diff --git a/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties
new file mode 100644
index 0000000000000000000000000000000000000000..7ae9067169995ceccf11499587ae253f8cab784f
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties
@@ -0,0 +1,73 @@
+inputs = hcs_image_raw, hcs_image_overview, hcs_image_segmentation, hcs_analysis_well_features, hcs_analysis_well_quality, hcs_analysis_well_features, hcs_analysis_cell_features_csv, hcs_analysis_cell_features_mat
+
+root = ~/data/dropboxes
+ibrain2-dropboxes-dir = ${root}/ibrain2-dropboxes-test
+staging-dir = ${root}/tmp
+scripts-dir = ${root}/scripts
+
+
+# --- hcs_image_raw ------------
+
+hcs_image_raw.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_image_raw
+hcs_image_raw.script-path = ${scripts-dir}/hcs_image_raw.py
+
+hcs_image_raw.incoming-data-completeness-condition = auto-detection
+hcs_image_raw.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+hcs_image_raw.staging-dir = ${staging-dir}
+
+hcs_image_raw.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+hcs_image_raw.storage-processor.data-source = imaging-db
+
+# --- hcs_image_overview
+
+# --- hcs_image_segmentation
+
+# --- hcs_analysis_cell_features_csv
+
+# --- hcs_analysis_cell_features_mat
+
+
+# --- hcs_analysis_well_quality -----------
+
+hcs_analysis_well_quality.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_analysis_well_quality
+hcs_analysis_well_quality.script-path = ${scripts-dir}/hcs_analysis_well_quality.py
+
+hcs_analysis_well_quality.incoming-data-completeness-condition = auto-detection
+hcs_analysis_well_quality.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+hcs_analysis_well_quality.staging-dir = ${staging-dir}
+
+hcs_analysis_well_quality.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
+hcs_analysis_well_quality.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+hcs_analysis_well_quality.storage-processor.data-source = imaging-db
+hcs_analysis_well_quality.storage-processor.separator = ,
+hcs_analysis_well_quality.storage-processor.ignore-comments = true
+hcs_analysis_well_quality.storage-processor.well-name-col-is-alphanum = true
+hcs_analysis_well_quality.storage-processor.well-name-row = File_Name
+hcs_analysis_well_quality.storage-processor.well-name-col = File_Name
+
+# --- hcs_analysis_well_features -----------
+
+hcs_analysis_well_features.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_analysis_well_features
+hcs_analysis_well_features.script-path = ${scripts-dir}/hcs_analysis_well_features.py
+
+hcs_analysis_well_features.incoming-data-completeness-condition = auto-detection
+hcs_analysis_well_features.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+hcs_analysis_well_features.staging-dir = ${staging-dir}
+
+hcs_analysis_well_features.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
+hcs_analysis_well_features.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+hcs_analysis_well_features.storage-processor.data-source = imaging-db
+
+# --- hcs_analysis_well_metadata -----------
+
+hcs_analysis_well_metadata.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_analysis_well_metadata
+hcs_analysis_well_metadata.script-path = ${scripts-dir}/hcs_analysis_well_metadata.py
+
+hcs_analysis_well_metadata.incoming-data-completeness-condition = auto-detection
+hcs_analysis_well_metadata.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+hcs_analysis_well_metadata.staging-dir = ${staging-dir}
+
+hcs_analysis_well_metadata.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
+hcs_analysis_well_metadata.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+hcs_analysis_well_metadata.storage-processor.data-source = imaging-db
+
diff --git a/integration-tests/templates/data-ibrain2/ibrain2-dropboxes-test.zip b/integration-tests/templates/data-ibrain2/ibrain2-dropboxes-test.zip
new file mode 100644
index 0000000000000000000000000000000000000000..15a65ebaa6306628e010d636bb094a084a85f6f4
Binary files /dev/null and b/integration-tests/templates/data-ibrain2/ibrain2-dropboxes-test.zip differ
diff --git a/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
new file mode 100755
index 0000000000000000000000000000000000000000..57886ecb685070f75b445bc3df0c7fa4adc30a2c
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/scripts/commonDropbox.py
@@ -0,0 +1,195 @@
+#! /usr/bin/env python
+
+import os
+
+class AbstractPropertiesParser:
+ _propertiesDict = None
+
+ def __init__(self, incoming, fileName):
+ path = os.path.join(incoming, fileName)
+ self._propertiesDict = self._parseMetadata(path)
+
+ # 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):
+ for key, value in self._propertiesDict.iteritems():
+ yield (key, value)
+
+ # All dataset properties.
