def decode_archive():
try:
print 'decoding archive...'
encoded_archive_bytes = FileUtils.readFileToByteArray(
File(node_archive_path))
decoded_archive_bytes = Base64.getMimeDecoder().decode(
encoded_archive_bytes)
FileUtils.writeByteArrayToFile(File(archive_name),
decoded_archive_bytes)
print 'successfully decoded archive'
except:
print 'Decoding application archive failed'
print dumpStack()
apply(traceback.print_exception, sys.exc_info())
exit(exitcode=1)
def processExperiment(self, experimentNode):
"""Register an IExperimentUpdatable based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@return IExperimentUpdatable experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
expDate = self.formatExpDateForPostgreSQL(experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Create the experiment (with corrected ID if needed: see above)
openBISExperiment = self.createExperiment(openBISIdentifier, expName)
if not openBISExperiment:
msg = "Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the experiment version
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_VERSION",
expVersion)
# Set the date
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DATE",
expDate)
# Set the description
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_DESCRIPTION",
description)
# Set the acquisition hardware
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_HARDWARE",
acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_ACQ_SOFTWARE",
acqSoftware)
# Set the experiment owner
openBISExperiment.setPropertyValue("LSR_FORTESSA_EXPERIMENT_OWNER",
owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(self._incoming.getAbsolutePath(),
f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName,
"", byteArray)
# Return the openBIS Experiment object
return openBISExperiment
def processExperiment(self, experimentNode):
"""Register an IExperimentUpdatable based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@return IExperimentUpdatable experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
expDate = self.formatExpDateForPostgreSQL(
experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Create the experiment (with corrected ID if needed: see above)
openBISExperiment = self.createExperiment(openBISIdentifier, expName)
if not openBISExperiment:
msg = "Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the experiment version
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_VERSION",
expVersion)
# Set the date
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_DATE",
expDate)
# Set the description
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_DESCRIPTION",
description)
# Set the acquisition hardware
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_ACQ_HARDWARE",
acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue(
"FACS_ARIA_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_ACQ_SOFTWARE",
acqSoftware)
# Set the experiment owner
openBISExperiment.setPropertyValue("FACS_ARIA_EXPERIMENT_OWNER", owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(
self._incoming.getAbsolutePath(), f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName, "",
byteArray)
# Return the openBIS Experiment object
return openBISExperiment
def processExperiment(self, experimentNode,
openBISExpType="MICROSCOPY_EXPERIMENT"):
"""Register an IExperiment based on the Experiment XML node.
@param experimentNode An XML node corresponding to an Experiment
@param openBISExpType The experiment type
@return IExperiment experiment
"""
# Get the experiment version
expVersion = experimentNode.attrib.get("version")
if expVersion is None:
expVersion = "0"
# Get the openBIS identifier
openBISIdentifier = experimentNode.attrib.get("openBISIdentifier")
# Get the experiment name
expName = experimentNode.attrib.get("name")
# Get the experiment date and reformat it to be compatible
# with postgreSQL
# TODO: Add this
# expDate = self.formatExpDateForPostgreSQL(experimentNode.attrib.get("date"))
# Get the description
description = experimentNode.attrib.get("description")
# Get the acquisition hardware
# TODO: Add this
# acqHardware = experimentNode.attrib.get("acq_hardware")
# Get the acquisition software
# TODO: Add this
# acqSoftware = experimentNode.attrib.get("acq_software")
# Get the owner name
# TODO: Add this
# owner = experimentNode.attrib.get("owner_name")
# Get attachments
attachments = experimentNode.attrib.get("attachments")
# Make sure to keep the code length within the limits imposed by
# openBIS for codes
if len(openBISIdentifier) > 41:
openBISIdentifier = openBISIdentifier[0:41]
# Create univocal ID
openBISIdentifier = openBISIdentifier + "_" + self.getCustomTimeStamp()
# Make sure to create a new Experiment
openBISExperiment = self._transaction.createNewExperiment(openBISIdentifier, openBISExpType)
print(type(openBISExperiment))
if not openBISExperiment:
msg = "PROCESSOR::processExperiment(): " + \
"Could not create experiment " + openBISIdentifier
self._logger.error(msg)
raise Exception(msg)
# Get comma-separated tag list
tagList = experimentNode.attrib.get("tags")
if tagList != None and tagList != "":
# Retrieve or create the tags
openBISTags = self.retrieveOrCreateTags(tagList)
# Set the metaprojects (tags)
for openBISTag in openBISTags:
openBISTag.addEntity(openBISExperiment)
# Set the date
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DATE",
# expDate)
# Store the name
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_NAME", expName)
# Set the experiment version
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_VERSION",
expVersion)
# Set the description -- but only if is not empty.
# This makes sure that the description of an already existing experiment
# is not overridden by an empty string.
if description != "":
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION",
description)
else:
currentDescription = openBISExperiment.getPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION")
if (currentDescription is None or currentDescription == ""):
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_DESCRIPTION", "")
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_HARDWARE",
# acqHardware)
# Set the acquisition hardware friendly name
openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_HARDWARE_FRIENDLY_NAME",
self._machinename)
# Set the acquisition software
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_ACQ_SOFTWARE",
# acqSoftware)
# Set the experiment owner
# TODO: Add this
# openBISExperiment.setPropertyValue("MICROSCOPY_EXPERIMENT_OWNER",
# owner)
# Add the attachments
if attachments is not None:
# Extract all relative file names
attachmentFiles = attachments.split(";")
for f in attachmentFiles:
# This is an additional security step
if f == '':
continue
# Inform
msg = "Adding file attachment " + f
self._logger.info(msg)
# Build the full path
attachmentFilePath = os.path.join(self._incoming.getAbsolutePath(),
f)
# Extract the file name
attachmentFileName = os.path.basename(attachmentFilePath)
# Read the attachment into a byte array
javaFile = java.io.File(attachmentFilePath)
byteArray = FileUtils.readFileToByteArray(javaFile)
# Add attachment
openBISExperiment.addAttachment(attachmentFilePath,
attachmentFileName,
"", byteArray)
# Return the openBIS Experiment object
return openBISExperiment
