1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944/ changeset: c015b82b3944 user: natefoo date: 2013-01-10 18:25:27 summary: DRMAA: Don't attempt to stop jobs that have no external ID set. affected #: 1 file diff -r caaab03824478384c256fc6b5678bb39dbf8f9f2 -r c015b82b3944f967e2c859d5552c00e3e38a2da0 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -400,16 +400,18 @@ def stop_job( self, job ): """Attempts to delete a job from the DRM queue""" try: + ext_id = job.get_job_runner_external_id() + assert ext_id not in ( None, 'None' ), 'External job id is None' if self.external_killJob_script is None: - self.ds.control( job.get_job_runner_external_id(), drmaa.JobControlAction.TERMINATE ) + self.ds.control( ext_id, drmaa.JobControlAction.TERMINATE ) else: # FIXME: hardcoded path - subprocess.Popen( [ '/usr/bin/sudo', '-E', self.external_killJob_script, str( job.get_job_runner_external_id() ), str( self.userid ) ], shell=False ) - log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.get_id(), job.get_job_runner_external_id() ) ) + subprocess.Popen( [ '/usr/bin/sudo', '-E', self.external_killJob_script, str( ext_id ), str( self.userid ) ], shell=False ) + log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.get_id(), ext_id ) ) except drmaa.InvalidJobException: - log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.get_id(), job.get_job_runner_external_id() ) ) + log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.get_id(), ext_id ) ) except Exception, e: - log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.get_id(), job.get_job_runner_external_id(), e ) ) + log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.get_id(), ext_id, e ) ) def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" 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.