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Source code for galaxy.jobs.runners.util.cli.job.torque

from logging import getLogger
try:
    import xml.etree.cElementTree as et
except:
    import xml.etree.ElementTree as et

try:
    from galaxy.model import Job
    job_states = Job.states
except ImportError:
    # Not in Galaxy, map Galaxy job states to Pulsar ones.
    from galaxy.util import enum
    job_states = enum(RUNNING='running', OK='complete', QUEUED='queued')

from ..job import BaseJobExec

log = getLogger(__name__)

ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'


argmap = {'destination': '-q',
          'Execution_Time': '-a',
          'Account_Name': '-A',
          'Checkpoint': '-c',
          'Error_Path': '-e',
          'Group_List': '-g',
          'Hold_Types': '-h',
          'Join_Paths': '-j',
          'Keep_Files': '-k',
          'Resource_List': '-l',
          'Mail_Points': '-m',
          'Mail_Users': '-M',
          'Job_Name': '-N',
          'Output_Path': '-o',
          'Priority': '-p',
          'Rerunable': '-r',
          'Shell_Path_List': '-S',
          'job_array_request': '-t',
          'User_List': '-u',
          'Variable_List': '-v'}


[docs]class Torque(BaseJobExec):
[docs] def __init__(self, **params): self.params = {} for k, v in params.items(): self.params[k] = v
[docs] def job_script_kwargs(self, ofile, efile, job_name): pbsargs = {'-o': ofile, '-e': efile, '-N': job_name} for k, v in self.params.items(): if k == 'plugin': continue try: if not k.startswith('-'): k = argmap[k] pbsargs[k] = v except KeyError: log.warning(ERROR_MESSAGE_UNRECOGNIZED_ARG % k) template_pbsargs = '' for k, v in pbsargs.items(): template_pbsargs += '#PBS %s %s\n' % (k, v) return dict(headers=template_pbsargs)
[docs] def submit(self, script_file): return 'qsub %s' % script_file
[docs] def delete(self, job_id): return 'qdel %s' % job_id
[docs] def get_status(self, job_ids=None): return 'qstat -x'
[docs] def get_single_status(self, job_id): return 'qstat -f %s' % job_id
[docs] def parse_status(self, status, job_ids): # in case there's noise in the output, find the big blob 'o xml tree = None rval = {} for line in status.strip().splitlines(): try: tree = et.fromstring(line.strip()) assert tree.tag == 'Data' break except Exception: tree = None if tree is None: log.warning('No valid qstat XML return from `qstat -x`, got the following: %s' % status) return None else: for job in tree.findall('Job'): id = job.find('Job_Id').text if id in job_ids: state = job.find('job_state').text # map PBS job states to Galaxy job states. rval[id] = self._get_job_state(state) return rval
[docs] def parse_single_status(self, status, job_id): for line in status.splitlines(): line = line.split(' = ') if line[0] == 'job_state': return self._get_job_state(line[1].strip()) # no state found, job has exited return job_states.OK
def _get_job_state(self, state): try: return { 'E': job_states.RUNNING, 'R': job_states.RUNNING, 'Q': job_states.QUEUED, 'C': job_states.OK }.get(state) except KeyError: raise KeyError("Failed to map torque status code [%s] to job state." % state)
__all__ = ('Torque',)