diff --git a/eu_basynthec/dist/etc/data-set-validator.py b/eu_basynthec/dist/etc/data-set-validator.py index 8af662eac42eb6a9e624b607e88acef2ad3d84f7..567cb2e9fad2dd613644815d4165803c24d3c458 100644 --- a/eu_basynthec/dist/etc/data-set-validator.py +++ b/eu_basynthec/dist/etc/data-set-validator.py @@ -1,6 +1,4 @@ -import os -import re - + def validate_data_set_file(file): 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 index 1cb69b52a57f62f49b747bf3ad764148b51c3268..30a4a053675e4c1eb26ad832398042e05859b980 100644 --- a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py +++ b/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py @@ -157,7 +157,7 @@ timeSeriesData = TimeSeriesDataExcel.createTimeSeriesDataExcel(incoming.getAbsol dataStart = getInitialDataRowAndCol(timeSeriesData.getMetadataMap()) # create the data set and assign the metadata from the file -dataset = tr.createNewDataSet("METABOLITE_INTENSITIES_GROUPED") +dataset = tr.createNewDataSet("METABOLITE_INTENSITIES") metadata = timeSeriesData.getMetadataMap() metadata["STRAIN_NAMES"] = extract_strains(dataStart[0], dataStart[1]) assign_properties(dataset, metadata) @@ -167,7 +167,7 @@ original_dataset = tr.createNewDataSet("EXCEL_ORIGINAL") set_data_type(original_dataset) store_original_data(tr, original_dataset, "xls") -tsv_dataset = tr.createNewDataSet("TSV_EXPORT") +tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT") set_data_type(tsv_dataset) convert_data_to_tsv(tr, tsv_dataset, "tsv") diff --git a/eu_basynthec/etc/service.properties b/eu_basynthec/etc/service.properties index a513c2e2f643466f06578dd93a005134966ef15b..2bd62a7a9aef67411c660c9ac5c85610a6a05dad 100644 --- a/eu_basynthec/etc/service.properties +++ b/eu_basynthec/etc/service.properties @@ -1,7 +1,7 @@ # Unique code of this Data Store Server. Not more than 40 characters. -data-store-server-code = BASYNTHEC +data-store-server-code = DSS1 -data-folder = targets/playground/data +data-folder = ../eu_basynthec/targets/data # The root directory of the data store storeroot-dir = ${data-folder}/store @@ -127,8 +127,8 @@ 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 = dist/etc/data-set-handler.py -main-thread.validation-script-path = dist/etc/data-set-validator.py +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 @@ -138,8 +138,8 @@ 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 = dist/etc/metabolomics2/data-set-handler.py -metabolomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/metabolomics2/data-set-validator.py +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 @@ -149,8 +149,8 @@ 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 = dist/etc/growth-profiles/data-set-handler.py -growth-profiles.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/growth-profiles/data-set-validator.py +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 @@ -160,8 +160,8 @@ 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 = dist/etc/transcriptomics/data-set-handler.py -transcriptomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/transcriptomics/data-set-validator.py +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 @@ -171,8 +171,8 @@ 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 = dist/etc/proteomics/data-set-handler.py -proteomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/proteomics/data-set-validator.py +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 #