listForType;
- }
- listForType.push(new DataSetWrapper(dataSet));
- return result;
- }, {});
-}
-
-/** Compute the dataSetsByStrain variable */
-AppModel.prototype.initializeDataSetsByStrain = function() {
- // group dataSets
- this.dataSetsByStrain = basynthec.dataSetList.reduce(
- function(result, dataSet) {
- var uniqueStrains = uniqueElements(basynthec.getStrains(dataSet).sort());
-
- uniqueStrains.forEach(function(strain) {
- if (!result[strain]) {
- result[strain] = new StrainWrapper(strain);
- }
- result[strain].dataSets.push(dataSet);
- });
- return result;
- }, {});
-}
-
-AppModel.prototype.initializeStrainGroups = function() {
- var strains = []
- for (strainName in this.dataSetsByStrain) {
- strains.push({name: strainName});
- }
- this.strainGroups = createStrainGroups(strains);
-}
-
-/** Initialize the state necessary for the OD600 visualization. This must be run after initializeDataSetsByType */
-AppModel.prototype.initializeOd600Model= function() {
- var colors = d3.scale.category20c();
- var dataSets = this.od600DataSets();
- var od600ExperimentIdentifiers = dataSets.map(function(ds) {
- return ds.dataSet.experimentIdentifier;
- });
-
- od600ExperimentIdentifiers.sort();
- this.od600Experiments = od600ExperimentIdentifiers.map(function(expId, i) {
- return { identifier: expId, color: colors(i) };
- });
-
- // Filter the strain groups to those that have OD600 data
- this.od600StrainGroups = this.strainGroups.map(function(group) {
- var strains = group.strains.filter(function(strain) {
- return model.dataSetsByStrain[strain.name].dataSets.some(function(ds) {
- return "OD600" == ds.dataSetTypeCode;
- })
- });
- return {groupName : group.groupName, strains : strains };
- });
-}
-
-AppModel.prototype.initializeOd600WithPhenotypesAndPredictionsModel = function(callback){
- var model = this;
-
- basynthec.getStrainsPhenotypesAndPredictions(function(strainDataMap){
-
- var strainsKnownToOpenbisWithPhenotypesOrPredictions = [];
- var strainsUnknownToOpenbisWithPhenotypesOrPredictions = [];
-
- for(strainName in model.dataSetsByStrain){
- var strainData = strainDataMap[strainName];
-
- if(!strainData){
- continue;
- }
-
- var strainDatasets = model.dataSetsByStrain[strainName];
- strainData.phenotypeMap = {};
- if (strainData.hasPhenotypes) {
- strainData.phenotypes.forEach(function(each) {
- strainData.phenotypeMap[each.media] = each.relativeGrowth;
- model.addGrowthMedium(each.media, strainName);
- });
- }
-
- var hasPhenotypesOrPredictions = strainData && (strainData.hasPhenotypes || strainData.hasPredictions);
- var hasOd600Datasets = strainDatasets && strainDatasets.dataSets.some(function(dataset){
- return "OD600" == dataset.dataSetTypeCode;
- });
-
- if (hasOd600Datasets) {
- if(hasPhenotypesOrPredictions){
- strainData.isKnown = true;
- strainsKnownToOpenbisWithPhenotypesOrPredictions.push(strainData);
- } else {
- strainData.isKnown = true;
- strainsKnownToOpenbisWithPhenotypesOrPredictions.push(strainData);
- }
- } else {
- if (strainDatasets && strainDatasets.dataSets.length > 0) {
- strainData.isKnown = true;
- strainsKnownToOpenbisWithPhenotypesOrPredictions.push(strainData);
- }
- }
- }
-
- for(strainName in strainDataMap){
- var strainData = strainDataMap[strainName];
- var strainDatasets = model.dataSetsByStrain[strainName];
-
- var hasPhenotypesOrPredictions = strainData && (strainData.hasPhenotypes || strainData.hasPredictions);
- var hasDatasets = strainDatasets && strainDatasets.dataSets.length > 0;
-
- if(hasPhenotypesOrPredictions && !hasDatasets) {
- strainData.isKnown = false;
- strainsUnknownToOpenbisWithPhenotypesOrPredictions.push(strainData);
- }
-
- strainData.phenotypeMap = {};
- if (strainData.hasPhenotypes) {
- strainData.phenotypes.forEach(function(each) {
- strainData.phenotypeMap[each.media] = each.relativeGrowth;
- model.addGrowthMedium(each.media, strainName);
- });
- }
- }
-
- model.od600StrainsWithPhenotypesAndPredictionsGroups = [];
- model.od600StrainsWithPhenotypesAndPredictionsGroups.push({
- "mainGroupName" : "Strains with data in openBIS",
- "groups" : createStrainGroups(strainsKnownToOpenbisWithPhenotypesOrPredictions)
- });
- model.od600StrainsWithPhenotypesAndPredictionsGroups.push({
- "mainGroupName" : "Strains without data in openBIS",
- "groups" : createStrainGroups(strainsUnknownToOpenbisWithPhenotypesOrPredictions)
- });
-
- var commonGrowthMedia = []
- var allGrowthMedia = []
- for (medium in model.growthMediaSet) {
- allGrowthMedia.push(medium);
- if (model.growthMediaSet[medium].length > 20) {
- commonGrowthMedia.push(medium);
- }
- }
- allGrowthMedia.sort();
- commonGrowthMedia.sort();
- model.allGrowthMedia = allGrowthMedia;
- model.commonGrowthMedia = commonGrowthMedia;
-
- callback();
- });
-
-}
-
-AppModel.prototype.od600DataSets = function() {
- var ds = this.dataSetsByType["OD600"];
- return ds ? ds : [];
-}
-
-/**
- * A utility function that groups strains together based on strain name
- */
-function createStrainGroups(strains) {
- if(!strains || strains.length == 0){
- return [];
- }
-
- // prefixes of strain names to be grouped togehter
- var STRAIN_GROUP_PREFIXES = [ "JJS-DIN", "JJS-MGP" ];
-
- // The names to show the user for the strain groups
- var STRAIN_GROUP_PREFIXES_DISPLAY_NAME = {"JJS-DIN" : "JJS-DIn", "JJS-MGP" : "JJS-MGP" };
-
- var groups = STRAIN_GROUP_PREFIXES.map(
- function(strainPrefix) {
- var filtered = strains.filter(function(strain) {
- return strain.name.indexOf(strainPrefix) >= 0
- });
- var groupStrains = filtered.map(function(strain) {
- return { name : strain.name, label : strain.name.substring(strainPrefix.length), data: strain};
- });
-
- return {groupName : STRAIN_GROUP_PREFIXES_DISPLAY_NAME[strainPrefix], strains : groupStrains};
- });
-
- var otherStrains = strains.filter(function(strain) {
- return false == STRAIN_GROUP_PREFIXES.some(function(prefix) { return strain.name.indexOf(prefix) >=0; } );
- });
- otherStrains = otherStrains.map(function(strain) { return {name:strain.name, label:strain.name, data: strain}});
- groups.push({groupName : "Other strains", strains : otherStrains});
-
- var sortFunction = sortByProp("name")
- groups.forEach(function(group) { group.strains.sort(sortFunction); });
-
- // only return groups that have strains
- return groups.filter(function(group) { return group.strains.length > 0 });
-}
-
-/**
- * View that groups data sets by type.
- */
-function DataSummaryView(group, typeName, id, type) {
- this.group = group;
- this.dataSetTypeName = typeName;
- this.dataSetType = type;
- this.nodeId = id;
- this.viewNode = this.createDataSetSummaryViewNode();
-}
-
-DataSummaryView.prototype.createDataSetSummaryViewNode = function()
-{
- var container, result;
- container = this.group.append("div");
-
- container.append("h2").attr("class", "datasetsummarytable").text(this.dataSetTypeName);
-
- result =
- container.append("div")
- .attr("id", this.nodeId)
- .attr("class", "datasummaryview");
-
- return result;
-}
-
-DataSummaryView.prototype.updateView = function()
-{
- var dataSetsForType = model.dataSetsByType[this.dataSetType];
-
- if (dataSetsForType == null) {
- this.viewNode.selectAll("p")
- .data(["No Data"])
- .enter()
- .append("p")
- .text("No Data");
- return;
- }
-
- this.viewNode.selectAll("table")
- .data([dataSetsForType])
- .enter()
- .append("table")
- .attr("class", "datasetsummarytable")
- .selectAll("tr")
- .data(function (d) { return d})
- .enter()
- .append("tr")
- .on("click", toggleInspected)
- .selectAll("td")
- .data(function (d) { return [d.dateString, d.userEmail, d.strainString] })
- .enter()
- .append("td")
- .style("width", "33%")
- .text(function (d) { return d});
-}
-
-
-function StrainView() {
-
-}
-
-function toggleInspected(d) { presenter.toggleInspected(d, this) }
-
-StrainView.prototype.updateView = function(duration)
-{
- var strainDiv = strainVis.selectAll("div.strains").data(model.strainGroups)
- .enter()
- .append("div")
- .attr("class", "strains");
-
- strainDiv
- .append("h2")
- .text(function(d) { return d.groupName });
- strainDiv
- .append("table")
- .selectAll("tr").data(function(d) {
- // Group the different sets of strains differently
- if (d.groupName.indexOf("Other") == 0) return d.strains.reduce(groupBy(3), []);
- if (d.groupName.indexOf("JJS-MGP") == 0) return d.strains.reduce(groupBy(10), []);
-
- // Group the JJS-DIn strains by runs
- return d.strains.reduce(groupByRuns(10), []) })
- .enter()
- .append("tr")
- .selectAll("td").data(function(d) { return d })
- .enter()
- .append("td")
- .on("click", toggleInspected)
- .text(function(d) { return d.label });
-}
-
-function toggleOd600Inspected(d) { presenter.toggleOd600Inspected(d, this) }
-
-function isOd600Inspected(d) {
- return od600Inspected.some(function(elem, index){
- return elem.name == d.name;
- });
-}
-
-/**
- * The view for the OD600 strains
- *
- * @constructor
- */
-function Od600StrainView() {
-
-}
-
-Od600StrainView.prototype.updateView = function(duration)
-{
- var strainDiv = od600StrainVis.selectAll("div.strains").data(model.od600StrainGroups)
- strainDiv.enter().append("div").attr("class", "strains").append("h2").text(function(d) {
- return d.groupName
- })
-
- var tables = strainDiv.selectAll("table").data(function(d){
- return [d];
- })
- tables.enter().append("table");
-
- var trs = tables.selectAll("tr").data(function(d) {
- // Group the different sets of strains differently
- if (d.groupName.indexOf("Other") == 0) return d.strains.reduce(groupBy(3), []);
- if (d.groupName.indexOf("JJS-MGP") == 0) return d.strains.reduce(groupBy(10), []);
-
- // Group the JJS-DIn strains by runs
- return d.strains.reduce(groupByRuns(10), []) })
- trs.enter().append("tr")
-
- var tds = trs.selectAll("td").data(function(d) { return d });
- tds.enter()
- .append("td")
- .on("click", toggleOd600Inspected)
- .text(function(d) { return d.label })
- tds.attr("class", function(d){
- if(isOd600Inspected(d)){
- return "inspected"
- }else{
- return "";
- }
- })
-}
-
-/**
- * The view for the OD600 strains with phenotypes and predictions
- *
- * @constructor
- */
-function Od600StrainWithPhenotypesAndPredictionsView(){
-}
-
-Od600StrainWithPhenotypesAndPredictionsView.prototype.updateView = function(duration)
-{
- var mainGroupDiv = od600StrainWithPhenotypesAndPredictionsVisScroll.selectAll("div.strainsMainGroup").data(model.od600StrainsWithPhenotypesAndPredictionsGroups);
- mainGroupDiv.enter().append("div").attr("class", "strainsMainGroup").append("h2").text(function(d) {
- return d.mainGroupName
- });
-
- var strainDiv = mainGroupDiv.selectAll("div.strains").data(function(d){
- return d.groups;
- })
- strainDiv.enter().append("div").attr("class", "strains").append("h3").text(function(d) {
- return d.groupName
- })
-
- var tables = strainDiv.selectAll("table").data(function(d){
- return [d];
- })
- tables.enter().append("table");
-
- var trs = tables.selectAll("tr").data(function(d) {
- // Group the different sets of strains differently
- if (d.groupName.indexOf("Other") == 0) return d.strains.reduce(groupBy(3), []);
- if (d.groupName.indexOf("JJS-MGP") == 0) return d.strains.reduce(groupBy(10), []);
-
- // Group the JJS-DIn strains by runs
- return d.strains.reduce(groupByRuns(10), []) })
- trs.enter().append("tr")
-
- var tds = trs.selectAll("td").data(function(d) { return d });
- tds.enter()
- .append("td")
- .on("click", function(d) { return toggleOd600Inspected(d); })
- .text(function(d) { return d.label })
- .style("color", function(d){
- if(d.data.hasPhenotypes && d.data.hasPredictions){
- return "green";
- }else if(d.data.hasPhenotypes){
- return "blue";
- } else if(d.data.hasPredictions){
- return "red";
- } else {
- return "black"
- }
- })
- tds.attr("class", function(d){
- var classes = [];
-
- if(isOd600Inspected(d)){
- classes.push("inspected");
- }
- if(!d.data.isKnown){
- classes.push("unknown");
- }
-
- return classes.join(" ");
- })
-
- var legend = od600StrainWithPhenotypesAndPredictionsVisLegend.selectAll("div.legend").data([model.od600StrainsWithPhenotypesAndPredictionsGroups]);
- legend.enter().append("div").attr("class","legend").append("h3").style("font-style","italic").text("Legend");
- var legendList = legend.selectAll("ul").data(function(d){ return [d] }).enter().append("ul");
- legendList.append("li").append("span").text("strain with phenotypes and predictions").style("color","green");
- legendList.append("li").append("span").text("strain with phenotypes only").style("color","blue");
- legendList.append("li").append("span").text("strain with predictions only").style("color","red");
- legendList.append("li").append("span").text("strain with no phenotypes or predictions").style("color","black");
-}
-
-/**
- * The view that shows data sets.
- *
- * @constructor
- */
-function DataSetInspectorView() {
-
-}
-
-DataSetInspectorView.prototype.updateView = function(duration)
-{
- var inspector = inspectors.selectAll("div.inspector").data(inspected, function (d) { return d.name });
-
- var box = inspector.enter().append("div")
- .attr("class", "inspector")
- .text(function(d) { return d.name });
-
- box.append("span")
- .attr("class", "close")
- .on("click", toggleInspected)
- .text("x");
-
- var dataSetList = inspector.selectAll("ul").data(function (d) { return [d] });
- dataSetList.enter()
- .append("ul")
- .attr('class', 'dataSets');
-
-
- var dataSetElt = dataSetList.selectAll("li").data(function (d) { return d.dataSets });
- dataSetElt.enter()
- .append("li")
- .text(function(d) { return dataSetLabel(d) });
-
- var dataSetDetailsElt = dataSetElt.selectAll("div.dataSetDetails").data(function(d) { return [d]; });
- dataSetDetailsElt
- .enter()
- .append("div")
- .attr("class", "dataSetDetails");
-
- var propsTable = dataSetDetailsElt.selectAll("table.properties").data(function(d) {return [d]});
-
- propsTable.enter()
- .append("table")
- .attr("class", "properties");
-
- propsTable.selectAll("tr").data(function(d) { return props_to_pairs(d.bis.properties) })
- .enter()
- .append("tr")
- .selectAll("td").data(function(d) { return d } ).enter()
- .append("td")
- .attr("class", function(d, i) { return (i == 0) ? "propkey" : "propvalue"})
- .style("opacity", "0")
- .text(function(d) { return d })
- .transition()
- .style("opacity", "1");
-
- var downloadTable = dataSetDetailsElt.selectAll("table.downloads").data(function(d) { return [d] });
-
- downloadTable
- .enter()
- .append("table")
- .attr("class", "downloads")
-
- // Add a caption, but make sure there is just one (this does not work with select())
- downloadTable.selectAll("caption").data(["Files"])
- .enter()
- .append("caption").text(function(d) { return d; });
-
- // We just want to see non-directories here
- var downloadTableRow = downloadTable.selectAll("tr").data(filesForDataSet, function(d) { return d.pathInDataSet });
- downloadTableRow
- .enter()
- .append("tr")
- .append("td")
- .on("click", downloadTableFile)
- .text(function(d) { return d.pathInListing });
- downloadTableRow
- .exit()
- .transition()
- .duration(duration)
- .style("opacity", "0")
- .remove();
-
- inspector.exit().transition()
- .duration(duration)
- .style("opacity", "0")
- .remove();
-}
-
-/** Removes all nodes from the view, without affecting the model */
-DataSetInspectorView.prototype.removeAll = function(duration)
-{
- var inspector = inspectors.selectAll("div.inspector").data([]);
- inspector.exit().transition()
- .duration(duration)
- .style("opacity", "0")
- .remove();
-}
-
-/**
- * The view that shows growth curves
- *
- * @constructor
- */
-function Od600InspectorView() {
-
-}
-
-Od600InspectorView.prototype.updateView = function(duration)
-{
- var GRAPH_SMALL_WIDTH = 160;
- var GRAPH_SMALL_HEIGHT = 100;
-
- var GRAPH_LARGE_WIDTH = 480;
- var GRAPH_LARGE_HEIGHT = 300;
-
- // Give duration a default
- duration = duration ? duration : 1000;
-
- var inspector = inspectors.selectAll("div.od600inspector").data(od600Inspected, function (d) { return d.name });
-
- // create
- var inspectorEnter = inspector.enter()
- .append("div")
- .attr("class", "od600inspector")
-
- inspectorEnter
- .append("div")
- .text(function(d) { return d.name })
- .append("span")
- .attr("class", "close")
- .on("click", toggleOd600Inspected)
- .text("x")
-
- inspectorEnter.append("svg:svg")
- .attr("width", function(d){
- d.showSmall = true;
- return GRAPH_SMALL_WIDTH
- })
- .attr("height", GRAPH_SMALL_HEIGHT)
- .on("click", function(d){
- d.showSmall = !d.showSmall;
- od600InspectorView.updateView();
- });
-
- appendGrowthSection(inspectorEnter);
- appendParentSection(inspectorEnter);
- appendIntervalsSection(inspectorEnter);
-
- appendObjectSection({
- getSectionContainer: function(){
- return inspectorEnter;
- },
- getSectionName: function(){
- return "Predictions";
- },
- getSectionClass: function(){
- return "predictionSection";
- },
- getSectionObjects: function(d){
- return d.data.predictions ? d.data.predictions : [];
- },
- getSectionObjectProperties: function(d){
- return prediction_props_to_pairs(d);
- }
- });
-
- function graphWidth(d) { return d.showSmall ? GRAPH_SMALL_WIDTH : GRAPH_LARGE_WIDTH }
- function graphHeight(d) { return d.showSmall ? GRAPH_SMALL_HEIGHT : GRAPH_LARGE_HEIGHT }
-
- // update
- inspector.select("svg").transition().duration(duration)
- .attr("width", graphWidth)
- .attr("height", graphHeight);
-
- var dataDisplay = inspector.select("svg").selectAll("g.curve").data(od600DataForStrain);
- dataDisplay.enter()
- .append("svg:g")
- .attr("class", "curve");
- // Reinitialize the variable
- dataDisplay = inspector.select("svg").selectAll("g.curve").data(od600DataForStrain);
-
- function x1(d, i) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- var lines = this.parentNode.__data__;
- return (i / (lines.length)) * graphWidth(graph);
- };
-
- function x2(d, i) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- var lines = this.parentNode.__data__;
- return ((i + 1) / (lines.length)) * graphWidth(graph);
- };
-
- // Draw the curves
- function colorForLine(node) { return this.parentNode.__data__.color; }
- var aCurve = dataDisplay.selectAll("g.lines").data(curveData);
- aCurve.enter().append("svg:g").attr("class", "lines");
- // The first two columns of data are the strain name and human-readable desc
- var line = aCurve.selectAll("line").data(lineData);
- line.enter().append("svg:line")
- .style("stroke-width", "1")
- .style("stroke", colorForLine)
- .attr("x1", x1).attr("y1", "0").attr("x2", x2).attr("y2", "0");
-
- line.transition().duration(duration)
- .attr("x1", x1)
- .attr("y1", function(d, i) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return graphHeight(graph) - (d[0] * graphHeight(graph));
- })
- .attr("x2", x2)
- .attr("y2", function(d) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return graphHeight(graph) - (d[1] * graphHeight(graph));
- })
- .style("stroke", function(d) {
- var lines = this.parentNode.__data__;
- return lines.color;
- });
-
- // Draw the scale
- function showScale(node) { return !node.parentNode.parentNode.parentNode.__data__.showSmall };
- function axisY(node) { return graphHeight(this.parentNode.parentNode.parentNode.__data__) } ;
- var scaleg = dataDisplay.selectAll("g.scale").data(scaleData);
- scaleg.enter().append("svg:g").attr("class", "scale");
- scaleg.style("visibility", function(d) { return showScale(this) ? "visible" : "hidden" })
- // The first two columns of data are the strain name and human-readable desc
- var scale = scaleg.selectAll("line").data([[1,0], [0,1]]);
- scale.enter().append("svg:line")
- .style("stroke-width", "1")
- .style("stroke", "black")
- .attr("x1", "0")
- .attr("y1", axisY)
- .attr("x2", "0")
- .attr("y2", axisY);
- scale.transition().duration(duration)
- .attr("y1", axisY)
- .attr("x2", function(d) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return d[0] * graphWidth(graph)
- })
- .attr("y2", function(d) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return graphHeight(graph) - (d[1] * graphHeight(graph))
- });
- var yscale = scaleg.selectAll("text.y").data([1, 0.5]);
- yscale.enter().append("svg:text")
- .attr("class", "y")
- .attr("x", "0").attr("dx", "5")
- .attr("y", "0").attr("dy", "15");
- yscale
- .attr("y", function(d) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return graphHeight(graph) - (d * graphHeight(graph));
- })
- .text(function(d) { return d * Y_MAX});
- var xscale = scaleg.selectAll("text.x").data(function(d, idx) {
- var numPointsToShow = 5;
- var len = d.timepoints.length;
- var delta = len / numPointsToShow;
- var points = [];
- for (var i = 0; i < numPointsToShow; ++i) {
- var position = Math.floor(i*delta);
- points.push({label : d.timepoints[position], pos : position / len, index : d.index });
- }
- return points;
- });
- xscale.enter().append("svg:text")
- .style("fill", colorForLine)
- .attr("class", "x")
- .attr("x", "0").attr("dx", "5")
- .attr("y", axisY)
- .attr("dy", function(d) { return -1 * (3 + 10 * d.index)});
-
- xscale
- .attr("x", function(d) {
- var graph = this.parentNode.parentNode.parentNode.__data__;
- return d.pos * graphWidth(graph);
- })
- .attr("y", axisY)
- .text(function(d) { return d.label});
-
- // remove
- inspector.exit().transition()
- .duration(duration)
- .style("opacity", "0")
- .remove();
-}
-
-function appendParentSection(inspectorEnter) {
- var parentSection = inspectorEnter.append("div");
- var parents = parentSection.selectAll("div.parent")
- .data(function(d) { return [d.data.parent]; });
- parents.enter().append("div")
- .attr("class", "parent")
- .text("Parent: ");
- parents.selectAll("span")
- .data(function(d) { return [d] })
- .enter().append("span")
- .text(function (d) { return (d) ? d : "None" });
-}
-
-function appendIntervalsSection(inspectorEnter) {
- var intervalsSection = inspectorEnter.append("div");
- var intervals = intervalsSection.selectAll("div.intervals")
- .data(function(d) { return [d.data.intervals]; });
- intervals.enter().append("div")
- .attr("class", "intervals")
- .text("Intervals: ");
- intervals.selectAll("span")
- .data(function(d) { return d; })
- .enter().append("span")
- .text(function (d) { return d + " " });
-}
-
-function appendGrowthSection(inspectorEnter) {
- var growthMediaSection = inspectorEnter.append("div");
- var growsSection = growthMediaSection.selectAll("div.growth")
- .data(function(d) { var growsOn = [];
- model.allGrowthMedia.forEach(function(m) {
- var value = d.data.phenotypeMap[m]
- if (value && value > 0) growsOn.push(m);
- });
- return growsOn.length > 0 ? [growsOn] : [];
- });
- growsSection.enter().append("div")
- .attr("class", "growth")
- .text("Grows on: ");
- growsSection.selectAll("span")
- .data(function(d) { return d })
- .enter().append("span")
- .text(function (d) { return d + " "});
-
- var doesNotGrowSection = growthMediaSection.selectAll("div.nogrow")
- .data(function(d) { var doesNotGrowOn = [];
- model.allGrowthMedia.forEach(function(m) {
- var value = d.data.phenotypeMap[m]
- if (value && value < 0.01) doesNotGrowOn.push(m);
- });
- return doesNotGrowOn.length > 0 ? [doesNotGrowOn] : [];
- });
- doesNotGrowSection.enter().append("div")
- .attr("class", "nogrow")
- .text("No growth on: ");
- doesNotGrowSection.selectAll("span")
- .data(function(d) { return d })
- .enter().append("span")
- .text(function (d) { return d + " "});
-
-
- var unknownGrowthSection = growthMediaSection.selectAll("div.unknown")
- .data(function(d) { var unknownGrowOn = [];
- model.commonGrowthMedia.forEach(function(m) {
- var value = d.data.phenotypeMap[m]
- if (!value) unknownGrowOn.push(m);
- });
- return unknownGrowOn.length > 0 ? [unknownGrowOn] : [];
- });
- unknownGrowthSection.enter().append("div")
- .attr("class", "unknown")
- .text("Unknown growth on: ");
-
- unknownGrowthSection.selectAll("span")
- .data(function(d) { return d})
- .enter().append("span")
- .text(function (d) { return d + " "});
-}
-
-function appendObjectSection(config){
-
- var section = config.getSectionContainer().append("div")
- .attr("class", config.getSectionClass())
- .style("display", function(d){
- var objects = config.getSectionObjects(d);
- if(objects && objects.length > 0){
- return "block";
- }else{
- return "none";
- }
- });
-
- var header = section.append("h3")
- .text(function(d){
- var name = config.getSectionName();
- var objects = config.getSectionObjects(d);
- return name + " (" + objects.length + ")";
- });
-
- var toggle = header.append("a")
- .text("show");
-
- var list = section.append("ul")
- .style("display","none");
-
- var items = list.selectAll("li")
- .data(function(d){ return config.getSectionObjects(d) });
-
- var item = items.enter()
- .append("li").append("table");
-
- item.selectAll("tr").data(function(d){ return config.getSectionObjectProperties(d) })
- .enter()
- .append("tr")
- .selectAll("td").data(function(d) { return d } ).enter()
- .append("td")
- .attr("class", function(d, i) { return (i == 0) ? "propkey" : "propvalue"})
- .style("opacity", "0")
- .text(function(d) { return d })
- .transition()
- .style("opacity", "1");
-
- toggle.on("click", function(){
- if(list.style("display") == "none"){
- list.style("display","block");
- toggle.text("hide");
- }else{
- list.style("display", "none");
- toggle.text("show");
- }
- });
-
-}
-
-/** Removes all nodes from the view, without affecting the model */
-Od600InspectorView.prototype.removeAll = function(duration)
-{
- var inspector = inspectors.selectAll("div.od600inspector").data([]);
- inspector.exit().transition()
- .duration(duration)
- .style("opacity", "0")
- .remove();
-}
-
-function od600DataForStrain(d) {
- if (null == d.dataSets) return [];
-
- var dataSets = d.dataSets.filter(function(ds) { return isOd600DataSet(ds) });
- var idx = -1;
- var data = [];
- dataSets.map(function(ds) {
- if (null == ds.od600Map) return {};
- var strainData = ds.od600Map[d.name];
- if (null == strainData) return {};
- strainData.map(function(curve) {
- if (curve) {
- idx = idx + 1;
- data.push({ strain: d, index: idx, values: curve, timepoints : ds.od600Timepoints});
- }
- });
- })
- return data;
-}
-
-function od600DataProperties(d){
- return d;
-}
-
-var Y_MAX = 2;
-
-function curveData(d, i)
-{
- var color = curveColors(d.index);
- // Don't normalize -- use 2 as the global max value
- // var maxValue = (0 == d.values.length) ? 0 : d3.max(d.values);
- return [{length : d.values.length, max : Y_MAX, values: d.values, color : color, timepoints : d.timepoints}]
-}
-
-function scaleData(d, i)
-{
- var color = curveColors(d.index);
- // Don't normalize -- use 2 as the global max value
- // var maxValue = (0 == d.values.length) ? 0 : d3.max(d.values);
- return [{length : d.timepoints.length, index : d.index, color : color, timepoints : d.timepoints}]
-}
-
-function lineData(d)
-{
- if (!d) return [];
-
- var data = d.values;
- // convert the data into pairs
- var pairs = data.reduce(function(sum, elt) {
- // initialization
- if (sum.length < 1) {
- sum.push([elt / d.max]);
- return sum;
- }
-
- // add the current elt as the second in the last pair and the first in the new pair
- sum[sum.length - 1].push(elt / d.max);
- // don't add the very last element
- if (sum.length < data.length - 1) sum.push([elt / d.max]);
- return sum;
- }, []);
-
- return pairs;
-}
-
-function dataSetLabel(d) { return d.bis.dataSetTypeCode + " registered on " + timeformat(new Date(d.bis.registrationDetails.registrationDate)); }
-
-function downloadTableFile(d) { presenter.downloadTableFile(d) }
-
-function filesForDataSet(d)
-{
- if (d.loadingFiles) return [{ pathInListing : "Loading..." }];
-
- var fileFilter = function(file) {
- if (file.isDirectory) return false;
- return true;
-/*
- if (!file.isDirectory) {
- if (endsWith(file.pathInDataSet, "xls")) {
- return true;
- }
- if (endsWith(file.pathInDataSet, "xls.tsv")) {
- return true;
- }
- }
- return false;
-*/
- };
-
- return (d.files) ? d.files.filter(fileFilter) : [];
-}
-
-
-var model = new AppModel();
-var presenter = new AppPresenter();
-
-// The data set type visualization
-var dataSetTypeVis, od600View, metabolomicsView, transcriptomicsView, proteomicsView, sequencesCm5View, sequencesGenbankView, intervalAnnotationsView, metabolicModelView;
-
-// The strain visualization
-var strainVis, strainView;
-
-// The OD600 strain visualization
-var od600StrainVis, od600StrainView;
-
-var IGNORED_DATASET_TYPES = [ "EXCEL_ORIGINAL", "TSV_EXPORT", "TSV_MULTISTRAIN_EXPORT", "UNKNOWN" ];
-
-//The inspected strains and data sets
-var inspected = [];
-var od600Inspected = [];
-
-//The node inspectors
-var inspectors, dataSetInspectorView, od600InspectorView;
-
-
-function isOd600DataSet(d) { return "OD600" == d.bis.dataSetTypeCode }
-
-function shouldRenderProperty(prop, value) {
- // strain properties are dealt with separately
- if (prop == STRAIN_PROP_NAME) return false;
-
- // do not show properties with no values
- if (!value) return false;
- return true;
-}
-
-/**
- * Convert properties to pairs
- */
-function props_to_pairs(d)
-{
- var pairs = [];
-
- var dataSetStrains = basynthec.getStrains({properties:d});
- dataSetStrains = dataSetStrains.map(function(strain){
- return { name : strain };
- });
- var strainGroups = createStrainGroups(dataSetStrains);
-
- strainGroups.forEach(function(group) {
- var shortedStrains = group.strains.map(function(elt) { return elt.label; });
- shortedStrains = uniqueElements(shortedStrains.sort())
- var pair = [ group.groupName, shortedStrains.join(" ") ];
- pairs.push(pair)
- });
-
- for (var prop in d) {
- if (shouldRenderProperty(prop, d[prop])) {
- var pair = [prop, d[prop]];
- pairs.push(pair);
- }
- }
- pairs.sort(function(a, b) {
- if (a[0] == b[0]) return 0;
- // Sort in reverse lexicographical
- return (a[0] < b[0]) ? -1 : 1;
- });
- return pairs;
-}
-
-function prediction_props_to_pairs(d){
- return object_props_to_pairs(d);
-}
-
-function phenotype_props_to_pairs(d){
- return object_props_to_pairs(d);
-}
-
-function object_props_to_pairs(d){
- var pairs = [];
-
- for (var prop in d) {
- var propValue = d[prop];
- if (propValue) {
- var pair = [prop, propValue];
- pairs.push(pair);
- }
- }
- pairs.sort(function(a, b) {
- if (a[0] == b[0]) return 0;
- // Sort in reverse lexicographical
- return (a[0] < b[0]) ? -1 : 1;
- });
-
- return pairs;
-}
-
-function enterApp()
-{
- $("#login-form-div").hide();
- $("#main").show();
- basynthec.listAllDataSets(function(data) {
- presenter.showDataSets(data.result);
- });
-
- $('#openbis-logo').height(50)
-
-}
-
-/**
- * Return true if str ends with suffix.
- */
-function endsWith(str, suffix)
-{
- var lastIndex = str.lastIndexOf(suffix);
- return (lastIndex != -1) && (lastIndex + suffix.length == str.length);
-}
-
-/**
- * A sort function that uses properties.
- *
- * @param propName a name of property
- * @returns {Function} a function that can be passed to sort
- */
-function sortByProp(propName)
-{
- var sortFunction = function(a, b) { if (a[propName] == b[propName]) return 0; return (a[propName] < b[propName]) ? -1 : 1};
- return sortFunction;
-}
-
-
-/**
- * @param arr an array
- * @returns the unique elements of an array
- */
-function uniqueElements(arr)
-{
- var reduceFunc = function(list, elt) {
- var size = list.length;
- if (size == 0 || list[size - 1] != elt)
- {
- list.push(elt);
- }
- return list;
- };
- return arr.reduce(reduceFunc, []);
-}
-
-/**
- * A function that groups a collection into collections of length numElts.
- *
- * @param numElts Number of elements
- * @returns {Function} a function that can be passed to reduce
- */
-function groupBy(numElts)
-{
- var groupBy = function(groups, elt) {
- if (groups.length < 1) {
- groups.push([elt]);
- return groups;
- }
-
- var lastGrp = groups[groups.length - 1];
- if (lastGrp.length < numElts) {
- lastGrp.push(elt);
- } else {
- groups.push([elt]);
- }
-
- return groups;
- }
- return groupBy;
-}
-
-/**
- * Check if the current elt number = last elt number + 1
- */
-function isRun(lastElt, currentElt) {
- var lastNumber = Number(lastElt.label);
- var currentNumber = Number(currentElt.label);
- // Assume that non numeric values are runs
- if (lastNumber == NaN || currentNumber == NaN) return true;
-
- return currentNumber == (lastNumber + 1);
-}
-
-/**
- * A function that groups a collection into sequential runs of length maxNumEltsPerGroup
- *
- * @param maxNumEltsPerGroup Number of elements
- * @returns {Function} a function that can be passed to reduce
- */
-function groupByRuns(maxNumEltsPerGroup)
-{
- var lastSeen = "";
- var groupBy = function(groups, elt) {
- // Initialize the groups
- if (groups.length < 1) { groups.push([elt]); return groups; }
-
- // Check if we should append to the last group or create a new one
- var lastGrp = groups[groups.length - 1];
- var createNewGroup = false;
- if (lastGrp.length >= maxNumEltsPerGroup) {
- // We've reached the size limit of the group
- createNewGroup = true;
- } else {
- // See if this is a run, if not create a new group
- createNewGroup = !isRun(lastGrp[lastGrp.length - 1], elt);
- }
-
- (createNewGroup) ? groups.push([elt]) : lastGrp.push(elt);
-
- return groups;
- }
- return groupBy;
-}
\ No newline at end of file
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-style.css b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-style.css
deleted file mode 100644
index 49414f6d7ce..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-style.css
+++ /dev/null
@@ -1,218 +0,0 @@
-body { font: 14px "Trebuchet MS", sans-serif; }
-
-h1 { font: 16px; }
-h2 {
- font-family: "Verdana", sans-serif;
- color: #222;
-}
-h3 { font: 12px; }
-
-.strainsMainGroup h2 { font-size: 22px;}
-
-.strains { padding-bottom: 10px; }
-
-.strains table {
- border-collapse: collapse;
-}
-
-.strains td {
- font-family: "Verdana", sans-serif;
- font-size: 12px;
- padding: 6px;
-}
-
-.strains td:hover {
- font-size: 14px;
- background-color: steelblue;
- font-weight: bold;
- color: white;
- padding: 2px;
- cursor: pointer;
-}
-
-.strains td.unknown:hover {
- cursor: auto;
-}
-
-.datasetsummarytable {
- font-family: "Verdana", sans-serif;
-}
-
-.datasetsummarytable tr {
- font-size: 12px;
-}
-
-.scale { font-size: 9px;}
-
-.datasetsummarytable tr:hover {
- background-color: steelblue;
- color: white;
- cursor: pointer;
-}
-
-div.datasummaryview {
- overflow: auto;
-}
-
-
-.sequenced text {
- fill: black;
-}
-
-td.inspected {
- font-size: 14px;
- font-weight: bold;
- padding: 2px;
-}
-
-.datasummaryview tr.inspected {
- font-weight: bold;
- padding: 0px;
-}
-
-/* Inspector */
-
-div.inspector {
- font: 14px "Verdana", sans-serif;
- padding: 10px;
- border: 1px solid gray;
- margin: 10px 2px;
- font-weight: bold;
-}
-
-.close {
- float: right;
-}
-
-.close:hover {
- opacity: 0.5;
- color: #AAA;
- cursor: pointer;
-}
-
-ul.dataSets {
- list-style-type: none;
- padding-left: 20px;
-}
-
-ul.dataSets li {
- font: 12px "Verdana", sans-serif;
- font-weight: bold;
- color: #222;
-
- padding-top: 10px;
- padding-bottom: 5px;
- border-bottom-style: solid;
- border-width:1px;
- border-color:#222;
-}
-
-/**
- * Downloads table
- */
-.downloads {
- color: steelblue;
- background-color: #E3E3E3;
-}
-
-table.downloads {
- font-family: "Trebuchet MS", sans-serif;
- font-size: 18px;
- font-variant: small-caps;
- table-layout: fixed;
- width: 100%;
-}
-
-.downloads td {
- width: 50%;
- text-align: left;
-}
-
-.downloads td:hover {
- cursor: pointer;
- font-weight: bold;
-}
-
-/**
- * properties table
- */
-table.properties {
- margin: 5px;
-}
-
-table.properties td, th {
- padding: 5px;
-}
-
-.propkey {
- font-size: 10px;
- white-space: nowrap;
-}
-
-.propvalue {
- font-size: 10px;
- font-weight: normal;
-}
-
-#explanation {
- font-family: "Verdana", sans-serif;
- width: 350px;
-}
-
-#explanation p {
- font-size: 14px
-}
-
-#explanation-show {
- padding: 10px 0px;
-}
-
-#explanation-show-text:hover {
- cursor: pointer;
- font-weight: bold;
-}
-
-#button-group{
- margin-bottom: 5px;
-}
-
-.od600inspector {
- margin-bottom: 20px;
- padding: 10px;
- border: 1px solid black;
-}
-
-.od600inspector svg {
- margin-bottom: 10px;
-}
-
-.predictionSection h3, .phenotypeSection h3 {
- font-size: 14px;
- font-weight: bold;
- margin-top: 0px;
- margin-bottom: 5px;
-}
-
-.predictionSection a, .phenotypeSection a {
- font-size: 12px;
- margin-left: 5px;
- cursor: pointer;
- text-decoration: underline;
-}
-
-.predictionSection ul, .phenotypeSection ul {
- font-size: 14px;
- list-style-type: none;
- padding: 0px;
- margin-left: 10px;
-}
-
-.predictionSection li .propkey, .phenotypeSection li .propkey {
- text-transform: uppercase;
- font-size: 11px;
- font-weight: bold;
-}
-
-.predictionSection li, .phenotypeSection li {
- margin-bottom: 5px;
-}
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/button.css b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/button.css
deleted file mode 100644
index b0c9944b189..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/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/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3-test.html b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3-test.html
deleted file mode 100644
index ea9cece3b24..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3-test.html
+++ /dev/null
@@ -1,87 +0,0 @@
-<html>
-<head>
- <title>openBIS BaSynthec Browser</title>
- <script type="text/javascript" src="d3.js"></script>
- <script type="text/javascript" src="jquery.js"></script>
- <script>
-
-var pos = 0;
-
-var testNodes;
-
-
-var didCreateVis = false;
-
-function createVis()
-{
- if (didCreateVis) return;
-
- vis = d3.select("#main").append("table")
- .attr("width", "100%")
- .attr("class", "downloads")
- .style("color", "steelblue");
-;
-
- didCreateVis = true;
-}
-
-function getData(d) {
- return [ 1, 2, 3 ];
-}
-
-
-function updateDiagram()
-{
-
- vis.selectAll("caption").data(["Files"])
- .enter()
- .append("caption").text(function(d) { return d; });
-
-// We just want to see non-directories here
-var downloadTableRow = vis.selectAll("tr").data(getData, function(d) { return d });
-
-// update
-downloadTableRow
- .append("tr")
- .append("td")
- .style("text-align", "left")
- .text(function(d) { return d + pos; });
-
-// add
-downloadTableRow
- .enter()
- .append("tr")
- .append("td")
- .style("text-align", "left")
- .text(function(d) { return d + pos; });
-// remove
-downloadTableRow
- .exit()
- .transition()
- .duration(500)
- .style("opacity", "0")
- .remove();
-
-}
-
-$(document).ready(function() {
-
- createVis()
- $('#button').click(function() { pos = pos + 5; updateDiagram() });
-
- });
-
- </script>
-</head>
-<body>
-
-<div id="main">
-
-<div id="button-group">
- <button id="button">Clickme</button>
-</div>
-
-</div>
-
-</body>
-</html>
\ No newline at end of file
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.js
deleted file mode 100755
index 13abb6dbc6f..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/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/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.layout.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.layout.js
deleted file mode 100755
index 6cc1d716167..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/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/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.time.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.time.js
deleted file mode 100644
index e1c0831c88e..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/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/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.tsv.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.tsv.js
deleted file mode 100644
index 8d9a5e4f703..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/d3.tsv.js
+++ /dev/null
@@ -1,101 +0,0 @@
-/**
- * TSV Parser from:
- * https://github.com/vlandham/d3.tsv
- */
-(function(){d3.tsv = function(url, callback) {
- d3.text(url, "text/tab-separated-values", function(text) {
- callback(text && d3.tsv.parse(text, "\t"));
- });
-};
-
-d3.tsv.version = "0.0.2"
-d3.tsv.parse = function(text, separator) {
- var header;
- return separator && d3.tsv.parseRows(text, separator, function(row, i) {
- if (i) {
- var o = {}, j = -1, m = header.length;
- while (++j < m) o[header[j]] = row[j];
- return o;
- } else {
- header = row;
- return null;
- }
- });
-};
-
-d3.tsv.parseRows = function(text, separator, f) {
- var EOL = {}, // sentinel value for end-of-line
- EOF = {}, // sentinel value for end-of-file
- rows = [], // output rows
- re = new RegExp("\r\n|[" + separator + "\r\n]", "g"), // field separator regex
- separatorCode = separator.charCodeAt(0), // code to match separator with
- n = 0, // the current line number
- t, // the current token
- eol; // is the current token followed by EOL?
-
- re.lastIndex = 0; // work-around bug in FF 3.6
-
- /** @private Returns the next token. */
- function token() {
- if (re.lastIndex >= text.length) return EOF; // special case: end of file
- if (eol) { eol = false; return EOL; } // special case: end of line
-
- // special case: quotes
- var j = re.lastIndex;
- if (text.charCodeAt(j) === 34) {
- var i = j;
- while (i++ < text.length) {
- if (text.charCodeAt(i) === 34) {
- if (text.charCodeAt(i + 1) !== 34) break;
- i++;
- }
- }
- re.lastIndex = i + 2;
- var c = text.charCodeAt(i + 1);
- if (c === 13) {
- eol = true;
- if (text.charCodeAt(i + 2) === 10) re.lastIndex++;
- } else if (c === 10) {
- eol = true;
- }
- return text.substring(j + 1, i).replace(/""/g, "\"");
- }
-
- // common case
- var m = re.exec(text);
- if (m) {
- eol = m[0].charCodeAt(0) !== separatorCode;
- return text.substring(j, m.index);
- }
- re.lastIndex = text.length;
- return text.substring(j);
- }
-
- while ((t = token()) !== EOF) {
- var a = [];
- while ((t !== EOL) && (t !== EOF)) {
- a.push(t);
- t = token();
- }
- if (f && !(a = f(a, n++))) continue;
- rows.push(a);
- }
-
- return rows;
-};
-d3.tsv.format = function(rows) {
- return rows.map(function (row) {
- return d3_formatRow(row, "\t");
- }).join("\n");
-};
-
-function d3_formatRow(row, separator) {
- return row.map(d3_formatValue).join(separator);
-}
-
-function d3_formatValue(text) {
- return /[",\n]/.test(text)
- ? "\"" + text.replace(/\"/g, "\"\"") + "\""
- : text;
-}
-})();
\ No newline at end of file
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/dendrogram-filter.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/dendrogram-filter.js
deleted file mode 100644
index 184771cdb48..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/dendrogram-filter.js
+++ /dev/null
@@ -1,55 +0,0 @@
-
-
-/**
- * @param inputBox the CSS selector of a text field, where users can enter restrictions
- * for the displayed tree nodes
- * @param renderTreeAction a function to be used to render the tree
- * @param
- */
-function addFilteringToDendrogram(inputBox, renderAction, maxLeafNodes)
-{
- $(inputBox).change(function() {
-
- var filterText = $(inputBox).text();
- var delayRenderActionInMs = 300;
-
- // execute filtering async and give user time to
- // continue typing
- setTimeout(function() {
- var filterText2 = $(inputBox).text()
-
- if (filterText != filterText2) {
- // user has changed filter in the meantime
- return;
- }
-
- var filteredTreeRoot = { name:root.name, children: [] };
- filterNode(root, filteredTreeRoot, filterText, maxLeafNodes);
- renderAction(filteredTreeRoot);
-
- }, delayRenderActionInMs)
-
- });
-}
-
-function filterTree(root, filterText, maxLeafNodes) {
-
-}
-
-function filterNode(sourceNode, resultNode, filterText, maxLeafNodes)
-{
-
-}
-
-function reduceNames(groups, name)
-{
- if (groups.length < 1) return groups.push([name]);
-
- var last = groups[groups.length - 1];
- if (last[last.length - 1].charAt(0) == name.charAt(0))
- last.push(name);
- else
- groups.push([name]);
-
- return groups;
-}
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/images/openBIS_Logo.png b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/images/openBIS_Logo.png
deleted file mode 100644
index 87ae5e81899908f3968ea230205322dc19ff4ee5..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.htm b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.htm
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-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en-US" lang="en-US">
-<head>
- <meta http-equiv="content-type" content="text/html; charset=utf-8" />
- <meta name="Author" content="Chandrasekhar Ramakrishnan" />
- <meta HTTP-EQUIV="REFRESH" content="0; url=index.html">
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diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.html b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.html
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--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/index.html
+++ /dev/null
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-<!DOCTYPE html>
-<html>
-<head>
- <!-- The browser for BaSynthec data sets. Data sets can be shown either by technology or by strain -->
- <title>openBIS BaSynthec Browser</title>
- <link type="text/css" rel="stylesheet" href="basynthec-style.css" />
- <link type="text/css" rel="stylesheet" href="button.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="d3.tsv.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="openbis-basynthec.js"></script>
- <script type="text/javascript" src="basynthec-browser.js"></script>
- <!-- To speed development, cache the requests -->
- <!-- <script type="text/javascript" src="/openbis/resources/js/openbis-request-cache.js"></script> -->
- <script>
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-var openBisUrl = 'http://localhost:20000/openbis/openbis';
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-// var openBisUrl = 'https://basynthec.ethz.ch/openbis/openbis';
-// var dssUrl = 'https://basynthec.ethz.ch/datastore_server';
-
-basynthec = new openbis_basynthec(openBisUrl, dssUrl);
-
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- if(data.result == null){
- $("#login-failed").show();
- $("#username").focus();
- return;
- } else {
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- }
-}
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-$(document).ready(function() {
-
- $("#main").hide();
-
- $("#groupradio1").change(function(event){
- presenter.switchToDataSetTypeView();
- });
- $("#groupradio2").change(function(event){
- presenter.switchToStrainView();
- });
- $("#groupradio3").change(function(event){
- presenter.switchToOD600View();
- });
- $("#groupradio4").change(function(event){
- presenter.switchToOD600WithPhenotypesAndPredictionsView();
- });
- $('#explanation-show-text').click(function() {
- presenter.showExplanation();
- });
-
- var context = new openbisWebAppContext();
-
- if(context.getSessionId()){
- $("#openbis-logo").hide();
- $("#login-form-div").hide();
- $("#logout-button").hide();
- basynthec.server.useSession(context.getSessionId());
- enterApp();
- }else{
- $('#logout-button').click(function() { basynthec.server.logout(function(data) {
- window.location.reload();
- })
- });
-
- $('#login-form').submit(function() {
- $("#login-failed").hide();
- basynthec.server.login(
- $.trim($('#username').val()),
- $.trim($('#password').val()),
- function(data) { enterAppOrShowLoginError(data) })
- });
-
- basynthec.server.ifRestoredSessionActive(function(data) { enterApp() });
- }
-
-});
-
- </script>
-</head>
-<body>
-<img id="openbis-logo" src="images/openBIS_Logo.png" alt="openBIS" height="100px" style="float: right;"/>
-<div id="login-form-div">
-<h1>openBIS BaSynthec</h1>
-
-<form id="login-form" action="javascript:">
-<input id="username" type="text" required="required"> <input id="password" type="password" required="required"> <button id="login-button">Login</button>
-</form>
-<div id="login-failed" style="display: none; position: relative; top: 10px;">
- <a href="https://crowd-bsse.ethz.ch/crowd/console/forgottenlogindetails!default.action" id="resetpassword" class="resetpassword">Forgot password?</a>
-</div>
-</div>
-
-<div id="main">
-
-<div id="button-group">
- <button id="logout-button">Logout</button>
- <div id="explanation-show" style="display: none;">
- <span id="explanation-show-text">[Guide]</span>
- </div>
- <div id="explanation">
- <p>
- This browser displays data registered in the BaSynthec project. Initially, data sets are displayed grouped by user upload. An alternate display mode shows all strains for which data has been collected.
- In either mode, clicking on an entry opens a small window that allows downloading of the data in several different formats.
- </p>
- <p>
- A third display mode, <em>From Strain DB</em>, is for browsing growth curves, phenotypes and model predictions.
- </p>
- </div>
- <div id="mode-selector">
- <span style="position: relative; font-weight: bold">View:</span>
- <input type="radio" name="groupgroup" id="groupradio1" checked> <label for="groupradio1">By Uploads</label>
- <input type="radio" name="groupgroup" id="groupradio2"> <label for="groupradio2">By Strain</label>
- <input type="radio" name="groupgroup" id="groupradio4"> <label for="groupradio4">From Strain DB</label>
- </div>
-</div>
-
-</div>
-
-</body>
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diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/LICENSE b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/LICENSE
deleted file mode 100644
index 2ac775d6e36..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/LICENSE
+++ /dev/null
@@ -1,38 +0,0 @@
-Apache-Style Software License for ColorBrewer software and ColorBrewer Color
-Schemes
-
-Copyright (c) 2002 Cynthia Brewer, Mark Harrower, and The Pennsylvania State
-University.
-
-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.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions as source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.
-
-2. The end-user documentation included with the redistribution, if any, must
-include the following acknowledgment: "This product includes color
-specifications and designs developed by Cynthia Brewer
-(http://colorbrewer.org/)." Alternately, this acknowledgment may appear in the
-software itself, if and wherever such third-party acknowledgments normally
-appear.
-
-4. The name "ColorBrewer" must not be used to endorse or promote products
-derived from this software without prior written permission. For written
-permission, please contact Cynthia Brewer at cbrewer@psu.edu.
-
-5. Products derived from this software may not be called "ColorBrewer", nor
-may "ColorBrewer" appear in their name, without prior written permission of
-Cynthia Brewer.
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.css b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.css
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diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.js
deleted file mode 100644
index e468640287c..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/lib/colorbrewer/colorbrewer.js
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * This product includes color specifications and designs developed by Cynthia
- * Brewer (http://colorbrewer.org/).
