def characterise(self, edna_input):
process_directory_path = edna_input.process_directory
# if there is no data collection id, the id will be a random number
# this is to give a unique number to the EDNA input and result files;
# something more clever might be done to give a more significant
# name, if there is no dc id.
try:
dc_id = edna_input.getDataCollectionId().getValue()
except:
dc_id = id(edna_input)
if hasattr(edna_input, "process_directory"):
edna_input_file = os.path.join(process_directory_path,"EDNAInput_%s.xml" % dc_id)
edna_input.exportToFile(edna_input_file)
edna_results_file = os.path.join(process_directory_path, "EDNAOutput_%s.xml" % dc_id)
if not os.path.isdir(process_directory_path):
os.makedirs(path)
else:
raise RuntimeError, "No process directory specified in edna_input"
logging.getLogger("queue_exec").info("Starting EDNA using xml file %r", edna_input_file)
edna_processing_thread = EdnaProcessingThread(self.start_edna_command, \
edna_input_file, \
edna_results_file,\
process_directory_path)
self.processing_done_event = edna_processing_thread.start()
self.processing_done_event.wait()
self.result = XSDataResultMXCuBE.parseFile(edna_results_file)
return self.result
def characterise(self, edna_input):
path = edna_input.process_directory
# if there is no data collection id, the id will be a random number
# this is to give a unique number to the EDNA input and result files;
# something more clever might be done to give a more significant
# name, if there is no dc id.
try:
dc_id = edna_input.getDataCollectionId().getValue()
except:
dc_id = id(edna_input)
if hasattr(edna_input, "process_directory"):
edna_input_file = os.path.join(path, "EDNAInput_%s.xml" % dc_id)
edna_input.exportToFile(edna_input_file)
edna_results_file = os.path.join(path, "EDNAOutput_%s.xml" % dc_id)
if not os.path.isdir(path):
os.makedirs(path)
else:
raise RuntimeError("No process directory specified in edna_input")
msg = "Starting EDNA using xml file %r", edna_input_file
logging.getLogger("queue_exec").info(msg)
edna_processing_thread = \
EdnaProcessingThread(self.start_edna_command, edna_input_file,
edna_results_file, path)
self.processing_done_event = edna_processing_thread.start()
self.processing_done_event.wait()
self.result = XSDataResultMXCuBE.parseFile(edna_results_file)
return self.result
def get_result(self):
jobstatus = self.job.status
# outname = self.input_file.replace("Input", "Output")
# outfile = os.path.join( self.edna_directory, outname)
logging.getLogger("HWR").debug("Job / state is COMPLETED")
logging.getLogger("HWR").debug(" job status dump: %s" % jobstatus)
logging.getLogger("HWR").debug(" looking for file: %s" %
self.results_file)
if os.path.exists(self.results_file):
# job_output = open(outfile).read()
# logging.getLogger("HWR").debug(" EDNA results file found. loading it")
# open(self.results_file, "w").write(job_output)
logging.getLogger("HWR").debug(" EDNA results file found 2")
result = XSDataResultMXCuBE.parseFile(self.results_file)
logging.getLogger("HWR").debug(" EDNA results file found 3")
logging.getLogger("HWR").debug(
"EDNA Result loaded from file / result is=%s" %
str(type(result)))
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / cannot find output file ")
result = ""
return result
def get_result(self):
jobstatus = self.job.status
# outname = self.input_file.replace("Input", "Output")
# outfile = os.path.join( self.edna_directory, outname)
logging.getLogger("HWR").debug("Job / state is COMPLETED")
logging.getLogger("HWR").debug(" job status dump: %s" % jobstatus)
logging.getLogger("HWR").debug(" looking for file: %s" % self.results_file)
if os.path.exists(self.results_file):
# job_output = open(outfile).read()
# logging.getLogger("HWR").debug(" EDNA results file found. loading it")
# open(self.results_file, "w").write(job_output)
logging.getLogger("HWR").debug(" EDNA results file found 2")
result = XSDataResultMXCuBE.parseFile(self.results_file)
logging.getLogger("HWR").debug(" EDNA results file found 3")
logging.getLogger("HWR").debug(
"EDNA Result loaded from file / result is=%s" % str(type(result))
)
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / cannot find output file "
)
result = ""
return result
def workflow_state_changed(self, new_state):
logging.debug('%s: new workflow state is %r', self.name(), new_state)
if type(new_state) == types.ListType or type(new_state) == types.TupleType:
new_state = str(new_state[0])
