class ALBAEdnaProcJob(ALBAClusterJob):
sls_script = os.path.join(root, 'edna-mx/ednaproc/edna-mx.ednaproc.sl')
def run(self, *args):
collect_id, input_file, output_dir = args
self.job = XalocJob("edna-ednaproc", str(collect_id), self.sls_script, input_file, output_dir)
self.job.submit()
class ALBAAutoprocJob(ALBAClusterJob):
sls_script = os.path.join(root, 'edna-mx/autoproc/edna-mx.autoproc.sl')
def run(self, *args):
jobname = os.path.basename(os.path.dirname(edna_directory))
self.job = XalocJob("edna-autoproc", jobname, self.sls_script, input_file, edna_directory)
self.job.submit()
class ALBAEdnaProcJob(ALBAClusterJob):
sls_script = os.path.join(root, "edna-mx/ednaproc/edna-mx.ednaproc.sl")
def run(self, *args):
collect_id, input_file, output_dir = args
self.job = XalocJob(
"edna-ednaproc", str(collect_id), self.sls_script, input_file, output_dir
)
self.job.submit()
class ALBAAutoprocJob(ALBAClusterJob):
sls_script = os.path.join(root, "edna-mx/autoproc/edna-mx.autoproc.sl")
def run(self, *args):
jobname = os.path.basename(os.path.dirname(edna_directory))
self.job = XalocJob(
"edna-autoproc", jobname, self.sls_script, input_file, edna_directory
)
self.job.submit()
class ALBAStrategyJob(ALBAClusterJob):
sls_script = os.path.join(root, "edna-mx/strategy/edna-mx.strategy.sl")
def run(self, *args):
logging.getLogger("HWR").debug("Starting StrategyJob - ")
input_file, results_file, edna_directory = args
jobname = os.path.basename(os.path.dirname(edna_directory))
self.job = XalocJob(
"edna-strategy", jobname, self.sls_script, input_file, edna_directory
)
self.job.submit()
logging.getLogger("HWR").debug(" StrategyJob - %s" % str(self.job))
self.edna_directory = os.path.dirname(input_file)
self.results_file = results_file
logging.getLogger("HWR").debug(" input file: %s" % input_file)
logging.getLogger("HWR").debug(" edna directory: %s" % self.edna_directory)
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
class ALBADataAnalysis(DataAnalysis):
def init(self):
DataAnalysis.init(self)
def prepare_edna_input(self, edna_input):
# used for strategy calculation (characterization) using data analysis cluster
# ALBA specific
firstImage = None
for dataSet in edna_input.getDataSet():
for imageFile in dataSet.imageFile:
if imageFile.getPath() is None:
continue
firstImage = imageFile.path.value
break
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.process_directory = edna_directory
output_dir = XSDataFile()
path = XSDataString()
path.setValue(edna_directory)
output_dir.setPath(path)
edna_input.setOutputFileDirectory(output_dir)
def run_edna(self, input_file, results_file, edna_directory):
return self.run(input_file, results_file, edna_directory)
def run(self, *args):
input_file, results_file, edna_directory = args
jobname = os.path.basename(os.path.dirname(edna_directory))
logging.getLogger("HWR").debug(" XalocJob submiting ")
logging.getLogger("HWR").debug(" job_name: %s" % jobname)
logging.getLogger("HWR").debug(" sls_script: %s, " % sls_script)
logging.getLogger("HWR").debug(" input file: %s" % input_file)
logging.getLogger("HWR").debug(" results file: %s" % results_file)
logging.getLogger("HWR").debug(" edna directory: %s" %
edna_directory)
self.job = XalocJob("edna-strategy", jobname, sls_script, input_file,
edna_directory)
self.job.submit()
logging.getLogger("HWR").debug(" XalocJob submitted %s" % self.job.id)
self.edna_directory = os.path.dirname(input_file)
self.input_file = os.path.basename(input_file)
# self.results_file = self.fix_path(results_file)
self.results_file = results_file
logging.getLogger("HWR").debug(" self.results file: %s" %
self.results_file)
state = self.wait_done()
if state == "COMPLETED":
logging.getLogger("HWR").debug("EDNA Job completed")
time.sleep(0.5)
result = self.get_result()
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / state was %s" %
(self.job.state))
result = ""
return result
