Python Toil.getWorkflowDir方法代码示例

# 需要导入模块: from toil.common import Toil [as 别名]
# 或者: from toil.common.Toil import getWorkflowDir [as 别名]
    def workerCleanup(info):
        """
        Cleans up the worker node on batch system shutdown. Also see :meth:`supportsWorkerCleanup`.

        :param WorkerCleanupInfo info: A named tuple consisting of all the relevant information
               for cleaning up the worker.
        """
        assert isinstance(info, WorkerCleanupInfo)
        workflowDir = Toil.getWorkflowDir(info.workflowID, info.workDir)
        if (info.cleanWorkDir == 'always'
            or info.cleanWorkDir in ('onSuccess', 'onError') and os.listdir(workflowDir) == []):
            shutil.rmtree(workflowDir)

# 需要导入模块: from toil.common import Toil [as 别名]
# 或者: from toil.common.Toil import getWorkflowDir [as 别名]
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.job import Job
    
    ########################################## 
    #Input args
    ##########################################
    
    jobStoreString = sys.argv[1]
    jobStoreID = sys.argv[2]
    
    ##########################################
    #Load the jobStore/config file
    ##########################################
    
    jobStore = Toil.loadOrCreateJobStore(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)
        # Ideally this would be a daemon thread but that causes an intermittent (but benign)
        # exception similar to the one described here:
        # http://stackoverflow.com/questions/20596918/python-exception-in-thread-thread-1-most-likely-raised-during-interpreter-shutd
        # Our exception is:
        #    Exception in thread Thread-1 (most likely raised during interpreter shutdown):
        #    <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'kill'
        # This attribute error is caused by the call os.kill() and apparently unavoidable with a
        # daemon
        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)

    toilWorkflowDir = Toil.getWorkflowDir(config.workflowID, config.workDir)

    ##########################################
    #Setup the temporary directories.
    ##########################################
        
    # Dir to put all this worker's temp files in.
    localWorkerTempDir = tempfile.mkdtemp(dir=toilWorkflowDir)
    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
#.........这里部分代码省略.........

# 需要导入模块: from toil.common import Toil [as 别名]
# 或者: from toil.common.Toil import getWorkflowDir [as 别名]
def physicalDisk(config, toilWorkflowDir=None):
    if toilWorkflowDir is None:
        from toil.common import Toil
        toilWorkflowDir = Toil.getWorkflowDir(config.workflowID, config.workDir)
    diskStats = os.statvfs(toilWorkflowDir)
    return diskStats.f_frsize * diskStats.f_bavail