Unverified Commit 66f25df2 authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #9761 from gmauro/release_19.09-cleanup_job

parents 2ff26d40 a206503d

lib/galaxy/jobs/runners/__init__.py

+3 −3
Original line number Diff line number Diff line
@@ -497,18 +497,18 @@ class BaseJobRunner(object): 
                job_stderr = None



            check_output_detected_state = job_wrapper.check_tool_output(tool_stdout, tool_stderr, tool_exit_code=exit_code, job=job, job_stdout=job_stdout, job_stderr=job_stderr)

            job_not_ok = check_output_detected_state != DETECTED_JOB_STATE.OK

            job_ok = check_output_detected_state == DETECTED_JOB_STATE.OK



            # clean up the job files

            cleanup_job = job_state.job_wrapper.cleanup_job

            if cleanup_job == "always" or (job_not_ok and cleanup_job == "onsuccess"):

            if cleanup_job == "always" or (job_ok and cleanup_job == "onsuccess"):

                job_state.cleanup()



            # Flush with streams...

            self.sa_session.add(job)

            self.sa_session.flush()



            if job_not_ok:

            if not job_ok:

                job_runner_state = JobState.runner_states.TOOL_DETECT_ERROR

                if check_output_detected_state == DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR:

                    job_runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED