Source code for pyworkflow.protocol.launch

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
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# *  All comments concerning this program package may be sent to the
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# **************************************************************************
This module is responsible for launching local protocol executions:

1- Check if the protocol will be submitted to a queue (using Queue template from config)
2- Build the command that will be launched.


import os
import re
import logging
logger = logging.getLogger(__file__)
from subprocess import Popen, PIPE
import pyworkflow as pw
from pyworkflow.exceptions import PyworkflowException
from pyworkflow.utils import (redStr, greenStr, makeFilePath, join, process,
from pyworkflow.protocol.constants import UNKNOWN_JOBID

# ******************************************************************
# *         Public functions provided by the module
# ******************************************************************

[docs]def launch(protocol, wait=False, stdin=None, stdout=None, stderr=None): """ This function should be used to launch a protocol. """ jobId = _launchLocal(protocol, wait, stdin, stdout, stderr) protocol.setJobId(jobId) return jobId
[docs]def stop(protocol): """ """ if protocol.useQueue() and not protocol.isScheduled(): jobId = protocol.getJobId() host = protocol.getHostConfig() cancelCmd = host.getCancelCommand() % {'JOB_ID': jobId} _run(cancelCmd, wait=True) else: process.killWithChilds(protocol.getPid())
[docs]def schedule(protocol, initialSleepTime=0, wait=False): """ Use this function to schedule protocols that are not ready to run yet. Right now it only make sense to schedule jobs locally. """ cmd = '%s %s' % (pw.PYTHON, pw.getScheduleScript()) cmd += ' "%s" "%s" %s "%s" --initial_sleep %s' % (protocol.getProject().path, protocol.getDbPath(), protocol.strId(), protocol.getScheduleLog(), initialSleepTime) jobId = _run(cmd, wait) protocol.setJobId(jobId) return jobId
# ****************************************************************** # * Internal utility functions # ****************************************************************** def _runsLocally(protocol): """ Return True if this protocol is running in this machine, where the PID makes sense. """ return protocol.getHostFullName() == getHostFullName() # ****************************************************************** # * Function related to LAUNCH # ****************************************************************** def _getAppsProgram(prog): """ Get a command to launch a program under the apps folder. """ return "%s %s" % (pw.PYTHON, pw.join(pw.APPS, prog)) def _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None): """ :param protocol: Protocol to launch :param wait: Pass true if you want to wait for the process to finish :param stdin: stdin object to direct stdin to :param stdout: stdout object to send process stdout :param stderr: stderr object to send process stderr :return: PID of queue's JOBID """ command = '{python} {prot_run} "{project_path}" "{db_path}" {prot_id} "{stdout_log}" "{stderr_log}"'.format( python=pw.PYTHON, prot_run=pw.join(pw.APPS, ''), project_path=protocol.getProject().path, db_path=protocol.getDbPath(), prot_id=protocol.strId(), # We make them absolute in case working dir is not passed to the node when running through a queue. # The reason is that since 3.0.27, the first thing that is affected by the current working dir is the # creation of the logs. Before event than loading the project, which was and is setting the working dir to # the project path. IMPORTANT: This assumes the paths before the queue and after the queue (nodes) are the same # Which I think is safe since we are passing here "project_path" that is absolute. stdout_log=os.path.abspath(protocol.getStdoutLog()), stderr_log=os.path.abspath(protocol.getStderrLog()) ) hostConfig = protocol.getHostConfig() useQueue = protocol.useQueue() # Empty PID: 0 protocol.setPid(0) # Check if need to submit to queue if useQueue and (protocol.getSubmitDict()["QUEUE_FOR_JOBS"] == "N"): submitDict = dict(hostConfig.getQueuesDefault()) submitDict.update(protocol.getSubmitDict()) submitDict['JOB_COMMAND'] = command jobId = _submit(hostConfig, submitDict) else: jobId = _run(command, wait, stdin, stdout, stderr) return jobId
[docs]def analyzeFormattingTypeError(string, dictionary): """ receives a string with %(VARS) to be replaced with a dictionary it splits te string by \n and test the formatting per line. Raises an exception if any line fails with all problems found""" # Do the replacement line by line lines = string.split("\n") problematicLines = [] for line in lines: try: line % dictionary except KeyError as e: problematicLines.append(line + " --> variable not present in this context.") except Exception as e: problematicLines.append(line + " --> " + str(e)) if problematicLines: return PyworkflowException('Following lines in %s seems to be problematic.\n' 'Values known in this context are: \n%s' 'Please review its format or content.\n%s' % (dictionary, pw.Config.SCIPION_HOSTS, "\n".join(problematicLines)), url=pw.DOCSITEURLS.HOST_CONFIG)
def _submit(hostConfig, submitDict, cwd=None, env=None): """ Submit a protocol to a queue system. Return its job id. """ # Create first the submission script to be launched # formatting using the template template = hostConfig.getSubmitTemplate() try: template = template % submitDict except Exception as e: # Capture parsing errors exception = analyzeFormattingTypeError(template, submitDict) if exception: raise exception else: # If there is no exception, then raise actual one raise e # FIXME: CREATE THE PATH FIRST scripPath = submitDict['JOB_SCRIPT'] f = open(scripPath, 'w') # Ensure the path exists makeFilePath(scripPath) # Add some line ends because in some clusters it fails # to submit jobs if the submit script does not have end of line f.write(template + '\n\n') f.close() # This should format the command using a template like: # "qsub %(JOB_SCRIPT)s" command = hostConfig.getSubmitCommand() % submitDict gcmd = greenStr(command)"** Submitting to queue: '%s'" % gcmd) p = Popen(command, shell=True, stdout=PIPE, cwd=cwd, env=env) out = p.communicate()[0] # Try to parse the result of qsub, searching for a number (jobId) # Review this, seems to exclusive to torque batch system s ='(\d+)', str(out)) if p.returncode == 0 and s: job = int("Launched job with id %s" % job) return job else:"Couldn't submit to queue for reason: %s " % redStr(out.decode())) return UNKNOWN_JOBID def _run(command, wait, stdin=None, stdout=None, stderr=None): """ Execute a command in a subprocess and return the pid. """ gcmd = greenStr(command)"** Running command: '%s'" % gcmd) p = Popen(command, shell=True, stdout=stdout, stderr=stderr) jobId = if wait: p.wait() return jobId