- */
-var colorbrewer = {
-YlGn:{3:["rgb(247,252,185)","rgb(173,221,142)","rgb(49,163,84)"],4:["rgb(255,255,204)","rgb(194,230,153)","rgb(120,198,121)","rgb(35,132,67)"],5:["rgb(255,255,204)","rgb(194,230,153)","rgb(120,198,121)","rgb(49,163,84)","rgb(0,104,55)"],6:["rgb(255,255,204)","rgb(217,240,163)","rgb(173,221,142)","rgb(120,198,121)","rgb(49,163,84)","rgb(0,104,55)"],7:["rgb(255,255,204)","rgb(217,240,163)","rgb(173,221,142)","rgb(120,198,121)","rgb(65,171,93)","rgb(35,132,67)","rgb(0,90,50)"],8:["rgb(255,255,229)","rgb(247,252,185)","rgb(217,240,163)","rgb(173,221,142)","rgb(120,198,121)","rgb(65,171,93)","rgb(35,132,67)","rgb(0,90,50)"],9:["rgb(255,255,229)","rgb(247,252,185)","rgb(217,240,163)","rgb(173,221,142)","rgb(120,198,121)","rgb(65,171,93)","rgb(35,132,67)","rgb(0,104,55)","rgb(0,69,41)"]},
-YlGnBu:{3:["rgb(237,248,177)","rgb(127,205,187)","rgb(44,127,184)"],4:["rgb(255,255,204)","rgb(161,218,180)","rgb(65,182,196)","rgb(34,94,168)"],5:["rgb(255,255,204)","rgb(161,218,180)","rgb(65,182,196)","rgb(44,127,184)","rgb(37,52,148)"],6:["rgb(255,255,204)","rgb(199,233,180)","rgb(127,205,187)","rgb(65,182,196)","rgb(44,127,184)","rgb(37,52,148)"],7:["rgb(255,255,204)","rgb(199,233,180)","rgb(127,205,187)","rgb(65,182,196)","rgb(29,145,192)","rgb(34,94,168)","rgb(12,44,132)"],8:["rgb(255,255,217)","rgb(237,248,177)","rgb(199,233,180)","rgb(127,205,187)","rgb(65,182,196)","rgb(29,145,192)","rgb(34,94,168)","rgb(12,44,132)"],9:["rgb(255,255,217)","rgb(237,248,177)","rgb(199,233,180)","rgb(127,205,187)","rgb(65,182,196)","rgb(29,145,192)","rgb(34,94,168)","rgb(37,52,148)","rgb(8,29,88)"]},
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-BuGn:{3:["rgb(229,245,249)","rgb(153,216,201)","rgb(44,162,95)"],4:["rgb(237,248,251)","rgb(178,226,226)","rgb(102,194,164)","rgb(35,139,69)"],5:["rgb(237,248,251)","rgb(178,226,226)","rgb(102,194,164)","rgb(44,162,95)","rgb(0,109,44)"],6:["rgb(237,248,251)","rgb(204,236,230)","rgb(153,216,201)","rgb(102,194,164)","rgb(44,162,95)","rgb(0,109,44)"],7:["rgb(237,248,251)","rgb(204,236,230)","rgb(153,216,201)","rgb(102,194,164)","rgb(65,174,118)","rgb(35,139,69)","rgb(0,88,36)"],8:["rgb(247,252,253)","rgb(229,245,249)","rgb(204,236,230)","rgb(153,216,201)","rgb(102,194,164)","rgb(65,174,118)","rgb(35,139,69)","rgb(0,88,36)"],9:["rgb(247,252,253)","rgb(229,245,249)","rgb(204,236,230)","rgb(153,216,201)","rgb(102,194,164)","rgb(65,174,118)","rgb(35,139,69)","rgb(0,109,44)","rgb(0,68,27)"]},
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-BuPu:{3:["rgb(224,236,244)","rgb(158,188,218)","rgb(136,86,167)"],4:["rgb(237,248,251)","rgb(179,205,227)","rgb(140,150,198)","rgb(136,65,157)"],5:["rgb(237,248,251)","rgb(179,205,227)","rgb(140,150,198)","rgb(136,86,167)","rgb(129,15,124)"],6:["rgb(237,248,251)","rgb(191,211,230)","rgb(158,188,218)","rgb(140,150,198)","rgb(136,86,167)","rgb(129,15,124)"],7:["rgb(237,248,251)","rgb(191,211,230)","rgb(158,188,218)","rgb(140,150,198)","rgb(140,107,177)","rgb(136,65,157)","rgb(110,1,107)"],8:["rgb(247,252,253)","rgb(224,236,244)","rgb(191,211,230)","rgb(158,188,218)","rgb(140,150,198)","rgb(140,107,177)","rgb(136,65,157)","rgb(110,1,107)"],9:["rgb(247,252,253)","rgb(224,236,244)","rgb(191,211,230)","rgb(158,188,218)","rgb(140,150,198)","rgb(140,107,177)","rgb(136,65,157)","rgb(129,15,124)","rgb(77,0,75)"]},
-RdPu:{3:["rgb(253,224,221)","rgb(250,159,181)","rgb(197,27,138)"],4:["rgb(254,235,226)","rgb(251,180,185)","rgb(247,104,161)","rgb(174,1,126)"],5:["rgb(254,235,226)","rgb(251,180,185)","rgb(247,104,161)","rgb(197,27,138)","rgb(122,1,119)"],6:["rgb(254,235,226)","rgb(252,197,192)","rgb(250,159,181)","rgb(247,104,161)","rgb(197,27,138)","rgb(122,1,119)"],7:["rgb(254,235,226)","rgb(252,197,192)","rgb(250,159,181)","rgb(247,104,161)","rgb(221,52,151)","rgb(174,1,126)","rgb(122,1,119)"],8:["rgb(255,247,243)","rgb(253,224,221)","rgb(252,197,192)","rgb(250,159,181)","rgb(247,104,161)","rgb(221,52,151)","rgb(174,1,126)","rgb(122,1,119)"],9:["rgb(255,247,243)","rgb(253,224,221)","rgb(252,197,192)","rgb(250,159,181)","rgb(247,104,161)","rgb(221,52,151)","rgb(174,1,126)","rgb(122,1,119)","rgb(73,0,106)"]},
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-YlOrBr:{3:["rgb(255,247,188)","rgb(254,196,79)","rgb(217,95,14)"],4:["rgb(255,255,212)","rgb(254,217,142)","rgb(254,153,41)","rgb(204,76,2)"],5:["rgb(255,255,212)","rgb(254,217,142)","rgb(254,153,41)","rgb(217,95,14)","rgb(153,52,4)"],6:["rgb(255,255,212)","rgb(254,227,145)","rgb(254,196,79)","rgb(254,153,41)","rgb(217,95,14)","rgb(153,52,4)"],7:["rgb(255,255,212)","rgb(254,227,145)","rgb(254,196,79)","rgb(254,153,41)","rgb(236,112,20)","rgb(204,76,2)","rgb(140,45,4)"],8:["rgb(255,255,229)","rgb(255,247,188)","rgb(254,227,145)","rgb(254,196,79)","rgb(254,153,41)","rgb(236,112,20)","rgb(204,76,2)","rgb(140,45,4)"],9:["rgb(255,255,229)","rgb(255,247,188)","rgb(254,227,145)","rgb(254,196,79)","rgb(254,153,41)","rgb(236,112,20)","rgb(204,76,2)","rgb(153,52,4)","rgb(102,37,6)"]},
-Purples:{3:["rgb(239,237,245)","rgb(188,189,220)","rgb(117,107,177)"],4:["rgb(242,240,247)","rgb(203,201,226)","rgb(158,154,200)","rgb(106,81,163)"],5:["rgb(242,240,247)","rgb(203,201,226)","rgb(158,154,200)","rgb(117,107,177)","rgb(84,39,143)"],6:["rgb(242,240,247)","rgb(218,218,235)","rgb(188,189,220)","rgb(158,154,200)","rgb(117,107,177)","rgb(84,39,143)"],7:["rgb(242,240,247)","rgb(218,218,235)","rgb(188,189,220)","rgb(158,154,200)","rgb(128,125,186)","rgb(106,81,163)","rgb(74,20,134)"],8:["rgb(252,251,253)","rgb(239,237,245)","rgb(218,218,235)","rgb(188,189,220)","rgb(158,154,200)","rgb(128,125,186)","rgb(106,81,163)","rgb(74,20,134)"],9:["rgb(252,251,253)","rgb(239,237,245)","rgb(218,218,235)","rgb(188,189,220)","rgb(158,154,200)","rgb(128,125,186)","rgb(106,81,163)","rgb(84,39,143)","rgb(63,0,125)"]},
-Blues:{3:["rgb(222,235,247)","rgb(158,202,225)","rgb(49,130,189)"],4:["rgb(239,243,255)","rgb(189,215,231)","rgb(107,174,214)","rgb(33,113,181)"],5:["rgb(239,243,255)","rgb(189,215,231)","rgb(107,174,214)","rgb(49,130,189)","rgb(8,81,156)"],6:["rgb(239,243,255)","rgb(198,219,239)","rgb(158,202,225)","rgb(107,174,214)","rgb(49,130,189)","rgb(8,81,156)"],7:["rgb(239,243,255)","rgb(198,219,239)","rgb(158,202,225)","rgb(107,174,214)","rgb(66,146,198)","rgb(33,113,181)","rgb(8,69,148)"],8:["rgb(247,251,255)","rgb(222,235,247)","rgb(198,219,239)","rgb(158,202,225)","rgb(107,174,214)","rgb(66,146,198)","rgb(33,113,181)","rgb(8,69,148)"],9:["rgb(247,251,255)","rgb(222,235,247)","rgb(198,219,239)","rgb(158,202,225)","rgb(107,174,214)","rgb(66,146,198)","rgb(33,113,181)","rgb(8,81,156)","rgb(8,48,107)"]},
-Greens:{3:["rgb(229,245,224)","rgb(161,217,155)","rgb(49,163,84)"],4:["rgb(237,248,233)","rgb(186,228,179)","rgb(116,196,118)","rgb(35,139,69)"],5:["rgb(237,248,233)","rgb(186,228,179)","rgb(116,196,118)","rgb(49,163,84)","rgb(0,109,44)"],6:["rgb(237,248,233)","rgb(199,233,192)","rgb(161,217,155)","rgb(116,196,118)","rgb(49,163,84)","rgb(0,109,44)"],7:["rgb(237,248,233)","rgb(199,233,192)","rgb(161,217,155)","rgb(116,196,118)","rgb(65,171,93)","rgb(35,139,69)","rgb(0,90,50)"],8:["rgb(247,252,245)","rgb(229,245,224)","rgb(199,233,192)","rgb(161,217,155)","rgb(116,196,118)","rgb(65,171,93)","rgb(35,139,69)","rgb(0,90,50)"],9:["rgb(247,252,245)","rgb(229,245,224)","rgb(199,233,192)","rgb(161,217,155)","rgb(116,196,118)","rgb(65,171,93)","rgb(35,139,69)","rgb(0,109,44)","rgb(0,68,27)"]},
-Oranges:{3:["rgb(254,230,206)","rgb(253,174,107)","rgb(230,85,13)"],4:["rgb(254,237,222)","rgb(253,190,133)","rgb(253,141,60)","rgb(217,71,1)"],5:["rgb(254,237,222)","rgb(253,190,133)","rgb(253,141,60)","rgb(230,85,13)","rgb(166,54,3)"],6:["rgb(254,237,222)","rgb(253,208,162)","rgb(253,174,107)","rgb(253,141,60)","rgb(230,85,13)","rgb(166,54,3)"],7:["rgb(254,237,222)","rgb(253,208,162)","rgb(253,174,107)","rgb(253,141,60)","rgb(241,105,19)","rgb(217,72,1)","rgb(140,45,4)"],8:["rgb(255,245,235)","rgb(254,230,206)","rgb(253,208,162)","rgb(253,174,107)","rgb(253,141,60)","rgb(241,105,19)","rgb(217,72,1)","rgb(140,45,4)"],9:["rgb(255,245,235)","rgb(254,230,206)","rgb(253,208,162)","rgb(253,174,107)","rgb(253,141,60)","rgb(241,105,19)","rgb(217,72,1)","rgb(166,54,3)","rgb(127,39,4)"]},
-Reds:{3:["rgb(254,224,210)","rgb(252,146,114)","rgb(222,45,38)"],4:["rgb(254,229,217)","rgb(252,174,145)","rgb(251,106,74)","rgb(203,24,29)"],5:["rgb(254,229,217)","rgb(252,174,145)","rgb(251,106,74)","rgb(222,45,38)","rgb(165,15,21)"],6:["rgb(254,229,217)","rgb(252,187,161)","rgb(252,146,114)","rgb(251,106,74)","rgb(222,45,38)","rgb(165,15,21)"],7:["rgb(254,229,217)","rgb(252,187,161)","rgb(252,146,114)","rgb(251,106,74)","rgb(239,59,44)","rgb(203,24,29)","rgb(153,0,13)"],8:["rgb(255,245,240)","rgb(254,224,210)","rgb(252,187,161)","rgb(252,146,114)","rgb(251,106,74)","rgb(239,59,44)","rgb(203,24,29)","rgb(153,0,13)"],9:["rgb(255,245,240)","rgb(254,224,210)","rgb(252,187,161)","rgb(252,146,114)","rgb(251,106,74)","rgb(239,59,44)","rgb(203,24,29)","rgb(165,15,21)","rgb(103,0,13)"]},
-Greys:{3:["rgb(240,240,240)","rgb(189,189,189)","rgb(99,99,99)"],4:["rgb(247,247,247)","rgb(204,204,204)","rgb(150,150,150)","rgb(82,82,82)"],5:["rgb(247,247,247)","rgb(204,204,204)","rgb(150,150,150)","rgb(99,99,99)","rgb(37,37,37)"],6:["rgb(247,247,247)","rgb(217,217,217)","rgb(189,189,189)","rgb(150,150,150)","rgb(99,99,99)","rgb(37,37,37)"],7:["rgb(247,247,247)","rgb(217,217,217)","rgb(189,189,189)","rgb(150,150,150)","rgb(115,115,115)","rgb(82,82,82)","rgb(37,37,37)"],8:["rgb(255,255,255)","rgb(240,240,240)","rgb(217,217,217)","rgb(189,189,189)","rgb(150,150,150)","rgb(115,115,115)","rgb(82,82,82)","rgb(37,37,37)"],9:["rgb(255,255,255)","rgb(240,240,240)","rgb(217,217,217)","rgb(189,189,189)","rgb(150,150,150)","rgb(115,115,115)","rgb(82,82,82)","rgb(37,37,37)","rgb(0,0,0)"]},
-PuOr:{3:["rgb(241,163,64)","rgb(247,247,247)","rgb(153,142,195)"],4:["rgb(230,97,1)","rgb(253,184,99)","rgb(178,171,210)","rgb(94,60,153)"],5:["rgb(230,97,1)","rgb(253,184,99)","rgb(247,247,247)","rgb(178,171,210)","rgb(94,60,153)"],6:["rgb(179,88,6)","rgb(241,163,64)","rgb(254,224,182)","rgb(216,218,235)","rgb(153,142,195)","rgb(84,39,136)"],7:["rgb(179,88,6)","rgb(241,163,64)","rgb(254,224,182)","rgb(247,247,247)","rgb(216,218,235)","rgb(153,142,195)","rgb(84,39,136)"],8:["rgb(179,88,6)","rgb(224,130,20)","rgb(253,184,99)","rgb(254,224,182)","rgb(216,218,235)","rgb(178,171,210)","rgb(128,115,172)","rgb(84,39,136)"],9:["rgb(179,88,6)","rgb(224,130,20)","rgb(253,184,99)","rgb(254,224,182)","rgb(247,247,247)","rgb(216,218,235)","rgb(178,171,210)","rgb(128,115,172)","rgb(84,39,136)"],10:["rgb(127,59,8)","rgb(179,88,6)","rgb(224,130,20)","rgb(253,184,99)","rgb(254,224,182)","rgb(216,218,235)","rgb(178,171,210)","rgb(128,115,172)","rgb(84,39,136)","rgb(45,0,75)"],11:["rgb(127,59,8)","rgb(179,88,6)","rgb(224,130,20)","rgb(253,184,99)","rgb(254,224,182)","rgb(247,247,247)","rgb(216,218,235)","rgb(178,171,210)","rgb(128,115,172)","rgb(84,39,136)","rgb(45,0,75)"]},
-BrBG:{3:["rgb(216,179,101)","rgb(245,245,245)","rgb(90,180,172)"],4:["rgb(166,97,26)","rgb(223,194,125)","rgb(128,205,193)","rgb(1,133,113)"],5:["rgb(166,97,26)","rgb(223,194,125)","rgb(245,245,245)","rgb(128,205,193)","rgb(1,133,113)"],6:["rgb(140,81,10)","rgb(216,179,101)","rgb(246,232,195)","rgb(199,234,229)","rgb(90,180,172)","rgb(1,102,94)"],7:["rgb(140,81,10)","rgb(216,179,101)","rgb(246,232,195)","rgb(245,245,245)","rgb(199,234,229)","rgb(90,180,172)","rgb(1,102,94)"],8:["rgb(140,81,10)","rgb(191,129,45)","rgb(223,194,125)","rgb(246,232,195)","rgb(199,234,229)","rgb(128,205,193)","rgb(53,151,143)","rgb(1,102,94)"],9:["rgb(140,81,10)","rgb(191,129,45)","rgb(223,194,125)","rgb(246,232,195)","rgb(245,245,245)","rgb(199,234,229)","rgb(128,205,193)","rgb(53,151,143)","rgb(1,102,94)"],10:["rgb(84,48,5)","rgb(140,81,10)","rgb(191,129,45)","rgb(223,194,125)","rgb(246,232,195)","rgb(199,234,229)","rgb(128,205,193)","rgb(53,151,143)","rgb(1,102,94)","rgb(0,60,48)"],11:["rgb(84,48,5)","rgb(140,81,10)","rgb(191,129,45)","rgb(223,194,125)","rgb(246,232,195)","rgb(245,245,245)","rgb(199,234,229)","rgb(128,205,193)","rgb(53,151,143)","rgb(1,102,94)","rgb(0,60,48)"]},
-PRGn:{3:["rgb(175,141,195)","rgb(247,247,247)","rgb(127,191,123)"],4:["rgb(123,50,148)","rgb(194,165,207)","rgb(166,219,160)","rgb(0,136,55)"],5:["rgb(123,50,148)","rgb(194,165,207)","rgb(247,247,247)","rgb(166,219,160)","rgb(0,136,55)"],6:["rgb(118,42,131)","rgb(175,141,195)","rgb(231,212,232)","rgb(217,240,211)","rgb(127,191,123)","rgb(27,120,55)"],7:["rgb(118,42,131)","rgb(175,141,195)","rgb(231,212,232)","rgb(247,247,247)","rgb(217,240,211)","rgb(127,191,123)","rgb(27,120,55)"],8:["rgb(118,42,131)","rgb(153,112,171)","rgb(194,165,207)","rgb(231,212,232)","rgb(217,240,211)","rgb(166,219,160)","rgb(90,174,97)","rgb(27,120,55)"],9:["rgb(118,42,131)","rgb(153,112,171)","rgb(194,165,207)","rgb(231,212,232)","rgb(247,247,247)","rgb(217,240,211)","rgb(166,219,160)","rgb(90,174,97)","rgb(27,120,55)"],10:["rgb(64,0,75)","rgb(118,42,131)","rgb(153,112,171)","rgb(194,165,207)","rgb(231,212,232)","rgb(217,240,211)","rgb(166,219,160)","rgb(90,174,97)","rgb(27,120,55)","rgb(0,68,27)"],11:["rgb(64,0,75)","rgb(118,42,131)","rgb(153,112,171)","rgb(194,165,207)","rgb(231,212,232)","rgb(247,247,247)","rgb(217,240,211)","rgb(166,219,160)","rgb(90,174,97)","rgb(27,120,55)","rgb(0,68,27)"]},
-PiYG:{3:["rgb(233,163,201)","rgb(247,247,247)","rgb(161,215,106)"],4:["rgb(208,28,139)","rgb(241,182,218)","rgb(184,225,134)","rgb(77,172,38)"],5:["rgb(208,28,139)","rgb(241,182,218)","rgb(247,247,247)","rgb(184,225,134)","rgb(77,172,38)"],6:["rgb(197,27,125)","rgb(233,163,201)","rgb(253,224,239)","rgb(230,245,208)","rgb(161,215,106)","rgb(77,146,33)"],7:["rgb(197,27,125)","rgb(233,163,201)","rgb(253,224,239)","rgb(247,247,247)","rgb(230,245,208)","rgb(161,215,106)","rgb(77,146,33)"],8:["rgb(197,27,125)","rgb(222,119,174)","rgb(241,182,218)","rgb(253,224,239)","rgb(230,245,208)","rgb(184,225,134)","rgb(127,188,65)","rgb(77,146,33)"],9:["rgb(197,27,125)","rgb(222,119,174)","rgb(241,182,218)","rgb(253,224,239)","rgb(247,247,247)","rgb(230,245,208)","rgb(184,225,134)","rgb(127,188,65)","rgb(77,146,33)"],10:["rgb(142,1,82)","rgb(197,27,125)","rgb(222,119,174)","rgb(241,182,218)","rgb(253,224,239)","rgb(230,245,208)","rgb(184,225,134)","rgb(127,188,65)","rgb(77,146,33)","rgb(39,100,25)"],11:["rgb(142,1,82)","rgb(197,27,125)","rgb(222,119,174)","rgb(241,182,218)","rgb(253,224,239)","rgb(247,247,247)","rgb(230,245,208)","rgb(184,225,134)","rgb(127,188,65)","rgb(77,146,33)","rgb(39,100,25)"]},
-RdBu:{3:["rgb(239,138,98)","rgb(247,247,247)","rgb(103,169,207)"],4:["rgb(202,0,32)","rgb(244,165,130)","rgb(146,197,222)","rgb(5,113,176)"],5:["rgb(202,0,32)","rgb(244,165,130)","rgb(247,247,247)","rgb(146,197,222)","rgb(5,113,176)"],6:["rgb(178,24,43)","rgb(239,138,98)","rgb(253,219,199)","rgb(209,229,240)","rgb(103,169,207)","rgb(33,102,172)"],7:["rgb(178,24,43)","rgb(239,138,98)","rgb(253,219,199)","rgb(247,247,247)","rgb(209,229,240)","rgb(103,169,207)","rgb(33,102,172)"],8:["rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(209,229,240)","rgb(146,197,222)","rgb(67,147,195)","rgb(33,102,172)"],9:["rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(247,247,247)","rgb(209,229,240)","rgb(146,197,222)","rgb(67,147,195)","rgb(33,102,172)"],10:["rgb(103,0,31)","rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(209,229,240)","rgb(146,197,222)","rgb(67,147,195)","rgb(33,102,172)","rgb(5,48,97)"],11:["rgb(103,0,31)","rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(247,247,247)","rgb(209,229,240)","rgb(146,197,222)","rgb(67,147,195)","rgb(33,102,172)","rgb(5,48,97)"]},
-RdGy:{3:["rgb(239,138,98)","rgb(255,255,255)","rgb(153,153,153)"],4:["rgb(202,0,32)","rgb(244,165,130)","rgb(186,186,186)","rgb(64,64,64)"],5:["rgb(202,0,32)","rgb(244,165,130)","rgb(255,255,255)","rgb(186,186,186)","rgb(64,64,64)"],6:["rgb(178,24,43)","rgb(239,138,98)","rgb(253,219,199)","rgb(224,224,224)","rgb(153,153,153)","rgb(77,77,77)"],7:["rgb(178,24,43)","rgb(239,138,98)","rgb(253,219,199)","rgb(255,255,255)","rgb(224,224,224)","rgb(153,153,153)","rgb(77,77,77)"],8:["rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(224,224,224)","rgb(186,186,186)","rgb(135,135,135)","rgb(77,77,77)"],9:["rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(255,255,255)","rgb(224,224,224)","rgb(186,186,186)","rgb(135,135,135)","rgb(77,77,77)"],10:["rgb(103,0,31)","rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(224,224,224)","rgb(186,186,186)","rgb(135,135,135)","rgb(77,77,77)","rgb(26,26,26)"],11:["rgb(103,0,31)","rgb(178,24,43)","rgb(214,96,77)","rgb(244,165,130)","rgb(253,219,199)","rgb(255,255,255)","rgb(224,224,224)","rgb(186,186,186)","rgb(135,135,135)","rgb(77,77,77)","rgb(26,26,26)"]},
-RdYlBu:{3:["rgb(252,141,89)","rgb(255,255,191)","rgb(145,191,219)"],4:["rgb(215,25,28)","rgb(253,174,97)","rgb(171,217,233)","rgb(44,123,182)"],5:["rgb(215,25,28)","rgb(253,174,97)","rgb(255,255,191)","rgb(171,217,233)","rgb(44,123,182)"],6:["rgb(215,48,39)","rgb(252,141,89)","rgb(254,224,144)","rgb(224,243,248)","rgb(145,191,219)","rgb(69,117,180)"],7:["rgb(215,48,39)","rgb(252,141,89)","rgb(254,224,144)","rgb(255,255,191)","rgb(224,243,248)","rgb(145,191,219)","rgb(69,117,180)"],8:["rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,144)","rgb(224,243,248)","rgb(171,217,233)","rgb(116,173,209)","rgb(69,117,180)"],9:["rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,144)","rgb(255,255,191)","rgb(224,243,248)","rgb(171,217,233)","rgb(116,173,209)","rgb(69,117,180)"],10:["rgb(165,0,38)","rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,144)","rgb(224,243,248)","rgb(171,217,233)","rgb(116,173,209)","rgb(69,117,180)","rgb(49,54,149)"],11:["rgb(165,0,38)","rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,144)","rgb(255,255,191)","rgb(224,243,248)","rgb(171,217,233)","rgb(116,173,209)","rgb(69,117,180)","rgb(49,54,149)"]},
-Spectral:{3:["rgb(252,141,89)","rgb(255,255,191)","rgb(153,213,148)"],4:["rgb(215,25,28)","rgb(253,174,97)","rgb(171,221,164)","rgb(43,131,186)"],5:["rgb(215,25,28)","rgb(253,174,97)","rgb(255,255,191)","rgb(171,221,164)","rgb(43,131,186)"],6:["rgb(213,62,79)","rgb(252,141,89)","rgb(254,224,139)","rgb(230,245,152)","rgb(153,213,148)","rgb(50,136,189)"],7:["rgb(213,62,79)","rgb(252,141,89)","rgb(254,224,139)","rgb(255,255,191)","rgb(230,245,152)","rgb(153,213,148)","rgb(50,136,189)"],8:["rgb(213,62,79)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(230,245,152)","rgb(171,221,164)","rgb(102,194,165)","rgb(50,136,189)"],9:["rgb(213,62,79)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(255,255,191)","rgb(230,245,152)","rgb(171,221,164)","rgb(102,194,165)","rgb(50,136,189)"],10:["rgb(158,1,66)","rgb(213,62,79)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(230,245,152)","rgb(171,221,164)","rgb(102,194,165)","rgb(50,136,189)","rgb(94,79,162)"],11:["rgb(158,1,66)","rgb(213,62,79)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(255,255,191)","rgb(230,245,152)","rgb(171,221,164)","rgb(102,194,165)","rgb(50,136,189)","rgb(94,79,162)"]},
-RdYlGn:{3:["rgb(252,141,89)","rgb(255,255,191)","rgb(145,207,96)"],4:["rgb(215,25,28)","rgb(253,174,97)","rgb(166,217,106)","rgb(26,150,65)"],5:["rgb(215,25,28)","rgb(253,174,97)","rgb(255,255,191)","rgb(166,217,106)","rgb(26,150,65)"],6:["rgb(215,48,39)","rgb(252,141,89)","rgb(254,224,139)","rgb(217,239,139)","rgb(145,207,96)","rgb(26,152,80)"],7:["rgb(215,48,39)","rgb(252,141,89)","rgb(254,224,139)","rgb(255,255,191)","rgb(217,239,139)","rgb(145,207,96)","rgb(26,152,80)"],8:["rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(217,239,139)","rgb(166,217,106)","rgb(102,189,99)","rgb(26,152,80)"],9:["rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(255,255,191)","rgb(217,239,139)","rgb(166,217,106)","rgb(102,189,99)","rgb(26,152,80)"],10:["rgb(165,0,38)","rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(217,239,139)","rgb(166,217,106)","rgb(102,189,99)","rgb(26,152,80)","rgb(0,104,55)"],11:["rgb(165,0,38)","rgb(215,48,39)","rgb(244,109,67)","rgb(253,174,97)","rgb(254,224,139)","rgb(255,255,191)","rgb(217,239,139)","rgb(166,217,106)","rgb(102,189,99)","rgb(26,152,80)","rgb(0,104,55)"]}};
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/openbis-basynthec.js b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/openbis-basynthec.js
deleted file mode 100644
index 9b064c27824..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/openbis-basynthec.js
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * OpenBIS-BaSynthec API
- *
- * A BaSynthec-specific API for accessing openBIS. Depends on openbis.js.
- */
-
-STRAIN_PROP_NAME = "STRAIN_NAMES";
-
-// A date formatter used to display data sets
-var timeformat = d3.time.format("%Y-%m-%d %H:%M");
-
-
-/**
- * The openbis_basynthec object provides a basynthec-specific interface to openbis.
- *
- * It creates objects for projects, experiments, samples, and datasets. These objects
- * are designed to be passed on to GUI libraries (like d3). The openbis version of each
- * object is stored in the bis variable.
- *
- * @constructor
- */
-function openbis_basynthec(url, dssUrl) {
- this.server = new openbis(url, dssUrl);
- // Initial projects
- var dataSets = [{code: "No Projects"}];
-}
-
-/**
- * List all data sets from the openBIS server.
- */
-openbis_basynthec.prototype.listAllDataSets = function(action)
-{
- var dataSetCriteria =
- {
- matchClauses : [
- {"@type":"AttributeMatchClause",
- attribute : "CODE",
- fieldType : "ATTRIBUTE",
- desiredValue : "*"
- }
- ],
- operator : "MATCH_ALL_CLAUSES"
- };
-
- this.server.searchForDataSets(dataSetCriteria, action);
-}
-
-/**
- * Return a list of strains for this data set. List could be empty.
- */
-openbis_basynthec.prototype.getStrains = function(dataSet)
-{
- var strains = dataSet.properties[STRAIN_PROP_NAME]
-
- if (strains)
- {
- return strains.split(",");
- }
- else
- {
- return [];
- }
-}
-
-openbis_basynthec.prototype.getStrainsPhenotypesAndPredictions = function(action){
- this.server.createReportFromAggregationService("DSS1","chicago", null, function(response){
- var result = {};
-
- if(response.result && response.result.rows){
- $.each(response.result.rows, function(index, row){
- strain = eval("(" + row[0].value + ")");
- strain.name = strain.id;
- strain.hasPredictions = strain.predictions != null && strain.predictions.length > 0;
- strain.hasPhenotypes = strain.phenotypes != null && strain.phenotypes.length > 0;
- strain.hasParent = strain.parent != null;
- strain.hasIntervals = strain.intervals != null;
- result[strain.id] = strain;
- });
- }
-
- action(result);
- });
-}
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/plugin.properties b/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/plugin.properties
deleted file mode 100644
index 94b969feb5b..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/plugin.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-webapp-folder = browser
-label = Strain Browser
-openbisui-contexts = modules-menu
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv
deleted file mode 100644
index 4748ec86fe2..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv
+++ /dev/null
@@ -1,518 +0,0 @@
-{"parent": "JJS-MGP006", "intervals": ["i648", "i492", "i687", "i623"], "id": "JJS-MGP009", "phenotypes": [{"relativeGrowth": "0.5", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
-{"parent": null, "intervals": ["i886"], "id": "JJS-DIN262", "phenotypes": [], "predictions": []}
-{"parent": null, "intervals": ["i613"], "id": "JJS-DIN112", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "1", "description": null, "media": "GMM_gln", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "1", "description": null, "media": "GMM_nh4", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}], "predictions": [{"relativeGrowth": "1.03867", "description": null, "media": "GMM_gln", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "1.03867", "description": null, "media": "GMM_gln_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "0.639786", "description": null, "media": "GMM_nh4", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "0.639786", "description": null, "media": "GMM_nh4_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "9.18482", "description": null, "media": "LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "7.45492", "description": null, "media": "old_LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:42", "noGrowthCompounds": null}, {"relativeGrowth": "3.93227", "description": null, "media": "GMM_gln", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "3.93227", "description": null, "media": "GMM_gln_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "3.3936", "description": null, "media": "GMM_nh4", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "3.41621", "description": null, "media": "GMM_nh4_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "7.64072", "description": null, "media": "LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "6.08382", "description": null, "media": "old_LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:21", "noGrowthCompounds": null}]}
-{"parent": null, "intervals": ["i844"], "id": "JJS-DIN237", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:41"}], "predictions": [{"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:46", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:46", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:25", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:25", "noGrowthCompounds": null}]}
-{"parent": null, "intervals": ["i263"], "id": "JJS-DIN039", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "0", "description": null, "media": "GMM_gln", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}, {"relativeGrowth": "0", "description": null, "media": "GMM_nh4", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:39"}], "predictions": [{"relativeGrowth": "1.03867", "description": null, "media": "GMM_gln", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "1.03867", "description": null, "media": "GMM_gln_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "0.639786", "description": null, "media": "GMM_nh4", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "0.639786", "description": null, "media": "GMM_nh4_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "9.18482", "description": null, "media": "LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "7.45492", "description": null, "media": "old_LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:41", "noGrowthCompounds": null}, {"relativeGrowth": "3.93227", "description": null, "media": "GMM_gln", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "3.93227", "description": null, "media": "GMM_gln_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "3.3936", "description": null, "media": "GMM_nh4", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "3.41621", "description": null, "media": "GMM_nh4_cit", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "7.64072", "description": null, "media": "LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "6.08382", "description": null, "media": "old_LB", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:20", "noGrowthCompounds": null}]}
-{"parent": "JJS-MGP021", "intervals": ["i648", "i687", "i623", "i725", "i651", "i661", "i719"], "id": "JJS-MGP028", "phenotypes": [{"relativeGrowth": "0.5", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
-{"parent": null, "intervals": ["i794"], "id": "JJS-DIN224", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:41"}], "predictions": [{"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}]}
-{"parent": "JJS-MGP076", "intervals": ["i648", "i687", "i623", "i725", "i249", "i651", "i84", "i719", "i260", "i692", "i612", "i614", "i727", "i729", "i215", "i716"], "id": "JJS-MGP109", "phenotypes": [{"relativeGrowth": "0.5", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
-{"parent": "JJS-MGP067", "intervals": ["i648", "i687", "i623", "i725", "i249", "i651", "i84", "i719", "i260", "i692", "i612", "i614", "i727", "i729", "i613"], "id": "JJS-MGP074", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
-{"parent": null, "intervals": ["i880"], "id": "JJS-DIN257", "phenotypes": [], "predictions": []}
-{"parent": null, "intervals": ["i800"], "id": "JJS-DIN208", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:41"}], "predictions": [{"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}]}
-{"parent": null, "intervals": ["i648", "i1001", "i1002", "i687", "i623", "i725", "i249", "i651", "i84", "i719", "i260", "i692", "i612", "i614", "i850", "i851", "i852", "i739", "i740", "i776", "i777", "i727", "i729", "i215", "i652", "i650", "i788", "i789", "i790", "i716"], "id": "JJS-MGP209", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:09"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:09"}], "predictions": []}
-{"parent": null, "intervals": ["i751"], "id": "JJS-DIN146", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:41"}], "predictions": [{"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}]}
-{"parent": null, "intervals": ["i790"], "id": "JJS-DIN214", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-05-22 17:45:41"}], "predictions": [{"relativeGrowth": "6.34894", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "6.34897", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuOld", "creationDate": "2011-05-22 17:57:45", "noGrowthCompounds": null}, {"relativeGrowth": "5.36054", "description": null, "media": "NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}, {"relativeGrowth": "5.36057", "description": null, "media": "old_NMS", "version": "0", "reactionKO": null, "modificationDate": null, "model": "iBsuNew", "creationDate": "2011-05-22 17:58:24", "noGrowthCompounds": null}]}
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-{"parent": "JJS-MGP098", "intervals": ["i648", "i687", "i623", "i725", "i249", "i651", "i84", "i719", "i260", "i692", "i612", "i614", "i727", "i729", "i652", "i716"], "id": "JJS-MGP108", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
-{"parent": "JJS-MGP030", "intervals": ["i648", "i687", "i623", "i725", "i651", "i84", "i719", "i692", "i312"], "id": "JJS-MGP043", "phenotypes": [{"relativeGrowth": "1", "description": null, "media": "NMS", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}, {"relativeGrowth": "1", "description": null, "media": "LB", "experimenter": "Kosei Tanaka", "modificationDate": null, "creationDate": "2011-06-15 04:29:08"}], "predictions": []}
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py
deleted file mode 100644
index 89c517fb870..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py
+++ /dev/null
@@ -1,78 +0,0 @@
-#! /usr/bin/env python
-
-import csv
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-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
-
-
-FIELD_STRAIN = 'strain'
-
-def loadDataFromFile(filePath):
- file = None
- try:
- file = open(filePath, 'r')
- dataList = []
-
- for line in file:
- dataList.append(line)
-
- return dataList
- except IOError, err:
- print 'Could not read the data from a file: ' + str(filePath)
- raise
- finally:
- if file != None:
- file.close()
-
-def indexDataByStrainId(data):
- dataById = {}
- for strainData in data:
- tokens = strainData.strip("{} \n").split(',')
- theIds = [token for token in tokens if token.strip().startswith('"id"')]
- if (len(theIds) < 1):
- continue
- theId = theIds[0].split(':')[1].strip('" \n')
- dataById[theId] = strainData
-
- return dataById
-
-def addDataToTable(dataList, table):
- table.addHeader(FIELD_STRAIN)
-
- for dataItem in dataList:
- row = table.addRow()
- row.setCell(FIELD_STRAIN, dataItem)
-
-def addStrainsNotInChicagoDb(strainsNotInChicagoDb, table):
- for strain in strainsNotInChicagoDb:
- row = table.addRow()
- dataItem = '{"id": "' + strain + '"}'
- row.setCell(FIELD_STRAIN, dataItem)
-
-def allDataSets():
- searchCriteria = SearchCriteria()
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, '*'))
- return searchService.searchForDataSets(searchCriteria)
-
-def filterToUnknownStrains(dataSets, dataById):
- unknownStrains = set()
- for dataSet in dataSets:
- strainNames = dataSet.getPropertyValue('STRAIN_NAMES')
- if (strainNames is None):
- continue
- strains = strainNames.split(",")
- for strain in strains:
- if dataById.get(strain) is None:
- unknownStrains.add(strain)
- return unknownStrains
-
-def aggregate(parameters, table):
- data = loadDataFromFile('TODO_PATH_TO_FILE_WITH_SERVER_DATA')
- addDataToTable(data, table)
-
- # Now get the strains in out db. We want to find the ones that might not be in their system
- dataById = indexDataByStrainId(data)
- dataSets = allDataSets()
- strainsNotInChicagoDb = filterToUnknownStrains(dataSets, dataById)
- addStrainsNotInChicagoDb(strainsNotInChicagoDb, table)
\ No newline at end of file
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py
deleted file mode 100644
index 79fd42ae0f0..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#! /usr/bin/env python
-
-import urllib
-import json
-import csv
-import shutil
-
-FIELD_ID = 'id'
-FIELD_PREDICTIONS = 'predictions'
-FIELD_PHENOTYPES = 'phenotypes'
-FIELD_PARENT = 'parent'
-FIELD_INTERVALS = 'intervals'
-
-def loadDataFromServer(serverUrl):
- url = urllib.urlopen(serverUrl)
- return url.read().decode('utf8')
-
-def loadDataFromFile(filePath):
- dataFile = open(filePath, 'r')
- data = file.read(dataFile)
- dataFile.close()
- return data
-
-def convertData(dataString):
- jsonList = json.loads(dataString)
- dataList = []
-
- for jsonItem in jsonList:
- id = jsonItem[FIELD_ID].upper()
- predictions = jsonItem[FIELD_PREDICTIONS]
- phenotypes = jsonItem[FIELD_PHENOTYPES]
- parent = jsonItem[FIELD_PARENT]
- intervals = jsonItem[FIELD_INTERVALS]
- dataList.append({FIELD_ID: id, FIELD_PREDICTIONS: predictions, FIELD_PHENOTYPES: phenotypes, FIELD_PARENT: parent, FIELD_INTERVALS: intervals})
-
- return dataList
-
-def writeDataToFile(filePath, dataList):
- file = None
- try:
-
- file = open(filePath,'w')
-
- for dataItem in dataList:
- file.write(json.dumps(dataItem) + '\n')
-
- except IOError as err:
- print 'Could not write the data to a file: ' + str(filePath)
- raise
- finally:
- if file != None:
- file.close()
-
-data = loadDataFromServer('http://pubseed.theseed.org/model-prod/StrainServer.cgi?user=reviewer&pass=reviewer&method=getAllPhenotypesAndPredictions&encoding=json')
-#data = loadDataFromFile('original-data-from-server.json')
-writeDataToFile('data-from-server.csv.tmp', convertData(data))
-shutil.move('data-from-server.csv.tmp', 'data-from-server.csv')
-
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/original-data-from-server.json b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/original-data-from-server.json
deleted file mode 100644
index e9b5757a18f..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/original-data-from-server.json
+++ /dev/null
@@ -1 +0,0 @@
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17:57:45","media":"old_NMS","relativeGrowth":"6.34897"},{"noGrowthCompounds":null,"reactionKO":null,"version":"0","model":"iBsuNew","description":null,"modificationDate":null,"creationDate":"2011-05-22 17:58:24","media":"NMS","relativeGrowth":"5.36054"},{"noGrowthCompounds":null,"reactionKO":null,"version":"0","model":"iBsuNew","description":null,"modificationDate":null,"creationDate":"2011-05-22 17:58:24","media":"old_NMS","relativeGrowth":"5.36057"}],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-05-22 17:45:41","media":"NMS","relativeGrowth":"1"}],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:00","resistance":"phleoR","experimentDate":"2011-05-22 17:28:00","public":"0","intervals":["i749"],"id":"JJS-DIn143","method":"Combination","attempted":"1"},{"competence":"Normal","parent":null,"predictions":[],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:01","resistance":"phleoR","experimentDate":"2011-05-22 17:28:01","public":"0","intervals":["i839"],"id":"JJS-DIn268","method":"Combination","attempted":"1"},{"competence":"Normal","parent":"JJS-MGP195","predictions":[],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:09","media":"NMS","relativeGrowth":"1"},{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:09","media":"LB","relativeGrowth":"1"}],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:07","resistance":"Phleo (Pr-Cm)","experimentDate":"2011-05-22 17:28:07","public":"0","intervals":["i648","i1001","i1002","i687","i623","i725","i249","i651","i84","i719","i260","i692","i612","i614","i850","i851","i852","i739","i740","i727","i729","i652","i650","i788","i789","i790","i613","i716"],"id":"JJS-MGP201","method":"Combination","attempted":"1"},{"competence":"Normal","parent":null,"predictions":[],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:09","media":"NMS","relativeGrowth":"1"},{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:09","media":"LB","relativeGrowth":"1"}],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:05","resistance":"Phleo (Pr-Cm)","experimentDate":"2011-05-22 17:28:05","public":"0","intervals":["i648","i1001","i1002","i687","i623","i725","i249","i651","i84","i719","i260","i692","i612","i614","i727","i729","i652","i650","i706","i716"],"id":"JJS-MGP163","method":"Combination","attempted":"1"},{"competence":"Normal","parent":"JJS-MGP098","predictions":[],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:08","media":"NMS","relativeGrowth":"1"},{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:08","media":"LB","relativeGrowth":"1"}],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:03","resistance":"Phleo (Pr-Neo)","experimentDate":"2011-05-22 17:28:03","public":"0","intervals":["i648","i687","i623","i725","i249","i651","i84","i719","i260","i692","i612","i614","i727","i729","i652","i716"],"id":"JJS-MGP108","method":"Combination","attempted":"1"},{"competence":"Normal","parent":"JJS-MGP030","predictions":[],"permission":{"admin":"1","read":"1","write":"1"},"phenotypes":[{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:08","media":"NMS","relativeGrowth":"1"},{"description":null,"experimenter":"Kosei Tanaka","modificationDate":null,"creationDate":"2011-06-15 04:29:08","media":"LB","relativeGrowth":"1"}],"implemented":"1","modificationDate":null,"experimenter":"Kosei Tanaka","creationDate":"2011-05-22 17:28:02","resistance":"Neo|Cm","experimentDate":"2011-05-22 17:28:02","public":"0","intervals":["i648","i687","i623","i725","i651","i84","i719","i692","i312"],"id":"JJS-MGP043","method":"Combination","attempted":"1"}]
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties
deleted file mode 100644
index b89889520dc..00000000000
--- a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-label = Load data from UChicago DB
-class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
-script-path = load-data-from-file-and-put-to-table.py
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/AbstractBaSynthecClient.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/AbstractBaSynthecClient.java
deleted file mode 100644
index 9ec69821de5..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/AbstractBaSynthecClient.java
+++ /dev/null
@@ -1,63 +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 eu.basynthec.cisd.client.examples;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-
-/**
- * Abstract superclass for code that interacts with the BaSynthec database via the IOpenbisServiceFacade interface.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class AbstractBaSynthecClient
-{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- BaSynthecClient.class);
-
- protected final IOpenbisServiceFacade openBis;
-
- /**
- * Utility method to log information.
- */
- protected static void logInfo(String msg)
- {
- operationLog.info(msg);
- }
-
- /**
- * Constructor that initializes the openBis facade.
- *
- * @param facade The facade for interacting with openBIS.
- */
- public AbstractBaSynthecClient(IOpenbisServiceFacade facade)
- {
- this.openBis = facade;
- }
-
- /**
- * Utility method for printing.
- */
- protected void println(String text)
- {
- System.out.println(text);
- }
-
-}
\ No newline at end of file
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.java
deleted file mode 100644
index 1434033733a..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/BaSynthecClient.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 eu.basynthec.cisd.client.examples;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.lang.time.DateUtils;
-import org.apache.log4j.PropertyConfigurator;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory;
-
-/**
- * An example of communcating with openBIS. This example retrieves metadata about an experiment and downaloads data from one data set.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class BaSynthecClient extends AbstractBaSynthecClient
-{
- private static final long CONNECTION_TIMEOUT_MILLIS = 15 * DateUtils.MILLIS_PER_SECOND;
-
- /**
- * The main method: logs into openBIS and runs the client.
- */
- public static void main(String[] args)
- {
- if (args.length < 2)
- {
- printUsage();
- return;
- }
-
- configureLogging();
-
- IOpenbisServiceFacade facade = createServiceFacade(args);
- if (facade == null)
- {
- System.err.println("Authentication failed: check the user name and password.");
- System.exit(1);
- return;
- }
-
- BaSynthecClient newMe = new BaSynthecClient(facade);
-
- newMe.run();
-
- newMe.logout();
-
- }
-
- private static IOpenbisServiceFacade createServiceFacade(String[] args)
- {
- String userId = args[0];
- String userPassword = args[1];
- String serverUrl;
- if (args.length > 2)
- {
- serverUrl = args[2];
- } else
- {
- // Default to the basynthec server
- serverUrl = "https://basynthec.ethz.ch";
- }
-
- logInfo(String.format("Connecting to the server '%s' as a user '%s'.", serverUrl, userId));
- IOpenbisServiceFacade facade =
- OpenbisServiceFacadeFactory.tryCreate(userId, userPassword, serverUrl,
- CONNECTION_TIMEOUT_MILLIS);
- return facade;
- }
-
- private static void printUsage()
- {
- System.err.println("Usage: <user> <password> [<openbis-server-url>]");
- System.err.println("Example: test-user my-password");
- System.err.println("Example: test-user my-password https://basynthec.ethz.ch");
- System.err.println("Example: test-user my-password http://localhost:8888");
- System.exit(1);
- }
-
- private static void configureLogging()
- {
- Properties props = new Properties();
- props.put("log4j.appender.STDOUT", "org.apache.log4j.ConsoleAppender");
- props.put("log4j.appender.STDOUT.layout", "org.apache.log4j.PatternLayout");
- props.put("log4j.appender.STDOUT.layout.ConversionPattern", "%d %-5p [%t] %c - %m%n");
- props.put("log4j.rootLogger", "INFO, STDOUT");
- PropertyConfigurator.configure(props);
- }
-
- /**
- * Private constructor.
- *
- * @param facade The facade for interacting with openBIS.
- */
- private BaSynthecClient(IOpenbisServiceFacade facade)
- {
- super(facade);
- }
-
- /**
- * Using the connection to openBIS, do the following:<br>
- * <ul>
- * <li>List the experiments, with their metadata, in the project <i>/PRIVATE/TEST</i></li>
- * <li>Search and print data sets that refer to a particular strain.</li>
- * </ul>
- */
- public void run()
- {
- List<String> projectIdentifiers = Arrays.asList("/PRIVATE/TEST");
- logInfo("Listing experiments in projects " + projectIdentifiers + "...");
- ExperimentLister experimentLister = new ExperimentLister(openBis);
- experimentLister.run(projectIdentifiers);
-
- println("\n");
-
- List<String> strainNames = Arrays.asList("MGP100");
- logInfo("Listing data sets containing data for strains " + strainNames + "...");
- File downloadFolder = new File("targets/downloads/");
- DataSetSearch dataSetSearch = new DataSetSearch(openBis, downloadFolder);
- dataSetSearch.run(strainNames);
-
- }
-
- private void logout()
- {
- openBis.logout();
- }
-}
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
deleted file mode 100644
index e1c1da6aee5..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/DataSetSearch.java
+++ /dev/null
@@ -1,294 +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 eu.basynthec.cisd.client.examples;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator;
-
-/**
- * A class that, given a live connection to openBIS, searches for data sets where one of the specified strains appear, downloads the data set and
- * prints information about the data set and experiment.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class DataSetSearch extends AbstractBaSynthecClient
-{
- private static final String STRAIN_NAMES_PROPERTY = "STRAIN_NAMES";
-
- private static final String STRAINS_HEADER = "Strains";
-
- private static final String REGISTERED_BY_HEADER = "Contact Person";
-
- private static final String DATA_SET_HEADER = "Data Set";
-
- private static final String PATH_HEADER = "Data Path";
-
- /**
- * An enum for keeping track of the metadata fields we are interested in, in the order we want to display them.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private enum MetadataField
- {
- EXPERIMENT_DATE("Date"), DESCRIPTION("Description"), MEDIUM("Medium"), TEMPERATURE(
- "Temperature"), MISC_GROWTH_CONDITIONS("Growth Conditions");
-
- MetadataField(String headerText)
- {
- this.headerText = headerText;
- }
-
- private final String headerText;
- }
-
- // Where to store the data we download
- private final File downloadFolder;
-
- // State we compute as part of the operation of this class
-
- // The data sets we are interested in
- private List<DataSet> matchingDataSets;
-
- // The experiments that contain the data sets we are interested in
- private List<Experiment> experiments;
-
- // A mapping from experiments to data sets
- private HashMap<String, ArrayList<DataSet>> experimentDataSets;
-
- // A mapping from data sets to paths where the data is stored
- private HashMap<DataSet, File> dataSetFiles;
-
- /**
- * The public constructor
- *
- * @param facade The facade for interacting with openBIS.
- */
- public DataSetSearch(IOpenbisServiceFacade facade, File downloadFolder)
- {
- super(facade);
- this.downloadFolder = downloadFolder;
- }
-
- /**
- * Using the connection to openBIS, get search for data sets that contain data on the specified strains. Download the data set and print
- * information about the data set and its experiment.<br>
- * <ul>
- * <li>Experiment Date</li>
- * <li>Description</li>
- * <li>Medium</li>
- * <li>Temperature</li>
- * <li>Growth Conditions</li>
- * <li>Data Set Strains</li>
- * <li>Data Set Path</li>
- * </ul>
- */
- public void run(List<String> strainNames)
- {
- retrieveInformationFromOpenBis(strainNames);
- downloadDataSets();
-
- printHeader();
- for (Experiment experiment : experiments)
- {
- printExperiment(experiment);
- }
- }
-
- /**
- * Connect to openBis to get the information we need.
- */
- private void retrieveInformationFromOpenBis(List<String> strainNames)
- {
- // Find all data sets that match the strain names
- matchingDataSets = retrieveDataSetsReferencingStrains(strainNames);
-
- // Get the experiments for the specified data sets
- List<String> experimentIdentifiers = new ArrayList<String>();
- for (DataSet dataSet : matchingDataSets)
- {
- experimentIdentifiers.add(dataSet.getExperimentIdentifier());
- }
- if (experimentIdentifiers.isEmpty())
- {
- experiments = new ArrayList<Experiment>();
- } else
- {
- experiments = openBis.getExperiments(experimentIdentifiers);
- }
-
- // Create a map from experiment to data set
- experimentDataSets = new HashMap<String, ArrayList<DataSet>>();
- for (DataSet dataSet : matchingDataSets)
- {
- ArrayList<DataSet> dataSetsForExperiment =
- experimentDataSets.get(dataSet.getExperimentIdentifier());
- if (null == dataSetsForExperiment)
- {
- dataSetsForExperiment = new ArrayList<DataSet>();
- experimentDataSets.put(dataSet.getExperimentIdentifier(), dataSetsForExperiment);
- }
- dataSetsForExperiment.add(dataSet);
- }
- }
-
- /**
- * Connect to openBis to download the data sets
- */
- private void downloadDataSets()
- {
- dataSetFiles = new HashMap<DataSet, File>();
- for (DataSet dataSet : matchingDataSets)
- {
- // This method retrieves a link to the data set if the file system it is on can be
- // mounted locally. In this case, it cannot be mounted locally, so don't even try.
- File location = dataSet.getLinkOrCopyOfContent(null, downloadFolder, "original/tsv");
- dataSetFiles.put(dataSet, location);
- }
- }
-
- /**
- * Find data sets that contain data for the specified strains.
- */
- private List<DataSet> retrieveDataSetsReferencingStrains(List<String> strainNames)
- {
- // Construct a search criteria that matches any of the strains specified.
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.setOperator(SearchOperator.MATCH_ANY_CLAUSES);
- for (String strainName : strainNames)
- {
- searchCriteria.addMatchClause(MatchClause.createPropertyMatch(STRAIN_NAMES_PROPERTY,
- strainName));
- }
- return openBis.searchForDataSets(searchCriteria);
- }
-
- private void printHeader()
- {
- StringBuffer sb = new StringBuffer();
- sb.append("Experiment");
- for (MetadataField field : MetadataField.values())
- {
- sb.append("\t");
- sb.append(field.headerText);
- }
- sb.append("\t");
- sb.append(REGISTERED_BY_HEADER);
- sb.append("\t");
- sb.append(DATA_SET_HEADER);
- sb.append("\t");
- sb.append(STRAINS_HEADER);
- sb.append("\t");
- sb.append(PATH_HEADER);
- println(sb.toString());
- }
-
- private void printEmptyExperimentInformationOn(StringBuffer sb)
- {
- // Experiment Identifier
- sb.append("\t");
- for (@SuppressWarnings("unused")
- MetadataField field : MetadataField.values())
- {
- sb.append("\t");
- }
- // REGISTERED_BY_HEADER
- sb.append("\t");
-
- // We have now tabbed to allign with the data set information
- }
-
- private void printExperiment(Experiment experiment)
- {
- StringBuffer sb = new StringBuffer();
- sb.append(experiment.getIdentifier());
- printExperimentPropertiesOn(experiment.getProperties(), sb);
- printRegisteredByOn(experiment.getRegistrationDetails(), sb);
- printDataSetsOn(experiment, sb);
- println(sb.toString());
- }
-
- private void printExperimentPropertiesOn(Map<String, String> properties, StringBuffer sb)
- {
- for (MetadataField field : MetadataField.values())
- {
- sb.append("\t");
- String value = properties.get(field.toString());
- if (null != value)
- {
- sb.append(value);
- }
- }
- }
-
- /**
- * Get the strains for the experiment and print them to the string buffer.
- *
- * @throws IOException
- */
- private void printDataSetsOn(Experiment experiment, StringBuffer sb)
- {
- sb.append("\t");
-
- // dataSets cannot be null, because we only have experiments that have data sets here
- ArrayList<DataSet> dataSets = experimentDataSets.get(experiment.getIdentifier());
-
- boolean isFirstLine = true;
- for (DataSet dataSet : dataSets)
- {
- String dataSetCode = dataSet.getCode();
- String strainNames = dataSet.getProperties().get(STRAIN_NAMES_PROPERTY);
- String path;
- try
- {
- path = dataSetFiles.get(dataSet).getCanonicalPath();
- } catch (IOException ex)
- {
- throw new IOExceptionUnchecked(ex);
- }
- if (false == isFirstLine)
- {
- sb.append("\n");
- printEmptyExperimentInformationOn(sb);
- }
- sb.append(dataSetCode);
- sb.append("\t");
- sb.append(strainNames);
- sb.append("\t");
- sb.append(path);
- isFirstLine = false;
- }
- }
-
- private void printRegisteredByOn(EntityRegistrationDetails registrationDetails, StringBuffer sb)
- {
- sb.append("\t");
- sb.append(registrationDetails.getUserEmail());
- }
-}
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java b/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java
deleted file mode 100644
index ab6444cf722..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/client/examples/ExperimentLister.java
+++ /dev/null
@@ -1,218 +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 eu.basynthec.cisd.client.examples;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-
-/**
- * A class that, given a live connection to openBIS, prints a listing of experiments with metadata.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class ExperimentLister extends AbstractBaSynthecClient
-{
- private static final String STRAIN_NAMES_PROPERTY = "STRAIN_NAMES";
-
- private static final String STRAINS_HEADER = "Strains";
-
- private static final String REGISTERED_BY_HEADER = "Contact Person";
-
- /**
- * An enum for keeping track of the metadata fields we are interested in, in the order we want to display them.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private enum MetadataField
- {
- EXPERIMENT_DATE("Date"), DESCRIPTION("Description"), MEDIUM("Medium"), TEMPERATURE(
- "Temperature"), MISC_GROWTH_CONDITIONS("Growth Conditions");
-
- MetadataField(String headerText)
- {
- this.headerText = headerText;
- }
-
- private final String headerText;
- }
-
- // State we compute as part of the operation of this class
-
- // The experiments we are interested in
- private List<Experiment> experiments;
-
- // A mapping from experiments to data sets
- private HashMap<String, ArrayList<DataSet>> experimentDataSets;
-
- /**
- * The public constructor
- *
- * @param facade The facade for interacting with openBIS.
- */
- public ExperimentLister(IOpenbisServiceFacade facade)
- {
- super(facade);
- }
-
- /**
- * Using the connection to openBIS, get all experiments in the specified projects and print the following information about the experiment:<br>
- * <ul>
- * <li>Experiment Date</li>
- * <li>Description</li>
- * <li>Medium</li>
- * <li>Temperature</li>
- * <li>Growth Conditions</li>
- * <li>Strains</li>
- * </ul>
- *
- * @param projectIdentifiers The projects in which the experiments we are interested in are housed.
- */
- public void run(List<String> projectIdentifiers)
- {
- retrieveInformationFromOpenBis(projectIdentifiers);
-
- printHeader();
- for (Experiment experiment : experiments)
- {
- printExperiment(experiment);
- }
- }
-
- /**
- * Connect to openBis to get the information we need.
- */
- private void retrieveInformationFromOpenBis(List<String> projectIdentifiers)
- {
- // Get the experiments for the specified project
- experiments = openBis.listExperimentsForProjects(projectIdentifiers);
-
- // Get the data sets
- List<String> experimentIdentifiers = new ArrayList<String>();
- for (Experiment experiment : experiments)
- {
- experimentIdentifiers.add(experiment.getIdentifier());
- }
-
- List<DataSet> dataSets = openBis.listDataSetsForExperiments(experimentIdentifiers);
-
- experimentDataSets = new HashMap<String, ArrayList<DataSet>>();
- for (DataSet dataSet : dataSets)
- {
- ArrayList<DataSet> dataSetsForExperiment =
- experimentDataSets.get(dataSet.getExperimentIdentifier());
- if (null == dataSetsForExperiment)
- {
- dataSetsForExperiment = new ArrayList<DataSet>();
- experimentDataSets.put(dataSet.getExperimentIdentifier(), dataSetsForExperiment);
- }
- dataSetsForExperiment.add(dataSet);
- }
- }
-
- private void printHeader()
- {
- StringBuffer sb = new StringBuffer();
- sb.append("Experiment");
- for (MetadataField field : MetadataField.values())
- {
- sb.append("\t");
- sb.append(field.headerText);
- }
- sb.append("\t");
- sb.append(STRAINS_HEADER);
- sb.append("\t");
- sb.append(REGISTERED_BY_HEADER);
- println(sb.toString());
- }
-
- private void printExperiment(Experiment experiment)
- {
- StringBuffer sb = new StringBuffer();
- sb.append(experiment.getIdentifier());
- printExperimentPropertiesOn(experiment.getProperties(), sb);
- printExperimentStrainsOn(experiment, sb);
- printRegisteredByOn(experiment.getRegistrationDetails(), sb);
- println(sb.toString());
- }
-
- private void printExperimentPropertiesOn(Map<String, String> properties, StringBuffer sb)
- {
- for (MetadataField field : MetadataField.values())
- {
- sb.append("\t");
- String value = properties.get(field.toString());
- if (null != value)
- {
- sb.append(value);
- }
- }
- }
-
- /**
- * Get the strains for the experiment and print them to the string buffer.
- */
- private void printExperimentStrainsOn(Experiment experiment, StringBuffer sb)
- {
- sb.append("\t");
-
- ArrayList<DataSet> dataSets = experimentDataSets.get(experiment.getIdentifier());
- if (null == dataSets)
- {
- return;
- }
-
- // collect all the strain names
- ArrayList<String> strains = new ArrayList<String>();
- for (DataSet dataSet : dataSets)
- {
- String strainNames = dataSet.getProperties().get(STRAIN_NAMES_PROPERTY);
- if (null != strainNames)
- {
- strains.add(strainNames);
- }
- }
-
- if (strains.size() < 1)
- {
- return;
- }
-
- // Append them to the StringBuffer
- sb.append(strains.get(0));
- for (int i = 1; i < strains.size(); ++i)
- {
- sb.append(",");
- sb.append(strains.get(i));
- }
- }
-
- private void printRegisteredByOn(EntityRegistrationDetails registrationDetails, StringBuffer sb)
- {
- sb.append("\t");
- if (null != registrationDetails)
- {
- sb.append(registrationDetails.getUserEmail());
- }
- }
-}
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/dss/TimeSeriesDataExcel.java b/eu_basynthec/source/java/eu/basynthec/cisd/dss/TimeSeriesDataExcel.java
deleted file mode 100644
index df3926c04a1..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/dss/TimeSeriesDataExcel.java
+++ /dev/null
@@ -1,149 +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 eu.basynthec.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.apache.poi.ss.usermodel.Workbook;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader;
-
-/**
- * An abstraction for accessing time series data following the BaSynthec conventions from an Excel file.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class TimeSeriesDataExcel
-{
- private static final String OPENBIS_METADATA_SHEET_NAME = "openbis-metadata";
-
- private static final String OPENBIS_DATA_SHEET_NAME = "openbis-data";
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- TimeSeriesDataExcel.class);
-
- /**
- * Create a time series data from the given file name.
- *
- * @param fileName
- * @return A TimeSeriesDataExcel or null if one could not be created.
- */
- public static TimeSeriesDataExcel createTimeSeriesDataExcel(String fileName)
- {
- File file = new File(fileName);
- Workbook workbook;
- try
- {
- workbook = ExcelFileReader.getExcelWorkbook(file);
- ExcelFileReader fileReader = new ExcelFileReader(workbook, true);
- return new TimeSeriesDataExcel(file, fileReader);
- } catch (IllegalArgumentException ex)
- {
- operationLog.error("Could not open file [" + fileName + "] as Excel data.", ex);
- } catch (IOException ex)
- {
- operationLog.error("Could not open file [" + fileName + "] as Excel data.", ex);
- }
-
- return null;
- }
-
- private final File file;
-
- private final ExcelFileReader fileReader;
-
- /**
- * Constructor
- */
- private TimeSeriesDataExcel(File file, ExcelFileReader fileReader)
- {
- super();
- this.file = file;
- this.fileReader = fileReader;
- }
-
- /**
- * Get the raw lines of the metadata sheet.
- */
- public List<String[]> getRawMetadataLines()
- {
- try
- {
- return fileReader.readLines(OPENBIS_METADATA_SHEET_NAME);
- } catch (IOException ex)
- {
- operationLog.error("Could not read data from [file: " + file.getPath() + ", sheet: "
- + OPENBIS_METADATA_SHEET_NAME + "]", ex);
- }
- return new ArrayList<String[]>();
- }
-
- /**
- * Get the raw lines of the data sheet.
- */
- public List<String[]> getRawDataLines()
- {
- try
- {
- return fileReader.readLines(OPENBIS_DATA_SHEET_NAME);
- } catch (IOException ex)
- {
- operationLog.error("Could not read data from [file: " + file.getPath() + ", sheet: "
- + OPENBIS_DATA_SHEET_NAME + "]", ex);
- }
- return new ArrayList<String[]>();
- }
-
- /**
- * Return the metadata has a hashmap, with all keys uppercased.
- * <p>
- * Assumes the metadata sheet corresponds to the following format: [Property] [Value] [... stuff that can be ignored], that is the property name
- * is in column 1 and property value is in column 2, and everything else can be ignored.
- */
- public Map<String, String> getMetadataMap()
- {
- HashMap<String, String> metadataMap = new HashMap<String, String>();
- List<String[]> metadataLines = getRawMetadataLines();
-
- // Skip the first line, this is just the header
- for (int i = 1; i < metadataLines.size(); ++i)
- {
- String[] line = metadataLines.get(i);
- String key = line[0];
- if (key == null)
- {
- continue;
- }
- String value = line[1];
- if ("BLANK".equals(value))
- {
- value = null;
- }
- metadataMap.put(line[0].toUpperCase(), value);
- }
-
- return metadataMap;
- }
-}
diff --git a/eu_basynthec/source/java/eu/basynthec/cisd/dss/ValidationHelper.java b/eu_basynthec/source/java/eu/basynthec/cisd/dss/ValidationHelper.java
deleted file mode 100644
index d5c861957c6..00000000000
--- a/eu_basynthec/source/java/eu/basynthec/cisd/dss/ValidationHelper.java
+++ /dev/null
@@ -1,53 +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 eu.basynthec.cisd.dss;
-
-import java.util.Collection;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-
-/**
- * Methods for simplifying validation in BaSynthec
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class ValidationHelper
-{
- private final Map<String, String> metadataMap;
-
- private final Collection<ValidationError> errors;
-
- public ValidationHelper(Map<String, String> metadataMap, Collection<ValidationError> errors)
- {
- this.metadataMap = metadataMap;
- this.errors = errors;
- }
-
- public boolean checkIsSpecified(String property, String displayName)
- {
- if (null == metadataMap.get(property))
- {
- errors.add(ValidationError.createFileValidationError("A " + displayName
- + " must be specified."));
-
- return false;
- }
-
- return true;
- }
-}
diff --git a/eu_basynthec/source/python/master-data.py b/eu_basynthec/source/python/master-data.py
deleted file mode 100644
index 72daef0e5c6..00000000000
--- a/eu_basynthec/source/python/master-data.py
+++ /dev/null
@@ -1,763 +0,0 @@
-# -*- coding: utf-8 -*-
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-tr = service.transaction()
-
-
-file_type_HDF5 = tr.createNewFileFormatType('HDF5')
-file_type_HDF5.setDescription('Hierarchical Data Format File, version 5')
-
-file_type_PROPRIETARY = tr.createNewFileFormatType('PROPRIETARY')
-file_type_PROPRIETARY.setDescription('Proprietary Format File')
-
-file_type_SRF = tr.createNewFileFormatType('SRF')
-file_type_SRF.setDescription('Sequence Read Format File')
-
-file_type_TIFF = tr.createNewFileFormatType('TIFF')
-file_type_TIFF.setDescription('TIFF File')
-
-file_type_TSV = tr.createNewFileFormatType('TSV')
-file_type_TSV.setDescription('Tab Separated Values File')
-
-file_type_XML = tr.createNewFileFormatType('XML')
-file_type_XML.setDescription('XML File')
-
-file_type_MULTI_STRAIN_EXCEL_V1 = tr.createNewFileFormatType('MULTI_STRAIN_EXCEL_V1')
-file_type_MULTI_STRAIN_EXCEL_V1.setDescription('An Excel file with data for multiple strains')
-
-vocabulary_STORAGE_FORMAT = tr.createNewVocabulary('STORAGE_FORMAT')
-vocabulary_STORAGE_FORMAT.setDescription('The on-disk storage format of a data set')
-vocabulary_STORAGE_FORMAT.setUrlTemplate(None)
-vocabulary_STORAGE_FORMAT.setManagedInternally(True)
-vocabulary_STORAGE_FORMAT.setInternalNamespace(True)
-vocabulary_STORAGE_FORMAT.setChosenFromList(True)
-
-vocabulary_term_STORAGE_FORMAT_BDS_DIRECTORY = tr.createNewVocabularyTerm('BDS_DIRECTORY')
-vocabulary_term_STORAGE_FORMAT_BDS_DIRECTORY.setDescription(None)
-vocabulary_term_STORAGE_FORMAT_BDS_DIRECTORY.setLabel(None)
-vocabulary_term_STORAGE_FORMAT_BDS_DIRECTORY.setOrdinal(2)
-vocabulary_STORAGE_FORMAT.addTerm(vocabulary_term_STORAGE_FORMAT_BDS_DIRECTORY)
-
-vocabulary_term_STORAGE_FORMAT_PROPRIETARY = tr.createNewVocabularyTerm('PROPRIETARY')
-vocabulary_term_STORAGE_FORMAT_PROPRIETARY.setDescription(None)
-vocabulary_term_STORAGE_FORMAT_PROPRIETARY.setLabel(None)
-vocabulary_term_STORAGE_FORMAT_PROPRIETARY.setOrdinal(1)
-vocabulary_STORAGE_FORMAT.addTerm(vocabulary_term_STORAGE_FORMAT_PROPRIETARY)
-
-vocabulary_CELL_LOCATION = tr.createNewVocabulary('CELL_LOCATION')
-vocabulary_CELL_LOCATION.setDescription('Cell Location')
-vocabulary_CELL_LOCATION.setUrlTemplate(None)
-vocabulary_CELL_LOCATION.setManagedInternally(False)
-vocabulary_CELL_LOCATION.setInternalNamespace(False)
-vocabulary_CELL_LOCATION.setChosenFromList(True)
-
-vocabulary_term_CELL_LOCATION_CE = tr.createNewVocabularyTerm('CE')
-vocabulary_term_CELL_LOCATION_CE.setDescription(None)
-vocabulary_term_CELL_LOCATION_CE.setLabel(None)
-vocabulary_term_CELL_LOCATION_CE.setOrdinal(1)
-vocabulary_CELL_LOCATION.addTerm(vocabulary_term_CELL_LOCATION_CE)
-
-vocabulary_term_CELL_LOCATION_ME = tr.createNewVocabularyTerm('ME')
-vocabulary_term_CELL_LOCATION_ME.setDescription(None)
-vocabulary_term_CELL_LOCATION_ME.setLabel(None)
-vocabulary_term_CELL_LOCATION_ME.setOrdinal(3)
-vocabulary_CELL_LOCATION.addTerm(vocabulary_term_CELL_LOCATION_ME)
-
-vocabulary_term_CELL_LOCATION_ES = tr.createNewVocabularyTerm('ES')
-vocabulary_term_CELL_LOCATION_ES.setDescription(None)
-vocabulary_term_CELL_LOCATION_ES.setLabel(None)
-vocabulary_term_CELL_LOCATION_ES.setOrdinal(2)
-vocabulary_CELL_LOCATION.addTerm(vocabulary_term_CELL_LOCATION_ES)
-
-vocabulary_term_CELL_LOCATION_NC = tr.createNewVocabularyTerm('NC')
-vocabulary_term_CELL_LOCATION_NC.setDescription(None)
-vocabulary_term_CELL_LOCATION_NC.setLabel(None)
-vocabulary_term_CELL_LOCATION_NC.setOrdinal(5)
-vocabulary_CELL_LOCATION.addTerm(vocabulary_term_CELL_LOCATION_NC)
-
-vocabulary_term_CELL_LOCATION_CY = tr.createNewVocabularyTerm('CY')
-vocabulary_term_CELL_LOCATION_CY.setDescription(None)
-vocabulary_term_CELL_LOCATION_CY.setLabel(None)
-vocabulary_term_CELL_LOCATION_CY.setOrdinal(4)
-vocabulary_CELL_LOCATION.addTerm(vocabulary_term_CELL_LOCATION_CY)
-
-vocabulary_CONTAINER = tr.createNewVocabulary('CONTAINER')
-vocabulary_CONTAINER.setDescription('Container in which the experiment was performed.')