try:
actor = self.workflow.current_actor.getValue()
self.refresh_workflow_state(new_state, actor)
except:
self.info_label.setText('Lost connection with workflow engine')
if new_state == "ON" and self.previous_workflow_state == "RUNNING":
# workflow finished, open the output file and use an EDNACaracterize method to
# continue the work
if self.workflow_output_file is not None and os.path.exists(self.workflow_output_file):
logging.debug('Workflow finished, sending the results to %r', self.edna)
logging.debug('Workflow file is %s', self.workflow_output_file)
try:
data = XSDataResultMXCuBE.parseFile(self.workflow_output_file)
self.edna.readEDNAResults(data.getCharacterisationResult(), self.workflow_output_file,
self.beamline_params['directory'], self.beamline_params['prefix'],
int(self.beamline_params['run_number']),
process_dir=self.process_dir, do_inducedraddam=False)
logging.debug('Results sent')
except:
logging.debug('Malformed or empty results file')
else:
logging.debug('Workflow finished, no result file')
# then remove the current widget with the parameters
if self.params_widget is not None:
self.layout().removeChild(self.params_widget)
self.previous_workflow_state = new_state
def workflow_state_changed(self, new_state):
logging.debug('%s: new workflow state is %r', self.name(), new_state)
if type(new_state) == list or type(new_state) == tuple:
new_state = str(new_state[0])
if new_state == "ON" and self.previous_workflow_state == "RUNNING":
# workflow finished, open the output file and use an EDNACaracterize method to
# continue the work
if self.workflow_output_file is not None and os.path.exists(
self.workflow_output_file):
logging.debug('Workflow finished, sending the results to %r',
self.edna)
logging.debug('Workflow file is %s', self.workflow_output_file)
try:
data = XSDataResultMXCuBE.parseFile(
self.workflow_output_file)
self.edna.readEDNAResults(
data.getCharacterisationResult(),
self.workflow_output_file,
self.beamline_params['directory'],
self.beamline_params['prefix'],
int(self.beamline_params['run_number']),
process_dir=self.process_dir,
do_inducedraddam=False)
logging.debug('Results sent')
except:
logging.debug('Malformed or empty results file')
else:
logging.debug('Workflow finished, no result file')
# then remove the current widget with the parameters
if self.params_widget is not None:
self.layout().removeChild(self.params_widget)
self.previous_workflow_state = new_state
def reallyGetEDNAResults(edna_process_id=edna_process_id, edna_results_file=edna_results_file, storage_dict={"i":0}):
storage_dict["i"]+=1
if storage_dict["i"]>=3:
logging.getLogger().error("Timeout: cannot open EDNA results file (%s)", edna_results_file)
self.EDNAWaitResultsTimers[edna_process_id].stop()
del self.EDNAWaitResultsTimers[edna_process_id]
del self.imagePathProperties[edna_process_id]
else:
results = XSDataResultMXCuBE.parseFile(edna_results_file)
self.EDNAWaitResultsTimers[edna_process_id].stop()
del self.EDNAWaitResultsTimers[edna_process_id]
imagePrefix = self.imagePathProperties[edna_process_id]["imagePrefix"]
imageDir = self.imagePathProperties[edna_process_id]["imageDir"]
lRunN = self.imagePathProperties[edna_process_id]["lRunN"]
del self.imagePathProperties[edna_process_id]
try:
html_path = results.htmlPage.path.value
self.emit('newEDNAHTML', (html_path, imagePrefix, lRunN))
except:
logging.getLogger().exception('EDNACharacterize: no html in results')
try:
screening_id = results.getScreeningId().getValue()
except:
screening_id = None
self.readEDNAResults(results.getCharacterisationResult(), edna_results_file, imageDir,
imagePrefix, lRunN, screeningId = screening_id)
def workflow_state_changed(self, new_state):
logging.debug("%s: new workflow state is %r", self.name(), new_state)
if isinstance(new_state, types.ListType) or isinstance(
new_state, types.TupleType
):
new_state = str(new_state[0])
if new_state == "ON" and self.previous_workflow_state == "RUNNING":
# workflow finished, open the output file and use an EDNACaracterize method to
# continue the work
if self.workflow_output_file is not None and os.path.exists(
self.workflow_output_file
):
logging.debug("Workflow finished, sending the results to %r", self.edna)
logging.debug("Workflow file is %s", self.workflow_output_file)
try:
data = XSDataResultMXCuBE.parseFile(self.workflow_output_file)
self.edna.readEDNAResults(
data.getCharacterisationResult(),
self.workflow_output_file,
