def test_hello_world(self):
system([sys.executable,
'-m', helloWorld.__name__,
'file:./toilTest',
'--batchSystem', 'mesos',
'--mesosMaster', 'localhost:5050',
'--logLevel', getLogLevelString()])
def testAWSProvisionerUtils(self):
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
try:
system([
self.toilMain, 'launch-cluster', '--nodeType=t2.micro',
'--keyPairName=jenkins@jenkins-master', clusterName,
'--provisioner=aws'
])
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
try:
# launch preemptable master with same name
system([
self.toilMain, 'launch-cluster', '--nodeType=m3.medium:0.2',
'--keyPairName=jenkins@jenkins-master', clusterName,
'--provisioner=aws', '--logLevel=DEBUG'
])
system([
self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName
])
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
def testUtilsStatsSort(self):
"""
Tests the stats commands on a complete run of the stats test.
"""
# Get the sort command to run
toilCommandString = ("{self.sort} "
"{self.toilDir} "
"--logLevel=DEBUG "
"--fileToSort={self.tempFile} "
"--N {self.N} --stats "
"--retryCount 99".format(**locals()))
# Run the script for the first time
system(toilCommandString)
self.assertTrue(os.path.exists(self.toilDir))
# Check we can run 'toil stats'
rootPath = os.path.join(toilPackageDirPath(), "utils")
toilStatsString = ("{self.toilMain} stats "
"{self.toilDir} --pretty".format(**locals()))
system(toilStatsString)
# Check the file is properly sorted
with open(self.tempFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
def testUtilsStatsSort(self):
"""
Tests the stats commands on a complete run of the stats test.
"""
# Get the sort command to run
toilCommand = [
sys.executable,
"-m",
toil.test.sort.sort.__name__,
self.toilDir,
"--logLevel=DEBUG",
"--fileToSort",
self.tempFile,
"--N",
str(self.N),
"--stats",
"--retryCount=99",
"--badWorker=0.5",
"--badWorkerFailInterval=0.01",
]
# Run the script for the first time
system(toilCommand)
self.assertTrue(os.path.exists(self.toilDir))
# Check we can run 'toil stats'
system(self.statsCommand)
# Check the file is properly sorted
with open(self.tempFile, "r") as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
def testUtilsStatsSort(self):
"""
Tests the stats commands on a complete run of the stats test.
"""
# Get the sort command to run
toilCommand = [sys.executable,
'-m', toil.test.sort.sort.__name__,
self.toilDir,
'--logLevel=DEBUG',
'--fileToSort', self.tempFile,
'--outputFile', self.outputFile,
'--N', str(self.N),
'--stats',
'--retryCount=99',
'--badWorker=0.5',
'--badWorkerFailInterval=0.01']
# Run the script for the first time
system(toilCommand)
self.assertTrue(os.path.exists(self.toilDir))
# Check we can run 'toil stats'
system(self.statsCommand)
# Check the file is properly sorted
with open(self.outputFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
# Delete output file
os.remove(self.outputFile)
def testUtilsStatsSort(self):
"""
Tests the stats commands on a complete run of the stats test.
"""
# Get the sort command to run
toilCommand = [
sys.executable, '-m', toil.test.sort.sort.__name__, self.toilDir,
'--logLevel=DEBUG', '--fileToSort', self.tempFile, '--outputFile',
self.outputFile, '--N',
str(self.N), '--stats', '--retryCount=99', '--badWorker=0.5',
'--badWorkerFailInterval=0.01'
]
# Run the script for the first time
system(toilCommand)
self.assertTrue(os.path.exists(self.toilDir))
# Check we can run 'toil stats'
system(self.statsCommand)
# Check the file is properly sorted
with open(self.outputFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEqual(self.correctSort, l2)
# Delete output file
os.remove(self.outputFile)
def test_hello_world(self):
system(
[
sys.executable,
"-m",
helloWorld.__name__,
"./toilTest",
"--batchSystem=mesos",
"--logLevel",
getLogLevelString(),
]
)
def testAWSProvisionerUtils(self):
"""
Runs a number of the cluster utilities in sequence.
Launches a cluster with custom tags.
Verifies the tags exist.
ssh's into the cluster.
Does some weird string comparisons.
Makes certain that TOIL_WORKDIR is set as expected in the ssh'ed cluster.
Rsyncs a file and verifies it exists on the leader.
Destroys the cluster.
:return:
"""
# TODO: Run these for the other clouds.
clusterName = f'cluster-utils-test{uuid.uuid4()}'
keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa'
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
aws_provisioner = AWSProvisioner.__module__
logger.debug(f"Found AWSProvisioner: {aws_provisioner}.")
# launch master with an assortment of custom tags
system([
self.toilMain, 'launch-cluster', '-t', 'key1=value1', '-t',
'key2=value2', '--tag', 'key3=value3',
'--leaderNodeType=m3.medium', '--keyPairName=' + keyName,
clusterName, '--provisioner=aws', '--zone=us-west-2a',
'--logLevel=DEBUG'
])
from toil.provisioners import cluster_factory
cluster = toil.provisioners.cluster_factory(
provisioner='aws', clusterName=clusterName)
leader = cluster.getLeader()
# check that the leader carries the appropriate tags
tags = {
'key1': 'value1',
'key2': 'value2',
'key3': 'value3',
'Name': clusterName,
'Owner': keyName
}
for key in tags:
self.assertEqual(tags[key], leader.tags.get(key))
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
def testAWSProvisionerUtils(self):
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
try:
system([
self.toilMain, 'launch-cluster', '--nodeType=t2.micro',
'--keyPairName=jenkins@jenkins-master', clusterName,
'--provisioner=aws'
])
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
# launch preemptable master with same name
system([
self.toilMain, 'launch-cluster', '--nodeType=m3.medium:0.2',
'--keyPairName=jenkins@jenkins-master', clusterName,
'--provisioner=aws', '--logLevel=DEBUG'
])
system([
self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName
])
testStrings = [
"'foo'", '"foo"', ' foo', '$PATH', '"', "'", '\\', '| cat',
'&& cat', '; cat'
]
for test in testStrings:
logger.info('Testing SSH with special string: %s', test)
compareTo = "import sys; assert sys.argv[1]==%r" % test
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['python', '-', test],
input=compareTo)
try:
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['nonsenseShouldFail'])
except RuntimeError:
pass
else:
self.fail(
'The remote command failed silently where it should have '
'raised an error')
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
def parasolIsInstalled():
"""
Returns True if parasol is installed, else False.
"""
try:
return system("parasol status") == 0
except CalledProcessError:
return False
def gridEngineIsInstalled():
"""
Returns True if grid-engine is installed, else False.
"""
try:
return system("qstat -help") == 0
except CalledProcessError:
return False
def parasolIsInstalled():
"""
Returns True if parasol is installed, else False.
"""
try:
return system("parasol status") == 0
except CalledProcessError:
return False
def gridEngineIsInstalled():
"""
Returns True if grid-engine is installed, else False.