-vocabulary_CONTAINER.setUrlTemplate(None)
-vocabulary_CONTAINER.setManagedInternally(False)
-vocabulary_CONTAINER.setInternalNamespace(False)
-vocabulary_CONTAINER.setChosenFromList(True)
-
-vocabulary_term_CONTAINER_96DWP = tr.createNewVocabularyTerm('96-DWP')
-vocabulary_term_CONTAINER_96DWP.setDescription(None)
-vocabulary_term_CONTAINER_96DWP.setLabel('96-well deep well (2mL) plate')
-vocabulary_term_CONTAINER_96DWP.setOrdinal(3)
-vocabulary_CONTAINER.addTerm(vocabulary_term_CONTAINER_96DWP)
-
-vocabulary_term_CONTAINER_FLASK = tr.createNewVocabularyTerm('FLASK')
-vocabulary_term_CONTAINER_FLASK.setDescription(None)
-vocabulary_term_CONTAINER_FLASK.setLabel('non-baffled shake flask')
-vocabulary_term_CONTAINER_FLASK.setOrdinal(1)
-vocabulary_CONTAINER.addTerm(vocabulary_term_CONTAINER_FLASK)
-
-vocabulary_term_CONTAINER_96MICRO = tr.createNewVocabularyTerm('96-MICRO')
-vocabulary_term_CONTAINER_96MICRO.setDescription(None)
-vocabulary_term_CONTAINER_96MICRO.setLabel('96-well microtiter (400ul) plate')
-vocabulary_term_CONTAINER_96MICRO.setOrdinal(2)
-vocabulary_CONTAINER.addTerm(vocabulary_term_CONTAINER_96MICRO)
-
-vocabulary_DEVICE = tr.createNewVocabulary('DEVICE')
-vocabulary_DEVICE.setDescription('Devices used to produce measurements.')
-vocabulary_DEVICE.setUrlTemplate(None)
-vocabulary_DEVICE.setManagedInternally(False)
-vocabulary_DEVICE.setInternalNamespace(False)
-vocabulary_DEVICE.setChosenFromList(True)
-
-vocabulary_term_DEVICE_ORBITRAP = tr.createNewVocabularyTerm('ORBITRAP')
-vocabulary_term_DEVICE_ORBITRAP.setDescription(None)
-vocabulary_term_DEVICE_ORBITRAP.setLabel(None)
-vocabulary_term_DEVICE_ORBITRAP.setOrdinal(1)
-vocabulary_DEVICE.addTerm(vocabulary_term_DEVICE_ORBITRAP)
-
-vocabulary_GROWTH_MEDIA = tr.createNewVocabulary('GROWTH_MEDIA')
-vocabulary_GROWTH_MEDIA.setDescription('Growth media for B. Subtilis.')
-vocabulary_GROWTH_MEDIA.setUrlTemplate(None)
-vocabulary_GROWTH_MEDIA.setManagedInternally(False)
-vocabulary_GROWTH_MEDIA.setInternalNamespace(False)
-vocabulary_GROWTH_MEDIA.setChosenFromList(True)
-
-vocabulary_term_GROWTH_MEDIA_MALATE = tr.createNewVocabularyTerm('MALATE')
-vocabulary_term_GROWTH_MEDIA_MALATE.setDescription(None)
-vocabulary_term_GROWTH_MEDIA_MALATE.setLabel(None)
-vocabulary_term_GROWTH_MEDIA_MALATE.setOrdinal(1)
-vocabulary_GROWTH_MEDIA.addTerm(vocabulary_term_GROWTH_MEDIA_MALATE)
-
-vocabulary_term_GROWTH_MEDIA_GLUCOSE = tr.createNewVocabularyTerm('GLUCOSE')
-vocabulary_term_GROWTH_MEDIA_GLUCOSE.setDescription(None)
-vocabulary_term_GROWTH_MEDIA_GLUCOSE.setLabel(None)
-vocabulary_term_GROWTH_MEDIA_GLUCOSE.setOrdinal(2)
-vocabulary_GROWTH_MEDIA.addTerm(vocabulary_term_GROWTH_MEDIA_GLUCOSE)
-
-vocabulary_term_GROWTH_MEDIA_NMS = tr.createNewVocabularyTerm('NMS')
-vocabulary_term_GROWTH_MEDIA_NMS.setDescription('glucose+citrate+amino acids. See SOPs or PPT in Kosei's email for complete recipe.')
-vocabulary_term_GROWTH_MEDIA_NMS.setLabel('NMS (4g/L glucose)')
-vocabulary_term_GROWTH_MEDIA_NMS.setOrdinal(3)
-vocabulary_GROWTH_MEDIA.addTerm(vocabulary_term_GROWTH_MEDIA_NMS)
-
-vocabulary_SCALE = tr.createNewVocabulary('SCALE')
-vocabulary_SCALE.setDescription('Scale')
-vocabulary_SCALE.setUrlTemplate(None)
-vocabulary_SCALE.setManagedInternally(False)
-vocabulary_SCALE.setInternalNamespace(False)
-vocabulary_SCALE.setChosenFromList(True)
-
-vocabulary_term_SCALE_LOG2 = tr.createNewVocabularyTerm('LOG2')
-vocabulary_term_SCALE_LOG2.setDescription(None)
-vocabulary_term_SCALE_LOG2.setLabel(None)
-vocabulary_term_SCALE_LOG2.setOrdinal(2)
-vocabulary_SCALE.addTerm(vocabulary_term_SCALE_LOG2)
-
-vocabulary_term_SCALE_LIN = tr.createNewVocabularyTerm('LIN')
-vocabulary_term_SCALE_LIN.setDescription(None)
-vocabulary_term_SCALE_LIN.setLabel(None)
-vocabulary_term_SCALE_LIN.setOrdinal(1)
-vocabulary_SCALE.addTerm(vocabulary_term_SCALE_LIN)
-
-vocabulary_term_SCALE_LOG10 = tr.createNewVocabularyTerm('LOG10')
-vocabulary_term_SCALE_LOG10.setDescription(None)
-vocabulary_term_SCALE_LOG10.setLabel(None)
-vocabulary_term_SCALE_LOG10.setOrdinal(3)
-vocabulary_SCALE.addTerm(vocabulary_term_SCALE_LOG10)
-
-vocabulary_term_SCALE_LN = tr.createNewVocabularyTerm('LN')
-vocabulary_term_SCALE_LN.setDescription(None)
-vocabulary_term_SCALE_LN.setLabel(None)
-vocabulary_term_SCALE_LN.setOrdinal(4)
-vocabulary_SCALE.addTerm(vocabulary_term_SCALE_LN)
-
-vocabulary_TECHNOLOGY = tr.createNewVocabulary('TECHNOLOGY')
-vocabulary_TECHNOLOGY.setDescription('Technologies used in BaSynthec')
-vocabulary_TECHNOLOGY.setUrlTemplate(None)
-vocabulary_TECHNOLOGY.setManagedInternally(False)
-vocabulary_TECHNOLOGY.setInternalNamespace(False)
-vocabulary_TECHNOLOGY.setChosenFromList(True)
-
-vocabulary_term_TECHNOLOGY_METABOLOMICS = tr.createNewVocabularyTerm('METABOLOMICS')
-vocabulary_term_TECHNOLOGY_METABOLOMICS.setDescription(None)
-vocabulary_term_TECHNOLOGY_METABOLOMICS.setLabel(None)
-vocabulary_term_TECHNOLOGY_METABOLOMICS.setOrdinal(1)
-vocabulary_TECHNOLOGY.addTerm(vocabulary_term_TECHNOLOGY_METABOLOMICS)
-
-vocabulary_term_TECHNOLOGY_PROTEOMICS = tr.createNewVocabularyTerm('PROTEOMICS')
-vocabulary_term_TECHNOLOGY_PROTEOMICS.setDescription(None)
-vocabulary_term_TECHNOLOGY_PROTEOMICS.setLabel(None)
-vocabulary_term_TECHNOLOGY_PROTEOMICS.setOrdinal(3)
-vocabulary_TECHNOLOGY.addTerm(vocabulary_term_TECHNOLOGY_PROTEOMICS)
-
-vocabulary_term_TECHNOLOGY_PHYSIOLOGY = tr.createNewVocabularyTerm('PHYSIOLOGY')
-vocabulary_term_TECHNOLOGY_PHYSIOLOGY.setDescription(None)
-vocabulary_term_TECHNOLOGY_PHYSIOLOGY.setLabel(None)
-vocabulary_term_TECHNOLOGY_PHYSIOLOGY.setOrdinal(2)
-vocabulary_TECHNOLOGY.addTerm(vocabulary_term_TECHNOLOGY_PHYSIOLOGY)
-
-vocabulary_term_TECHNOLOGY_TRANSCRIPTOMICS = tr.createNewVocabularyTerm('TRANSCRIPTOMICS')
-vocabulary_term_TECHNOLOGY_TRANSCRIPTOMICS.setDescription(None)
-vocabulary_term_TECHNOLOGY_TRANSCRIPTOMICS.setLabel(None)
-vocabulary_term_TECHNOLOGY_TRANSCRIPTOMICS.setOrdinal(4)
-vocabulary_TECHNOLOGY.addTerm(vocabulary_term_TECHNOLOGY_TRANSCRIPTOMICS)
-
-vocabulary_TEMPERATURE = tr.createNewVocabulary('TEMPERATURE')
-vocabulary_TEMPERATURE.setDescription('Temperature the experiment was conducted under')
-vocabulary_TEMPERATURE.setUrlTemplate(None)
-vocabulary_TEMPERATURE.setManagedInternally(False)
-vocabulary_TEMPERATURE.setInternalNamespace(False)
-vocabulary_TEMPERATURE.setChosenFromList(True)
-
-vocabulary_term_TEMPERATURE_40 = tr.createNewVocabularyTerm('40')
-vocabulary_term_TEMPERATURE_40.setDescription(None)
-vocabulary_term_TEMPERATURE_40.setLabel(None)
-vocabulary_term_TEMPERATURE_40.setOrdinal(3)
-vocabulary_TEMPERATURE.addTerm(vocabulary_term_TEMPERATURE_40)
-
-vocabulary_term_TEMPERATURE_30 = tr.createNewVocabularyTerm('30')
-vocabulary_term_TEMPERATURE_30.setDescription(None)
-vocabulary_term_TEMPERATURE_30.setLabel(None)
-vocabulary_term_TEMPERATURE_30.setOrdinal(2)
-vocabulary_TEMPERATURE.addTerm(vocabulary_term_TEMPERATURE_30)
-
-vocabulary_term_TEMPERATURE_20 = tr.createNewVocabularyTerm('20')
-vocabulary_term_TEMPERATURE_20.setDescription(None)
-vocabulary_term_TEMPERATURE_20.setLabel(None)
-vocabulary_term_TEMPERATURE_20.setOrdinal(1)
-vocabulary_TEMPERATURE.addTerm(vocabulary_term_TEMPERATURE_20)
-
-vocabulary_TIMEPOINT_TYPE = tr.createNewVocabulary('TIMEPOINT_TYPE')
-vocabulary_TIMEPOINT_TYPE.setDescription('Timepoint Type')
-vocabulary_TIMEPOINT_TYPE.setUrlTemplate(None)
-vocabulary_TIMEPOINT_TYPE.setManagedInternally(False)
-vocabulary_TIMEPOINT_TYPE.setInternalNamespace(False)
-vocabulary_TIMEPOINT_TYPE.setChosenFromList(True)
-
-vocabulary_term_TIMEPOINT_TYPE_IN = tr.createNewVocabularyTerm('IN')
-vocabulary_term_TIMEPOINT_TYPE_IN.setDescription(None)
-vocabulary_term_TIMEPOINT_TYPE_IN.setLabel(None)
-vocabulary_term_TIMEPOINT_TYPE_IN.setOrdinal(2)
-vocabulary_TIMEPOINT_TYPE.addTerm(vocabulary_term_TIMEPOINT_TYPE_IN)
-
-vocabulary_term_TIMEPOINT_TYPE_EX = tr.createNewVocabularyTerm('EX')
-vocabulary_term_TIMEPOINT_TYPE_EX.setDescription(None)
-vocabulary_term_TIMEPOINT_TYPE_EX.setLabel(None)
-vocabulary_term_TIMEPOINT_TYPE_EX.setOrdinal(1)
-vocabulary_TIMEPOINT_TYPE.addTerm(vocabulary_term_TIMEPOINT_TYPE_EX)
-
-vocabulary_term_TIMEPOINT_TYPE_SI = tr.createNewVocabularyTerm('SI')
-vocabulary_term_TIMEPOINT_TYPE_SI.setDescription(None)
-vocabulary_term_TIMEPOINT_TYPE_SI.setLabel(None)
-vocabulary_term_TIMEPOINT_TYPE_SI.setOrdinal(3)
-vocabulary_TIMEPOINT_TYPE.addTerm(vocabulary_term_TIMEPOINT_TYPE_SI)
-
-vocabulary_VALUE_TYPE = tr.createNewVocabulary('VALUE_TYPE')
-vocabulary_VALUE_TYPE.setDescription('Value Type')
-vocabulary_VALUE_TYPE.setUrlTemplate(None)
-vocabulary_VALUE_TYPE.setManagedInternally(False)
-vocabulary_VALUE_TYPE.setInternalNamespace(False)
-vocabulary_VALUE_TYPE.setChosenFromList(True)
-
-vocabulary_term_VALUE_TYPE_IQR = tr.createNewVocabularyTerm('IQR')
-vocabulary_term_VALUE_TYPE_IQR.setDescription(None)
-vocabulary_term_VALUE_TYPE_IQR.setLabel(None)
-vocabulary_term_VALUE_TYPE_IQR.setOrdinal(7)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_IQR)
-
-vocabulary_term_VALUE_TYPE_VAR = tr.createNewVocabularyTerm('VAR')
-vocabulary_term_VALUE_TYPE_VAR.setDescription(None)
-vocabulary_term_VALUE_TYPE_VAR.setLabel(None)
-vocabulary_term_VALUE_TYPE_VAR.setOrdinal(5)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_VAR)
-
-vocabulary_term_VALUE_TYPE_ERROR = tr.createNewVocabularyTerm('ERROR')
-vocabulary_term_VALUE_TYPE_ERROR.setDescription(None)
-vocabulary_term_VALUE_TYPE_ERROR.setLabel(None)
-vocabulary_term_VALUE_TYPE_ERROR.setOrdinal(6)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_ERROR)
-
-vocabulary_term_VALUE_TYPE_VALUE = tr.createNewVocabularyTerm('VALUE')
-vocabulary_term_VALUE_TYPE_VALUE.setDescription(None)
-vocabulary_term_VALUE_TYPE_VALUE.setLabel(None)
-vocabulary_term_VALUE_TYPE_VALUE.setOrdinal(1)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_VALUE)
-
-vocabulary_term_VALUE_TYPE_MEAN = tr.createNewVocabularyTerm('MEAN')
-vocabulary_term_VALUE_TYPE_MEAN.setDescription(None)
-vocabulary_term_VALUE_TYPE_MEAN.setLabel(None)
-vocabulary_term_VALUE_TYPE_MEAN.setOrdinal(2)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_MEAN)
-
-vocabulary_term_VALUE_TYPE_STD = tr.createNewVocabularyTerm('STD')
-vocabulary_term_VALUE_TYPE_STD.setDescription(None)
-vocabulary_term_VALUE_TYPE_STD.setLabel(None)
-vocabulary_term_VALUE_TYPE_STD.setOrdinal(4)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_STD)
-
-vocabulary_term_VALUE_TYPE_MEDIAN = tr.createNewVocabularyTerm('MEDIAN')
-vocabulary_term_VALUE_TYPE_MEDIAN.setDescription(None)
-vocabulary_term_VALUE_TYPE_MEDIAN.setLabel(None)
-vocabulary_term_VALUE_TYPE_MEDIAN.setOrdinal(3)
-vocabulary_VALUE_TYPE.addTerm(vocabulary_term_VALUE_TYPE_MEDIAN)
-
-vocabulary_VALUE_UNIT = tr.createNewVocabulary('VALUE_UNIT')
-vocabulary_VALUE_UNIT.setDescription('Value Unit')
-vocabulary_VALUE_UNIT.setUrlTemplate(None)
-vocabulary_VALUE_UNIT.setManagedInternally(False)
-vocabulary_VALUE_UNIT.setInternalNamespace(False)
-vocabulary_VALUE_UNIT.setChosenFromList(True)
-
-vocabulary_term_VALUE_UNIT_PERCENT = tr.createNewVocabularyTerm('PERCENT')
-vocabulary_term_VALUE_UNIT_PERCENT.setDescription(None)
-vocabulary_term_VALUE_UNIT_PERCENT.setLabel(None)
-vocabulary_term_VALUE_UNIT_PERCENT.setOrdinal(3)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_PERCENT)
-
-vocabulary_term_VALUE_UNIT_MM = tr.createNewVocabularyTerm('MM')
-vocabulary_term_VALUE_UNIT_MM.setDescription(None)
-vocabulary_term_VALUE_UNIT_MM.setLabel(None)
-vocabulary_term_VALUE_UNIT_MM.setOrdinal(1)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_MM)
-
-vocabulary_term_VALUE_UNIT_RATIOCS = tr.createNewVocabularyTerm('RATIOCS')
-vocabulary_term_VALUE_UNIT_RATIOCS.setDescription(None)
-vocabulary_term_VALUE_UNIT_RATIOCS.setLabel(None)
-vocabulary_term_VALUE_UNIT_RATIOCS.setOrdinal(5)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_RATIOCS)
-
-vocabulary_term_VALUE_UNIT_RATIOT1 = tr.createNewVocabularyTerm('RATIOT1')
-vocabulary_term_VALUE_UNIT_RATIOT1.setDescription(None)
-vocabulary_term_VALUE_UNIT_RATIOT1.setLabel(None)
-vocabulary_term_VALUE_UNIT_RATIOT1.setOrdinal(4)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_RATIOT1)
-
-vocabulary_term_VALUE_UNIT_AU = tr.createNewVocabularyTerm('AU')
-vocabulary_term_VALUE_UNIT_AU.setDescription(None)
-vocabulary_term_VALUE_UNIT_AU.setLabel(None)
-vocabulary_term_VALUE_UNIT_AU.setOrdinal(6)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_AU)
-
-vocabulary_term_VALUE_UNIT_UM = tr.createNewVocabularyTerm('UM')
-vocabulary_term_VALUE_UNIT_UM.setDescription(None)
-vocabulary_term_VALUE_UNIT_UM.setLabel(None)
-vocabulary_term_VALUE_UNIT_UM.setOrdinal(2)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_UM)
-
-vocabulary_term_VALUE_UNIT_DIMENSIONLESS = tr.createNewVocabularyTerm('DIMENSIONLESS')
-vocabulary_term_VALUE_UNIT_DIMENSIONLESS.setDescription(None)
-vocabulary_term_VALUE_UNIT_DIMENSIONLESS.setLabel(None)
-vocabulary_term_VALUE_UNIT_DIMENSIONLESS.setOrdinal(7)
-vocabulary_VALUE_UNIT.addTerm(vocabulary_term_VALUE_UNIT_DIMENSIONLESS)
-
-exp_type_BASYNTHEC = tr.createNewExperimentType('BASYNTHEC')
-exp_type_BASYNTHEC.setDescription('The BaSynthec experiment type.')
-
-data_set_type_EXCEL_ORIGINAL = tr.createNewDataSetType('EXCEL_ORIGINAL')
-data_set_type_EXCEL_ORIGINAL.setDescription('Excel data')
-data_set_type_EXCEL_ORIGINAL.setContainerType(False)
-
-data_set_type_METABOLITE_INTENSITIES = tr.createNewDataSetType('METABOLITE_INTENSITIES')
-data_set_type_METABOLITE_INTENSITIES.setDescription('Metabolite intensities')
-data_set_type_METABOLITE_INTENSITIES.setContainerType(True)
-
-data_set_type_OD600 = tr.createNewDataSetType('OD600')
-data_set_type_OD600.setDescription('Growth profiles')
-data_set_type_OD600.setContainerType(True)
-
-data_set_type_PROTEIN_QUANTIFICATIONS = tr.createNewDataSetType('PROTEIN_QUANTIFICATIONS')
-data_set_type_PROTEIN_QUANTIFICATIONS.setDescription('Protein quantifications')
-data_set_type_PROTEIN_QUANTIFICATIONS.setContainerType(True)
-
-data_set_type_RAW = tr.createNewDataSetType('RAW')
-data_set_type_RAW.setDescription('Raw data')
-data_set_type_RAW.setContainerType(False)
-
-data_set_type_TRANSCRIPTOMICS = tr.createNewDataSetType('TRANSCRIPTOMICS')
-data_set_type_TRANSCRIPTOMICS.setDescription('Transcriptomics data')
-data_set_type_TRANSCRIPTOMICS.setContainerType(True)
-
-data_set_type_TSV_EXPORT = tr.createNewDataSetType('TSV_EXPORT')
-data_set_type_TSV_EXPORT.setDescription('An export of the data containing one strain per file.')
-data_set_type_TSV_EXPORT.setContainerType(False)
-
-data_set_type_TSV_MULTISTRAIN_EXPORT = tr.createNewDataSetType('TSV_MULTISTRAIN_EXPORT')
-data_set_type_TSV_MULTISTRAIN_EXPORT.setDescription('An export of the data containing multiple strains per file.')
-data_set_type_TSV_MULTISTRAIN_EXPORT.setContainerType(False)
-
-data_set_type_UNKNOWN = tr.createNewDataSetType('UNKNOWN')
-data_set_type_UNKNOWN.setDescription('Unknown')
-data_set_type_UNKNOWN.setContainerType(False)
-
-material_type_STRAIN = tr.createNewMaterialType('STRAIN')
-material_type_STRAIN.setDescription('Strain')
-
-prop_type_CELL_LOCATION = tr.createNewPropertyType('CELL_LOCATION', DataType.CONTROLLEDVOCABULARY)
-prop_type_CELL_LOCATION.setLabel('Cell Location')
-prop_type_CELL_LOCATION.setManagedInternally(False)
-prop_type_CELL_LOCATION.setInternalNamespace(False)
-
-prop_type_CELL_LOCATION.setVocabulary(vocabulary_CELL_LOCATION)
-
-prop_type_COMMENTS = tr.createNewPropertyType('COMMENTS', DataType.MULTILINE_VARCHAR)
-prop_type_COMMENTS.setLabel('Comments')
-prop_type_COMMENTS.setManagedInternally(False)
-prop_type_COMMENTS.setInternalNamespace(False)
-
-
-prop_type_CONTAINER = tr.createNewPropertyType('CONTAINER', DataType.CONTROLLEDVOCABULARY)
-prop_type_CONTAINER.setLabel('Container')
-prop_type_CONTAINER.setManagedInternally(False)
-prop_type_CONTAINER.setInternalNamespace(False)
-
-prop_type_CONTAINER.setVocabulary(vocabulary_CONTAINER)
-
-prop_type_CONTAINER_VOLUME = tr.createNewPropertyType('CONTAINER_VOLUME', DataType.VARCHAR)
-prop_type_CONTAINER_VOLUME.setLabel('Container Volume')
-prop_type_CONTAINER_VOLUME.setManagedInternally(False)
-prop_type_CONTAINER_VOLUME.setInternalNamespace(False)
-
-
-prop_type_DATA_TYPE = tr.createNewPropertyType('DATA_TYPE', DataType.VARCHAR)
-prop_type_DATA_TYPE.setLabel('Data Type')
-prop_type_DATA_TYPE.setManagedInternally(False)
-prop_type_DATA_TYPE.setInternalNamespace(False)
-
-
-prop_type_DESCRIPTION = tr.createNewPropertyType('DESCRIPTION', DataType.VARCHAR)
-prop_type_DESCRIPTION.setLabel('Description')
-prop_type_DESCRIPTION.setManagedInternally(False)
-prop_type_DESCRIPTION.setInternalNamespace(False)
-
-
-prop_type_DEVICE = tr.createNewPropertyType('DEVICE', DataType.CONTROLLEDVOCABULARY)
-prop_type_DEVICE.setLabel('Device')
-prop_type_DEVICE.setManagedInternally(False)
-prop_type_DEVICE.setInternalNamespace(False)
-
-prop_type_DEVICE.setVocabulary(vocabulary_DEVICE)
-
-prop_type_EXPERIMENT_DATE = tr.createNewPropertyType('EXPERIMENT_DATE', DataType.TIMESTAMP)
-prop_type_EXPERIMENT_DATE.setLabel('Experiment Date')
-prop_type_EXPERIMENT_DATE.setManagedInternally(False)
-prop_type_EXPERIMENT_DATE.setInternalNamespace(False)
-
-
-prop_type_MEDIUM = tr.createNewPropertyType('MEDIUM', DataType.CONTROLLEDVOCABULARY)
-prop_type_MEDIUM.setLabel('Medium')
-prop_type_MEDIUM.setManagedInternally(False)
-prop_type_MEDIUM.setInternalNamespace(False)
-
-prop_type_MEDIUM.setVocabulary(vocabulary_GROWTH_MEDIA)
-
-prop_type_MISC_GROWTH_CONDITIONS = tr.createNewPropertyType('MISC_GROWTH_CONDITIONS', DataType.MULTILINE_VARCHAR)
-prop_type_MISC_GROWTH_CONDITIONS.setLabel('Growth Conditions')
-prop_type_MISC_GROWTH_CONDITIONS.setManagedInternally(False)
-prop_type_MISC_GROWTH_CONDITIONS.setInternalNamespace(False)
-
-
-prop_type_OPERATOR = tr.createNewPropertyType('OPERATOR', DataType.VARCHAR)
-prop_type_OPERATOR.setLabel('Operator')
-prop_type_OPERATOR.setManagedInternally(False)
-prop_type_OPERATOR.setInternalNamespace(False)
-
-
-prop_type_REFERENCE_STRAIN = tr.createNewPropertyType('REFERENCE_STRAIN', DataType.MATERIAL)
-prop_type_REFERENCE_STRAIN.setLabel('Reference Strain')
-prop_type_REFERENCE_STRAIN.setManagedInternally(False)
-prop_type_REFERENCE_STRAIN.setInternalNamespace(False)
-prop_type_REFERENCE_STRAIN.setMaterialType(material_type_STRAIN)
-
-prop_type_SCALE = tr.createNewPropertyType('SCALE', DataType.CONTROLLEDVOCABULARY)
-prop_type_SCALE.setLabel('Scale')
-prop_type_SCALE.setManagedInternally(False)
-prop_type_SCALE.setInternalNamespace(False)
-
-prop_type_SCALE.setVocabulary(vocabulary_SCALE)
-
-prop_type_SHAKER_RPM = tr.createNewPropertyType('SHAKER_RPM', DataType.INTEGER)
-prop_type_SHAKER_RPM.setLabel('Shaker RPM')
-prop_type_SHAKER_RPM.setManagedInternally(False)
-prop_type_SHAKER_RPM.setInternalNamespace(False)
-
-
-prop_type_STRAIN = tr.createNewPropertyType('STRAIN', DataType.MATERIAL)
-prop_type_STRAIN.setLabel('Strain')
-prop_type_STRAIN.setManagedInternally(False)
-prop_type_STRAIN.setInternalNamespace(False)
-prop_type_STRAIN.setMaterialType(material_type_STRAIN)
-
-prop_type_STRAIN_NAME = tr.createNewPropertyType('STRAIN_NAME', DataType.VARCHAR)
-prop_type_STRAIN_NAME.setLabel('Name')
-prop_type_STRAIN_NAME.setManagedInternally(False)
-prop_type_STRAIN_NAME.setInternalNamespace(False)
-
-
-prop_type_STRAIN_NAMES = tr.createNewPropertyType('STRAIN_NAMES', DataType.VARCHAR)
-prop_type_STRAIN_NAMES.setLabel('Strain Names')
-prop_type_STRAIN_NAMES.setManagedInternally(False)
-prop_type_STRAIN_NAMES.setInternalNamespace(False)
-
-
-prop_type_TECHNOLOGY = tr.createNewPropertyType('TECHNOLOGY', DataType.CONTROLLEDVOCABULARY)
-prop_type_TECHNOLOGY.setLabel('Technology')
-prop_type_TECHNOLOGY.setManagedInternally(False)
-prop_type_TECHNOLOGY.setInternalNamespace(False)
-
-prop_type_TECHNOLOGY.setVocabulary(vocabulary_TECHNOLOGY)
-
-prop_type_TEMPERATURE = tr.createNewPropertyType('TEMPERATURE', DataType.REAL)
-prop_type_TEMPERATURE.setLabel('Temperature')
-prop_type_TEMPERATURE.setManagedInternally(False)
-prop_type_TEMPERATURE.setInternalNamespace(False)
-
-
-prop_type_TIMEPOINT_TYPE = tr.createNewPropertyType('TIMEPOINT_TYPE', DataType.CONTROLLEDVOCABULARY)
-prop_type_TIMEPOINT_TYPE.setLabel('Timepoint Type')
-prop_type_TIMEPOINT_TYPE.setManagedInternally(False)
-prop_type_TIMEPOINT_TYPE.setInternalNamespace(False)
-
-prop_type_TIMEPOINT_TYPE.setVocabulary(vocabulary_TIMEPOINT_TYPE)
-
-prop_type_VALUE_TYPE = tr.createNewPropertyType('VALUE_TYPE', DataType.CONTROLLEDVOCABULARY)
-prop_type_VALUE_TYPE.setLabel('Value Type')
-prop_type_VALUE_TYPE.setManagedInternally(False)
-prop_type_VALUE_TYPE.setInternalNamespace(False)
-
-prop_type_VALUE_TYPE.setVocabulary(vocabulary_VALUE_TYPE)
-
-prop_type_VALUE_UNIT = tr.createNewPropertyType('VALUE_UNIT', DataType.CONTROLLEDVOCABULARY)
-prop_type_VALUE_UNIT.setLabel('Value Unit')
-prop_type_VALUE_UNIT.setManagedInternally(False)
-prop_type_VALUE_UNIT.setInternalNamespace(False)
-
-prop_type_VALUE_UNIT.setVocabulary(vocabulary_VALUE_UNIT)
-
-assignment_EXPERIMENT_BASYNTHEC_DESCRIPTION = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_DESCRIPTION)
-assignment_EXPERIMENT_BASYNTHEC_DESCRIPTION.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_DESCRIPTION.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_DESCRIPTION.setPositionInForms(1)
-
-assignment_EXPERIMENT_BASYNTHEC_MEDIUM = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_MEDIUM)
-assignment_EXPERIMENT_BASYNTHEC_MEDIUM.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_MEDIUM.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_MEDIUM.setPositionInForms(2)
-
-assignment_EXPERIMENT_BASYNTHEC_TEMPERATURE = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_TEMPERATURE)
-assignment_EXPERIMENT_BASYNTHEC_TEMPERATURE.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_TEMPERATURE.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_TEMPERATURE.setPositionInForms(3)
-
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_CONTAINER)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER.setPositionInForms(5)
-
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER_VOLUME = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_CONTAINER_VOLUME)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER_VOLUME.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER_VOLUME.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_CONTAINER_VOLUME.setPositionInForms(6)
-
-assignment_EXPERIMENT_BASYNTHEC_MISC_GROWTH_CONDITIONS = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_MISC_GROWTH_CONDITIONS)
-assignment_EXPERIMENT_BASYNTHEC_MISC_GROWTH_CONDITIONS.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_MISC_GROWTH_CONDITIONS.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_MISC_GROWTH_CONDITIONS.setPositionInForms(7)
-
-assignment_EXPERIMENT_BASYNTHEC_SHAKER_RPM = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_SHAKER_RPM)
-assignment_EXPERIMENT_BASYNTHEC_SHAKER_RPM.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_SHAKER_RPM.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_SHAKER_RPM.setPositionInForms(8)
-
-assignment_EXPERIMENT_BASYNTHEC_COMMENTS = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_COMMENTS)
-assignment_EXPERIMENT_BASYNTHEC_COMMENTS.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_COMMENTS.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_COMMENTS.setPositionInForms(9)
-
-assignment_EXPERIMENT_BASYNTHEC_EXPERIMENT_DATE = tr.assignPropertyType(exp_type_BASYNTHEC, prop_type_EXPERIMENT_DATE)
-assignment_EXPERIMENT_BASYNTHEC_EXPERIMENT_DATE.setMandatory(False)
-assignment_EXPERIMENT_BASYNTHEC_EXPERIMENT_DATE.setSection(None)
-assignment_EXPERIMENT_BASYNTHEC_EXPERIMENT_DATE.setPositionInForms(10)
-
-assignment_DATA_SET_EXCEL_ORIGINAL_DATA_TYPE = tr.assignPropertyType(data_set_type_EXCEL_ORIGINAL, prop_type_DATA_TYPE)
-assignment_DATA_SET_EXCEL_ORIGINAL_DATA_TYPE.setMandatory(False)
-assignment_DATA_SET_EXCEL_ORIGINAL_DATA_TYPE.setSection(None)
-assignment_DATA_SET_EXCEL_ORIGINAL_DATA_TYPE.setPositionInForms(1)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_STRAIN)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN.setPositionInForms(1)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN_NAMES = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_STRAIN_NAMES)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN_NAMES.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN_NAMES.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_STRAIN_NAMES.setPositionInForms(2)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_TIMEPOINT_TYPE = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_TIMEPOINT_TYPE)
-assignment_DATA_SET_METABOLITE_INTENSITIES_TIMEPOINT_TYPE.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_TIMEPOINT_TYPE.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_TIMEPOINT_TYPE.setPositionInForms(3)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_CELL_LOCATION = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_CELL_LOCATION)
-assignment_DATA_SET_METABOLITE_INTENSITIES_CELL_LOCATION.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_CELL_LOCATION.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_CELL_LOCATION.setPositionInForms(4)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_TYPE = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_VALUE_TYPE)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_TYPE.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_TYPE.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_TYPE.setPositionInForms(5)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_UNIT = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_VALUE_UNIT)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_UNIT.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_UNIT.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_VALUE_UNIT.setPositionInForms(6)
-
-assignment_DATA_SET_METABOLITE_INTENSITIES_SCALE = tr.assignPropertyType(data_set_type_METABOLITE_INTENSITIES, prop_type_SCALE)
-assignment_DATA_SET_METABOLITE_INTENSITIES_SCALE.setMandatory(False)
-assignment_DATA_SET_METABOLITE_INTENSITIES_SCALE.setSection(None)
-assignment_DATA_SET_METABOLITE_INTENSITIES_SCALE.setPositionInForms(7)
-
-assignment_DATA_SET_OD600_STRAIN = tr.assignPropertyType(data_set_type_OD600, prop_type_STRAIN)
-assignment_DATA_SET_OD600_STRAIN.setMandatory(False)
-assignment_DATA_SET_OD600_STRAIN.setSection(None)
-assignment_DATA_SET_OD600_STRAIN.setPositionInForms(1)
-
-assignment_DATA_SET_OD600_STRAIN_NAMES = tr.assignPropertyType(data_set_type_OD600, prop_type_STRAIN_NAMES)
-assignment_DATA_SET_OD600_STRAIN_NAMES.setMandatory(False)
-assignment_DATA_SET_OD600_STRAIN_NAMES.setSection(None)
-assignment_DATA_SET_OD600_STRAIN_NAMES.setPositionInForms(2)
-
-assignment_DATA_SET_OD600_TIMEPOINT_TYPE = tr.assignPropertyType(data_set_type_OD600, prop_type_TIMEPOINT_TYPE)
-assignment_DATA_SET_OD600_TIMEPOINT_TYPE.setMandatory(False)
-assignment_DATA_SET_OD600_TIMEPOINT_TYPE.setSection(None)
-assignment_DATA_SET_OD600_TIMEPOINT_TYPE.setPositionInForms(3)
-
-assignment_DATA_SET_OD600_CELL_LOCATION = tr.assignPropertyType(data_set_type_OD600, prop_type_CELL_LOCATION)
-assignment_DATA_SET_OD600_CELL_LOCATION.setMandatory(False)
-assignment_DATA_SET_OD600_CELL_LOCATION.setSection(None)
-assignment_DATA_SET_OD600_CELL_LOCATION.setPositionInForms(4)
-
-assignment_DATA_SET_OD600_VALUE_TYPE = tr.assignPropertyType(data_set_type_OD600, prop_type_VALUE_TYPE)
-assignment_DATA_SET_OD600_VALUE_TYPE.setMandatory(False)
-assignment_DATA_SET_OD600_VALUE_TYPE.setSection(None)
-assignment_DATA_SET_OD600_VALUE_TYPE.setPositionInForms(5)
-
-assignment_DATA_SET_OD600_VALUE_UNIT = tr.assignPropertyType(data_set_type_OD600, prop_type_VALUE_UNIT)
-assignment_DATA_SET_OD600_VALUE_UNIT.setMandatory(False)
-assignment_DATA_SET_OD600_VALUE_UNIT.setSection(None)
-assignment_DATA_SET_OD600_VALUE_UNIT.setPositionInForms(6)
-
-assignment_DATA_SET_OD600_SCALE = tr.assignPropertyType(data_set_type_OD600, prop_type_SCALE)
-assignment_DATA_SET_OD600_SCALE.setMandatory(False)
-assignment_DATA_SET_OD600_SCALE.setSection(None)
-assignment_DATA_SET_OD600_SCALE.setPositionInForms(7)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_STRAIN)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN.setPositionInForms(1)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN_NAMES = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_STRAIN_NAMES)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN_NAMES.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN_NAMES.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_STRAIN_NAMES.setPositionInForms(2)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_TIMEPOINT_TYPE = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_TIMEPOINT_TYPE)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_TIMEPOINT_TYPE.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_TIMEPOINT_TYPE.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_TIMEPOINT_TYPE.setPositionInForms(3)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_CELL_LOCATION = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_CELL_LOCATION)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_CELL_LOCATION.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_CELL_LOCATION.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_CELL_LOCATION.setPositionInForms(4)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_VALUE_UNIT = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_VALUE_UNIT)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_VALUE_UNIT.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_VALUE_UNIT.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_VALUE_UNIT.setPositionInForms(6)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_SCALE = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_SCALE)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_SCALE.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_SCALE.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_SCALE.setPositionInForms(7)
-
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_REFERENCE_STRAIN = tr.assignPropertyType(data_set_type_PROTEIN_QUANTIFICATIONS, prop_type_REFERENCE_STRAIN)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_REFERENCE_STRAIN.setMandatory(False)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_REFERENCE_STRAIN.setSection(None)
-assignment_DATA_SET_PROTEIN_QUANTIFICATIONS_REFERENCE_STRAIN.setPositionInForms(8)
-
-assignment_DATA_SET_RAW_STRAIN = tr.assignPropertyType(data_set_type_RAW, prop_type_STRAIN)
-assignment_DATA_SET_RAW_STRAIN.setMandatory(True)
-assignment_DATA_SET_RAW_STRAIN.setSection(None)
-assignment_DATA_SET_RAW_STRAIN.setPositionInForms(1)
-
-assignment_DATA_SET_RAW_TECHNOLOGY = tr.assignPropertyType(data_set_type_RAW, prop_type_TECHNOLOGY)
-assignment_DATA_SET_RAW_TECHNOLOGY.setMandatory(True)
-assignment_DATA_SET_RAW_TECHNOLOGY.setSection(None)
-assignment_DATA_SET_RAW_TECHNOLOGY.setPositionInForms(2)
-
-assignment_DATA_SET_RAW_DEVICE = tr.assignPropertyType(data_set_type_RAW, prop_type_DEVICE)
-assignment_DATA_SET_RAW_DEVICE.setMandatory(False)
-assignment_DATA_SET_RAW_DEVICE.setSection(None)
-assignment_DATA_SET_RAW_DEVICE.setPositionInForms(3)
-
-assignment_DATA_SET_RAW_OPERATOR = tr.assignPropertyType(data_set_type_RAW, prop_type_OPERATOR)
-assignment_DATA_SET_RAW_OPERATOR.setMandatory(False)
-assignment_DATA_SET_RAW_OPERATOR.setSection(None)
-assignment_DATA_SET_RAW_OPERATOR.setPositionInForms(4)
-
-assignment_MATERIAL_STRAIN_STRAIN_NAME = tr.assignPropertyType(material_type_STRAIN, prop_type_STRAIN_NAME)
-assignment_MATERIAL_STRAIN_STRAIN_NAME.setMandatory(True)
-assignment_MATERIAL_STRAIN_STRAIN_NAME.setSection(None)
-assignment_MATERIAL_STRAIN_STRAIN_NAME.setPositionInForms(1)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_STRAIN)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN.setPositionInForms(1)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN_NAMES = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_STRAIN_NAMES)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN_NAMES.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN_NAMES.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_STRAIN_NAMES.setPositionInForms(2)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_TIMEPOINT_TYPE = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_TIMEPOINT_TYPE)
-assignment_DATA_SET_TRANSCRIPTOMICS_TIMEPOINT_TYPE.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_TIMEPOINT_TYPE.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_TIMEPOINT_TYPE.setPositionInForms(3)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_CELL_LOCATION = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_CELL_LOCATION)
-assignment_DATA_SET_TRANSCRIPTOMICS_CELL_LOCATION.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_CELL_LOCATION.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_CELL_LOCATION.setPositionInForms(4)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_TYPE = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_VALUE_TYPE)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_TYPE.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_TYPE.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_TYPE.setPositionInForms(5)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_UNIT = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_VALUE_UNIT)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_UNIT.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_UNIT.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_VALUE_UNIT.setPositionInForms(6)
-
-assignment_DATA_SET_TRANSCRIPTOMICS_SCALE = tr.assignPropertyType(data_set_type_TRANSCRIPTOMICS, prop_type_SCALE)
-assignment_DATA_SET_TRANSCRIPTOMICS_SCALE.setMandatory(False)
-assignment_DATA_SET_TRANSCRIPTOMICS_SCALE.setSection(None)
-assignment_DATA_SET_TRANSCRIPTOMICS_SCALE.setPositionInForms(7)
-
-assignment_DATA_SET_TSV_EXPORT_DATA_TYPE = tr.assignPropertyType(data_set_type_TSV_EXPORT, prop_type_DATA_TYPE)
-assignment_DATA_SET_TSV_EXPORT_DATA_TYPE.setMandatory(False)
-assignment_DATA_SET_TSV_EXPORT_DATA_TYPE.setSection(None)
-assignment_DATA_SET_TSV_EXPORT_DATA_TYPE.setPositionInForms(1)
-
-assignment_DATA_SET_TSV_MULTISTRAIN_EXPORT_DATA_TYPE = tr.assignPropertyType(data_set_type_TSV_MULTISTRAIN_EXPORT, prop_type_DATA_TYPE)
-assignment_DATA_SET_TSV_MULTISTRAIN_EXPORT_DATA_TYPE.setMandatory(False)
-assignment_DATA_SET_TSV_MULTISTRAIN_EXPORT_DATA_TYPE.setSection(None)
-assignment_DATA_SET_TSV_MULTISTRAIN_EXPORT_DATA_TYPE.setPositionInForms(1)
diff --git a/eu_basynthec/sourceTest/examples/Metabolomics-BadData.xlsx b/eu_basynthec/sourceTest/examples/Metabolomics-BadData.xlsx
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diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
deleted file mode 100644
index ebd678574f0..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
+++ /dev/null
@@ -1,212 +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 eu.basynthec.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.io.FileUtils;
-import org.jmock.Expectations;
-
-import ch.systemsx.cisd.common.filesystem.FileConstants;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.etlserver.registrator.AbstractJythonDataSetHandlerTest;
-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.builders.ExperimentBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public abstract class AbstractBaSynthecDataSetRegistratorTest extends
- AbstractJythonDataSetHandlerTest
-{
-
- private static final String TEST_EXPERIMENT_IDENTIFIER = "/TEST/TEST/TEST";
-
- protected static final String STRAIN_NAMES_PROP = "STRAIN_NAMES";
-
- protected static final String VALUE_UNIT_PROP = "VALUE_UNIT";
-
- protected static final DataSetType TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE = new DataSetType(
- "TSV_MULTISTRAIN_EXPORT");
-
- protected static final DataSetType TSV_DATA_SET_TYPE = new DataSetType("TSV_EXPORT");
-
- /**
- *
- *
- */
- public AbstractBaSynthecDataSetRegistratorTest()
- {
- super();
- }
-
- protected RecordingMatcher<AtomicEntityOperationDetails> setUpDataSetRegistrationExpectations(
- final DataSetType dataSetType, final DataSetType tsvDataSetType)
- {
- return setUpDataSetRegistrationExpectations(
- dataSetType, tsvDataSetType, true);
- }
-
- protected RecordingMatcher<AtomicEntityOperationDetails> setUpDataSetRegistrationExpectations(
- final DataSetType dataSetType, final DataSetType tsvDataSetType,
- final boolean requireSingleStrainTsvExport)
- {
- ExperimentBuilder builder = new ExperimentBuilder().identifier(TEST_EXPERIMENT_IDENTIFIER);
- final Experiment experiment = builder.getExperiment();
- final RecordingMatcher<AtomicEntityOperationDetails> atomicatOperationDetails =
- new RecordingMatcher<AtomicEntityOperationDetails>();
- context.checking(new Expectations()
- {
- {
- allowing(openBisService).heartbeat();
-
- one(
- openBisService).createPermId();
- will(returnValue(DATA_SET_CODE));
-
- String excelDataSetCode = DATA_SET_CODE + "-EXCEL";
- one(
- openBisService).createPermId();
- will(returnValue(excelDataSetCode));
-
- // Some if there is a multistrain data set type, it needs to be taken care of in
- // addition to the normal one
- if (tsvDataSetType == TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE)
- {
- String tsvMultistrain = DATA_SET_CODE + "-TSV-MULTISTRAIN";
- one(
- openBisService).createPermId();
- will(returnValue(tsvMultistrain));
- }
-
- String tsvDataSetCode = DATA_SET_CODE + "-TSV";
- if (requireSingleStrainTsvExport)
- {
- one(
- openBisService).createPermId();
- will(returnValue(tsvDataSetCode));
- }
-
- atLeast(
- 1).of(
- openBisService).tryGetExperiment(
- new ExperimentIdentifierFactory(experiment.getIdentifier())
- .createIdentifier());
- will(returnValue(experiment));
-
- allowing(
- openBisService).tryGetExperiment(
- null);
- will(returnValue(null));
-
- one(
- dataSetValidator).assertValidDataSet(
- dataSetType, null);
-
- one(
- dataSetValidator).assertValidDataSet(
- new DataSetType("EXCEL_ORIGINAL"),
- new File(new File(stagingDirectory, excelDataSetCode), "xls"));
-
- if (tsvDataSetType == TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE)
- {
- one(
- dataSetValidator).assertValidDataSet(
- TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE,
- new File(new File(stagingDirectory, DATA_SET_CODE
- + "-TSV-MULTISTRAIN"), "tsv-multi"));
- }
-
- if (requireSingleStrainTsvExport)
- {
- one(
- dataSetValidator).assertValidDataSet(
- TSV_DATA_SET_TYPE,
- new File(new File(stagingDirectory, tsvDataSetCode), "tsv"));
- }
-
- one(
- openBisService).drawANewUniqueID();
- will(returnValue(new Long(1)));
-
- one(
- openBisService).performEntityOperations(
- with(atomicatOperationDetails));
-
- will(returnValue(new AtomicEntityOperationResult()));
-
- allowing(
- openBisService).setStorageConfirmed(
- with(any(List.class)));
-
- }
- });
- return atomicatOperationDetails;
- }
-
- protected Properties createThreadProperties()
- {
- return createThreadPropertiesRelativeToScriptsFolder(
- "data-set-handler.py", "dist/etc/shared/shared-classes.py,"
- + getRegistrationScriptsFolderPath() + "/data-set-validator.py");
- }
-
- protected void createData(String fileName) throws IOException
- {
- File dataFile = new File("sourceTest/examples/" + fileName);
- FileUtils.copyFileToDirectory(
- dataFile, workingDirectory);
- incomingDataSetFile = new File(workingDirectory, dataFile.getName());
-
- markerFile = new File(workingDirectory, FileConstants.IS_FINISHED_PREFIX + dataFile.getName());
- FileUtilities.writeToFile(
- markerFile, "");
- }
-
- protected HashMap<String, NewProperty> getDataSetPropertiesMap(
- List<NewProperty> dataSetProperties)
- {
- HashMap<String, NewProperty> propertyMap = new HashMap<String, NewProperty>();
- for (NewProperty prop : dataSetProperties)
- {
- propertyMap.put(
- prop.getPropertyCode(), prop);
- }
- return propertyMap;
- }
-
- protected void checkDataTypeProperty(NewExternalData dataSet, String expectedValue)
- {
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty property = propertyMap.get("DATA_TYPE");
- assertEquals(
- expectedValue, property.getValue());
- }
-
-}
\ No newline at end of file
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/TimeSeriesDataExcelTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/TimeSeriesDataExcelTest.java
deleted file mode 100644
index c9525d17d8e..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/TimeSeriesDataExcelTest.java
+++ /dev/null
@@ -1,132 +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 eu.basynthec.cisd.dss;
-
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class TimeSeriesDataExcelTest extends AssertJUnit
-{
-
- @Test
- public void testReadingMetaboliteData()
- {
- TimeSeriesDataExcel data =
- TimeSeriesDataExcel
- .createTimeSeriesDataExcel("sourceTest/examples/Metabolomics1-Example.xlsx");
- List<String[]> metadataLines = data.getRawMetadataLines();
- assertTrue("Metadata lines should not be empty", metadataLines.size() > 0);
- String[][] expectedMetadata =
- {
- { "Property", "Value" },
- { "Experiment", "/TEST/TEST/TEST" },
- { "Strain", "CHASSIS 1" },
- { "Timepoint Type", "EX" },
- { "Cell Location", "CE" },
- { "Value Type", "Std" },
- { "Value Unit", "RatioCs" },
- { "Scale", "Lin" } };
- assertLinesAreEqual(metadataLines, expectedMetadata);
-
- List<String[]> dataLines = data.getRawDataLines();
- assertTrue("Data lines should not be empty", dataLines.size() > 0);
- String[][] expectedData =
- {
- { "CompoundID", "HumanReadable", "-703.0", "-603.0" },
- { "CHEBI:15521", "phosphate1", "0.095157063", "0.083137933" },
- { "CHEBI:18311", "phosphate2", "0.059749697", "0.044605606" } };
- assertLinesAreEqual(dataLines, expectedData);
- }
-
- @Test
- public void testReadingMetaboliteTemplate()
- {
- TimeSeriesDataExcel data =
- TimeSeriesDataExcel
- .createTimeSeriesDataExcel("sourceTest/examples/Metabolomics1-Template.xlsx");
- List<String[]> metadataLines = data.getRawMetadataLines();
- assertTrue("Metadata lines should not be empty", metadataLines.size() > 0);
- String[][] expectedMetadata =
- {
- { "Property", "Value" },
- { "Experiment", "BLANK" },
- { "Strain", null },
- { "Timepoint Type", null },
- { "Cell Location", null },
- { "Value Type", null },
- { "Value Unit", null },
- { "Scale", null } };
- assertLinesAreEqual(metadataLines, expectedMetadata);
- }
-
- @Test
- public void testReadingOD600Data()
- {
- TimeSeriesDataExcel data =
- TimeSeriesDataExcel
- .createTimeSeriesDataExcel("sourceTest/examples/OD600-Example.xlsx");
- List<String[]> metadataLines = data.getRawMetadataLines();
- assertTrue("Metadata lines should not be empty", metadataLines.size() > 0);
- String[][] expectedMetadata =
- {
- { "Property", "Value" },
- { "Experiment", "/TEST/TEST/TEST" },
- { "Timepoint Type", "IN" },
- { "Cell Location", "ES" },
- { "Value Type", "Value" },
- { "Value Unit", "Dimensionless" },
- { "Scale", "Lin" } };
- assertLinesAreEqual(metadataLines, expectedMetadata);
-
- List<String[]> dataLines = data.getRawDataLines();
- assertTrue("Data lines should not be empty", dataLines.size() > 0);
- String[][] expectedData =
- {
- { "Strain", "HumanReadable", "-19020.0", "-17220.0" },
- { "JJS-MGP001", "OD600", "0.05", "0.064" },
- { "JJS-MGP100", "OD600", "0.05", "0.064" },
- { "JJS-MGP020", "OD600", "0.05", "0.064" },
- { "JJS-MGP999", "OD600", "0.05", "0.064" },
- { "JJS-MGP001", "OD600", "0.05", "0.064" },
- { "MS", "OD600", "0.05", "0.064" },
- { "WT 168 trp+", "OD600", "0.05", "0.064" } };
- assertLinesAreEqual(dataLines, expectedData);
- }
-
- /**
- * Check that the lines in expected show up in actual in the same order. Actual may have additional columns, though -- these are ignored.
