details: http://www.bx.psu.edu/hg/galaxy/rev/c9f19b8b21ba changeset: 1582:c9f19b8b21ba user: Nate Coraor <nate@bx.psu.edu> date: Wed Oct 29 12:35:50 2008 -0400 description: Re-add JOB_ERROR since some finish hooks use it (albeit improperly). 2 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/jobs/runners/pbs.py diffs (33 lines): diff -r 4841a9e393c7 -r c9f19b8b21ba lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Oct 28 14:31:02 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Wed Oct 29 12:35:50 2008 -0400 @@ -15,7 +15,7 @@ log = logging.getLogger( __name__ ) # States for running a job. These are NOT the same as data states -JOB_WAIT, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted' +JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted' class Sleeper( object ): """ @@ -163,6 +163,8 @@ if job_state == JOB_WAIT: if not self.track_jobs_in_database: new_waiting.append( job ) + elif job_state == JOB_ERROR: + log.info( "job %d ended with an error" % job.job_id ) elif job_state == JOB_INPUT_ERROR: log.info( "job %d unable to run: one or more inputs in error state" % job.job_id ) elif job_state == JOB_INPUT_DELETED: diff -r 4841a9e393c7 -r c9f19b8b21ba lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Tue Oct 28 14:31:02 2008 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Oct 29 12:35:50 2008 -0400 @@ -358,7 +358,7 @@ pbs_job_state.job_wrapper.finish( stdout, stderr ) except: log.exception("Job wrapper finish method failed") - job_wrapper.fail("Unable to finish job", exception=True) + pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True) # clean up the pbs files self.cleanup( ( ofile, efile, job_file ) )