def fix_path(self, path):
outpath = path.replace("PROCESS_DATA", "PROCESS_DATA/RESULTS")
# dirname = os.path.dirname(path)
# basename = os.path.basename(path)
# outpath = os.path.join(dirname,'RESULTS',basename)
return outpath
def wait_done(self):
logging.getLogger("HWR").debug("Polling for Job state")
time.sleep(0.5)
logging.getLogger("HWR").debug("Polling for Job state 2")
try:
state = self.job.state
logging.getLogger("HWR").debug("Job / is %s" % str(state))
except BaseException:
import traceback
logging.getLogger("HWR").debug(
"Polling for Job state 3. exception happened")
logging.getLogger("HWR").debug(" %s " % traceback.format_exc())
while state in ["RUNNING", "PENDING"]:
logging.getLogger("HWR").debug("Job / is %s" % state)
time.sleep(0.5)
state = self.job.state
logging.getLogger("HWR").debug("Returning")
logging.getLogger("HWR").debug("Returning %s" % str(state))
return state
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
class ALBADataAnalysis(DataAnalysis):
def init(self):
DataAnalysis.init(self)
def prepare_edna_input(self, edna_input):
# used for strategy calculation (characterization) using data analysis cluster
# ALBA specific
firstImage = None
for dataSet in edna_input.getDataSet():
for imageFile in dataSet.imageFile:
if imageFile.getPath() is None:
continue
firstImage = imageFile.path.value
break
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.process_directory = edna_directory
output_dir = XSDataFile()
path = XSDataString()
path.setValue(edna_directory)
output_dir.setPath(path)
edna_input.setOutputFileDirectory(output_dir)
def run_edna(self, input_file, results_file, edna_directory):
return self.run(input_file, results_file, edna_directory)
def run(self, *args):
input_file, results_file, edna_directory = args
jobname = os.path.basename(os.path.dirname(edna_directory))
logging.getLogger("HWR").debug(" XalocJob submiting ")
logging.getLogger("HWR").debug(" job_name: %s" % jobname)
logging.getLogger("HWR").debug(" sls_script: %s, " % sls_script)
logging.getLogger("HWR").debug(" input file: %s" % input_file)
logging.getLogger("HWR").debug(" results file: %s" % results_file)
logging.getLogger("HWR").debug(" edna directory: %s" % edna_directory)
self.job = XalocJob(
"edna-strategy", jobname, sls_script, input_file, edna_directory
)
self.job.submit()
logging.getLogger("HWR").debug(" XalocJob submitted %s" % self.job.id)
self.edna_directory = os.path.dirname(input_file)
self.input_file = os.path.basename(input_file)
# self.results_file = self.fix_path(results_file)
self.results_file = results_file
logging.getLogger("HWR").debug(
" self.results file: %s" % self.results_file
)
state = self.wait_done()
if state == "COMPLETED":
logging.getLogger("HWR").debug("EDNA Job completed")
time.sleep(0.5)
result = self.get_result()
else:
logging.getLogger("HWR").debug(
"EDNA Job finished without success / state was %s" % (self.job.state)
)
result = ""
return result
def fix_path(self, path):
outpath = path.replace("PROCESS_DATA", "PROCESS_DATA/RESULTS")
# dirname = os.path.dirname(path)
# basename = os.path.basename(path)
# outpath = os.path.join(dirname,'RESULTS',basename)
return outpath
def wait_done(self):
logging.getLogger("HWR").debug("Polling for Job state")
time.sleep(0.5)
logging.getLogger("HWR").debug("Polling for Job state 2")
try:
state = self.job.state
logging.getLogger("HWR").debug("Job / is %s" % str(state))
except BaseException:
import traceback
logging.getLogger("HWR").debug(
"Polling for Job state 3. exception happened"
)
logging.getLogger("HWR").debug(" %s " % traceback.format_exc())
while state in ["RUNNING", "PENDING"]:
logging.getLogger("HWR").debug("Job / is %s" % state)
time.sleep(0.5)
state = self.job.state
logging.getLogger("HWR").debug("Returning")
logging.getLogger("HWR").debug("Returning %s" % str(state))
return state
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