- */
- private void assertLinesAreEqual(List<String[]> actual, String[][] expected)
- {
- assertTrue("Number of lines does not match: " + expected.length + " vs. " + actual.size(),
- actual.size() == expected.length);
- for (int i = 0; i < expected.length; ++i)
- {
- String[] actualLine = actual.get(i);
- String[] expectedLine = expected[i];
- for (int j = 0; j < expectedLine.length; ++j)
- {
- assertEquals("Line " + i, expectedLine[j], actualLine[j]);
- }
- }
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
deleted file mode 100644
index cc342f27e79..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
+++ /dev/null
@@ -1,110 +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 eu.basynthec.cisd.dss.growthprofiles;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Properties;
-
-import org.apache.commons.io.FileUtils;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class OD600DataSetRegistratorTest extends AbstractBaSynthecDataSetRegistratorTest
-{
- private static final DataSetType OD600 = new DataSetType("OD600");
-
- @Test
- public void testSimpleTransaction() throws IOException
- {
- setUpHomeDataBaseExpectations();
- Properties properties = createThreadProperties();
- createHandler(properties, false, true);
- createData("OD600-Example.xlsx");
-
- final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
- setUpDataSetRegistrationExpectations(OD600, TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE);
-
- handler.handle(markerFile);
-
- assertEquals(4, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
-
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(1), "OD600");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(2), "OD600");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(3), "OD600");
-
- NewExternalData dataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
-
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(OD600, dataSet.getDataSetType());
-
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty strainProperty = propertyMap.get(STRAIN_NAMES_PROP);
-
- assertNotNull(strainProperty);
- assert null != strainProperty;
-
- NewExternalData tsvSplitDataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(3);
- String location = tsvSplitDataSet.getLocation() + "/tsv";
- File tsvSplitFolder = new File(workingDirectory, "/1/" + location);
- String[] contents = tsvSplitFolder.list();
- Arrays.sort(contents);
- String[] expectedContents =
- { "OD600-Example.xlsx_JJS-MGP001.tsv", "OD600-Example.xlsx_JJS-MGP020.tsv",
- "OD600-Example.xlsx_JJS-MGP100.tsv",
- "OD600-Example.xlsx_JJS-MGP999.tsv", "OD600-Example.xlsx_MS.tsv",
- "OD600-Example.xlsx_WT 168 trp+.tsv" };
- assertEquals(Arrays.asList(expectedContents), Arrays.asList(contents));
- File tsvSplitFile = new File(tsvSplitFolder, "OD600-Example.xlsx_JJS-MGP001.tsv");
- checkTsvSplitContent(tsvSplitFile);
-
- context.assertIsSatisfied();
- }
-
- @Override
- protected String getRegistrationScriptsFolderPath()
- {
- return "dist/etc/growth-profiles/";
- }
-
- private void checkTsvSplitContent(File tsvFile) throws IOException
- {
- String content = FileUtils.readFileToString(tsvFile);
- assertEquals(
- "RunNumber\tHumanReadable\t-19020.0\t-17220.0\t-15360.0\t-13620.0\t-11820.0\t-10020.0\t-8220.0\t-7020.0\t-4920.0\t-2820.0\t-1020.0\t-120.0\t720.0\t1500.0\t3660.0\t5460.0\t6060.0\t7200.0\t9000.0\n"
- + "0\tOD600\t0.05\t0.064\t0.077\t0.089\t0.107\t0.127\t0.155\t0.176\t0.24\t0.33\t0.43\t0.49\t0.58\t0.66\t0.975\t1.42\t1.49\t2.09\t3.22\n"
- + "1\tOD600\t0.05\t0.064\t0.077\t0.089\t0.107\t0.127\t0.155\t0.176\t0.24\t0.33\t0.43\t0.49\t0.58\t0.66\t0.975\t1.42\t1.49\t2.09\t3.22",
- content);
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600ValidatorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600ValidatorTest.java
deleted file mode 100644
index 3d168a7159a..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600ValidatorTest.java
+++ /dev/null
@@ -1,72 +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 eu.basynthec.cisd.dss.growthprofiles;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class OD600ValidatorTest extends AssertJUnit
-{
- private static final String[] VALIDATION_SCRIPT_PATH = new String[]
- { "dist/etc/shared/shared-classes.py", "dist/etc/growth-profiles/data-set-validator.py" };
-
- @Test
- public void testGoodData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/OD600-Example.xlsx"));
- assertTrue("The example should have no errors", errors.isEmpty());
- }
-
- @Test
- public void testBadData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/OD600-BadData.xlsx"));
- assertEquals("The bad data should have two errors", 2, errors.size());
- assertEquals(
- "Line 2, column 1 must be either JJS-MGP[0-999], JJS-DIN[0-999], MS, CHASSIS [1-3], or WT 168 TRP+ (instead of OD600).",
- errors.get(0).getErrorMessage());
- assertEquals(
- "Line 3, column 1 must be either JJS-MGP[0-999], JJS-DIN[0-999], MS, CHASSIS [1-3], or WT 168 TRP+ (instead of JJS-MGP1000).",
- errors.get(1).getErrorMessage());
- }
-
- @Test
- public void testTemplate()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/OD600-Template.xlsx"));
- assertEquals("The template should have five errors", 4, errors.size());
- }
-
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java
deleted file mode 100644
index f864068bc51..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.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 eu.basynthec.cisd.dss.metabolomics;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class MetabolomicsDataSetRegistrator2Test extends AbstractBaSynthecDataSetRegistratorTest
-{
- private static final DataSetType METABOLITE_INTENSITIES = new DataSetType(
- "METABOLITE_INTENSITIES");
-
- @Test
- public void testSimpleTransaction() throws IOException
- {
- setUpHomeDataBaseExpectations();
- Properties properties = createThreadProperties();
- createHandler(properties, false, true);
- createData("Metabolomics-Example.xlsx");
-
- final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
- setUpDataSetRegistrationExpectations(METABOLITE_INTENSITIES,
- TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE, false);
-
- handler.handle(markerFile);
-
- assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
-
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(1), "METABOLITE_INTENSITIES");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(2), "METABOLITE_INTENSITIES");
-
- NewExternalData dataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
-
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(METABOLITE_INTENSITIES, dataSet.getDataSetType());
-
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty strainProperty = propertyMap.get(STRAIN_NAMES_PROP);
-
- assertNotNull(strainProperty);
- assertEquals("CHASSIS 1,JJS-MGP192", strainProperty.getValue());
-
- NewProperty valueUnitProperty = propertyMap.get(VALUE_UNIT_PROP);
- assertNotNull(valueUnitProperty);
- assertEquals("MM", valueUnitProperty.getValue());
-
- context.assertIsSatisfied();
- }
-
- @Override
- protected String getRegistrationScriptsFolderPath()
- {
- return "dist/etc/metabolomics2/";
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
deleted file mode 100644
index b6eb0eeaee6..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.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 eu.basynthec.cisd.dss.metabolomics;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class MetabolomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRegistratorTest
-{
- private static final DataSetType METABOLITE_INTENSITIES = new DataSetType("METABOLITE_INTENSITIES");
-
- @Test
- public void testSimpleTransaction() throws IOException
- {
- setUpHomeDataBaseExpectations();
- Properties properties = createThreadProperties();
- createHandler(properties, false, true);
- createData("Metabolomics1-Example.xlsx");
-
- final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
- setUpDataSetRegistrationExpectations(METABOLITE_INTENSITIES, TSV_DATA_SET_TYPE);
-
- handler.handle(markerFile);
-
- assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
-
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(1), "METABOLITE_INTENSITIES");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(2), "METABOLITE_INTENSITIES");
-
- NewExternalData dataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
-
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(METABOLITE_INTENSITIES, dataSet.getDataSetType());
-
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty strainProperty = propertyMap.get(STRAIN_NAMES_PROP);
-
- assertNotNull(strainProperty);
- assert null != strainProperty;
- assertEquals("CHASSIS 1", strainProperty.getValue());
- context.assertIsSatisfied();
- }
-
- @Override
- protected String getRegistrationScriptsFolderPath()
- {
- return "dist/etc/metabolomics/";
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java
deleted file mode 100644
index 98a4fcbc80e..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.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 eu.basynthec.cisd.dss.metabolomics;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class MetabolomicsValidator2Test extends AssertJUnit
-{
- private static final String[] VALIDATION_SCRIPT_PATH = new String[]
- { "dist/etc/shared/shared-classes.py", "dist/etc/metabolomics2/data-set-validator.py" };
-
- @Test
- public void testGoodData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics-Example.xlsx"));
- assertTrue("The example should have no errors", errors.isEmpty());
- }
-
- @Test
- public void testTemplate()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics-Template.xlsx"));
- assertEquals("The template should have four errors", 4, errors.size());
- }
-
- @Test
- public void testBadData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics-BadData.xlsx"));
- assertEquals("The bad data should have thirteen errors", 13, errors.size());
- }
-
- @Test
- public void testGarbageData()
- {
- // Test the data that is completely unusable
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner
- .validate(new File("sourceTest/examples/Metabolomics-GarbageData.xlsx"));
- assertEquals("The garbage data should have eight errors", 8, errors.size());
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidatorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidatorTest.java
deleted file mode 100644
index 8145f3f0c51..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidatorTest.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 eu.basynthec.cisd.dss.metabolomics;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class MetabolomicsValidatorTest extends AssertJUnit
-{
- private static final String[] VALIDATION_SCRIPT_PATH = new String[]
- { "dist/etc/shared/shared-classes.py", "dist/etc/metabolomics/data-set-validator.py" };
-
- @Test
- public void testGoodData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics1-Example.xlsx"));
- assertTrue("The example should have no errors", errors.isEmpty());
- }
-
- @Test
- public void testTemplate()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics1-Template.xlsx"));
- assertEquals("The template should have six errors", 6, errors.size());
- }
-
- @Test
- public void testBadData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Metabolomics1-BadData.xlsx"));
- assertEquals("The bad data should have 8 errors", 8, errors.size());
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
deleted file mode 100644
index 70cdb7f09df..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.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 eu.basynthec.cisd.dss.proteomics;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class ProteomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRegistratorTest
-{
-
- private static final DataSetType PROTEIN_QUANTIFICATIONS = new DataSetType(
- "PROTEIN_QUANTIFICATIONS");
-
- @Test
- public void testSimpleTransaction() throws IOException
- {
- setUpHomeDataBaseExpectations();
- Properties properties = createThreadProperties();
- createHandler(properties, false, true);
- createData("Proteomics-Example.xlsx");
-
- final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
- setUpDataSetRegistrationExpectations(PROTEIN_QUANTIFICATIONS, TSV_DATA_SET_TYPE);
-
- handler.handle(markerFile);
-
- assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
-
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(1), "PROTEIN_QUANTIFICATIONS");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(2), "PROTEIN_QUANTIFICATIONS");
-
- NewExternalData dataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
-
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(PROTEIN_QUANTIFICATIONS, dataSet.getDataSetType());
-
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty strainProperty = propertyMap.get(STRAIN_NAMES_PROP);
-
- assertNotNull(strainProperty);
- assert null != strainProperty;
- assertEquals("JJS-MGP90", strainProperty.getValue());
- context.assertIsSatisfied();
- }
-
- @Override
- protected String getRegistrationScriptsFolderPath()
- {
- return "dist/etc/proteomics/";
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsValidatorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsValidatorTest.java
deleted file mode 100644
index d2dd9da712d..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsValidatorTest.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 eu.basynthec.cisd.dss.proteomics;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class ProteomicsValidatorTest extends AssertJUnit
-{
- private static final String[] VALIDATION_SCRIPT_PATH = new String[]
- { "dist/etc/shared/shared-classes.py", "dist/etc/proteomics/data-set-validator.py" };
-
- @Test
- public void testGoodData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Proteomics-Example.xlsx"));
- assertTrue("The example should have no errors", errors.isEmpty());
- }
-
- @Test
- public void testTemplate()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Proteomics-Template.xlsx"));
- assertEquals("The template should have five errors", 5, errors.size());
- }
-
- @Test
- public void testBadHeader()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Proteomics-BadHeader.xlsx"));
- assertEquals("The bad data should have four errors", 4, errors.size());
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
deleted file mode 100644
index a2c6e4d8b6f..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
+++ /dev/null
@@ -1,140 +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 eu.basynthec.cisd.dss.transcriptomics;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Properties;
-
-import org.apache.commons.io.FileUtils;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRegistratorTest
-{
- private static final DataSetType TRANSCRIPTOMICS = new DataSetType("TRANSCRIPTOMICS");
-
- @Test
- public void testSimpleTransaction() throws IOException
- {
- setUpHomeDataBaseExpectations();
- Properties properties = createThreadProperties();
- createHandler(properties, false, true);
- createData("Transcriptomics-Example.xlsx");
-
- final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
- setUpDataSetRegistrationExpectations(TRANSCRIPTOMICS,
- TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE);
-
- handler.handle(markerFile);
-
- assertEquals(4, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
-
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(1), "TRANSCRIPTOMICS");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(2), "TRANSCRIPTOMICS");
- checkDataTypeProperty(atomicOperationDetails.recordedObject().getDataSetRegistrations()
- .get(3), "TRANSCRIPTOMICS");
-
- NewExternalData dataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
-
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(TRANSCRIPTOMICS, dataSet.getDataSetType());
-
- HashMap<String, NewProperty> propertyMap =
- getDataSetPropertiesMap(dataSet.getDataSetProperties());
- NewProperty strainProperty = propertyMap.get(STRAIN_NAMES_PROP);
-
- assertNotNull(strainProperty);
- assert null != strainProperty;
- assertEquals("JJS-MGP253,JJS-MGP776", strainProperty.getValue());
-
- NewExternalData tsvDataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(2);
- String location = tsvDataSet.getLocation() + "/tsv-multi/";
- File tsvFile =
- new File(new File(workingDirectory, "/1/" + location),
- "Transcriptomics-Example.xlsx.tsv");
- checkTsvContent(tsvFile);
-
- NewExternalData tsvSplitDataSet =
- atomicOperationDetails.recordedObject().getDataSetRegistrations().get(3);
- location = tsvSplitDataSet.getLocation() + "/tsv/";
- File tsvSplitFolder = new File(workingDirectory, "/1/" + location);
- String[] contents = tsvSplitFolder.list();
- Arrays.sort(contents);
- String[] expectedContents =
- { "Transcriptomics-Example.xlsx_JJS-MGP253.tsv",
- "Transcriptomics-Example.xlsx_JJS-MGP776.tsv" };
- assertEquals(Arrays.asList(expectedContents), Arrays.asList(contents));
- File tsvSplitFile = new File(tsvSplitFolder, "Transcriptomics-Example.xlsx_JJS-MGP253.tsv");
- checkSplitTsvContent(tsvSplitFile);
- context.assertIsSatisfied();
- }
-
- @Override
- protected String getRegistrationScriptsFolderPath()
- {
- return "dist/etc/transcriptomics/";
- }
-
- private void checkTsvContent(File tsvFile) throws IOException
- {
- String content = FileUtils.readFileToString(tsvFile);
- assertEquals("Locustag\tJJS-MGP253-1 66687802\tJJS-MGP776-2 66730002\n"
- + "BSU00010\t13.7953\t13.5517\n" + "BSU00020\t13.5907\t13.3277\n"
- + "BSU00030\t13.8489\t13.6306\n" + "BSU00040\t14.3564\t14.1073\n"
- + "BSU00050\t14.5239\t14.1992\n" + "BSU00060\t14.3293\t13.933\n"
- + "BSU00070\t14.481\t14.1348\n" + "BSU00090\t15.474\t15.2813\n"
- + "BSU00100\t14.4332\t14.1945\n" + "BSU00110\t15.2669\t14.9582\n"
- + "BSU00120\t15.3344\t15.112\n" + "BSU_misc_RNA_1\t15.4497\t15.2485\n"
- + "BSU00130\t13.6604\t13.5385\n" + "BSU00180\t9.8208\t9.971\n"
- + "BSU_misc_RNA_2\t13.6614\t14.0933\n" + "BSU00190\t13.464\t13.1213\n"
- + "BSU00200\t14.6102\t14.4169\n" + "BSU00210\t13.5285\t13.2043\n"
- + "BSU00220\t13.1007\t12.8862\n" + "BSU00230\t11.8547\t11.6761\n"
- + "BSU00240\t10.8623\t11.1397\n" + "BSU00250\t11.6694\t11.429\n"
- + "BSU00260\t11.7669\t11.4658\n" + "BSU00270\t12.2675\t11.8745\n"
- + "BSU00280\t12.5574\t12.1608\n", content);
- }
-
- private void checkSplitTsvContent(File tsvFile) throws IOException
- {
- String content = FileUtils.readFileToString(tsvFile);
- assertEquals("Locustag\t1 66687802\n" + "BSU00010\t13.7953\n" + "BSU00020\t13.5907\n"
- + "BSU00030\t13.8489\n" + "BSU00040\t14.3564\n" + "BSU00050\t14.5239\n"
- + "BSU00060\t14.3293\n" + "BSU00070\t14.481\n" + "BSU00090\t15.474\n"
- + "BSU00100\t14.4332\n" + "BSU00110\t15.2669\n" + "BSU00120\t15.3344\n"
- + "BSU_misc_RNA_1\t15.4497\n" + "BSU00130\t13.6604\n" + "BSU00180\t9.8208\n"
- + "BSU_misc_RNA_2\t13.6614\n" + "BSU00190\t13.464\n" + "BSU00200\t14.6102\n"
- + "BSU00210\t13.5285\n" + "BSU00220\t13.1007\n" + "BSU00230\t11.8547\n"
- + "BSU00240\t10.8623\n" + "BSU00250\t11.6694\n" + "BSU00260\t11.7669\n"
- + "BSU00270\t12.2675\n" + "BSU00280\t12.5574", content);
- }
-}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsValidatorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsValidatorTest.java
deleted file mode 100644
index ad7e40bdb62..00000000000
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsValidatorTest.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 eu.basynthec.cisd.dss.transcriptomics;
-
-import java.io.File;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class TranscriptomicsValidatorTest extends AssertJUnit
-{
- private static final String[] VALIDATION_SCRIPT_PATH = new String[]
- { "dist/etc/shared/shared-classes.py", "dist/etc/transcriptomics/data-set-validator.py" };
-
- @Test
- public void testGoodData()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner.validate(new File("sourceTest/examples/Transcriptomics-Example.xlsx"));
- assertTrue("The example should have no errors", errors.isEmpty());
- }
-
- @Test
- public void testTemplate()
- {
- ValidationScriptRunner scriptRunner =
- ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
- List<ValidationError> errors =
- scriptRunner
- .validate(new File("sourceTest/examples/Transcriptomics-Template.xlsx"));
- assertEquals("The template should have seven errors", 7, errors.size());
- }
-}
diff --git a/eu_basynthec/sourceTest/java/tests.xml b/eu_basynthec/sourceTest/java/tests.xml
deleted file mode 100644
index 082bf00ea75..00000000000
--- a/eu_basynthec/sourceTest/java/tests.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<!DOCTYPE suite SYSTEM "http://beust.com/testng/testng-1.0.dtd" >
-
-<suite name="All" verbose="1">
- <test name="All">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="eu.basynthec.cisd.dss.*" />
- </packages>
- </test>
-</suite>
diff --git a/eu_basysbio/.classpath b/eu_basysbio/.classpath
deleted file mode 100644
index a93a8e7b26d..00000000000
--- a/eu_basysbio/.classpath
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry combineaccessrules="false" kind="src" path="/common"/>
- <classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
- <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
- <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
- <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
- <classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
- <classpathentry kind="lib" path="/libraries/restrictionchecker/restrictionchecker.jar"/>
- <classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
- <classpathentry kind="lib" path="/libraries/gwt2.4/gwt-user.jar"/>
- <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
- <classpathentry kind="output" path="targets/classes"/>
-</classpath>
diff --git a/eu_basysbio/.gitignore b/eu_basysbio/.gitignore
deleted file mode 100644
index df207ad5192..00000000000
--- a/eu_basysbio/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-/.settings
-/targets
-/test-output
-/.shredder
-/.updater
-/.idea/
-*.iml
-*.eml
\ No newline at end of file
diff --git a/eu_basysbio/.project b/eu_basysbio/.project
deleted file mode 100644
index 21bb9696867..00000000000
--- a/eu_basysbio/.project
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu_basysbio</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
- <filteredResources>
- <filter>
- <id>1332321366607</id>
- <name></name>
- <type>26</type>
- <matcher>
- <id>org.eclipse.ui.ide.multiFilter</id>
- <arguments>1.0-name-matches-true-false-.git</arguments>
- </matcher>
- </filter>
- </filteredResources>
-</projectDescription>
diff --git a/eu_basysbio/build/antrun.sh b/eu_basysbio/build/antrun.sh
deleted file mode 100755
index 5ff1a62b259..00000000000
--- a/eu_basysbio/build/antrun.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#! /bin/bash
-
-ME="$0"
-MYDIR=${ME%/*}
-cd $MYDIR
-ant -lib ../../build_resources/lib/ecj.jar "$@"
diff --git a/eu_basysbio/build/build.xml b/eu_basysbio/build/build.xml
deleted file mode 100644
index 74f119627e5..00000000000
--- a/eu_basysbio/build/build.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<project name="eu_basysbio" default="ci" basedir="..">
- <import file="../../datastore_server/build/build.xml" />
- <import file="../../openbis/build/build.xml" />
- <project-classpath name="ecp" classes="${classes}" />
-
- <property name="variant" value="-basysbio" />
- <property name="original.dist" value="dist" />
- <property name="mainfolder" value="eu_basysbio" />
-
- <target name="compile" depends="build-common.compile, clean" />
-
- <target name="run-tests">
- <antcall target="build-common.run-tests">
- <param name="test.suite" value="tests.xml" />
- </antcall>
- </target>
-
- <target name="jar" depends="compile">
- <mkdir dir="${dist}" />
- <build-info revision="revision.number" version="version.number" clean="clean.flag" />
- <echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
- <jar destfile="${plugin-jar.file}">
- <fileset dir="${classes}">
- <include name="eu/**/*.class" />
- <include name="${build.info.filename}" />
- </fileset>
- <fileset dir="source">
- <include name="**/*.sql" />
- </fileset>
- <manifest>
- <attribute name="Version" value="${version.number}" />
- <attribute name="Build-Number"
- value="${version.number} (r${revision.number},${clean.flag})" />
- </manifest>
- </jar>
- </target>
- <!--
- // Task for creating distributions
- -->
- <target name="dist" depends="jar, datastore_server.make-plugin-dist" />
-
- <!--
- // Task for continuous integration server.
- -->
- <target name="ci" depends="build-common.ci, dist, check-dependencies" />
-
-</project>
\ No newline at end of file
diff --git a/eu_basysbio/dist/etc/log.xml b/eu_basysbio/dist/etc/log.xml
deleted file mode 100644
index f9104bc9f0a..00000000000
--- a/eu_basysbio/dist/etc/log.xml
+++ /dev/null
@@ -1,56 +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="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender">
-
- <param name="File" value="log/datastore_server_log.txt"/>
- <param name="DatePattern" value="'.'yyyy-MM-dd"/>
-
- <layout class="org.apache.log4j.PatternLayout">
- <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
- </layout>
-
- </appender>
-
- <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" />
-
- <appender name="EMAIL" class="org.apache.log4j.net.SMTPAppender">
-
- <param name="BufferSize" value="512" />
- <param name="SMTPHost" value="localhost" />
- <param name="From" value="datastore_server@localhost" />
- <param name="To" value="root@localhost" />
- <param name="Subject" value="ATTENTION: etl server" />
- <param name="EvaluatorClass" value="ch.systemsx.cisd.common.logging.AlwaysTrueTriggeringEventEvaluator" />
-
- <layout class="org.apache.log4j.PatternLayout">
- <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
- </layout>
-
- <!--filter class="org.apache.log4j.varia.LevelRangeFilter">
- <param name="LevelMin" value="ERROR"/>
- <param name="LevelMax" value="FATAL"/>
- </filter-->
-
- </appender>
-
- <category name="NOTIFY">
- <priority value="info" />
- <appender-ref ref="DEFAULT" />
- <appender-ref ref="EMAIL" />
- </category>
-
- <root>
- <priority value="info" />
- <appender-ref ref="DEFAULT" />
- </root>
-
-</log4j:configuration>
diff --git a/eu_basysbio/dist/etc/service.properties b/eu_basysbio/dist/etc/service.properties
deleted file mode 100644
index c45e0f0c06c..00000000000
--- a/eu_basysbio/dist/etc/service.properties
+++ /dev/null
@@ -1,205 +0,0 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS1
-
-# The root directory of the data store
-storeroot-dir = data/store
-
-# The directory where the command queue file is located; defaults to storeroot-dir
-commandqueue-dir =
-
-# Port
-port = 8444
-
-# Session timeout in minutes
-session-timeout = 720
-
-# Path to the keystore
-keystore.path = 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 = 60
-
-# 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
-
-# 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
-
-# The URL of the openBIS server
-server-url = https://localhost:8443/openbis/openbis
-
-# 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 = https://localhost:8444
-
-# SMTP properties (must start with 'mail' to be considered).
-# mail.smtp.host = localhost
-# mail.from = datastore_server@localhost
-# If this property is set a test e-mail will be sent to the specified address after DSS successfully started-up.
-# mail.test.address = test@localhost
-
-# ---------------- Database parameters
-
-basysbio-databaseEngineCode = postgresql
-basysbio-basicDatabaseName = basysbio
-basysbio-databaseKind = productive
-basysbio-readOnlyGroup = basysbio_readonly
-basysbio-readWriteGroup = basysbio_readwrite
-basysbio-scriptFolder = sql
-
-# ---------------- 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
-
-
-maintenance-plugins = post-registration-upload
-
-post-registration-upload.class = eu.basysbio.cisd.dss.PostRegistrationDatabaseUploadTask
-post-registration-upload.interval = 1440000
-post-registration-upload.database.databaseEngineCode = ${basysbio-databaseEngineCode}
-post-registration-upload.database.basicDatabaseName = ${basysbio-basicDatabaseName}
-post-registration-upload.database.databaseKind = ${basysbio-databaseKind}
-post-registration-upload.database.readOnlyGroup = ${basysbio-readOnlyGroup}
-post-registration-upload.database.readWriteGroup = ${basysbio-readWriteGroup}
-post-registration-upload.database.scriptFolder = ${basysbio-scriptFolder}
-
-
-# Data Set Validators
-data-set-validators = time-series-validator
-
-time-point-data-set-types = AgilentRNA2color, NimbleGenRNA1colorBsubT1, \
- NimbleGenRNA1colorBsubT1MedianNorm, NimbleGenRNA1colorBsubT1QQnorm, MetaboliteLCMS, \
- PhysRFR, PhysOD, LcaMicCFD
-
-time-series-validator.data-set-type = TIME_SERIES
-time-series-validator.path-patterns = *
-time-series-validator.exclude-path-patterns = request.properties
-time-series-validator.columns = id, human-readable, controlled-gene, data-column
-time-series-validator.id.header-pattern = CompoundID|GeneLocus|Abs
-time-series-validator.id.mandatory = true
-time-series-validator.id.order = 1
-time-series-validator.id.value-validator = ch.systemsx.cisd.etlserver.validation.HeaderBasedValueValidatorFactory
-time-series-validator.id.header-types = compound, gene-locus, abs
-time-series-validator.id.compound.header-pattern = CompoundID
-time-series-validator.id.compound.value-type = unique
-time-series-validator.id.compound.value-pattern = BSBME:[0-9]+(BSBME:[0-9])*|CHEBI:[0-9]+(_CHEBI:[0-9]+)*
-time-series-validator.id.gene-locus.header-pattern = GeneLocus
-time-series-validator.id.gene-locus.value-type = unique
-time-series-validator.id.gene-locus.value-pattern = BSU[0-9]+|BSU_misc_RNA_[0-9]+|VMG_[0-9]+_[0-9]+|VMG_[0-9]+_[0-9]+_c
-time-series-validator.id.abs.header-pattern = Abs
-time-series-validator.id.abs.value-type = unique
-time-series-validator.id.abs.value-pattern = OD600
-time-series-validator.human-readable.header-pattern = HumanReadable
-time-series-validator.human-readable.order = 2
-time-series-validator.controlled-gene.header-pattern = ControlledGene
-time-series-validator.controlled-gene.order = 3
-time-series-validator.data-column.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-time-series-validator.data-column.header-validator.elements = experiment-code, cultivation-method, biological-replicate-code, \
- time-point, time-point-type, technical-replicate-code, cel-loc, data-set-type, value-type, scale, bi-id, cg
-time-series-validator.data-column.header-validator.experiment-code.type = vocabulary
-time-series-validator.data-column.header-validator.experiment-code.terms = Ma, GI, GM, MG
-time-series-validator.data-column.header-validator.cultivation-method.type = vocabulary
-time-series-validator.data-column.header-validator.cultivation-method.terms = BR, SF, MW, MS
-time-series-validator.data-column.header-validator.biological-replicate-code.type = string
-time-series-validator.data-column.header-validator.biological-replicate-code.pattern = B[0-9]+(_B[0-9]+)*
-time-series-validator.data-column.header-validator.time-point.type = integer
-time-series-validator.data-column.header-validator.time-point-type.type = vocabulary
-time-series-validator.data-column.header-validator.time-point-type.terms = EX, IN, SI
-time-series-validator.data-column.header-validator.technical-replicate-code.type = string
-time-series-validator.data-column.header-validator.technical-replicate-code.pattern = T[0-9]+(_T[0-9]+)*
-time-series-validator.data-column.header-validator.cel-loc.type = vocabulary
-time-series-validator.data-column.header-validator.cel-loc.terms = CE, ES, ME, CY, NC
-time-series-validator.data-column.header-validator.data-set-type.type = vocabulary
-time-series-validator.data-column.header-validator.data-set-type.terms = ${time-point-data-set-types}
-time-series-validator.data-column.header-validator.value-type.type = string
-time-series-validator.data-column.header-validator.value-type.pattern = (Value|Mean|Median|Std|Var|Error|Iqr)\\[(mM|Ratio1|RatioCs)\\]
-time-series-validator.data-column.header-validator.scale.type = vocabulary
-time-series-validator.data-column.header-validator.scale.terms = LIN, Log2, Log10, Ln
-time-series-validator.data-column.header-validator.bi-id.type = string
-time-series-validator.data-column.header-validator.bi-id.pattern = NB|BBA[0-9]*
-time-series-validator.data-column.header-validator.cg.type = string
-time-series-validator.data-column.header-validator.cg.pattern = NC|BSU[0-9]+_[0-9]
-time-series-validator.data-column.can-define-multiple-columns = true
-time-series-validator.data-column.value-type = numeric
-
-
-# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
-# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs = main-thread
-
-# ---------------------------------------------------------------------------
-# main thread configuration
-# ---------------------------------------------------------------------------
-# The directory to watch for incoming data.
-main-thread.incoming-dir = ${data-folder}/incoming
-main-thread.incoming-data-completeness-condition = auto-detection
-main-thread.delete-unidentified = true
-main-thread.data-set-info-extractor = eu.basysbio.cisd.dss.TimeSeriesDataSetInfoExtractor
-main-thread.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
-main-thread.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
-main-thread.storage-processor.keep-file-regex = .*(?<!request\.properties)$
-main-thread.storage-processor.processor = eu.basysbio.cisd.dss.StorageProcessor
-main-thread.storage-processor.processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.storage-processor.processor.time-point-data-set-drop-box-path = ${data-folder}/incoming-time-point
-main-thread.storage-processor.processor.data-set-properties-file-name = data-set.properties
-main-thread.storage-processor.processor.translation.data-set-types = ${time-point-data-set-types}
-main-thread.storage-processor.processor.translation.time-point-data-set-file-name-separator = .
-main-thread.storage-processor.processor.translation.AgilentRNA2color = AGILENT_RNA_2_COLOR
-main-thread.storage-processor.processor.translation.NimbleGenRNA1colorBsubT1 = NIMBLE_GEN_RNA1_COLOR_BSUB_T1
-main-thread.storage-processor.processor.translation.NimbleGenRNA1colorBsubT1MedianNorm = NIMBLE_GEN_RNA1_COLOR_BSUB_T1_MEDIAN_NORM
-main-thread.storage-processor.processor.translation.NimbleGenRNA1colorBsubT1QQnorm = NIMBLE_GEN_RNA1_COLOR_BSUB_T1_QQ_NORM
-main-thread.storage-processor.processor.translation.MetaboliteLCMS = METABOLITE_LCMS
-main-thread.storage-processor.processor.database.databaseEngineCode = ${basysbio-databaseEngineCode}
-main-thread.storage-processor.processor.database.basicDatabaseName = ${basysbio-basicDatabaseName}
-main-thread.storage-processor.processor.database.databaseKind = ${basysbio-databaseKind}
-main-thread.storage-processor.processor.database.readOnlyGroup = ${basysbio-readOnlyGroup}
-main-thread.storage-processor.processor.database.readWriteGroup = ${basysbio-readWriteGroup}
-main-thread.storage-processor.processor.database.scriptFolder = ${basysbio-scriptFolder}
-
-main-thread.dataset-handler = eu.basysbio.cisd.dss.TimeSeriesAndTimePointDataSetHandler
-main-thread.dataset-handler.time-point.incoming-dir = ${data-folder}/incoming-time-point
-main-thread.dataset-handler.time-point.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
-main-thread.dataset-handler.time-point.data-set-info-extractor.strip-file-extension = true
-main-thread.dataset-handler.time-point.data-set-info-extractor.entity-separator = ${main-thread.storage-processor.processor.translation.time-point-data-set-file-name-separator}
-main-thread.dataset-handler.time-point.data-set-info-extractor.index-of-sample-code = 0
-main-thread.dataset-handler.time-point.data-set-info-extractor.group-code = TEST
-main-thread.dataset-handler.time-point.data-set-info-extractor.data-set-properties-file-name = data-set.properties
-main-thread.dataset-handler.time-point.type-extractor = eu.basysbio.cisd.dss.TypeExtractor
-main-thread.dataset-handler.time-point.type-extractor.file-format-type = PROPRIETARY
-main-thread.dataset-handler.time-point.type-extractor.locator-type = RELATIVE_LOCATION
-main-thread.dataset-handler.time-point.type-extractor.is-measured = true
-main-thread.dataset-handler.time-point.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
diff --git a/eu_basysbio/etc/log.xml b/eu_basysbio/etc/log.xml
deleted file mode 100644
index 5cee0a68436..00000000000
--- a/eu_basysbio/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/eu_basysbio/etc/service.properties b/eu_basysbio/etc/service.properties
deleted file mode 100644
index 2ae72702576..00000000000
--- a/eu_basysbio/etc/service.properties
+++ /dev/null
@@ -1,487 +0,0 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
-data-store-server-code = DSS2
-
-data-folder = targets/playground/data
-
-# The root directory of the data store
-storeroot-dir = ${data-folder}/store
-
-# The directory where the command queue file is located; defaults to storeroot-dir
-commandqueue-dir =
-
-# Port
-port = 8890
-
-use-ssl = false
-
-# Session timeout in minutes
-session-timeout = 720
-
-# Path to the keystore
-keystore.path = ../datastore_server/dist/etc/openBIS.keystore
-
-# Password of the keystore
-keystore.password = changeit
-
-# Key password of the keystore
-keystore.key-password = changeit
-
-# The check interval (in seconds)
-check-interval = 5
-
-# The time-out for clean up work in the shutdown sequence (in seconds).
-# Note that that the maximal time for the shutdown sequence to complete can be as large
-# as twice this time.
-# Remark: On a network file system, it is not recommended to turn this value to something
-# lower than 180.
-shutdown-timeout = 2
-
-# If free disk space goes below value defined here, a notification email will be sent.
-# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
-# specified or if value is negative, the system will not be watching.
-highwater-mark = -1
-
-# If a data set is successfully registered it sends out an email to the registrator.
-# If this property is not specified, no email is sent to the registrator. This property
-# does not affect the mails which are sent, when the data set could not be registered.
-notify-successful-registration = false
-
-# The URL of the openBIS server
-server-url = http://localhost:8888/openbis
-
-# The username to use when contacting the openBIS server
-username = etlserver
-
-# The password to use when contacting the openBIS server
-password = etlserver
-
-# The base URL for Web client access.
-download-url = http://localhost:${port}
-use-ssl = false
-
-# SMTP properties (must start with 'mail' to be considered).
-mail.smtp.host = file://targets/email
-mail.from = datastore_server@localhost
-# If this property is set a test e-mail will be sent to the specified address after DSS successfully started-up.
-mail.test.address = test@localhost
-
-# ---------------- Database parameters
-
-basysbio-databaseEngineCode = postgresql
-basysbio-basicDatabaseName = basysbio
-basysbio-databaseKind = dev
-basysbio-readOnlyGroup = basysbio_readonly
-basysbio-readWriteGroup = basysbio_readwrite
-basysbio-scriptFolder = source/sql
-
-# Define names of data sources
-data-sources = data-source
-data-source.databaseEngineCode = postgresql
-data-source.basicDatabaseName = basysbio
-data-source.databaseKind = dev
-
-
-# ---------------- 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
-
-# -----------------------------------------------------------------------------
-# Maintenance Plugins
-#
-
-maintenance-plugins = data-set-clean-up, post-registration-upload
-
-data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-data-set-clean-up.interval = 300
-data-set-clean-up.data-source = data-source
-
-post-registration-upload.class = eu.basysbio.cisd.dss.PostRegistrationDatabaseUploadTask
-post-registration-upload.execute-only-once = true
-post-registration-upload.database.databaseEngineCode = ${basysbio-databaseEngineCode}
-post-registration-upload.database.basicDatabaseName = ${basysbio-basicDatabaseName}
-post-registration-upload.database.databaseKind = ${basysbio-databaseKind}
-post-registration-upload.database.readOnlyGroup = ${basysbio-readOnlyGroup}
-post-registration-upload.database.readWriteGroup = ${basysbio-readWriteGroup}
-post-registration-upload.database.scriptFolder = ${basysbio-scriptFolder}
-
-# -----------------------------------------------------------------------------
-# Reporting Plugins
-#
-reporting-plugins = time-series-reporter, tsv-viewer, trans-tsv-viewer, demo
-
-time-series-reporter.label = Header Properties
-time-series-reporter.dataset-types = CHIP_CHIP, TIME_SERIES, LCA_MTP_TIME_SERIES
-time-series-reporter.class = eu.basysbio.cisd.dss.TimeSeriesPropertiesReportingPlugin
-time-series-reporter.properties-file =
-
-tsv-viewer.label = TSV View
-tsv-viewer.dataset-types = CHIP_CHIP, TIME_SERIES, LCA_MTP_TIME_SERIES
-tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
-tsv-viewer.properties-file =
-
-trans-tsv-viewer.label = Transposed TSV View
-trans-tsv-viewer.dataset-types = TIME_SERIES, LCA_MTP_TIME_SERIES
-trans-tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
-trans-tsv-viewer.properties-file =
-trans-tsv-viewer.transpose = true
-
-demo.label = Demo
-demo.dataset-types = CHIP_CHIP
-demo.class ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin
-
-# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
-# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs = main-thread
-
-main-thread.incoming-dir = ${data-folder}/incoming
-main-thread.incoming-data-completeness-condition = auto-detection
-main-thread.delete-unidentified = true
-main-thread.data-set-info-extractor = eu.basysbio.cisd.dss.DataSetInfoExtractor
-main-thread.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
-main-thread.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
-main-thread.storage-processor.keep-file-regex = .*(?<!request\.properties)$
-main-thread.storage-processor.processor = eu.basysbio.cisd.dss.StorageProcessor
-main-thread.storage-processor.processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.storage-processor.processor.data-set-type-pattern-for-default-handling = .*_TIME_SERIES|CHIP_CHIP
-main-thread.storage-processor.processor.data-set-properties-file-name = data-set.properties
-main-thread.storage-processor.processor.database.databaseEngineCode = ${basysbio-databaseEngineCode}
-main-thread.storage-processor.processor.database.basicDatabaseName = ${basysbio-basicDatabaseName}
-main-thread.storage-processor.processor.database.databaseKind = ${basysbio-databaseKind}
-main-thread.storage-processor.processor.database.readOnlyGroup = ${basysbio-readOnlyGroup}
-main-thread.storage-processor.processor.database.readWriteGroup = ${basysbio-readWriteGroup}
-main-thread.storage-processor.processor.database.scriptFolder = ${basysbio-scriptFolder}
-
-main-thread.dataset-handler = eu.basysbio.cisd.dss.TimeSeriesAndTimePointDataSetHandler
-main-thread.dataset-handler.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-
-#####################################################################################################
-# Data Set Validators
-
-data-set-validators = ChIP-chip-validator, \
- metabolite-lcms-abs-validator, \
- metabolite-lcms-rel-validator, \
- phys-rfr-validator, \
- tf-activity-validator, \
- quantified-peptides-validator, \
- protein-lcms-ratio-validator, \
- protein-2de-combined-lcms-validator, \
- nimblegen-rna-1-color-bsubt1-validator, \
- nimblegen-rna-1-color-bsubt1-median-norm-validator, \
- nimblegen-rna-1-color-bsubt1-qq-norm-validator, \
- agilent-rna-2-color-validator, \
- absolute-protein-number-gfp-validator, \
- absolute-protein-concentration-aqua-2d-page-validator, \
- 2d-gel-spot-vol-validator, \
- phys-od600-validator, \
- lca-mtp-time-series-validator, \
- LCA-MTP-PCAV-time-series-validator, \
- LCA-MIC-time-series-validator
-
-####### ChIP-chip Validator #########################################################################
-
-ChIP-chip-validator.data-set-type = CHIP_CHIP
-ChIP-chip-validator.path-patterns = *
-ChIP-chip-validator.exclude-path-patterns = request.properties
-ChIP-chip-validator.columns = transcription-factor, gene-name, gene-function, array-design, \
- microarray-id, chip-peak-position, chip-local-height, chip-score, intergenic, \
- nearby-gene, bsu-number, distance-from-start
-ChIP-chip-validator.transcription-factor.header-pattern = TfBSU
-ChIP-chip-validator.transcription-factor.order = 1
-ChIP-chip-validator.transcription-factor.value-type = string
-ChIP-chip-validator.transcription-factor.value-pattern = ${bsu-number-pattern}
-
-ChIP-chip-validator.gene-name.header-pattern = GeneName/HumanReadable
-ChIP-chip-validator.gene-name.order = 2
-ChIP-chip-validator.gene-name.value-type = any
-
-ChIP-chip-validator.gene-function.header-pattern = GeneFunction/HumanReadable
-ChIP-chip-validator.gene-function.order = 3
-ChIP-chip-validator.gene-function.value-type = any
-
-ChIP-chip-validator.array-design.header-pattern = ArrayDesign
-ChIP-chip-validator.array-design.order = 4
-ChIP-chip-validator.array-design.value-type = string
-ChIP-chip-validator.array-design.value-pattern = 070910_BaSysBio_expr|090325_CBS_DTU_Bsu_T2
-
-ChIP-chip-validator.microarray-id.header-pattern = MicroarrayID
-ChIP-chip-validator.microarray-id.order = 5
-ChIP-chip-validator.microarray-id.value-type = numeric
-ChIP-chip-validator.microarray-id.value-range = (0,Infinity)
-
-ChIP-chip-validator.chip-peak-position.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-ChIP-chip-validator.chip-peak-position.header-validator. = ChIP-chip-validator.data-column-header-validator.
-ChIP-chip-validator.chip-peak-position.header-validator.data-set-type.terms = ChipPeakPosition[GBAL009126v3]
-ChIP-chip-validator.chip-peak-position.order = 6
-ChIP-chip-validator.chip-peak-position.value-type = numeric
-ChIP-chip-validator.chip-peak-position.value-range = (0,Infinity)
-
-ChIP-chip-validator.chip-local-height.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-ChIP-chip-validator.chip-local-height.header-validator. = ChIP-chip-validator.data-column-header-validator.
-ChIP-chip-validator.chip-local-height.header-validator.data-set-type.terms = ChipLocalHeight
-ChIP-chip-validator.chip-local-height.order = 7
-ChIP-chip-validator.chip-local-height.value-type = numeric
-ChIP-chip-validator.chip-local-height.value-range = (0,Infinity)
-
-ChIP-chip-validator.chip-score.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-ChIP-chip-validator.chip-score.header-validator. = ChIP-chip-validator.data-column-header-validator.
-ChIP-chip-validator.chip-score.header-validator.data-set-type.terms = ChipScore
-ChIP-chip-validator.chip-score.order = 8
-ChIP-chip-validator.chip-score.value-type = numeric
-
-ChIP-chip-validator.data-column-header-validator. = default-data-colum-header-validator.
-ChIP-chip-validator.data-column-header-validator.elements = ${default-data-colum-header-validator.elements}, growth-phase, genotype
-ChIP-chip-validator.data-column-header-validator.experiment-code.terms = \
- LB, LB_Gl, LB_Ma, LB_Gl_Ma, M9, M9_Gl, M9_Ma, M9_Gl_Ma
-ChIP-chip-validator.data-column-header-validator.cultivation-method.terms = BR, SF
-ChIP-chip-validator.data-column-header-validator.time-point.type = string
-ChIP-chip-validator.data-column-header-validator.time-point.pattern = NT
-ChIP-chip-validator.data-column-header-validator.cel-loc.terms = CE
-ChIP-chip-validator.data-column-header-validator.data-set-type.terms =
-ChIP-chip-validator.data-column-header-validator.value-type.pattern = Value\\[\\]
-ChIP-chip-validator.data-column-header-validator.bi-id.pattern = NB
-ChIP-chip-validator.data-column-header-validator.cg.pattern = NC
-ChIP-chip-validator.data-column-header-validator.growth-phase.type = vocabulary
-ChIP-chip-validator.data-column-header-validator.growth-phase.terms = lat, exp, trans, stat
-ChIP-chip-validator.data-column-header-validator.genotype.type = string
-ChIP-chip-validator.data-column-header-validator.genotype.pattern = .*
-
-ChIP-chip-validator.intergenic.header-pattern = Intergenic\\[GBAL009126v3\\]
-ChIP-chip-validator.intergenic.order = 9
-ChIP-chip-validator.intergenic.value-type = string
-ChIP-chip-validator.intergenic.value-pattern = FALSE|TRUE
-
-ChIP-chip-validator.nearby-gene.header-pattern = NearbyGene\\[GBAL009126v3\\]
-ChIP-chip-validator.nearby-gene.order = 10
-ChIP-chip-validator.nearby-gene.value-type = any
-
-ChIP-chip-validator.bsu-number.header-pattern = BsuNumber\\[GBAL009126v3\\]
-ChIP-chip-validator.bsu-number.order = 11
-ChIP-chip-validator.bsu-number.value-type = string
-ChIP-chip-validator.bsu-number.value-pattern = NA|${bsu-number-pattern}(;${bsu-number-pattern})*
-
-ChIP-chip-validator.distance-from-start.header-pattern = DistanceFromStart\\[GBAL009126v3\\]
-ChIP-chip-validator.distance-from-start.order = 12
-ChIP-chip-validator.distance-from-start.value-type = string
-ChIP-chip-validator.distance-from-start.value-pattern = NA|(-?[0-9]+(;-?[0-9]+)*)
-
-####### LCA MIC Time Series Validator ###############################################################
-
-LCA-MIC-time-series-validator.data-set-type = LCA_MIC_TIME_SERIES
-LCA-MIC-time-series-validator.path-patterns = *
-LCA-MIC-time-series-validator.exclude-path-patterns = request.properties
-LCA-MIC-time-series-validator.columns = id, data-column
-LCA-MIC-time-series-validator.id.header-pattern = BBA ID
-LCA-MIC-time-series-validator.id.mandatory = true
-LCA-MIC-time-series-validator.id.order = 1
-LCA-MIC-time-series-validator.id.value-type = unique
-LCA-MIC-time-series-validator.id.value-pattern = BBA[0-9]{4}#[A,B,C]_S20[0-9]{2}[0,1][0-9][0,1,2,3][0-9]-[1-8]
-LCA-MIC-time-series-validator.data-column.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-LCA-MIC-time-series-validator.data-column.header-validator. = default-data-colum-header-validator.
-LCA-MIC-time-series-validator.data-column.header-validator.data-set-type.terms = LcaMicCfd, LcaMicAbsFl
-LCA-MIC-time-series-validator.data-column.header-validator.value-type.pattern = Value\\[um\\]|Mean\\[Au\\]|Std\\[Au\\]
-LCA-MIC-time-series-validator.data-column.header-validator.bi-id.pattern = NB
-LCA-MIC-time-series-validator.data-column.header-validator.cg.pattern = NC
-LCA-MIC-time-series-validator.data-column.can-define-multiple-columns = true
-LCA-MIC-time-series-validator.data-column.value-type = numeric
-
-####### LCA MTP PCAV Time Series Validator ##########################################################
-
-LCA-MTP-PCAV-time-series-validator.data-set-type = LCA_MTP_PCAV_TIME_SERIES
-LCA-MTP-PCAV-time-series-validator.path-patterns = *
-LCA-MTP-PCAV-time-series-validator.exclude-path-patterns = request.properties
-LCA-MTP-PCAV-time-series-validator.columns = id, no-of-replicates, confidence-level, data-column
-LCA-MTP-PCAV-time-series-validator.id.header-pattern = BSB_ID
-LCA-MTP-PCAV-time-series-validator.id.mandatory = true
-LCA-MTP-PCAV-time-series-validator.id.order = 1
-LCA-MTP-PCAV-time-series-validator.id.value-type = unique
-LCA-MTP-PCAV-time-series-validator.id.value-pattern = BBA[0-9]+
-LCA-MTP-PCAV-time-series-validator.no-of-replicates.header-pattern = no of replicates
-LCA-MTP-PCAV-time-series-validator.no-of-replicates.order = 2
-LCA-MTP-PCAV-time-series-validator.no-of-replicates.value-type = string
-LCA-MTP-PCAV-time-series-validator.no-of-replicates.value-pattern = [0-9]+
-LCA-MTP-PCAV-time-series-validator.confidence-level.header-pattern = confidence level
-LCA-MTP-PCAV-time-series-validator.confidence-level.order = 3
-LCA-MTP-PCAV-time-series-validator.confidence-level.value-type = string
-LCA-MTP-PCAV-time-series-validator.confidence-level.value-pattern = [A-Z]
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator. = default-data-colum-header-validator.
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator.biological-replicate-code.pattern = BN
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator.data-set-type.terms = LcaMtpPaCav
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator.value-type.pattern = Average\\[U\\]
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator.bi-id.pattern = NB
-LCA-MTP-PCAV-time-series-validator.data-column.header-validator.cg.pattern = NC
-LCA-MTP-PCAV-time-series-validator.data-column.can-define-multiple-columns = true
-LCA-MTP-PCAV-time-series-validator.data-column.value-type = numeric
-
-####### LCA MTP Time Series Validator ###############################################################
-
-lca-mtp-data-set-types = LcaMicCFD, LcaMicabsFl, LcaMtpOD600, LcaMtpAbs900, LcaMtpAbs977, LcaMtpGFP, LcaMtpPa
-
-lca-mtp-time-series-validator.data-set-type = LCA_MTP_TIME_SERIES
-lca-mtp-time-series-validator.path-patterns = *
-lca-mtp-time-series-validator.exclude-path-patterns = request.properties
-lca-mtp-time-series-validator.columns = id, bsb, data-column
-# Identifier column
-lca-mtp-time-series-validator.id.header-pattern = LCAMtpID
-lca-mtp-time-series-validator.id.mandatory = true
-lca-mtp-time-series-validator.id.order = 1
-lca-mtp-time-series-validator.id.value-type = unique
-lca-mtp-time-series-validator.id.value-pattern = ((BBA[0-9]{4}#[A-Z])|BSB168|Empty|(FLUO(100|010|001)))_P[0-9]{2}-[0-9]{2}-[0-9]{2}U[1-8](ID|FP|NG)-[A-H](0[1-9]|1(0|1|2))
-# BSB identifier column
-lca-mtp-time-series-validator.bsb.header-pattern = BSB_ID
-lca-mtp-time-series-validator.bsb.order = 2
-lca-mtp-time-series-validator.bsb.value-type = string
-lca-mtp-time-series-validator.bsb.value-pattern = BBA[0-9]{4}|BSB168|Empty|FLUO100|FLUO010|FLUO001
-# Data columns
-lca-mtp-time-series-validator.data-column.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-lca-mtp-time-series-validator.data-column.header-validator. = default-data-colum-header-validator.
-lca-mtp-time-series-validator.data-column.header-validator.data-set-type.terms = ${lca-mtp-data-set-types}
-# LcaMtpOD and LcaMtpGFP should be positive
-lca-mtp-time-series-validator.data-column.value-validator = ch.systemsx.cisd.etlserver.validation.HeaderBasedValueValidatorFactory
-lca-mtp-time-series-validator.data-column.header-types = positive, real
-lca-mtp-time-series-validator.data-column.positive.header-pattern = .*LcaMtpOD.*|.*LcaMtpGFP.*
-lca-mtp-time-series-validator.data-column.positive.value-type = numeric
-lca-mtp-time-series-validator.data-column.positive.value-range = [0,Infinity)
-# Other values should be real
-lca-mtp-time-series-validator.data-column.real.header-pattern = .*
-lca-mtp-time-series-validator.data-column.real.value-type = numeric
-lca-mtp-time-series-validator.data-column.real.value-range = (-Infinity,Infinity)
-# Many data columns can be defined
-lca-mtp-time-series-validator.data-column.can-define-multiple-columns = true
-
-
-####### Time Series Validator #######################################################################
-metabolite-lcms-abs-validator.data-set-type = METABOLITE_LCMS_ABS_TIME_SERIES
-metabolite-lcms-abs-validator. = compound-time-series-validator.
-metabolite-lcms-abs-validator.data-column.header-validator.data-set-type.terms = MetaboliteLcmsAbs
-
-metabolite-lcms-rel-validator.data-set-type = METABOLITE_LCMS_REL_TIME_SERIES
-metabolite-lcms-rel-validator. = compound-time-series-validator.
-metabolite-lcms-rel-validator.data-column.header-validator.data-set-type.terms = MetaboliteLcmsRel
-
-phys-rfr-validator.data-set-type = PHYS_RFR_TIME_SERIES
-phys-rfr-validator. = compound-time-series-validator.
-phys-rfr-validator.data-column.header-validator.data-set-type.terms = PhysRFR
-
-tf-activity-validator.data-set-type = TF_ACTIVITY_TIME_SERIES
-tf-activity-validator. = genelocus-time-series-validator.
-tf-activity-validator.data-column.header-validator.data-set-type.terms = TFactivity
-
-quantified-peptides-validator.data-set-type = QUANTIFIED_PEPTIDES_TIME_SERIES
-quantified-peptides-validator. = genelocus-time-series-validator.
-quantified-peptides-validator.data-column.header-validator.data-set-type.terms = QuantifiedPeptides
-
-protein-lcms-ratio-validator.data-set-type = PROTEIN_LCMS_RATIO_TIME_SERIES
-protein-lcms-ratio-validator. = genelocus-time-series-validator.
-protein-lcms-ratio-validator.data-column.header-validator.data-set-type.terms = ProteinLcmsRatio, QuantifiedPeptides
-
-protein-2de-combined-lcms-validator.data-set-type = PROTEIN_2DE_COMBINED_LCMS_TIME_SERIES
-protein-2de-combined-lcms-validator. = genelocus-time-series-validator.
-protein-2de-combined-lcms-validator.data-column.header-validator.data-set-type.terms = Protein2DEcombinedLCMS
-
-nimblegen-rna-1-color-bsubt1-validator.data-set-type = NIMBLEGEN_RNA_1_COLOR_BSUBT1_TIME_SERIES
-nimblegen-rna-1-color-bsubt1-validator. = genelocus-time-series-validator.
-nimblegen-rna-1-color-bsubt1-validator.data-column.header-validator.data-set-type.terms = NimbleGenRNA1colorBsubT1
-
-nimblegen-rna-1-color-bsubt1-median-norm-validator.data-set-type = NIMBLEGEN_RNA_1_COLOR_BSUBT1_MEDIAN_NORM_TIME_SERIES
-nimblegen-rna-1-color-bsubt1-median-norm-validator. = genelocus-time-series-validator.
-nimblegen-rna-1-color-bsubt1-median-norm-validator.data-column.header-validator.data-set-type.terms = NimbleGenRNA1colorBsubT1MedianNorm
-
-nimblegen-rna-1-color-bsubt1-qq-norm-validator.data-set-type = NIMBLEGEN_RNA_1_COLOR_BSUBT1_QQ_NORM_TIME_SERIES
-nimblegen-rna-1-color-bsubt1-qq-norm-validator. = genelocus-time-series-validator.
-nimblegen-rna-1-color-bsubt1-qq-norm-validator.data-column.header-validator.data-set-type.terms = NimbleGenRNA1colorBsubT1QQnorm
-
-agilent-rna-2-color-validator.data-set-type = AGILENT_RNA_2_COLOR_TIME_SERIES
-agilent-rna-2-color-validator. = genelocus-time-series-validator.
-agilent-rna-2-color-validator.data-column.header-validator.data-set-type.terms = AgilentRNA2color
-
-absolute-protein-number-gfp-validator.data-set-type = ABSOLUTE_PROTEIN_NUMBERS_GFP_TIME_SERIES
-absolute-protein-number-gfp-validator. = genelocus-time-series-validator.
-absolute-protein-number-gfp-validator.data-column.header-validator.data-set-type.terms = AbsoluteProteinNumbersGFP
-
-absolute-protein-concentration-aqua-2d-page-validator.data-set-type = ABSOLUTE_PROTEIN_CONCENTRATION_AQUA_2D_PAGE_TIME_SERIES
-absolute-protein-concentration-aqua-2d-page-validator. = genelocus-time-series-validator.
-absolute-protein-concentration-aqua-2d-page-validator.data-column.header-validator.data-set-type.terms = AbsoluteProteinConcentrationAqua2DPAGE
-
-2d-gel-spot-vol-validator.data-set-type = 2D_GEL_SPOT_VOL_TIME_SERIES
-2d-gel-spot-vol-validator. = genelocus-time-series-validator.
-2d-gel-spot-vol-validator.data-column.header-validator.data-set-type.terms = 2DgelSpotvol
-
-phys-od600-validator.data-set-type = PHYS_OD600_TIME_SERIES
-phys-od600-validator. = time-series-validator.
-phys-od600-validator.data-column.header-validator.data-set-type.terms = PhysOD600
-phys-od600-validator.id.header-pattern = Abs
-phys-od600-validator.id.value-pattern = OD600
-
-######## Common compound-based validator ############################################################
-compound-time-series-validator. = time-series-validator.
-compound-time-series-validator.id.header-pattern = CompoundID
-compound-time-series-validator.id.value-pattern = BSBME:[0-9]+(BSBME:[0-9])*|CHEBI:[0-9]+(_CHEBI:[0-9]+)*
-
-######## GeneLocus compound-based validator #########################################################
-genelocus-time-series-validator. = time-series-validator.
-genelocus-time-series-validator.id.header-pattern = GeneLocus
-genelocus-time-series-validator.id.value-pattern = ${bsu-vmg-number-multiple-pattern}
-
-######## Common *_TIME_SERIES validator #############################################################
-time-series-validator.path-patterns = *
-time-series-validator.exclude-path-patterns = request.properties
-time-series-validator.columns = id, human-readable, controlled-gene, data-column
-time-series-validator.id.mandatory = true
-time-series-validator.id.order = 1
-time-series-validator.id.value-type = unique
-time-series-validator.human-readable.header-pattern = HumanReadable
-time-series-validator.human-readable.order = 2
-time-series-validator.controlled-gene.header-pattern = ControlledGene
-time-series-validator.controlled-gene.order = 3
-time-series-validator.data-column.header-validator = eu.basysbio.cisd.dss.DataColumnHeaderValidator
-time-series-validator.data-column.header-validator. = default-data-colum-header-validator.
-time-series-validator.data-column.can-define-multiple-columns = true
-time-series-validator.data-column.value-type = numeric
-
-
-####### Default Data Column Header Validator ########################################################
-default-data-colum-header-validator.elements = experiment-code, cultivation-method, biological-replicate-code, \
- time-point, time-point-type, technical-replicate-code, cel-loc, data-set-type, value-type, scale, bi-id, cg
-default-data-colum-header-validator.experiment-code.type = vocabulary
-default-data-colum-header-validator.experiment-code.terms = Ma, Gl, GM, MG
-default-data-colum-header-validator.cultivation-method.type = vocabulary
-default-data-colum-header-validator.cultivation-method.terms = BR, SF, MW, MS
-default-data-colum-header-validator.biological-replicate-code.type = string
-default-data-colum-header-validator.biological-replicate-code.pattern = B[0-9]+(_B[0-9]+)*
-default-data-colum-header-validator.time-point.type = integer
-default-data-colum-header-validator.time-point-type.type = vocabulary
-default-data-colum-header-validator.time-point-type.terms = EX, IN, SI
-default-data-colum-header-validator.technical-replicate-code.type = string
-default-data-colum-header-validator.technical-replicate-code.pattern = T[0-9]+(_T[0-9]+)*
-default-data-colum-header-validator.cel-loc.type = vocabulary
-default-data-colum-header-validator.cel-loc.terms = CE, ES, ME, CY, NC
-default-data-colum-header-validator.data-set-type.type = vocabulary
-default-data-colum-header-validator.value-type.type = string
-default-data-colum-header-validator.value-type.pattern = (Value|Mean|Median|Std|Var|Error|Iqr)\\[(mM|uM|RatioT1|RatioCs||AU||| |\\%)\\]
-default-data-colum-header-validator.scale.type = vocabulary
-default-data-colum-header-validator.scale.terms = LIN, Lin, Log2, Log10, Ln
-default-data-colum-header-validator.bi-id.type = string
-default-data-colum-header-validator.bi-id.pattern = NB|BBA[0-9]*
-default-data-colum-header-validator.cg.type = string
-default-data-colum-header-validator.cg.pattern = NC|${bsu-number-pattern}_(3|5)
-
-bsu-number-pattern = (BSU(_(misc_|r|t)RNA_)?[0-9]+)
-bsu-vmg-number-pattern = ${bsu-number-pattern}|VMG_[0-9]+_[0-9]+|VMG_[0-9]+_[0-9]+_c
-bsu-vmg-number-multiple-pattern = (${bsu-vmg-number-pattern})(_(${bsu-vmg-number-pattern}))*
-
-
-#### End of Data Set Validators #####################################################################
-
diff --git a/eu_basysbio/resource/dependency-structure.ddf b/eu_basysbio/resource/dependency-structure.ddf
deleted file mode 100644
index 8af4fcc730b..00000000000
--- a/eu_basysbio/resource/dependency-structure.ddf
+++ /dev/null
@@ -1,16 +0,0 @@
-#show allResults
-
-{root} = eu.basysbio.cisd
-{dss} = ${root}.dss
-{openbis} = ch.systemsx.cisd.openbis
-
-######################################################################
-# Check dependencies to openbis
-
-[dss] = ${dss}.*
-[private_openbis] = ${openbis}.* excluding [dss] ${openbis}.dss.generic.shared.* ${openbis}.generic.shared.* ${openbis}.dss.generic.server.plugins.* ${openbis}.common.*
-
-check sets [dss]
-
-check [dss] independentOf [private_openbis]
-
diff --git a/eu_basysbio/resource/openBIS-script.txt b/eu_basysbio/resource/openBIS-script.txt
deleted file mode 100644
index 0fc03589f55..00000000000
--- a/eu_basysbio/resource/openBIS-script.txt
+++ /dev/null
@@ -1,75 +0,0 @@
---
--- Creating data set types for BaSysBio
---
-
--- For issue LMS-1480
-
-
-set type = LCA_MTP_PCAV_TIME_SERIES
-
-register-type DATA_SET ${type}
-assign-to DATA_SET:${type} BIOLOGICAL_REPLICATE_CODE
-assign-to DATA_SET:${type} BI_ID
-assign-to DATA_SET:${type} CEL_LOC
-assign-to DATA_SET:${type} CG_LIST
-assign-to DATA_SET:${type} CULTIVATION_METHOD_EXPERIMENT_CODE
-assign-to DATA_SET:${type} EXPERIMENT_CODE
-assign-to DATA_SET:${type} SCALE_LIST
-assign-to DATA_SET:${type} TECHNICAL_REPLICATE_CODE_LIST
-assign-to DATA_SET:${type} TIME_POINT_LIST
-assign-to DATA_SET:${type} TIME_POINT_TYPE
-assign-to DATA_SET:${type} TIME_SERIES_DATA_SET_TYPE
-assign-to DATA_SET:${type} UPLOADER_EMAIL
-assign-to DATA_SET:${type} VALUE_TYPE_LIST
-
-set type = LCA_MTP_PA_CAV
-
-register-type DATA_SET ${type}
-assign-to DATA_SET:${type} BI_ID
-assign-to DATA_SET:${type} CEL_LOC
-assign-to DATA_SET:${type} CG
-assign-to DATA_SET:${type} SCALE
-assign-to DATA_SET:${type} TECHNICAL_REPLICATE_CODE
-assign-to DATA_SET:${type} TIME_SERIES_DATA_SET_TYPE
-assign-to DATA_SET:${type} UPLOADER_EMAIL
-assign-to DATA_SET:${type} VALUE_TYPE
-
--- For issue LMS-1488
-
-set type = LCA_MIC
-
-register-type DATA_SET ${type}
-assign-to DATA_SET:${type} GROWTH_RATE mandatory
-assign-to DATA_SET:${type} BIOLOGICAL_REPLICATE_CODE
-assign-to DATA_SET:${type} BI_ID
-assign-to DATA_SET:${type} CEL_LOC
-assign-to DATA_SET:${type} CG_LIST
-assign-to DATA_SET:${type} CULTIVATION_METHOD_EXPERIMENT_CODE
-assign-to DATA_SET:${type} EXPERIMENT_CODE
-assign-to DATA_SET:${type} SCALE_LIST
-assign-to DATA_SET:${type} TECHNICAL_REPLICATE_CODE_LIST
-assign-to DATA_SET:${type} TIME_POINT_LIST
-assign-to DATA_SET:${type} TIME_POINT_TYPE
-assign-to DATA_SET:${type} TIME_SERIES_DATA_SET_TYPE
-assign-to DATA_SET:${type} UPLOADER_EMAIL
-assign-to DATA_SET:${type} VALUE_TYPE_LIST
-
-set type = LCA_MIC_TIME_SERIES
-
-register-type DATA_SET ${type}
-assign-to DATA_SET:${type} BIOLOGICAL_REPLICATE_CODE
-assign-to DATA_SET:${type} BI_ID
-assign-to DATA_SET:${type} CEL_LOC
-assign-to DATA_SET:${type} CG_LIST
-assign-to DATA_SET:${type} CULTIVATION_METHOD_EXPERIMENT_CODE
-assign-to DATA_SET:${type} EXPERIMENT_CODE
-assign-to DATA_SET:${type} SCALE_LIST
-assign-to DATA_SET:${type} TECHNICAL_REPLICATE_CODE_LIST
-assign-to DATA_SET:${type} TIME_POINT_LIST
-assign-to DATA_SET:${type} TIME_POINT_TYPE
-assign-to DATA_SET:${type} TIME_SERIES_DATA_SET_TYPE
-assign-to DATA_SET:${type} UPLOADER_EMAIL
-assign-to DATA_SET:${type} VALUE_TYPE_LIST
-
-
-
diff --git a/eu_basysbio/source/bash/create-data-set-type.txt b/eu_basysbio/source/bash/create-data-set-type.txt
deleted file mode 100644
index a1b3d5e4d94..00000000000
--- a/eu_basysbio/source/bash/create-data-set-type.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-set time-series-type = ${type}_TIME_SERIES
-
-register-type DATA_SET ${time-series-type} description="Time series of type ${type}" main-pattern=.*\.txt
-assign-to DATA_SET:${time-series-type} BIOLOGICAL_REPLICATE_CODE
-assign-to DATA_SET:${time-series-type} BI_ID
-assign-to DATA_SET:${time-series-type} CG_LIST
-assign-to DATA_SET:${time-series-type} CEL_LOC
-assign-to DATA_SET:${time-series-type} CULTIVATION_METHOD_EXPERIMENT_CODE
-assign-to DATA_SET:${time-series-type} EXPERIMENT_CODE
-assign-to DATA_SET:${time-series-type} SCALE_LIST
-assign-to DATA_SET:${time-series-type} TECHNICAL_REPLICATE_CODE_LIST
-assign-to DATA_SET:${time-series-type} TIME_POINT_LIST
-assign-to DATA_SET:${time-series-type} TIME_SERIES_DATA_SET_TYPE
-assign-to DATA_SET:${time-series-type} UPLOADER_EMAIL
-assign-to DATA_SET:${time-series-type} VALUE_TYPE_LIST
-assign-to DATA_SET:${time-series-type} TIME_POINT_TYPE
-
-
diff --git a/eu_basysbio/source/bash/create-data-set-types.sh b/eu_basysbio/source/bash/create-data-set-types.sh
deleted file mode 100755
index 69ace8d40de..00000000000
--- a/eu_basysbio/source/bash/create-data-set-types.sh
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/bin/bash
-#
-# Script to create data set types *_TIME_SERIES.
-#
-# Prerequisites:
-# 1. openbis-admin-console.zip is unpacked at the same place as this script is located
-# 2. create-data-set-type.txt is in the same directory as this script
-#
-# Usage:
-# ./create-data-set-types.sh <base-url> <user id>
-#
-# The user will be prompted for his/her password.
-# Note: The script continuous running in case of an error. Only an error message will be printed.
