Fixes to the tool now running on the dev server

microscopy-migration-tool/microscopy-migration-dropbox/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py

+import os
+
+from ch.systemsx.cisd.openbis.generic.client.web.client.exception import UserFailureException
+from ch.ethz.sis.openbis.generic.asapi.v3 import IApplicationServerApi
+from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer
+from ch.systemsx.cisd.common.spring import HttpInvokerUtils;
+
+INVALID_FORMAT_ERROR_MESSAGE = "Invalid format for the folder name, should follow the pattern <ENTITY_KIND>+<SPACE_CODE>+<PROJECT_CODE>[<EXPERIMENT_CODE|<SAMPLE_CODE>]+<OPTIONAL_DATASET_TYPE>+<OPTIONAL_NAME>";
+FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE = "Failed to parse sample";
+FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE = "Failed to parse experiment";
+SAMPLE_MISSING_ERROR_MESSAGE = "Sample not found";
+EXPERIMENT_MISSING_ERROR_MESSAGE = "Experiment not found";
+MORE_THAN_ONE_FOLDER_ERROR_MESSAGE = "More than one folder found";
+
+def process(transaction):
+	incoming = transaction.getIncoming();
+	folderName = incoming.getName();
+	
+	if not folderName.startswith('.'):
+		datasetInfo = folderName.split("+");
+		entityKind = None;
+		sample = None;
+		experiment = None;
+		datasetType = None;
+		name = None;
+		
+		# Parse entity Kind
+		if len(datasetInfo) >= 1:
+			entityKind = datasetInfo[0];
+		else:
+			raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_ERROR_MESSAGE);
+		
+		# Parse entity Kind Format
+		if entityKind == "O":
+			
+			if len(datasetInfo) >= 4:
+				sampleSpace = datasetInfo[1];
+				projectCode = datasetInfo[2];
+				sampleCode = datasetInfo[3];
+				
+				OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis"
+				v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
+				projectSamplesEnabled = v3.getServerInformation(transaction.getOpenBisServiceSessionToken())['project-samples-enabled'] == 'true'
+				
+				sample = None
+				if projectSamplesEnabled:
+					sample = transaction.getSample("/" +sampleSpace + "/" + projectCode + "/" + sampleCode);
+				else:
+					sample = transaction.getSample("/" +sampleSpace + "/" + sampleCode);
+				
+				if sample is None:
+					raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE);
+				if len(datasetInfo) >= 5:
+					datasetType = datasetInfo[4];
+				if len(datasetInfo) >= 6:
+					name = datasetInfo[5];
+				if len(datasetInfo) > 6:
+					raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
+			else:
+				raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
+		
+		if entityKind == "E":
+			if len(datasetInfo) >= 4:
+				experimentSpace = datasetInfo[1];
+				projectCode = datasetInfo[2];
+				experimentCode = datasetInfo[3];
+				experiment = transaction.getExperiment("/" +experimentSpace + "/" + projectCode + "/" + experimentCode);
+				if experiment is None:
+					raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + EXPERIMENT_MISSING_ERROR_MESSAGE);
+				if len(datasetInfo) >= 5:
+					datasetType = datasetInfo[4];
+				if len(datasetInfo) >= 6:
+					name = datasetInfo[5];
+				if len(datasetInfo) > 6:
+					raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE);
+			else:
+				raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_EXPERIMENT_ERROR_MESSAGE);
+		
+		# Create dataset
+		dataSet = None;
+		if datasetType is not None: #Set type if found
+			dataSet = transaction.createNewDataSet(datasetType);
+		else:
+			dataSet = transaction.createNewDataSet();
+		
+		if name is not None:
+			dataSet.setPropertyValue("NAME", name); #Set name if found
+		
+		# Set sample or experiment
+		if sample is not None:
+			dataSet.setSample(sample);
+		else:
+			dataSet.setExperiment(experiment);
+		
+		# Move folder to dataset
+		filesInFolder = incoming.listFiles();
+		
+		# Discard folders started with a . (hidden files)
+		itemsInFolder = 0;
+		datasetItem = None;
+		for item in filesInFolder:
+			#Exclude files starting with .
+			#Exclude Mac .DS_Store
+			#Exclude Windows Thumbs.db
+			if (not item.getName().startswith('.')) and (not item.getName() == ".DS_Store") and (not item.getName() == "Thumbs.db"):
+				itemsInFolder = itemsInFolder + 1;
+				datasetItem = item;
+		
+		if itemsInFolder > 1:
+			raise UserFailureException(MORE_THAN_ONE_FOLDER_ERROR_MESSAGE);
+		else:
+			transaction.moveFile(datasetItem.getAbsolutePath(), dataSet);
\ No newline at end of file

microscopy-migration-tool/microscopy-migration-dropbox/1/dss/drop-boxes/eln-lims-dropbox/plugin.properties

+incoming-dir = ${incoming-root-dir}/eln-lims-dropbox
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = eln-lims-dropbox.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+incoming-share-id = 1
+h5-folders = ${dataset-uploader.h5-folders:false}
+h5ar-folders = ${dataset-uploader.h5ar-folders:true}

microscopy-migration-tool/readme.txt

@@ -9,7 +9,10 @@ dss-rpc.put.ATTACHMENT = eln-lims-dropbox
 
 The information can be retrieved from the database using the next SQL:
 
-SELECT m.name as "tag", ea.perm_id as "experiment" 
+psql -U postgres -d openbis_standard
+\o tags.txt
+
+SELECT '"' || m.name || '"	"' || ea.perm_id ||'"'
 FROM metaproject_assignments_all ma 
 LEFT JOIN metaprojects m ON (m.id = ma.mepr_id) 
 LEFT JOIN experiments_all ea ON (ea.id = ma.expe_id);