self.beamline_params["directory"],
self.beamline_params["prefix"],
int(self.beamline_params["run_number"]),
process_dir=self.process_dir,
do_inducedraddam=False,
)
logging.debug("Results sent")
except BaseException:
logging.debug("Malformed or empty results file")
else:
logging.debug("Workflow finished, no result file")
# then remove the current widget with the parameters
if self.params_widget is not None:
self.layout().removeChild(self.params_widget)
self.previous_workflow_state = new_state
def workflow_state_changed(self, new_state):
logging.debug("%s: new workflow state is %r", self.name(), new_state)
if isinstance(new_state, types.ListType) or isinstance(
new_state, types.TupleType):
new_state = str(new_state[0])
if new_state == "ON" and self.previous_workflow_state == "RUNNING":
# workflow finished, open the output file and use an EDNACaracterize method to
# continue the work
if self.workflow_output_file is not None and os.path.exists(
self.workflow_output_file):
logging.debug("Workflow finished, sending the results to %r",
self.edna)
logging.debug("Workflow file is %s", self.workflow_output_file)
try:
data = XSDataResultMXCuBE.parseFile(
self.workflow_output_file)
self.edna.readEDNAResults(
data.getCharacterisationResult(),
self.workflow_output_file,
self.beamline_params["directory"],
self.beamline_params["prefix"],
int(self.beamline_params["run_number"]),
process_dir=self.process_dir,
do_inducedraddam=False,
)
logging.debug("Results sent")
except BaseException:
logging.debug("Malformed or empty results file")
else:
logging.debug("Workflow finished, no result file")
# then remove the current widget with the parameters
if self.params_widget is not None:
self.layout().removeChild(self.params_widget)
self.previous_workflow_state = new_state
def characterise(self, edna_input):
# if there is no data collection id, the id will be a random number
# this is to give a unique number to the EDNA input and result files;
# something more clever might be done to give a more significant
# name, if there is no dc id.
try:
dc_id = edna_input.getDataCollectionId().getValue()
except:
dc_id = id(edna_input)
for dataSet in edna_input.dataSet:
for imageFile in dataSet.imageFile:
firstImage = imageFile.path.value
break
self.edna_processing_thread = None
listImageName = os.path.basename(firstImage).split("_")
prefix = "_".join(listImageName[:-2])
run_number = listImageName[-2]
i = 1
if hasattr(edna_input, "process_directory"):
edna_directory = os.path.join(
edna_input.process_directory,
"characterisation_%s_run%s_%d" % (prefix, run_number, i))
while os.path.exists(edna_directory):
i += 1
edna_directory = os.path.join(
edna_input.process_directory,
"characterisation_%s_run%s_%d" % (prefix, run_number, i))
os.makedirs(edna_directory)
else:
raise RuntimeError("No process directory specified in edna_input")
edna_input_file = os.path.join(edna_directory,
"EDNAInput_%s.xml" % dc_id)
edna_input.exportToFile(edna_input_file)
edna_results_file = os.path.join(edna_directory,
"EDNAOutput_%s.xml" % dc_id)
msg = "Starting EDNA using xml file %r", edna_input_file
logging.getLogger("queue_exec").info(msg)
self.edna_processing_thread = \
EdnaProcessingThread(self.start_edna_command, edna_input_file,
edna_results_file, edna_directory)
self.processing_done_event = self.edna_processing_thread.start()
self.processing_done_event.wait()
self.result = None
if os.path.exists(edna_results_file):
self.result = XSDataResultMXCuBE.parseFile(edna_results_file)
return self.result
def _run_edna(self, input_file, results_file, process_directory):
"""Starts EDNA"""
msg = "Starting EDNA characterisation using xml file %s" % input_file
logging.getLogger("queue_exec").info(msg)
args = (self.start_edna_command, input_file, results_file, process_directory)
subprocess.call("%s %s %s %s" % args, shell=True)
self.result = None
if os.path.exists(results_file):
self.result = XSDataResultMXCuBE.parseFile(results_file)
return self.result
def run_edna(self, input_file, results_file, process_directory):
msg = "Starting EDNA characterisation using xml file %s" % input_file
logging.getLogger("queue_exec").info(msg)
args = (self.start_edna_command, input_file, results_file, process_directory)
subprocess.call("%s %s %s %s" % args, shell=True)
self.result = None
if os.path.exists(results_file):
self.result = XSDataResultMXCuBE.parseFile(results_file)
return self.result
def characterise(self, edna_input):
