diff --git a/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
index 75ae339ff3c67c35f8d3ab60246940c0ce692aa6..c6ddb2ffa478b74b2738ffadbd24f921c92fb68c 100755
--- a/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
+++ b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
@@ -184,7 +184,7 @@ class RegistrationConfirmationUtils:
# --------------
-def setPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory):
+def setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory):
imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
for propertyCode, value in metadataParser.getDatasetPropertiesIter():
imageRegistrationDetails.setPropertyValue(propertyCode, value)
@@ -193,11 +193,31 @@ def setPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, inc
dataset = tr.createNewDataSet(imageRegistrationDetails)
dataset.setParentDatasets([metadataParser.getParentDatasetPermId()])
imageDataSetFolder = tr.moveFile(incoming.getPath(), dataset)
- ok = tr.commit()
- if ok:
- print "success", iBrain2DatasetId
+ if tr.commit():
createSuccessStatus(iBrain2DatasetId, dataset, incoming.getPath())
+
+def registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, datasetType, fileFormatType):
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+ openbisDatasetParent = metadataParser.getParentDatasetPermId()
+
+ (space, plate) = tryGetConnectedPlate(state, openbisDatasetParent, iBrain2DatasetId, incoming.getPath())
+ if plate == None:
+ return
+ transaction = service.transaction(incoming, factory)
+ dataset = transaction.createNewDataSet()
+ dataset.setDataSetType(datasetType)
+ dataset.setFileFormatType(fileFormatType)
+ dataset.setSample(transaction.getSample('/'+space+'/'+plate))
+ dataset.setMeasuredData(False)
+ for propertyCode, value in metadataParser.getDatasetPropertiesIter():
+ dataset.setPropertyValue(propertyCode, value)
+ dataset.setParentDatasets([metadataParser.getParentDatasetPermId()])
+
+ transaction.moveFile(incoming.getPath(), dataset)
+ if transaction.commit():
+ createSuccessStatus(iBrain2DatasetId, dataset, incoming.getPath())
+
"""
Returns:
(plateSpace, plateCode) tuple for the plate connected with the specified dataset
@@ -214,6 +234,7 @@ def tryGetConnectedPlate(state, openbisDatasetId, iBrain2DatasetId, incomingPath
errorMsg = "No plate is connected to the dataset: "+openbisDatasetId+"."
else:
errorMsg = "Dataset does not exist or is not accessible: "+openbisDatasetId+". Maybe the dataset has not been registered yet. Try again later."
+ print errorMsg
RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, errorMsg, incomingPath)
return (None, None)
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_csv.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_csv.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..a3276bb96e4c3c9f038c501d56d9eb33110e95f4 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_csv.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_csv.py
@@ -0,0 +1,19 @@
+#! /usr/bin/env python
+
+import commonImageDropbox
+import commonDropbox
+
+reload(commonImageDropbox)
+reload(commonDropbox)
+
+# Global variable where we set the iBrain2 id of the dataset at the beginning,
+# so that the rollback can use it as well.
+iBrain2DatasetId = None
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+if incoming.isDirectory():
+ metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+ commonDropbox.registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, 'HCS_ANALYSIS_CELL_FEATURES_CSV', 'CSV')
\ No newline at end of file
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_mat.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_mat.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..aafd2dce1758da6e868e4c6d2076667a9f2238fa 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_mat.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_cell_features_mat.py
@@ -0,0 +1,19 @@
+#! /usr/bin/env python
+
+import commonImageDropbox
+import commonDropbox
+
+reload(commonImageDropbox)
+reload(commonDropbox)
+
+# Global variable where we set the iBrain2 id of the dataset at the beginning,
+# so that the rollback can use it as well.
+iBrain2DatasetId = None
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+if incoming.isDirectory():
+ metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+ commonDropbox.registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, 'HCS_ANALYSIS_CELL_FEATURES_MAT', 'MAT')
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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..f78ec67e6c3506a3a3ba7ea1a06c7998fe8c805d 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
@@ -0,0 +1,37 @@
+#! /usr/bin/env python
+
+import commonImageDropbox
+import commonDropbox
+
+reload(commonImageDropbox)
+reload(commonDropbox)
+
+# Global variable where we set the iBrain2 id of the dataset at the beginning,
+# so that the rollback can use it as well.
+iBrain2DatasetId = None
+
+def register(incomingPath):
+ metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+ openbisDatasetParent = metadataParser.getParentDatasetPermId()
+
+ (space, plate) = commonDropbox.tryGetConnectedPlate(state, openbisDatasetParent, iBrain2DatasetId, incomingPath)
+ if plate == None:
+ return
+
+ imageDataset = commonImageDropbox.IBrain2ImageDataSetConfig()
+ imageDataset.setOverviewImageDatasetType()
+ imageDataset.setPlate(space, plate)
+ imageDataset.setFileFormatType("JPG")
+ imageDataset.setRecognizedImageExtensions(["jpg", "jpeg", "png", "gif"])
+ imageDataset.setStoreChannelsOnExperimentLevel(False)
+ imageDataset.setGenerateThumbnails(True)
+ imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
+
+ commonDropbox.setPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+if incoming.isDirectory():
+ register(incoming.getPath())
\ No newline at end of file
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py b/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
index 40ea989248d019d60f59a70bdbf90a379a2d8d61..500dc57059e20890a77f0965563cc074064a2cf2 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
@@ -12,6 +12,7 @@ iBrain2DatasetId = None
def register(incomingPath):
metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
+ global iBrain2DatasetId
iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
openbisDatasetParent = metadataParser.getParentDatasetPermId()
@@ -28,7 +29,7 @@ def register(incomingPath):
imageDataset.setGenerateThumbnails(True)
imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
- commonDropbox.setPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
+ commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
def rollback_transaction(service, transaction, algorithmRunner, throwable):
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py b/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
index 3f728a455a90e997444ff0cd7f0ca50fb75a2b50..b514027f8a30d12935478509b093be9d96b50feb 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
@@ -33,10 +33,9 @@ def register(incomingPath):
imageDataset.setStoreChannelsOnExperimentLevel(False)
imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
- commonDropbox.setPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
+ commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
def rollback_transaction(service, transaction, algorithmRunner, throwable):
- print 'failure', iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
if incoming.isDirectory():