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

# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from logging import getLogger

from . import (

log = getLogger(__name__)

argmap = {"time": "-t", "ncpus": "-c", "partition": "-p"}

[docs]class Slurm(BaseJobExec):
[docs] def job_script_kwargs(self, ofile, efile, job_name): scriptargs = {"-o": ofile, "-e": efile, "-J": job_name} # Map arguments using argmap. for k, v in self.params.items(): if k == "plugin": continue try: if not k.startswith("-"): k = argmap[k] scriptargs[k] = v except Exception: log.warning(f"Unrecognized long argument passed to Slurm CLI plugin: {k}") # Generated template. template_scriptargs = "" for k, v in scriptargs.items(): template_scriptargs += f"#SBATCH {k} {v}\n" return dict(headers=template_scriptargs)
[docs] def submit(self, script_file): return f"sbatch {script_file}"
[docs] def delete(self, job_id): return f"scancel {job_id}"
[docs] def get_status(self, job_ids=None): return "squeue -a -o '%A %t'"
[docs] def get_single_status(self, job_id): return f"squeue -a -o '%A %t' -j {job_id}"
[docs] def parse_status(self, status, job_ids): # Get status for each job, skipping header. rval = {} for line in status.splitlines()[1:]: id, state = line.split() if id in job_ids: # map job states to Galaxy job states. rval[id] = self._get_job_state(state) return rval
[docs] def parse_single_status(self, status, job_id): status = status.splitlines() if len(status) > 1: # Job still on cluster and has state. id, state = status[1].split() return self._get_job_state(state) # else line like "slurm_load_jobs error: Invalid job id specified" return job_states.OK
def _get_job_state(self, state): try: return { "F": job_states.ERROR, "R": job_states.RUNNING, "CG": job_states.RUNNING, "PD": job_states.QUEUED, "CD": job_states.OK, }.get(state) except KeyError: raise KeyError(f"Failed to map slurm status code [{state}] to job state.")
__all__ = ("Slurm",)