# if there is no data collection id, the id will be a random number
# this is to give a unique number to the EDNA input and result files;
# something more clever might be done to give a more significant
# name, if there is no dc id.
try:
dc_id = edna_input.getDataCollectionId().getValue()
except:
dc_id = id(edna_input)
for dataSet in edna_input.dataSet:
for imageFile in dataSet.imageFile:
firstImage = imageFile.path.value
break
self.edna_processing_thread = None
listImageName = os.path.basename(firstImage).split("_")
prefix = "_".join(listImageName[:-2])
run_number = listImageName[-2]
i = 1
if hasattr(edna_input, "process_directory"):
edna_directory = os.path.join(edna_input.process_directory, "characterisation_%s_run%s_%d" % (prefix, run_number, i))
while os.path.exists(edna_directory):
i += 1
edna_directory = os.path.join(edna_input.process_directory, "characterisation_%s_run%s_%d" % (prefix, run_number, i))
os.makedirs(edna_directory)
else:
raise RuntimeError("No process directory specified in edna_input")
edna_input_file = os.path.join(edna_directory, "EDNAInput_%s.xml" % dc_id)
edna_input.exportToFile(edna_input_file)
edna_results_file = os.path.join(edna_directory, "EDNAOutput_%s.xml" % dc_id)
msg = "Starting EDNA using xml file %r", edna_input_file
logging.getLogger("queue_exec").info(msg)
self.edna_processing_thread = \
EdnaProcessingThread(self.start_edna_command, edna_input_file,
edna_results_file, edna_directory)
self.processing_done_event = self.edna_processing_thread.start()
self.processing_done_event.wait()
self.result = None
if os.path.exists(edna_results_file):
self.result = XSDataResultMXCuBE.parseFile(edna_results_file)
return self.result
def get_result(self, state):
if state == "COMPLETED":
outfile = os.path.join( self.edna_directory, "ControlInterfaceToMXCuBEv1_3_dataOutput.xml")
logging.getLogger("HWR").debug("Job / state is COMPLETED")
logging.getLogger("HWR").debug(" looking for file: %s" % outfile)
if os.path.exists(outfile):
job_output = open(outfile).read()
open(self.results_file, "w").write(job_output)
result = XSDataResultMXCuBE.parseFile(self.results_file)
else:
logging.getLogger("HWR").debug("EDNA Job finished without success / cannot find output file ")
result = ""
else:
logging.getLogger("HWR").debug("EDNA Job finished without success / state was %s" % (job.state))
result = ""
return result
def get_result(self, state):
if state == "COMPLETED":
outfile = os.path.join(
self.edna_directory, "ControlInterfaceToMXCuBEv1_3_dataOutput.xml"
)
logging.getLogger("HWR").debug("Job / state is COMPLETED")
logging.getLogger("HWR").debug(" looking for file: %s" % outfile)
if os.path.exists(outfile):
job_output = open(outfile).read()
open(self.results_file, "w").write(job_output)
result = XSDataResultMXCuBE.parseFile(self.results_file)
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / cannot find output file "
)
result = ""
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / state was %s" % (job.state)
)
result = ""
return result