"""
try:
return system("qstat -help") == 0
except CalledProcessError:
return False
def testAWSProvisionerUtils(self):
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
try:
system([self.toilMain, 'launch-cluster', '--nodeType=t2.micro', '--keyPairName=jenkins@jenkins-master',
clusterName, '--provisioner=aws'])
finally:
system([self.toilMain, 'destroy-cluster', '--provisioner=aws', clusterName])
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
# launch preemptable master with same name
system([self.toilMain, 'launch-cluster', '--nodeType=m3.medium:0.2', '--keyPairName=jenkins@jenkins-master',
clusterName, '--provisioner=aws', '--logLevel=DEBUG'])
system([self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName])
testStrings = ["'foo'",
'"foo"',
' foo',
'$PATH',
'"',
"'",
'\\',
'| cat',
'&& cat',
'; cat'
]
for test in testStrings:
logger.info('Testing SSH with special string: %s', test)
compareTo = "import sys; assert sys.argv[1]==%r" % test
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['python', '-', test],
input=compareTo)
try:
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['nonsenseShouldFail'])
except RuntimeError:
pass
else:
self.fail('The remote command failed silently where it should have '
'raised an error')
finally:
system([self.toilMain, 'destroy-cluster', '--provisioner=aws', clusterName])
def testToilStats_SortSimple(self):
"""
Tests the toilStats utility using the scriptTree_sort example.
"""
for test in xrange(self.testNo):
tempDir = getTempDirectory(os.getcwd())
tempFile = getTempFile(rootDir=tempDir)
outputFile = getTempFile(rootDir=tempDir)
toilDir = os.path.join(tempDir, "testToil")
lines = 10000
maxLineLength = 10
N = 1000
makeFileToSort(tempFile, lines, maxLineLength)
# Sort the file
rootPath = os.path.join(toilPackageDirPath(), "test", "sort")
system("{rootPath}/sort.py "
"--toil {toilDir} "
"--logLevel=DEBUG "
"--fileToSort={tempFile} "
"--N {N} --stats "
"--jobTime 0.5 "
"--retryCount 99".format(**locals()))
# Now get the stats
toilStats = self.getScriptPath('toilStats')
system("{toilStats} "
"--toil {toilDir} "
"--outputFile {outputFile}".format(**locals()))
# Cleanup
system("rm -rf %s" % tempDir)
def testAWSProvisionerUtils(self):
"""
Runs a number of the cluster utilities in sequence.
Launches a cluster with custom tags.
Verifies the tags exist.
ssh's into the cluster.
Does some weird string comparisons.
Makes certain that TOIL_WORKDIR is set as expected in the ssh'ed cluster.
Rsyncs a file and verifies it exists on the leader.
Destroys the cluster.
:return:
"""
# TODO: Run these for the other clouds.
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
keyName = os.getenv('TOIL_AWS_KEYNAME')
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
# launch master with an assortment of custom tags
system([
self.toilMain, 'launch-cluster', '-t', 'key1=value1', '-t',
'key2=value2', '--tag', 'key3=value3',
'--leaderNodeType=m3.medium', '--keyPairName=' + keyName,
clusterName, '--provisioner=aws', '--zone=us-west-2a',
'--logLevel=DEBUG'
])
cluster = clusterFactory(provisioner='aws',
clusterName=clusterName)
leader = cluster.getLeader()
# check that the leader carries the appropriate tags
tags = {
'key1': 'value1',
'key2': 'value2',
'key3': 'value3',
'Name': clusterName,
'Owner': keyName
}
for key in tags:
self.assertEqual(tags[key], leader.tags.get(key))
# Test strict host key checking
# Doesn't work when run locally.
if keyName == 'jenkins@jenkins-master':
try:
leader.sshAppliance(strict=True)
except RuntimeError:
pass
else:
self.fail(
"Host key verification passed where it should have failed"
)
# Add the host key to known_hosts so that the rest of the tests can
# pass without choking on the verification prompt.
leader.sshAppliance('bash',
strict=True,
sshOptions=['-oStrictHostKeyChecking=no'])
system([
self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName
])
testStrings = [
"'foo'", '"foo"', ' foo', '$PATH', '"', "'", '\\', '| cat',
'&& cat', '; cat'
]
for test in testStrings:
logger.debug('Testing SSH with special string: %s', test)
compareTo = "import sys; assert sys.argv[1]==%r" % test
leader.sshAppliance('python', '-', test, input=compareTo)
try:
leader.sshAppliance('nonsenseShouldFail')
except RuntimeError:
pass
else:
self.fail(
'The remote command failed silently where it should have raised an error'
)
leader.sshAppliance(
'python', '-c',
"import os; assert os.environ['TOIL_WORKDIR']=='/var/lib/toil'"
)
# `toil rsync-cluster`
# Testing special characters - string.punctuation
fname = '!"#$%&\'()*+,-.;<=>:\ ?@[\\\\]^_`{|}~'
testData = os.urandom(3 * (10**6))
with tempfile.NamedTemporaryFile(suffix=fname) as tmpFile:
relpath = os.path.basename(tmpFile.name)
tmpFile.write(testData)
tmpFile.flush()
# Upload file to leader
leader.coreRsync(args=[tmpFile.name, ":"])
# Ensure file exists
leader.sshAppliance("test", "-e", relpath)
tmpDir = tempfile.mkdtemp()
# Download the file again and make sure it's the same file
# `--protect-args` needed because remote bash chokes on special characters
leader.coreRsync(args=["--protect-args", ":" + relpath, tmpDir])
with open(os.path.join(tmpDir, relpath), "r") as f:
self.assertEqual(
f.read(), testData,
"Downloaded file does not match original file")
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
try:
shutil.rmtree(tmpDir)
except NameError:
pass
def decompressFastaFile(fileName, tempFileName):
"""Copies the file from the central dir to a temporary file, returning the temp file name.
"""
system("bunzip2 --stdout %s > %s" % (fileName, tempFileName))
return tempFileName
def testUtilsSort(self):
"""
Tests the status and stats commands of the toil command line utility using the
sort example with the --restart flag.
"""
# Get the sort command to run
toilCommand = [
sys.executable, '-m', toil.test.sort.sort.__name__, self.toilDir,
'--logLevel=DEBUG', '--fileToSort', self.tempFile, '--N',
str(self.N), '--stats', '--retryCount=2', '--badWorker=0.5',
'--badWorkerFailInterval=0.05'
]
# Try restarting it to check that a JobStoreException is thrown
self.assertRaises(CalledProcessError, system,
toilCommand + ['--restart'])
# Check that trying to run it in restart mode does not create the jobStore
self.assertFalse(os.path.exists(self.toilDir))
# Status command
# Run the script for the first time
try:
system(toilCommand)
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system, self.statusCommand)
finished = False
self.assertTrue(os.path.exists(self.toilDir))
# Try running it without restart and check an exception is thrown
self.assertRaises(CalledProcessError, system, toilCommand)
# Now restart it until done
totalTrys = 1
while not finished:
try:
system(toilCommand + ['--restart'])
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system,
self.statusCommand)
if totalTrys > 16:
self.fail() # Exceeded a reasonable number of restarts
totalTrys += 1
# Check the toil status command does not issue an exception
system(self.statusCommand)
# Check if we try to launch after its finished that we get a JobException
self.assertRaises(CalledProcessError, system,
toilCommand + ['--restart'])
# Check we can run 'toil stats'
system(self.statsCommand)
# Check the file is properly sorted
with open(self.tempFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
# Check we can run 'toil clean'
system(self.cleanCommand)
def main():
logging.basicConfig()
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import makePublicDir
from toil.lib.bioio import system
from toil.common import loadJobStore
from toil.job import Job
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Create the worker killer, if requested
##########################################
if config.badWorker > 0 and random.random() < config.badWorker:
def badWorker():
#This will randomly kill the worker process at a random time
time.sleep(config.badWorkerFailInterval * random.random())
os.kill(os.getpid(), signal.SIGKILL) #signal.SIGINT)
#TODO: FIX OCCASIONAL DEADLOCK WITH SIGINT (tested on single machine)
t = Thread(target=badWorker)
t.daemon = True
t.start()
##########################################
#Load the environment for the jobWrapper
##########################################
#First load the environment for the jobWrapper.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(fileHandle)
for i in environment:
if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
os.environ[i] = environment[i]
# sys.path is used by __import__ to find modules
if "PYTHONPATH" in environment:
for e in environment["PYTHONPATH"].split(':'):
if e != '':
sys.path.append(e)
setLogLevel(config.logLevel)
tempRootDir = config.workDir
if tempRootDir is not None and not os.path.exists(tempRootDir):
raise RuntimeError("The temporary directory specified by workDir: %s does not exist" % tempRootDir)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in. If tempRootDir is None, tempdir looks at environment variables to determine
# where to put the tempDir.
localWorkerTempDir = tempfile.mkdtemp(dir=tempRootDir)
os.chmod(localWorkerTempDir, 0755)
##########################################
#Setup the logging
##########################################
#This is mildly tricky because we don't just want to
#redirect stdout and stderr for this Python process; we want to redirect it
#for this process and all children. Consequently, we can't just replace
#sys.stdout and sys.stderr; we need to mess with the underlying OS-level
#file descriptors. See <http://stackoverflow.com/a/11632982/402891>
#When we start, standard input is file descriptor 0, standard output is
#file descriptor 1, and standard error is file descriptor 2.
#What file do we want to point FDs 1 and 2 to?
tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")
#Save the original stdout and stderr (by opening new file descriptors to the
#same files)
origStdOut = os.dup(1)
origStdErr = os.dup(2)
#Open the file to send stdout/stderr to.
logFh = os.open(tempWorkerLogPath, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logFh, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logFh, 2)
#Since we only opened the file once, all the descriptors duped from the
#original will share offset information, and won't clobber each others'
#writes. See <http://stackoverflow.com/a/5284108/402891>. This shouldn't
#matter, since O_APPEND seeks to the end of the file before every write, but
#maybe there's something odd going on...
#Close the descriptor we used to open the file
os.close(logFh)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
statsDict = MagicExpando()
statsDict.jobs = []
messages = []
blockFn = lambda : True
cleanCacheFn = lambda x : True
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the jobWrapper
##########################################
jobWrapper = jobStore.load(jobStoreID)
logger.debug("Parsed jobWrapper")
##########################################
#Cleanup from any earlier invocation of the jobWrapper
##########################################
if jobWrapper.command == None:
while len(jobWrapper.stack) > 0:
jobs = jobWrapper.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
jobWrapper.stack.pop()
#This cleans the old log file which may
#have been left if the jobWrapper is being retried after a jobWrapper failure.
oldLogFile = jobWrapper.logJobStoreFileID
jobWrapper.logJobStoreFileID = None
jobStore.update(jobWrapper) #Update first, before deleting the file
if oldLogFile != None:
jobStore.delete(oldLogFile)
#Make a temporary file directory for the jobWrapper
localTempDir = makePublicDir(os.path.join(localWorkerTempDir, "localTempDir"))
##########################################
#Setup the stats, if requested
##########################################
if config.stats:
startTime = time.time()
startClock = getTotalCpuTime()
startTime = time.time()
while True:
##########################################
#Run the jobWrapper, if there is one
##########################################
if jobWrapper.command != None:
if jobWrapper.command.startswith( "_toil " ):
#Load the job
job = Job._loadJob(jobWrapper.command, jobStore)
#Cleanup the cache from the previous job
cleanCacheFn(job.effectiveRequirements(jobStore.config).cache)
#Create a fileStore object for the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir,
blockFn)
#Get the next block function and list that will contain any messages
blockFn = fileStore._blockFn
messages = fileStore.loggingMessages
job._execute(jobWrapper=jobWrapper,
stats=statsDict if config.stats else None,
localTempDir=localTempDir,
jobStore=jobStore,
fileStore=fileStore)
#Set the clean cache function
cleanCacheFn = fileStore._cleanLocalTempDir
else: #Is another command (running outside of jobs may be deprecated)
#Cleanup the cache from the previous job
cleanCacheFn(0)
system(jobWrapper.command)
#Set a dummy clean cache fn
cleanCacheFn = lambda x : None
else:
#The command may be none, in which case
#the jobWrapper is either a shell ready to be deleted or has
#been scheduled after a failure to cleanup
break
if Job.FileStore._terminateEvent.isSet():
raise RuntimeError("The termination flag is set")
##########################################
#Establish if we can run another jobWrapper within the worker
##########################################
#No more jobs to run so quit
if len(jobWrapper.stack) == 0:
break
#Get the next set of jobs to run
jobs = jobWrapper.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the jobWrapper to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCores, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > jobWrapper.memory:
logger.debug("We need more memory for the next jobWrapper, so finishing")
break
if successorCores > jobWrapper.cores:
logger.debug("We need more cores for the next jobWrapper, so finishing")
break
if successorsDisk > jobWrapper.disk:
logger.debug("We need more disk for the next jobWrapper, so finishing")
break
if successorPredecessorID != None:
logger.debug("The jobWrapper has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor jobWrapper.
#We load the successor jobWrapper and transplant its command and stack
#into the current jobWrapper so that it can be run
#as if it were a command that were part of the current jobWrapper.
#We can then delete the successor jobWrapper in the jobStore, as it is
#wholly incorporated into the current jobWrapper.
##########################################
#Clone the jobWrapper and its stack
jobWrapper = copy.deepcopy(jobWrapper)
#Remove the successor jobWrapper
jobWrapper.stack.pop()
#Load the successor jobWrapper
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cores == successorCores
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current jobWrapper
jobWrapper.command = successorJob.command
jobWrapper.stack += successorJob.stack
assert jobWrapper.memory >= successorJob.memory
assert jobWrapper.cores >= successorJob.cores
#Build a fileStore to update the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir, blockFn)
#Update blockFn
blockFn = fileStore._blockFn
#Add successorJob to those to be deleted
fileStore.jobsToDelete.add(successorJob.jobStoreID)
#This will update the job once the previous job is done
fileStore._updateJobWhenDone()
#Clone the jobWrapper and its stack again, so that updates to it do
#not interfere with this update
jobWrapper = copy.deepcopy(jobWrapper)
logger.debug("Starting the next jobWrapper")
##########################################
#Finish up the stats
##########################################
if config.stats:
totalCPUTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
statsDict.workers.time = str(time.time() - startTime)
statsDict.workers.clock = str(totalCPUTime - startClock)
statsDict.workers.memory = str(totalMemoryUsage)
statsDict.workers.log = messages
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds", time.time() - startTime)
##########################################
#Trapping where worker goes wrong
##########################################
except: #Case that something goes wrong in worker
traceback.print_exc()
logger.error("Exiting the worker because of a failed jobWrapper on host %s", socket.gethostname())
Job.FileStore._terminateEvent.set()
##########################################
#Wait for the asynchronous chain of writes/updates to finish
##########################################
blockFn()
##########################################
#All the asynchronous worker/update threads must be finished now,
#so safe to test if they completed okay
##########################################
if Job.FileStore._terminateEvent.isSet():
jobWrapper = jobStore.load(jobStoreID)
jobWrapper.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#Flush at the OS level
os.fsync(1)
os.fsync(2)
#Close redirected stdout and replace with the original standard output.
os.dup2(origStdOut, 1)
#Close redirected stderr and replace with the original standard error.
os.dup2(origStdOut, 2)
#sys.stdout and sys.stderr don't need to be modified at all. We don't need
#to call redirectLoggerStreamHandlers since they still log to sys.stderr
#Close our extra handles to the original standard output and standard error
#streams, so we don't leak file handles.
os.close(origStdOut)
os.close(origStdErr)
#Now our file handles are in exactly the state they were in before.
