LMS-2305 iBrain dropboxes have been moved to...

LMS-2305 iBrain dropboxes have been moved to https://systemsx02.ethz.ch/svn/iBrain/trunk/ibrain2/source/python/openbis/dss/dropboxes/scripts

SVN: 21700

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

-#! /usr/bin/env python
-
-import os
-from java.io import File
-
-class AbstractPropertiesParser:
-	_propertiesDict = None
-
-	def __init__(self, incoming, fileName):
-		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):
-				return file
-		raise Exception("No file with prefix '"+prefix+"' has been found!")
-
-	# Parses the metadata file from the given incoming directory.
-	# Each line should have a form:
-	#   key = value
-	# Keys should be unique in the file.
-	# Returns: 
-	#	a dictionary with keys and values from the file.
-	def _parseMetadata(self, path):		
-		f = open(path)
-		myDict = {}
-		for line in f:
-			line = line.strip()
-			if len(line) == 0 or line.startswith("#"):
-				continue
-	
-			ix = line.find("=")
-			if ix == -1:
-				raise Exception("Cannot find '=' in line '"+line+"' in file: "+path)
-			key = line[:ix].strip()
-			value = line[ix+1:].strip()
-			if key in myDict:
-				raise Exception("Duplicated key '"+key+"' in file: "+path)		
-			myDict[key] = value
-		return myDict
-
-	def get(self, propertyName):
-		return self._propertiesDict[propertyName]
-
-	# All properties in the file.
-	# Returns:
-	#	an iterator which yields (propertyName, propertyValue) pairs 
-	def getPropertiesIter(self):
-		return [ (key, value) for key, value in self._propertiesDict.iteritems() ]
-
-	# All dataset properties.
-	# Returns:
-	#	an iterator which yields (propertyCode, propertyValue) pairs 
-	def getDatasetPropertiesIter(self):
-		return [ (key, value) for key, value in self._propertiesDict.iteritems() if key.startswith(self.DATASET_PROPERTY_PREFIX) ]
-
-class AbstractMetadataParser(AbstractPropertiesParser):
-	METADATA_FILE="metadata.properties"
-
-	IBRAIN2_DATASET_ID_PROPERTY = "ibrain2.dataset.id" 
-	DATASET_PROPERTY_PREFIX = "ibrain2."
-	DATASET_TYPE_PROPERTY = "dataset.type"
-
-	def __init__(self, incoming):
-		AbstractPropertiesParser.__init__(self, incoming, self.METADATA_FILE)
-
-	def getDatasetType(self):
-		return self.get(self.DATASET_TYPE_PROPERTY)
-
-	def getIBrain2DatasetId(self):
-		return self.get(self.IBRAIN2_DATASET_ID_PROPERTY)
-
-# --- concrete parser classes ----------------------
-
-class AcquiredDatasetMetadataParser(AbstractMetadataParser):
-	PLATE_CODE_PRPOPERTY = "barcode"
-	INSTRUMENT_PROPERTY = "instrument.id"
-	TIMESTAMP_PROPERTY = "timestamp"
-	
-	# All dataset properties.
-	# Returns:
-	#	an iterator which yields (propertyCode, propertyValue) pairs 
-	def getDatasetPropertiesIter(self):
-		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):
-		return self.get(self.PLATE_CODE_PRPOPERTY)
-
-class DerivedDatasetMetadataParser(AbstractMetadataParser):
-	WORKFLOW_FILE_PREFIX = "workflow_"
-	PARENT_DATSASET_PERMID_PRPOPERTY = "storage_provider.parent.dataset.id"
-	DATASET_TYPE_PROPERTY = "dataset.type"
-	WORKFLOW_NAME_PROPERTY = "ibrain2.workflow.name"
-	WORKFLOW_AUTHOR_PROPERTY = "ibrain2.workflow.author"
-		
-	_workflowName = None
-	_workflowAuthor = None
-	
-	def __init__(self, incoming):
-		AbstractMetadataParser.__init__(self, incoming)
-		workflowFile = self._findFile(incoming, self.WORKFLOW_FILE_PREFIX)
-		basename = os.path.splitext(workflowFile)[0]
-		tokens = basename.split("_")
-		if len(tokens) < 3:
-			raise Exception("Cannot parse workflow name and author from: "+workflowFile)
-		self._workflowName = tokens[1]
-		self._workflowAuthor = tokens[2]
-
-	def getDatasetPropertiesIter(self):
-		properties = AbstractMetadataParser.getDatasetPropertiesIter(self)
-		properties.append((self.WORKFLOW_NAME_PROPERTY, self._workflowName))
-		properties.append((self.WORKFLOW_AUTHOR_PROPERTY, self._workflowAuthor))
-		return properties
-		
-	def getParentDatasetPermId(self):
-		return self.get(self.PARENT_DATSASET_PERMID_PRPOPERTY)
-	
-	def getDatasetType(self):
-		return self.get(self.DATASET_TYPE_PROPERTY)
-
-class AssayParser(AbstractPropertiesParser):
-	ASSAY_FILE_PREFIX="assay_"
-
-	ASSAY_ID_PROPERTY = "assay.id"
-	ASSAY_TYPE_PROPERTY = "assay.type"
-	ASSAY_DESC_PROPERTY = "assay.description"
-	LAB_LEADER_PROPERTY = "labinfo.pi"
-	EXPERIMENTER_PROPERTY = "experimenter.login"
-	WORKFLOW_NAME_PROPERTY = "workflow.name"
-	WORKFLOW_AUTHOR_PROPERTY = "workflow.author"
-
-	def __init__(self, incoming):
-		AbstractPropertiesParser.__init__(self, incoming, self._findFile(incoming, self.ASSAY_FILE_PREFIX))
-
-class RegistrationConfirmationUtils:
