SSDM-10264: missing removals of proteomics modul references

js-test/servers/common/core-plugins/proteomics-optional/1/as/initialize-master-data.py

-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-tr = service.transaction()
-
-file_type_HTML = tr.getOrCreateNewFileFormatType('HTML')
-file_type_HTML.setDescription('HTML File')
-
-file_type_MZDATA = tr.getOrCreateNewFileFormatType('MZDATA')
-file_type_MZDATA.setDescription('Mass spectrometry data format.')
-
-file_type_MZML = tr.getOrCreateNewFileFormatType('MZML')
-file_type_MZML.setDescription('Mass spectrometry data format. \
-Unifiying mzXML and mzData formats, as released at the \
-2008 American Society for Mass Spectrometry Meeting.')
-
-file_type_MZXML = tr.getOrCreateNewFileFormatType('MZXML')
-file_type_MZXML.setDescription('Mass spectrometry data format.')
-
-file_type_RAW = tr.getOrCreateNewFileFormatType('RAW')
-file_type_RAW.setDescription('Proprietary file format for Thermo mass sepectrometry data.')
-
-file_type_TGZ = tr.getOrCreateNewFileFormatType('TGZ')
-file_type_TGZ.setDescription('gzipped tar')
-
-file_type_WIFF = tr.getOrCreateNewFileFormatType('WIFF')
-file_type_WIFF.setDescription('Proprieatry file format for Sciex and Agilent mass spectrometry data.')
-
-file_type_ZIP = tr.getOrCreateNewFileFormatType('ZIP')
-file_type_ZIP.setDescription('A zipped package')
-
-vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE')
-
-vocabulary_term_TREATMENT_TYPE_PH = tr.createNewVocabularyTerm('PH')
-vocabulary_term_TREATMENT_TYPE_PH.setDescription(None)
-vocabulary_term_TREATMENT_TYPE_PH.setUrl(None)
-vocabulary_term_TREATMENT_TYPE_PH.setLabel('ph')
-vocabulary_term_TREATMENT_TYPE_PH.setOrdinal(1)
-vocabulary_TREATMENT_TYPE.addTerm(vocabulary_term_TREATMENT_TYPE_PH)
-
-exp_type_BIOLOGICAL_EXPERIMENT = tr.getOrCreateNewExperimentType('BIOLOGICAL_EXPERIMENT')
-exp_type_BIOLOGICAL_EXPERIMENT.setDescription('A biological experiment')
-
-exp_type_MS_INJECT = tr.getOrCreateNewExperimentType('MS_INJECT')
-exp_type_MS_INJECT.setDescription('MS injection experiment')
-
-exp_type_MS_QUANTIFICATION = tr.getOrCreateNewExperimentType('MS_QUANTIFICATION')
-exp_type_MS_QUANTIFICATION.setDescription('Quantification of LC-MS data')
-
-data_set_type_MZXML_DATA = tr.getOrCreateNewDataSetType('MZXML_DATA')
-data_set_type_MZXML_DATA.setDescription('standardized format for ms data')
-
-data_set_type_RAW_DATA = tr.getOrCreateNewDataSetType('RAW_DATA')
-data_set_type_RAW_DATA.setDescription(None)
-
-prop_type_PARENTDATASETCODES = tr.getOrCreateNewPropertyType('PARENT-DATA-SET-CODES', DataType.VARCHAR)
-prop_type_PARENTDATASETCODES.setLabel('Parent Dataset Codes')
-prop_type_PARENTDATASETCODES.setManagedInternally(False)
-prop_type_PARENTDATASETCODES.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE1 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE1', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE1.setLabel('Treatment Type 1')
-prop_type_TREATMENT_TYPE1.setManagedInternally(False)
-prop_type_TREATMENT_TYPE1.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE1.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-prop_type_TREATMENT_TYPE2 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE2', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE2.setLabel('Treatment Type 2')
-prop_type_TREATMENT_TYPE2.setManagedInternally(False)
-prop_type_TREATMENT_TYPE2.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE2.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-prop_type_TREATMENT_TYPE3 = tr.getOrCreateNewPropertyType('TREATMENT_TYPE3', DataType.CONTROLLEDVOCABULARY)
-prop_type_TREATMENT_TYPE3.setLabel('Treatment Type 3')
-prop_type_TREATMENT_TYPE3.setManagedInternally(False)
-prop_type_TREATMENT_TYPE3.setInternalNamespace(False)
-
-prop_type_TREATMENT_TYPE3.setVocabulary(vocabulary_TREATMENT_TYPE)
-
-

js-test/servers/common/core-plugins/proteomics/1/as/dss-data-sources/DSS1/plugin.properties