#Copy back the log file to the global dir, if needed
if workerFailed:
truncateFile(tempWorkerLogPath)
jobWrapper.logJobStoreFileID = jobStore.writeFile( tempWorkerLogPath, jobWrapper.jobStoreID )
os.remove(tempWorkerLogPath)
jobStore.update(jobWrapper)
elif debugging: # write log messages
truncateFile(tempWorkerLogPath)
with open(tempWorkerLogPath, 'r') as logFile:
logMessages = logFile.read().splitlines()
statsDict.logs = [Expando(jobStoreID=jobStoreID,text=logMessage) for logMessage in logMessages]
if (debugging or config.stats or messages) and not workerFailed: # We have stats/logging to report back
jobStore.writeStatsAndLogging(json.dumps(statsDict))
#Remove the temp dir
shutil.rmtree(localWorkerTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not workerFailed) and jobWrapper.command == None and len(jobWrapper.stack) == 0:
#We can now safely get rid of the jobWrapper
jobStore.delete(jobWrapper.jobStoreID)
def test_hello_world(self):
system([sys.executable,
'-m', helloWorld.__name__,
'./toilTest',
'--batchSystem=mesos',
'--logLevel', getLogLevelString()])
def tearDown(self):
ToilTest.tearDown(self)
system("rm -rf %s" % self.tempDir)
def tearDown(self):
self.contextManager.__exit__(None, None, None)
system("rm -rf %s" % self.testToil)
super(JobTest, self).tearDown()
def compressFastaFile(fileName):
"""Compress a fasta file.
"""
system("bzip2 --keep --fast %s" % fileName)
return fileName + ".bz2"
def testAWSProvisionerUtils(self):
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
keyName = os.getenv('TOIL_AWS_KEYNAME')
try:
# --provisioner flag should default to aws, so we're not explicitly
# specifying that here
system([self.toilMain, 'launch-cluster', '--nodeType=t2.micro',
'--keyPairName=' + keyName, clusterName])
finally:
system([self.toilMain, 'destroy-cluster', '--provisioner=aws', clusterName])
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
userTags = {'key1': 'value1', 'key2': 'value2', 'key3': 'value3'}
tags = {'Name': clusterName, 'Owner': keyName}
tags.update(userTags)
# launch preemptable master with same name
system([self.toilMain, 'launch-cluster', '-t', 'key1=value1', '-t', 'key2=value2', '--tag', 'key3=value3',
'--nodeType=m3.medium:0.2', '--keyPairName=' + keyName, clusterName,
'--provisioner=aws', '--logLevel=DEBUG'])
# test leader tags
leaderTags = AWSProvisioner._getLeader(clusterName).tags
self.assertEqual(tags, leaderTags)
# Test strict host key checking
# Doesn't work when run locally.
if(keyName == 'jenkins@jenkins-master'):
try:
AWSProvisioner.sshLeader(clusterName=clusterName, strict=True)
except RuntimeError:
pass
else:
self.fail("Host key verification passed where it should have failed")
# Add the host key to known_hosts so that the rest of the tests can
# pass without choking on the verification prompt.
AWSProvisioner.sshLeader(clusterName=clusterName, strict=True, sshOptions=['-oStrictHostKeyChecking=no'])
system([self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName])
testStrings = ["'foo'",
'"foo"',
' foo',
'$PATH',
'"',
"'",
'\\',
'| cat',
'&& cat',
'; cat'
]
for test in testStrings:
logger.info('Testing SSH with special string: %s', test)
compareTo = "import sys; assert sys.argv[1]==%r" % test
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['python', '-', test],
input=compareTo)
try:
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['nonsenseShouldFail'])
except RuntimeError:
pass
else:
self.fail('The remote command failed silently where it should have '
'raised an error')
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['python', '-c', "import os; assert os.environ['TOIL_WORKDIR']=='/var/lib/toil'"])
# `toil rsync-cluster`
# Testing special characters - string.punctuation
fname = '!"#$%&\'()*+,-.;<=>:\ ?@[\\\\]^_`{|}~'
testData = os.urandom(3 * (10**6))
with tempfile.NamedTemporaryFile(suffix=fname) as tmpFile:
relpath = os.path.basename(tmpFile.name)
tmpFile.write(testData)
tmpFile.flush()
# Upload file to leader
AWSProvisioner.rsyncLeader(clusterName=clusterName, args=[tmpFile.name, ":"])
# Ensure file exists
AWSProvisioner.sshLeader(clusterName=clusterName, args=["test", "-e", relpath])
tmpDir = tempfile.mkdtemp()
# Download the file again and make sure it's the same file
# `--protect-args` needed because remote bash chokes on special characters
AWSProvisioner.rsyncLeader(clusterName=clusterName, args=["--protect-args", ":" + relpath, tmpDir])
with open(os.path.join(tmpDir, relpath), "r") as f:
self.assertEqual(f.read(), testData, "Downloaded file does not match original file")
finally:
system([self.toilMain, 'destroy-cluster', '--provisioner=aws', clusterName])
try:
shutil.rmtree(tmpDir)
except NameError:
pass
def tearDown(self):
self.contextManager.__exit__(None, None, None)
system("rm -rf %s" % self.testToil)
super( JobTest, self ).tearDown( )
def testUtilsSort(self):
"""
Tests the restart, status and stats commands of the toil command line utility using the
sort example.
"""
# Get the sort command to run
toilCommandString = ("{self.sort} "
"{self.toilDir} "
"--logLevel=DEBUG "
"--fileToSort={self.tempFile} "
"--N {self.N} --stats "
"--retryCount 2".format(**locals()))
# Try restarting it to check that a JobStoreException is thrown
self.assertRaises(CalledProcessError, system, toilCommandString + " --restart")
# Check that trying to run it in restart mode does not create the jobStore
self.assertFalse(os.path.exists(self.toilDir))
# Status command
toilStatusCommandString = ("{self.toilMain} status "
"{self.toilDir} "
"--failIfNotComplete".format(**locals()))
# Run the script for the first time
try:
system(toilCommandString)
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system, toilStatusCommandString)
finished = False
self.assertTrue(os.path.exists(self.toilDir))
# Try running it without restart and check an exception is thrown
self.assertRaises(CalledProcessError, system, toilCommandString)
# Now restart it until done
while not finished:
try:
system(toilCommandString + " --restart")
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system, toilStatusCommandString)
# Check the toil status command does not issue an exception
system(toilStatusCommandString)
# Check if we try to launch after its finished that we get a JobException
self.assertRaises(CalledProcessError, system, toilCommandString + " --restart")
# Check we can run 'toil stats'
toilStatsString = ("{self.toilMain} stats "
"{self.toilDir} "
"--pretty".format(**locals()))
system(toilStatsString)
# Check the file is properly sorted
with open(self.tempFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
# Check we can run 'toil clean'
toilCleanString = ("{self.toilMain} clean "
"{self.toilDir}".format(**locals()))
system(toilCleanString)
def testAWSProvisionerUtils(self):
clusterName = 'cluster-utils-test' + str(uuid.uuid4())
keyName = os.getenv('TOIL_AWS_KEYNAME')
try:
# --provisioner flag should default to aws, so we're not explicitly
# specifying that here
system([
self.toilMain, 'launch-cluster', '--leaderNodeType=t2.micro',
'--keyPairName=' + keyName, clusterName
])
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
userTags = {'key1': 'value1', 'key2': 'value2', 'key3': 'value3'}
tags = {'Name': clusterName, 'Owner': keyName}
tags.update(userTags)
# launch preemptable master with same name
system([
self.toilMain, 'launch-cluster', '-t', 'key1=value1', '-t',
'key2=value2', '--tag', 'key3=value3',
'--leaderNodeType=m3.medium:0.2', '--keyPairName=' + keyName,
clusterName, '--provisioner=aws', '--logLevel=DEBUG'
])
# test leader tags
leaderTags = AWSProvisioner._getLeader(clusterName).tags
self.assertEqual(tags, leaderTags)
# Test strict host key checking
# Doesn't work when run locally.
if (keyName == 'jenkins@jenkins-master'):
try:
AWSProvisioner.sshLeader(clusterName=clusterName,
strict=True)
except RuntimeError:
pass
else:
self.fail(
"Host key verification passed where it should have failed"
)
# Add the host key to known_hosts so that the rest of the tests can
# pass without choking on the verification prompt.
AWSProvisioner.sshLeader(clusterName=clusterName,
strict=True,
sshOptions=['-oStrictHostKeyChecking=no'])
system([
self.toilMain, 'ssh-cluster', '--provisioner=aws', clusterName
])
testStrings = [
"'foo'", '"foo"', ' foo', '$PATH', '"', "'", '\\', '| cat',
'&& cat', '; cat'
]
for test in testStrings:
logger.info('Testing SSH with special string: %s', test)
compareTo = "import sys; assert sys.argv[1]==%r" % test
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['python', '-', test],
input=compareTo)
try:
AWSProvisioner.sshLeader(clusterName=clusterName,
args=['nonsenseShouldFail'])
except RuntimeError:
pass
else:
self.fail(
'The remote command failed silently where it should have '
'raised an error')
AWSProvisioner.sshLeader(
clusterName=clusterName,
args=[
'python', '-c',
"import os; assert os.environ['TOIL_WORKDIR']=='/var/lib/toil'"
])
# `toil rsync-cluster`
# Testing special characters - string.punctuation
fname = '!"#$%&\'()*+,-.;<=>:\ ?@[\\\\]^_`{|}~'
testData = os.urandom(3 * (10**6))
with tempfile.NamedTemporaryFile(suffix=fname) as tmpFile:
relpath = os.path.basename(tmpFile.name)
tmpFile.write(testData)
tmpFile.flush()
# Upload file to leader
AWSProvisioner.rsyncLeader(clusterName=clusterName,
args=[tmpFile.name, ":"])
# Ensure file exists
AWSProvisioner.sshLeader(clusterName=clusterName,
args=["test", "-e", relpath])
tmpDir = tempfile.mkdtemp()
# Download the file again and make sure it's the same file
# `--protect-args` needed because remote bash chokes on special characters
AWSProvisioner.rsyncLeader(
clusterName=clusterName,
args=["--protect-args", ":" + relpath, tmpDir])
with open(os.path.join(tmpDir, relpath), "r") as f:
self.assertEqual(
f.read(), testData,
"Downloaded file does not match original file")
finally:
system([
self.toilMain, 'destroy-cluster', '--provisioner=aws',
clusterName
])
try:
shutil.rmtree(tmpDir)
except NameError:
pass
def testUtilsSort(self):
"""
Tests the status and stats commands of the toil command line utility using the
sort example with the --restart flag.
"""
# Get the sort command to run
toilCommand = [
sys.executable,
"-m",
toil.test.sort.sort.__name__,
self.toilDir,
"--logLevel=DEBUG",
"--fileToSort",
self.tempFile,
"--N",
str(self.N),
"--stats",
"--retryCount=2",
"--badWorker=0.5",
"--badWorkerFailInterval=0.05",
]
# Try restarting it to check that a JobStoreException is thrown
self.assertRaises(CalledProcessError, system, toilCommand + ["--restart"])
# Check that trying to run it in restart mode does not create the jobStore
self.assertFalse(os.path.exists(self.toilDir))
# Status command
# Run the script for the first time
try:
system(toilCommand)
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system, self.statusCommand)
finished = False
self.assertTrue(os.path.exists(self.toilDir))
# Try running it without restart and check an exception is thrown
self.assertRaises(CalledProcessError, system, toilCommand)
# Now restart it until done
totalTrys = 1
while not finished:
try:
system(toilCommand + ["--restart"])
finished = True
except CalledProcessError: # This happens when the script fails due to having unfinished jobs
self.assertRaises(CalledProcessError, system, self.statusCommand)
if totalTrys > 16:
self.fail() # Exceeded a reasonable number of restarts
totalTrys += 1
# Check the toil status command does not issue an exception
system(self.statusCommand)
# Check if we try to launch after its finished that we get a JobException
self.assertRaises(CalledProcessError, system, toilCommand + ["--restart"])
# Check we can run 'toil stats'
system(self.statsCommand)
# Check the file is properly sorted
with open(self.tempFile, "r") as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
# Check we can run 'toil clean'
system(self.cleanCommand)
def main():
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
# FIXME: prepending to sys.path should fix #103
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import getTempDirectory
from toil.lib.bioio import makeSubDir
from toil.lib.bioio import system
from toil.common import loadJobStore
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Load the environment for the batchjob
##########################################
#First load the environment for the batchjob.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(fileHandle)
for i in environment:
if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
os.environ[i] = environment[i]
# sys.path is used by __import__ to find modules
if "PYTHONPATH" in environment:
for e in environment["PYTHONPATH"].split(':'):
if e != '':
sys.path.append(e)
setLogLevel(config.attrib["log_level"])
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localWorkerTempDir = getTempDirectory()
##########################################
#Setup the logging
##########################################
#This is mildly tricky because we don't just want to
#redirect stdout and stderr for this Python process; we want to redirect it
#for this process and all children. Consequently, we can't just replace
#sys.stdout and sys.stderr; we need to mess with the underlying OS-level
#file descriptors. See <http://stackoverflow.com/a/11632982/402891>
#When we start, standard input is file descriptor 0, standard output is
#file descriptor 1, and standard error is file descriptor 2.
#What file do we want to point FDs 1 and 2 to?
tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")
#Save the original stdout and stderr (by opening new file descriptors to the
#same files)
origStdOut = os.dup(1)
origStdErr = os.dup(2)
#Open the file to send stdout/stderr to.
logFh = os.open(tempWorkerLogPath, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logFh, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logFh, 2)
#Since we only opened the file once, all the descriptors duped from the
#original will share offset information, and won't clobber each others'
#writes. See <http://stackoverflow.com/a/5284108/402891>. This shouldn't
#matter, since O_APPEND seeks to the end of the file before every write, but
#maybe there's something odd going on...
#Close the descriptor we used to open the file
os.close(logFh)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the batchjob
##########################################
batchjob = jobStore.load(jobStoreID)
logger.debug("Parsed batchjob")
##########################################
#Cleanup from any earlier invocation of the batchjob
##########################################
if batchjob.command == None:
while len(batchjob.stack) > 0:
jobs = batchjob.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
batchjob.stack.pop()
#This cleans the old log file which may
#have been left if the batchjob is being retried after a batchjob failure.
if batchjob.logJobStoreFileID != None:
batchjob.clearLogFile(jobStore)
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("worker")
else:
stats = None
startTime = time.time()
while True:
##########################################
#Run the batchjob, if there is one
##########################################
if batchjob.command != None:
if batchjob.command[:11] == "scriptTree ":
#Make a temporary file directory for the job
localTempDir = makeSubDir(os.path.join(localWorkerTempDir, "localTempDir"))
#Is a job command
messages = loadJob(batchjob.command, jobStore)._execute(batchjob=batchjob,
stats=stats, localTempDir=localTempDir,
jobStore=jobStore)
#Remove the temporary file directory
shutil.rmtree(localTempDir)
else: #Is another command (running outside of jobs may be deprecated)
system(batchjob.command)
messages = []
else:
#The command may be none, in which case
#the batchjob is just a shell ready to be deleted
assert len(batchjob.stack) == 0
messages = []
break
##########################################
#Establish if we can run another batchjob within the worker
##########################################
#Exceeded the amount of time the worker is allowed to run for so quit
if time.time() - startTime > float(config.attrib["job_time"]):
logger.debug("We are breaking because the maximum time the batchjob should run for has been exceeded")
break
#No more jobs to run so quit
if len(batchjob.stack) == 0:
break
#Get the next set of jobs to run
jobs = batchjob.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the batchjob to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCpu, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > batchjob.memory:
logger.debug("We need more memory for the next batchjob, so finishing")
break
if successorCpu > batchjob.cpu:
logger.debug("We need more cpus for the next batchjob, so finishing")
break
if successorsDisk > batchjob.disk:
logger.debug("We need more disk for the next batchjob, so finishing")
break
if successorPredecessorID != None:
logger.debug("The batchjob has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor batchjob.
#We load the successor batchjob and transplant its command and stack
#into the current batchjob so that it can be run
#as if it were a command that were part of the current batchjob.
#We can then delete the successor batchjob in the jobStore, as it is
#wholly incorporated into the current batchjob.
##########################################
#Remove the successor batchjob
batchjob.stack.pop()
#Load the successor batchjob
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cpu == successorCpu
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current batchjob
batchjob.command = successorJob.command
batchjob.stack += successorJob.stack
assert batchjob.memory >= successorJob.memory
assert batchjob.cpu >= successorJob.cpu
#Checkpoint the batchjob and delete the successorJob
batchjob.jobsToDelete = [ successorJob.jobStoreID ]
jobStore.update(batchjob)
jobStore.delete(successorJob.jobStoreID)
logger.debug("Starting the next batchjob")
##########################################
#Finish up the stats
##########################################
if stats != None:
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["memory"] = str(totalMemoryUsage)
m = ET.SubElement(stats, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(stats))
elif len(messages) > 0: #No stats, but still need to report log messages
l = ET.Element("worker")
m = ET.SubElement(l, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(l))
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds", time.time() - startTime)
##########################################
#Trapping where worker goes wrong
##########################################
except: #Case that something goes wrong in worker
traceback.print_exc()
logger.error("Exiting the worker because of a failed batchjob on host %s", socket.gethostname())
batchjob = jobStore.load(jobStoreID)
batchjob.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#Flush at the OS level
os.fsync(1)
os.fsync(2)
#Close redirected stdout and replace with the original standard output.
os.dup2(origStdOut, 1)
#Close redirected stderr and replace with the original standard error.
os.dup2(origStdOut, 2)
#sys.stdout and sys.stderr don't need to be modified at all. We don't need
#to call redirectLoggerStreamHandlers since they still log to sys.stderr
#Close our extra handles to the original standard output and standard error
#streams, so we don't leak file handles.
os.close(origStdOut)
os.close(origStdErr)
#Now our file handles are in exactly the state they were in before.
#Copy back the log file to the global dir, if needed
if workerFailed:
truncateFile(tempWorkerLogPath)
batchjob.setLogFile(tempWorkerLogPath, jobStore)
os.remove(tempWorkerLogPath)
jobStore.update(batchjob)
#Remove the temp dir
shutil.rmtree(localWorkerTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not workerFailed) and batchjob.command == None and len(batchjob.stack) == 0:
#We can now safely get rid of the batchjob
jobStore.delete(batchjob.jobStoreID)
def decompressFastaFile(fileName, tempFileName):
"""Copies the file from the central dir to a temporary file, returning the temp file name.
"""
system("bunzip2 --stdout %s > %s" % (fileName, tempFileName))
return tempFileName
def test_hello_world(self):
system([sys.executable,
'-m', helloWorld.__name__,
'./toilTest',
'--batchSystem=mesos',
'--logLevel', getLogLevelString()])
def tearDown(self):
ToilTest.tearDown(self)
system("rm -rf %s" % self.tempDir)
def main():
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
# FIXME: prepending to sys.path should fix #103
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import getTempDirectory
from toil.lib.bioio import makeSubDir
from toil.lib.bioio import system
from toil.common import loadJobStore
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Load the environment for the batchjob
##########################################
#First load the environment for the batchjob.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(fileHandle)
for i in environment:
if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
os.environ[i] = environment[i]
# sys.path is used by __import__ to find modules
if "PYTHONPATH" in environment:
for e in environment["PYTHONPATH"].split(':'):
if e != '':
sys.path.append(e)
setLogLevel(config.attrib["log_level"])
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localWorkerTempDir = getTempDirectory()
##########################################
#Setup the logging
##########################################
#This is mildly tricky because we don't just want to
#redirect stdout and stderr for this Python process; we want to redirect it
#for this process and all children. Consequently, we can't just replace
#sys.stdout and sys.stderr; we need to mess with the underlying OS-level
#file descriptors. See <http://stackoverflow.com/a/11632982/402891>
#When we start, standard input is file descriptor 0, standard output is
#file descriptor 1, and standard error is file descriptor 2.
#What file do we want to point FDs 1 and 2 to?
tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")
#Save the original stdout and stderr (by opening new file descriptors to the
#same files)
origStdOut = os.dup(1)
origStdErr = os.dup(2)
#Open the file to send stdout/stderr to.
logFh = os.open(tempWorkerLogPath, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logFh, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logFh, 2)
#Since we only opened the file once, all the descriptors duped from the
#original will share offset information, and won't clobber each others'
#writes. See <http://stackoverflow.com/a/5284108/402891>. This shouldn't
#matter, since O_APPEND seeks to the end of the file before every write, but
#maybe there's something odd going on...