-	""" path to the registration confirmation directory relative to the incoming dataset """
-	CONFIRMATION_DIRECTORY = "registration-status"
-	
-	STATUS_PROPERTY = "storage_provider.storage.status"
-	STATUS_OK = "STORAGE_SUCCESSFUL"
-	STATUS_ERROR = "STORAGE_FAILED"
-	ERROR_MSG_PROPERTY = "storage_provider.message"
-
-	OPENBIS_DATASET_ID_PROPERTY = "storage_provider.dataset.id"
-	IBRAIN2_STATUS_FILE_PREFIX = "ibrain2_dataset_id_"
-	IBRAIN2_STATUS_FILE_SUFFIX = ".properties"
-
-	def _getDestinationDir(self, incoming):
-		return File(incoming).getParentFile().getParentFile().getParent() + "/" + self.CONFIRMATION_DIRECTORY
-	
-	def _getConfirmationFileName(self, ibrain2DatasetId):
-		return self.IBRAIN2_STATUS_FILE_PREFIX + ibrain2DatasetId + self.IBRAIN2_STATUS_FILE_SUFFIX
-
-	def _getStatusFilePath(self, ibrain2DatasetId, incoming):
-		return self._getDestinationDir(incoming) + "/" + self._getConfirmationFileName(ibrain2DatasetId)
-
-	def _prop(self, name, value):
-		return "" + name + " = " + value + "\n"
-	
-	def _writeConfirmationFile(self, ibrain2DatasetId, fileContent, incoming):
-		confirmationFile = self._getStatusFilePath(ibrain2DatasetId, incoming)
-		self._writeFile(confirmationFile, fileContent)
-		
-	def _writeFile(self, file, fileContent):
-		file = open(file, "w")
-		file.write(fileContent)
-		file.close()
-
-	def createSuccessStatus(self, ibrain2DatasetId, openbisDatasetId, incoming):
-		fileContent  = self._prop(self.STATUS_PROPERTY, self.STATUS_OK)
-		fileContent += self._prop(AbstractMetadataParser.IBRAIN2_DATASET_ID_PROPERTY, ibrain2DatasetId)
-		fileContent += self._prop(self.OPENBIS_DATASET_ID_PROPERTY, openbisDatasetId)
-		self._writeConfirmationFile(ibrain2DatasetId, fileContent, incoming)
-			
-	def createFailureStatus(self, ibrain2DatasetId, errorMessage, incoming):
-		fileContent  = self._prop(self.STATUS_PROPERTY, self.STATUS_ERROR)
-		fileContent += self._prop(AbstractMetadataParser.IBRAIN2_DATASET_ID_PROPERTY, ibrain2DatasetId)
-		fileContent += self._prop(self.ERROR_MSG_PROPERTY, errorMessage)
-		self._writeConfirmationFile(ibrain2DatasetId, fileContent, incoming)
-
-# --------------
-
-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
-    
-    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())
-
-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
-   or (None, None) if the dataset does not exist or is not connected to the plate.
-"""
-def tryGetConnectedPlate(state, openbisDatasetId, iBrain2DatasetId, incomingPath):
-	openbis = state.getOpenBisService()		
-	dataset = openbis.tryGetDataSet(openbisDatasetId)
-	if dataset != None:
-		plate = dataset.getSample()
-		if plate != None:
-			return (plate.getSpace().getCode(), plate.getCode())
-		else:
-			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)
-
-def createSuccessStatus(iBrain2DatasetId, dataset, incomingPath):
-	datasetCode = dataset.getDataSetCode()
-	RegistrationConfirmationUtils().createSuccessStatus(iBrain2DatasetId, datasetCode, incomingPath)
-
-def createFailureStatus(iBrain2DatasetId, throwable, incoming):
-	msg = throwable.getMessage()
-	if msg == None:
-		msg = throwable.toString()
-	RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, msg, incoming.getPath())
-	
-# -------------- TODO: remove tests
-
-TEST_DIR = "/Users/tpylak/main/src/screening-demo/biozentrum/dropboxes/ibrain2-dropboxes-test"
-
-def testMetadataParsers():
-	print "-- acquired ---------------------------------"
-	parser = AcquiredDatasetMetadataParser(TEST_DIR+"/HCS_IMAGE_RAW/ibrain2_dataset_id_32")
-	print "dataset type:", parser.getDatasetType()
-	print "plate:", parser.getPlateCode()
-	print "properties"
-	for key, value in parser.getDatasetPropertiesIter():
-		print key, value
-		
-	print "\n-- derived ---------------------------------"
-	parser = DerivedDatasetMetadataParser(TEST_DIR+"/HCS_IMAGE_OVERVIEW/ibrain2_dataset_id_48")
-	print "dataset type:", parser.getDatasetType()
-	print "parent perm id:", parser.getParentDatasetPermId()
-	print "properties"
-	for key, value in parser.getDatasetPropertiesIter():
-		print key, value
-
-def testAssayParsers():
-	print "-- assay ---------------------------------"
-	parser = AssayParser(TEST_DIR+"/HCS_IMAGE_RAW/ibrain2_dataset_id_32")
-	print "properties"
-	for key, value in parser.getPropertiesIter():
-		print key, value
-
-def testConfirmationFiles():
-	IBRAIN2Utils().createSuccessStatus("123", "123123123123-12312", TEST_DIR+"/HCS_IMAGE_RAW/ibrain2_dataset_id_32")
-	IBRAIN2Utils().createFailureStatus("321", "Global catastrophy!", TEST_DIR+"/HCS_IMAGE_RAW/ibrain2_dataset_id_32")
-
-#testAssayParsers()
-#testMetadataParsers()
-#testConfirmationFiles()
-

