diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py
deleted file mode 100755
index abd66bdc8abbc547a600d2a4947bd5ac46364534..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py
+++ /dev/null
@@ -1,298 +0,0 @@
-#! /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()
-
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonImageDropbox.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonImageDropbox.py
deleted file mode 100755
index c65b119c3e68f8c02c6fe653472c683b43c78a13..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonImageDropbox.py
+++ /dev/null
@@ -1,60 +0,0 @@
-#! /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
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py
deleted file mode 100755
index f66dfcbd1e41300e3117b9967e508995a3746994..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#! /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
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py
deleted file mode 100755
index a7dfb919cdec9e55f189f8c06467225ab8ab4360..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#! /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')
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py
deleted file mode 100755
index 4c6ba29fba35b171280b160fcd048d5ddf7245f2..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#! /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
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_metadata.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_metadata.py
deleted file mode 100755
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py
deleted file mode 100755
index df79b0349a2196cbbd93b69f62ececf7dd8dc409..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py
+++ /dev/null
@@ -1,48 +0,0 @@
-#! /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
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py
deleted file mode 100755
index 873126de5e3dfa3988063c8edb53b69694e415d3..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#! /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())
-
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py
deleted file mode 100755
index 3a6e287e10e77ac30bd03c3b8377efe1302756e4..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py
+++ /dev/null
@@ -1,79 +0,0 @@
-#! /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
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py
deleted file mode 100755
index a05c08dde09a1d9cc361d7558d99fb158e2b18fe..0000000000000000000000000000000000000000
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py
+++ /dev/null
@@ -1,46 +0,0 @@
-#! /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())