#Close the descriptor we used to open the file
os.close(logFh)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the batchjob
##########################################
batchjob = jobStore.load(jobStoreID)
logger.debug("Parsed batchjob")
##########################################
#Cleanup from any earlier invocation of the batchjob
##########################################
if batchjob.command == None:
while len(batchjob.stack) > 0:
jobs = batchjob.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
batchjob.stack.pop()
#This cleans the old log file which may
#have been left if the batchjob is being retried after a batchjob failure.
if batchjob.logJobStoreFileID != None:
batchjob.clearLogFile(jobStore)
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("worker")
else:
stats = None
startTime = time.time()
while True:
##########################################
#Run the batchjob, if there is one
##########################################
if batchjob.command != None:
if batchjob.command[:11] == "scriptTree ":
#Make a temporary file directory for the job
localTempDir = makeSubDir(
os.path.join(localWorkerTempDir, "localTempDir"))
#Is a job command
messages = loadJob(batchjob.command, jobStore)._execute(
batchjob=batchjob,
stats=stats,
localTempDir=localTempDir,
jobStore=jobStore)
#Remove the temporary file directory
shutil.rmtree(localTempDir)
else: #Is another command (running outside of jobs may be deprecated)
system(batchjob.command)
messages = []
else:
#The command may be none, in which case
#the batchjob is just a shell ready to be deleted
assert len(batchjob.stack) == 0
messages = []
break
##########################################
#Establish if we can run another batchjob within the worker
##########################################
#Exceeded the amount of time the worker is allowed to run for so quit
if time.time() - startTime > float(config.attrib["job_time"]):
logger.debug(
"We are breaking because the maximum time the batchjob should run for has been exceeded"
)
break
#No more jobs to run so quit
if len(batchjob.stack) == 0:
break
#Get the next set of jobs to run
jobs = batchjob.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug(
"No more jobs can run in series by this worker,"
" it's got %i children",
len(jobs) - 1)
break
#We check the requirements of the batchjob to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCpu, successorsDisk, successorPredecessorID = jobs[
0]
if successorMemory > batchjob.memory:
logger.debug(
"We need more memory for the next batchjob, so finishing")
break
if successorCpu > batchjob.cpu:
logger.debug(
"We need more cpus for the next batchjob, so finishing")
break
if successorsDisk > batchjob.disk:
logger.debug(
"We need more disk for the next batchjob, so finishing")
break
if successorPredecessorID != None:
logger.debug(
"The batchjob has multiple predecessors, we must return to the leader."
)
break
##########################################
#We have a single successor batchjob.
#We load the successor batchjob and transplant its command and stack
#into the current batchjob so that it can be run
#as if it were a command that were part of the current batchjob.
#We can then delete the successor batchjob in the jobStore, as it is
#wholly incorporated into the current batchjob.
##########################################
#Remove the successor batchjob
batchjob.stack.pop()
#Load the successor batchjob
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cpu == successorCpu
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current batchjob
batchjob.command = successorJob.command
batchjob.stack += successorJob.stack
assert batchjob.memory >= successorJob.memory
assert batchjob.cpu >= successorJob.cpu
#Checkpoint the batchjob and delete the successorJob
batchjob.jobsToDelete = [successorJob.jobStoreID]
jobStore.update(batchjob)
jobStore.delete(successorJob.jobStoreID)
logger.debug("Starting the next batchjob")
##########################################
#Finish up the stats
##########################################
if stats != None:
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["memory"] = str(totalMemoryUsage)
m = ET.SubElement(stats, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(stats))
elif len(messages
) > 0: #No stats, but still need to report log messages
l = ET.Element("worker")
m = ET.SubElement(l, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(l))
logger.info(
"Finished running the chain of jobs on this node, we ran for a total of %f seconds",
time.time() - startTime)
##########################################
#Trapping where worker goes wrong
##########################################
except: #Case that something goes wrong in worker
traceback.print_exc()
logger.error(
"Exiting the worker because of a failed batchjob on host %s",
socket.gethostname())
batchjob = jobStore.load(jobStoreID)
batchjob.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#Flush at the OS level
os.fsync(1)
os.fsync(2)
#Close redirected stdout and replace with the original standard output.
os.dup2(origStdOut, 1)
#Close redirected stderr and replace with the original standard error.
os.dup2(origStdOut, 2)
#sys.stdout and sys.stderr don't need to be modified at all. We don't need
#to call redirectLoggerStreamHandlers since they still log to sys.stderr
#Close our extra handles to the original standard output and standard error
#streams, so we don't leak file handles.
os.close(origStdOut)
os.close(origStdErr)
#Now our file handles are in exactly the state they were in before.
#Copy back the log file to the global dir, if needed
if workerFailed:
truncateFile(tempWorkerLogPath)
batchjob.setLogFile(tempWorkerLogPath, jobStore)
os.remove(tempWorkerLogPath)
jobStore.update(batchjob)
#Remove the temp dir
shutil.rmtree(localWorkerTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not workerFailed) and batchjob.command == None and len(
batchjob.stack) == 0:
#We can now safely get rid of the batchjob
jobStore.delete(batchjob.jobStoreID)
def main():
logging.basicConfig()
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import makePublicDir
from toil.lib.bioio import system
from toil.common import loadJobStore
from toil.job import Job
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Create the worker killer, if requested
##########################################
if config.badWorker > 0 and random.random() < config.badWorker:
def badWorker():
#This will randomly kill the worker process at a random time
time.sleep(config.badWorkerFailInterval * random.random())
os.kill(os.getpid(), signal.SIGKILL) #signal.SIGINT)
#TODO: FIX OCCASIONAL DEADLOCK WITH SIGINT (tested on single machine)
t = Thread(target=badWorker)
t.daemon = True
t.start()
##########################################
#Load the environment for the jobWrapper
##########################################
#First load the environment for the jobWrapper.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(fileHandle)
for i in environment:
if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
os.environ[i] = environment[i]
# sys.path is used by __import__ to find modules
if "PYTHONPATH" in environment:
for e in environment["PYTHONPATH"].split(':'):
if e != '':
sys.path.append(e)
setLogLevel(config.logLevel)
tempRootDir = config.workDir
if tempRootDir is not None and not os.path.exists(tempRootDir):
raise RuntimeError("The temporary directory specified by workDir: %s does not exist" % tempRootDir)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in. If tempRootDir is None, tempdir looks at environment variables to determine
# where to put the tempDir.
localWorkerTempDir = tempfile.mkdtemp(dir=tempRootDir)
os.chmod(localWorkerTempDir, 0755)
##########################################
#Setup the logging
##########################################
#This is mildly tricky because we don't just want to
#redirect stdout and stderr for this Python process; we want to redirect it
#for this process and all children. Consequently, we can't just replace
#sys.stdout and sys.stderr; we need to mess with the underlying OS-level
#file descriptors. See <http://stackoverflow.com/a/11632982/402891>
#When we start, standard input is file descriptor 0, standard output is
#file descriptor 1, and standard error is file descriptor 2.
