3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c5fa48633c0b/ changeset: c5fa48633c0b branch: job_scripts user: peterjc date: 2011-07-29 15:18:15 summary: Catch problems creating job script affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Jul 28 11:50:56 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Jul 29 14:18:15 2011 +0100 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: http://bitbucket.org/galaxy/galaxy-central/changeset/769e04ccce29/ changeset: 769e04ccce29 branch: job_scripts user: natefoo date: 2011-08-19 19:30:21 summary: Closed branch job_scripts affected #: 0 files (0 bytes) http://bitbucket.org/galaxy/galaxy-central/changeset/8d8d9e8ef1a0/ changeset: 8d8d9e8ef1a0 user: natefoo date: 2011-08-19 19:30:36 summary: merge affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Aug 18 14:20:48 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Aug 19 13:30:36 2011 -0400 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.