Unverified Commit e29f927f authored by mvdbeek's avatar mvdbeek
Browse files

Write exit code file when when setting metadata outside of pulsar 

We need this to figure out the right stdout/stderr and job state with
the `check_output` function.
parent 8019207d

lib/galaxy/jobs/runners/pulsar.py

+5 −0
Original line number Diff line number Diff line
@@ -646,6 +646,11 @@ class PulsarJobRunner(AsynchronousJobRunner): 
            log.exception("failure finishing job %d", job_wrapper.job_id)

            return

        if not PulsarJobRunner.__remote_metadata(client):

            # we need an actual exit code file in the job working directory to detect job errors in the metadata script

            with open(

                os.path.join(job_wrapper.working_directory, f"galaxy_{job_wrapper.job_id}.ec"), "w"

            ) as exit_code_file:

                exit_code_file.write(str(exit_code))

            self._handle_metadata_externally(job_wrapper, resolve_requirements=True)

        # Finish the job

        try:

lib/galaxy/metadata/set_metadata.py

+12 −12
Original line number Diff line number Diff line
@@ -283,7 +283,7 @@ def set_metadata_portable( 
        import_model_store = None



    tool_script_file = tool_job_working_directory / "tool_script.sh"

    job = None

    job: Optional[Job] = None

    if import_model_store and export_store:

        job = next(iter(import_model_store.sa_session.objects[Job].values()))
@@ -328,7 +328,7 @@ def set_metadata_portable( 
            final_job_state = Job.states.ERROR

            job_messages.append(str(e))

        if job:

            job.job_messages = job_messages

            job.set_streams(tool_stdout=tool_stdout, tool_stderr=tool_stderr, job_messages=job_messages)

            job.state = final_job_state

            if os.path.exists(tool_script_file):

                with open(tool_script_file) as command_fh: