def processFinishedJob(self, jobBatchSystemID, resultStatus, wallTime=None):
"""
Function reads a processed jobWrapper file and updates it state.
"""
if wallTime is not None and self.clusterScaler is not None:
issuedJob = self.jobBatchSystemIDToIssuedJob[jobBatchSystemID]
self.clusterScaler.addCompletedJob(issuedJob, wallTime)
jobStoreID = self.removeJobID(jobBatchSystemID)
if self.jobStore.exists(jobStoreID):
logger.debug("Job %s continues to exist (i.e. has more to do)" % jobStoreID)
jobWrapper = self.jobStore.load(jobStoreID)
if jobWrapper.logJobStoreFileID is not None:
logger.warn("The jobWrapper seems to have left a log file, indicating failure: %s", jobStoreID)
with jobWrapper.getLogFileHandle( self.jobStore ) as logFileStream:
logStream( logFileStream, jobStoreID, logger.warn )
if resultStatus != 0:
# If the batch system returned a non-zero exit code then the worker
# is assumed not to have captured the failure of the job, so we
# reduce the retry count here.
if jobWrapper.logJobStoreFileID is None:
logger.warn("No log file is present, despite jobWrapper failing: %s", jobStoreID)
jobWrapper.setupJobAfterFailure(self.config)
self.jobStore.update(jobWrapper)
elif jobStoreID in self.toilState.hasFailedSuccessors:
# If the job has completed okay, we can remove it from the list of jobs with failed successors
self.toilState.hasFailedSuccessors.remove(jobStoreID)
self.toilState.updatedJobs.add((jobWrapper, resultStatus)) #Now we know the
#jobWrapper is done we can add it to the list of updated jobWrapper files
logger.debug("Added jobWrapper: %s to active jobs", jobStoreID)
else: #The jobWrapper is done
if resultStatus != 0:
logger.warn("Despite the batch system claiming failure the "
"jobWrapper %s seems to have finished and been removed", jobStoreID)
self._updatePredecessorStatus(jobStoreID)
def processFinishedJob(self, jobBatchSystemID, resultStatus, wallTime=None):
"""
Function reads a processed jobWrapper file and updates it state.
"""
if wallTime is not None and self.clusterScaler is not None:
issuedJob = self.jobBatchSystemIDToIssuedJob[jobBatchSystemID]
self.clusterScaler.addCompletedJob(issuedJob, wallTime)
jobStoreID = self.removeJobID(jobBatchSystemID)
if self.jobStore.exists(jobStoreID):
logger.debug("Job %s continues to exist (i.e. has more to do)" % jobStoreID)
jobWrapper = self.jobStore.load(jobStoreID)
if jobWrapper.logJobStoreFileID is not None:
logger.warn("The jobWrapper seems to have left a log file, indicating failure: %s", jobStoreID)
with jobWrapper.getLogFileHandle( self.jobStore ) as logFileStream:
logStream( logFileStream, jobStoreID, logger.warn )
if resultStatus != 0:
# If the batch system returned a non-zero exit code then the worker
# is assumed not to have captured the failure of the job, so we
# reduce the retry count here.
if jobWrapper.logJobStoreFileID is None:
logger.warn("No log file is present, despite jobWrapper failing: %s", jobStoreID)
jobWrapper.setupJobAfterFailure(self.config)
self.jobStore.update(jobWrapper)
elif jobStoreID in self.toilState.hasFailedSuccessors:
# If the job has completed okay, we can remove it from the list of jobs with failed successors
self.toilState.hasFailedSuccessors.remove(jobStoreID)
self.toilState.updatedJobs.add((jobWrapper, resultStatus)) #Now we know the
#jobWrapper is done we can add it to the list of updated jobWrapper files
logger.debug("Added jobWrapper: %s to active jobs", jobStoreID)
else: #The jobWrapper is done
if resultStatus != 0:
logger.warn("Despite the batch system claiming failure the "
"jobWrapper %s seems to have finished and been removed", jobStoreID)
self._updatePredecessorStatus(jobStoreID)
def processFinishedJob(self, jobBatchSystemID, resultStatus):
"""
Function reads a processed jobWrapper file and updates it state.
"""
jobStoreID = self.removeJob(jobBatchSystemID).jobStoreID
if self.jobStore.exists(jobStoreID):
jobWrapper = self.jobStore.load(jobStoreID)
if jobWrapper.logJobStoreFileID is not None:
logger.warn(
"The jobWrapper seems to have left a log file, indicating failure: %s",
jobStoreID)
with jobWrapper.getLogFileHandle(
self.jobStore) as logFileStream:
logStream(logFileStream, jobStoreID, logger.warn)
if resultStatus != 0:
if jobWrapper.logJobStoreFileID is None:
logger.warn(
"No log file is present, despite jobWrapper failing: %s",
jobStoreID)
jobWrapper.setupJobAfterFailure(self.config)
self.toilState.updatedJobs.add(
(jobWrapper, resultStatus)) #Now we know the
#jobWrapper is done we can add it to the list of updated jobWrapper files
logger.debug("Added jobWrapper: %s to active jobs", jobStoreID)
else: #The jobWrapper is done
if resultStatus != 0:
logger.warn(
"Despite the batch system claiming failure the "
"jobWrapper %s seems to have finished and been removed",
jobStoreID)
self._updatePredecessorStatus(jobStoreID)
def processFinishedJob(self, jobBatchSystemID, resultStatus, wallTime=None):
"""
Function reads a processed jobWrapper file and updates it state.
"""
def processRemovedJob(jobStoreID):
if resultStatus != 0:
logger.warn("Despite the batch system claiming failure the "
"jobWrapper %s seems to have finished and been removed", jobStoreID)
self._updatePredecessorStatus(jobStoreID)
if wallTime is not None and self.clusterScaler is not None:
issuedJob = self.jobBatchSystemIDToIssuedJob[jobBatchSystemID]
self.clusterScaler.addCompletedJob(issuedJob, wallTime)
jobStoreID = self.removeJobID(jobBatchSystemID)
if self.jobStore.exists(jobStoreID):
logger.debug("Job %s continues to exist (i.e. has more to do)" % jobStoreID)
try:
jobWrapper = self.jobStore.load(jobStoreID)
except NoSuchJobException:
# Avoid importing AWSJobStore as the corresponding extra might be missing
if self.jobStore.__class__.__name__ == 'AWSJobStore':
# We have a ghost job - the job has been deleted but a stale read from
# SDB gave us a false positive when we checked for its existence.
# Process the job from here as any other job removed from the job store.
# This is a temporary work around until https://github.com/BD2KGenomics/toil/issues/1091
# is completed
logger.warn('Got a stale read from SDB for job %s', jobStoreID)
processRemovedJob(jobStoreID)
return
else:
raise
if jobWrapper.logJobStoreFileID is not None:
logger.warn("The jobWrapper seems to have left a log file, indicating failure: %s", jobStoreID)
with jobWrapper.getLogFileHandle( self.jobStore ) as logFileStream:
logStream( logFileStream, jobStoreID, logger.warn )
if resultStatus != 0:
# If the batch system returned a non-zero exit code then the worker
# is assumed not to have captured the failure of the job, so we
# reduce the retry count here.
if jobWrapper.logJobStoreFileID is None:
logger.warn("No log file is present, despite jobWrapper failing: %s", jobStoreID)
jobWrapper.setupJobAfterFailure(self.config)
self.jobStore.update(jobWrapper)
elif jobStoreID in self.toilState.hasFailedSuccessors:
# If the job has completed okay, we can remove it from the list of jobs with failed successors
self.toilState.hasFailedSuccessors.remove(jobStoreID)
self.toilState.updatedJobs.add((jobWrapper, resultStatus)) #Now we know the
#jobWrapper is done we can add it to the list of updated jobWrapper files
logger.debug("Added jobWrapper: %s to active jobs", jobStoreID)
else: #The jobWrapper is done
processRemovedJob(jobStoreID)
def processFinishedJob(self, jobBatchSystemID, resultStatus):
"""
Function reads a processed jobWrapper file and updates it state.
"""
jobStoreID = self.removeJob(jobBatchSystemID).jobStoreID
if self.jobStore.exists(jobStoreID):
jobWrapper = self.jobStore.load(jobStoreID)
if jobWrapper.logJobStoreFileID is not None:
logger.warn("The jobWrapper seems to have left a log file, indicating failure: %s", jobStoreID)
with jobWrapper.getLogFileHandle( self.jobStore ) as logFileStream:
logStream( logFileStream, jobStoreID, logger.warn )
if resultStatus != 0:
if jobWrapper.logJobStoreFileID is None:
logger.warn("No log file is present, despite jobWrapper failing: %s", jobStoreID)
jobWrapper.setupJobAfterFailure(self.config)
self.toilState.updatedJobs.add((jobWrapper, resultStatus)) #Now we know the
#jobWrapper is done we can add it to the list of updated jobWrapper files
logger.debug("Added jobWrapper: %s to active jobs", jobStoreID)
else: #The jobWrapper is done
if resultStatus != 0:
logger.warn("Despite the batch system claiming failure the "
"jobWrapper %s seems to have finished and been removed", jobStoreID)
self._updatePredecessorStatus(jobStoreID)
def main():
"""Reports the state of the toil.
"""
##########################################
# Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=(
"Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" ExistingJobStoreException exception will be thrown."
),
)
parser.add_argument(
"--verbose",
dest="verbose",
action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False,
)
parser.add_argument(
"--failIfNotComplete",
dest="failIfNotComplete",
action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False,
)
parser.add_argument("--version", action="version", version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
# Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.jobStore != None
##########################################
# Survey the status of the job and report.
##########################################
jobStore = loadJobStore(options.jobStore)
try:
rootJob = Job._loadRootJob(jobStore)
except JobException:
print "The root job of the jobStore is not present, the toil workflow has probably completed okay"
sys.exit(0)
toilState = ToilState(jobStore, rootJob)
failedJobs = [
job for job in toilState.updatedJobs | set(toilState.successorCounts.keys()) if job.remainingRetryCount == 0
]
print "There are %i active jobs, %i parent jobs with children, and \
%i totally failed jobs currently in toil workflow: %s" % (
len(toilState.updatedJobs),
len(toilState.successorCounts),
len(failedJobs),
options.jobStore,
)
if options.verbose: # Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print "Log file for job %s is not present" % job.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help=("Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" JobStoreCreationException exception will be thrown."))
parser.add_argument("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for Toil")
assert options.jobStore is not None
##########################################
#Survey the status of the job and report.
##########################################
jobStore = Toil.loadOrCreateJobStore(options.jobStore)
try:
rootJob = jobStore.loadRootJob()
except JobException:
print('The root job of the job store is absent, the workflow completed successfully.',
file=sys.stderr)
sys.exit(0)
toilState = ToilState(jobStore, rootJob )
# The first element of the toilState.updatedJobs tuple is the jobWrapper we want to inspect
totalJobs = set(toilState.successorCounts.keys()) | \
{jobTuple[0] for jobTuple in toilState.updatedJobs}
failedJobs = [ job for job in totalJobs if job.remainingRetryCount == 0 ]
print('There are %i active jobs, %i parent jobs with children, and %i totally failed jobs '
'currently in %s.' % (len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), options.jobStore), file=sys.stderr)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print('Log file for job %s is absent.' % job.jobStoreID, file=sys.stderr)
if len(failedJobs) == 0:
print('There are no failed jobs to report.', file=sys.stderr)
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help=("Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" ExistingJobStoreException exception will be thrown."))
parser.add_argument("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.jobStore != None
##########################################
#Survey the status of the job and report.
##########################################
jobStore = loadJobStore(options.jobStore)
try:
rootJob = Job._loadRootJob(jobStore)
except JobException:
print "The root job of the jobStore is not present, the toil workflow has probably completed okay"
sys.exit(0)
toilState = ToilState(jobStore, rootJob )
# The first element of the toilState.updatedJobs tuple is the jobWrapper we want to inspect
totalJobs = set(toilState.successorCounts.keys()) | \
{jobTuple[0] for jobTuple in toilState.updatedJobs}
failedJobs = [ job for job in totalJobs if job.remainingRetryCount == 0 ]
print "There are %i active jobs, %i parent jobs with children, and \
%i totally failed jobs currently in toil workflow: %s" % \
(len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), options.jobStore)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print "Log file for job %s is not present" % job.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of a job store that holds the information about the "
"workflow whose status is to be reported on." + jobStoreLocatorHelp)
parser.add_argument("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for Toil")
assert options.jobStore is not None
config = Config()
config.setOptions(options)
##########################################
#Survey the status of the job and report.
##########################################
jobStore = Toil.resumeJobStore(config.jobStore)
try:
rootJob = jobStore.loadRootJob()
except JobException:
print('The root job of the job store is absent, the workflow completed successfully.',
file=sys.stderr)
sys.exit(0)
toilState = ToilState(jobStore, rootJob )
# The first element of the toilState.updatedJobs tuple is the jobGraph we want to inspect
totalJobs = set(toilState.successorCounts.keys()) | \
{jobTuple[0] for jobTuple in toilState.updatedJobs}
failedJobs = [ job for job in totalJobs if job.remainingRetryCount == 0 ]
print('There are %i active jobs, %i parent jobs with children, and %i totally failed jobs '
'currently in %s.' % (len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), config.jobStore), file=sys.stderr)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print('Log file for job %s is absent.' % job.jobStoreID, file=sys.stderr)
if len(failedJobs) == 0:
print('There are no failed jobs to report.', file=sys.stderr)
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help="The location of a job store that holds the information about the "
"workflow whose status is to be reported on." + jobStoreLocatorHelp)
parser.add_argument(
"--verbose",
dest="verbose",
action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument(
"--failIfNotComplete",
dest="failIfNotComplete",
action="store_true",
help=
"Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for Toil")
assert options.jobStore is not None
##########################################
#Survey the status of the job and report.
##########################################
jobStore = Toil.resumeJobStore(options.jobStore)
try:
rootJob = jobStore.loadRootJob()
except JobException:
print(
'The root job of the job store is absent, the workflow completed successfully.',
file=sys.stderr)
sys.exit(0)
toilState = ToilState(jobStore, rootJob)
# The first element of the toilState.updatedJobs tuple is the jobWrapper we want to inspect
totalJobs = set(toilState.successorCounts.keys()) | \
{jobTuple[0] for jobTuple in toilState.updatedJobs}
failedJobs = [job for job in totalJobs if job.remainingRetryCount == 0]
print(
'There are %i active jobs, %i parent jobs with children, and %i totally failed jobs '
'currently in %s.' %
(len(toilState.updatedJobs), len(
toilState.successorCounts), len(failedJobs), options.jobStore),
file=sys.stderr)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print('Log file for job %s is absent.' % job.jobStoreID,
file=sys.stderr)
if len(failedJobs) == 0:
print('There are no failed jobs to report.', file=sys.stderr)
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser(
"usage: %prog [--jobStore] JOB_TREE_DIR [options]", "%prog 0.1")
parser.add_option(
"--jobStore",
dest="jobStore",
help=
"Job store path. Can also be specified as the single argument to the script.\
default=%default",
default=os.path.abspath("./toil"))
parser.add_option(
"--verbose",
dest="verbose",
action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%default",
default=False)
parser.add_option(
"--failIfNotComplete",
dest="failIfNotComplete",
action="store_true",
help=
"Return exit value of 1 if toil jobs not all completed. default=%default",
default=False)
options, args = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
assert len(args) <= 1 #Only toil may be specified as argument
if len(args) == 1: #Allow toil directory as arg
options.jobStore = args[0]
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.jobStore != None
##########################################
#Survey the status of the job and report.
##########################################
jobStore = loadJobStore(options.jobStore)
try:
rootJob = Job._loadRootJob(jobStore)
except JobException:
print "The root job of the jobStore is not present, the toil workflow has probably completed okay"
sys.exit(0)
toilState = ToilState(jobStore, rootJob)
failedJobs = [ job for job in toilState.updatedJobs | \
set(toilState.successorCounts.keys()) \
if job.remainingRetryCount == 0 ]
print "There are %i active jobs, %i parent jobs with children, and \
%i totally failed jobs currently in toil workflow: %s" % \
(len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), options.jobStore)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print "Log file for job %s is not present" % job.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser("usage: %prog [--jobStore] JOB_TREE_DIR [options]", "%prog 0.1")
parser.add_option("--jobStore", dest="jobStore",
help="Job store path. Can also be specified as the single argument to the script.\
default=%default", default=os.path.abspath("./toil"))
parser.add_option("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%default",
default=False)
parser.add_option("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%default",
default=False)
options, args = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
assert len(args) <= 1 #Only toil may be specified as argument
if len(args) == 1: #Allow toil directory as arg
options.jobStore = args[0]
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.jobStore != None
##########################################
#Survey the status of the job and report.
