diff --git a/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
index c6ddb2ffa478b74b2738ffadbd24f921c92fb68c..97c8f1d22984c8f3048f4d8dd9602a22ffaa0f9e 100755
--- a/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
+++ b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
@@ -10,6 +10,7 @@ class AbstractPropertiesParser:
path = os.path.join(incoming, fileName)
self._propertiesDict = self._parseMetadata(path)
+ # Returns: name of the file
def _findFile(self, incoming, prefix):
for file in os.listdir(incoming):
if file.startswith(prefix):
@@ -184,30 +185,34 @@ class RegistrationConfirmationUtils:
# --------------
-def setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory):
- imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
- for propertyCode, value in metadataParser.getDatasetPropertiesIter():
- imageRegistrationDetails.setPropertyValue(propertyCode, value)
-
- tr = service.transaction(incoming, factory)
- dataset = tr.createNewDataSet(imageRegistrationDetails)
- dataset.setParentDatasets([metadataParser.getParentDatasetPermId()])
- imageDataSetFolder = tr.moveFile(incoming.getPath(), dataset)
- if tr.commit():
+def setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory):
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+ imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+ for propertyCode, value in metadataParser.getDatasetPropertiesIter():
+ imageRegistrationDetails.setPropertyValue(propertyCode, value)
+
+ tr = service.transaction(incoming, factory)
+ dataset = tr.createNewDataSet(imageRegistrationDetails)
+ dataset.setParentDatasets([metadataParser.getParentDatasetPermId()])
+ imageDataSetFolder = tr.moveFile(incoming.getPath(), dataset)
+ if tr.commit():
createSuccessStatus(iBrain2DatasetId, dataset, incoming.getPath())
def registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, datasetType, fileFormatType):
+ transaction = service.transaction(incoming, factory)
+ dataset = transaction.createNewDataSet()
+ dataset.setDataSetType(datasetType)
+ dataset.setFileFormatType(fileFormatType)
+ registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
+
+def registerDerivedDataset(state, transaction, dataset, incoming, metadataParser):
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():
@@ -218,6 +223,12 @@ def registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataPa
if transaction.commit():
createSuccessStatus(iBrain2DatasetId, dataset, incoming.getPath())
+def findCSVFile(dir):
+ for file in os.listdir(dir):
+ if file.endswith(".csv"):
+ return dir + "/" + file
+ raise Exception("No CSV file has been found in "+dir)
+
"""
Returns:
(plateSpace, plateCode) tuple for the plate connected with the specified dataset
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_features.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_features.py
index 6486b490795426a271bc3d6571e08ac2653eeefe..1558b858e53580e9ddf0c73a27eb1fcdf13fc15f 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_features.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_features.py
@@ -1,19 +1,26 @@
#! /usr/bin/env python
# This is an example Jython dropbox for importing feature vectors coming from analysis of image datasets
-import os
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import *
+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
+
SEPARATOR = ","
-# Specific code which defines the feature vector values for the dataset..
+# Specific code which defines the feature vector values for the dataset.
# Usually you will parse the content of the incoming file or directory to get the values.
-# Here all the values are hard-coded for simplicity,
-# but the example shows which calls you need to perform in your parser.
# Parameters
-# incoming: java.io.File which points to the incoming dataset
-def defineFeatures(featuresBuilder, incoming):
- file = open(incoming.getPath())
+# incomingCsvPath: path which points to the incoming CSV file
+def defineFeatures(incomingCsvFile):
+ featuresBuilder = factory.createFeaturesBuilder()
+ file = open(incomingCsvFile)
for header in file:
headerTokens = header.split(SEPARATOR)
featureCode = headerTokens[0]
@@ -27,40 +34,24 @@ def defineFeatures(featuresBuilder, incoming):
value = rowTokens[column].strip()
well = rowLabel + str(column)
featureValues.addValue(well, value)
-
-# Returns the code of the plate to which the dataset should be connected.
-# Parameters
-# incoming: java.io.File which points to the incoming dataset
-def extractPlateCode(incoming):
- return os.path.splitext(incoming.getName())[0]
-
-def extractSpaceCode(incoming):
- return "TEST"
-
-# ----------------------------
-# --- boilerplate code which register one dataset with image analysis results on the well level
-# --- Nothing has to be modified if your case is not complicated.
-# ----------------------------
-
-featuresBuilder = factory.createFeaturesBuilder()
-defineFeatures(featuresBuilder, incoming)
-
-analysisRegistrationDetails = factory.createFeatureVectorRegistrationDetails(featuresBuilder, incoming)
-tr = service.transaction(incoming, factory)
-analysisDataset = tr.createNewDataSet(analysisRegistrationDetails)
-
-# set plate to which the dataset should be connected
-sampleIdentifier = "/"+extractSpaceCode(incoming)+"/"+extractPlateCode(incoming)
-plate = tr.getSample(sampleIdentifier)
-analysisDataset.setSample(plate)
-
-# store the original file in the dataset.
-tr.moveFile(incoming.getPath(), analysisDataset)
-
-# ----------------------------
-# --- optional: other standard operations on analysisDataset can be performed (see IDataSet interface)
-# ----------------------------
-
-analysisDataset.setFileFormatType("CSV")
-analysisDataset.setDataSetType("HCS_ANALYSIS_WELL_FEATURES")
-#analysisDataset.setParentDatasets(["20110302085840150-90"])
\ No newline at end of file
+ return featuresBuilder
+
+def register(incomingPath):
+ metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
+ global iBrain2DatasetId
+ iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
+
+ transaction = service.transaction(incoming, factory)
+ incomingCsvFile = commonDropbox.findCSVFile(incomingPath)
+ featuresBuilder = defineFeatures(incomingCsvFile)
+ analysisRegistrationDetails = factory.createFeatureVectorRegistrationDetails(featuresBuilder, incoming)
+ dataset = transaction.createNewDataSet(analysisRegistrationDetails)
+ dataset.setDataSetType('HCS_ANALYSIS_WELL_FEATURES')
+ dataset.setFileFormatType('CSV')
+ commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
+
+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_analysis_well_quality.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py
index f78ec67e6c3506a3a3ba7ea1a06c7998fe8c805d..ed49cae01e7244bd352252d2ea6c4ea997a393e1 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
@@ -19,16 +19,7 @@ def register(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)
+ #TODO: finish me !!!!
def rollback_transaction(service, transaction, algorithmRunner, throwable):
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
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 500dc57059e20890a77f0965563cc074064a2cf2..a596c43cc6dc1308138ef078fbc0448b28532571 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
@@ -29,7 +29,7 @@ def register(incomingPath):
imageDataset.setGenerateThumbnails(True)
imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
- commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
+ commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, 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 b514027f8a30d12935478509b093be9d96b50feb..a0d9f775c2d4f222b4749c5af5495ea154dd9a3d 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
@@ -33,7 +33,7 @@ def register(incomingPath):
imageDataset.setStoreChannelsOnExperimentLevel(False)
imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
- commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, iBrain2DatasetId, metadataParser, incoming, service, factory)
+ commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
def rollback_transaction(service, transaction, algorithmRunner, throwable):
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)