details: http://www.bx.psu.edu/hg/galaxy/rev/b02b8d9196a8 changeset: 1567:b02b8d9196a8 user: Nate Coraor nate@bx.psu.edu date: Wed Oct 22 12:15:06 2008 -0400 description: Like the local runner, if job preparation fails, catch and log.
2 file(s) affected in this change:
lib/galaxy/jobs/runners/pbs.py lib/galaxy/jobs/runners/sge.py
diffs (42 lines):
diff -r 510ff36caaf3 -r b02b8d9196a8 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Tue Oct 21 10:40:08 2008 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Oct 22 12:15:06 2008 -0400 @@ -114,8 +114,15 @@
def queue_job( self, job_wrapper ): """Create PBS script for a job and submit it to the PBS queue""" - job_wrapper.prepare() - command_line = job_wrapper.get_command_line() + + try: + job_wrapper.prepare() + command_line = job_wrapper.get_command_line() + except: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + runner_url = job_wrapper.tool.job_runner
# This is silly, why would we queue a job with no command line? diff -r 510ff36caaf3 -r b02b8d9196a8 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Tue Oct 21 10:40:08 2008 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Wed Oct 22 12:15:06 2008 -0400 @@ -103,8 +103,15 @@
def queue_job( self, job_wrapper ): """Create SGE script for a job and submit it to the SGE queue""" - job_wrapper.prepare() - command_line = job_wrapper.get_command_line() + + try: + job_wrapper.prepare() + command_line = job_wrapper.get_command_line() + except: + job_wrapper.fail( "failure preparing job", exception=True ) + log.exception("failure running job %d" % job_wrapper.job_id) + return + runner_url = job_wrapper.tool.job_runner
# This is silly, why would we queue a job with no command line?