##########################################
jobStore = loadJobStore(options.jobStore)
try:
rootJob = Job._loadRootJob(jobStore)
except JobException:
print "The root job of the jobStore is not present, the toil workflow has probably completed okay"
sys.exit(0)
toilState = ToilState(jobStore, rootJob )
failedJobs = [ job for job in toilState.updatedJobs | \
set(toilState.successorCounts.keys()) \
if job.remainingRetryCount == 0 ]
print "There are %i active jobs, %i parent jobs with children, and \
%i totally failed jobs currently in toil workflow: %s" % \
(len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), options.jobStore)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print "Log file for job %s is not present" % job.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser(
"usage: %prog [--toil] JOB_TREE_DIR [options]", "%prog 0.1")
parser.add_option(
"--toil",
dest="toil",
help=
"Batchjob store path. Can also be specified as the single argument to the script.\
default=%default",
default='./toil')
parser.add_option(
"--verbose",
dest="verbose",
action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%default",
default=False)
parser.add_option(
"--failIfNotComplete",
dest="failIfNotComplete",
action="store_true",
help=
"Return exit value of 1 if toil jobs not all completed. default=%default",
default=False)
options, args = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
assert len(args) <= 1 #Only toil may be specified as argument
if len(args) == 1: #Allow toil directory as arg
options.toil = args[0]
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.toil != None
##########################################
#Survey the status of the batchjob and report.
##########################################
jobStore = loadJobStore(options.toil)
config = jobStore.config
toilState = jobStore.loadToilState(
) #This initialises the object toil.toilState used to track the active toil
failedJobs = [ batchjob for batchjob in toilState.updatedJobs | \
set(toilState.childCounts.keys()) \
if batchjob.remainingRetryCount == 0 ]
print "There are %i active jobs, %i parent jobs with children, \
%i totally failed jobs and %i empty jobs (i.e. finished but not cleaned up) \
currently in toil: %s" % \
(len(toilState.updatedJobs), len(toilState.childCounts),
len(failedJobs), len(toilState.shellJobs), options.toil)
if options.verbose: #Verbose currently means outputting the files that have failed.
for batchjob in failedJobs:
if batchjob.logJobStoreFileID is not None:
with batchjob.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, batchjob.jobStoreID, logger.warn)
else:
print "Log file for batchjob %s is not present" % batchjob.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.childCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser("usage: %prog [--toil] JOB_TREE_DIR [options]", "%prog 0.1")
parser.add_option("--toil", dest="toil",
help="Batchjob store path. Can also be specified as the single argument to the script.\
default=%default", default='./toil')
parser.add_option("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%default",
default=False)
parser.add_option("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%default",
default=False)
options, args = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
assert len(args) <= 1 #Only toil may be specified as argument
if len(args) == 1: #Allow toil directory as arg
options.toil = args[0]
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for toil")
assert options.toil != None
##########################################
#Survey the status of the batchjob and report.
##########################################
jobStore = loadJobStore(options.toil)
config = jobStore.config
toilState = jobStore.loadToilState() #This initialises the object toil.toilState used to track the active toil
failedJobs = [ batchjob for batchjob in toilState.updatedJobs | \
set(toilState.childCounts.keys()) \
if batchjob.remainingRetryCount == 0 ]
print "There are %i active jobs, %i parent jobs with children, \
%i totally failed jobs and %i empty jobs (i.e. finished but not cleaned up) \
currently in toil: %s" % \
(len(toilState.updatedJobs), len(toilState.childCounts),
len(failedJobs), len(toilState.shellJobs), options.toil)
if options.verbose: #Verbose currently means outputting the files that have failed.
for batchjob in failedJobs:
if batchjob.logJobStoreFileID is not None:
with batchjob.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, batchjob.jobStoreID, logger.warn)
else:
print "Log file for batchjob %s is not present" % batchjob.jobStoreID
if len(failedJobs) == 0:
print "There are no failed jobs to report"
if (len(toilState.updatedJobs) + len(toilState.childCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)