-#
-# author: Franz-Josef Elmer
-
-if [ $# -lt 2 ]; then
- echo "Usage: $0 <base url> <user id>"
- exit 1
-fi
-
-url=$1/openbis
-user=$2
-read -s -p "Password: " password
-
-jar=openbis-admin-console/openbis-admin-console.jar
-
-types=`echo METABOLITE_LCMS_ABS \
- METABOLITE_LCMS_REL \
- PHYS_RFR \
- TF_ACTIVITY \
- QUANTIFIED_PEPTIDES \
- PROTEIN_LCMS_RATIO \
- PROTEIN_2DE_COMBINED_LCMS \
- NIMBLEGEN_RNA_1_COLOR_BSUBT1 \
- NIMBLEGEN_RNA_1_COLOR_BSUBT1_MEDIAN_NORM \
- NIMBLEGEN_RNA_1_COLOR_BSUBT1_QQ_NORM \
- AGILENT_RNA_2_COLOR \
- ABSOLUTE_PROTEIN_NUMBERS_GFP \
- ABSOLUTE_PROTEIN_CONCENTRATION_AQUA_2D_PAGE \
- 2D_GEL_SPOT_VOL \
- PHYS_OD600
- `
-for type in $types;do
- java -Dopenbis.type=$type -jar $jar $url create-data-set-type.txt $user $password
-done
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractColumnInjection.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractColumnInjection.java
deleted file mode 100644
index e5beebd8ce8..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractColumnInjection.java
+++ /dev/null
@@ -1,45 +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 eu.basysbio.cisd.dss;
-
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-abstract class AbstractColumnInjection<T extends AbstractDataValue> implements IColumnInjection<T>
-{
- protected final Column column;
-
- AbstractColumnInjection(Column column)
- {
- this.column = column;
- }
-
- @Override
- public void inject(T dataValue, int rowIndex)
- {
- String value = column.getValues().get(rowIndex);
- try
- {
- inject(dataValue, value);
- } catch (Exception ex)
- {
- throw new IllegalArgumentException("Column '" + column.getHeader()
- + "' has an invalid value in row " + (rowIndex + 2) + ": " + value, ex);
- }
- }
-
- abstract void inject(T dataValue, String value);
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataSetUploader.java
deleted file mode 100644
index e433f7893c9..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataSetUploader.java
+++ /dev/null
@@ -1,159 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.sql.Connection;
-import java.sql.SQLException;
-
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.QueryTool;
-
-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.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractDataSetUploader implements IDataSetUploader
-{
- protected final ITimeSeriesDAO dao;
-
- protected final IEncapsulatedOpenBISService service;
-
- protected final TimeSeriesDataSetUploaderParameters parameters;
-
- protected final IDatabaseFeeder databaseFeeder;
-
- private Connection connection;
-
- AbstractDataSetUploader(DataSource dataSource, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- this.service = service;
- this.parameters = parameters;
- try
- {
- connection = dataSource.getConnection();
- connection.setAutoCommit(false);
- dao = QueryTool.getQuery(connection, ITimeSeriesDAO.class);
- databaseFeeder = new DatabaseFeeder(dao, service, parameters);
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- AbstractDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- this(dao, new DatabaseFeeder(dao, service, parameters), service, parameters);
- }
-
- AbstractDataSetUploader(ITimeSeriesDAO dao, IDatabaseFeeder databaseFeeder,
- IEncapsulatedOpenBISService service, TimeSeriesDataSetUploaderParameters parameters)
- {
- this.dao = dao;
- this.service = service;
- this.parameters = parameters;
- this.databaseFeeder = databaseFeeder;
- }
-
- /** the uploader should not be used after calling this method */
- @Override
- public void commit()
- {
- try
- {
- if (connection != null)
- {
- connection.commit();
- }
- dao.close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- connection = null;
- }
- }
-
- /** the uploader should not be used after calling this method */
- @Override
- public void rollback()
- {
- try
- {
- if (connection != null)
- {
- connection.rollback();
- }
- dao.close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- connection = null;
- }
- }
-
- @Override
- public void upload(File originalData, DataSetInformation dataSetInformation)
- {
- ExperimentIdentifier experimentIdentifier = dataSetInformation.getExperimentIdentifier();
- if (experimentIdentifier == null)
- {
- throw new UserFailureException(
- "Data set should be registered for an experiment and not for a sample.");
- }
- if (originalData.isFile())
- {
- handleTSVFile(originalData, dataSetInformation);
- } else
- {
- File[] tsvFiles = originalData.listFiles(new FilenameFilter()
- {
- @Override
- public boolean accept(File dir, String name)
- {
- String lowerCaseName = name.toLowerCase();
- return lowerCaseName.endsWith(".txt") || lowerCaseName.endsWith(".tsv");
- }
- });
- if (tsvFiles == null || tsvFiles.length == 0)
- {
- throw new UserFailureException("No files of type "
- + "'.txt', '.TXT', '.tsv', or '.TSV'. found in " + originalData);
- }
- for (File tsvFile : tsvFiles)
- {
- handleTSVFile(tsvFile, dataSetInformation);
- }
- }
-
- }
-
- protected abstract void handleTSVFile(File tsvFile, DataSetInformation dataSetInformation);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataValue.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataValue.java
deleted file mode 100644
index 478bffa3f3f..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractDataValue.java
+++ /dev/null
@@ -1,72 +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 eu.basysbio.cisd.dss;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractDataValue
-{
- private int rowIndex;
-
- private int columnIndex;
-
- private long valueGroupId;
-
- private TimeSeriesColumnDescriptor descriptor;
-
- public final int getRowIndex()
- {
- return rowIndex;
- }
-
- public final void setRowIndex(int rowIndex)
- {
- this.rowIndex = rowIndex;
- }
-
- public final int getColumnIndex()
- {
- return columnIndex;
- }
-
- public final void setColumnIndex(int columnIndex)
- {
- this.columnIndex = columnIndex;
- }
-
- public final long getValueGroupId()
- {
- return valueGroupId;
- }
-
- public final void setValueGroupId(long valueGroupId)
- {
- this.valueGroupId = valueGroupId;
- }
-
- public final TimeSeriesColumnDescriptor getDescriptor()
- {
- return descriptor;
- }
-
- public final void setDescriptor(TimeSeriesColumnDescriptor descriptor)
- {
- this.descriptor = descriptor;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractSQLArray.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractSQLArray.java
deleted file mode 100644
index c401132cc46..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/AbstractSQLArray.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 eu.basysbio.cisd.dss;
-
-import java.sql.Array;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.Map;
-
-/**
- * An abstract super class that implements {@link Array}. All methods throw an {@link UnsupportedOperationException}.
- *
- * @author Bernd Rinn
- */
-abstract class AbstractSQLArray implements Array
-{
-
- AbstractSQLArray()
- {
- // Call from sub-class.
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public Object getArray(Map<String, Class<?>> map) throws SQLException,
- UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public Object getArray(long index, int count) throws SQLException,
- UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public Object getArray(long index, int count, Map<String, Class<?>> map) throws SQLException,
- UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public ResultSet getResultSet() throws SQLException, UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public ResultSet getResultSet(Map<String, Class<?>> map) throws SQLException,
- UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public ResultSet getResultSet(long index, int count) throws SQLException,
- UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public ResultSet getResultSet(long index, int count, Map<String, Class<?>> map)
- throws SQLException, UnsupportedOperationException
- {
- throw new UnsupportedOperationException();
- }
-
- /**
- * @throws UnsupportedOperationException
- */
- @Override
- public void free() throws SQLException
- {
- throw new UnsupportedOperationException();
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipData.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipData.java
deleted file mode 100644
index 37d3b9b8ccf..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipData.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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ChipChipData extends AbstractDataValue
-{
- private String bsuIdentifier;
-
- private String geneName;
-
- private String geneFunction;
-
- private String arrayDesign;
-
- private Integer microArrayID;
-
- private Integer chipPeakPosition;
-
- private String chipPeakPositionScale;
-
- private Double chipLocalHeight;
-
- private String chipLocalHeightScale;
-
- private Double chipScore;
-
- private String chipScoreScale;
-
- private boolean intergenic;
-
- private String nearbyGeneNames;
-
- private String nearbyGeneIDs;
-
- private String distancesFromStart;
-
- public final String getBsuIdentifier()
- {
- return bsuIdentifier;
- }
-
- public final void setBsuIdentifier(String bsuIdentifier)
- {
- this.bsuIdentifier = bsuIdentifier;
- }
-
- public final String getGeneName()
- {
- return geneName;
- }
-
- public final void setGeneName(String geneName)
- {
- this.geneName = geneName;
- }
-
- public final String getGeneFunction()
- {
- return geneFunction;
- }
-
- public final void setGeneFunction(String geneFunction)
- {
- this.geneFunction = geneFunction;
- }
-
- public final String getArrayDesign()
- {
- return arrayDesign;
- }
-
- public final void setArrayDesign(String arrayDesign)
- {
- this.arrayDesign = arrayDesign;
- }
-
- public final Integer getMicroArrayID()
- {
- return microArrayID;
- }
-
- public final void setMicroArrayID(Integer microArrayID)
- {
- this.microArrayID = microArrayID;
- }
-
- public final Integer getChipPeakPosition()
- {
- return chipPeakPosition;
- }
-
- public final void setChipPeakPosition(Integer chipPeakPosition)
- {
- this.chipPeakPosition = chipPeakPosition;
- }
-
- public final String getChipPeakPositionScale()
- {
- return chipPeakPositionScale;
- }
-
- public final void setChipPeakPositionScale(String chipPeakPositionScale)
- {
- this.chipPeakPositionScale = chipPeakPositionScale;
- }
-
- public final Double getChipLocalHeight()
- {
- return chipLocalHeight;
- }
-
- public final void setChipLocalHeight(Double chipLocalHeight)
- {
- this.chipLocalHeight = chipLocalHeight;
- }
-
- public final String getChipLocalHeightScale()
- {
- return chipLocalHeightScale;
- }
-
- public final void setChipLocalHeightScale(String chipLocalHeightScale)
- {
- this.chipLocalHeightScale = chipLocalHeightScale;
- }
-
- public final Double getChipScore()
- {
- return chipScore;
- }
-
- public final void setChipScore(Double chipScore)
- {
- this.chipScore = chipScore;
- }
-
- public final String getChipScoreScale()
- {
- return chipScoreScale;
- }
-
- public final void setChipScoreScale(String chipScoreScale)
- {
- this.chipScoreScale = chipScoreScale;
- }
-
- public final boolean isIntergenic()
- {
- return intergenic;
- }
-
- public final void setIntergenic(boolean intergenic)
- {
- this.intergenic = intergenic;
- }
-
- public final String getNearbyGeneNames()
- {
- return nearbyGeneNames;
- }
-
- public final void setNearbyGeneNames(String nearbyGeneNames)
- {
- this.nearbyGeneNames = nearbyGeneNames;
- }
-
- public final String getNearbyGeneIDs()
- {
- return nearbyGeneIDs;
- }
-
- public final void setNearbyGeneIDs(String nearbyGeneIDs)
- {
- this.nearbyGeneIDs = nearbyGeneIDs;
- }
-
- public final String getDistancesFromStart()
- {
- return distancesFromStart;
- }
-
- public final void setDistancesFromStart(String distancesFromStart)
- {
- this.distancesFromStart = distancesFromStart;
- }
-
- ChipChipData createFor(int rowIndex, Integer position, Double height, Double score, List<IColumnInjection<ChipChipData>> injections)
- {
- ChipChipData data = new ChipChipData();
- for (IColumnInjection<ChipChipData> injection : injections)
- {
- injection.inject(data, rowIndex);
- }
- data.setDescriptor(getDescriptor());
- data.setRowIndex(rowIndex);
- data.setChipPeakPosition(position);
- data.setChipPeakPositionScale(getChipPeakPositionScale());
- data.setChipLocalHeight(height);
- data.setChipLocalHeightScale(getChipLocalHeightScale());
- data.setChipScore(score);
- data.setChipScoreScale(getChipScoreScale());
- return data;
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipInjectionFactory.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipInjectionFactory.java
deleted file mode 100644
index c5a49ed06b1..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ChipChipInjectionFactory.java
+++ /dev/null
@@ -1,192 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-/**
- * @author Franz-Josef Elmer
- */
-enum ChipChipInjectionFactory implements IInjectionFactory<ChipChipData>
-{
- BSU_IDENTIFIER(1)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setBsuIdentifier(value);
- }
- };
- }
- },
- GENE_NAME(2)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setGeneName(value);
- }
- };
- }
- },
- GENE_FUNCTION(3)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setGeneFunction(value);
- }
- };
- }
- },
- ARRAY_DESIGN(4)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setArrayDesign(value);
- }
- };
- }
- },
- MICRO_ARRAY_ID(5)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- Integer number = null;
- if (StringUtils.isNotBlank(value))
- {
- number = Integer.parseInt(value);
- }
- dataValue.setMicroArrayID(number);
- }
- };
- }
- },
- INTERGENIC(9)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setIntergenic("true".equalsIgnoreCase(value));
- }
- };
- }
- },
- NEARBY_GENE_NAMES(10)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setNearbyGeneNames(value);
- }
- };
- }
- },
- NEARBY_GENE_IDS(11)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setNearbyGeneIDs(value);
- }
- };
- }
- },
- DISTANCE_FROM_START(12)
- {
- @Override
- public IColumnInjection<ChipChipData> create(final Column column)
- {
- return new AbstractColumnInjection<ChipChipData>(column)
- {
- @Override
- void inject(ChipChipData dataValue, String value)
- {
- dataValue.setDistancesFromStart(value);
- }
- };
- }
- };
-
- private final int columnNumber;
-
- private ChipChipInjectionFactory(int columnNumber)
- {
- this.columnNumber = columnNumber;
- }
-
- @Override
- public IColumnInjection<ChipChipData> tryToCreate(List<Column> columns)
- {
- int colIndex = columnNumber - 1;
- if (colIndex >= columns.size())
- {
- return null;
- }
- Column column = columns.get(colIndex);
- return create(column);
- }
-
- public abstract IColumnInjection<ChipChipData> create(final Column column);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DBUtils.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DBUtils.java
deleted file mode 100644
index 5eeac33631f..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DBUtils.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 eu.basysbio.cisd.dss;
-
-import java.util.Properties;
-import java.util.concurrent.ConcurrentHashMap;
-
-import net.lemnik.eodsql.QueryTool;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.properties.ExtendedProperties;
-import ch.systemsx.cisd.common.reflection.BeanUtils;
-import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-
-/**
- * Method for initializing the BaSysBio database.
- *
- * @author Franz-Josef Elmer
- */
-public class DBUtils
-{
- static
- {
- QueryTool.getTypeMap().put(String[].class, new StringArrayMapper());
- }
-
- /** Current version of the database. */
- public static final String DATABASE_VERSION = "008";
-
- private static final String DATABASE_PROPERTIES_PREFIX = "database.";
-
- private static ConcurrentHashMap<Properties, DatabaseConfigurationContext> dbContexts =
- new ConcurrentHashMap<Properties, DatabaseConfigurationContext>();
-
- /**
- * Return the {@link DatabaseConfigurationContext} corresponding to the specified {@link Properties} input. The method maintains a cache with
- * {@link DatabaseConfigurationContext} objects and it does not create a new DB connection for earch invokation.
- */
- public static synchronized DatabaseConfigurationContext getOrCreateDBContext(
- Properties properties)
- {
- DatabaseConfigurationContext dbContext = dbContexts.get(properties);
- if (dbContext == null)
- {
- dbContext = createAndInitDBContext(properties);
- dbContexts.put(properties, dbContext);
- }
- return dbContext;
- }
-
- public static DatabaseConfigurationContext createAndInitDBContext(Properties properties)
- {
- final DatabaseConfigurationContext dbContext = createDBContext(properties);
- DBUtils.init(dbContext);
- return dbContext;
- }
-
- public static DatabaseConfigurationContext createDBContext(Properties properties)
- {
- final Properties dbProps =
- ExtendedProperties.getSubset(properties, DATABASE_PROPERTIES_PREFIX, true);
- DatabaseConfigurationContext context =
- BeanUtils.createBean(DatabaseConfigurationContext.class, dbProps);
- if (context.getBasicDatabaseName() == null)
- {
- throw new EnvironmentFailureException("db basic name not specified in " + dbProps);
- }
- if (context.getDatabaseEngineCode() == null)
- {
- throw new EnvironmentFailureException("db engine code not specified in " + dbProps);
- }
- final DatabaseConfigurationContext dbContext = context;
- return dbContext;
- }
-
- /**
- * Checks the database specified by <var>context</var> and migrates it to the current version if necessary.
- */
- public static void init(DatabaseConfigurationContext context)
- {
- DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
- }
-
- private DBUtils()
- {
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeader.java
deleted file mode 100644
index 573a262de52..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeader.java
+++ /dev/null
@@ -1,290 +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 eu.basysbio.cisd.dss;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-
-public final class DataColumnHeader
-{
- private static final class PropertyManager
- {
- private final Map<String, String> propertiesMap;
-
- private final String dataSetCode;
-
- PropertyManager(AbstractExternalData dataSet)
- {
- dataSetCode = dataSet.getCode();
- List<IEntityProperty> properties = dataSet.getProperties();
- propertiesMap = new HashMap<String, String>();
- for (IEntityProperty property : properties)
- {
- propertiesMap.put(property.getPropertyType().getCode(), property.tryGetAsString());
- }
- }
-
- String getProperty(TimePointPropertyType timePointPropertyType)
- {
- String value = propertiesMap.get(timePointPropertyType.toString());
- if (value == null)
- {
- throw new UserFailureException("Data Set '" + dataSetCode + "' has no property "
- + timePointPropertyType + ".");
- }
- return value;
- }
- }
-
- static final String SEPARATOR = "::";
-
- static final TimePointPropertyType[] HEADER_ELEMENTS =
- new TimePointPropertyType[]
- { TimePointPropertyType.TECHNICAL_REPLICATE_CODE, TimePointPropertyType.CEL_LOC,
- TimePointPropertyType.TIME_SERIES_DATA_SET_TYPE,
- TimePointPropertyType.VALUE_TYPE, TimePointPropertyType.SCALE,
- TimePointPropertyType.BI_ID, TimePointPropertyType.CG };
-
- private static final int HEADER_PARTS = 12;
-
- private static final int TIME_POINT_INDEX = 3;
-
- private static final int TIME_POINT_TYPE_INDEX = 4;
-
- private final Pattern VALUE_TYPE_PATTERN =
- Pattern.compile("([a-zA-Z0-9]+)\\[([a-zA-Z0-9%]*)\\]");
-
- private final String experimentCode;
-
- private final String cultivationMethod;
-
- private final String biologicalReplicateCode;
-
- private final int timePoint;
-
- private final String timePointType;
-
- private final String technicalReplicateCode;
-
- private final String celLoc;
-
- private final String timeSeriesDataSetType;
-
- private final String valueTypeAndUnit;
-
- private final String scale;
-
- private final String biID;
-
- private final String controlledGene;
-
- private final String growthPhase;
-
- private final String genotype;
-
- private final String normalizedHeader;
-
- private final String header;
-
- DataColumnHeader(DataColumnHeader header, AbstractExternalData dataSet)
- {
- PropertyManager propertyManager = new PropertyManager(dataSet);
- experimentCode = header.getExperimentCode();
- cultivationMethod = header.getCultivationMethod();
- biologicalReplicateCode = header.getBiologicalReplicateCode();
- timePoint = header.getTimePoint();
- timePointType = header.getTimePointType();
- technicalReplicateCode = propertyManager.getProperty(TimePointPropertyType.TECHNICAL_REPLICATE_CODE);
- celLoc = propertyManager.getProperty(TimePointPropertyType.CEL_LOC);
- timeSeriesDataSetType = propertyManager.getProperty(TimePointPropertyType.TIME_SERIES_DATA_SET_TYPE);
- valueTypeAndUnit = propertyManager.getProperty(TimePointPropertyType.VALUE_TYPE);
- scale = propertyManager.getProperty(TimePointPropertyType.SCALE);
- biID = propertyManager.getProperty(TimePointPropertyType.BI_ID);
- controlledGene = propertyManager.getProperty(TimePointPropertyType.CG);
- growthPhase = null;
- genotype = null;
- normalizedHeader = createNormalizedHeader();
- this.header = normalizedHeader;
- }
-
- DataColumnHeader(String header)
- {
- this.header = header;
- String[] parts = header.split(SEPARATOR);
- if (parts.length < HEADER_PARTS)
- {
- throw new IllegalArgumentException("At least " + HEADER_PARTS
- + " elements of the following header separated by '" + DataColumnHeader.SEPARATOR
- + "' expected: " + header);
- }
- experimentCode = parts[0];
- cultivationMethod = parts[1];
- biologicalReplicateCode = parts[2];
- timePoint = parseTimePoint(parts[TIME_POINT_INDEX], header);
- timePointType = parts[TIME_POINT_TYPE_INDEX];
- technicalReplicateCode = parts[5];
- celLoc = parts[6];
- timeSeriesDataSetType = parts[7];
- valueTypeAndUnit = parts[8];
- scale = parts[9];
- biID = parts[10];
- controlledGene = parts[11];
- growthPhase = parts.length > 12 ? parts[12] : null;
- genotype = parts.length > 13 ? parts[13] : null;
- normalizedHeader = createNormalizedHeader();
- }
-
- private String createNormalizedHeader()
- {
- StringBuilder builder = new StringBuilder();
- builder.append(experimentCode).append(SEPARATOR);
- builder.append(cultivationMethod).append(SEPARATOR);
- builder.append(biologicalReplicateCode).append(SEPARATOR);
- builder.append(timePoint).append(SEPARATOR);
- builder.append(timePointType);
- for (TimePointPropertyType type : HEADER_ELEMENTS)
- {
- builder.append(SEPARATOR).append(type.getElement(this));
- }
- if (growthPhase != null)
- {
- builder.append(SEPARATOR).append(growthPhase).append(SEPARATOR).append(genotype);
- }
- return builder.toString();
- }
-
- private int parseTimePoint(String value, String originalHeader)
- {
- try
- {
- return Util.parseIntegerWithPlusSign(value);
- } catch (NumberFormatException ex)
- {
- return 0;
- }
- }
-
- public String getExperimentCode()
- {
- return experimentCode;
- }
-
- public String getCultivationMethod()
- {
- return cultivationMethod;
- }
-
- public String getBiologicalReplicateCode()
- {
- return biologicalReplicateCode;
- }
-
- public int getTimePoint()
- {
- return timePoint;
- }
-
- public String getTimePointType()
- {
- return timePointType;
- }
-
- public String getTechnicalReplicateCode()
- {
- return technicalReplicateCode;
- }
-
- public String getCelLoc()
- {
- return celLoc;
- }
-
- public String getTimeSeriesDataSetType()
- {
- return timeSeriesDataSetType;
- }
-
- public String getValueTypeAndUnit()
- {
- return valueTypeAndUnit;
- }
-
- public String getValueType()
- {
- Matcher matcher = VALUE_TYPE_PATTERN.matcher(valueTypeAndUnit);
- return matcher.matches() ? matcher.group(1) : valueTypeAndUnit;
- }
-
- public String getUnit()
- {
- Matcher matcher = VALUE_TYPE_PATTERN.matcher(valueTypeAndUnit);
- return matcher.matches() ? matcher.group(2) : "?";
- }
-
- public String getScale()
- {
- return scale;
- }
-
- public String getBiID()
- {
- return biID;
- }
-
- public String getControlledGene()
- {
- return controlledGene;
- }
-
- public String getGrowthPhase()
- {
- return growthPhase;
- }
-
- public String getGenotype()
- {
- return genotype;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- return obj == this
- || (obj instanceof DataColumnHeader && ((DataColumnHeader) obj).normalizedHeader
- .equals(normalizedHeader));
- }
-
- @Override
- public int hashCode()
- {
- return toString().hashCode();
- }
-
- @Override
- public String toString()
- {
- return header;
- }
-
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeaderValidator.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeaderValidator.java
deleted file mode 100644
index 9cbf2598589..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataColumnHeaderValidator.java
+++ /dev/null
@@ -1,241 +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 eu.basysbio.cisd.dss;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.regex.Pattern;
-import java.util.regex.PatternSyntaxException;
-
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.properties.PropertyParametersUtil;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.common.properties.PropertyParametersUtil.SectionProperties;
-import ch.systemsx.cisd.etlserver.validation.IColumnHeaderValidator;
-import ch.systemsx.cisd.etlserver.validation.Result;
-
-/**
- * Special {@link IColumnHeaderValidator} for Data Columns in time series data sets.
- *
- * @author Franz-Josef Elmer
- */
-public class DataColumnHeaderValidator implements IColumnHeaderValidator
-{
- static final String ELEMENTS_KEY = "elements";
-
- static final String TYPE_KEY = "type";
-
- static final String TYPE_VOCABULARY = "vocabulary";
-
- static final String TERMS_KEY = "terms";
-
- static final String TYPE_INTEGER = "integer";
-
- static final String TYPE_STRING = "string";
-
- static final String PATTERN_KEY = "pattern";
-
- private static interface IElementValidator
- {
- public String validate(String element);
- }
-
- private static interface IElementValidatorFactory
- {
- public String getType();
-
- public IElementValidator createValidator(Properties properties);
- }
-
- private static final class VocabularyValidatorFactory implements IElementValidatorFactory
- {
-
- @Override
- public String getType()
- {
- return TYPE_VOCABULARY;
- }
-
- @Override
- public IElementValidator createValidator(Properties properties)
- {
- String termsSequence = PropertyUtils.getMandatoryProperty(properties, TERMS_KEY);
- final HashSet<String> set = new HashSet<String>();
- String[] terms = PropertyParametersUtil.parseItemisedProperty(termsSequence, TERMS_KEY);
- set.addAll(Arrays.asList(terms));
- return new IElementValidator()
- {
- @Override
- public String validate(String element)
- {
- if (set.contains(element))
- {
- return null;
- }
- return "It is not a term from the following vocabulary: " + set;
- }
- };
- }
- }
-
- private static final class IntegerValidatorFactory implements IElementValidatorFactory
- {
-
- @Override
- public String getType()
- {
- return TYPE_INTEGER;
- }
-
- @Override
- public IElementValidator createValidator(Properties properties)
- {
- return new IElementValidator()
- {
- @Override
- public String validate(String element)
- {
- try
- {
- Util.parseIntegerWithPlusSign(element);
- return null;
- } catch (NumberFormatException ex)
- {
- return "It is not an integer number.";
- }
- }
- };
- }
- }
-
- private static final class StringValidatorFactory implements IElementValidatorFactory
- {
-
- @Override
- public String getType()
- {
- return TYPE_STRING;
- }
-
- @Override
- public IElementValidator createValidator(Properties properties)
- {
- String regex = PropertyUtils.getMandatoryProperty(properties, PATTERN_KEY);
- final Pattern pattern;
- try
- {
- pattern = Pattern.compile(regex);
- } catch (PatternSyntaxException ex)
- {
- throw new ConfigurationFailureException("Invalid regular expression: " + regex);
- }
- return new IElementValidator()
- {
-
- @Override
- public String validate(String element)
- {
- if (pattern.matcher(element).matches())
- {
- return null;
- }
- return "It does not match the following regular expression: " + pattern;
- }
- };
- }
-
- }
-
- private final List<IElementValidator> elementValidators;
-
- public DataColumnHeaderValidator(Properties properties)
- {
- Map<String, IElementValidatorFactory> factories = createValidatorFactories();
- SectionProperties[] sections =
- PropertyParametersUtil.extractSectionProperties(properties, ELEMENTS_KEY, false);
- elementValidators = new ArrayList<IElementValidator>(sections.length);
- for (SectionProperties sectionProperties : sections)
- {
- String key = sectionProperties.getKey();
- Properties validatorProperties = sectionProperties.getProperties();
- String type = validatorProperties.getProperty(TYPE_KEY);
- if (type == null)
- {
- throw new ConfigurationFailureException("Missing property '" + TYPE_KEY
- + "' for element '" + key + "' of data column header validator.");
- }
- IElementValidatorFactory factory = factories.get(type);
- if (factory == null)
- {
- throw new ConfigurationFailureException("Unknown validator type '" + type
- + "' for element '" + key + "' of data column header validator.");
- }
- try
- {
- elementValidators.add(factory.createValidator(validatorProperties));
- } catch (ConfigurationFailureException e)
- {
- throw new ConfigurationFailureException(
- "Error in validator definition for element '" + key
- + "' of data column header validator: " + e.getMessage());
- }
- }
- }
-
- private Map<String, IElementValidatorFactory> createValidatorFactories()
- {
- Map<String, IElementValidatorFactory> map = new HashMap<String, IElementValidatorFactory>();
- register(map, new VocabularyValidatorFactory());
- register(map, new IntegerValidatorFactory());
- register(map, new StringValidatorFactory());
- return map;
- }
-
- private void register(Map<String, IElementValidatorFactory> map,
- IElementValidatorFactory factory)
- {
- map.put(factory.getType(), factory);
- }
-
- @Override
- public Result validateHeader(String header)
- {
- String[] elements = header.split(DataColumnHeader.SEPARATOR);
- if (elements.length < elementValidators.size())
- {
- return Result.failure(elementValidators.size() + " elements separated by '"
- + DataColumnHeader.SEPARATOR + "' expected instead of only " + elements.length
- + ".");
- }
- for (int i = 0, n = Math.min(elements.length, elementValidators.size()); i < n; i++)
- {
- String element = elements[i];
- String result = elementValidators.get(i).validate(element);
- if (result != null)
- {
- return Result.failure("Element '" + element + "' is invalid: " + result);
- }
- }
- return Result.OK;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataHeaderProperty.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataHeaderProperty.java
deleted file mode 100644
index dd382b56040..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataHeaderProperty.java
+++ /dev/null
@@ -1,145 +0,0 @@
-package eu.basysbio.cisd.dss;
-
-/**
- * Properties of data header.
- *
- * @author Izabela Adamczyk
- */
-public enum DataHeaderProperty
-{
-
- ExperimentCode
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getExperimentCode();
- }
- },
- CultivationMethodExperimentCode
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getCultivationMethod();
- }
- },
- BiologicalReplicatateCode
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getBiologicalReplicateCode();
- }
- },
- TimePoint
- {
- /**
- * String value of integer.
- */
- @Override
- String getValue(DataColumnHeader header)
- {
- return Integer.toString(header.getTimePoint());
- }
- },
- TimePointType
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getTimePointType();
- }
- },
- TechnicalReplicateCode
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getTechnicalReplicateCode();
- }
- },
- CelLoc
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getCelLoc();
- }
- },
- DataSetType
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getTimeSeriesDataSetType();
- }
- },
- ValueType
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getValueTypeAndUnit();
- }
- },
- Scale
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getScale();
- }
- },
- BiID
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getBiID();
- }
- },
- CG
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getControlledGene();
- }
- },
- GROWTH_PHASE(true)
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getGrowthPhase();
- }
- },
- GENOTYPE(true)
- {
- @Override
- String getValue(DataColumnHeader header)
- {
- return header.getGenotype();
- }
- };
-
- private final boolean optional;
-
- private DataHeaderProperty()
- {
- this(false);
- }
-
- private DataHeaderProperty(boolean optional)
- {
- this.optional = optional;
- }
-
- public final boolean isOptional()
- {
- return optional;
- }
-
- abstract String getValue(DataColumnHeader header);
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetHandler.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetHandler.java
deleted file mode 100644
index 9e78327ecbc..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetHandler.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.Map;
-import java.util.Properties;
-import java.util.regex.Pattern;
-
-import javax.sql.DataSource;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.common.filesystem.IFileOperations;
-import ch.systemsx.cisd.etlserver.AbstractPostRegistrationDataSetHandlerForFileBasedUndo;
-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;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetHandler extends AbstractPostRegistrationDataSetHandlerForFileBasedUndo implements IDataSetUploader, IFileManager
-{
- static final String TIME_SERIES = "TIME_SERIES";
-
- static final String LCA_MTP_TIME_SERIES = "LCA_MTP_TIME_SERIES";
-
- static final String LCA_MTP_PCAV_TIME_SERIES = "LCA_MTP_PCAV_TIME_SERIES";
-
- static final String LCA_MIC_TIME_SERIES = "LCA_MIC_TIME_SERIES";
-
- static final String LCA_MIC = "LCA_MIC";
-
- private final IEncapsulatedOpenBISService service;
-
- private final DataSource dataSource;
-
- private final TimeSeriesDataSetUploaderParameters parameters;
-
- final DataSetUploaderFactory factory;
-
- private eu.basysbio.cisd.dss.IDataSetUploader uploader;
-
- DataSetHandler(Properties properties, IEncapsulatedOpenBISService service)
- {
- this(properties, DBUtils.getOrCreateDBContext(properties).getDataSource(), service);
- }
-
- DataSetHandler(Properties properties, DataSource dataSource,
- IEncapsulatedOpenBISService service)
- {
- super(FileOperations.getInstance());
- this.dataSource = dataSource;
- this.service = service;
- parameters = new TimeSeriesDataSetUploaderParameters(properties);
- Pattern patternForDefaultHandling = parameters.getPatternForDefaultHandling();
- factory = new DataSetUploaderFactory(TimeSeriesDataSetUploader.FACTORY, patternForDefaultHandling);
- factory.register(LCA_MIC, LcaMicDataSetUploader.FACTORY);
- }
-
- @Override
- public IFileOperations getFileOperations()
- {
- return super.getFileOperations();
- }
-
- @Override
- public void addFileForUndo(File file)
- {
- super.addFileForUndo(file);
- }
-
- @Override
- public void commit()
- {
- if (uploader != null)
- {
- uploader.commit();
- }
- }
-
- @Override
- public void rollback()
- {
- if (uploader != null)
- {
- uploader.rollback();
- }
- }
-
- @Override
- public void upload(File dataSet, DataSetInformation dataSetInformation)
- throws EnvironmentFailureException
- {
- handle(dataSet, dataSetInformation, null);
- }
-
- @Override
- public Status handle(File originalData, DataSetInformation dataSetInformation, Map<String, String> parameterBindings)
- {
- uploader = createUploader(dataSetInformation);
- uploader.upload(originalData, dataSetInformation);
- return Status.OK;
- }
-
- @Private
- eu.basysbio.cisd.dss.IDataSetUploader createUploader(
- DataSetInformation dataSetInformation)
- {
- return factory.create(dataSetInformation, dataSource, service, parameters);
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetInfoExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetInfoExtractor.java
deleted file mode 100644
index 46c874f19d9..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetInfoExtractor.java
+++ /dev/null
@@ -1,89 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor;
-import ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetInfoExtractor implements IDataSetInfoExtractor
-{
- private final CifexDataSetInfoExtractor infoExtractor;
-
- private final CifexTypeExtractor typeExtractor;
-
- private final Map<String, IDataSetPropertiesExtractor> propertiesExtractors =
- new HashMap<String, IDataSetPropertiesExtractor>();
-
- private IDataSetPropertiesExtractor defaultExtractor;
-
- public DataSetInfoExtractor(Properties properties)
- {
- infoExtractor = new CifexDataSetInfoExtractor(properties);
- typeExtractor = new CifexTypeExtractor(properties);
- defaultExtractor = new DataSetPropertiesExtractor(properties, true);
- DataSetPropertiesExtractor timeSeriesExtractor =
- new DataSetPropertiesExtractor(properties, false);
- propertiesExtractors.put(DataSetHandler.TIME_SERIES, timeSeriesExtractor);
- propertiesExtractors.put(DataSetHandler.LCA_MTP_TIME_SERIES, timeSeriesExtractor);
- propertiesExtractors.put(DataSetHandler.LCA_MTP_PCAV_TIME_SERIES, timeSeriesExtractor);
- propertiesExtractors.put(DataSetHandler.LCA_MIC_TIME_SERIES, timeSeriesExtractor);
-
- propertiesExtractors.put(DataSetHandler.LCA_MIC, new LcaMicDataSetPropertiesExtractor(
- properties));
- }
-
- @Override
- public DataSetInformation getDataSetInformation(File incomingDataSetPath,
- IEncapsulatedOpenBISService openbisService) throws UserFailureException,
- EnvironmentFailureException
- {
- DataSetInformation info =
- infoExtractor.getDataSetInformation(incomingDataSetPath, openbisService);
- String email = info.tryGetUploadingUserEmail();
- if (email != null)
- {
- info.getDataSetProperties().add(
- new NewProperty(TimeSeriesPropertyType.UPLOADER_EMAIL.toString(), email));
- }
- DataSetType dataSetType = typeExtractor.getDataSetType(incomingDataSetPath);
- IDataSetPropertiesExtractor extractor = propertiesExtractors.get(dataSetType.getCode());
- if (extractor == null)
- {
- extractor = defaultExtractor;
- }
- List<NewProperty> headerProperties =
- extractor.extractDataSetProperties(incomingDataSetPath);
- info.getDataSetProperties().addAll(headerProperties);
- return info;
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesExtractor.java
deleted file mode 100644
index ea5a9c0bf38..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesExtractor.java
+++ /dev/null
@@ -1,50 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetPropertiesExtractor implements IDataSetPropertiesExtractor
-{
- protected final boolean ignoreEmptyLines;
-
- private final boolean allowMultipleValues;
-
- DataSetPropertiesExtractor(Properties properties, boolean allowMultipleValues)
- {
- this.allowMultipleValues = allowMultipleValues;
- ignoreEmptyLines =
- PropertyUtils.getBoolean(properties,
- TimeSeriesDataSetUploaderParameters.IGNORE_EMPTY_LINES_KEY, true);
- }
-
- @Override
- public List<NewProperty> extractDataSetProperties(File incomingDataSetPath)
- {
- return HeaderUtils.extractHeaderProps(incomingDataSetPath, ignoreEmptyLines, false,
- allowMultipleValues);
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesValidator.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesValidator.java
deleted file mode 100644
index a1e620e8857..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetPropertiesValidator.java
+++ /dev/null
@@ -1,151 +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 eu.basysbio.cisd.dss;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.HighLevelException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyTypeWithVocabulary;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetPropertiesValidator
-{
- private final Map<String, Map<String, PropertyTypeWithVocabulary>> dataSetType2PropertyTypeMap =
- new HashMap<String, Map<String, PropertyTypeWithVocabulary>>();
-
- DataSetPropertiesValidator(Collection<String> translatedDataSetTypes,
- IEncapsulatedOpenBISService service)
- {
- StringBuilder builder = new StringBuilder();
- for (String dataSetTypeCode : translatedDataSetTypes)
- {
- DataSetTypeWithVocabularyTerms dataSetType = null;
- try
- {
- dataSetType = service.getDataSetType(dataSetTypeCode);
- add(dataSetType);
- } catch (HighLevelException ex)
- {
- builder.append(ex.getMessage()).append('\n');
- }
- }
- if (builder.length() > 0)
- {
- throw new ConfigurationFailureException(builder.toString());
- }
- }
-
- void assertValidFor(String dataSetType, TimePointPropertyType key, String value)
- {
- Map<String, PropertyTypeWithVocabulary> map = dataSetType2PropertyTypeMap.get(dataSetType);
- if (map == null)
- {
- throw new IllegalArgumentException("Unknown data set type: " + dataSetType);
- }
- PropertyTypeWithVocabulary propertyType = map.get(key.toString());
- if (propertyType.isVocabulary())
- {
- Set<String> terms = propertyType.getVocabularyTerms();
- if (terms.contains(value) == false)
- {
- throw new IllegalArgumentException("Value of property " + key
- + " is not from the vocabulary " + terms + ": " + value);
- }
- }
- }
-
- private void add(DataSetTypeWithVocabularyTerms dataSetType)
- {
- List<PropertyTypeWithVocabulary> assignedPropertyTypes = dataSetType.getPropertyTypes();
- Map<String, PropertyTypeWithVocabulary> map = new HashMap<String, PropertyTypeWithVocabulary>();
- for (PropertyTypeWithVocabulary dataSetTypePropertyType : assignedPropertyTypes)
- {
- map.put(dataSetTypePropertyType.getCode(), dataSetTypePropertyType);
- }
- TimePointPropertyType[] values = TimePointPropertyType.values();
- List<TimePointPropertyType> missingPropertyTypes = new ArrayList<TimePointPropertyType>();
- List<TimePointPropertyType> wrongDataTypePropertyTypes = new ArrayList<TimePointPropertyType>();
- for (TimePointPropertyType timePointPropertyType : values)
- {
- PropertyTypeWithVocabulary propertyType = map.get(timePointPropertyType.toString());
- if (propertyType == null)
- {
- missingPropertyTypes.add(timePointPropertyType);
- } else
- {
- if (timePointPropertyType.isVocabulary() != propertyType.isVocabulary())
- {
- wrongDataTypePropertyTypes.add(timePointPropertyType);
- }
- }
- }
- StringBuilder errorMessage =
- createErrorMessage(missingPropertyTypes, wrongDataTypePropertyTypes);
- String dataSetTypeCode = dataSetType.getDataSetType().getCode();
- if (errorMessage.length() > 0)
- {
- throw new ConfigurationFailureException("Wrong property assignments for data set type "
- + dataSetTypeCode + ":\n" + errorMessage);
- }
- dataSetType2PropertyTypeMap.put(dataSetTypeCode, map);
- }
-
- private StringBuilder createErrorMessage(List<TimePointPropertyType> missingPropertyTypes,
- List<TimePointPropertyType> wrongDataTypePropertyTypes)
- {
- StringBuilder errorMessage = new StringBuilder();
- if (missingPropertyTypes.isEmpty() == false)
- {
- gotoNewLine(errorMessage);
- errorMessage.append("The following property types are not assigned: ");
- errorMessage.append(missingPropertyTypes);
- }
- if (wrongDataTypePropertyTypes.isEmpty() == false)
- {
- for (TimePointPropertyType timePointPropertyType : wrongDataTypePropertyTypes)
- {
- gotoNewLine(errorMessage);
- errorMessage.append("Property type ").append(timePointPropertyType).append(" has ");
- if (timePointPropertyType.isVocabulary())
- {
- errorMessage.append("not ");
- }
- errorMessage.append("to be a vocabulary.");
- }
- }
- return errorMessage;
- }
-
- private void gotoNewLine(StringBuilder builder)
- {
- if (builder.length() != 0)
- {
- builder.append('\n');
- }
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetTypeTranslator.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetTypeTranslator.java
deleted file mode 100644
index c0e79f8993a..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetTypeTranslator.java
+++ /dev/null
@@ -1,77 +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 eu.basysbio.cisd.dss;
-
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.Properties;
-
-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.common.properties.PropertyParametersUtil;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-
-/**
- * Translator of data set types into openBIS conform upper-case data set types.
- *
- * @author Franz-Josef Elmer
- */
-class DataSetTypeTranslator
-{
- static final String DATA_SET_TYPES_KEY = "data-set-types";
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, DataSetTypeTranslator.class);
-
- private final Map<String, String> map = new LinkedHashMap<String, String>();
-
- DataSetTypeTranslator(Properties properties)
- {
- String sequence = PropertyUtils.getMandatoryProperty(properties, DATA_SET_TYPES_KEY);
- String[] types = PropertyParametersUtil.parseItemisedProperty(sequence, DATA_SET_TYPES_KEY);
- for (String type : types)
- {
- String translatedType = properties.getProperty(type);
- if (translatedType == null)
- {
- translatedType = type.toUpperCase();
- operationLog.warn("No translation found for data set type '" + type
- + "' using default translation '" + translatedType + "'.");
- }
- map.put(type, translatedType);
- }
- }
-
- String translate(String type)
- {
- String translatedType = map.get(type);
- if (translatedType == null)
- {
- throw new UserFailureException("Unknown data set type: " + type);
- }
- return translatedType;
- }
-
- Collection<String> getTranslatedDataSetTypes()
- {
- return map.values();
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetUploaderFactory.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetUploaderFactory.java
deleted file mode 100644
index 18a56d633dc..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DataSetUploaderFactory.java
+++ /dev/null
@@ -1,83 +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 eu.basysbio.cisd.dss;
-
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.regex.Pattern;
-
-import javax.sql.DataSource;
-
-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;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DataSetUploaderFactory implements IDataSetUploaderFactory
-{
- private final Map<String, IDataSetUploaderFactory> factories =
- new LinkedHashMap<String, IDataSetUploaderFactory>();
-
- private final IDataSetUploaderFactory defaultFactory;
-
- private final Pattern pattern;
-
- DataSetUploaderFactory(IDataSetUploaderFactory defaultFactory, Pattern pattern)
- {
- this.defaultFactory = defaultFactory;
- this.pattern = pattern;
- }
-
- void register(String dataSetType, IDataSetUploaderFactory uploaderFactory)
- {
- factories.put(dataSetType, uploaderFactory);
- }
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation, DataSource dataSource,
- IEncapsulatedOpenBISService service, TimeSeriesDataSetUploaderParameters parameters)
- {
- IDataSetUploaderFactory factory = getFactory(dataSetInformation);
- return factory.create(dataSetInformation, dataSource, service, parameters);
- }
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation, ITimeSeriesDAO dao,
- IEncapsulatedOpenBISService service, TimeSeriesDataSetUploaderParameters parameters)
- {
- IDataSetUploaderFactory factory = getFactory(dataSetInformation);
- return factory.create(dataSetInformation, dao, service, parameters);
- }
-
- private IDataSetUploaderFactory getFactory(DataSetInformation dataSetInformation)
- {
- String dataSetType = dataSetInformation.getDataSetType().getCode();
- IDataSetUploaderFactory factory = factories.get(dataSetType);
- if (factory != null)
- {
- return factory;
- }
- if (pattern.matcher(dataSetType).matches() == false)
- {
- throw new UserFailureException("Unable to handle data sets of type " + dataSetType);
- }
- return defaultFactory;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DatabaseFeeder.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/DatabaseFeeder.java
deleted file mode 100644
index e8f2aa977bd..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/DatabaseFeeder.java
+++ /dev/null
@@ -1,335 +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 eu.basysbio.cisd.dss;
-
-import java.io.Reader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-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.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TabSeparatedValueTable;
-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.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-class DatabaseFeeder implements IDatabaseFeeder
-{
- static final String UPLOADER_EMAIL_KEY = "UPLOADER_EMAIL";
-
- private static final int POSITION_COLUMN_INDEX = 5;
-
- private static final int HEIGHT_COLUMN_INDEX = 6;
-
- private static final int SCORE_COLUMN_INDEX = 7;
-
- private static interface IDataSetProvider
- {
- List<String> getDataSetsByDataColumnHeader(DataColumnHeader dataColumnHeader);
- }
-
- private final class DataSetProviderForTimeSeriesData implements IDataSetProvider
- {
- @Override
- public List<String> getDataSetsByDataColumnHeader(DataColumnHeader dataColumnHeader)
- {
- return dao.listDataSetsByTimeSeriesDataColumnHeader(dataColumnHeader);
- }
- }
-
- private final class DataSetProviderForChipChipData implements IDataSetProvider
- {
- @Override
- public List<String> getDataSetsByDataColumnHeader(DataColumnHeader dataColumnHeader)
- {
- return dao.listDataSetsByChipChipDataColumnHeader(dataColumnHeader);
- }
- }
-
- private final ITimeSeriesDAO dao;
-
- private final IEncapsulatedOpenBISService service;
-
- private final TimeSeriesDataSetUploaderParameters parameters;
-
- private final ValueGroupIdGenerator valueGroupIdGenerator;
-
- private final Map<ExperimentIdentifier, Experiment> experimentCache =
- new HashMap<ExperimentIdentifier, Experiment>();
-
- DatabaseFeeder(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- this.dao = dao;
- this.service = service;
- this.parameters = parameters;
- valueGroupIdGenerator = new ValueGroupIdGenerator(dao);
- }
-
- @Override
- public void resetValueGroupIDGenerator()
- {
- valueGroupIdGenerator.clear();
- }
-
- @Override
- public void feedDatabase(DataSetInformation dataSetInformation, Reader reader,
- String nameOfReaderSource)
- {
- feedDatabase(dataSetInformation, reader, nameOfReaderSource, null);
- }
-
- @Override
- public void feedDatabase(DataSetInformation dataSetInformation, Reader reader,
- String nameOfReaderSource, String biIdOrNull)
- {
- TabSeparatedValueTable table =
- new TabSeparatedValueTable(reader, nameOfReaderSource, parameters
- .isIgnoreEmptyLines(), true, false);
- List<Column> columns = table.getColumns();
- feedDatabase(dataSetInformation, columns, biIdOrNull);
- }
-
- private void feedDatabase(DataSetInformation dataSetInformation, List<Column> columns,
- String biIdOrNull)
- {
- assertExperiment(dataSetInformation, columns);
- long dataSetID = getOrCreateDataSet(dataSetInformation);
- String dataSetType = dataSetInformation.getDataSetType().getCode();
- if (dataSetType.equals("CHIP_CHIP"))
- {
- feedDatabaseWithChipChipData(columns, dataSetID);
- } else
- {
- feedDatabaseWithTimeSeriesData(columns, dataSetID, biIdOrNull);
- }
- }
-
- private void feedDatabaseWithTimeSeriesData(List<Column> columns, long dataSetID,
- String biIdOrNull)
- {
- List<IColumnInjection<TimeSeriesValue>> columnInjections =
- createInjections(columns, TimeSeriesInjectionFactory.values());
- List<TimeSeriesValue> dataValues = new ArrayList<TimeSeriesValue>();
- Set<DataColumnHeader> headers = new HashSet<DataColumnHeader>();
- for (int colIndex = 0; colIndex < columns.size(); colIndex++)
- {
- Column column = columns.get(colIndex);
- String header = column.getHeader();
- if (HeaderUtils.isDataColumnHeader(header))
- {
- TimeSeriesValue timeSeriesValue = new TimeSeriesValue();
- timeSeriesValue.setColumnIndex(colIndex);
- DataColumnHeader dataColumnHeader = new DataColumnHeader(header);
- assertUniqueDataColumnHeader(dataColumnHeader, biIdOrNull, headers,
- new DataSetProviderForTimeSeriesData());
- ValueGroupDescriptor valueGroupDescriptor =
- new ValueGroupDescriptor(dataColumnHeader);
- timeSeriesValue.setValueGroupId(valueGroupIdGenerator
- .getValueGroupIdFor(valueGroupDescriptor));
- timeSeriesValue.setDescriptor(new TimeSeriesColumnDescriptor(valueGroupDescriptor,
- dataColumnHeader));
- for (int i = 0, n = column.getValues().size(); i < n; i++)
- {
- Double value = Util.parseDouble(column, i);
- dataValues.add(timeSeriesValue.createFor(i, value, columnInjections));
- }
- }
- }
- String identifierType = columns.get(0).getHeader();
- dao.insertTimeSeriesValues(dataSetID, identifierType, dataValues);
- }
-
- private void feedDatabaseWithChipChipData(List<Column> columns, long dataSetID)
- {
- List<IColumnInjection<ChipChipData>> columnInjections =
- createInjections(columns, ChipChipInjectionFactory.values());
- List<ChipChipData> dataValues = new ArrayList<ChipChipData>();
- ChipChipData chipChipData = new ChipChipData();
- TimeSeriesColumnDescriptor peakColumnDescriptor =
- createDataColumnDescriptor(columns, POSITION_COLUMN_INDEX);
- chipChipData.setDescriptor(peakColumnDescriptor);
- chipChipData.setChipPeakPositionScale(peakColumnDescriptor.getScale());
- chipChipData.setChipLocalHeightScale(createDataColumnDescriptor(columns,
- HEIGHT_COLUMN_INDEX).getScale());
- chipChipData.setChipScoreScale(createDataColumnDescriptor(columns, SCORE_COLUMN_INDEX)
- .getScale());
- Column positions = columns.get(POSITION_COLUMN_INDEX);
- Column heights = columns.get(HEIGHT_COLUMN_INDEX);
- Column scores = columns.get(SCORE_COLUMN_INDEX);
- for (int rowIndex = 0, n = positions.getValues().size(); rowIndex < n; rowIndex++)
- {
- Integer position = Util.parseInteger(positions, rowIndex);
- Double height = Util.parseDouble(heights, rowIndex);
- Double score = Util.parseDouble(scores, rowIndex);
- dataValues.add(chipChipData.createFor(rowIndex, position, height, score,
- columnInjections));
- }
- dao.insertChipChipValues(dataSetID, dataValues);
- }
-
- private TimeSeriesColumnDescriptor createDataColumnDescriptor(List<Column> columns,
- int columnIndex)
- {
- Column column = columns.get(columnIndex);
- DataColumnHeader dataColumnHeader = new DataColumnHeader(column.getHeader());
- assertUniqueDataColumnHeader(dataColumnHeader, null, new HashSet<DataColumnHeader>(),
- new DataSetProviderForChipChipData());
- ValueGroupDescriptor valueGroupDescriptor = new ValueGroupDescriptor(dataColumnHeader);
- return new TimeSeriesColumnDescriptor(valueGroupDescriptor, dataColumnHeader);
- }
-
- private <T extends AbstractDataValue> List<IColumnInjection<T>> createInjections(
- List<Column> columns, IInjectionFactory<T>[] enums)
- {
- List<IColumnInjection<T>> columnInjections = new ArrayList<IColumnInjection<T>>();
- for (IInjectionFactory<T> factory : enums)
- {
- IColumnInjection<T> injection = factory.tryToCreate(columns);
- if (injection != null)
- {
- columnInjections.add(injection);
- }
- }
- return columnInjections;
- }
-
- private void assertUniqueDataColumnHeader(DataColumnHeader dataColumnHeader, String biIdOrNull,
- Set<DataColumnHeader> headers, IDataSetProvider dataSetProvider)
- {
- if (headers.contains(dataColumnHeader))
- {
- throw new UserFailureException("Data column '" + dataColumnHeader + "' appears twice.");
- }
- List<String> dataSets = dataSetProvider.getDataSetsByDataColumnHeader(dataColumnHeader);
- if (biIdOrNull != null)
- {
- final Set<String> biIds =
- dao.getIdentifiersForTimeSeriesDataSet(dataSets.toArray(new String[dataSets
- .size()]));
- if (biIds.contains(biIdOrNull))
- {
- throw new UserFailureException("The data sets " + dataSets
- + " measure the identifiers " + biIds + " for data column '"
- + dataColumnHeader
- + "', which duplicates time series measurements for identifier "
- + biIdOrNull);
- }
- } else if (dataSets.isEmpty() == false)
- {
- throw new UserFailureException("For data column '" + dataColumnHeader
- + "' following data sets have already been registered: " + dataSets);
- }
- headers.add(dataColumnHeader);
- }
-
- private void assertExperiment(DataSetInformation dataSetInformation, List<Column> columns)
- {
- String code = dataSetInformation.getExperimentIdentifier().getExperimentCode();
- Set<String> invalidExperimentCodes = new LinkedHashSet<String>();
- Set<String> experimentCodes = new LinkedHashSet<String>();
- for (Column column : columns)
- {
- String header = column.getHeader();
- if (HeaderUtils.isDataColumnHeader(header))
- {
- DataColumnHeader dataColumnHeader = new DataColumnHeader(header);
- String experimentCode = createExperimentCode(dataColumnHeader);
- experimentCodes.add(experimentCode);
- if (code.equalsIgnoreCase(experimentCode) == false)
- {
- invalidExperimentCodes.add(experimentCode);
- }
- }
- }
- if (invalidExperimentCodes.isEmpty() == false)
- {
- if (experimentCodes.size() == 1 && invalidExperimentCodes.size() == 1)
- {
- throw new UserFailureException("Data should be uploaded for experiment '"
- + invalidExperimentCodes.iterator().next() + "' instead of '" + code + "'.");
- } else
- {
- throw new UserFailureException("Data columns found for more than one experiment: "
- + experimentCodes);
- }
- }
- }
-
- private long getOrCreateDataSet(DataSetInformation dataSetInformation)
- {
- ExperimentIdentifier experimentIdentifier = dataSetInformation.getExperimentIdentifier();
- Experiment experiment = tryToGetExperiment(experimentIdentifier);
- if (experiment == null)
- {
- throw new UserFailureException("Unknown experiment: " + experimentIdentifier);
- }
- String dataSetCode = dataSetInformation.getDataSetCode();
- Long dataSetID = dao.tryToGetDataSetIDByPermID(dataSetCode);
- if (dataSetID == null)
- {
- String eMailAddress = getUploaderEMailAddress(dataSetInformation);
- dataSetID = dao.createDataSet(dataSetCode, eMailAddress, experiment);
- }
- return dataSetID;
- }
-
- private String getUploaderEMailAddress(DataSetInformation dataSetInformation)
- {
- List<NewProperty> properties = dataSetInformation.getDataSetProperties();
- for (NewProperty property : properties)
- {
- if (property.getPropertyCode().equals(UPLOADER_EMAIL_KEY))
- {
- return property.getValue();
- }
- }
- throw new IllegalArgumentException("No uploader email address specified: "
- + dataSetInformation);
- }
-
- private String createExperimentCode(DataColumnHeader dataColumnHeader)
- {
- return parameters.getExperimentCodeFormat().format(
- new Object[]
- { dataColumnHeader.getExperimentCode(),
- dataColumnHeader.getCultivationMethod(),
- dataColumnHeader.getBiologicalReplicateCode() });
- }
-
- private Experiment tryToGetExperiment(ExperimentIdentifier experimentIdentifier)
- {
- Experiment experiment = experimentCache.get(experimentIdentifier);
- if (experiment == null)
- {
- experiment = service.tryGetExperiment(experimentIdentifier);
- experimentCache.put(experimentIdentifier, experiment);
- }
- return experiment;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/HeaderUtils.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/HeaderUtils.java
deleted file mode 100644
index b26517b2874..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/HeaderUtils.java
+++ /dev/null
@@ -1,415 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Pattern;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TabSeparatedValueTable;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * Tools for working with headers.
- *
- * @author Izabela Adamczyk
- */
-
-class HeaderUtils
-{
- private static final String DOTS = "...";
-
- private static final String QUANTIFIED_PEPTIDES = "QuantifiedPeptides";
-
- private static final String PROTEIN_LCMS_RATIO = "ProteinLcmsRatio";
-
- private static final Pattern DATA_COLUMN_HEADER_PATTERN =
- Pattern.compile(".*(" + DataColumnHeader.SEPARATOR + ".*)+");
-
- private static final String LIST_SEPARATOR = ", ";
-
- private static final String[] TSV_EXTENSIONS =
- { "tsv", "TSV", "txt", "TXT" };
-
- public static final TimeSeriesPropertyType[] TIME_SERIES_HEADER_PROPERTIES =
- { TimeSeriesPropertyType.TECHNICAL_REPLICATE_CODE_LIST,
- TimeSeriesPropertyType.BIOLOGICAL_REPLICATE_CODE,
- TimeSeriesPropertyType.TIME_SERIES_DATA_SET_TYPE,
- TimeSeriesPropertyType.CEL_LOC, TimeSeriesPropertyType.CG_LIST,
- TimeSeriesPropertyType.CULTIVATION_METHOD_EXPERIMENT_CODE,
- TimeSeriesPropertyType.EXPERIMENT_CODE, TimeSeriesPropertyType.GENOTYPE,
- TimeSeriesPropertyType.GROWTH_PHASE, TimeSeriesPropertyType.SCALE_LIST,
- TimeSeriesPropertyType.TIME_POINT_LIST,
- TimeSeriesPropertyType.TIME_POINT_TYPE, TimeSeriesPropertyType.BI_ID,
- TimeSeriesPropertyType.VALUE_TYPE_LIST };
-
- /**
- * Extracts data column headers, skips other columns.
- */
- private static Collection<DataColumnHeader> extractDataColumnHeaders(Collection<Column> columns)
- {
- ArrayList<DataColumnHeader> result = new ArrayList<DataColumnHeader>();
- for (Column c : columns)
- {
- String header = c.getHeader();
- if (isDataColumnHeader(header))
- {
- result.add(new DataColumnHeader(header));
- }
- }
- return result;
- }
-
- /**
- * Returns a map of {@link DataHeaderProperty}s and sets of values defined in given headers.