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

-#! /usr/bin/env python
-
-import os
-from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import *
-from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
-     
-class IBrain2ImageDataSetConfig(SimpleImageDataConfig):
-    THUMBANAIL_SIZE = 200
-    
-    def extractImageMetadata(self, imagePath):
-        basename = self.getFileBasename(imagePath)
-        token_dict = {}
-        for token in basename.split("_"):
-            token_dict[token[:1]] = token[1:]
-
-        image_tokens = ImageMetadata()
-        image_tokens.well = token_dict["w"]
-        image_tokens.tileNumber = self.fieldAsInt(token_dict["s"], basename)
-        image_tokens.channelCode = self.extractChannelCode(token_dict, basename)
-        return image_tokens
-
-    def extractChannelCode(self, token_dict, basename):
-        return token_dict["c"]
-    
-    def getFileBasename(self, filePath):
-        return os.path.splitext(filePath)[0]
-    
-    def fieldAsInt(self, fieldText, basename):
-        try:
-            return int(fieldText)
-        except ValueError:
-            raise Exception("Cannot parse field number from '" + fieldText + "' in '" + basename + "' file name.")
-
-    def geom(self, row, col):
-		return Geometry.createFromRowColDimensions(row, col)
-
-    """ 
-    Parameters:
-        image_tokens_list - list of ImageTokens
-    Returns:  (rows, columns) tuple describing the matrix of tiles (aka fields or sides) in the well  
-    """
-    def getTileGeometry(self, imageTokens, maxTileNumber):
-        # if a number of tiles is strange, assume that one tile is missing
-        if maxTileNumber == 5 or maxTileNumber == 7 or maxTileNumber == 11 or maxTileNumber == 13:
-            maxTileNumber = maxTileNumber + 1
-    
-        if maxTileNumber % 4 == 0 and maxTileNumber != 4:
-            return self.geom(4, maxTileNumber / 4) # (4,2), (4,4)
-        elif maxTileNumber % 3 == 0:
-            return self.geom(maxTileNumber / 3, 3) # (3,3), (4,3), (5,3)
-        elif maxTileNumber % 2 == 0:
-            return self.geom(maxTileNumber / 2, 2) # (2,2), (3,2), (5,2), (7,2)
-        else:
-            return self.geom(maxTileNumber, 1)
-           
-class IBrain2SegmentationImageDataSetConfig(IBrain2ImageDataSetConfig):
-    def extractChannelCode(self, token_dict, basename):
-        return basename.split("_")[-1] + " ("+ token_dict["c"] + ")"
-    
-            
\ No newline at end of file

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

-#! /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_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())
-    iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
-    commonDropbox.registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, 'HCS_ANALYSIS_CELL_FEATURES_CSV', 'CSV')
\ No newline at end of file

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

-#! /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_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())
-    iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
-    commonDropbox.registerDerivedBlackBoxDataset(state, service, factory, incoming, metadataParser, 'HCS_ANALYSIS_CELL_FEATURES_MAT', 'MAT')

