diff --git a/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties index f8eeeef7b61059cff4df23b203e94b59cea0027e..8675a12131027652fd7cbec3d5e82aadc893d27b 100644 --- a/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties +++ b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties @@ -5,6 +5,7 @@ ibrain2-dropboxes-dir = ${root}/incoming staging-dir = ${root}/tmp scripts-dir = ${root}/scripts + # --- hcs_image_raw ------------ hcs_image_raw.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_image_raw @@ -70,11 +71,6 @@ hcs_analysis_well_quality.staging-dir = ${staging-dir} hcs_analysis_well_quality.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor hcs_analysis_well_quality.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor hcs_analysis_well_quality.storage-processor.data-source = imaging-db -hcs_analysis_well_quality.storage-processor.separator = , -hcs_analysis_well_quality.storage-processor.ignore-comments = true -hcs_analysis_well_quality.storage-processor.well-name-col-is-alphanum = true -hcs_analysis_well_quality.storage-processor.well-name-row = File_Name -hcs_analysis_well_quality.storage-processor.well-name-col = File_Name # --- hcs_analysis_well_features ----------- @@ -101,4 +97,3 @@ hcs_analysis_well_metadata.staging-dir = ${staging-dir} hcs_analysis_well_metadata.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor hcs_analysis_well_metadata.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor hcs_analysis_well_metadata.storage-processor.data-source = imaging-db - diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py index ed49cae01e7244bd352252d2ea6c4ea997a393e1..bb97d6e3f4adca68d2bdcd61a99651b5acfec0d7 100755 --- a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py +++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py @@ -2,6 +2,7 @@ import commonImageDropbox import commonDropbox +from java.util import Properties reload(commonImageDropbox) reload(commonDropbox) @@ -10,17 +11,32 @@ reload(commonDropbox) # so that the rollback can use it as well. iBrain2DatasetId = None +def rollback_transaction(service, transaction, algorithmRunner, throwable): + commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming) + +def getConfigurationProperties(): + config = Properties() + config.setProperty("separator", ",") + config.setProperty("well-name-row", "File_Name") + config.setProperty("well-name-col", "File_Name") + config.setProperty("well-name-col-is-alphanum", "true") + return config + def register(incomingPath): metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath) + global iBrain2DatasetId iBrain2DatasetId = metadataParser.getIBrain2DatasetId() - openbisDatasetParent = metadataParser.getParentDatasetPermId() - (space, plate) = commonDropbox.tryGetConnectedPlate(state, openbisDatasetParent, iBrain2DatasetId, incomingPath) - if plate == None: - return - - #TODO: finish me !!!! + transaction = service.transaction(incoming, factory) + configProps = getConfigurationProperties() + incomingCsvFile = commonDropbox.findCSVFile(incomingPath) + analysisRegistrationDetails = factory.createFeatureVectorRegistrationDetails(incomingCsvFile, configProps) + dataset = transaction.createNewDataSet(analysisRegistrationDetails) + dataset.setDataSetType('HCS_ANALYSIS_WELL_QUALITY') + dataset.setFileFormatType('CSV') + commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser) + def rollback_transaction(service, transaction, algorithmRunner, throwable): commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)