Commit 902025e0 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '128-stdout-not-none' into 'dev' 

Ensure stdout/stderr from pulsar is not processed as None

Closes #128

See merge request !104
parents dca01854 0b1f04cf

.gitlab-ci.yml

+2 −2
Original line number Diff line number Diff line
@@ -9,8 +9,8 @@ variables: 
  CONTAINER_GALAXY_URL: "${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}"

  CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"

  CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"

  GALAXY_VERSION_PYTHON: 24.1.dev3+ornl

  GALAXY_VERSION_DOCKER: 24.1.dev3.ornl

  GALAXY_VERSION_PYTHON: 24.1.dev4+ornl

  GALAXY_VERSION_DOCKER: 24.1.dev4.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/jobs/handler.py

+5 −2
Original line number Diff line number Diff line
@@ -1240,7 +1240,7 @@ class DefaultJobDispatcher: 
            log.debug(f"({job_wrapper.job_id}) Dispatching to {job_wrapper.job_destination.runner} runner")

        runner.put(job_wrapper)



    def stop(self, job, job_wrapper):

    def stop(self, job, job_wrapper, soft_kill=False):

        """

        Stop the given job. The input variable job may be either a Job or a Task.

        """
@@ -1260,6 +1260,9 @@ class DefaultJobDispatcher: 
            runner_name = job_runner_name.split(":", 1)[0]

            log.debug(f"Stopping job {job_wrapper.get_id_tag()} in {runner_name} runner")

            try:

                try:

                    self.job_runners[runner_name].stop_job(job_wrapper, soft_kill=soft_kill)

                except:

                    self.job_runners[runner_name].stop_job(job_wrapper)

            except KeyError:

                log.error(f"stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}")

lib/galaxy/jobs/runners/pulsar.py

+5 −1
Original line number Diff line number Diff line
@@ -684,6 +684,10 @@ class PulsarJobRunner(AsynchronousJobRunner): 
                        tool_stderr = file_content.read()

                except Exception:

                    pass

            if not tool_stdout:

                tool_stdout = ''

            if not tool_stderr:

                tool_stderr = ''

            job_stdout = run_results.get("job_stdout")

            job_stderr = run_results.get("job_stderr")

            exit_code = run_results.get("returncode")
@@ -758,7 +762,7 @@ class PulsarJobRunner(AsynchronousJobRunner): 
                )

            return False



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

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

        job = job_wrapper.get_job()

        if not job.job_runner_external_id:

            return

lib/galaxy/managers/jobs.py

+3 −1
Original line number Diff line number Diff line
@@ -337,12 +337,14 @@ class JobManager: 
        if not job.finished:

            try:

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

                job_wrapper = self.app.job_manager.job_handler.job_queue.job_wrapper(job)

                self.app.job_manager.job_handler.dispatcher.stop(job, job_wrapper, soft_kill=True)

                session = self.app.model.session

                with transaction(session):

                    session.commit()

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

                return True

            except Exception:

            except Exception as e:

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

        return False