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

-#! /usr/bin/env python
-# This is an example Jython dropbox for importing feature vectors coming from analysis of image datasets
- 
-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.
-# Usually you will parse the content of the incoming file or directory to get the values.
-# Parameters
-#     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]
-        featureValues = featuresBuilder.defineFeature(featureCode)
-        for rowValues in file:
-            rowTokens = rowValues.split(SEPARATOR)
-            rowLabel = rowTokens[0].strip()
-            if len(rowLabel) == 0:
-                break
-            for column in range(1,len(headerTokens)):
-                value = rowTokens[column].strip()
-                well = rowLabel + str(column)
-                featureValues.addValue(well, value)
-    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_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

-#! /usr/bin/env python
-
-import commonImageDropbox
-import commonDropbox
-from java.util import Properties
-
-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)
-
-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()
-
-    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_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

-#! /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)
-    global iBrain2DatasetId
-    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.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
-
-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

-#! /usr/bin/env python
-
-import commonImageDropbox
-import commonDropbox
-
-reload(commonImageDropbox)
-reload(commonDropbox)
-
-""" sample type code of the plate, needed if a new sample is registered automatically """
-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)
-    experimentDesc = assayParser.get(assayParser.ASSAY_DESC_PROPERTY)   
-    experimentType = assayParser.get(assayParser.ASSAY_TYPE_PROPERTY)
-    
-    if transaction.getSpace(spaceCode) == None:
-        transaction.createNewSpace(spaceCode, None)
-    
-    sampleIdentifier = "/"+spaceCode+"/"+plateCode
-    plate = transaction.getSample(sampleIdentifier)
-    if plate == None:
-        projectIdent = "/" + spaceCode +"/" + projectCode
-        if transaction.getProject(projectIdent) == None:
-            transaction.createNewProject(projectIdent)
-        expIdentifier = projectIdent + "/"+experiment
-        experiment = transaction.getExperiment(expIdentifier)
-        if experiment == None:
-            experiment = transaction.createNewExperiment(expIdentifier, SIRNA_EXP_TYPE)
-            openbisExpDesc = experimentDesc + " (type: "+experimentType + ")"
-            experiment.setPropertyValue("DESCRIPTION", openbisExpDesc)
-
-        plate = transaction.createNewSample(sampleIdentifier, PLATE_TYPE_CODE)
-        plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, plateGeometry)
-        plate.setExperiment(experiment)
-    return plate
-
-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)
-    iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
-    assayParser = commonDropbox.AssayParser(incomingPath)
-
-    imageDataset = commonImageDropbox.IBrain2ImageDataSetConfig()
-    imageDataset.setRawImageDatasetType()
-    imageDataset.setFileFormatType("TIFF")
-    imageDataset.setRecognizedImageExtensions(["tif", "tiff"])    
-    imageDataset.setStoreChannelsOnExperimentLevel(False)
-    imageDataset.setGenerateThumbnails(True)
-    imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
-
-    imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
-    for propertyCode, value in metadataParser.getDatasetPropertiesIter():
-		imageRegistrationDetails.setPropertyValue(propertyCode, value)
-    
-    tr = service.transaction(incoming, factory)
-
-    plate = metadataParser.getPlateCode()
-    space = assayParser.get(assayParser.LAB_LEADER_PROPERTY)
-    plateGeometry = factory.figureGeometry(imageRegistrationDetails)
-    plate = createPlateWithExperimentIfNeeded(tr, assayParser, plate, space, plateGeometry)	    
-
-    dataset = tr.createNewDataSet(imageRegistrationDetails)
-    dataset.setSample(plate)
-    imageDataSetFolder = tr.moveFile(incomingPath, dataset)
-    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

-#! /usr/bin/env python
-# This is a dropbox for importing HCS segmentation image datasets
-
-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
-
-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
-    iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
-    openbisDatasetParent = metadataParser.getParentDatasetPermId()
-
-    (space, plate) = commonDropbox.tryGetConnectedPlate(state, openbisDatasetParent, iBrain2DatasetId, incomingPath)
-    if plate == None:
-        return
-    
-    imageDataset = commonImageDropbox.IBrain2SegmentationImageDataSetConfig()
-    imageDataset.setSegmentationImageDatasetType()
-    imageDataset.setPlate(space, plate)
-    imageDataset.setFileFormatType("TIFF")
-    imageDataset.setRecognizedImageExtensions(["tif"])
-    imageDataset.setGenerateThumbnails(True)
-    imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
-    imageDataset.setGenerateHighQualityThumbnails(True)
-    imageDataset.setStoreChannelsOnExperimentLevel(False)
-    imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
-  
-    commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
-          
-if incoming.isDirectory():
-    register(incoming.getPath())