- */
- private static Map<DataHeaderProperty, Set<String>> extractHeaderPropertyValues(
- Collection<DataColumnHeader> headers)
- {
- return extractHeaderPropertyValues(headers, Arrays.asList(DataHeaderProperty.values()));
- }
-
- private static Map<DataHeaderProperty, Set<String>> extractHeaderPropertyValues(
- Collection<DataColumnHeader> headers, Collection<DataHeaderProperty> properties)
- {
- Map<DataHeaderProperty, Set<String>> map = new HashMap<DataHeaderProperty, Set<String>>();
- for (DataColumnHeader dataColumnHeader : headers)
- {
- for (DataHeaderProperty p : properties)
- {
- updateMap(map, p, p.getValue(dataColumnHeader));
- }
- }
- return map;
- }
-
- private static void updateMap(Map<DataHeaderProperty, Set<String>> map,
- DataHeaderProperty property, String value)
- {
- if (map.containsKey(property) == false)
- {
- map.put(property, new HashSet<String>());
- }
- map.get(property).add(value);
- }
-
- private static Collection<DataColumnHeader> loadHeaders(File dir, boolean ignoreEmptyLines,
- boolean ignoreHashedLines)
- {
- Collection<DataColumnHeader> headers = new ArrayList<DataColumnHeader>();
- List<File> tsvFiles = listFiles(dir);
- for (File tsvFile : tsvFiles)
- {
- headers.addAll(HeaderUtils.loadHeadersFromFile(tsvFile, ignoreEmptyLines, ignoreHashedLines));
- }
- return headers;
- }
-
- static File getTabSeparatedValueFile(File dir)
- {
- List<File> files = listFiles(dir);
- if (files.size() > 1)
- {
- throw new UserFailureException("Exactly one file with extensions ["
- + StringUtils.join(TSV_EXTENSIONS) + "] expected instead of " + files.size());
- }
- return files.get(0);
- }
-
- private static List<File> listFiles(File dir)
- {
- List<File> tsvFiles =
- FileUtilities.listFiles(dir, HeaderUtils.TSV_EXTENSIONS, true, null);
- if (tsvFiles.size() == 0)
- {
- throw new UserFailureException(String.format(
- "Could not find any files with extensions [%s].", StringUtils.join(
- HeaderUtils.TSV_EXTENSIONS, ",")));
- }
- return tsvFiles;
- }
-
- private static Collection<DataColumnHeader> loadHeadersFromFile(File tsvFile,
- boolean ignoreEmptyLines, boolean ignoreHashedLines)
- {
- FileReader reader = null;
- try
- {
- reader = new FileReader(tsvFile);
- String fileName = tsvFile.toString();
- TabSeparatedValueTable table =
- new TabSeparatedValueTable(reader, fileName, ignoreEmptyLines, false,
- ignoreHashedLines);
- List<Column> columns = table.getColumns();
- return extractDataColumnHeaders(columns);
- } catch (RuntimeException ex)
- {
- throw ex;
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(reader);
- }
- }
-
- private static NewProperty extractProperty(TimeSeriesPropertyType timeSeriesPropertyType,
- boolean multipleValuesAllowed,
- Map<DataHeaderProperty, Set<String>> map)
- {
- String propertyValue =
- HeaderUtils.getPropertyValue(timeSeriesPropertyType.getHeaderProperty(),
- map, multipleValuesAllowed || timeSeriesPropertyType.isMultipleValues());
- if (propertyValue == null)
- {
- return null;
- }
- NewProperty newProperty = new NewProperty(timeSeriesPropertyType.name(), propertyValue);
- return newProperty;
- }
-
- @Private
- static String getPropertyValue(DataHeaderProperty property,
- Map<DataHeaderProperty, Set<String>> map, boolean multipleValuesAllowed)
- {
- return getPropertyValue(property, map, multipleValuesAllowed, true);
- }
-
- @Private
- static String getPropertyValue(DataHeaderProperty property,
- Map<DataHeaderProperty, Set<String>> map, boolean multipleValuesAllowed,
- boolean treatQuantifiedPeptidesAsProteins)
- {
- Set<String> set = map.get(property);
- if (set == null || set.size() < 1)
- {
- String message = String.format("%s not defined", property.name());
- throw new UserFailureException(message);
- }
- Iterator<String> iterator = set.iterator();
- if (set.size() == 1)
- {
- return iterator.next();
- }
- if (multipleValuesAllowed == false)
- {
- if (treatQuantifiedPeptidesAsProteins
- && property.equals(DataHeaderProperty.DataSetType) && set.size() == 2)
- {
- String first = iterator.next();
- String second = iterator.next();
- if (equal(first, second, PROTEIN_LCMS_RATIO, QUANTIFIED_PEPTIDES))
- {
- return PROTEIN_LCMS_RATIO;
- }
- }
- String message =
- String.format("Inconsistent header values of '%s'. "
- + "Expected the same value in all the columns, found: [%s].", property
- .name(), StringUtils.join(set, HeaderUtils.LIST_SEPARATOR));
- throw new UserFailureException(message);
- }
- List<String> list = new ArrayList<String>(set);
- Collections.sort(list, new Comparator<String>()
- {
- @Override
- public int compare(String s1, String s2)
- {
- try
- {
- int i1 = Integer.parseInt(s1);
- int i2 = Integer.parseInt(s2);
- return i1 - i2;
- } catch (NumberFormatException ex)
- {
- return s1.compareTo(s2);
- }
- }
- });
- return join(list);
- }
-
- static String join(List<String> list)
- {
- return join(list, HeaderUtils.LIST_SEPARATOR, 200);
- }
-
- @Private
- static String join(List<String> list, String separator, int maxSize)
- {
- String lastElement = list.get(list.size() - 1);
- int maxSizeWithoutLastElement = maxSize - separator.length() - lastElement.length();
- int n = 0;
- int totalLength = 0;
- for (; n < list.size() - 1; n++)
- {
- int length = calculateLengthOfElement(list, n, separator);
- totalLength += length;
- if (totalLength > maxSizeWithoutLastElement)
- {
- totalLength -= length;
- length = (n == 0 ? 0 : separator.length()) + DOTS.length();
- if (totalLength + length > maxSizeWithoutLastElement)
- {
- n--;
- }
- break;
- }
- }
- StringBuilder builder = new StringBuilder();
- for (int i = 0; i < n; i++)
- {
- if (builder.length() > 0)
- {
- builder.append(separator);
- }
- builder.append(list.get(i));
- }
- if (n < list.size() - 1)
- {
- if (builder.length() > 0)
- {
- builder.append(separator);
- }
- builder.append(DOTS);
- }
- builder.append(separator).append(lastElement);
- return builder.toString();
- }
-
- private static int calculateLengthOfElement(List<String> list, int i, String separator)
- {
- return (i == 0 ? 0 : separator.length()) + list.get(i).length();
- }
-
- private static boolean equal(String first, String second, String expectedFirst,
- String expectedSecond)
- {
- return first.equals(expectedFirst) && second.equals(expectedSecond)
- || first.equals(expectedSecond) && second.equals(expectedFirst);
- }
-
- /**
- * Extracts a list of "time series" data sets properties defined in the tsv files located in chosen directory.
- */
- public static List<NewProperty> extractHeaderProperties(File dir, boolean ignoreEmptyLines)
- {
- return extractHeaderProps(dir, ignoreEmptyLines, false, false);
- }
-
- /**
- * Extracts a list of "time series" data sets properties defined in the tsv files located in chosen directory.
- *
- * @param multipleValuesAllowed If <code>true</code> multiple values for same header element allowed.
- */
- public static List<NewProperty> extractHeaderPropertiesIgnoringTimeSeriesDataSetType(File dir,
- boolean ignoreEmptyLines, boolean ignoreHashedLines, boolean multipleValuesAllowed)
- {
- return extractHeaderProps(dir, ignoreEmptyLines, ignoreHashedLines, multipleValuesAllowed,
- TimeSeriesPropertyType.TIME_SERIES_DATA_SET_TYPE);
- }
-
- static List<NewProperty> extractHeaderProps(File dir, boolean ignoreEmptyLines,
- boolean ignoreHashedLines, boolean multipleValuesAllowed,
- TimeSeriesPropertyType... ignoredTypes)
- {
- HashSet<TimeSeriesPropertyType> typesToBeIgnored = new HashSet<TimeSeriesPropertyType>(Arrays.asList(ignoredTypes));
- Collection<DataColumnHeader> headers = loadHeaders(dir, ignoreEmptyLines, ignoreHashedLines);
- Map<DataHeaderProperty, Set<String>> values = extractHeaderPropertyValues(headers);
-
- List<NewProperty> headerProperties = new ArrayList<NewProperty>();
- for (TimeSeriesPropertyType pt : TIME_SERIES_HEADER_PROPERTIES)
- {
- if (typesToBeIgnored.contains(pt))
- {
- continue;
- }
- NewProperty property = extractProperty(pt, multipleValuesAllowed, values);
- if (property == null)
- {
- if (pt.isOptional() == false)
- {
- throw new UserFailureException("Header property '" + pt + "' missing.");
- }
- } else
- {
- headerProperties.add(property);
- }
- }
- return headerProperties;
- }
-
- /**
- * Checks weather given header matches data column pattern.
- */
- static public boolean isDataColumnHeader(String header)
- {
- return DATA_COLUMN_HEADER_PATTERN.matcher(header).matches();
- }
-
- /**
- * Chosen data columns should have the same metadata.
- *
- * @throws UserFailureException when chosen {@link DataHeaderProperty}s are not the same in the headers
- */
- public static void assertMetadataConsistent(Collection<DataColumnHeader> headers,
- Collection<DataHeaderProperty> consistentProperties)
- {
- Map<DataHeaderProperty, Set<String>> map =
- extractHeaderPropertyValues(headers, consistentProperties);
- StringBuilder sb = new StringBuilder();
- for (DataHeaderProperty key : map.keySet())
- {
- if (map.get(key).size() > 1)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(key);
- sb.append("(");
- sb.append(StringUtils.join(map.get(key), ","));
- sb.append(")");
- }
- }
- if (sb.length() > 0)
- {
- throw new UserFailureException("Inconsistent data column headers: [" + sb + "]");
- }
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IColumnInjection.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IColumnInjection.java
deleted file mode 100644
index c1802cb9d59..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IColumnInjection.java
+++ /dev/null
@@ -1,26 +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 eu.basysbio.cisd.dss;
-
-/**
- * @author Franz-Josef Elmer
- */
-interface IColumnInjection<T extends AbstractDataValue>
-{
- public void inject(T dataValue, int rowIndex);
-
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetPropertiesExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetPropertiesExtractor.java
deleted file mode 100644
index d99a9007999..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetPropertiesExtractor.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-interface IDataSetPropertiesExtractor
-{
- public List<NewProperty> extractDataSetProperties(File incomingDataSetPath);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java
deleted file mode 100644
index 78dbbeaf64d..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * @author Franz-Josef Elmer
- */
-interface IDataSetUploader
-{
-
- public void upload(File originalData, DataSetInformation dataSetInformation);
-
- public void commit();
-
- public void rollback();
-
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploaderFactory.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploaderFactory.java
deleted file mode 100644
index 2cc7f579784..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploaderFactory.java
+++ /dev/null
@@ -1,34 +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 eu.basysbio.cisd.dss;
-
-import javax.sql.DataSource;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * @author Franz-Josef Elmer
- */
-interface IDataSetUploaderFactory
-{
- public IDataSetUploader create(DataSetInformation dataSetInformation, DataSource dataSource,
- IEncapsulatedOpenBISService service, TimeSeriesDataSetUploaderParameters parameters);
-
- public IDataSetUploader create(DataSetInformation dataSetInformation, ITimeSeriesDAO dao,
- IEncapsulatedOpenBISService service, TimeSeriesDataSetUploaderParameters parameters);
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDatabaseFeeder.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDatabaseFeeder.java
deleted file mode 100644
index d5b4ef28633..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDatabaseFeeder.java
+++ /dev/null
@@ -1,43 +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 eu.basysbio.cisd.dss;
-
-import java.io.Reader;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * Interface for database feeders.
- *
- * @author Franz-Josef Elmer
- */
-interface IDatabaseFeeder
-{
-
- public void resetValueGroupIDGenerator();
-
- public void feedDatabase(DataSetInformation dataSetInformation, Reader reader,
- String nameOfReaderSource);
-
- /**
- * For LCA Microscopy data types who need to allow uploading of many data sets with the same header information but different biIds.
- * <code>biId==null</code> stands for a "regular" time seris data set.
- */
- public void feedDatabase(DataSetInformation dataSetInformation, Reader reader,
- String nameOfReaderSource, String biIdOrNull);
-
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IFileManager.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IFileManager.java
deleted file mode 100644
index 0299db747fd..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IFileManager.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-
-import ch.systemsx.cisd.common.filesystem.IFileOperations;
-
-/**
- * @author Franz-Josef Elmer
- */
-interface IFileManager
-{
- public IFileOperations getFileOperations();
-
- public void addFileForUndo(File file);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IInjectionFactory.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IInjectionFactory.java
deleted file mode 100644
index 85eaf4a833a..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IInjectionFactory.java
+++ /dev/null
@@ -1,26 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-interface IInjectionFactory<T extends AbstractDataValue>
-{
- IColumnInjection<T> tryToCreate(List<Column> columns);
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ITimeSeriesDAO.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/ITimeSeriesDAO.java
deleted file mode 100644
index 840cd519386..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ITimeSeriesDAO.java
+++ /dev/null
@@ -1,107 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-
-import net.lemnik.eodsql.BaseQuery;
-import net.lemnik.eodsql.DataSet;
-import net.lemnik.eodsql.Select;
-import net.lemnik.eodsql.Update;
-
-/**
- * @author Franz-Josef Elmer
- */
-public interface ITimeSeriesDAO extends BaseQuery
-{
- @Select("select nextval('time_series_value_group_id_seq')")
- public long getNextValueGroupId();
-
- @Select("select id from data_sets where perm_id = ?{1}")
- public Long tryToGetDataSetIDByPermID(String dataSetID);
-
- @Select("insert into data_sets (perm_id, uploader_email, exp_code, exp_perm_id) "
- + "values (?{1}, ?{2}, ?{3.code}, ?{3.permId}) returning id")
- public long createDataSet(String dataSetPermID, String uploaderEMail, Experiment experiment);
-
- @Select("select perm_id from data_sets where id in (select dase_id from time_series where "
- + "experiment_type = ?{1.experimentCode} and cultivation_method = ?{1.cultivationMethod} "
- + "and biological_replicates = ?{1.biologicalReplicateCode} "
- + "and time_point = ?{1.timePoint} and time_point_type = ?{1.timePointType} "
- + "and technical_replicates = ?{1.technicalReplicateCode} and cell_location = ?{1.celLoc} "
- + "and data_set_type = ?{1.timeSeriesDataSetType} "
- + "and value_type = ?{1.valueType} and unit = ?{1.unit} and scale = ?{1.scale})")
- public List<String> listDataSetsByTimeSeriesDataColumnHeader(
- DataColumnHeader dataColumnHeader);
-
- @Select(" select distinct ts.identifier from time_series ts join data_sets ds on ds.id = ts.dase_id "
- + "where ds.perm_id = ANY(?{1})")
- public Set<String> getIdentifiersForTimeSeriesDataSet(String[] permId);
-
- @Update(sql = "insert into time_series "
- + "(dase_id, identifier_type, row_index, column_index, value_group_id, "
- + " identifier, identifier_human_readable, bsb_id, confidence_level, "
- + " controlled_gene, number_of_replicates, "
- + " experiment_type, cultivation_method, biological_replicates, time_point, "
- + " time_point_type, technical_replicates, cell_location, data_set_type, "
- + " value_type, unit, scale, value) "
- + "values (?{1}, ?{2}, ?{3.rowIndex}, ?{3.columnIndex}, ?{3.valueGroupId}, "
- + " ?{3.identifier}, ?{3.humanReadable}, ?{3.bsbId}, ?{3.confidenceLevel}, "
- + " ?{3.controlledGene}, ?{3.numberOfReplicates}, "
- + " ?{3.descriptor.experimentType}, ?{3.descriptor.cultivationMethod}, "
- + " ?{3.descriptor.biologicalReplicates}, ?{3.descriptor.timePoint}, "
- + " ?{3.descriptor.timePointType}, ?{3.descriptor.technicalReplicates}, "
- + " ?{3.descriptor.cellLocation}, ?{3.descriptor.dataSetType}, "
- + " ?{3.descriptor.valueType}, ?{3.descriptor.unit}, ?{3.descriptor.scale}, "
- + " ?{3.value})", batchUpdate = true)
- public void insertTimeSeriesValues(long dataSetID, String identifierType,
- List<TimeSeriesValue> timeSeriesValues);
-
- @Select("select perm_id from data_sets where id in (select dase_id from chip_chip_data where "
- + "experiment_type = ?{1.experimentCode} and cultivation_method = ?{1.cultivationMethod} "
- + "and biological_replicates = ?{1.biologicalReplicateCode} "
- + "and technical_replicates = ?{1.technicalReplicateCode} and cell_location = ?{1.celLoc} "
- + "and growth_phase = ?{1.growthPhase} and genotype = ?{1.genotype})")
- public List<String> listDataSetsByChipChipDataColumnHeader(DataColumnHeader dataColumnHeader);
-
- @Update(sql = "insert into chip_chip_data "
- + "(dase_id, row_index, bsu_identifier, gene_name, gene_function, "
- + " array_design, microarray_id, "
- + " experiment_type, cultivation_method, biological_replicates, technical_replicates, "
- + " cell_location, growth_phase, genotype, "
- + " chip_peak_position_value, chip_peak_position_scale, "
- + " chip_local_height_value, chip_local_height_scale, "
- + " chip_score_value, chip_score_scale, "
- + " intergenic, nearby_gene_names, nearby_gene_ids, distances_from_start) "
- + "values (?{1}, ?{2.rowIndex}, ?{2.bsuIdentifier}, ?{2.geneName}, ?{2.geneFunction}, "
- + " ?{2.arrayDesign}, ?{2.microArrayID}, "
- + " ?{2.descriptor.experimentType}, ?{2.descriptor.cultivationMethod}, "
- + " ?{2.descriptor.biologicalReplicates}, ?{2.descriptor.technicalReplicates}, "
- + " ?{2.descriptor.cellLocation}, ?{2.descriptor.growthPhase}, ?{2.descriptor.genotype}, "
- + " ?{2.chipPeakPosition}, ?{2.chipPeakPositionScale}, "
- + " ?{2.chipLocalHeight}, ?{2.chipLocalHeightScale}, "
- + " ?{2.chipScore}, ?{2.chipScoreScale}, "
- + " ?{2.intergenic}, ?{2.nearbyGeneNames}, ?{2.nearbyGeneIDs}, ?{2.distancesFromStart})", batchUpdate = true)
- public void insertChipChipValues(long dataSetID, List<ChipChipData> dataValues);
-
- @Select("select perm_id from data_sets")
- public DataSet<String> findDataSets();
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
deleted file mode 100644
index e36332e2e53..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
+++ /dev/null
@@ -1,59 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-class LcaMicDataSetPropertiesExtractor extends DataSetPropertiesExtractor
-{
-
- static final String GROWTH_RATE = "GROWTH_RATE";
-
- LcaMicDataSetPropertiesExtractor(Properties properties)
- {
- super(properties, true);
- }
-
- @Override
- public List<NewProperty> extractDataSetProperties(File incomingDataSetPath)
- {
- File file = HeaderUtils.getTabSeparatedValueFile(incomingDataSetPath);
- List<String> lines = FileUtilities.loadToStringList(file);
- if (lines.isEmpty())
- {
- throw new UserFailureException("Empty file: " + file);
- }
- String[] items = StringUtils.split(lines.get(0), " \t");
- NewProperty growthRate = new NewProperty(GROWTH_RATE, items[items.length - 1]);
- List<NewProperty> properties =
- HeaderUtils.extractHeaderProps(incomingDataSetPath, ignoreEmptyLines, true, true);
- properties.add(growthRate);
- return properties;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
deleted file mode 100644
index 918c233d055..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
+++ /dev/null
@@ -1,190 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.StringReader;
-import java.util.List;
-
-import javax.sql.DataSource;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.Parameters;
-import ch.systemsx.cisd.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TabSeparatedValueTable;
-import ch.systemsx.cisd.etlserver.validation.DataSetValidator;
-import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-class LcaMicDataSetUploader extends AbstractDataSetUploader
-{
- static final String LCA_MIC_TIME_SERIES = "LCA_MIC_TIME_SERIES";
-
- static final IDataSetUploaderFactory FACTORY = new IDataSetUploaderFactory()
- {
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation,
- DataSource dataSource, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- return new LcaMicDataSetUploader(dataSource, service, parameters);
- }
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation,
- ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- return new LcaMicDataSetUploader(dao, service, parameters);
- }
- };
-
- private final IDataSetValidator dataSetValidator;
-
- LcaMicDataSetUploader(DataSource dataSource, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- super(dataSource, service, parameters);
- dataSetValidator =
- new DataSetValidator(Parameters.createParametersForApiUse().getProperties());
- }
-
- LcaMicDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- super(dao, service, parameters);
- dataSetValidator =
- new DataSetValidator(Parameters.createParametersForApiUse().getProperties());
- }
-
- LcaMicDataSetUploader(ITimeSeriesDAO dao, IDatabaseFeeder databaseFeeder,
- IEncapsulatedOpenBISService service, IDataSetValidator dataSetValidator,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- super(dao, databaseFeeder, service, parameters);
- this.dataSetValidator = dataSetValidator;
- }
-
- @Override
- protected void handleTSVFile(File tsvFile, DataSetInformation dataSetInformation)
- {
- FileReader reader = null;
- try
- {
- reader = new FileReader(tsvFile);
- String fileName = tsvFile.toString();
- TabSeparatedValueTable table =
- new TabSeparatedValueTable(reader, fileName, parameters.isIgnoreEmptyLines(), true, true);
- List<Column> columns = table.getColumns();
- List<String> timeValues = columns.get(0).getValues();
- List<NewProperty> properties = dataSetInformation.getDataSetProperties();
- for (NewProperty property : properties)
- {
- if (property.getPropertyCode().equals(TimeSeriesPropertyType.TIME_POINT_LIST.toString()))
- {
- property.setValue(HeaderUtils.join(timeValues));
- }
- }
- String lastBBAID = null;
- String lastControlledGene = null;
- databaseFeeder.resetValueGroupIDGenerator();
- for (int i = 1; i < columns.size(); i++)
- {
- Column column = columns.get(i);
- String header = column.getHeader();
- String[] items = header.split(DataColumnHeader.SEPARATOR);
- if (items.length < 11)
- {
- throw new UserFailureException("Invalid header: Missing BBA ID: " + header);
- }
- String bbaIDOfColumn = items[10];
- if (bbaIDOfColumn.startsWith("BBA") == false)
- {
- throw new UserFailureException("Invalid header: BBA ID doesn't start with 'BBA': " + header);
- }
- if (lastBBAID != null && bbaIDOfColumn.equals(lastBBAID) == false)
- {
- throw new UserFailureException(
- "Invalid headers: All BBA IDs should be the same. "
- + "The folowing two different BBA IDs found: " + lastBBAID
- + " " + bbaIDOfColumn);
- }
- lastBBAID = bbaIDOfColumn;
- items[10] = "NB";
- if (items.length > 11 && "NC".equals(items[11]) == false)
- {
- String controlledGeneOfColumn = items[11];
- if (lastControlledGene != null && controlledGeneOfColumn.equals(lastControlledGene) == false)
- {
- throw new UserFailureException(
- "Invalid headers: All ControlledGenes should be the same. "
- + "The folowing two ControlledGenes found: " + lastControlledGene
- + " " + controlledGeneOfColumn);
- }
- lastControlledGene = controlledGeneOfColumn;
- items[11] = "NC";
- }
- StringBuilder builder = new StringBuilder("BBA ID");
- if (lastControlledGene != null)
- {
- builder.append("\tControlledGene");
- }
- for (String value : timeValues)
- {
- items[3] = value;
- builder.append("\t").append(StringUtils.join(items, DataColumnHeader.SEPARATOR));
- }
- builder.append("\n").append(bbaIDOfColumn);
- if (lastControlledGene != null)
- {
- builder.append("\t").append(lastControlledGene);
- }
- List<String> values = column.getValues();
- for (String value : values)
- {
- builder.append("\t").append(value);
- }
- builder.append("\n");
- String timeSeriesDataSet = builder.toString();
- DataSetType dataSetType = new DataSetType(LCA_MIC_TIME_SERIES);
- String timeSeriesDataSetName = LCA_MIC_TIME_SERIES + i;
- dataSetValidator.assertValidDataSet(dataSetType, new StringReader(
- timeSeriesDataSet), timeSeriesDataSetName);
- databaseFeeder.feedDatabase(dataSetInformation,
- new StringReader(timeSeriesDataSet), timeSeriesDataSetName, bbaIDOfColumn);
- }
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(reader);
- }
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/PostRegistrationDatabaseUploadTask.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/PostRegistrationDatabaseUploadTask.java
deleted file mode 100644
index a4aa480f950..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/PostRegistrationDatabaseUploadTask.java
+++ /dev/null
@@ -1,217 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Properties;
-import java.util.Set;
-
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.DataSet;
-import net.lemnik.eodsql.QueryTool;
-
-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.logging.LogInitializer;
-import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
-import ch.systemsx.cisd.common.properties.ExtendedProperties;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.etlserver.Parameters;
-import ch.systemsx.cisd.etlserver.plugins.HierarchicalStorageUpdater;
-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.dss.generic.shared.utils.DssPropertyParametersUtil;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-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.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
-{
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, PostRegistrationDatabaseUploadTask.class);
-
- private final IEncapsulatedOpenBISService service;
-
- private final File storeRoot;
-
- private DataSource dataSource;
-
- private DataSetHandler dataSetHandler;
-
- public PostRegistrationDatabaseUploadTask()
- {
- LogInitializer.init();
- service = ServiceProvider.getOpenBISService();
- Properties properties = DssPropertyParametersUtil.loadServiceProperties();
- storeRoot =
- new File(PropertyUtils.getMandatoryProperty(properties,
- HierarchicalStorageUpdater.STOREROOT_DIR_KEY));
- }
-
- @Override
- public void setUp(String pluginName, Properties properties)
- {
- dataSource = DBUtils.createDBContext(properties).getDataSource();
- Properties allProperties = Parameters.createParametersForApiUse().getProperties();
- dataSetHandler =
- new DataSetHandler(ExtendedProperties.getSubset(allProperties,
- "main-thread.storage-processor.processor.", true), dataSource, service);
- }
-
- @Override
- public void execute()
- {
- Set<String> knownDataSets = getKnownDataSets();
- List<SimpleDataSetInformationDTO> dataSets = service.listPhysicalDataSets();
- Collections.sort(dataSets, new Comparator<SimpleDataSetInformationDTO>()
- {
- @Override
- public int compare(SimpleDataSetInformationDTO o1, SimpleDataSetInformationDTO o2)
- {
- return o1.getDataSetCode().compareTo(o2.getDataSetCode());
- }
- });
- for (SimpleDataSetInformationDTO dataSet : dataSets)
- {
- if (knownDataSets.contains(dataSet.getDataSetCode()) == false)
- {
- File share = new File(storeRoot, dataSet.getDataSetShareId());
- File pathToDataSet = new File(share, dataSet.getDataSetLocation());
- File[] dataSetFiles = new File(pathToDataSet, "original").listFiles();
- if (dataSetFiles != null && dataSetFiles.length > 0)
- {
- for (File dataSetFile : dataSetFiles)
- {
- printMemoryUsage();
- DataSetInformation dataSetInformation = createDataSetInformation(dataSet);
- try
- {
- dataSetHandler.upload(dataSetFile, dataSetInformation);
- dataSetHandler.commit();
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("Data set " + dataSet.getDataSetCode()
- + " successfully uploaded.");
- }
- } catch (Exception ex)
- {
- try
- {
- operationLog.error("Uploading of data set " + dataSet.getDataSetCode()
- + " failed: ", ex);
- dataSetHandler.rollback();
- } catch (Exception ex1)
- {
- operationLog.error("Rollback of uploading data set "
- + dataSet.getDataSetCode() + " failed: ", ex1);
- }
- }
- }
- }
- }
- }
- }
-
- private void printMemoryUsage()
- {
- long mb = 1024 * 1024;
- Runtime runtime = Runtime.getRuntime();
- long totalMemory = runtime.totalMemory() / mb;
- long freeMemory = runtime.freeMemory() / mb;
- long maxMemory = runtime.maxMemory() / mb;
- operationLog.info("MEMORY: used=" + (totalMemory - freeMemory) + ", total=" + totalMemory
- + " max=" + maxMemory);
- }
-
- private DataSetInformation createDataSetInformation(SimpleDataSetInformationDTO dataSet)
- {
- DataSetInformation dataSetInformation = new DataSetInformation();
- String dataSetCode = dataSet.getDataSetCode();
- dataSetInformation.setDataSetCode(dataSetCode);
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(dataSet.getDataSetType());
- dataSetInformation.setDataSetType(dataSetType);
- String groupCode = dataSet.getSpaceCode();
- dataSetInformation.setSpaceCode(groupCode);
- String databaseInstanceCode = dataSet.getDatabaseInstanceCode();
- String projectCode = dataSet.getProjectCode();
- String experimentCode = dataSet.getExperimentCode();
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(databaseInstanceCode,
- groupCode, projectCode, experimentCode));
- AbstractExternalData fullDataSet = service.tryGetDataSet(dataSetCode);
- List<IEntityProperty> properties = fullDataSet.getProperties();
- List<NewProperty> dataSetProperties = new ArrayList<NewProperty>();
- for (IEntityProperty property : properties)
- {
- String name = property.getPropertyType().getCode();
- String value = property.tryGetAsString();
- dataSetProperties.add(new NewProperty(name, value));
- }
- dataSetInformation.setDataSetProperties(dataSetProperties);
- return dataSetInformation;
- }
-
- private Set<String> getKnownDataSets()
- {
- Connection connection = null;
- try
- {
- connection = dataSource.getConnection();
- ITimeSeriesDAO dao = QueryTool.getQuery(connection, ITimeSeriesDAO.class);
- DataSet<String> dataSet = dao.findDataSets();
- Set<String> dataSets = new HashSet<String>();
- dataSets.addAll(dataSet);
- dataSet.close();
- return dataSets;
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- if (connection != null)
- {
- try
- {
- connection.close();
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
- }
-
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/SimpleSQLStringArray.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/SimpleSQLStringArray.java
deleted file mode 100644
index 95c55aca984..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/SimpleSQLStringArray.java
+++ /dev/null
@@ -1,100 +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 eu.basysbio.cisd.dss;
-
-import java.sql.SQLException;
-import java.sql.Types;
-
-/**
- * A simple implementation of {@link java.sql.Array} for <code>String[]</code>.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class SimpleSQLStringArray extends AbstractSQLArray
-{
-
- private final String[] value;
-
- SimpleSQLStringArray(String[] array)
- {
- value = array;
- }
-
- /**
- * Get the object array.
- *
- * @return the object array
- */
- @Override
- public Object getArray()
- {
- return value;
- }
-
- /**
- * Get the base type of this array.
- *
- * @return VARCHAR
- */
- @Override
- public int getBaseType()
- {
- return Types.VARCHAR;
- }
-
- /**
- * Get the base type name of this array.
- *
- * @return "varchar"
- */
- @Override
- public String getBaseTypeName()
- {
- return "varchar";
- }
-
- @Override
- public void free() throws SQLException
- {
- // do nothing
- }
-
- @Override
- /*
- * * For the PostgreSQL JDBC driver to work with this class, this method needs to return '{x,y,z,...}'.
- */
- public String toString()
- {
- final StringBuilder builder = new StringBuilder();
- builder.append("{");
- for (String v : value)
- {
- builder.append("\"");
- builder.append(v);
- builder.append("\"");
- builder.append(',');
- }
- // Remove the trailing ','
- if (value.length > 0)
- {
- builder.setLength(builder.length() - 1);
- }
- builder.append("}");
- return builder.toString();
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/StorageProcessor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/StorageProcessor.java
deleted file mode 100644
index caf49711ea7..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/StorageProcessor.java
+++ /dev/null
@@ -1,158 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessorTransaction;
-import ch.systemsx.cisd.etlserver.AbstractStrorageProcessorWithUploader;
-import ch.systemsx.cisd.etlserver.DelegatingStorageProcessorWithDropbox;
-import ch.systemsx.cisd.etlserver.IDataSetUploader;
-import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.etlserver.NullStorageProcessorTransaction;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IPostRegistrationDatasetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class StorageProcessor extends DelegatingStorageProcessorWithDropbox
-{
-
- public StorageProcessor(Properties properties)
- {
- super(properties);
- }
-
- @Override
- public IPostRegistrationDatasetHandler createPostRegistrationDataSetHandler()
- {
- return new DataSetHandler(properties, ServiceProvider.getOpenBISService());
- }
-
- @Override
- public IStorageProcessorTransaction createTransaction(
- final StorageProcessorTransactionParameters parameters)
- {
- StorageProcessorWithDropboxTransaction superTransaction =
- (StorageProcessorWithDropboxTransaction) super.createTransaction(parameters);
-
- StorageProcessorWithUploader storageProcessorWithUploader =
- new StorageProcessorWithUploader(new DummyStorageProcessor(),
- (IDataSetUploader) superTransaction.getPostReigstrationHandler());
-
- IStorageProcessorTransaction uploaderTransaction =
- storageProcessorWithUploader.createTransaction(parameters);
-
- return new StorageProcessorTransaction(parameters, superTransaction, uploaderTransaction);
-
- }
-
- private static final class StorageProcessorWithUploader extends
- AbstractStrorageProcessorWithUploader
- {
- public StorageProcessorWithUploader(IStorageProcessorTransactional processor,
- IDataSetUploader uploader)
- {
- super(processor, uploader);
- }
-
- @Override
- protected void logDataSetFileError(File incomingDataSetDirectory, Throwable exception)
- {
- }
-
- }
-
- static class StorageProcessorTransaction extends AbstractDelegatingStorageProcessorTransaction
- {
-
- private static final long serialVersionUID = 1L;
-
- private final IStorageProcessorTransaction uploaderTransaction;
-
- StorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
- IStorageProcessorTransaction nestedTransaction,
- IStorageProcessorTransaction uploaderTransaction)
- {
- super(parameters, nestedTransaction);
- this.uploaderTransaction = uploaderTransaction;
- }
-
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
- nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
-
- uploaderTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
-
- return nestedTransaction.getStoredDataDirectory();
- }
-
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- nestedTransaction.rollback(ex);
- return uploaderTransaction.rollback(ex);
- }
-
- @Override
- protected void executeCommit()
- {
- uploaderTransaction.commit();
- nestedTransaction.commit();
- }
- }
-
- private final class DummyStorageProcessor implements IStorageProcessorTransactional
- {
- @Override
- public File getStoreRootDirectory()
- {
- return null;
- }
-
- @Override
- public void setStoreRootDirectory(File storeRootDirectory)
- {
- }
-
- @Override
- public IStorageProcessorTransaction createTransaction(
- StorageProcessorTransactionParameters parameters)
- {
- return new NullStorageProcessorTransaction();
- }
-
- @Override
- public StorageFormat getStorageFormat()
- {
- return null;
- }
-
- @Override
- public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
- {
- return null;
- }
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/StringArrayMapper.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/StringArrayMapper.java
deleted file mode 100644
index 1bc22930e24..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/StringArrayMapper.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 eu.basysbio.cisd.dss;
-
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Types;
-
-import net.lemnik.eodsql.TypeMapper;
-
-/**
- * A class for mapping <code>String[]</code> to {@link java.sql.Array}.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class StringArrayMapper implements TypeMapper<String[]>
-{
- @Override
- public String[] get(ResultSet results, int column) throws SQLException
- {
- return (String[]) results.getArray(column).getArray();
- }
-
- @Override
- public void set(PreparedStatement statement, int column, String[] obj) throws SQLException
- {
- if (obj != null)
- {
- statement.setArray(column, new SimpleSQLStringArray(obj));
- } else
- {
- statement.setNull(column, Types.ARRAY);
- }
- }
-
- @Override
- public void set(ResultSet results, int column, String[] obj) throws SQLException
- {
- results.updateArray(column, new SimpleSQLStringArray(obj));
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TSVOutputWriter.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TSVOutputWriter.java
deleted file mode 100644
index cd096c4f138..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TSVOutputWriter.java
+++ /dev/null
@@ -1,98 +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 eu.basysbio.cisd.dss;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.base.io.IOutputStream;
-import ch.systemsx.cisd.base.utilities.OSUtilities;
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-/**
- * Helper class to write a table (i.e. a list of {@link Column} objects) onto an {@link IOutputStream} in TAB-separated format.
- *
- * @author Franz-Josef Elmer
- */
-class TSVOutputWriter
-{
- private static final class Printer
- {
- private final IOutputStream outputStream;
-
- public Printer(IOutputStream outputStream)
- {
- this.outputStream = outputStream;
- }
-
- public void println(Object object)
- {
- print(object + OSUtilities.LINE_SEPARATOR);
- }
-
- public void print(Object object)
- {
- outputStream.write(String.valueOf(object).getBytes());
- }
- }
-
- private final IOutputStream outputStream;
-
- TSVOutputWriter(IOutputStream outputStream)
- {
- this.outputStream = outputStream;
- }
-
- /**
- * Writes specified columns.
- */
- void write(List<Column> columns)
- {
- Printer printer = new Printer(outputStream);
- List<List<String>> cols = new ArrayList<List<String>>();
- int numberOfRows = Integer.MAX_VALUE;
- String delim = "";
- for (Column column : columns)
- {
- printer.print(delim + column.getHeader());
- delim = "\t";
- List<String> values = column.getValues();
- numberOfRows = Math.min(numberOfRows, values.size());
- cols.add(values);
- }
- printer.println("");
- for (int i = 0; i < numberOfRows; i++)
- {
- delim = "";
- for (List<String> col : cols)
- {
- printer.print(delim + col.get(i));
- delim = "\t";
- }
- printer.println("");
- }
- outputStream.flush();
- }
-
- /**
- * Closes wrapped output stream.
- */
- void close()
- {
- outputStream.close();
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimePointPropertyType.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimePointPropertyType.java
deleted file mode 100644
index 03e7f28421e..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimePointPropertyType.java
+++ /dev/null
@@ -1,116 +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 eu.basysbio.cisd.dss;
-
-/**
- * Property type specification of a time point data set type.
- *
- * @author Franz-Josef Elmer
- */
-enum TimePointPropertyType
-{
- BI_ID
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getBiID();
- }
- },
- CEL_LOC(true)
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getCelLoc();
- }
- },
- CG
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getControlledGene();
- }
- },
- SCALE(true)
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getScale();
- }
- },
- TECHNICAL_REPLICATE_CODE
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getTechnicalReplicateCode();
- }
- },
- TIME_SERIES_DATA_SET_TYPE
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getTimeSeriesDataSetType();
- }
- },
- UPLOADER_EMAIL
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return null;
- }
- },
- VALUE_TYPE
- {
- @Override
- public String getElementPlain(DataColumnHeader header)
- {
- return header.getValueTypeAndUnit();
- }
- };
-
- private final boolean vocabulary;
-
- private TimePointPropertyType()
- {
- this(false);
- }
-
- private TimePointPropertyType(boolean vocabulary)
- {
- this.vocabulary = vocabulary;
- }
-
- boolean isVocabulary()
- {
- return vocabulary;
- }
-
- String getElement(DataColumnHeader header)
- {
- String element = getElementPlain(header);
- return isVocabulary() ? element.toUpperCase() : element;
- }
-
- protected abstract String getElementPlain(DataColumnHeader header);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
deleted file mode 100644
index 89ea6011797..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
+++ /dev/null
@@ -1,251 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.log4j.Logger;
-
-import ch.rinn.restrictions.Private;
-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.mail.IMailClient;
-import ch.systemsx.cisd.common.mail.MailClient;
-import ch.systemsx.cisd.common.time.DateFormatThreadLocal;
-import ch.systemsx.cisd.common.utilities.ITimeProvider;
-import ch.systemsx.cisd.common.utilities.SystemTimeProvider;
-import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-
-/**
- * Data set handler for time series data sets and time point data sets.
- *
- * @author Franz-Josef Elmer
- */
-public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
-{
- private static final String CIFEX_DIR_ENDING = ".dir";
-
- @Private
- static final String HELPDESK_EMAIL = "helpdesk.openbis.basysbio@bsse.ethz.ch";
-
- private static enum TypeOfDerivedDataSet
- {
- TIME_POINT("time point"), LCA_MIC_TIME_SERIES("LCA MIC time series");
-
- private final String name;
-
- TypeOfDerivedDataSet(String name)
- {
- this.name = name;
- }
- }
-
- private static final class MessageBuilder
- {
-
- private final String userEMail;
-
- private final ITimeProvider timeProvider;
-
- private String dataSetFileName;
-
- private int numberOfDerivedDataSets;
-
- private int count;
-
- private TypeOfDerivedDataSet type;
-
- MessageBuilder(String userEMail, ITimeProvider timeProvider)
- {
- this.userEMail = userEMail;
- this.timeProvider = timeProvider;
- }
-
- void setDataSetFileName(File dataSet)
- {
- dataSetFileName = dataSet.getName();
- if (dataSetFileName.endsWith(CIFEX_DIR_ENDING))
- {
- int until = dataSetFileName.length() - CIFEX_DIR_ENDING.length();
- dataSetFileName = dataSetFileName.substring(0, until);
- }
- }
-
- void setNumberOfExpectedDerivedDataSets(TypeOfDerivedDataSet type,
- int numberOfDerivedDataSets)
- {
- this.type = type;
- this.numberOfDerivedDataSets = numberOfDerivedDataSets;
- }
-
- void addDerivedDataSetCode(String code)
- {
- count++;
- }
-
- void logSendEMailAndHandlerError(Logger logger, IMailClient mailClient, boolean sendEMail)
- {
- if (count < numberOfDerivedDataSets)
- {
- int numberOfFailures = numberOfDerivedDataSets - count;
- operationLog.error(numberOfFailures + " " + type.name
- + " data sets couldn't be registered.");
- if (sendEMail)
- {
- String subject =
- "BaSysBio: Failed uploading of data set '" + dataSetFileName + "'";
- String timeStamp =
- DateFormatThreadLocal.DATE_FORMAT.get().format(
- new Date(timeProvider.getTimeInMilliseconds()));
- String message =
- "Uploading of data set '" + dataSetFileName + "' failed because "
- + numberOfFailures + " of " + numberOfDerivedDataSets + " "
- + type.name + " data sets couldn't be registered.\n\n"
- + "Please, contact the help desk for support: "
- + HELPDESK_EMAIL + "\n(Time stamp of failure: " + timeStamp
- + ")";
- mailClient.sendMessage(subject, message, null, null, userEMail, HELPDESK_EMAIL);
- }
- throw new UserFailureException("Not all data sets could be registered. "
- + "For more details see error messages in the log.");
- } else
- {
- if (count > 0 && operationLog.isInfoEnabled())
- {
- operationLog.info(count + " " + type.name + " data sets have been registered.");
- }
- if (sendEMail)
- {
- String subject =
- "BaSysBio: Successful uploading of data set '" + dataSetFileName + "'";
- String message =
- "The data set '" + dataSetFileName
- + "' has been successfully uploaded and registered in openBIS.";
-
- mailClient.sendMessage(subject, message, null, null, userEMail);
- }
- }
- }
-
- }
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- TimeSeriesAndTimePointDataSetHandler.class);
-
- private static final FilenameFilter LCA_MIC_TIME_SERIES_FILE_FILTER = new FilenameFilter()
- {
-
- @Override
- public boolean accept(File dir, String name)
- {
- return name.startsWith(DataSetHandler.LCA_MIC_TIME_SERIES);
- }
- };
-
- private final IDataSetHandler delegator;
-
- private final IMailClient mailClient;
-
- private final ITimeProvider timeProvider;
-
- public TimeSeriesAndTimePointDataSetHandler(Properties parentProperties,
- IDataSetHandler delegator)
- {
- this.delegator = delegator;
- this.mailClient = new MailClient(parentProperties);
- timeProvider = SystemTimeProvider.SYSTEM_TIME_PROVIDER;
- }
-
- @Private
- TimeSeriesAndTimePointDataSetHandler(IDataSetHandler delegator, IMailClient mailClient,
- ITimeProvider timeProvider)
- {
- this.delegator = delegator;
- this.mailClient = mailClient;
- this.timeProvider = timeProvider;
- }
-
- @Override
- public List<DataSetInformation> handleDataSet(File dataSet)
- {
- List<DataSetInformation> dataSetInfos = new ArrayList<DataSetInformation>();
- List<DataSetInformation> result = delegator.handleDataSet(dataSet);
- dataSetInfos.addAll(result);
- boolean successful = result.isEmpty() == false;
- if (successful)
- {
- try
- {
- DataSetInformation dataSetInformation = result.get(0);
- MessageBuilder builder =
- new MessageBuilder(dataSetInformation.tryGetUploadingUserEmail(),
- timeProvider);
- builder.setDataSetFileName(dataSet);
- File[] files = dataSet.getParentFile().listFiles(LCA_MIC_TIME_SERIES_FILE_FILTER);
- handleDerivedDataSets(files, TypeOfDerivedDataSet.LCA_MIC_TIME_SERIES, delegator,
- dataSetInfos, builder);
- DataSetType dataSetType = dataSetInformation.getDataSetType();
- boolean lcaMicTimeSeries =
- dataSetType.getCode().equals(DataSetHandler.LCA_MIC_TIME_SERIES);
- builder.logSendEMailAndHandlerError(operationLog, mailClient,
- lcaMicTimeSeries == false);
- } catch (RuntimeException ex)
- {
- // NOTE: the code to delete data sets is not supported any more
- throw new RuntimeException("Exception can't be handled properly any more.", ex);
- }
- }
- return dataSetInfos;
- }
-
- private void handleDerivedDataSets(File[] files, TypeOfDerivedDataSet type,
- IDataSetHandler handler, List<DataSetInformation> dataSetInfos, MessageBuilder builder)
- {
- if (files != null && files.length > 0)
- {
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("Starting registration of " + files.length + " " + type.name
- + " data sets.");
- }
- builder.setNumberOfExpectedDerivedDataSets(type, files.length);
- for (File file : files)
- {
- List<DataSetInformation> result = handler.handleDataSet(file);
- dataSetInfos.addAll(result);
- if (result.isEmpty() == false)
- {
- builder.addDerivedDataSetCode(getDataSetCode(result));
- }
- }
- }
- }
-
- private String getDataSetCode(List<DataSetInformation> result)
- {
- return result.get(0).getDataSetCode();
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesColumnDescriptor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesColumnDescriptor.java
deleted file mode 100644
index 6091c67642c..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesColumnDescriptor.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 eu.basysbio.cisd.dss;
-
-import org.apache.commons.lang.builder.ToStringBuilder;
-
-import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
-
-/**
- * Descriptor of a column in a time series data set file.
- *
- * @author Bernd Rinn
- */
-public class TimeSeriesColumnDescriptor
-{
- private final ValueGroupDescriptor valueGroupDescriptor;
-
- private final String valueType;
-
- private final String unit;
-
- private final String scale;
-
- public TimeSeriesColumnDescriptor(ValueGroupDescriptor descriptor,
- DataColumnHeader dataColumnHeader)
- {
- valueGroupDescriptor = descriptor;
- valueType = dataColumnHeader.getValueType();
- unit = dataColumnHeader.getUnit();
- scale = dataColumnHeader.getScale();
- }
-
- public String getExperimentType()
- {
- return valueGroupDescriptor.getExperimentType();
- }
-
- public String getCultivationMethod()
- {
- return valueGroupDescriptor.getCultivationMethod();
- }
-
- public String getBiologicalReplicates()
- {
- return valueGroupDescriptor.getBiologicalReplicates();
- }
-
- public int getTimePoint()
- {
- return valueGroupDescriptor.getTimePoint();
- }
-
- public String getTimePointType()
- {
- return valueGroupDescriptor.getTimePointType();
- }
-
- public String getTechnicalReplicates()
- {
- return valueGroupDescriptor.getTechnicalReplicates();
- }
-
- public String getCellLocation()
- {
- return valueGroupDescriptor.getCellLocation();
- }
-
- public String getDataSetType()
- {
- return valueGroupDescriptor.getDataSetType();
- }
-
- public String getValueType()
- {
- return valueType;
- }
-
- public String getUnit()
- {
- return unit;
- }
-
- public String getScale()
- {
- return scale;
- }
-
- public String getBiId()
- {
- return valueGroupDescriptor.getBiId();
- }
-
- public String getControlledGene()
- {
- return valueGroupDescriptor.getControlledGene();
- }
-
- public final String getGenotype()
- {
- return valueGroupDescriptor.getGenotype();
- }
-
- public final String getGrowthPhase()
- {
- return valueGroupDescriptor.getGrowthPhase();
- }
-
- public ValueGroupDescriptor getValueGroupDescriptor()
- {
- return valueGroupDescriptor;
- }
-
- @Override
- public String toString()
- {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploader.java
deleted file mode 100644
index bf0f21fa78c..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploader.java
+++ /dev/null
@@ -1,89 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FileReader;
-
-import javax.sql.DataSource;
-
-import org.apache.commons.io.IOUtils;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * @author Franz-Josef Elmer
- */
-class TimeSeriesDataSetUploader extends AbstractDataSetUploader
-{
- static final IDataSetUploaderFactory FACTORY = new IDataSetUploaderFactory()
- {
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation,
- DataSource dataSource, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- return new TimeSeriesDataSetUploader(dataSource, service, parameters);
- }
-
- @Override
- public IDataSetUploader create(DataSetInformation dataSetInformation,
- ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- return new TimeSeriesDataSetUploader(dao, service, parameters);
- }
- };
-
- TimeSeriesDataSetUploader(DataSource dataSource, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- super(dataSource, service, parameters);
- }
-
- TimeSeriesDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
- TimeSeriesDataSetUploaderParameters parameters)
- {
- super(dao, service, parameters);
- }
-
- @Override
- protected void handleTSVFile(File tsvFile, DataSetInformation dataSetInformation)
- {
- FileReader reader = null;
- try
- {
- reader = new FileReader(tsvFile);
- String fileName = tsvFile.toString();
- databaseFeeder.resetValueGroupIDGenerator();
- databaseFeeder.feedDatabase(dataSetInformation, reader, fileName);
- } catch (RuntimeException ex)
- {
- throw ex;
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(reader);
- }
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderParameters.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderParameters.java
deleted file mode 100644
index 0e2029b17a0..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderParameters.java
+++ /dev/null
@@ -1,70 +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 eu.basysbio.cisd.dss;
-
-import java.text.MessageFormat;
-import java.util.Properties;
-import java.util.regex.Pattern;
-
-import ch.systemsx.cisd.common.properties.PropertyUtils;
-
-/**
- * @author Franz-Josef Elmer
- */
-class TimeSeriesDataSetUploaderParameters
-{
- static final String DATA_SET_TYPE_PATTERN_FOR_DEFAULT_HANDLING = "data-set-type-pattern-for-default-handling";
-
- static final String EXPERIMENT_CODE_TEMPLATE_KEY = "experiment-code-template";
-
- static final String DEFAULT_EXPERIMENT_CODE_TEMPLATE = "{0}_{1}_{2}";
-
- static final String IGNORE_EMPTY_LINES_KEY = "ignore-empty-lines";
-
- private final MessageFormat experimentCodeFormat;
-
- private final boolean ignoreEmptyLines;
-
- private final Pattern patternForDefaultHandling;
-
- TimeSeriesDataSetUploaderParameters(Properties properties)
- {
- patternForDefaultHandling =
- Pattern.compile(PropertyUtils.getMandatoryProperty(properties,
- DATA_SET_TYPE_PATTERN_FOR_DEFAULT_HANDLING));
- ignoreEmptyLines = PropertyUtils.getBoolean(properties, IGNORE_EMPTY_LINES_KEY, false);
- experimentCodeFormat =
- new MessageFormat(properties.getProperty(EXPERIMENT_CODE_TEMPLATE_KEY,
- DEFAULT_EXPERIMENT_CODE_TEMPLATE));
- }
-
- MessageFormat getExperimentCodeFormat()
- {
- return experimentCodeFormat;
- }
-
- boolean isIgnoreEmptyLines()
- {
- return ignoreEmptyLines;
- }
-
- Pattern getPatternForDefaultHandling()
- {
- return patternForDefaultHandling;
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesInjectionFactory.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesInjectionFactory.java
deleted file mode 100644
index 868bde2dd31..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesInjectionFactory.java
+++ /dev/null
@@ -1,151 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-import java.util.regex.Pattern;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-/**
- * @author Franz-Josef Elmer
- */
-enum TimeSeriesInjectionFactory implements IInjectionFactory<TimeSeriesValue>
-{
- IDENTIFIER(1, ".+")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- dataValue.setIdentifier(value);
- }
- };
- }
- },
- HUMAN_READABLE(2, "HumanReadable")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- dataValue.setHumanReadable(value);
- }
- };
- }
- },
- BSB_ID(2, "BSB_ID")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- dataValue.setBsbId(value);
- }
- };
- }
- },
- CONFIDENCE_LEVEL(3, "confidence level")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- dataValue.setConfidenceLevel(value);
- }
- };
- }
- },
- CONTROLLED_GENE(3, "ControlledGene")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- dataValue.setControlledGene(value);
- }
- };
- }
- },
- NUMBER_OF_REPLICATES(2, "no of replicates")
- {
- @Override
- public IColumnInjection<TimeSeriesValue> create(final Column column)
- {
- return new AbstractColumnInjection<TimeSeriesValue>(column)
- {
- @Override
- void inject(TimeSeriesValue dataValue, String value)
- {
- Integer number = null;
- if (StringUtils.isNotBlank(value))
- {
- number = Integer.parseInt(value);
- }
- dataValue.setNumberOfReplicates(number);
- }
- };
- }
- };
-
- private final int columnNumber;
-
- private final Pattern pattern;
-
- private TimeSeriesInjectionFactory(int columnNumber, String columnHeaderPattern)
- {
- this.columnNumber = columnNumber;
- pattern = Pattern.compile(columnHeaderPattern);
- }
-
- @Override
- public IColumnInjection<TimeSeriesValue> tryToCreate(List<Column> columns)
- {
- int colIndex = columnNumber - 1;
- if (colIndex >= columns.size())
- {
- return null;
- }
- Column column = columns.get(colIndex);
- return pattern.matcher(column.getHeader()).matches() ? create(column) : null;
- }
-
- public abstract IColumnInjection<TimeSeriesValue> create(final Column column);
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPlugin.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPlugin.java
deleted file mode 100644
index 443d66f12de..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPlugin.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-
-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.generic.shared.basic.dto.ISerializableComparable;
-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.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
-
-/**
- * Shows the header properties of time series data sets.
- *
- * @author Izabela Adamczyk
- */
-public class TimeSeriesPropertiesReportingPlugin extends AbstractTableModelReportingPlugin
-{
- private static final long serialVersionUID = 1L;
-
- public TimeSeriesPropertiesReportingPlugin(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
-
- @Override
- public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
- {
- List<String> headers = new ArrayList<String>();
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- addHeader(builder, headers, "CODE");
- for (TimeSeriesPropertyType pt : HeaderUtils.TIME_SERIES_HEADER_PROPERTIES)
- {
- addHeader(builder, headers, pt.name());
- }
- for (DatasetDescription dataset : datasets)
- {
- List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
- for (int i = 0, n = headers.size(); i < n; i++)
- {
- row.add(new StringTableCell(""));
- }
- addTableCellValue(row, headers, "CODE", dataset.getDataSetCode());
- File file = getDataSubDir(context.getDirectoryProvider(), dataset);
- List<NewProperty> properies = HeaderUtils.extractHeaderProps(file, true, false, true);
- for (NewProperty p : properies)
- {
- addTableCellValue(row, headers, p.getPropertyCode(), p.getValue());
- }
- builder.addRow(row);
- }
- return builder.getTableModel();
- }
-
- private static void addTableCellValue(List<ISerializableComparable> row, List<String> headers,
- String key, String value)
- {
- row.set(headers.indexOf(key), new StringTableCell(value));
-
- }
-
- private static void addHeader(SimpleTableModelBuilder builder, List<String> headers,
- String title)
- {
- builder.addHeader(title);
- headers.add(title);
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesUpdateProcessingPlugin.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesUpdateProcessingPlugin.java
deleted file mode 100644
index 44112772719..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesUpdateProcessingPlugin.java
+++ /dev/null
@@ -1,81 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
-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.ProcessingStatus;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-
-/**
- * Extracts header properties from TSV file belonging to data set and updates data set properties.
- *
- * @author Izabela Adamczyk
- */
-public class TimeSeriesPropertiesUpdateProcessingPlugin extends AbstractDatastorePlugin implements
- IProcessingPluginTask
-{
-
- public TimeSeriesPropertiesUpdateProcessingPlugin(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
-
- private static final long serialVersionUID = 1L;
-
- @Override
- public ProcessingStatus process(List<DatasetDescription> datasets,
- DataSetProcessingContext context)
- {
- final ProcessingStatus result = new ProcessingStatus();
- for (DatasetDescription dataset : datasets)
- {
- Status status = processDataset(context.getDirectoryProvider(), dataset);
- result.addDatasetStatus(dataset, status);
- }
- return result;
- }
-
- private Status processDataset(IDataSetDirectoryProvider directoryProvider,
- DatasetDescription dataset)
- {
- try
- {
- File file = getDataSubDir(directoryProvider, dataset);
- List<NewProperty> newProperties = HeaderUtils.extractHeaderProperties(file, true);
- SpaceIdentifier space =
- new SpaceIdentifier(dataset.getDatabaseInstanceCode(), dataset.getSpaceCode());
- ServiceProvider.getOpenBISService().updateDataSet(dataset.getDataSetCode(),
- newProperties, space);
- return Status.OK;
- } catch (UserFailureException ex)
- {
- return Status.createError(ex.getMessage());
- }
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertyType.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertyType.java
deleted file mode 100644
index 5f1c5743f37..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesPropertyType.java
+++ /dev/null
@@ -1,98 +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 eu.basysbio.cisd.dss;
-
-/**
- * Property type specification of a time series data set type.
- *
- * @author Izabela Adamczyk
- */
-enum TimeSeriesPropertyType
-{
- VALUE_TYPE_LIST(DataHeaderProperty.ValueType, true),
-
- CEL_LOC(DataHeaderProperty.CelLoc),
-
- CG_LIST(DataHeaderProperty.CG, true),
-
- CULTIVATION_METHOD_EXPERIMENT_CODE(
- DataHeaderProperty.CultivationMethodExperimentCode),
-
- EXPERIMENT_CODE(DataHeaderProperty.ExperimentCode),
-
- GENOTYPE(DataHeaderProperty.GENOTYPE),
-
- GROWTH_PHASE(DataHeaderProperty.GROWTH_PHASE),
-
- SCALE_LIST(DataHeaderProperty.Scale, true),
-
- TIME_POINT_LIST(DataHeaderProperty.TimePoint, true),
-
- TIME_POINT_TYPE(DataHeaderProperty.TimePointType),
-
- BI_ID(DataHeaderProperty.BiID),
-
- BIOLOGICAL_REPLICATE_CODE(DataHeaderProperty.BiologicalReplicatateCode),
-
- TECHNICAL_REPLICATE_CODE_LIST(DataHeaderProperty.TechnicalReplicateCode, true),
-
- TIME_SERIES_DATA_SET_TYPE(DataHeaderProperty.DataSetType),
-
- UPLOADER_EMAIL;
-
- private final DataHeaderProperty headerPropertyOrNull;
-
- private final boolean multipleValues;
-
- public boolean isMultipleValues()
- {
- return multipleValues;
- }
-
- private TimeSeriesPropertyType()
- {
- this(null);
- }
-
- private TimeSeriesPropertyType(DataHeaderProperty headerPropertyOrNull)
- {
- this(headerPropertyOrNull, false);
- }
-
- private TimeSeriesPropertyType(DataHeaderProperty headerPropertyOrNull,
- boolean multipleValues)
- {
- assert multipleValues == false || name().endsWith("_LIST") : "Inconsistent property: " + name();
- this.headerPropertyOrNull = headerPropertyOrNull;
- this.multipleValues = multipleValues;
- }
-
- boolean isOptional()
- {
- return headerPropertyOrNull == null ? false : headerPropertyOrNull.isOptional();
- }
-
- public DataHeaderProperty getHeaderProperty()
- {
- if (headerPropertyOrNull == null)
- {
- throw new UnsupportedOperationException(name()
- + " does not have header property.");
- }
- return headerPropertyOrNull;
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesValue.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesValue.java
deleted file mode 100644
index 9656cef6215..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesValue.java
+++ /dev/null
@@ -1,136 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-
-import org.apache.commons.lang.builder.ToStringBuilder;
-
-import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TimeSeriesValue extends AbstractDataValue
-{
- private String identifier;
-
- private String humanReadable;
-
- private String bsbId;
-
- private String confidenceLevel;
-
- private String controlledGene;
-
- private Integer numberOfReplicates;
-
- private Double value;
-
- public final String getIdentifier()
- {
- return identifier;
- }
-
- public final void setIdentifier(String identifier)
- {
- this.identifier = identifier;
- }
-
- public final String getHumanReadable()
- {
- return humanReadable;
- }
-
- public final void setHumanReadable(String humanReadable)
- {
- this.humanReadable = humanReadable;
- }
-
- public final String getBsbId()
- {
- return bsbId;
- }
-
- public final void setBsbId(String bsbId)
- {
- this.bsbId = bsbId;
- }
-
- public final String getConfidenceLevel()
- {
- return confidenceLevel;
- }
-
- public final void setConfidenceLevel(String confidenceLevel)
- {
- this.confidenceLevel = confidenceLevel;
- }
-
- public final String getControlledGene()
- {
- return controlledGene;
- }
-
- public final void setControlledGene(String controlledGene)
- {
- this.controlledGene = controlledGene;
- }
-
- public final Integer getNumberOfReplicates()
- {
- return numberOfReplicates;
- }
-
- public final void setNumberOfReplicates(Integer numberOfReplicates)
- {
- this.numberOfReplicates = numberOfReplicates;
- }
-
- public final Double getValue()
- {
- return value;
- }
-
- public final void setValue(Double value)
- {
- this.value = value;
- }
-
- TimeSeriesValue createFor(int rowIndex, Double cellValue, List<IColumnInjection<TimeSeriesValue>> injections)
- {
- TimeSeriesValue v = new TimeSeriesValue();
- for (IColumnInjection<TimeSeriesValue> injection : injections)
- {
- injection.inject(v, rowIndex);
- }
- v.setDescriptor(getDescriptor());
- v.setColumnIndex(getColumnIndex());
- v.setRowIndex(rowIndex);
- v.setValue(cellValue);
- v.setValueGroupId(getValueGroupId());
- return v;
- }
-
- @Override
- public String toString()
- {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TypeExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TypeExtractor.java
deleted file mode 100644
index 83d0b77c37f..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TypeExtractor.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.etlserver.SimpleTypeExtractor;
-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;
-
-/**
- * Type extractor based on {@link SimpleTypeExtractor}. Data set type code is extracted from the name of the one and only one file of type
- * {@link #DATA_TYPE}.
