def veto_injections(workflow, inj_file, veto_file, veto_name, out_dir, tags=None):
tags = [] if tags is None else tags
make_analysis_dir(out_dir)
node = Executable(workflow.cp, 'strip_injections', ifos=workflow.ifos,
out_dir=out_dir, tags=tags).create_node()
node.add_opt('--segment-name', veto_name)
node.add_input_opt('--veto-file', veto_file)
node.add_input_opt('--injection-file', inj_file)
node.add_opt('--ifos', ' '.join(workflow.ifos))
node.new_output_file_opt(workflow.analysis_time, '.xml', '--output-file')
workflow += node
return node.output_files[0]
def veto_injections(workflow, inj_file, veto_file, veto_name, out_dir, tags=None):
tags = [] if tags is None else tags
make_analysis_dir(out_dir)
node = Executable(workflow.cp, 'strip_injections', ifos=workflow.ifos,
out_dir=out_dir, tags=tags).create_node()
node.add_opt('--segment-name', veto_name)
node.add_input_opt('--veto-file', veto_file)
node.add_input_opt('--injection-file', inj_file)
node.add_opt('--ifos', ' '.join(workflow.ifos))
node.new_output_file_opt(workflow.analysis_time, '.xml', '--output-file')
workflow += node
return node.output_files[0]
def create_segs_from_cats_job(cp, out_dir, ifo_string, tag=None):
"""
This function creates the CondorDAGJob that will be used to run
ligolw_segments_from_cats as part of the workflow
Parameters
-----------
cp : pycbc.workflow.configuration.WorkflowConfigParser
The in-memory representation of the configuration (.ini) files
out_dir : path
Directory in which to put output files
ifo_string : string
String containing all active ifos, ie. "H1L1V1"
tag : string, optional (default=None)
Use this to specify a tag. This can be used if this module is being
called more than once to give call specific configuration (by setting
options in [workflow-datafind-${TAG}] rather than [workflow-datafind]). This
is also used to tag the Files returned by the class to uniqueify
the Files and uniqueify the actual filename.
FIXME: Filenames may not be unique with current codes!
Returns
--------
job : Job instance
The Job instance that will run segments_from_cats jobs
"""
segServerUrl = cp.get_opt_tags("workflow-segments",
"segments-database-url", [tag])
vetoDefFile = cp.get_opt_tags("workflow-segments",
"segments-veto-definer-file", [tag])
if tag:
currTags = [tag]
else:
currTags = []
job = Executable(cp, 'segments_from_cats', universe='local',
ifos=ifo_string, out_dir=out_dir, tags=currTags)
job.add_opt('--separate-categories')
job.add_opt('--segment-url', segServerUrl)
job.add_opt('--veto-file', vetoDefFile)
# FIXME: Would like the proxy in the Workflow instance
# FIXME: Explore using the x509 condor commands
# Set up proxy to be accessible in a NFS location
# If the user has logged in with gsissh then X509_USER_PROXY will be set
# However, certain users log in with an ssh key and then ligo-proxy-init
# This route does not set X509_USER_PROXY, so use the default file location
if os.environ.has_key('X509_USER_PROXY'):
proxy = os.getenv('X509_USER_PROXY')
else:
proxy = "/tmp/x509up_u%d" % os.getuid()
proxyfile = os.path.join(out_dir, 'x509up.file')
try:
shutil.copyfile(proxy, proxyfile)
except IOError:
raise RuntimeError('Cannot find certificate in %s. '
'Make sure that ligo-proxy-init '
'has been run.' % proxy)
job.add_profile('condor', 'environment',
'USER=$ENV(USER);X509_USER_PROXY=%s' % proxyfile)
return job
def rerank_coinc_followup(workflow,
statmap_file,
bank_file,
out_dir,
tags=None,
injection_file=None,
ranking_file=None):
if tags is None:
tags = []
make_analysis_dir(out_dir)
if not workflow.cp.has_section("workflow-rerank"):
logging.info("No reranking done in this workflow")
return statmap_file
else:
logging.info("Setting up reranking of candidates")
# Generate reduced data files (maybe this could also be used elsewhere?)
stores = FileList([])
for ifo in workflow.ifos:
make_analysis_dir('strain_files')
node = Executable(workflow.cp,
'strain_data_reduce',
ifos=[ifo],
out_dir='strain_files',
tags=tags).create_node()
node.add_opt('--gps-start-time', workflow.analysis_time[0])
node.add_opt('--gps-end-time', workflow.analysis_time[1])
if injection_file:
node.add_input_opt('--injection-file', injection_file)
fil = node.new_output_file_opt(workflow.analysis_time, '.hdf',
'--output-file')
stores.append(fil)
workflow += node
# Generate trigger input file
node = Executable(workflow.cp,
'rerank_trigger_input',
ifos=workflow.ifos,
out_dir=out_dir,
tags=tags).create_node()
node.add_input_opt('--statmap-file', statmap_file)
node.add_input_opt('--bank-file', bank_file)
trigfil = node.new_output_file_opt(workflow.analysis_time, '.hdf',
'--output-file')
workflow += node
# Parallelize coinc trigger followup
factor = int(
workflow.cp.get_opt_tags("workflow-rerank", "parallelization-factor",
tags))
exe = Executable(workflow.cp,
'coinc_followup',
ifos=workflow.ifos,
out_dir=out_dir,
tags=tags)
stat_files = FileList([])
for i in range(factor):
node = exe.create_node()
node.new_output_file_opt(workflow.analysis_time,
'.hdf',
'--output-file',
tags=[str(i)])
node.add_multiifo_input_list_opt('--hdf-store', stores)
node.add_input_opt('--input-file', trigfil)
node.add_opt('--start-index', str(i))
node.add_opt('--stride', factor)
workflow += node
stat_files += node.output_files
exe = Executable(workflow.cp,
'rerank_coincs',
ifos=workflow.ifos,
out_dir=out_dir,
tags=tags)
node = exe.create_node()
node.add_input_list_opt('--stat-files', stat_files)
node.add_input_opt('--statmap-file', statmap_file)
node.add_input_opt('--followup-file', trigfil)
if ranking_file:
node.add_input_opt('--ranking-file', ranking_file)
node.new_output_file_opt(workflow.analysis_time, '.hdf', '--output-file')
workflow += node
return node.output_file