Commit 2e81c346 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Add stop function to enable finishing jobs early to job manager and pulsar runner

parent 843d2efb

lib/galaxy/jobs/runners/pulsar.py

+5 −2
Original line number Diff line number Diff line
@@ -736,7 +736,7 @@ class PulsarJobRunner(AsynchronousJobRunner): 
                )

            return False



    def stop_job(self, job_wrapper):

    def stop_job(self, job_wrapper, soft_kill=True):

        job = job_wrapper.get_job()

        if not job.job_runner_external_id:

            return
@@ -775,6 +775,9 @@ class PulsarJobRunner(AsynchronousJobRunner): 
            job_id = job.job_runner_external_id

            log.debug(f"Attempt remote Pulsar kill of job with url {pulsar_url} and id {job_id}")

            client = self.get_client(job.destination_params, job_id)

            if soft_kill:

                client.kill(soft_kill=soft_kill)

            else:

                client.kill()



    def recover(self, job, job_wrapper):

lib/galaxy/managers/jobs.py

+13 −0
Original line number Diff line number Diff line
@@ -29,6 +29,7 @@ from galaxy.exceptions import ( 
    ObjectNotFound,

    RequestParameterInvalidException,

)

from galaxy.jobs import JobConfiguration, MinimalJobWrapper

from galaxy.job_metrics import (

    RawMetric,

    Safety,
@@ -266,6 +267,18 @@ class JobManager: 
        else:

            return False



    def finish_early(self, job):

        if not job.finished:

            try:

                job.mark_stopped(self.app.config.track_jobs_in_database)

                session = self.app.model.session

                with transaction(session):

                    session.commit()

                self.app.job_manager.stop(job, message="")

                return True

            except Exception as e:

                log.error("Job Runner does not support stopping job early.")

        return False



class JobSearch:

    """Search for jobs using tool inputs or other jobs"""