diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties index c41aca0a3da83ad96e0d9462d9769a1b7755862c..b2400892d2ac5a98da3cf8b417b115fab9c15c75 100644 --- a/screening/dist/etc/service.properties +++ b/screening/dist/etc/service.properties @@ -91,13 +91,19 @@ imaging-db.databaseEngineCode = postgresql imaging-db.basicDatabaseName = imaging imaging-db.databaseKind = productive imaging-db.scriptFolder = sql +imaging-db.owner = +imaging-db.owner-password = +# Credentials of a database user which is able to create a new database. +# Leave empty to use the db engines default +imaging-db.admin-user = +imaging-db.admin-password = # --------------------------------------------------------------------------- # reporting and processing plugins configuration # --------------------------------------------------------------------------- # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. -reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph, plate-image-params-reporter +reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph default-plate-image-analysis.label = Image Analysis Results default-plate-image-analysis.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE @@ -110,15 +116,6 @@ plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.p plate-image-analysis-graph.servlet-path = datastore_server_graph/ plate-image-analysis-graph.properties-file = etc/tabular-data-graph.properties -# Label of the plugin which will be shown for the users. -plate-image-params-reporter.label = Plate Image Parameters -# Comma separated list of dataset type codes which can be handled by this plugin. -plate-image-params-reporter.dataset-types = HCS_IMAGE -# Plugin class specification (together with the list of packages this class belongs to). -plate-image-params-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ScreeningPlateImageParamsReportingPlugin -# The property file. Its content will be passed as a parameter to the plugin. -plate-image-params-reporter.properties-file = - # --------------------------------------------------------------------------- # screening specific extension servlets # --------------------------------------------------------------------------- @@ -172,7 +169,7 @@ bds-migrator.bds-remover.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.B feature-migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask feature-migrator.execute-only-once = true feature-migrator.storeRoot = ${storeroot-dir} -feature-migrator.migrators = csv, genedata +feature-migrator.migrators = csv feature-migrator.csv.class = ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorMigrator feature-migrator.csv.data-source = imaging-db # semi-colon (;) by default @@ -181,8 +178,6 @@ feature-migrator.csv.data-source = imaging-db #feature-migrator.csv.well-name-row = row #feature-migrator.csv.well-name-col = col #feature-migrator.csv.well-name-col-is-alphanum = true -feature-migrator.genedata.class = ch.systemsx.cisd.openbis.dss.etl.genedata.GenedataFeatureVectorMigrator -feature-migrator.genedata.data-source = imaging-db # --------------------------------------------------------------------------- # DROPBOXES CONFIGURATION diff --git a/screening/etc/service.properties b/screening/etc/service.properties index 6d2f7c43a16ab8ef139a89852f7821507e466404..31c0a913abb6169d322979c35d0b3667db69b74e 100644 --- a/screening/etc/service.properties +++ b/screening/etc/service.properties @@ -97,7 +97,7 @@ imaging-db.scriptFolder = source/sql # --------------------------------------------------------------------------- # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. -reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph, plate-image-params-reporter +reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph default-plate-image-analysis.label = Image Analysis Results default-plate-image-analysis.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE @@ -110,15 +110,6 @@ plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.p plate-image-analysis-graph.servlet-path = datastore_server_graph/ plate-image-analysis-graph.properties-file = etc/tabular-data-graph.properties -# Label of the plugin which will be shown for the users. -plate-image-params-reporter.label = Plate Image Parameters -# Comma separated list of dataset type codes which can be handled by this plugin. -plate-image-params-reporter.dataset-types = HCS_IMAGE -# Plugin class specification (together with the list of packages this class belongs to). -plate-image-params-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ScreeningPlateImageParamsReportingPlugin -# The property file. Its content will be passed as a parameter to the plugin. -plate-image-params-reporter.properties-file = - # --------------------------------------------------------------------------- # screening specific extension servlets # --------------------------------------------------------------------------- @@ -142,7 +133,7 @@ screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api-v1 # --------------------------------------------------------------------------- maintenance-plugins=data-set-clean-up -# hierarchical-storage-updater, feature-migrator, bds-migrator +# hierarchical-storage-updater # the plugin which is run periodically to create a mirror structure of the store with the same files # but with user-readable structure of directories @@ -157,33 +148,6 @@ data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DataSetDeletionMain data-set-clean-up.interval = 86400 data-set-clean-up.data-source = imaging-db -bds-migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask -bds-migrator.execute-only-once = true -bds-migrator.storeRoot = ${storeroot-dir} -#bds-migrator.migrators = bds-image-db, bds-original-relocator, bds-remover -bds-migrator.migrators = bds-image-db -bds-migrator.bds-image-db.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSImagingDatabaseMigrator -bds-migrator.bds-image-db.data-source = imaging-db -bds-migrator.bds-image-db.channel-names = dapi, gfp -#bds-migrator.bds-image-db.extract-single-image-channels = BLUE, GREEN -bds-migrator.bds-original-relocator.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSOriginalDataRelocatorMigrator -bds-migrator.bds-remover.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSDataRemoverMigrator - -feature-migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask -feature-migrator.execute-only-once = true -feature-migrator.storeRoot = ${storeroot-dir} -feature-migrator.migrators = csv, genedata -feature-migrator.csv.class = ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorMigrator -feature-migrator.csv.data-source = imaging-db -# semi-colon (;) by default -#feature-migrator.csv.separator = , -#feature-migrator.csv.ignore-comments = true -#feature-migrator.csv.well-name-row = row -#feature-migrator.csv.well-name-col = col -#feature-migrator.csv.well-name-col-is-alphanum = true -feature-migrator.genedata.class = ch.systemsx.cisd.openbis.dss.etl.genedata.GenedataFeatureVectorMigrator -feature-migrator.genedata.data-source = imaging-db - # --------------------------------------------------------------------------- # DROPBOXES CONFIGURATION # ---------------------------------------------------------------------------