+ # Returns:
+ # an iterator which yields (propertyCode, propertyValue) pairs
+ def getDatasetPropertiesIter(self):
+ for key, value in self._propertiesDict.iteritems():
+ if key.startswith(self.DATASET_PROPERTY_PREFIX):
+ yield (key, value)
+
+class AbstractMetadataParser(AbstractPropertiesParser):
+ METADATA_FILE="metadata.properties"
+
+ IBRAIN2_DATASET_ID_PROPERTY = "brain2.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" # not used
+
+ # All dataset properties.
+ # Returns:
+ # an iterator which yields (propertyCode, propertyValue) pairs
+ def getDatasetPropertiesIter(self):
+ for propertyCode, value in AbstractPropertiesParser.getDatasetPropertiesIter(self):
+ yield (propertyCode, value)
+ yield (self.INSTRUMENT_PROPERTY, self.get(self.INSTRUMENT_PROPERTY))
+
+ def getPlateCode(self):
+ return self.get(self.PLATE_CODE_PRPOPERTY)
+
+class DerivedDatasetMetadataParser(AbstractMetadataParser):
+ PARENT_DATSASET_PERMID_PRPOPERTY = "storage_provider.parent.dataset.id"
+ DATASET_TYPE_PROPERTY = "dataset.type"
+
+ def getDatasetPropertiesIter(self):
+ return AbstractMetadataParser.getDatasetPropertiesIter(self)
+
+ 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 _findAssayFile(self, incoming):
+ for file in os.listdir(incoming):
+ print file
+ if file.startswith(self.ASSAY_FILE_PREFIX):
+ return file
+ raise Exception("Assay file not found!")
+
+ def __init__(self, incoming):
+ AbstractPropertiesParser.__init__(self, incoming, self._findAssayFile(incoming))
+
+class IBRAIN2Utils:
+ """ path to the registration confirmation directory relative to the incoming dataset """
+ CONFIRMATION_DIRECTORY = "../../registration-status"
+
+ STATUS_PROPERTY = "storage_provider.storage.status"
+ OK = "STORAGE_SUCCESS"
+ 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 _getStatusFileName(self, ibrain2DatasetId, incoming):
+ return incoming + "/" + self.CONFIRMATION_DIRECTORY + "/" + self.IBRAIN2_STATUS_FILE_PREFIX + ibrain2DatasetId + self.IBRAIN2_STATUS_FILE_SUFFIX
+
+ def _prop(self, name, value):
+ return name + " = " + value + "\n"
+
+ def _writeConfirmationFile(self, ibrain2DatasetId, fileContent, incoming):
+ confirmationFile = self._getStatusFileName(ibrain2DatasetId, incoming)
+ file = open(confirmationFile, "w")
+ file.write(fileContent)
+ file.close()
+
+ def createSuccessStatus(self, ibrain2DatasetId, openbisDatasetId, incoming):
+ fileContent = self._prop(self.STATUS_PROPERTY, self.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.ERROR)
+ fileContent += self._prop(AbstractMetadataParser.IBRAIN2_DATASET_ID_PROPERTY, ibrain2DatasetId)
+ fileContent += self._prop(self.ERROR_MSG_PROPERTY, errorMessage)
+ self._writeConfirmationFile(ibrain2DatasetId, fileContent, incoming)
+
+
+# -------------- 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/scripts/commonImageDropbox.py b/integration-tests/templates/data-ibrain2/scripts/commonImageDropbox.py
new file mode 100755
index 0000000000000000000000000000000000000000..60372dc0da410aeaefabd3af4084edc86f689af7
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/scripts/commonImageDropbox.py
@@ -0,0 +1,51 @@
+#! /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):
+ image_tokens = ImageMetadata()
+
+ basename = os.path.splitext(imagePath)[0]
+ #
+ token_dict = {}
+ for token in basename.split("_"):
+ token_dict[token[:1]] = token[1:]
+
+ image_tokens.well = token_dict["w"]
+ fieldText = token_dict["s"]
+ try:
+ image_tokens.tileNumber = int(fieldText)
+ except ValueError:
+ raise Exception("Cannot parse field number from '" + fieldText + "' in '" + basename + "' file name.")
+
+ image_tokens.channelCode = basename.split("_")[-1] + " ("+ token_dict["c"] + ")"
+ return image_tokens
+
+ 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)
+
+
\ No newline at end of file
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
new file mode 100755
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100755
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100755
index 0000000000000000000000000000000000000000..6486b490795426a271bc3d6571e08ac2653eeefe
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_features.py
@@ -0,0 +1,66 @@
+#! /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 *
+
+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.