#What file do we want to point FDs 1 and 2 to?
tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")
#Save the original stdout and stderr (by opening new file descriptors to the
#same files)
origStdOut = os.dup(1)
origStdErr = os.dup(2)
#Open the file to send stdout/stderr to.
logFh = os.open(tempWorkerLogPath, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logFh, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logFh, 2)
#Since we only opened the file once, all the descriptors duped from the
#original will share offset information, and won't clobber each others'
#writes. See <http://stackoverflow.com/a/5284108/402891>. This shouldn't
#matter, since O_APPEND seeks to the end of the file before every write, but
#maybe there's something odd going on...
#Close the descriptor we used to open the file
os.close(logFh)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
statsDict = MagicExpando()
messages = []
blockFn = lambda : True
cleanCacheFn = lambda x : True
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the jobWrapper
##########################################
jobWrapper = jobStore.load(jobStoreID)
logger.debug("Parsed jobWrapper")
##########################################
#Cleanup from any earlier invocation of the jobWrapper
##########################################
if jobWrapper.command == None:
while len(jobWrapper.stack) > 0:
jobs = jobWrapper.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
jobWrapper.stack.pop()
#This cleans the old log file which may
#have been left if the jobWrapper is being retried after a jobWrapper failure.
oldLogFile = jobWrapper.logJobStoreFileID
jobWrapper.logJobStoreFileID = None
jobStore.update(jobWrapper) #Update first, before deleting the file
if oldLogFile != None:
jobStore.delete(oldLogFile)
#Make a temporary file directory for the jobWrapper
localTempDir = makePublicDir(os.path.join(localWorkerTempDir, "localTempDir"))
##########################################
#Setup the stats, if requested
##########################################
if config.stats:
startTime = time.time()
startClock = getTotalCpuTime()
startTime = time.time()
while True:
##########################################
#Run the jobWrapper, if there is one
##########################################
if jobWrapper.command != None:
if jobWrapper.command.startswith( "_toil " ):
#Load the job
job = Job._loadJob(jobWrapper.command, jobStore)
#Cleanup the cache from the previous job
cleanCacheFn(job.effectiveRequirements(jobStore.config).cache)
#Create a fileStore object for the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir,
blockFn)
#Get the next block function and list that will contain any messages
blockFn = fileStore._blockFn
messages = fileStore.loggingMessages
job._execute(jobWrapper=jobWrapper,
stats=statsDict if config.stats else None,
localTempDir=localTempDir,
jobStore=jobStore,
fileStore=fileStore)
#Set the clean cache function
cleanCacheFn = fileStore._cleanLocalTempDir
else: #Is another command (running outside of jobs may be deprecated)
#Cleanup the cache from the previous job
cleanCacheFn(0)
system(jobWrapper.command)
#Set a dummy clean cache fn
cleanCacheFn = lambda x : None
else:
#The command may be none, in which case
#the jobWrapper is either a shell ready to be deleted or has
#been scheduled after a failure to cleanup
break
if Job.FileStore._terminateEvent.isSet():
raise RuntimeError("The termination flag is set")
##########################################
#Establish if we can run another jobWrapper within the worker
##########################################
#No more jobs to run so quit
if len(jobWrapper.stack) == 0:
break
#Get the next set of jobs to run
jobs = jobWrapper.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the jobWrapper to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCores, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > jobWrapper.memory:
logger.debug("We need more memory for the next jobWrapper, so finishing")
break
if successorCores > jobWrapper.cores:
logger.debug("We need more cores for the next jobWrapper, so finishing")
break
if successorsDisk > jobWrapper.disk:
logger.debug("We need more disk for the next jobWrapper, so finishing")
break
if successorPredecessorID != None:
logger.debug("The jobWrapper has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor jobWrapper.
#We load the successor jobWrapper and transplant its command and stack
#into the current jobWrapper so that it can be run
#as if it were a command that were part of the current jobWrapper.
#We can then delete the successor jobWrapper in the jobStore, as it is
#wholly incorporated into the current jobWrapper.
##########################################
#Clone the jobWrapper and its stack
jobWrapper = copy.deepcopy(jobWrapper)
#Remove the successor jobWrapper
jobWrapper.stack.pop()
#Load the successor jobWrapper
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cores == successorCores
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current jobWrapper
jobWrapper.command = successorJob.command
jobWrapper.stack += successorJob.stack
assert jobWrapper.memory >= successorJob.memory
assert jobWrapper.cores >= successorJob.cores
#Build a fileStore to update the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir, blockFn)
#Update blockFn
blockFn = fileStore._blockFn
#Add successorJob to those to be deleted
fileStore.jobsToDelete.add(successorJob.jobStoreID)
#This will update the job once the previous job is done
fileStore._updateJobWhenDone()
#Clone the jobWrapper and its stack again, so that updates to it do
#not interfere with this update
jobWrapper = copy.deepcopy(jobWrapper)
logger.debug("Starting the next jobWrapper")
##########################################
#Finish up the stats
##########################################
if config.stats:
totalCPUTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
statsDict.workers.time = str(time.time() - startTime)
statsDict.workers.clock = str(totalCPUTime - startClock)
statsDict.workers.memory = str(totalMemoryUsage)
statsDict.workers.log = messages
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds", time.time() - startTime)
##########################################
#Trapping where worker goes wrong
##########################################
except: #Case that something goes wrong in worker
traceback.print_exc()
logger.error("Exiting the worker because of a failed jobWrapper on host %s", socket.gethostname())
Job.FileStore._terminateEvent.set()
##########################################
#Wait for the asynchronous chain of writes/updates to finish
##########################################
blockFn()
##########################################
#All the asynchronous worker/update threads must be finished now,
#so safe to test if they completed okay
##########################################
if Job.FileStore._terminateEvent.isSet():
jobWrapper = jobStore.load(jobStoreID)
jobWrapper.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#Flush at the OS level
os.fsync(1)
os.fsync(2)
#Close redirected stdout and replace with the original standard output.
os.dup2(origStdOut, 1)
#Close redirected stderr and replace with the original standard error.
os.dup2(origStdOut, 2)
#sys.stdout and sys.stderr don't need to be modified at all. We don't need
#to call redirectLoggerStreamHandlers since they still log to sys.stderr
#Close our extra handles to the original standard output and standard error
#streams, so we don't leak file handles.
os.close(origStdOut)
os.close(origStdErr)
#Now our file handles are in exactly the state they were in before.
#Copy back the log file to the global dir, if needed
if workerFailed:
truncateFile(tempWorkerLogPath)
jobWrapper.logJobStoreFileID = jobStore.writeFile( tempWorkerLogPath, jobWrapper.jobStoreID )
os.remove(tempWorkerLogPath)
jobStore.update(jobWrapper)
elif debugging: # write log messages
truncateFile(tempWorkerLogPath)
with open(tempWorkerLogPath, 'r') as logFile:
logMessages = logFile.read().splitlines()
statsDict.logs = [Expando(jobStoreID=jobStoreID,text=logMessage) for logMessage in logMessages]
if (debugging or config.stats or messages) and not workerFailed: # We have stats/logging to report back
jobStore.writeStatsAndLogging(json.dumps(statsDict))
#Remove the temp dir
shutil.rmtree(localWorkerTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not workerFailed) and jobWrapper.command == None and len(jobWrapper.stack) == 0:
#We can now safely get rid of the jobWrapper
jobStore.delete(jobWrapper.jobStoreID)
def compressFastaFile(fileName):
"""Compress a fasta file.
"""
system("bzip2 --keep --fast %s" % fileName)
return fileName + ".bz2"