- *
- * @author Franz-Josef Elmer
- */
-public class TypeExtractor implements ITypeExtractor
-{
- static final String DATA_TYPE = ".data.txt";
-
- private final SimpleTypeExtractor extractor;
-
- public TypeExtractor(Properties properties)
- {
- extractor = new SimpleTypeExtractor(properties);
- }
-
- @Override
- public final DataSetType getDataSetType(File incomingDataSetPath)
- {
- if (incomingDataSetPath.isDirectory() == false)
- {
- throw new UserFailureException("Data set should be a folder: "
- + incomingDataSetPath.getAbsolutePath());
- }
- String[] files = incomingDataSetPath.list(new FilenameFilter()
- {
- @Override
- public boolean accept(File dir, String name)
- {
- return name.endsWith(DATA_TYPE);
- }
- });
- if (files.length != 1)
- {
- throw new UserFailureException("Exactly one file of type '" + DATA_TYPE
- + "' expected instead of " + files.length + ".");
- }
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(files[0].substring(0, files[0].length() - DATA_TYPE.length()));
- return dataSetType;
- }
-
- @Override
- public final FileFormatType getFileFormatType(File incomingDataSetPath)
- {
- return extractor.getFileFormatType(incomingDataSetPath);
- }
-
- @Override
- public final LocatorType getLocatorType(File incomingDataSetPath)
- {
- return extractor.getLocatorType(incomingDataSetPath);
- }
-
- @Override
- public String getProcessorType(File incomingDataSetPath)
- {
- return extractor.getProcessorType(incomingDataSetPath);
- }
-
- @Override
- public boolean isMeasuredData(File incomingDataSetPath)
- {
- return extractor.isMeasuredData(incomingDataSetPath);
- }
-
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/Util.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/Util.java
deleted file mode 100644
index d89151327ee..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/Util.java
+++ /dev/null
@@ -1,77 +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 eu.basysbio.cisd.dss;
-
-import java.util.List;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.etlserver.utils.Column;
-
-/**
- * @author Franz-Josef Elmer
- */
-class Util
-{
- static int parseIntegerWithPlusSign(String number)
- {
- return Integer.parseInt(number.startsWith("+") ? number.substring(1) : number);
- }
-
- static Double parseDouble(String number)
- {
- double value = Double.parseDouble(number);
- return Double.isNaN(value) ? null : value;
- }
-
- static Integer parseInteger(Column column, int rowIndex)
- {
- String value = getValueAt(column, rowIndex);
- try
- {
- return StringUtils.isBlank(value) ? null : new Integer(value);
- } catch (NumberFormatException e)
- {
- throw new IllegalArgumentException((rowIndex + 1) + " data point of column '"
- + column.getHeader() + "' is not an integer number: " + value);
- }
- }
-
- static Double parseDouble(Column column, int rowIndex)
- {
- String value = getValueAt(column, rowIndex);
- try
- {
- return parseDouble(value);
- } catch (NumberFormatException e)
- {
- throw new IllegalArgumentException((rowIndex + 1) + " data point of column '"
- + column.getHeader() + "' is not a floating-point number: " + value);
- }
- }
-
- private static String getValueAt(Column column, int rowIndex)
- {
- List<String> values = column.getValues();
- if (rowIndex >= values.size())
- {
- throw new IllegalArgumentException("Column '" + column.getHeader() + "' has only "
- + values.size() + " data points instead of " + (rowIndex + 1) + " or more.");
- }
- return values.get(rowIndex);
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupDescriptor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupDescriptor.java
deleted file mode 100644
index f33ddb5f5b8..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupDescriptor.java
+++ /dev/null
@@ -1,192 +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 eu.basysbio.cisd.dss;
-
-import org.apache.commons.lang.builder.ToStringBuilder;
-
-import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
-
-/**
- * A value group groups all value types of one data set file together.
- *
- * @author Bernd Rinn
- */
-public class ValueGroupDescriptor
-{
- private final String experimentType;
-
- private final String cultivationMethod;
-
- private final String biologicalReplicates;
-
- private final int timePoint;
-
- private final String timePointType;
-
- private final String technicalReplicates;
-
- private final String cellLocation;
-
- private final String dataSetType;
-
- private final String biId;
-
- private final String controlledGene;
-
- private final String growthPhase;
-
- private final String genotype;
-
- public ValueGroupDescriptor(DataColumnHeader dataColumnHeader)
- {
- experimentType = dataColumnHeader.getExperimentCode();
- cultivationMethod = dataColumnHeader.getCultivationMethod();
- biologicalReplicates = dataColumnHeader.getBiologicalReplicateCode();
- timePoint = dataColumnHeader.getTimePoint();
- timePointType = dataColumnHeader.getTimePointType();
- technicalReplicates = dataColumnHeader.getTechnicalReplicateCode();
- cellLocation = dataColumnHeader.getCelLoc();
- dataSetType = dataColumnHeader.getTimeSeriesDataSetType();
- biId = dataColumnHeader.getBiID();
- controlledGene = dataColumnHeader.getControlledGene();
- growthPhase = dataColumnHeader.getGrowthPhase();
- genotype = dataColumnHeader.getGenotype();
- }
-
- public String getExperimentType()
- {
- return experimentType;
- }
-
- public String getCultivationMethod()
- {
- return cultivationMethod;
- }
-
- public String getBiologicalReplicates()
- {
- return biologicalReplicates;
- }
-
- public int getTimePoint()
- {
- return timePoint;
- }
-
- public String getTimePointType()
- {
- return timePointType;
- }
-
- public String getTechnicalReplicates()
- {
- return technicalReplicates;
- }
-
- public String getCellLocation()
- {
- return cellLocation;
- }
-
- public String getDataSetType()
- {
- return dataSetType;
- }
-
- public String getBiId()
- {
- return biId;
- }
-
- public String getControlledGene()
- {
- return controlledGene;
- }
-
- public final String getGrowthPhase()
- {
- return growthPhase;
- }
-
- public final String getGenotype()
- {
- return genotype;
- }
-
- @Override
- public int hashCode()
- {
- final int prime = 31;
- int result = 1;
- result = prime * result + ((biId == null) ? 0 : biId.hashCode());
- result =
- prime * result
- + ((biologicalReplicates == null) ? 0 : biologicalReplicates.hashCode());
- result = prime * result + ((cellLocation == null) ? 0 : cellLocation.hashCode());
- result = prime * result + ((controlledGene == null) ? 0 : controlledGene.hashCode());
- result = prime * result + ((cultivationMethod == null) ? 0 : cultivationMethod.hashCode());
- result = prime * result + ((dataSetType == null) ? 0 : dataSetType.hashCode());
- result = prime * result + ((experimentType == null) ? 0 : experimentType.hashCode());
- result = prime * result + ((genotype == null) ? 0 : genotype.hashCode());
- result = prime * result + ((growthPhase == null) ? 0 : growthPhase.hashCode());
- result =
- prime * result
- + ((technicalReplicates == null) ? 0 : technicalReplicates.hashCode());
- result = prime * result + timePoint;
- result = prime * result + ((timePointType == null) ? 0 : timePointType.hashCode());
- return result;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (this == obj)
- {
- return true;
- }
- if (obj == null)
- {
- return false;
- }
- if (getClass() != obj.getClass())
- {
- return false;
- }
- final ValueGroupDescriptor other = (ValueGroupDescriptor) obj;
- return equals(biId, other.biId) && equals(biologicalReplicates, other.biologicalReplicates)
- && equals(cellLocation, other.cellLocation)
- && equals(controlledGene, other.controlledGene)
- && equals(cultivationMethod, other.cultivationMethod)
- && equals(dataSetType, other.dataSetType)
- && equals(experimentType, other.experimentType) && equals(genotype, other.genotype)
- && equals(growthPhase, other.growthPhase)
- && equals(technicalReplicates, other.technicalReplicates)
- && timePoint == other.timePoint && equals(timePointType, other.timePointType);
- }
-
- private boolean equals(Object obj1, Object obj2)
- {
- return obj1 == null ? obj1 == obj2 : obj1.equals(obj2);
- }
-
- @Override
- public String toString()
- {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
-}
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupIdGenerator.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupIdGenerator.java
deleted file mode 100644
index 27589c59ff9..00000000000
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/ValueGroupIdGenerator.java
+++ /dev/null
@@ -1,48 +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 eu.basysbio.cisd.dss;
-
-import java.util.HashMap;
-import java.util.Map;
-
-class ValueGroupIdGenerator
-{
- private final Map<ValueGroupDescriptor, Long> valueGroupIDs = new HashMap<ValueGroupDescriptor, Long>();
-
- private final ITimeSeriesDAO dao;
-
- ValueGroupIdGenerator(ITimeSeriesDAO dao)
- {
- this.dao = dao;
- }
-
- void clear()
- {
- valueGroupIDs.clear();
- }
-
- long getValueGroupIdFor(ValueGroupDescriptor descriptor)
- {
- Long id = valueGroupIDs.get(descriptor);
- if (id == null)
- {
- id = dao.getNextValueGroupId();
- valueGroupIDs.put(descriptor, id);
- }
- return id;
- }
-}
\ No newline at end of file
diff --git a/eu_basysbio/source/sql/postgresql/001/schema-001.pdf b/eu_basysbio/source/sql/postgresql/001/schema-001.pdf
deleted file mode 100755
index d518190f0f89ab8f91919c0744029a009bb0128c..0000000000000000000000000000000000000000
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diff --git a/eu_basysbio/source/sql/postgresql/001/schema-001.sql b/eu_basysbio/source/sql/postgresql/001/schema-001.sql
deleted file mode 100755
index 0639856d4e6..00000000000
--- a/eu_basysbio/source/sql/postgresql/001/schema-001.sql
+++ /dev/null
@@ -1,168 +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: 2010-02-08 11:50 */
-/* Model version: Version 2010-02-08 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-CREATE DOMAIN IDENTIFIER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN HEADER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(100);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMN_VALUES (
- DACO_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE REAL,
- CONSTRAINT PK_DATA_COLUMN_VALUES PRIMARY KEY (DACO_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_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)
-);
-
-/* ---------------------------------------------------------------------- */
-/* 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 "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMNS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- HEADER HEADER NOT NULL,
- CONSTRAINT PK_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMNS (
- ID BIGSERIAL NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- EXPERIMENT_CODE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATE_CODE PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATE_CODE PROPERTY NOT NULL,
- CELLOC PROPERTY NOT NULL,
- TIME_SERIES_DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CONTROLLED_GENE PROPERTY NOT NULL,
- CONSTRAINT PK_DATA_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMN_VALUES (
- COLU_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE IDENTIFIER,
- CONSTRAINT PK_COLUMN_VALUES PRIMARY KEY (COLU_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ROWS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ROWS (
- ID BIGSERIAL NOT NULL,
- CONSTRAINT PK_ROWS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT ROWS_DATA_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT EXPERIMENTS_DATA_SETS
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT SAMPLES_DATA_COLUMNS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT ROWS_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
diff --git a/eu_basysbio/source/sql/postgresql/002/grants-002.sql b/eu_basysbio/source/sql/postgresql/002/grants-002.sql
deleted file mode 100644
index b5d8b745f80..00000000000
--- a/eu_basysbio/source/sql/postgresql/002/grants-002.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE SAMPLES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE ROWS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readonly;
-
-GRANT ALL PRIVILEGES ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE ROWS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readwrite;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/002/schema-002.pdf b/eu_basysbio/source/sql/postgresql/002/schema-002.pdf
deleted file mode 100755
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diff --git a/eu_basysbio/source/sql/postgresql/002/schema-002.sql b/eu_basysbio/source/sql/postgresql/002/schema-002.sql
deleted file mode 100755
index 0639856d4e6..00000000000
--- a/eu_basysbio/source/sql/postgresql/002/schema-002.sql
+++ /dev/null
@@ -1,168 +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: 2010-02-08 11:50 */
-/* Model version: Version 2010-02-08 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-CREATE DOMAIN IDENTIFIER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN HEADER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(100);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMN_VALUES (
- DACO_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE REAL,
- CONSTRAINT PK_DATA_COLUMN_VALUES PRIMARY KEY (DACO_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_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)
-);
-
-/* ---------------------------------------------------------------------- */
-/* 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 "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMNS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- HEADER HEADER NOT NULL,
- CONSTRAINT PK_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMNS (
- ID BIGSERIAL NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- EXPERIMENT_CODE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATE_CODE PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATE_CODE PROPERTY NOT NULL,
- CELLOC PROPERTY NOT NULL,
- TIME_SERIES_DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CONTROLLED_GENE PROPERTY NOT NULL,
- CONSTRAINT PK_DATA_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMN_VALUES (
- COLU_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE IDENTIFIER,
- CONSTRAINT PK_COLUMN_VALUES PRIMARY KEY (COLU_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ROWS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ROWS (
- ID BIGSERIAL NOT NULL,
- CONSTRAINT PK_ROWS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT ROWS_DATA_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT EXPERIMENTS_DATA_SETS
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT SAMPLES_DATA_COLUMNS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT ROWS_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
diff --git a/eu_basysbio/source/sql/postgresql/003/grants-003.sql b/eu_basysbio/source/sql/postgresql/003/grants-003.sql
deleted file mode 100644
index b5d8b745f80..00000000000
--- a/eu_basysbio/source/sql/postgresql/003/grants-003.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE SAMPLES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE ROWS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readonly;
-
-GRANT ALL PRIVILEGES ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE ROWS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readwrite;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/003/schema-003.png b/eu_basysbio/source/sql/postgresql/003/schema-003.png
deleted file mode 100755
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diff --git a/eu_basysbio/source/sql/postgresql/003/schema-003.sql b/eu_basysbio/source/sql/postgresql/003/schema-003.sql
deleted file mode 100755
index 6db8e70d364..00000000000
--- a/eu_basysbio/source/sql/postgresql/003/schema-003.sql
+++ /dev/null
@@ -1,168 +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: 2010-04-13 14:59 */
-/* Model version: Version 2010-04-13 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-CREATE DOMAIN IDENTIFIER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN HEADER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(100);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMN_VALUES (
- DACO_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE REAL,
- CONSTRAINT PK_DATA_COLUMN_VALUES PRIMARY KEY (DACO_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_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)
-);
-
-/* ---------------------------------------------------------------------- */
-/* 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 "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMNS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- HEADER HEADER NOT NULL,
- CONSTRAINT PK_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMNS (
- ID BIGSERIAL NOT NULL,
- SAMP_ID TECH_ID,
- DASE_ID TECH_ID NOT NULL,
- EXPERIMENT_CODE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATE_CODE PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATE_CODE PROPERTY NOT NULL,
- CELLOC PROPERTY NOT NULL,
- TIME_SERIES_DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CONTROLLED_GENE PROPERTY NOT NULL,
- CONSTRAINT PK_DATA_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMN_VALUES (
- COLU_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE IDENTIFIER,
- CONSTRAINT PK_COLUMN_VALUES PRIMARY KEY (COLU_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ROWS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ROWS (
- ID BIGSERIAL NOT NULL,
- CONSTRAINT PK_ROWS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT ROWS_DATA_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT EXPERIMENTS_DATA_SETS
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT SAMPLES_DATA_COLUMNS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT ROWS_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
diff --git a/eu_basysbio/source/sql/postgresql/004/grants-004.sql b/eu_basysbio/source/sql/postgresql/004/grants-004.sql
deleted file mode 100644
index b5d8b745f80..00000000000
--- a/eu_basysbio/source/sql/postgresql/004/grants-004.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE SAMPLES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE ROWS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readonly;
-
-GRANT ALL PRIVILEGES ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE ROWS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readwrite;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/004/schema-004.png b/eu_basysbio/source/sql/postgresql/004/schema-004.png
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diff --git a/eu_basysbio/source/sql/postgresql/004/schema-004.sql b/eu_basysbio/source/sql/postgresql/004/schema-004.sql
deleted file mode 100755
index b3cffe07f27..00000000000
--- a/eu_basysbio/source/sql/postgresql/004/schema-004.sql
+++ /dev/null
@@ -1,170 +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: 2010-05-25 10:30 */
-/* Model version: Version 2010-05-25 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-CREATE DOMAIN IDENTIFIER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN HEADER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(100);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMN_VALUES (
- DACO_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE REAL,
- CONSTRAINT PK_DATA_COLUMN_VALUES PRIMARY KEY (DACO_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_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)
-);
-
-/* ---------------------------------------------------------------------- */
-/* 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 "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMNS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- HEADER HEADER NOT NULL,
- CONSTRAINT PK_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMNS (
- ID BIGSERIAL NOT NULL,
- SAMP_ID TECH_ID,
- DASE_ID TECH_ID NOT NULL,
- EXPERIMENT_CODE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATE_CODE PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATE_CODE PROPERTY NOT NULL,
- CELLOC PROPERTY NOT NULL,
- TIME_SERIES_DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CONTROLLED_GENE PROPERTY NOT NULL,
- GROWTH_PHASE PROPERTY,
- GENOTYPE PROPERTY,
- CONSTRAINT PK_DATA_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMN_VALUES (
- COLU_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE IDENTIFIER,
- CONSTRAINT PK_COLUMN_VALUES PRIMARY KEY (COLU_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ROWS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ROWS (
- ID BIGSERIAL NOT NULL,
- CONSTRAINT PK_ROWS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT ROWS_DATA_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID);
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT EXPERIMENTS_DATA_SETS
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT SAMPLES_DATA_COLUMNS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID);
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT ROWS_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
diff --git a/eu_basysbio/source/sql/postgresql/005/grants-005.sql b/eu_basysbio/source/sql/postgresql/005/grants-005.sql
deleted file mode 100644
index b5d8b745f80..00000000000
--- a/eu_basysbio/source/sql/postgresql/005/grants-005.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE SAMPLES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE ROWS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readonly;
-
-GRANT ALL PRIVILEGES ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE ROWS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readwrite;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/005/schema-005.png b/eu_basysbio/source/sql/postgresql/005/schema-005.png
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diff --git a/eu_basysbio/source/sql/postgresql/005/schema-005.sql b/eu_basysbio/source/sql/postgresql/005/schema-005.sql
deleted file mode 100755
index 1b72c4fc69e..00000000000
--- a/eu_basysbio/source/sql/postgresql/005/schema-005.sql
+++ /dev/null
@@ -1,170 +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: 2010-06-14 08:19 */
-/* Model version: Version 2010-06-14 */
-/* ---------------------------------------------------------------------- */
-
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-CREATE DOMAIN IDENTIFIER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS CHARACTER VARYING(40);
-
-CREATE DOMAIN HEADER AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(100);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-/* ---------------------------------------------------------------------- */
-/* Tables */
-/* ---------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMN_VALUES (
- DACO_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE REAL,
- CONSTRAINT PK_DATA_COLUMN_VALUES PRIMARY KEY (DACO_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "SAMPLES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE SAMPLES (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
- CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- EXPE_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)
-);
-
-/* ---------------------------------------------------------------------- */
-/* 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 "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMNS (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- HEADER HEADER NOT NULL,
- CONSTRAINT PK_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_COLUMNS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_COLUMNS (
- ID BIGSERIAL NOT NULL,
- SAMP_ID TECH_ID,
- DASE_ID TECH_ID NOT NULL,
- EXPERIMENT_CODE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATE_CODE PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATE_CODE PROPERTY NOT NULL,
- CELLOC PROPERTY NOT NULL,
- TIME_SERIES_DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CONTROLLED_GENE PROPERTY NOT NULL,
- GROWTH_PHASE PROPERTY,
- GENOTYPE PROPERTY,
- CONSTRAINT PK_DATA_COLUMNS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "COLUMN_VALUES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE COLUMN_VALUES (
- COLU_ID TECH_ID NOT NULL,
- ROW_ID TECH_ID NOT NULL,
- VALUE IDENTIFIER,
- CONSTRAINT PK_COLUMN_VALUES PRIMARY KEY (COLU_ID, ROW_ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "ROWS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE ROWS (
- ID BIGSERIAL NOT NULL,
- CONSTRAINT PK_ROWS PRIMARY KEY (ID)
-);
-
-/* ---------------------------------------------------------------------- */
-/* Foreign key constraints */
-/* ---------------------------------------------------------------------- */
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT ROWS_DATA_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
-
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID) ON DELETE CASCADE;
-
-ALTER TABLE DATA_SETS ADD CONSTRAINT EXPERIMENTS_DATA_SETS
- FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
-
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT SAMPLES_DATA_COLUMNS
- FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
-
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID) ON DELETE CASCADE;
-
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT ROWS_COLUMN_VALUES
- FOREIGN KEY (ROW_ID) REFERENCES ROWS (ID);
diff --git a/eu_basysbio/source/sql/postgresql/006/schema-006.dez b/eu_basysbio/source/sql/postgresql/006/schema-006.dez
deleted file mode 100644
index dd7d394d2ef..00000000000
--- a/eu_basysbio/source/sql/postgresql/006/schema-006.dez
+++ /dev/null
@@ -1,2426 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?><dezign>
-
-<FILEFORMATVERSION>51</FILEFORMATVERSION>
-<VERSION>
-<PROJECTSETTINGS>
-<PROJECTFILENAME>U:\basysbio\schema-006.dez</PROJECTFILENAME>
-<MODIFIED>2010-09-08</MODIFIED>
-<CREATED>2010-09-08</CREATED>
-<CREATED2></CREATED2>
-<PROJECTNAME></PROJECTNAME>
-<DESCRIPTION></DESCRIPTION>
-<AUTHOR></AUTHOR>
-<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES></LASTGENERATEDFILES>
-</PROJECTSETTINGS>
-<CONNECTIONSETTINGS>
-<SQLFILE>U:\basysbio\schema-006.sql</SQLFILE>
-<CONNECTIONTYPE>SQLFILE</CONNECTIONTYPE>
-<DBID>postgresql83</DBID>
-</CONNECTIONSETTINGS>
-<DATADICT>
-<DBID>postgresql83</DBID>
-<LASTID>14</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>
-</DDSETTINGS>
-<DOMAINS>
-<DOMAIN>
-<NAME>TECH_ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
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-<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>PROPERTY</NAME>
-<ID>4</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>INTEGER</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-</DT>
-</DOMAIN>
-<DOMAIN>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
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-</DT>
-</DOMAIN>
-</DOMAINS>
-<ENTITIES>
-<ENT>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
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-<NAMETEMPLATE>DATA_PK</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
-<DT>
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-<INC>1</INC>
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-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
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-<ATTRIBUTEIDS>
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-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UPLOADER_EMAIL</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
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-</ATTR>
-<ATTR>
-<NAME>EXP_PERM_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>3</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>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>DATA_BK_UK</NAME>
-<NAMETEMPLATE>DATA_BK_UK</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>TIME_SERIES</NAME>
-<NAMETEMPLATE>TISE_PK</NAMETEMPLATE>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>27</ATTRLASTID>
-<IDXLASTID>17</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>TISE_PK</NAME>
-<NAMETEMPLATE>TISE_PK</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>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>ROW_INDEX</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>COLUMN_INDEX</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>VALUE_GROUP_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>IDENTIFIER</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>IDENTIFIER_TYPE</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>8</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>IDENTIFIER_HUMAN_READABLE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>BSB_ID</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CONFIDENCE_LEVEL</NAME>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CONTROLLED_GENE</NAME>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>NUMBER_OF_REPLICATES</NAME>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>14</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CULTIVATION_METHOD</NAME>
-<ID>15</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>15</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>16</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TIME_POINT</NAME>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>17</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TIME_POINT_TYPE</NAME>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>18</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>19</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CELL_LOCATION</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>20</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DATA_SET_TYPE</NAME>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>21</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE_TYPE</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>22</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIT</NAME>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>23</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SCALE</NAME>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>24</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BI_ID</NAME>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>25</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CG</NAME>
-<ID>26</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>26</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<ID>27</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>TISE_DASE_FK_I</NAME>
-<NAMETEMPLATE>TISE_DASE_FK_I</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>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_GROUP_ID_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_GROUP_ID_I</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_GROUP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_IDENTIFIER_I</NAME>
-<NAMETEMPLATE>TISE_IDENTIFIER_I</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDENTIFIER</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>7</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_EXPERIMENT_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_EXPERIMENT_TYPE_I</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>14</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CULTIVATION_METHOD_I</NAME>
-<NAMETEMPLATE>TISE_CULTIVATION_METHOD_I</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CULTIVATION_METHOD</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<NAMETEMPLATE>TISE_BIOLOGICAL_REPLICATES_I</NAMETEMPLATE>
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-<SCHEMA></SCHEMA>
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-<IDXCOLS>
-<IDXCOL>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>16</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TIME_POINT_I</NAME>
-<NAMETEMPLATE>TISE_TIME_POINT_I</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
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-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>17</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
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-<NAMETEMPLATE>TISE_TIME_POINT_TYPE_I</NAMETEMPLATE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>18</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TECHNICAL_REPLICATES_I</NAME>
-<NAMETEMPLATE>TISE_TECHNICAL_REPLICATES_I</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TECHNICAL_REPLICATES</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>19</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CELL_LOCATION_I</NAME>
-<NAMETEMPLATE>TISE_CELL_LOCATION_I</NAMETEMPLATE>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CELL_LOCATION</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>20</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_DATA_SET_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_DATA_SET_TYPE_I</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DATA_SET_TYPE</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>21</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_TYPE_I</NAMETEMPLATE>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
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-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_TYPE</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>22</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_UNIT_I</NAME>
-<NAMETEMPLATE>TISE_UNIT_I</NAMETEMPLATE>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIT</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>23</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_SCALE_I</NAME>
-<NAMETEMPLATE>TISE_SCALE_I</NAMETEMPLATE>
-<ID>15</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SCALE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>24</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_BI_ID_I</NAME>
-<NAMETEMPLATE>TISE_BI_ID_I</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>BI_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>25</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CG_I</NAME>
-<NAMETEMPLATE>TISE_CG_I</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CG</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>26</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>CHIP_CHIP_DATA</NAME>
-<NAMETEMPLATE>CHCH_PK</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>26</ATTRLASTID>
-<IDXLASTID>8</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>CHCH_PK</NAME>
-<NAMETEMPLATE>CHCH_PK</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>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>ROW_INDEX</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BSU_IDENTIFIER</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>GENE_NAME</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>GENE_FUNCTION</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ARRAY_DESIGN</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MICROARRAY_ID</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>
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-<ATTR>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>11</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>12</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>13</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CELL_LOCATION</NAME>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>14</ATTRIBUTEID>
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-</NNCON>
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-<NAME>GROWTH_PHASE</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>15</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>GENOTYPE</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>16</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>CHIP_PEAK_POSITION_VALUE</NAME>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHIP_PEAK_POSITION_SCALE</NAME>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>18</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHIP_LOCAL_HEIGHT_VALUE</NAME>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHIP_LOCAL_HEIGHT_SCALE</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>20</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CHIP_SCORE_VALUE</NAME>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CHIP_SCORE_SCALE</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>22</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>INTERGENIC</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>-1</DOMAINID>
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-<DTLISTNAME>BOOLEAN</DTLISTNAME>
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-<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>23</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
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-<ATTR>
-<NAME>NEARBY_GENE_NAMES</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
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diff --git a/eu_basysbio/source/sql/postgresql/006/schema-006.sql b/eu_basysbio/source/sql/postgresql/006/schema-006.sql
deleted file mode 100644
index 80ffc17fb97..00000000000
--- a/eu_basysbio/source/sql/postgresql/006/schema-006.sql
+++ /dev/null
@@ -1,153 +0,0 @@
-/**************************************************************************/
-/* Schema Version: 006 */
-/* Author: Bernd Rinn, 2010, CISD */
-/**************************************************************************/
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS VARCHAR(40);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- UPLOADER_EMAIL PROPERTY NOT NULL,
- EXP_CODE CODE NOT NULL,
- EXP_PERM_ID CODE NOT NULL,
- CONSTRAINT DATA_PK PRIMARY KEY (ID),
- CONSTRAINT DATA_BK_UK UNIQUE (PERM_ID)
-);
-
-
-/* ---------------------------------------------------------------------- */
-/* Add table "TIME_SERIES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE TIME_SERIES_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE TIME_SERIES (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
- COLUMN_INDEX INTEGER NOT NULL,
- VALUE_GROUP_ID TECH_ID NOT NULL,
-
- IDENTIFIER PROPERTY NOT NULL,
- IDENTIFIER_TYPE PROPERTY NOT NULL,
- IDENTIFIER_HUMAN_READABLE PROPERTY,
- BSB_ID PROPERTY,
- CONFIDENCE_LEVEL PROPERTY,
- CONTROLLED_GENE PROPERTY,
- NUMBER_OF_REPLICATES INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- UNIT PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CG PROPERTY NOT NULL,
- VALUE REAL,
-
- CONSTRAINT TISE_PK PRIMARY KEY (ID),
- CONSTRAINT TISE_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add indices */
-/* ---------------------------------------------------------------------- */
-
-CREATE INDEX TISE_DASE_FK_I ON TIME_SERIES (DASE_ID);
-CREATE INDEX TISE_VALUE_GROUP_ID_I ON TIME_SERIES (VALUE_GROUP_ID);
-CREATE INDEX TISE_IDENTIFIER_I ON TIME_SERIES (IDENTIFIER);
-CREATE INDEX TISE_EXPERIMENT_TYPE_I ON TIME_SERIES (EXPERIMENT_TYPE);
-CREATE INDEX TISE_CULTIVATION_METHOD_I ON TIME_SERIES (CULTIVATION_METHOD);
-CREATE INDEX TISE_BIOLOGICAL_REPLICATES_I ON TIME_SERIES (BIOLOGICAL_REPLICATES);
-CREATE INDEX TISE_TIME_POINT_I ON TIME_SERIES (TIME_POINT);
-CREATE INDEX TISE_TIME_POINT_TYPE_I ON TIME_SERIES (TIME_POINT_TYPE);
-CREATE INDEX TISE_TECHNICAL_REPLICATES_I ON TIME_SERIES (TECHNICAL_REPLICATES);
-CREATE INDEX TISE_CELL_LOCATION_I ON TIME_SERIES (CELL_LOCATION);
-CREATE INDEX TISE_DATA_SET_TYPE_I ON TIME_SERIES (DATA_SET_TYPE);
-CREATE INDEX TISE_VALUE_TYPE_I ON TIME_SERIES (VALUE_TYPE);
-CREATE INDEX TISE_UNIT_I ON TIME_SERIES (UNIT);
-CREATE INDEX TISE_SCALE_I ON TIME_SERIES (SCALE);
-CREATE INDEX TISE_BI_ID_I ON TIME_SERIES (BI_ID);
-CREATE INDEX TISE_CG_I ON TIME_SERIES (CG);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "CHIP_CHIP_DATA" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE CHIP_CHIP_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE CHIP_CHIP_DATA (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
-
- BSU_IDENTIFIER PROPERTY NOT NULL,
- GENE_NAME PROPERTY,
- GENE_FUNCTION PROPERTY,
- ARRAY_DESIGN PROPERTY,
- MICROARRAY_ID INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- GROWTH_PHASE PROPERTY NOT NULL,
- GENOTYPE PROPERTY NOT NULL,
-
- CHIP_PEAK_POSITION_VALUE INTEGER,
- CHIP_PEAK_POSITION_SCALE PROPERTY NOT NULL,
- CHIP_LOCAL_HEIGHT_VALUE REAL,
- CHIP_LOCAL_HEIGHT_SCALE PROPERTY NOT NULL,
- CHIP_SCORE_VALUE REAL,
- CHIP_SCORE_SCALE PROPERTY NOT NULL,
-
- INTERGENIC BOOLEAN NOT NULL,
- NEARBY_GENE_NAMES PROPERTY,
- NEARBY_GENE_IDS PROPERTY,
- DISTANCES_FROM_START PROPERTY,
-
- CONSTRAINT CHCH_PK PRIMARY KEY (ID),
- CONSTRAINT CHCH_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-CREATE INDEX CHCH_EXPERIMENT_TYPE_I ON CHIP_CHIP_DATA (EXPERIMENT_TYPE);
-CREATE INDEX CHCH_CULTIVATION_METHOD_I ON CHIP_CHIP_DATA (CULTIVATION_METHOD);
-CREATE INDEX CHCH_BIOLOGICAL_REPLICATES_I ON CHIP_CHIP_DATA (BIOLOGICAL_REPLICATES);
-CREATE INDEX CHCH_TECHNICAL_REPLICATES_I ON CHIP_CHIP_DATA (TECHNICAL_REPLICATES);
-CREATE INDEX CHCH_CELL_LOCATION_I ON CHIP_CHIP_DATA (CELL_LOCATION);
-CREATE INDEX CHCH_GROWTH_PHASE_I ON CHIP_CHIP_DATA (GROWTH_PHASE);
-CREATE INDEX CHCH_GENOTYPE_I ON CHIP_CHIP_DATA (GENOTYPE);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-
diff --git a/eu_basysbio/source/sql/postgresql/007/grants-007.sql b/eu_basysbio/source/sql/postgresql/007/grants-007.sql
deleted file mode 100644
index d22de08a7f3..00000000000
--- a/eu_basysbio/source/sql/postgresql/007/grants-007.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE TIME_SERIES TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readonly;
-
-GRANT ALL ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE TIME_SERIES TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readwrite;
diff --git a/eu_basysbio/source/sql/postgresql/007/schema-007.dez b/eu_basysbio/source/sql/postgresql/007/schema-007.dez
deleted file mode 100644
index dd7d394d2ef..00000000000
--- a/eu_basysbio/source/sql/postgresql/007/schema-007.dez
+++ /dev/null
@@ -1,2426 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?><dezign>
-
-<FILEFORMATVERSION>51</FILEFORMATVERSION>
-<VERSION>
-<PROJECTSETTINGS>
-<PROJECTFILENAME>U:\basysbio\schema-006.dez</PROJECTFILENAME>
-<MODIFIED>2010-09-08</MODIFIED>
-<CREATED>2010-09-08</CREATED>
-<CREATED2></CREATED2>
-<PROJECTNAME></PROJECTNAME>
-<DESCRIPTION></DESCRIPTION>
-<AUTHOR></AUTHOR>
-<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES></LASTGENERATEDFILES>
-</PROJECTSETTINGS>
-<CONNECTIONSETTINGS>
-<SQLFILE>U:\basysbio\schema-006.sql</SQLFILE>
-<CONNECTIONTYPE>SQLFILE</CONNECTIONTYPE>
-<DBID>postgresql83</DBID>
-</CONNECTIONSETTINGS>
-<DATADICT>
-<DBID>postgresql83</DBID>
-<LASTID>14</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>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
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-<DTLISTNAME>BIGINT</DTLISTNAME>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<DTLISTNAME>INTEGER</DTLISTNAME>
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-<NAME></NAME>
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-<DTLISTNAME>INTEGER</DTLISTNAME>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
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-<NAME></NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<NAME>IDENTIFIER</NAME>
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-<SCHEMA></SCHEMA>
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-<DOMAINID>4</DOMAINID>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
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-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
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-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>
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-<CONTYPE>5</CONTYPE>
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-</NNCON>
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-<NAME>IDENTIFIER_HUMAN_READABLE</NAME>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
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-<ATTR>
-<NAME>BSB_ID</NAME>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
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-</DT>
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-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
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-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
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-<SCHEMA></SCHEMA>
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-<DTLISTNAME>INTEGER</DTLISTNAME>
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-<LE>1000</LE>
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-<NAME></NAME>
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-<SCHEMA></SCHEMA>
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-<SCHEMA></SCHEMA>
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-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>23</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SCALE</NAME>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>24</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BI_ID</NAME>
-<ID>25</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>25</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CG</NAME>
-<ID>26</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>26</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<ID>27</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>TISE_DASE_FK_I</NAME>
-<NAMETEMPLATE>TISE_DASE_FK_I</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>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_GROUP_ID_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_GROUP_ID_I</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_GROUP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_IDENTIFIER_I</NAME>
-<NAMETEMPLATE>TISE_IDENTIFIER_I</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDENTIFIER</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>7</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_EXPERIMENT_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_EXPERIMENT_TYPE_I</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>14</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CULTIVATION_METHOD_I</NAME>
-<NAMETEMPLATE>TISE_CULTIVATION_METHOD_I</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CULTIVATION_METHOD</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>15</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_BIOLOGICAL_REPLICATES_I</NAME>
-<NAMETEMPLATE>TISE_BIOLOGICAL_REPLICATES_I</NAMETEMPLATE>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>16</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TIME_POINT_I</NAME>
-<NAMETEMPLATE>TISE_TIME_POINT_I</NAMETEMPLATE>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>17</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TIME_POINT_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_TIME_POINT_TYPE_I</NAMETEMPLATE>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>18</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TECHNICAL_REPLICATES_I</NAME>
-<NAMETEMPLATE>TISE_TECHNICAL_REPLICATES_I</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>19</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CELL_LOCATION_I</NAME>
-<NAMETEMPLATE>TISE_CELL_LOCATION_I</NAMETEMPLATE>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CELL_LOCATION</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>20</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_DATA_SET_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_DATA_SET_TYPE_I</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DATA_SET_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>21</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_TYPE_I</NAMETEMPLATE>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>22</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_UNIT_I</NAME>
-<NAMETEMPLATE>TISE_UNIT_I</NAMETEMPLATE>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIT</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>23</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_SCALE_I</NAME>
-<NAMETEMPLATE>TISE_SCALE_I</NAMETEMPLATE>
-<ID>15</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SCALE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>24</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_BI_ID_I</NAME>
-<NAMETEMPLATE>TISE_BI_ID_I</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>BI_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>25</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CG_I</NAME>
-<NAMETEMPLATE>TISE_CG_I</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CG</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>26</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>CHIP_CHIP_DATA</NAME>
-<NAMETEMPLATE>CHCH_PK</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>26</ATTRLASTID>
-<IDXLASTID>8</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>CHCH_PK</NAME>
-<NAMETEMPLATE>CHCH_PK</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>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>ROW_INDEX</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BSU_IDENTIFIER</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>GENE_NAME</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>GENE_FUNCTION</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ARRAY_DESIGN</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>MICROARRAY_ID</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>CULTIVATION_METHOD</NAME>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>11</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>12</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>13</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CELL_LOCATION</NAME>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
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diff --git a/eu_basysbio/source/sql/postgresql/007/schema-007.sql b/eu_basysbio/source/sql/postgresql/007/schema-007.sql
deleted file mode 100644
index 80ffc17fb97..00000000000
--- a/eu_basysbio/source/sql/postgresql/007/schema-007.sql
+++ /dev/null
@@ -1,153 +0,0 @@
-/**************************************************************************/
-/* Schema Version: 006 */
-/* Author: Bernd Rinn, 2010, CISD */
-/**************************************************************************/
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS VARCHAR(40);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- UPLOADER_EMAIL PROPERTY NOT NULL,
- EXP_CODE CODE NOT NULL,
- EXP_PERM_ID CODE NOT NULL,
- CONSTRAINT DATA_PK PRIMARY KEY (ID),
- CONSTRAINT DATA_BK_UK UNIQUE (PERM_ID)
-);
-
-
-/* ---------------------------------------------------------------------- */
-/* Add table "TIME_SERIES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE TIME_SERIES_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE TIME_SERIES (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
- COLUMN_INDEX INTEGER NOT NULL,
- VALUE_GROUP_ID TECH_ID NOT NULL,
-
- IDENTIFIER PROPERTY NOT NULL,
- IDENTIFIER_TYPE PROPERTY NOT NULL,
- IDENTIFIER_HUMAN_READABLE PROPERTY,
- BSB_ID PROPERTY,
- CONFIDENCE_LEVEL PROPERTY,
- CONTROLLED_GENE PROPERTY,
- NUMBER_OF_REPLICATES INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- UNIT PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- BI_ID PROPERTY NOT NULL,
- CG PROPERTY NOT NULL,
- VALUE REAL,
-
- CONSTRAINT TISE_PK PRIMARY KEY (ID),
- CONSTRAINT TISE_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add indices */
-/* ---------------------------------------------------------------------- */
-
-CREATE INDEX TISE_DASE_FK_I ON TIME_SERIES (DASE_ID);
-CREATE INDEX TISE_VALUE_GROUP_ID_I ON TIME_SERIES (VALUE_GROUP_ID);
-CREATE INDEX TISE_IDENTIFIER_I ON TIME_SERIES (IDENTIFIER);
-CREATE INDEX TISE_EXPERIMENT_TYPE_I ON TIME_SERIES (EXPERIMENT_TYPE);
-CREATE INDEX TISE_CULTIVATION_METHOD_I ON TIME_SERIES (CULTIVATION_METHOD);
-CREATE INDEX TISE_BIOLOGICAL_REPLICATES_I ON TIME_SERIES (BIOLOGICAL_REPLICATES);
-CREATE INDEX TISE_TIME_POINT_I ON TIME_SERIES (TIME_POINT);
-CREATE INDEX TISE_TIME_POINT_TYPE_I ON TIME_SERIES (TIME_POINT_TYPE);
-CREATE INDEX TISE_TECHNICAL_REPLICATES_I ON TIME_SERIES (TECHNICAL_REPLICATES);
-CREATE INDEX TISE_CELL_LOCATION_I ON TIME_SERIES (CELL_LOCATION);
-CREATE INDEX TISE_DATA_SET_TYPE_I ON TIME_SERIES (DATA_SET_TYPE);
-CREATE INDEX TISE_VALUE_TYPE_I ON TIME_SERIES (VALUE_TYPE);
-CREATE INDEX TISE_UNIT_I ON TIME_SERIES (UNIT);
-CREATE INDEX TISE_SCALE_I ON TIME_SERIES (SCALE);
-CREATE INDEX TISE_BI_ID_I ON TIME_SERIES (BI_ID);
-CREATE INDEX TISE_CG_I ON TIME_SERIES (CG);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "CHIP_CHIP_DATA" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE CHIP_CHIP_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE CHIP_CHIP_DATA (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
-
- BSU_IDENTIFIER PROPERTY NOT NULL,
- GENE_NAME PROPERTY,
- GENE_FUNCTION PROPERTY,
- ARRAY_DESIGN PROPERTY,
- MICROARRAY_ID INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- GROWTH_PHASE PROPERTY NOT NULL,
- GENOTYPE PROPERTY NOT NULL,
-
- CHIP_PEAK_POSITION_VALUE INTEGER,
- CHIP_PEAK_POSITION_SCALE PROPERTY NOT NULL,
- CHIP_LOCAL_HEIGHT_VALUE REAL,
- CHIP_LOCAL_HEIGHT_SCALE PROPERTY NOT NULL,
- CHIP_SCORE_VALUE REAL,
- CHIP_SCORE_SCALE PROPERTY NOT NULL,
-
- INTERGENIC BOOLEAN NOT NULL,
- NEARBY_GENE_NAMES PROPERTY,
- NEARBY_GENE_IDS PROPERTY,
- DISTANCES_FROM_START PROPERTY,
-
- CONSTRAINT CHCH_PK PRIMARY KEY (ID),
- CONSTRAINT CHCH_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-CREATE INDEX CHCH_EXPERIMENT_TYPE_I ON CHIP_CHIP_DATA (EXPERIMENT_TYPE);
-CREATE INDEX CHCH_CULTIVATION_METHOD_I ON CHIP_CHIP_DATA (CULTIVATION_METHOD);
-CREATE INDEX CHCH_BIOLOGICAL_REPLICATES_I ON CHIP_CHIP_DATA (BIOLOGICAL_REPLICATES);
-CREATE INDEX CHCH_TECHNICAL_REPLICATES_I ON CHIP_CHIP_DATA (TECHNICAL_REPLICATES);
-CREATE INDEX CHCH_CELL_LOCATION_I ON CHIP_CHIP_DATA (CELL_LOCATION);
-CREATE INDEX CHCH_GROWTH_PHASE_I ON CHIP_CHIP_DATA (GROWTH_PHASE);
-CREATE INDEX CHCH_GENOTYPE_I ON CHIP_CHIP_DATA (GENOTYPE);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-
diff --git a/eu_basysbio/source/sql/postgresql/008/grants-008.sql b/eu_basysbio/source/sql/postgresql/008/grants-008.sql
deleted file mode 100644
index d22de08a7f3..00000000000
--- a/eu_basysbio/source/sql/postgresql/008/grants-008.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE TIME_SERIES TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readonly;
-
-GRANT ALL ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE TIME_SERIES TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readwrite;
diff --git a/eu_basysbio/source/sql/postgresql/008/schema-008.dez b/eu_basysbio/source/sql/postgresql/008/schema-008.dez
deleted file mode 100644
index cafbf45ebb1..00000000000
--- a/eu_basysbio/source/sql/postgresql/008/schema-008.dez
+++ /dev/null
@@ -1,2356 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?><dezign>
-
-<FILEFORMATVERSION>51</FILEFORMATVERSION>
-<VERSION>
-<PROJECTSETTINGS>
-<PROJECTFILENAME>U:\basysbio\schema-006.dez</PROJECTFILENAME>
-<MODIFIED>2010-10-03</MODIFIED>
-<CREATED>2010-09-08</CREATED>
-<CREATED2></CREATED2>
-<PROJECTNAME></PROJECTNAME>
-<DESCRIPTION></DESCRIPTION>
-<AUTHOR></AUTHOR>
-<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES></LASTGENERATEDFILES>
-</PROJECTSETTINGS>
-<CONNECTIONSETTINGS>
-<SQLFILE>U:\basysbio\schema-006.sql</SQLFILE>
-<CONNECTIONTYPE>SQLFILE</CONNECTIONTYPE>
-<DBID>postgresql83</DBID>
-</CONNECTIONSETTINGS>
-<DATADICT>
-<DBID>postgresql83</DBID>
-<LASTID>14</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>
-</DDSETTINGS>
-<DOMAINS>
-<DOMAIN>
-<NAME>TECH_ID</NAME>
-<ID>2</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>BIGINT</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>CODE</NAME>
-<ID>3</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>PROPERTY</NAME>
-<ID>4</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>INTEGER</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-<DOMAIN>
-<NAME>REAL</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</DOMAIN>
-</DOMAINS>
-<ENTITIES>
-<ENT>
-<NAME>DATA_SETS</NAME>
-<NAMETEMPLATE>DATA_PK</NAMETEMPLATE>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
-<IDXLASTID>1</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>2</CONLASTID>
-<PKCON>
-<NAME>DATA_PK</NAME>
-<NAMETEMPLATE>DATA_PK</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>3</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>UPLOADER_EMAIL</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXP_CODE</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>3</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>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>EXP_PERM_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>3</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>6</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-</ATTRIBUTES>
-<CONSTRAINTS>
-<CONSTRAINT>
-<NAME>DATA_BK_UK</NAME>
-<NAMETEMPLATE>DATA_BK_UK</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>TIME_SERIES</NAME>
-<NAMETEMPLATE>TISE_PK</NAMETEMPLATE>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>27</ATTRLASTID>
-<IDXLASTID>17</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>TISE_PK</NAME>
-<NAMETEMPLATE>TISE_PK</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>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>ROW_INDEX</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>COLUMN_INDEX</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>VALUE_GROUP_ID</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>IDENTIFIER</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>7</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>IDENTIFIER_TYPE</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>8</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>IDENTIFIER_HUMAN_READABLE</NAME>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>BSB_ID</NAME>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CONFIDENCE_LEVEL</NAME>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>CONTROLLED_GENE</NAME>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>NUMBER_OF_REPLICATES</NAME>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</DOMAINID>
-<DT>
-<DTLISTNAME>INTEGER</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>14</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CULTIVATION_METHOD</NAME>
-<ID>15</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>15</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>16</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TIME_POINT</NAME>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>17</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TIME_POINT_TYPE</NAME>
-<ID>18</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>18</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>19</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>19</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>CELL_LOCATION</NAME>
-<ID>20</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>20</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>DATA_SET_TYPE</NAME>
-<ID>21</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>21</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE_TYPE</NAME>
-<ID>22</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>22</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>UNIT</NAME>
-<ID>23</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>23</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>SCALE</NAME>
-<ID>24</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>24</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>VALUE</NAME>
-<ID>27</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>6</DOMAINID>
-<DT>
-<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-</ATTRIBUTES>
-<INDEXES>
-<INDEX>
-<NAME>TISE_DASE_FK_I</NAME>
-<NAMETEMPLATE>TISE_DASE_FK_I</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>3</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_GROUP_ID_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_GROUP_ID_I</NAMETEMPLATE>
-<ID>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_GROUP_ID</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>6</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_IDENTIFIER_I</NAME>
-<NAMETEMPLATE>TISE_IDENTIFIER_I</NAMETEMPLATE>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>IDENTIFIER</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>7</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_EXPERIMENT_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_EXPERIMENT_TYPE_I</NAMETEMPLATE>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>EXPERIMENT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>14</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CULTIVATION_METHOD_I</NAME>
-<NAMETEMPLATE>TISE_CULTIVATION_METHOD_I</NAMETEMPLATE>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CULTIVATION_METHOD</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>15</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_BIOLOGICAL_REPLICATES_I</NAME>
-<NAMETEMPLATE>TISE_BIOLOGICAL_REPLICATES_I</NAMETEMPLATE>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>BIOLOGICAL_REPLICATES</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>16</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TIME_POINT_I</NAME>
-<NAMETEMPLATE>TISE_TIME_POINT_I</NAMETEMPLATE>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>17</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TIME_POINT_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_TIME_POINT_TYPE_I</NAMETEMPLATE>
-<ID>9</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TIME_POINT_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>18</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_TECHNICAL_REPLICATES_I</NAME>
-<NAMETEMPLATE>TISE_TECHNICAL_REPLICATES_I</NAMETEMPLATE>
-<ID>10</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>TECHNICAL_REPLICATES</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>19</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CELL_LOCATION_I</NAME>
-<NAMETEMPLATE>TISE_CELL_LOCATION_I</NAMETEMPLATE>
-<ID>11</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>CELL_LOCATION</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>20</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_DATA_SET_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_DATA_SET_TYPE_I</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>DATA_SET_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>21</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_VALUE_TYPE_I</NAME>
-<NAMETEMPLATE>TISE_VALUE_TYPE_I</NAMETEMPLATE>
-<ID>13</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>VALUE_TYPE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>22</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_UNIT_I</NAME>
-<NAMETEMPLATE>TISE_UNIT_I</NAMETEMPLATE>
-<ID>14</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>UNIT</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>23</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_SCALE_I</NAME>
-<NAMETEMPLATE>TISE_SCALE_I</NAMETEMPLATE>
-<ID>15</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-<IDXCOL>
-<NAME>SCALE</NAME>
-<ID>0</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<IDXCOLATTRID>24</IDXCOLATTRID>
-</IDXCOL>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_BI_ID_I</NAME>
-<NAMETEMPLATE>TISE_BI_ID_I</NAMETEMPLATE>
-<ID>16</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-</IDXCOLS>
-</INDEX>
-<INDEX>
-<NAME>TISE_CG_I</NAME>
-<NAMETEMPLATE>TISE_CG_I</NAMETEMPLATE>
-<ID>17</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<RELID>0</RELID>
-<AUTOIDXTYPE>0</AUTOIDXTYPE>
-<IDXCOLS>
-</IDXCOLS>
-</INDEX>
-</INDEXES>
-</ENT>
-<ENT>
-<NAME>CHIP_CHIP_DATA</NAME>
-<NAMETEMPLATE>CHCH_PK</NAMETEMPLATE>
-<ID>12</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<ATTRLASTID>26</ATTRLASTID>
-<IDXLASTID>8</IDXLASTID>
-<TRGLASTID>1</TRGLASTID>
-<CONLASTID>1</CONLASTID>
-<PKCON>
-<NAME>CHCH_PK</NAME>
-<NAMETEMPLATE>CHCH_PK</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>3</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>2</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>ROW_INDEX</NAME>
-<ID>4</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>5</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>4</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>BSU_IDENTIFIER</NAME>
-<ID>5</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</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>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
-</ATTR>
-<ATTR>
-<NAME>GENE_NAME</NAME>
-<ID>6</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>GENE_FUNCTION</NAME>
-<ID>7</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
-</ATTR>
-<ATTR>
-<NAME>ARRAY_DESIGN</NAME>
-<ID>8</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<DOMAINID>4</DOMAINID>
-<DT>
-<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
-<LE>1000</LE>
-<SD>0</SD>
-<INC>1</INC>
-</DT>
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diff --git a/eu_basysbio/source/sql/postgresql/008/schema-008.sql b/eu_basysbio/source/sql/postgresql/008/schema-008.sql
deleted file mode 100644
index da01fb2292b..00000000000
--- a/eu_basysbio/source/sql/postgresql/008/schema-008.sql
+++ /dev/null
@@ -1,150 +0,0 @@
-/**************************************************************************/
-/* Schema Version: 006 */
-/* Author: Bernd Rinn, 2010, CISD */
-/**************************************************************************/
-
-/* ---------------------------------------------------------------------- */
-/* Domains */
-/* ---------------------------------------------------------------------- */
-
-CREATE DOMAIN TECH_ID AS BIGINT;
-
-CREATE DOMAIN CODE AS VARCHAR(40);
-
-CREATE DOMAIN PROPERTY AS CHARACTER VARYING(1000);
-
-CREATE DOMAIN INTEGER AS INTEGER;
-
-CREATE DOMAIN REAL AS DOUBLE PRECISION;
-
-/* ---------------------------------------------------------------------- */
-/* Add table "DATA_SETS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE DATA_SETS (
- ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
- UPLOADER_EMAIL PROPERTY NOT NULL,
- EXP_CODE CODE NOT NULL,
- EXP_PERM_ID CODE NOT NULL,
- CONSTRAINT DATA_PK PRIMARY KEY (ID),
- CONSTRAINT DATA_BK_UK UNIQUE (PERM_ID)
-);
-
-
-/* ---------------------------------------------------------------------- */
-/* Add table "TIME_SERIES" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE TIME_SERIES_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE TIME_SERIES (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
- COLUMN_INDEX INTEGER NOT NULL,
- VALUE_GROUP_ID TECH_ID NOT NULL,
-
- IDENTIFIER PROPERTY NOT NULL,
- IDENTIFIER_TYPE PROPERTY NOT NULL,
- IDENTIFIER_HUMAN_READABLE PROPERTY,
- BSB_ID PROPERTY,
- CONFIDENCE_LEVEL PROPERTY,
- CONTROLLED_GENE PROPERTY,
- NUMBER_OF_REPLICATES INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TIME_POINT INTEGER NOT NULL,
- TIME_POINT_TYPE PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- DATA_SET_TYPE PROPERTY NOT NULL,
- VALUE_TYPE PROPERTY NOT NULL,
- UNIT PROPERTY NOT NULL,
- SCALE PROPERTY NOT NULL,
- VALUE REAL,
-
- CONSTRAINT TISE_PK PRIMARY KEY (ID),
- CONSTRAINT TISE_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-/* ---------------------------------------------------------------------- */
-/* Add indices */
-/* ---------------------------------------------------------------------- */
-
-CREATE INDEX TISE_DASE_FK_I ON TIME_SERIES (DASE_ID);
-CREATE INDEX TISE_VALUE_GROUP_ID_I ON TIME_SERIES (VALUE_GROUP_ID);
-CREATE INDEX TISE_IDENTIFIER_I ON TIME_SERIES (IDENTIFIER);
-CREATE INDEX TISE_EXPERIMENT_TYPE_I ON TIME_SERIES (EXPERIMENT_TYPE);
-CREATE INDEX TISE_CONTROLLED_GENE_ID ON TIME_SERIES (CONTROLLED_GENE);
-CREATE INDEX TISE_CULTIVATION_METHOD_I ON TIME_SERIES (CULTIVATION_METHOD);
-CREATE INDEX TISE_BIOLOGICAL_REPLICATES_I ON TIME_SERIES (BIOLOGICAL_REPLICATES);
-CREATE INDEX TISE_TIME_POINT_I ON TIME_SERIES (TIME_POINT);
-CREATE INDEX TISE_TIME_POINT_TYPE_I ON TIME_SERIES (TIME_POINT_TYPE);
-CREATE INDEX TISE_TECHNICAL_REPLICATES_I ON TIME_SERIES (TECHNICAL_REPLICATES);
-CREATE INDEX TISE_CELL_LOCATION_I ON TIME_SERIES (CELL_LOCATION);
-CREATE INDEX TISE_DATA_SET_TYPE_I ON TIME_SERIES (DATA_SET_TYPE);
-CREATE INDEX TISE_VALUE_TYPE_I ON TIME_SERIES (VALUE_TYPE);
-CREATE INDEX TISE_UNIT_I ON TIME_SERIES (UNIT);
-CREATE INDEX TISE_SCALE_I ON TIME_SERIES (SCALE);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "CHIP_CHIP_DATA" */
-/* ---------------------------------------------------------------------- */
-
-CREATE SEQUENCE CHIP_CHIP_VALUE_GROUP_ID_SEQ;
-
-CREATE TABLE CHIP_CHIP_DATA (
- ID BIGSERIAL NOT NULL,
- DASE_ID TECH_ID NOT NULL,
- ROW_INDEX INTEGER NOT NULL,
-
- BSU_IDENTIFIER PROPERTY NOT NULL,
- GENE_NAME PROPERTY,
- GENE_FUNCTION PROPERTY,
- ARRAY_DESIGN PROPERTY,
- MICROARRAY_ID INTEGER,
-
- EXPERIMENT_TYPE PROPERTY NOT NULL,
- CULTIVATION_METHOD PROPERTY NOT NULL,
- BIOLOGICAL_REPLICATES PROPERTY NOT NULL,
- TECHNICAL_REPLICATES PROPERTY NOT NULL,
- CELL_LOCATION PROPERTY NOT NULL,
- GROWTH_PHASE PROPERTY NOT NULL,
- GENOTYPE PROPERTY NOT NULL,
-
- CHIP_PEAK_POSITION_VALUE INTEGER,
- CHIP_PEAK_POSITION_SCALE PROPERTY NOT NULL,
- CHIP_LOCAL_HEIGHT_VALUE REAL,
- CHIP_LOCAL_HEIGHT_SCALE PROPERTY NOT NULL,
- CHIP_SCORE_VALUE REAL,
- CHIP_SCORE_SCALE PROPERTY NOT NULL,
-
- INTERGENIC BOOLEAN NOT NULL,
- NEARBY_GENE_NAMES PROPERTY,
- NEARBY_GENE_IDS PROPERTY,
- DISTANCES_FROM_START PROPERTY,
-
- CONSTRAINT CHCH_PK PRIMARY KEY (ID),
- CONSTRAINT CHCH_DASE_FK FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE
-);
-
-CREATE INDEX CHCH_EXPERIMENT_TYPE_I ON CHIP_CHIP_DATA (EXPERIMENT_TYPE);
-CREATE INDEX CHCH_CULTIVATION_METHOD_I ON CHIP_CHIP_DATA (CULTIVATION_METHOD);
-CREATE INDEX CHCH_BIOLOGICAL_REPLICATES_I ON CHIP_CHIP_DATA (BIOLOGICAL_REPLICATES);
-CREATE INDEX CHCH_TECHNICAL_REPLICATES_I ON CHIP_CHIP_DATA (TECHNICAL_REPLICATES);
-CREATE INDEX CHCH_CELL_LOCATION_I ON CHIP_CHIP_DATA (CELL_LOCATION);
-CREATE INDEX CHCH_GROWTH_PHASE_I ON CHIP_CHIP_DATA (GROWTH_PHASE);
-CREATE INDEX CHCH_GENOTYPE_I ON CHIP_CHIP_DATA (GENOTYPE);
-
-/* ---------------------------------------------------------------------- */
-/* Add table "EVENTS" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE EVENTS (
- LAST_SEEN_DELETION_EVENT_ID BIGINT NOT NULL
-);
-
-
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-001-002.sql b/eu_basysbio/source/sql/postgresql/migration/migration-001-002.sql
deleted file mode 100644
index b5d8b745f80..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-001-002.sql
+++ /dev/null
@@ -1,33 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE SAMPLES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EXPERIMENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_COLUMNS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE COLUMN_VALUES TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE ROWS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readonly;
-
-GRANT ALL PRIVILEGES ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE DATA_COLUMNS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE DATA_COLUMNS_ID_SEQ TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE COLUMN_VALUES TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON TABLE ROWS TO GROUP basysbio_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE ROWS_ID_SEQ TO GROUP basysbio_readwrite;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-002-003.sql b/eu_basysbio/source/sql/postgresql/migration/migration-002-003.sql
deleted file mode 100644
index 85d38e2347d..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-002-003.sql
+++ /dev/null
@@ -1 +0,0 @@
-ALTER TABLE DATA_COLUMNS ALTER SAMP_ID DROP NOT NULL;
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-003-004.sql b/eu_basysbio/source/sql/postgresql/migration/migration-003-004.sql
deleted file mode 100644
index 9e93f1dd172..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-003-004.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-ALTER TABLE DATA_COLUMNS ADD COLUMN GROWTH_PHASE PROPERTY;
-ALTER TABLE DATA_COLUMNS ADD COLUMN GENOTYPE PROPERTY;
-
-
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-004-005.sql b/eu_basysbio/source/sql/postgresql/migration/migration-004-005.sql
deleted file mode 100644
index 66b4a2dd31a..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-004-005.sql
+++ /dev/null
@@ -1,18 +0,0 @@
-
-ALTER TABLE COLUMN_VALUES DROP CONSTRAINT COLUMNS_COLUMN_VALUES;
-ALTER TABLE COLUMN_VALUES ADD CONSTRAINT COLUMNS_COLUMN_VALUES
- FOREIGN KEY (COLU_ID) REFERENCES COLUMNS (ID) ON DELETE CASCADE;
-
-ALTER TABLE DATA_COLUMNS DROP CONSTRAINT DATA_SETS_DATA_COLUMNS;
-ALTER TABLE DATA_COLUMNS ADD CONSTRAINT DATA_SETS_DATA_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-ALTER TABLE DATA_COLUMN_VALUES DROP CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES;
-ALTER TABLE DATA_COLUMN_VALUES ADD CONSTRAINT DATA_COLUMNS_DATA_COLUMN_VALUES
- FOREIGN KEY (DACO_ID) REFERENCES DATA_COLUMNS (ID) ON DELETE CASCADE;
-
-ALTER TABLE COLUMNS DROP CONSTRAINT DATA_SETS_COLUMNS;
-ALTER TABLE COLUMNS ADD CONSTRAINT DATA_SETS_COLUMNS
- FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
-
-
\ No newline at end of file
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-006-007.sql b/eu_basysbio/source/sql/postgresql/migration/migration-006-007.sql
deleted file mode 100644
index d22de08a7f3..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-006-007.sql
+++ /dev/null
@@ -1,19 +0,0 @@
-GRANT SELECT ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE DATA_SETS TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE EVENTS TO GROUP basysbio_readonly;
-GRANT SELECT ON TABLE TIME_SERIES TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_id_seq TO GROUP basysbio_readonly;
-GRANT SELECT ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readonly;
-
-GRANT ALL ON TABLE DATABASE_VERSION_LOGS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE CHIP_CHIP_DATA TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE chip_chip_data_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE DATA_SETS TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE data_sets_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE EVENTS TO GROUP basysbio_readwrite;
-GRANT ALL ON TABLE TIME_SERIES TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_id_seq TO GROUP basysbio_readwrite;
-GRANT ALL ON SEQUENCE time_series_value_group_id_seq TO GROUP basysbio_readwrite;
diff --git a/eu_basysbio/source/sql/postgresql/migration/migration-007-008.sql b/eu_basysbio/source/sql/postgresql/migration/migration-007-008.sql
deleted file mode 100644
index a886e2da19f..00000000000
--- a/eu_basysbio/source/sql/postgresql/migration/migration-007-008.sql
+++ /dev/null
@@ -1,10 +0,0 @@
----------------------------------------------
--- Remove unused columns from TIME_SERIES
----------------------------------------------
-ALTER TABLE TIME_SERIES DROP COLUMN BI_ID;
-ALTER TABLE TIME_SERIES DROP COLUMN CG;
-
----------------------------------------------
--- Create index on CONTROLLED_GENE column
----------------------------------------------
-CREATE INDEX TISE_CONTROLLED_GENE_ID ON TIME_SERIES (CONTROLLED_GENE);
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataColumnHeaderValidatorTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataColumnHeaderValidatorTest.java
deleted file mode 100644
index 6a723251801..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataColumnHeaderValidatorTest.java
+++ /dev/null
@@ -1,222 +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 eu.basysbio.cisd.dss;
-
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.ELEMENTS_KEY;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.PATTERN_KEY;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.TERMS_KEY;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.TYPE_INTEGER;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.TYPE_KEY;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.TYPE_STRING;
-import static eu.basysbio.cisd.dss.DataColumnHeaderValidator.TYPE_VOCABULARY;
-
-import java.util.Properties;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.etlserver.validation.Result;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataColumnHeaderValidatorTest extends AssertJUnit
-{
- private DataColumnHeaderValidator validator;
-
- @BeforeMethod
- public void beforeMethod()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a, b, c");
- properties.setProperty("a." + TYPE_KEY, TYPE_STRING);
- properties.setProperty("a." + PATTERN_KEY, "a[0-9]+");
- properties.setProperty("b." + TYPE_KEY, TYPE_VOCABULARY);
- properties.setProperty("b." + TERMS_KEY, "alpha, beta, gamma");
- properties.setProperty("c." + TYPE_KEY, TYPE_INTEGER);
- validator = new DataColumnHeaderValidator(properties);
- }
-
- @Test
- public void testUnrestricted()
- {
- Result result = new DataColumnHeaderValidator(new Properties()).validateHeader("blabla");
-
- assertEquals(true, result.isValid());
- }
-
- @Test
- public void testMissingElementValidatorDefinition()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a, b");
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Missing property '" + TYPE_KEY
- + "' for element 'a' of data column header validator.", ex.getMessage());
- }
- }
-
- @Test
- public void testUnknownValidatorType()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a");
- properties.setProperty("a." + TYPE_KEY, "blabla");
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Unknown validator type 'blabla' "
- + "for element 'a' of data column header validator.", ex.getMessage());
- }
- }
-
- @Test
- public void testMissingTermsOfVocabularyValidatorDefinition()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a");
- properties.setProperty("a." + TYPE_KEY, TYPE_VOCABULARY);
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Error in validator definition for element 'a' "
- + "of data column header validator: Given key '" + TERMS_KEY
- + "' not found in properties '[" + TYPE_KEY + "]'", ex.getMessage());
- }
- }
-
- @Test
- public void testDuplicatedTermsOfVocabularyValidatorDefinition()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a");
- properties.setProperty("a." + TYPE_KEY, TYPE_VOCABULARY);
- properties.setProperty("a." + TERMS_KEY, "alpha, alpha");
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Error in validator definition for element 'a' "
- + "of data column header validator: Duplicated name 'alpha' in '" + TERMS_KEY
- + "' property.", ex.getMessage());
- }
- }
-
- @Test
- public void testMissingPatternOfStringValidatorDefinition()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a");
- properties.setProperty("a." + TYPE_KEY, TYPE_STRING);
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Error in validator definition for element 'a' "
- + "of data column header validator: Given key '" + PATTERN_KEY
- + "' not found in properties '[" + TYPE_KEY + "]'", ex.getMessage());
- }
- }
-
- @Test
- public void testInvalidPatternOfStringValidatorDefinition()
- {
- Properties properties = new Properties();
- properties.setProperty(ELEMENTS_KEY, "a");
- properties.setProperty("a." + TYPE_KEY, TYPE_STRING);
- properties.setProperty("a." + PATTERN_KEY, "[?");
-
- try
- {
- new DataColumnHeaderValidator(properties);
- fail("ConfigurationFailureException expected");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Error in validator definition for element 'a' "
- + "of data column header validator: Invalid regular expression: [?",
- ex.getMessage());
- }
- }
-
- @Test
- public void testValidHeaders()
- {
- assertEquals(Result.OK, validator.validateHeader("a42::beta::-34"));
- assertEquals(Result.OK, validator.validateHeader("a4711::gamma::0"));
- assertEquals(Result.OK, validator.validateHeader("a0::alpha::+42::additional element"));
- }
-
- @Test
- public void testNotEnoughHeaders()
- {
- assertInvalid("3 elements separated by '::' expected instead of only 2.", "a42::beta");
- }
-
- @Test
- public void testInvalidVocabularyTypeHeaderElement()
- {
- String regexp =
- "Element 'Beta' is invalid: It is not a term from the following vocabulary: "
- + "\\[(gamma|beta|alpha), (gamma|beta|alpha), (gamma|beta|alpha)\\]";
- String message = validator.validateHeader("a42::Beta::12").toString();
-
- assertTrue("Error message does not match given expresstion, expected: '" + regexp
- + "', was: '" + message + "'.", message.matches(regexp));
- }
-
- @Test
- public void testInvalidStringTypeHeaderElement()
- {
- assertInvalid(
- "Element 'A42' is invalid: It does not match the following regular expression: "
- + "a[0-9]+", "A42::beta::12");
- }
-
- @Test
- public void testInvalidIntegerTypeHeaderElement()
- {
- assertInvalid("Element '1.2' is invalid: It is not an integer number.", "a42::beta::1.2");
- }
-
- private void assertInvalid(String expectedFailure, String header)
- {
- assertEquals(expectedFailure, validator.validateHeader(header).toString());
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetHandlerTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetHandlerTest.java
deleted file mode 100644
index 955294e9891..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetHandlerTest.java
+++ /dev/null
@@ -1,390 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Properties;
-
-import javax.sql.DataSource;
-
-import org.apache.commons.io.IOUtils;
-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.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TableBuilder;
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = DataSetHandler.class)
-public class DataSetHandlerTest extends AbstractFileSystemTestCase
-{
- private static final String E_MAIL_ADDRESS = "e-mail";
-
- private static final String DATA_SET_CODE = "DS1";
-
- private static final long DATA_SET_SPECIAL_ID = 4711;
-
- private static final String GROUP_CODE = "/G1";
-
- private static final long EXP_ID = 42L;
-
- private static final String EXP_PERM_ID = "perm-" + EXP_ID;
-
- private static final long VALUE_GROUP_ID1 = 42;
-
- private static final long VALUE_GROUP_ID2 = 43;
-
- private static final String PROJECT_CODE = "P1";
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService service;
-
- private File dropBox;
-
- private DataSource dataSource;
-
- private ITimeSeriesDAO dao;
-
- @BeforeMethod
- public void beforeMethod() throws Exception
- {
- super.setUp();
- LogInitializer.init();
- context = new Mockery();
- service = context.mock(IEncapsulatedOpenBISService.class);
- dataSource = context.mock(DataSource.class);
- dao = context.mock(ITimeSeriesDAO.class);
- dropBox = new File(workingDirectory, "drop-box");
- dropBox.mkdirs();
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one does not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testMissingExperiment() throws IOException
- {
- DataSetHandler handler = createHandler();
-
- File file = createDataExample();
-
- try
- {
- handler.handle(file, createDataSetInformation(DataSetHandler.TIME_SERIES), null);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Data set should be registered for an experiment and not for a sample.",
- ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWrongExperiment() throws IOException
- {
- DataSetHandler handler = createHandler();
- File file = createDataExample();
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE, "exp1"));
-
- try
- {
- handler.handle(file, dataSetInformation, null);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Data should be uploaded for experiment 'GM_BR_B1' instead of 'EXP1'.", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDataSetAlreadyExists()
- {
- DataSetHandler handler = createHandler();
- File file = createDataExample();
- final Experiment experiment = createExperiment("GM_BR_B1");
- prepareGetOrCreateDataSet(experiment, true);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(PROJECT_CODE, "GM_BR_B1"));
- will(returnValue(experiment));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::200::EX::T1::CE::"
- + "MetaboliteLCMS::Value[mM]::Log10::NB::NC"));
- MockDataSet<String> dataSets = new MockDataSet<String>();
- dataSets.add("ds1");
- will(returnValue(dataSets));
- }
-
- });
-
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE,
- "GM_BR_B1"));
- try
- {
- handler.handle(file, dataSetInformation, null);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals(
- "For data column 'GM::BR::B1::200::EX::T1::CE::MetaboliteLCMS::Value[mM]::Log10::NB::NC' "
- + "following data sets have already been registered: [ds1]", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testTimeSeries()
- {
- DataSetHandler handler = createHandler();
- File file = createDataExample();
- final Experiment experiment = createExperiment("GM_BR_B1");
- prepareGetOrCreateDataSet(experiment, false);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(PROJECT_CODE, "GM_BR_B1"));
- will(returnValue(experiment));
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::200::EX::T1::CE::"
- + "MetaboliteLCMS::Value[mM]::Log10::NB::NC"));
- MockDataSet<String> dataSets = new MockDataSet<String>();
- will(returnValue(dataSets));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::+7200::EX::T2::CE::"
- + "b::Value[mM]::LIN::NB::NC"));
- will(returnValue(dataSets));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID1));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID2));
-
- one(dao).insertTimeSeriesValues(with(DATA_SET_SPECIAL_ID), with("ID"),
- with(Expectations.<List<TimeSeriesValue>> anything()));
- }
- });
-
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE,
- "GM_BR_B1"));
- handler.handle(file, dataSetInformation, null);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGeneric()
- {
- DataSetHandler handler = createHandler();
- File file = createDataExample();
- final Experiment experiment = createExperiment("GM_BR_B1");
- prepareGetOrCreateDataSet(experiment, false);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(PROJECT_CODE, "GM_BR_B1"));
- will(returnValue(experiment));
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::200::EX::T1::CE::"
- + "MetaboliteLCMS::Value[mM]::Log10::NB::NC"));
- MockDataSet<String> dataSets = new MockDataSet<String>();
- will(returnValue(dataSets));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::+7200::EX::T2::CE::"
- + "b::Value[mM]::LIN::NB::NC"));
- will(returnValue(dataSets));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID1));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID2));
-
- one(dao).insertTimeSeriesValues(with(DATA_SET_SPECIAL_ID), with("ID"),
- with(Expectations.<List<TimeSeriesValue>> anything()));
- }
- });
-
- DataSetInformation dataSetInformation =
- createDataSetInformation("GENERIC");
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE,
- "GM_BR_B1"));
- handler.handle(file, dataSetInformation, null);
-
- context.assertIsSatisfied();
- }
-
- private void prepareGetOrCreateDataSet(final Experiment experiment, final boolean get)
- {
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetDataSetIDByPermID(DATA_SET_CODE);
- if (get)
- {
- will(returnValue(DATA_SET_SPECIAL_ID));
- } else
- {
- will(returnValue(null));
-
- one(dao).createDataSet(DATA_SET_CODE, E_MAIL_ADDRESS, experiment);
- will(returnValue(DATA_SET_SPECIAL_ID));
- }
- }
- });
- }
-
- private DataSetHandler createHandler()
- {
- final Properties properties = new Properties();
- properties.setProperty(TimeSeriesDataSetUploaderParameters.DATA_SET_TYPE_PATTERN_FOR_DEFAULT_HANDLING, ".*");
- return new DataSetHandler(properties, dataSource, service)
- {
- @Override
- IDataSetUploader createUploader(DataSetInformation dataSetInformation)
- {
- return factory.create(dataSetInformation, dao, service,
- new TimeSeriesDataSetUploaderParameters(properties));
- }
- };
- }
-
- private File createDataExample()
- {
- TableBuilder builder =
- new TableBuilder("ID", "HumanReadable",
- "GM::BR::B1::200::EX::T1::CE::MetaboliteLCMS::Value[mM]::Log10::NB::NC",
- "GM::BR::B1::+7200::EX::T2::CE::b::Value[mM]::LIN::NB::NC");
- builder.addRow("CHEBI:15721", "sedoheptulose 7-phosphate", "0.34", "0.799920281");
- builder.addRow("CHEBI:18211", "citrulline", "0.87", "1.203723714");
- File file = new File(workingDirectory, "data.txt");
- write(builder, file);
- return file;
- }
-
- private void write(TableBuilder builder, File file)
- {
- PrintWriter writer = null;
- try
- {
- writer = new PrintWriter(file);
- List<Column> columns = builder.getColumns();
- String delim = "";
- for (Column column : columns)
- {
- writer.print(delim);
- writer.print(column.getHeader());
- delim = "\t";
- }
- writer.println();
- int numberOfRows = columns.get(0).getValues().size();
- for (int i = 0; i < numberOfRows; i++)
- {
- delim = "";
- for (Column column : columns)
- {
- writer.print(delim);
- writer.print(column.getValues().get(i));
- delim = "\t";
- }
- writer.println();
- }
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(writer);
- }
- }
-
- private Experiment createExperiment(String code)
- {
- Experiment experiment = new Experiment();
- experiment.setId(EXP_ID);
- experiment.setCode(code);
- experiment.setPermId(EXP_PERM_ID);
- Project project = new Project();
- project.setCode(PROJECT_CODE);
- Space space = new Space();
- space.setIdentifier(GROUP_CODE);
- project.setSpace(space);
- experiment.setProject(project);
- return experiment;
- }
-
- private DataSetInformation createDataSetInformation(String dataSetTypeCode)
- {
- DataSetInformation dataSetInformation = new DataSetInformation();
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(dataSetTypeCode);
- dataSetInformation.setDataSetType(dataSetType);
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetProperties(Arrays.asList(new NewProperty(
- DatabaseFeeder.UPLOADER_EMAIL_KEY, E_MAIL_ADDRESS)));
- return dataSetInformation;
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetTypeTranslatorTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetTypeTranslatorTest.java
deleted file mode 100644
index 0f544d41ba3..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/DataSetTypeTranslatorTest.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 eu.basysbio.cisd.dss;
-
-import java.util.Properties;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetTypeTranslatorTest extends AssertJUnit
-{
- @Test
- public void testMissingTypes()
- {
- try
- {
- new DataSetTypeTranslator(new Properties());
- fail("ConfigurationFailureException");
- } catch (ConfigurationFailureException ex)
- {
- assertEquals("Given key '" + DataSetTypeTranslator.DATA_SET_TYPES_KEY
- + "' not found in properties '[]'", ex.getMessage());
- }
- }
-
- @Test
- public void test()
- {
- Properties properties = new Properties();
- properties.setProperty(DataSetTypeTranslator.DATA_SET_TYPES_KEY, "a, b");
- properties.setProperty("a", "alpha");
- DataSetTypeTranslator translator = new DataSetTypeTranslator(properties);
-
- assertEquals("alpha", translator.translate("a"));
- assertEquals("B", translator.translate("b"));
- try
- {
- translator.translate("B");
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Unknown data set type: B", ex.getMessage());
- }
- }
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/HeaderUtilsTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/HeaderUtilsTest.java
deleted file mode 100644
index 8df16546d27..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/HeaderUtilsTest.java
+++ /dev/null
@@ -1,57 +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 eu.basysbio.cisd.dss;
-
-import java.util.Arrays;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = HeaderUtils.class)
-public class HeaderUtilsTest extends AssertJUnit
-{
- @Test
- public void testJoin()
- {
- assertEquals("a, b, c", HeaderUtils.join(Arrays.asList("a", "b", "c"), ", ", 8));
- assertEquals("a, b, c", HeaderUtils.join(Arrays.asList("a", "b", "c"), ", ", 7));
- assertEquals("..., c", HeaderUtils.join(Arrays.asList("a", "b", "c"), ", ", 6));
-
- assertEquals("123, 345, 789", HeaderUtils.join(Arrays.asList("123", "345", "789"), ", ", 14));
- assertEquals("123, 345, 789", HeaderUtils.join(Arrays.asList("123", "345", "789"), ", ", 13));
- assertEquals("..., 789", HeaderUtils.join(Arrays.asList("123", "345", "789"), ", ", 12));
-
- assertEquals("100, 1000, 10000", HeaderUtils.join(Arrays.asList("100", "1000", "10000"), ", ", 17));
- assertEquals("100, 1000, 10000", HeaderUtils.join(Arrays.asList("100", "1000", "10000"), ", ", 16));
- assertEquals("100, ..., 10000", HeaderUtils.join(Arrays.asList("100", "1000", "10000"), ", ", 15));
- assertEquals("..., 10000", HeaderUtils.join(Arrays.asList("100", "1000", "10000"), ", ", 14));
-
- assertEquals("1, 10, 100, 1000, 10000", HeaderUtils.join(Arrays.asList("1", "10", "100",
- "1000", "10000"), ", ", 24));
- assertEquals("1, 10, 100, 1000, 10000", HeaderUtils.join(Arrays.asList("1", "10", "100",
- "1000", "10000"), ", ", 23));
- assertEquals("1, 10, 100, ..., 10000", HeaderUtils.join(Arrays.asList("1", "10", "100",
- "1000", "10000"), ", ", 22));
- assertEquals("1, 10, ..., 10000", HeaderUtils.join(Arrays.asList("1", "10", "100",
- "1000", "10000"), ", ", 21));
- }
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
deleted file mode 100644
index f7283edf78e..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
+++ /dev/null
@@ -1,75 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class LcaMicDataSetPropertiesExtractorTest extends AbstractFileSystemTestCase
-{
- static final String EXAMPLE =
- "# Ma::MS::B1::NT::EX::T1::NC::GrowthRate::Value[h^(-1)]::LIN::BBA9001#A_S20090325-2::NC\t0.68\n"
- + "Time (s)\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicCfd::Value[um]::LIN::BBA9001#A_S20090325-2::NC\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::BBA9001#A_S20090325-2::NC\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::BBA9001#A_S20090325-2::NC\n";
-
- @Test
- public void test() throws IOException
- {
- File ds = new File(workingDirectory, "ds");
- ds.mkdirs();
- File file = new File(ds, "t.txt");
- FileUtilities.writeToFile(file, EXAMPLE);
- IDataSetPropertiesExtractor extractor =
- new LcaMicDataSetPropertiesExtractor(new Properties());
- List<NewProperty> props = extractor.extractDataSetProperties(ds);
- assertEquals(13, props.size());
- Map<String, String> map = new HashMap<String, String>();
- for (NewProperty property : props)
- {
- map.put(property.getPropertyCode(), property.getValue());
- }
- assertEquals("BBA9001#A_S20090325-2", map.get(TimeSeriesPropertyType.BI_ID.toString()));
- assertEquals("B1", map.get(TimeSeriesPropertyType.BIOLOGICAL_REPLICATE_CODE.toString()));
- assertEquals("NC", map.get(TimeSeriesPropertyType.CEL_LOC.toString()));
- assertEquals("NC", map.get(TimeSeriesPropertyType.CG_LIST.toString()));
- assertEquals("MS", map.get(TimeSeriesPropertyType.CULTIVATION_METHOD_EXPERIMENT_CODE.toString()));
- assertEquals("Ma", map.get(TimeSeriesPropertyType.EXPERIMENT_CODE.toString()));
- assertEquals("LIN", map.get(TimeSeriesPropertyType.SCALE_LIST.toString()));
- assertEquals("T1", map.get(TimeSeriesPropertyType.TECHNICAL_REPLICATE_CODE_LIST.toString()));
- assertEquals("0", map.get(TimeSeriesPropertyType.TIME_POINT_LIST.toString()));
- assertEquals("EX", map.get(TimeSeriesPropertyType.TIME_POINT_TYPE.toString()));
- assertEquals(null, map.get(TimeSeriesPropertyType.UPLOADER_EMAIL.toString()));
- assertEquals("Mean[Au], Std[Au], Value[um]", map.get(TimeSeriesPropertyType.VALUE_TYPE_LIST.toString()));
- assertEquals("0.68", map.get(LcaMicDataSetPropertiesExtractor.GROWTH_RATE));
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
deleted file mode 100644
index 1c8266fb2f5..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
+++ /dev/null
@@ -1,207 +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 eu.basysbio.cisd.dss;
-
-import static eu.basysbio.cisd.dss.LcaMicDataSetUploader.LCA_MIC_TIME_SERIES;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.Reader;
-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.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.filesystem.FileUtilities;
-import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class LcaMicDataSetUploaderTest extends UploaderTestCase
-{
- private final class ReaderMatcher extends BaseMatcher<Reader>
- {
- private final String content;
-
- private ReaderMatcher(String content)
- {
- this.content = content;
- }
-
- @Override
- public boolean matches(Object item)
- {
- try
- {
- String actualContent = IOUtils.toString((Reader) item);
- assertEquals(content, actualContent);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- return true;
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendText(content);
- }
- }
-
- private Mockery context;
-
- private ITimeSeriesDAO dao;
-
- private IEncapsulatedOpenBISService service;
-
- private IDatabaseFeeder databaseFeeder;
-
- private IDataSetValidator validator;
-
- private LcaMicDataSetUploader uploader;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- dao = context.mock(ITimeSeriesDAO.class);
- service = context.mock(IEncapsulatedOpenBISService.class);
- databaseFeeder = context.mock(IDatabaseFeeder.class);
- validator = context.mock(IDataSetValidator.class);
- Properties properties = new Properties();
- properties.setProperty(TimeSeriesDataSetUploaderParameters.DATA_SET_TYPE_PATTERN_FOR_DEFAULT_HANDLING, ".*");
- uploader =
- new LcaMicDataSetUploader(dao, databaseFeeder, service, validator,
- new TimeSeriesDataSetUploaderParameters(properties));
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one does not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNonUniqueBbaIDs()
- {
- File tsvFile = new File(workingDirectory, "data.tsv");
- FileUtilities
- .writeToFile(
- tsvFile,
- "# Ma::MS::B1::NT::EX::T1::NC::GrowthRate::Value[h^(-1)]::LIN::BBA9001#A_S20090325-2::NC\t0.68\n"
- + "Time (s)\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicCfd::Value[um]::LIN::BBA9001#A_S20090325-2::NC\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::BBA9002#A_S20090325-2::NC\t"
- + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::BBA9001#A_S20090325-2::NC\n"
- + "12\t2.5\t5.5\tN/A\n42\t42.5\t45.5\t3.25\n");
-
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier("p1", "e1"));
- dataSetInformation.setDataSetCode("abc-1");
- dataSetInformation.setUploadingUserEmail("ab@c.de");
- prepareResetDatabaseFeeder();
- prepareValidatorAndFeeder(dataSetInformation,
- "BBA ID\tMa::MS::B1::12::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\t"
- + "Ma::MS::B1::42::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\n"
- + "BBA9001#A_S20090325-2\t2.5\t42.5\n", 1, "BBA9001#A_S20090325-2");
-
- try
- {
- uploader.handleTSVFile(tsvFile, dataSetInformation);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Invalid headers: All BBA IDs should be the same. "
- + "The folowing two different BBA IDs found: "
- + "BBA9001#A_S20090325-2 BBA9002#A_S20090325-2", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testHappyCase()
- {
- File tsvFile = new File(workingDirectory, "data.tsv");
- FileUtilities.writeToFile(tsvFile, LcaMicDataSetPropertiesExtractorTest.EXAMPLE
- + "12\t2.5\t5.5\tN/A\n42\t42.5\t45.5\t3.25\n");
- DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier("p1", "MA_MS_B1"));
- dataSetInformation.setDataSetCode("abc-1");
- dataSetInformation.setUploadingUserEmail("ab@c.de");
- prepareResetDatabaseFeeder();
- prepareValidatorAndFeeder(dataSetInformation,
- "BBA ID\tMa::MS::B1::12::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\t"
- + "Ma::MS::B1::42::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\n"
- + "BBA9001#A_S20090325-2\t2.5\t42.5\n", 1, "BBA9001#A_S20090325-2");
- prepareValidatorAndFeeder(dataSetInformation,
- "BBA ID\tMa::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC\t"
- + "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC\n"
- + "BBA9001#A_S20090325-2\t5.5\t45.5\n", 2, "BBA9001#A_S20090325-2");
- prepareValidatorAndFeeder(dataSetInformation,
- "BBA ID\tMa::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC\t"
- + "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC\n"
- + "BBA9001#A_S20090325-2\tN/A\t3.25\n", 3, "BBA9001#A_S20090325-2");
-
- uploader.handleTSVFile(tsvFile, dataSetInformation);
-
- context.assertIsSatisfied();
- }
-
- private void prepareResetDatabaseFeeder()
- {
- context.checking(new Expectations()
- {
- {
- one(databaseFeeder).resetValueGroupIDGenerator();
- }
- });
- }
-
- private void prepareValidatorAndFeeder(final DataSetInformation dataSetInformation,
- final String content, final int numberOfDataSet, final String biIdOrNull)
- {
- context.checking(new Expectations()
- {
- {
- ReaderMatcher matcher = new ReaderMatcher(content);
- String sourceName = LCA_MIC_TIME_SERIES + numberOfDataSet;
- one(validator).assertValidDataSet(with(new DataSetType(LCA_MIC_TIME_SERIES)),
- with(matcher), with(sourceName));
- one(databaseFeeder).feedDatabase(with(dataSetInformation), with(matcher),
- with(sourceName), with(biIdOrNull));
- }
- });
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TSVOutputWriterTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TSVOutputWriterTest.java
deleted file mode 100644
index 9ddda053e39..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TSVOutputWriterTest.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 eu.basysbio.cisd.dss;
-
-import static ch.systemsx.cisd.base.utilities.OSUtilities.LINE_SEPARATOR;
-
-import java.io.ByteArrayOutputStream;
-import java.io.StringReader;
-import java.util.List;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.io.AdapterOutputStreamToIOutputStream;
-import ch.systemsx.cisd.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TabSeparatedValueTable;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TSVOutputWriterTest extends AssertJUnit
-{
- @Test
- public void testIgnoringEmptyLines()
- {
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- TSVOutputWriter writer =
- new TSVOutputWriter(new AdapterOutputStreamToIOutputStream(outputStream));
- String content = "a\tb\n11\t12\n\n";
- TabSeparatedValueTable table =
- new TabSeparatedValueTable(new StringReader(content), content, true);
- List<Column> columns = table.getColumns();
-
- writer.write(columns);
-
- assertEquals("a\tb" + LINE_SEPARATOR + "11\t12" + LINE_SEPARATOR, outputStream.toString());
- }
-
- @Test
- public void testWithEmptyLines()
- {
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- TSVOutputWriter writer =
- new TSVOutputWriter(new AdapterOutputStreamToIOutputStream(outputStream));
- String content = "a\tb\n11\t12\n\n";
- TabSeparatedValueTable table =
- new TabSeparatedValueTable(new StringReader(content), content, false);
- List<Column> columns = table.getColumns();
-
- writer.write(columns);
-
- assertEquals("a\tb" + LINE_SEPARATOR + "11\t12" + LINE_SEPARATOR + "\t" + LINE_SEPARATOR,
- outputStream.toString());
- }
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
deleted file mode 100644
index 25704e216ac..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
+++ /dev/null
@@ -1,215 +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 eu.basysbio.cisd.dss;
-
-import static eu.basysbio.cisd.dss.TimeSeriesAndTimePointDataSetHandler.HELPDESK_EMAIL;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hamcrest.collection.IsArray;
-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.logging.LogInitializer;
-import ch.systemsx.cisd.common.mail.From;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.utilities.ITimeProvider;
-import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = TimeSeriesAndTimePointDataSetHandler.class)
-public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystemTestCase
-{
- private static final class StringMatcher extends BaseMatcher<String>
- {
- private final String expectedString;
-
- StringMatcher(String expectedString)
- {
- this.expectedString = expectedString;
- }
-
- @Override
- public boolean matches(Object item)
- {
- if (item instanceof String)
- {
- String string = (String) item;
- assertEquals(expectedString, string);
- return true;
- }
- return false;
- }
-
- @Override
- public void describeTo(Description description)
- {
- description.appendText(expectedString);
- }
- }
-
- private Mockery context;
-
- private IDataSetHandler delegator;
-
- private IMailClient mailClient;
-
- private IDataSetHandler handler;
-
- private File dropBox;
-
- private File timePointFolder;
-
- private ITimeProvider timeProvider;
-
- @BeforeMethod
- public void beforeMethod() throws Exception
- {
- super.setUp();
- LogInitializer.init();
- context = new Mockery();
- delegator = context.mock(IDataSetHandler.class, "delegator");
- mailClient = context.mock(IMailClient.class);
- timeProvider = context.mock(ITimeProvider.class);
- dropBox = new File(workingDirectory, "drop-box");
- timePointFolder = new File(workingDirectory, "time-point-folder");
- timePointFolder.mkdirs();
- handler = new TimeSeriesAndTimePointDataSetHandler(delegator, mailClient, timeProvider);
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one does not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testFailingTimeSeriesRegistration()
- {
- context.checking(new Expectations()
- {
- {
- one(delegator).handleDataSet(dropBox);
- will(returnValue(Arrays.asList()));
- }
- });
-
- List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
-
- assertEquals(0, dataSets.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testHandleSuccesfullyTwoTimePointDataSets() throws IOException
- {
- final File tp1 = new File(timePointFolder, "tp1");
- tp1.createNewFile();
- final File tp2 = new File(timePointFolder, "tp2");
- tp2.createNewFile();
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setUploadingUserEmail("john.doe@abc.de");
- dataSetInformation.setDataSetType(new DataSetType(DataSetHandler.TIME_SERIES));
- String expectedSubject = "BaSysBio: Successful uploading of data set 'drop-box'";
- String expectedMessage =
- "The data set 'drop-box' "
- + "has been successfully uploaded and registered in openBIS.";
- prepareSendingEMail(expectedSubject, expectedMessage, dataSetInformation, false);
- context.checking(new Expectations()
- {
- {
- one(delegator).handleDataSet(dropBox);
- will(returnValue(Arrays.asList(dataSetInformation)));
- }
- });
-
- List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
-
- assertEquals(1, dataSets.size());
- assertSame(dataSetInformation, dataSets.get(0));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testHandleLcaMicTimeSeriesDataSet() throws IOException
- {
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setUploadingUserEmail("john.doe@abc.de");
- dataSetInformation.setDataSetType(new DataSetType(DataSetHandler.LCA_MIC));
- String expectedSubject = "BaSysBio: Successful uploading of data set 'drop-box'";
- String expectedMessage =
- "The data set 'drop-box' "
- + "has been successfully uploaded and registered in openBIS.";
- prepareSendingEMail(expectedSubject, expectedMessage, dataSetInformation, false);
- context.checking(new Expectations()
- {
- {
- one(delegator).handleDataSet(dropBox);
- will(returnValue(Arrays.asList(dataSetInformation)));
- }
- });
-
- List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
-
- assertEquals(1, dataSets.size());
- assertSame(dataSetInformation, dataSets.get(0));
- context.assertIsSatisfied();
- }
-
- private void prepareSendingEMail(final String expectedSubject, final String expectedMessage,
- final DataSetInformation dataSetInformation, final boolean alsoToHelpDesk)
- {
- context.checking(new Expectations()
- {
- {
- StringMatcher[] recipients = new StringMatcher[alsoToHelpDesk ? 2 : 1];
- recipients[0] =
- new StringMatcher(dataSetInformation.tryGetUploadingUserEmail());
- if (alsoToHelpDesk)
- {
- recipients[1] = new StringMatcher(HELPDESK_EMAIL);
- }
- one(mailClient).sendMessage(string(expectedSubject), string(expectedMessage),
- with(new IsNull<String>()), with(new IsNull<From>()),
- with(new IsArray<String>(recipients)));
- }
-
- private String string(String expectedString)
- {
- return with(new StringMatcher(expectedString));
- }
- });
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderTest.java
deleted file mode 100644
index f7702ccb1e7..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesDataSetUploaderTest.java
+++ /dev/null
@@ -1,361 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.Arrays;
-import java.util.List;
-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.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.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.etlserver.utils.Column;
-import ch.systemsx.cisd.etlserver.utils.TableBuilder;
-import ch.systemsx.cisd.openbis.common.eodsql.MockDataSet;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses = TimeSeriesDataSetUploader.class)
-public class TimeSeriesDataSetUploaderTest extends UploaderTestCase
-{
- private static final String E_MAIL_ADDRESS = "e-mail";
-
- private static final String DATA_SET_CODE = "DS1";
-
- private static final long DATA_SET_SPECIAL_ID = 4711;
-
- private static final long VALUE_GROUP_ID1 = 42;
-
- private static final long VALUE_GROUP_ID2 = 43;
-
- private Mockery context;
-
- private ITimeSeriesDAO dao;
-
- private IEncapsulatedOpenBISService service;
-
- private IDataSetUploader uploader;
-
- private File dropBox;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- dao = context.mock(ITimeSeriesDAO.class);
- service = context.mock(IEncapsulatedOpenBISService.class);
- dropBox = new File(workingDirectory, "drop-box");
- dropBox.mkdirs();
- Properties properties = new Properties();
- properties.setProperty(TimeSeriesDataSetUploaderParameters.DATA_SET_TYPE_PATTERN_FOR_DEFAULT_HANDLING, ".*");
- uploader =
- new TimeSeriesDataSetUploader(dao, service,
- new TimeSeriesDataSetUploaderParameters(properties));
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one does not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUploadNotForExperiment()
- {
- DataSetInformation info = new DataSetInformation();
- try
- {
- uploader.upload(new File(workingDirectory, "example.txt"), info);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Data set should be registered for an experiment and not for a sample.",
- ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testWrongExperiment() throws IOException
- {
- File file = createDataExample();
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE, "exp1"));
-
- try
- {
- uploader.upload(file, dataSetInformation);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Data should be uploaded for experiment 'GM_BR_B1' instead of 'EXP1'.", ex
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDataSetAlreadyExists()
- {
- File file = createDataExample();
- final Experiment experiment = createExperiment("GM_BR_B1");
- prepareGetOrCreateDataSet(experiment, true);
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(PROJECT_CODE, "GM_BR_B1"));
- will(returnValue(experiment));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::200::EX::T1::CE::"
- + "MetaboliteLCMS::Value[mM]::Log10::NB::NC"));
- MockDataSet<String> dataSets = new MockDataSet<String>();
- dataSets.add("ds1");
- will(returnValue(dataSets));
- }
-
- });
-
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE,
- "GM_BR_B1"));
- try
- {
- uploader.upload(file, dataSetInformation);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals(
- "For data column 'GM::BR::B1::200::EX::T1::CE::MetaboliteLCMS::Value[mM]::Log10::NB::NC' "
- + "following data sets have already been registered: [ds1]", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void test()
- {
- File file = createDataExample();
- final Experiment experiment = createExperiment("GM_BR_B1");
- prepareGetOrCreateDataSet(experiment, true);
- final String v1 =
- "TimeSeriesValue{identifier=CHEBI:15721,humanReadable=sedoheptulose 7-phosphate,"
- + "bsbId=<null>,confidenceLevel=<null>,controlledGene=<null>,numberOfReplicates=<null>,"
- + "value=0.125,rowIndex=0,columnIndex=2,valueGroupId=42,"
- + "descriptor=TimeSeriesColumnDescriptor{"
- + "valueGroupDescriptor=ValueGroupDescriptor{experimentType=GM,cultivationMethod=BR,"
- + "biologicalReplicates=B1,timePoint=200,timePointType=EX,technicalReplicates=T1,"
- + "cellLocation=CE,dataSetType=MetaboliteLCMS,biId=NB,controlledGene=NC,"
- + "growthPhase=<null>,genotype=<null>},"
- + "valueType=Value,unit=mM,scale=Log10}}";
- final String v2 =
- "TimeSeriesValue{identifier=CHEBI:18211,humanReadable=citrulline,"
- + "bsbId=<null>,confidenceLevel=<null>,controlledGene=<null>,numberOfReplicates=<null>,"
- + "value=0.625,rowIndex=1,columnIndex=2,valueGroupId=42,"
- + "descriptor=TimeSeriesColumnDescriptor{"
- + "valueGroupDescriptor=ValueGroupDescriptor{experimentType=GM,cultivationMethod=BR,"
- + "biologicalReplicates=B1,timePoint=200,timePointType=EX,technicalReplicates=T1,"
- + "cellLocation=CE,dataSetType=MetaboliteLCMS,biId=NB,controlledGene=NC,"
- + "growthPhase=<null>,genotype=<null>},"
- + "valueType=Value,unit=mM,scale=Log10}}";
- final String v3 =
- "TimeSeriesValue{identifier=CHEBI:15721,humanReadable=sedoheptulose 7-phosphate,"
- + "bsbId=<null>,confidenceLevel=<null>,controlledGene=<null>,numberOfReplicates=<null>,"
- + "value=0.75,rowIndex=0,columnIndex=3,valueGroupId=43,"
- + "descriptor=TimeSeriesColumnDescriptor{"
- + "valueGroupDescriptor=ValueGroupDescriptor{experimentType=GM,cultivationMethod=BR,"
- + "biologicalReplicates=B1,timePoint=7200,timePointType=EX,technicalReplicates=T2,"
- + "cellLocation=CE,dataSetType=b,biId=NB,controlledGene=NC,"
- + "growthPhase=<null>,genotype=<null>},"
- + "valueType=Value,unit=mM,scale=LIN}}";
- final String v4 =
- "TimeSeriesValue{identifier=CHEBI:18211,humanReadable=citrulline,"
- + "bsbId=<null>,confidenceLevel=<null>,controlledGene=<null>,numberOfReplicates=<null>,"
- + "value=1.25,rowIndex=1,columnIndex=3,valueGroupId=43,"
- + "descriptor=TimeSeriesColumnDescriptor{"
- + "valueGroupDescriptor=ValueGroupDescriptor{experimentType=GM,cultivationMethod=BR,"
- + "biologicalReplicates=B1,timePoint=7200,timePointType=EX,technicalReplicates=T2,"
- + "cellLocation=CE,dataSetType=b,biId=NB,controlledGene=NC,"
- + "growthPhase=<null>,genotype=<null>},"
- + "valueType=Value,unit=mM,scale=LIN}}";
- context.checking(new Expectations()
- {
- {
- one(service).tryGetExperiment(
- new ExperimentIdentifier(PROJECT_CODE, "GM_BR_B1"));
- will(returnValue(experiment));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::200::EX::T1::CE::"
- + "MetaboliteLCMS::Value[mM]::Log10::NB::NC"));
- MockDataSet<String> dataSets = new MockDataSet<String>();
- will(returnValue(dataSets));
-
- one(dao).listDataSetsByTimeSeriesDataColumnHeader(
- new DataColumnHeader("GM::BR::B1::+7200::EX::T2::CE::"
- + "b::Value[mM]::LIN::NB::NC"));
- will(returnValue(dataSets));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID1));
-
- one(dao).getNextValueGroupId();
- will(returnValue(VALUE_GROUP_ID2));
-
- one(dao).insertTimeSeriesValues(with(DATA_SET_SPECIAL_ID), with("ID"),
- with(new BaseMatcher<List<TimeSeriesValue>>()
- {
- @Override
- @SuppressWarnings("unchecked")
- public boolean matches(Object item)
- {
- List<TimeSeriesValue> values = (List<TimeSeriesValue>) item;
- assertEquals(v1, values.get(0).toString());
- assertEquals(v2, values.get(1).toString());
- assertEquals(v3, values.get(2).toString());
- assertEquals(v4, values.get(3).toString());
- assertEquals(4, values.size());
- return true;
- }
-
- @Override
- public void describeTo(Description description)
- {
- }
- }));
- }
- });
-
- DataSetInformation dataSetInformation =
- createDataSetInformation(DataSetHandler.TIME_SERIES);
- dataSetInformation.setUploadingUserEmail("ab@c.de");
- dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(PROJECT_CODE,
- "GM_BR_B1"));
- uploader.upload(file, dataSetInformation);
-
- context.assertIsSatisfied();
- }
-
- private void prepareGetOrCreateDataSet(final Experiment experiment, final boolean get)
- {
- context.checking(new Expectations()
- {
- {
- one(dao).tryToGetDataSetIDByPermID(DATA_SET_CODE);
- if (get)
- {
- will(returnValue(DATA_SET_SPECIAL_ID));
- } else
- {
- will(returnValue(null));
-
- one(dao).createDataSet(DATA_SET_CODE, E_MAIL_ADDRESS, experiment);
- will(returnValue(DATA_SET_SPECIAL_ID));
- }
- }
- });
- }
-
- private DataSetInformation createDataSetInformation(String dataSetTypeCode)
- {
- DataSetInformation dataSetInformation = new DataSetInformation();
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(dataSetTypeCode);
- dataSetInformation.setDataSetType(dataSetType);
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- dataSetInformation.setDataSetProperties(Arrays.asList(new NewProperty(
- DatabaseFeeder.UPLOADER_EMAIL_KEY, E_MAIL_ADDRESS)));
- return dataSetInformation;
- }
-
- private File createDataExample()
- {
- TableBuilder builder =
- new TableBuilder("ID", "HumanReadable",
- "GM::BR::B1::200::EX::T1::CE::MetaboliteLCMS::Value[mM]::Log10::NB::NC",
- "GM::BR::B1::+7200::EX::T2::CE::b::Value[mM]::LIN::NB::NC");
- builder.addRow("CHEBI:15721", "sedoheptulose 7-phosphate", "0.125", "0.75");
- builder.addRow("CHEBI:18211", "citrulline", "0.625", "1.25");
- File file = new File(workingDirectory, "data.txt");
- write(builder, file);
- return file;
- }
-
- private void write(TableBuilder builder, File file)
- {
- PrintWriter writer = null;
- try
- {
- writer = new PrintWriter(file);
- List<Column> columns = builder.getColumns();
- String delim = "";
- for (Column column : columns)
- {
- writer.print(delim);
- writer.print(column.getHeader());
- delim = "\t";
- }
- writer.println();
- int numberOfRows = columns.get(0).getValues().size();
- for (int i = 0; i < numberOfRows; i++)
- {
- delim = "";
- for (Column column : columns)
- {
- writer.print(delim);
- writer.print(column.getValues().get(i));
- delim = "\t";
- }
- writer.println();
- }
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(writer);
- }
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesHeaderUtilsTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesHeaderUtilsTest.java
deleted file mode 100644
index 57e95cd26a8..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesHeaderUtilsTest.java
+++ /dev/null
@@ -1,369 +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 eu.basysbio.cisd.dss;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang.StringUtils;
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- * Test cases for {@link HeaderUtils}.
- *
- * @author Izabela Adamczyk
- */
-@Friend(toClasses = HeaderUtils.class)
-public class TimeSeriesHeaderUtilsTest extends AssertJUnit
-{
- private static final String QUANTIFIED_PEPTIDES = "QuantifiedPeptides";
-
- private static final String PROTEIN_LCMS_RATIO = "ProteinLcmsRatio";
-
- private static final String CG_NEW1 = "CG1";
-
- private static final String TR_NEW1 = "TR1";
-
- private static final String TR_NEW2 = "TR2";
-
- private static final String INCONSISTENT_HEADERS_MESSAGE = "Inconsistent data column headers";
-
- private static final String DEFAULT_HEADER = "0::1::2::3::4::5::6::7::8::9::10::11::12::13";
-
- @Test
- public void testConsistentOneHeaderNoRequirement() throws Exception
- {
- String header = new Header().toString();
- assertEquals(DEFAULT_HEADER, header);
- Collection<DataColumnHeader> headers = Arrays.asList(new DataColumnHeader(header));
- HeaderUtils
- .assertMetadataConsistent(headers, new ArrayList<DataHeaderProperty>());
- }
-
- @Test
- public void testConsistentOneHeaderOneRequirement() throws Exception
- {
- String header = new Header().toString();
- assertEquals(DEFAULT_HEADER, header);
- Collection<DataColumnHeader> headers = Arrays.asList(new DataColumnHeader(header));
- HeaderUtils.assertMetadataConsistent(headers, Arrays
- .asList(DataHeaderProperty.BiologicalReplicatateCode));
- }
-
- @Test
- public void testConsistentOneHeaderTwoRequirements() throws Exception
- {
- String header = new Header().toString();
- assertEquals(DEFAULT_HEADER, header);
- Collection<DataColumnHeader> headers = Arrays.asList(new DataColumnHeader(header));
- HeaderUtils.assertMetadataConsistent(headers, Arrays.asList(
- DataHeaderProperty.BiologicalReplicatateCode, DataHeaderProperty.TimePoint));
- }
-
- @Test
- public void testConsistentTwoSameHeadersOneRequirement() throws Exception
- {
- String header1 = new Header().toString();
- assertEquals(DEFAULT_HEADER, header1);
- String header2 = new Header().toString();
- assertTrue(header1.equals(header2));
- Collection<DataColumnHeader> headers =
- Arrays.asList(new DataColumnHeader(header1), new DataColumnHeader(header2));
- HeaderUtils.assertMetadataConsistent(headers, Arrays
- .asList(DataHeaderProperty.BiologicalReplicatateCode));
- }
-
- @Test
- public void testConsistentTwoDifferentConsistentHeadersOneRequirement() throws Exception
- {
- String header1 = new Header().toString();
- assertEquals(DEFAULT_HEADER, header1);
- String header2 =
- new Header().set(DataHeaderProperty.TechnicalReplicateCode, "TR1").toString();
- assertFalse(header1.equals(header2));
- Collection<DataColumnHeader> headers =
- Arrays.asList(new DataColumnHeader(header1), new DataColumnHeader(header2));
- HeaderUtils.assertMetadataConsistent(headers, Arrays
- .asList(DataHeaderProperty.BiologicalReplicatateCode));
- }
-
- @Test
- public void testConsistentTwoDifferentInconsistentHeadersOneRequirement() throws Exception
- {
- String header1 = new Header().toString();
- assertEquals(DEFAULT_HEADER, header1);
- DataHeaderProperty property = DataHeaderProperty.TechnicalReplicateCode;
- String header2 = new Header().set(property, TR_NEW1).toString();
- assertFalse(header1.equals(header2));
- Collection<DataColumnHeader> headers =
- Arrays.asList(new DataColumnHeader(header1), new DataColumnHeader(header2));
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.assertMetadataConsistent(headers, Arrays.asList(property));
- } catch (UserFailureException ex)
- {
- exceptionThrown = true;
- assertTrue(ex.getMessage().contains(INCONSISTENT_HEADERS_MESSAGE)
- && ex.getMessage().contains(property.name())
- && ex.getMessage().contains(property.ordinal() + "")
- && ex.getMessage().contains(TR_NEW1));
- }
- assertTrue(exceptionThrown);
- }
-
- @Test
- public void testConsistentManyInconsistentHeadersOneRequirement() throws Exception
- {
- DataHeaderProperty property = DataHeaderProperty.TechnicalReplicateCode;
- String header1 = new Header().toString();
-
- String header2 = new Header().set(property, TR_NEW1).toString();
- assertFalse(header1.equals(header2));
-
- String header3 =
- new Header().set(property, TR_NEW2).set(DataHeaderProperty.CG, CG_NEW1).toString();
- assertFalse(header1.equals(header3));
- assertFalse(header2.equals(header3));
-
- Collection<DataColumnHeader> headers =
- Arrays.asList(new DataColumnHeader(header1), new DataColumnHeader(header1),
- new DataColumnHeader(header2), new DataColumnHeader(header3));
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.assertMetadataConsistent(headers, Arrays.asList(property));
- } catch (UserFailureException ex)
- {
- exceptionThrown = true;
- assertTrue(ex.getMessage().contains(INCONSISTENT_HEADERS_MESSAGE)
- && ex.getMessage().contains(property.name())
- && ex.getMessage().contains(property.ordinal() + "")
- && ex.getMessage().contains(TR_NEW1) && ex.getMessage().contains(TR_NEW2));
- }
- assertTrue(exceptionThrown);
- }
-
- @Test
- public void testConsistentManyInconsistentHeadersManyRequirements() throws Exception
- {
- DataHeaderProperty firstRequirement = DataHeaderProperty.TechnicalReplicateCode;
- DataHeaderProperty secondRequirement = DataHeaderProperty.CG;
- String header1 = new Header().toString();
-
- String header2 = new Header().set(firstRequirement, TR_NEW1).toString();
- assertFalse(header1.equals(header2));
-
- String header3 =
- new Header().set(firstRequirement, TR_NEW2).set(secondRequirement, CG_NEW1)
- .toString();
- assertFalse(header1.equals(header3));
- assertFalse(header2.equals(header3));
-
- Collection<DataColumnHeader> headers =
- Arrays.asList(new DataColumnHeader(header1), new DataColumnHeader(header1),
- new DataColumnHeader(header2), new DataColumnHeader(header3));
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.assertMetadataConsistent(headers, Arrays.asList(firstRequirement,
- secondRequirement));
- } catch (UserFailureException ex)
- {
- exceptionThrown = true;
- assertTrue(ex.getMessage().contains(INCONSISTENT_HEADERS_MESSAGE));
- assertTrue(ex.getMessage().contains(firstRequirement.name()));
- assertTrue(ex.getMessage().contains(firstRequirement.ordinal() + ""));
- assertTrue(ex.getMessage().contains(TR_NEW1));
- assertTrue(ex.getMessage().contains(TR_NEW2));
- assertTrue(ex.getMessage().contains(secondRequirement.name()));
- assertTrue(ex.getMessage().contains(secondRequirement.ordinal() + ""));
- assertTrue(ex.getMessage().contains(CG_NEW1));
- }
- assertTrue(exceptionThrown);
- }
-
- class Header
- {
- private final String[] header;
-
- public Header()
- {
- header = new String[DataHeaderProperty.values().length];
- for (DataHeaderProperty p : DataHeaderProperty.values())
- {
- set(p, Integer.toString(p.ordinal()));
- }
- }
-
- public Header set(DataHeaderProperty property, String value)
- {
- header[property.ordinal()] = value;
- return this;
- }
-
- @Override
- public String toString()
- {
- return StringUtils.join(header, "::");
- }
-
- }
-
- private static final String VAL1 = "val1";
-
- private static final String VAL2 = "val2";
-
- @Test
- public void testGetPropertyValuePropertyNotDefined() throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.BiID;
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.getPropertyValue(property, map, true);
- } catch (UserFailureException ex)
- {
- exceptionThrown = true;
- assertEquals("BiID not defined", ex.getMessage());
- }
- assertTrue(exceptionThrown);
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedButEmpty() throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.BiID;
- HashSet<String> set = new HashSet<String>();
- map.put(property, set);
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.getPropertyValue(property, map, true);
- } catch (UserFailureException ex)
- {
- exceptionThrown = true;
- assertEquals("BiID not defined", ex.getMessage());
- }
- assertTrue(exceptionThrown);
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedOnce() throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.BiID;
- HashSet<String> set = new HashSet<String>();
- set.add(VAL1);
- map.put(property, set);
- assertEquals(VAL1, HeaderUtils.getPropertyValue(property, map, true));
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedMoreThanOnce() throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.BiID;
- HashSet<String> set = new HashSet<String>();
- set.add(VAL1);
- set.add(VAL2);
- map.put(property, set);
- String result = HeaderUtils.getPropertyValue(property, map, true);
- assertTrue((VAL1 + ", " + VAL2).equals(result) || (VAL2 + ", " + VAL1).equals(result));
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedMoreThanOnceButOnlyOneExpected()
- throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.BiID;
- HashSet<String> set = new HashSet<String>();
- set.add(VAL1);
- set.add(VAL2);
- map.put(property, set);
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.getPropertyValue(property, map, false);
- } catch (UserFailureException e)
- {
- exceptionThrown = true;
- assertEquals("Inconsistent header values of 'BiID'. "
- + "Expected the same value in all the columns, found: [val1, val2].", e
- .getMessage());
- }
- assertTrue(exceptionThrown);
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedMoreThanOnceOneExpectedQuantPeptides()
- throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.DataSetType;
- HashSet<String> set = new HashSet<String>();
- set.add(PROTEIN_LCMS_RATIO);
- set.add(QUANTIFIED_PEPTIDES);
- map.put(property, set);
- assertEquals(PROTEIN_LCMS_RATIO, HeaderUtils.getPropertyValue(property, map,
- false, true));
- }
-
- @Test
- public void testGetPropertyValuePropertyDefinedMoreThanOnceOneExpectedQuantPeptidesTurnedOff()
- throws Exception
- {
- HashMap<DataHeaderProperty, Set<String>> map =
- new HashMap<DataHeaderProperty, Set<String>>();
- DataHeaderProperty property = DataHeaderProperty.DataSetType;
- HashSet<String> set = new HashSet<String>();
- set.add(QUANTIFIED_PEPTIDES);
- set.add(PROTEIN_LCMS_RATIO);
- map.put(property, set);
- boolean exceptionThrown = false;
- try
- {
- HeaderUtils.getPropertyValue(property, map, false, false);
- } catch (UserFailureException e)
- {
- exceptionThrown = true;
- assertEquals(
- "Inconsistent header values of 'DataSetType'. "
- + "Expected the same value in all the columns, found: [ProteinLcmsRatio, QuantifiedPeptides].",
- e.getMessage());
- }
- assertTrue(exceptionThrown);
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPluginTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPluginTest.java
deleted file mode 100644
index e9bcfb9a0a4..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertiesReportingPluginTest.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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Properties;
-
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.MockDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TimeSeriesPropertiesReportingPluginTest extends AbstractFileSystemTestCase
-{
- private static final String SHARE_ID = "42";
-
- @Test
- public void test()
- {
- DatasetDescription ds1 =
- createDataSet("ds1", "1::2::3::4::5::6::7::8::9::10::11::12\t"
- + "1::2::3::44::5::66::7::8::99::101::11::121");
- DatasetDescription ds2 =
- createDataSet("ds2", "1::2::3::4::5::6::7::8::9::10::11::12::13::14");
- IReportingPluginTask plugin =
- new TimeSeriesPropertiesReportingPlugin(new Properties(), workingDirectory);
-
- TableModel table =
- plugin.createReport(Arrays.asList(ds1, ds2), new DataSetProcessingContext(null,
- new MockDataSetDirectoryProvider(workingDirectory, SHARE_ID), null, null,
- "test-user", null));
- assertEquals("[CODE, TECHNICAL_REPLICATE_CODE_LIST, BIOLOGICAL_REPLICATE_CODE, "
- + "TIME_SERIES_DATA_SET_TYPE, CEL_LOC, CG_LIST, "
- + "CULTIVATION_METHOD_EXPERIMENT_CODE, EXPERIMENT_CODE, GENOTYPE, "
- + "GROWTH_PHASE, SCALE_LIST, TIME_POINT_LIST, "
- + "TIME_POINT_TYPE, BI_ID, VALUE_TYPE_LIST]", table.getHeader().toString());
- List<TableModelRow> rows = table.getRows();
- Collections.sort(rows, new Comparator<TableModelRow>()
- {
- @Override
- public int compare(TableModelRow r1, TableModelRow r2)
- {
- return r1.getValues().toString().compareTo(r2.getValues().toString());
- }
- });
- assertEquals("[ds1, 6, 66, 3, 8, 7, 12, 121, 2, 1, , , 10, 101, 4, 44, 5, 11, 9, 99]", rows
- .get(0).getValues().toString());
- assertEquals("[ds2, 6, 3, 8, 7, 12, 2, 1, 14, 13, 10, 4, 5, 11, 9]", rows.get(1)
- .getValues().toString());
- assertEquals(2, rows.size());
- }
-
- private DatasetDescription createDataSet(String dataSetCode, String header)
- {
- File dir = new File(new File(workingDirectory, SHARE_ID), dataSetCode + "/original");
- dir.mkdirs();
- File file = new File(dir, "data.tsv");
- FileUtilities.writeToFile(file, header);
- DatasetDescription datasetDescription = new DatasetDescription();
- datasetDescription.setDataSetLocation(dataSetCode);
- datasetDescription.setDataSetCode(dataSetCode);
- return datasetDescription;
- }
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertyTypeTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertyTypeTest.java
deleted file mode 100644
index 928ebe8a446..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesPropertyTypeTest.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 eu.basysbio.cisd.dss;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-/**
- * Test cases for TimeSeriesPropertyType.
- *
- * @author Izabela Adamczyk
- */
-public class TimeSeriesPropertyTypeTest extends AssertJUnit
-{
- @Test
- public void testInitialization()
- {
- TimeSeriesPropertyType.values();
- }
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TypeExtractorTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TypeExtractorTest.java
deleted file mode 100644
index 4311ceb2309..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TypeExtractorTest.java
+++ /dev/null
@@ -1,99 +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 eu.basysbio.cisd.dss;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Properties;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TypeExtractorTest extends AbstractFileSystemTestCase
-{
- private TypeExtractor extractor;
-
- private File dataSet;
-
- @BeforeMethod
- public void beforeMethod()
- {
- extractor = new TypeExtractor(new Properties());
- dataSet = new File(workingDirectory, "data-set");
- }
-
- @Test
- public void testNonExistentDataSet()
- {
- try
- {
- extractor.getDataSetType(dataSet);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Data set should be a folder: " + dataSet.getAbsolutePath(), ex
- .getMessage());
- }
- }
-
- @Test
- public void testMissingDataFile()
- {
- dataSet.mkdirs();
- try
- {
- extractor.getDataSetType(dataSet);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Exactly one file of type '.data.txt' expected instead of 0.", ex
- .getMessage());
- }
- }
-
- @Test
- public void testMoreThanOneDataFile() throws IOException
- {
- dataSet.mkdirs();
- new File(dataSet, "MY_TYPE" + TypeExtractor.DATA_TYPE).createNewFile();
- new File(dataSet, "MY_TYPE2" + TypeExtractor.DATA_TYPE).createNewFile();
- try
- {
- extractor.getDataSetType(dataSet);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Exactly one file of type '.data.txt' expected instead of 2.", ex
- .getMessage());
- }
- }
-
- @Test
- public void testExtractDataSetType() throws IOException
- {
- dataSet.mkdirs();
- new File(dataSet, "MY_TYPE" + TypeExtractor.DATA_TYPE).createNewFile();
- assertEquals("MY_TYPE", extractor.getDataSetType(dataSet).getCode());
- }
-
-}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/UploaderTestCase.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/UploaderTestCase.java
deleted file mode 100644
index a1891b8d7d0..00000000000
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/UploaderTestCase.java
+++ /dev/null
@@ -1,70 +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 eu.basysbio.cisd.dss;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class UploaderTestCase extends AbstractFileSystemTestCase
-{
-
- protected static final String PROJECT_CODE = "P1";
-
- static final String GROUP_CODE = "/G1";
-
- protected static final long EXP_ID = 42L;
-
- protected static final String EXP_PERM_ID = "perm-" + EXP_ID;
-
- /**
- *
- *
- */
- public UploaderTestCase()
- {
- super();
- }
-
- /**
- * @param cleanAfterMethod
- */
- public UploaderTestCase(boolean cleanAfterMethod)
- {
- super(cleanAfterMethod);
- }
-
- protected Experiment createExperiment(String code)
- {
- Experiment experiment = new Experiment();
- experiment.setId(EXP_ID);
- experiment.setCode(code);
- experiment.setPermId(EXP_PERM_ID);
- Project project = new Project();
- project.setCode(PROJECT_CODE);
- Space space = new Space();
- space.setIdentifier(GROUP_CODE);
- project.setSpace(space);
- experiment.setProject(project);
- return experiment;
- }
-
-}
\ No newline at end of file
diff --git a/eu_basysbio/sourceTest/java/tests.xml b/eu_basysbio/sourceTest/java/tests.xml
deleted file mode 100644
index d37abf70329..00000000000
--- a/eu_basysbio/sourceTest/java/tests.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<!DOCTYPE suite SYSTEM "http://beust.com/testng/testng-1.0.dtd" >
-
-<suite name="All" verbose="1">
- <test name="All">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="eu.basysbio.cisd.dss.*" />
- </packages>
- </test>
-</suite>
diff --git a/openbis_all/build/build.xml b/openbis_all/build/build.xml
index 8cf9e436fd0..10889f83ce3 100644
--- a/openbis_all/build/build.xml
+++ b/openbis_all/build/build.xml
@@ -32,10 +32,6 @@
<param name="project" value="screening" />
<param name="pattern" value="*"/>
</antcall>
- <antcall target="_dist">
- <param name="project" value="eu_basysbio" />
- <param name="pattern" value="*"/>
- </antcall>
<antcall target="_dist">
<param name="project" value="rtd_cina" />
<param name="pattern" value="*"/>
@@ -44,10 +40,6 @@
<param name="project" value="plasmid" />
<param name="pattern" value="*"/>
</antcall>
- <antcall target="_dist">
- <param name="project" value="eu_basynthec" />
- <param name="pattern" value="*"/>
- </antcall>
<antcall target="_dist">
<param name="project" value="openbis_standard_technologies" />
<param name="pattern" value="*server-standard*"/>
@@ -116,18 +108,12 @@
<antcall target="_clean">
<param name="project" value="screening"/>
</antcall>
- <antcall target="_clean">
- <param name="project" value="eu_basysbio"/>
- </antcall>
<antcall target="_clean">
<param name="project" value="rtd_cina"/>
</antcall>
<antcall target="_clean">
<param name="project" value="plasmid"/>
</antcall>
- <antcall target="_clean">
- <param name="project" value="eu_basynthec"/>
- </antcall>
<antcall target="_clean">
<param name="project" value="openbis_standard_technologies"/>
</antcall>
--
GitLab