-#
-# Data Store Server data source for the database storing protein identification and quantification results.
-#
-# Variables:
-#   proteomics-basic-database-name
-#     First part of the database name. Default value is 'proteomics'.
-#   proteomics-database-kind
-#     Second part of the database name. Default value is 'productive'.
-#
-database-driver = org.postgresql.Driver
-database-url = jdbc:postgresql://localhost/${proteomics-basic-database-name:proteomics}_test_js_common

js-test/servers/common/core-plugins/proteomics/1/as/initialize-master-data.py

-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-tr = service.transaction()
-
-vocabulary_TREATMENT_TYPE = tr.getOrCreateNewVocabulary('TREATMENT_TYPE')
-vocabulary_TREATMENT_TYPE.setDescription('Type of treatment of a biological sample.')
-vocabulary_TREATMENT_TYPE.setUrlTemplate(None)
-vocabulary_TREATMENT_TYPE.setManagedInternally(False)
-vocabulary_TREATMENT_TYPE.setInternalNamespace(False)
-vocabulary_TREATMENT_TYPE.setChosenFromList(True)
-
-exp_type_MS_SEARCH = tr.getOrCreateNewExperimentType('MS_SEARCH')
-exp_type_MS_SEARCH.setDescription('MS_SEARCH experiment')
-
-samp_type_MS_INJECTION = tr.getOrCreateNewSampleType('MS_INJECTION')
-samp_type_MS_INJECTION.setDescription('injection of a biological sample into a MS')
-samp_type_MS_INJECTION.setListable(True)
-samp_type_MS_INJECTION.setSubcodeUnique(False)
-samp_type_MS_INJECTION.setAutoGeneratedCode(False)
-samp_type_MS_INJECTION.setGeneratedCodePrefix('S')
-
-samp_type_SEARCH = tr.getOrCreateNewSampleType('SEARCH')
-samp_type_SEARCH.setDescription('pointer to an MS_INJECTION sample used as placeholder for searches')
-samp_type_SEARCH.setListable(True)
-samp_type_SEARCH.setSubcodeUnique(False)
-samp_type_SEARCH.setAutoGeneratedCode(False)
-samp_type_SEARCH.setGeneratedCodePrefix('S')
-
-data_set_type_PROT_RESULT = tr.getOrCreateNewDataSetType('PROT_RESULT')
-data_set_type_PROT_RESULT.setDescription('protXML file')
-

js-test/servers/common/core-plugins/proteomics/1/as/miscellaneous/proteomics-application/plugin.properties

-proteomics-application-context-required = true

js-test/servers/common/core-plugins/proteomics/1/dss/data-sources/proteomics-db/plugin.properties

-#
-# Data source for the database stroing protein identification and quantification results.
-#
-# Variables:
-#   proteomics-database.url-host-part
-#     The host and optionally port. Default is 'localhost'.
-#   proteomics-basic-database-name
-#     First part of the database name. Default value is 'proteomics'.
-#   proteomics-database-kind
-#     Second part of the database name. Default value is 'productive'.
-#   proteomics-sql-root-folder
-#     Path to root folder of SQL scripts. Default value is an empty string.
-#
-version-holder-class = ch.systemsx.cisd.openbis.etlserver.proteomics.DatabaseVersionHolder
-databaseEngineCode = postgresql
-urlHostPart = ${proteomics-database.url-host-part:localhost}
-basicDatabaseName = ${proteomics-basic-database-name:proteomics}
-databaseKind = ${proteomics-database-kind:productive}
-scriptFolder = ${proteomics-sql-root-folder:}sql/proteomics

js-test/servers/common/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties

-# 
-# Drop box for MS spectra data.
-#
-# Variables:
-#   incoming-root-dir
-#     Path to the directory which contains incoming directories for drop boxes.
-incoming-dir = ${incoming-root-dir}/incoming-ms-injection
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values: 
-#  - auto-detection - when no write access will be detected for a specified 'quite-period'
-#  - marker-file		- when an appropriate marker file for the data exists. 
-# The default value is 'marker-file'.
-incoming-data-completeness-condition = marker-file
-
-data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection
-storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection

js-test/servers/common/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties

-# 
-# Drop box for protein identification and quantification data.
-#
-# Variables:
-#   incoming-root-dir
-#     Path to the directory which contains incoming directories for drop boxes.
-#
-# This drop box assumes that data source 'proteomics-db' has been defined.
-#
-incoming-dir = ${incoming-root-dir}/incoming-ms-search
-
-incoming-data-completeness-condition = marker-file
-
-data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults
-data-set-info-extractor.separator = +
-
-type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
-type-extractor.file-format-type = XML
-type-extractor.locator-type = RELATIVE_LOCATION
-type-extractor.data-set-type = PROT_RESULT
-type-extractor.is-measured = false
-
-storage-processor = ch.systemsx.cisd.openbis.etlserver.proteomics.StorageProcessorWithResultDataSetUploader
-storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-storage-processor.assuming-extended-prot-xml = false
-storage-processor.database.basic-name = ${proteomics-db.basicDatabaseName}
-storage-processor.database.kind = ${proteomics-db.databaseKind}
-storage-processor.database.owner = 
-storage-processor.database.password = 
\ No newline at end of file

js-test/servers/common/core-plugins/proteomics/1/dss/maintenance-tasks/proteomics-db-clean-up/plugin.properties

-#
-# Maintenance task which does a database clean up by deleting all data sets deleted in application server. 
-# This task assumes that data source 'proteomics-db' has been defined. 
-#
-class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-interval = 300
-data-source = proteomics-db
-data-set-table-name = data_sets