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

import json
from logging import getLogger

from .torque import Torque

log = getLogger(__name__)

[docs]class OpenPBS(Torque): ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to OpenPBS CLI plugin: %s'
[docs] def get_status(self, job_ids=None): return 'qstat -f -F json'
[docs] def get_single_status(self, job_id): return f'qstat -f {job_id}'
[docs] def parse_status(self, status, job_ids): try: data = json.loads(status) except Exception: log.warning(f'No valid qstat JSON return from `qstat -f -F json`, got the following: {status}') rval = {} for job_id, job in data.get('Jobs', {}).items(): if job_id in job_ids: # map PBS job states to Galaxy job states. rval[id] = self._get_job_state(job['job_state']) return rval
__all__ = ('OpenPBS',)