Unverified Commit 65e9605f authored by mvdbeek's avatar mvdbeek
Browse files

Don't fail _finish_or_resubmit if tool_stdout / tool_stderr not written 

These are only written if the command actually ran, so we'd fail here
for instance if the outputs are deleted before the job had a chance to
run.
parent 8bc3f215

lib/galaxy/jobs/runners/__init__.py

+17 −4
Original line number Diff line number Diff line
@@ -625,10 +625,23 @@ class BaseJobRunner: 


            tool_stdout_path = os.path.join(outputs_directory, "tool_stdout")

            tool_stderr_path = os.path.join(outputs_directory, "tool_stderr")

            try:

                with open(tool_stdout_path, "rb") as stdout_file:

                    tool_stdout = self._job_io_for_db(stdout_file)

                with open(tool_stderr_path, "rb") as stderr_file:

                    tool_stderr = self._job_io_for_db(stderr_file)

            except FileNotFoundError:

                if job.state in (model.Job.states.DELETING, model.Job.states.DELETED):

                    # We killed the job, so we may not even have the tool stdout / tool stderr

                    tool_stdout = ""

                    tool_stderr = "Job cancelled"

                else:

                    # Should we instead just move on ?

                    # In the end the only consequence here is that we won't be able to determine

                    # if the job failed for known tool reasons (check_tool_output).

                    # OTOH I don't know if this can even be reached

                    # Deal with it if we ever get reports about this.

                    raise



            check_output_detected_state = job_wrapper.check_tool_output(

                tool_stdout,