+# 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())
+ 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)
+
+# 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
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_metadata.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_metadata.py
new file mode 100755
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100755
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py b/integration-tests/templates/data-ibrain2/scripts/hcs_image_overview.py
new file mode 100755
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_image_raw.py b/integration-tests/templates/data-ibrain2/scripts/hcs_image_raw.py
new file mode 100755
index 0000000000000000000000000000000000000000..b5446e3157640066d4340c5373748f152b048ef3
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_raw.py
@@ -0,0 +1,71 @@
+#! /usr/bin/env python
+
+from commonImageDropbox import IBrain2ImageDataSetConfig
+from commonDropbox import AcquiredDatasetMetadataParser
+
+""" Plate geometry which will be used. Other possible value: 96_WELLS_8X12 """
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+""" 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"
+
+def createPlateWithExperimentIfNeeded(transaction, assayParser, plate, space):
+ project = 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)
+
+ sampleIdentifier = "/"+space+"/"+plate
+ plate = transaction.getSample(sampleIdentifier)
+ if plate == None:
+ expIdentifier = "/"+space+"/"+project+"/"+experiment
+ experiment = transaction.getExperiment(expIdentifier)
+ if experiment == None:
+ experiment = transaction.createNewExperiment(expIdentifier, SIRNA_EXP_TYPE)
+ openbisExpDesc = experimentDesc + "\ntype: "+experimentType
+ experiment.setPropertyValue("DESCRIPTION", openbisExpDesc)
+
+ plate = transaction.createNewSample(sampleIdentifier, PLATE_TYPE_CODE)
+ plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+ plate.setExperiment(experiment)
+
+"""
+TODO:
+-
+"""
+if incoming.isDirectory():
+ imageDataset = IBrain2ImageDataSetConfig()
+ imageDataset.setRawImageDatasetType()
+ metadataParser = AcquiredDatasetMetadataParser(incoming)
+ assayParser = AssayParser(incoming)
+
+ plate = metadataParser.getPlateCode()
+ space = assayParser.get(assayParser.LAB_LEADER_PROPERTY)
+
+ imageDataset.setPlate(space, plate)
+ imageDataset.setFileFormatType("TIFF")
+ imageDataset.setGenerateThumbnails(True)
+ imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
+ imageDataset.setRecognizedImageExtensions(["tif, tiff"])
+ imageDataset.setStoreChannelsOnExperimentLevel(False)
+
+ imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+ for propertyCode, value in metadataParser.getPropertiesIter():
+ imageRegistrationDetails.setPropertyValue(propertyCode, value)
+
+ tr = service.transaction(incoming, factory)
+
+ createPlateWithExperimentIfNeeded(tr, assayParser, plate, space)
+ dataset = tr.createNewDataSet(imageRegistrationDetails)
+ imageDataSetFolder = tr.moveFile(incoming.getPath(), dataset)
+ imageDatasetCode = dataset.getDataSetCode()
+ IBRAIN2Utils().createSuccessStatus(metadataParser.getIBrain2DatasetId(), imageDatasetCode, incoming)
+ print "Registered dataset:", imageDatasetCode
+
+# TODO: test this !!!
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ incoming = service.incomingDataSetFile
+ iBrain2DatasetId = AcquiredDatasetMetadataParser(incoming).getIBrain2DatasetId()
+ IBRAIN2Utils().createFailureStatus(iBrain2DatasetId, throwable.getMessage(), 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
new file mode 100755
index 0000000000000000000000000000000000000000..409e1a3331de11a9a13efa829300df5468789208
--- /dev/null
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_image_segmentation.py
@@ -0,0 +1,34 @@
+#! /usr/bin/env python
+# This is a dropbox for importing HCS segmentation image datasets
+
+import IBrain2ImageDataSetConfig from common-image-dropbox
+
+"""
+TODO:
+- check if parent exists and exit otherwise (ask Eva)
+-
+"""
+if incoming.isDirectory():
+ imageDataset = IBrain2ImageDataSetConfig()
+ imageDataset.setSegmentationImageDatasetType()
+ plate = incoming.getName().split("_")[2][1:]
+ space = "IBRAIN2"
+ #space = "TEST"
+ imageDataset.setPlate(space, plate)
+ imageDataset.setFileFormatType("PNG")
+ imageDataset.setGenerateThumbnails(True)
+ imageDataset.setMaxThumbnailWidthAndHeight(imageDataset.THUMBANAIL_SIZE)
+ imageDataset.setRecognizedImageExtensions(["png"])
+ imageDataset.setStoreChannelsOnExperimentLevel(False)
+ imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
+
+ imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+ info = imageRegistrationDetails.getDataSetInformation()
+ info.getImageStorageConfiguraton().getThumbnailsStorageFormat().setHighQuality(True)
+ tr = service.transaction(incoming, factory)
+
+ dataset = tr.createNewDataSet(imageRegistrationDetails)
+ imageDataSetFolder = tr.moveFile(incoming.getPath(), dataset)
+ imageDatasetCode = dataset.getDataSetCode()
+ print "Registered dataset:", imageDatasetCode
+
\ No newline at end of file