diff --git a/screening/etc/service.properties b/screening/etc/service.properties index 32409fbca4b575a15d9028978454ad3df55bb7ea..fe2e7fd966efbe9c7568f70a177544b282abc50e 100644 --- a/screening/etc/service.properties +++ b/screening/etc/service.properties @@ -124,8 +124,8 @@ hierarchical-storage-updater.hierarchy-root-dir = targets/hierarchical-store # list of additional web servlets which will be exposed plugin-services = screening-image-download-servlet, tabular-data-graph-servlet, screening-dss-api-exporter-servlet # class of the web servlet -#screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet -screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.SplittingImagesDownloadServlet +screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet +#screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.SplittingImagesDownloadServlet # URL which will be mapped to this servlet screening-image-download-servlet.path = /datastore_server_screening/* @@ -151,7 +151,7 @@ imaging-db.scriptFolder = source/sql # 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=raw-data, plate-analysis-data, lmc-raw-data, lmc-jpg-data, lmc-segmented-jpg-data, image-db-data, pelk-raw-img-db, lmc-raw-img-db +inputs=raw-data, plate-analysis-data, lmc-raw-data, lmc-jpg-data, lmc-segmented-jpg-data, genedata-raw-img-db, pelk-raw-img-db, lmc-raw-img-db, genedata-image-analysis-results # --------------------------------------------------------------------------- # 'raw-data' thread configuration @@ -168,7 +168,7 @@ raw-data.data-set-info-extractor.entity-separator = ${data-set-file-name-entity- raw-data.data-set-info-extractor.index-of-sample-code = -1 raw-data.data-set-info-extractor.index-of-data-producer-code = 1 raw-data.data-set-info-extractor.index-of-data-production-date = 0 -raw-data.data-set-info-extractor.space-code = HCS-LAB-STOCKLI +raw-data.data-set-info-extractor.space-code = DEMO # The extractor class to use for type extraction raw-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor @@ -335,29 +335,54 @@ lmc-segmented-jpg-data.storage-processor.file_extension = jpg # --------------------------------------------------------------------------- # The directory to watch for incoming data. -image-db-data.incoming-dir = targets/raw-images-db -image-db-data.incoming-data-completeness-condition = auto-detection +genedata-raw-img-db.incoming-dir = targets/raw-images-db +genedata-raw-img-db.incoming-data-completeness-condition = auto-detection # The extractor class to use for code extraction -image-db-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor +genedata-raw-img-db.data-set-info-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.DataSetInfoExtractorForDataAcquisition # Separator used to extract the barcode in the data set file name -image-db-data.data-set-info-extractor.entity-separator = . -image-db-data.data-set-info-extractor.index-of-sample-code = 0 -image-db-data.data-set-info-extractor.index-of-data-producer-code = -image-db-data.data-set-info-extractor.space-code = DEMO +genedata-raw-img-db.data-set-info-extractor.entity-separator = . +genedata-raw-img-db.data-set-info-extractor.index-of-sample-code = 0 +genedata-raw-img-db.data-set-info-extractor.index-of-data-producer-code = +genedata-raw-img-db.data-set-info-extractor.space-code = DEMO # The extractor class to use for type extraction -image-db-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor -image-db-data.type-extractor.file-format-type = JPG -image-db-data.type-extractor.locator-type = RELATIVE_LOCATION -image-db-data.type-extractor.data-set-type = HCS_IMAGE -image-db-data.type-extractor.is-measured = true - -image-db-data.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor -image-db-data.storage-processor.channel-names = dapi, gfp -image-db-data.storage-processor.well_geometry = 1x1 -image-db-data.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.HCSImageFileExtractor -image-db-data.storage-processor.data-source = imaging-db +genedata-raw-img-db.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +genedata-raw-img-db.type-extractor.file-format-type = JPG +genedata-raw-img-db.type-extractor.locator-type = RELATIVE_LOCATION +genedata-raw-img-db.type-extractor.data-set-type = HCS_IMAGE +genedata-raw-img-db.type-extractor.is-measured = true + +genedata-raw-img-db.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor +genedata-raw-img-db.storage-processor.channel-names = dapi, gfp +genedata-raw-img-db.storage-processor.well_geometry = 1x1 +genedata-raw-img-db.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.HCSImageFileExtractor +genedata-raw-img-db.storage-processor.data-source = imaging-db + +# --------------------------------------------------------------------------- +# GENEDATA images analysis results +# --------------------------------------------------------------------------- + +# The directory to watch for incoming data. +genedata-image-analysis-results.incoming-dir = targets/incoming-genedata-feature-vectors +genedata-image-analysis-results.incoming-data-completeness-condition = auto-detection + +# The extractor class to use for code extraction +genedata-image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.openbis.dss.etl.genedata.DataSetInfoExtractorForImageAnalysis +# Separator used to extract the barcode in the data set file name +genedata-image-analysis-results.data-set-info-extractor.entity-separator = . +genedata-image-analysis-results.data-set-info-extractor.index-of-sample-code = 0 +genedata-image-analysis-results.data-set-info-extractor.space-code = DEMO + +# The extractor class to use for type extraction +genedata-image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +genedata-image-analysis-results.type-extractor.file-format-type = CSV +genedata-image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION +genedata-image-analysis-results.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA +genedata-image-analysis-results.type-extractor.is-measured = false + +# The storage processor (IStorageProcessor implementation) +genedata-image-analysis-results.storage-processor = ch.systemsx.cisd.openbis.dss.etl.genedata.FeatureStorageProcessor # --------------------------------------------------------------------------- @@ -412,7 +437,6 @@ lmc-raw-img-db.storage-processor.channel-names = dapi, gfp lmc-raw-img-db.storage-processor.well_geometry = 3x3 lmc-raw-img-db.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.openbis.dss.etl.lmc.HCSImageFileExtractor lmc-raw-img-db.storage-processor.data-source = imaging-db -#lmc-raw-img-db.storage-processor. #lmc-raw-img-db.storage-processor.compute_file_checksums = false # ---------------------------------------------------------------------------