LMS-2164 bugfixes in iBrain dropboxes

SVN: 20658

integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py

@@ -77,7 +77,7 @@ class AbstractMetadataParser(AbstractPropertiesParser):
 class AcquiredDatasetMetadataParser(AbstractMetadataParser):
 	PLATE_CODE_PRPOPERTY = "barcode"
 	INSTRUMENT_PROPERTY = "instrument.id"
-	TIMESTAMP_PROPERTY = "timestamp" # not used
+	TIMESTAMP_PROPERTY = "timestamp"
 	
 	# All dataset properties.
 	# Returns:
@@ -86,6 +86,7 @@ class AcquiredDatasetMetadataParser(AbstractMetadataParser):
 		properties = AbstractPropertiesParser.getDatasetPropertiesIter(self)
 		properties = [ (key, value) for (key, value) in properties if key != "ibrain2.assay.id" ]
 		properties.append((self.INSTRUMENT_PROPERTY, self.get(self.INSTRUMENT_PROPERTY)))
+		properties.append((self.TIMESTAMP_PROPERTY, self.get(self.TIMESTAMP_PROPERTY)))	
 		return properties
 	
 	def getPlateCode(self):
@@ -254,7 +255,10 @@ def createSuccessStatus(iBrain2DatasetId, dataset, incomingPath):
 	RegistrationConfirmationUtils().createSuccessStatus(iBrain2DatasetId, datasetCode, incomingPath)
 
 def createFailureStatus(iBrain2DatasetId, throwable, incoming):
-    RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, throwable.getMessage(), incoming.getPath())
+	msg = throwable.getMessage()
+	if msg == None:
+		msg = throwable.toString()
+	RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, msg, incoming.getPath())
 	
 # -------------- TODO: remove tests
 

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py

@@ -10,8 +10,12 @@ reload(commonDropbox)
 # so that the rollback can use it as well.
 iBrain2DatasetId = None
 
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
     commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
             
 if incoming.isDirectory():
     metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py

@@ -10,8 +10,12 @@ reload(commonDropbox)
 # so that the rollback can use it as well.
 iBrain2DatasetId = None
 
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
     commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
 
 if incoming.isDirectory():
     metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py

@@ -50,8 +50,12 @@ def register(incomingPath):
     dataset.setFileFormatType('CSV')
     commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
  
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
     commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
             
 if incoming.isDirectory():
     register(incoming.getPath())
\ No newline at end of file

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py

@@ -37,8 +37,12 @@ def register(incomingPath):
     dataset.setFileFormatType('CSV')
     commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
  
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
     commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
             
 if incoming.isDirectory():
     register(incoming.getPath())
\ No newline at end of file

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py

@@ -31,9 +31,13 @@ def register(incomingPath):
 
     commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
 
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
     commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
-            
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
+                
 if incoming.isDirectory():
     register(incoming.getPath())
 

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py

@@ -11,6 +11,8 @@ PLATE_TYPE_CODE = "PLATE"
 SIRNA_EXP_TYPE = "SIRNA_HCS"
 PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
 
+iBrain2DatasetId = None
+
 def createPlateWithExperimentIfNeeded(transaction, assayParser, plateCode, spaceCode, plateGeometry):
     projectCode = assayParser.get(assayParser.EXPERIMENTER_PROPERTY)
     experiment = assayParser.get(assayParser.ASSAY_ID_PROPERTY)
@@ -38,9 +40,13 @@ def createPlateWithExperimentIfNeeded(transaction, assayParser, plateCode, space
         plate.setExperiment(experiment)
     return plate
 
-
-iBrain2DatasetId = None
-
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
+    commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
+    
 if incoming.isDirectory():
     incomingPath = incoming.getPath()
     metadataParser = commonDropbox.AcquiredDatasetMetadataParser(incomingPath)
@@ -69,8 +75,5 @@ if incoming.isDirectory():
     dataset = tr.createNewDataSet(imageRegistrationDetails)
     dataset.setSample(plate)
     imageDataSetFolder = tr.moveFile(incomingPath, dataset)
-    tr.commit()
-    commonDropbox.createSuccessStatus(iBrain2DatasetId, dataset, incomingPath)
-
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
-    commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
\ No newline at end of file
+    if tr.commit():
+        commonDropbox.createSuccessStatus(iBrain2DatasetId, dataset, incomingPath)
\ No newline at end of file

integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py

@@ -12,6 +12,13 @@ reload(commonDropbox)
 # so that the rollback can use it as well.
 iBrain2DatasetId = None
 
+def rollback_service(service, throwable):
+    global iBrain2DatasetId
+    commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+        
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+    rollback_service(service, throwable)
+    
 def register(incomingPath):
     metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
     global iBrain2DatasetId
@@ -34,9 +41,6 @@ def register(incomingPath):
     imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
   
     commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
-
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
-    commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
-            
+          
 if incoming.isDirectory():
     register(incoming.getPath())