1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/238207122b68/ changeset: 238207122b68 user: natefoo date: 2012-02-02 19:25:59 summary: DRMAA runner no longer needs to clean up its stdout/stderr since they live in the working directory which is cleaned up by the job wrapper. affected #: 1 file
diff -r 37e787787128662a1aba3c6c831f9dabc9de3289 -r 238207122b68e961dac14238fe1af0a585a9e903 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -196,7 +196,6 @@ if job_wrapper.get_state() == model.Job.states.DELETED: log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): - self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return
@@ -334,25 +333,12 @@ except: log.exception("Job wrapper finish method failed")
- # clean up the drm files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) - def fail_job( self, drm_job_state ): """ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) ) drm_job_state.job_wrapper.fail( drm_job_state.fail_message ) - if self.app.config.cleanup_job == "always": - self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) ) - - def cleanup( self, files ): - for file in files: - try: - os.unlink( file ) - except Exception, e: - log.warning( "Unable to cleanup: %s" % str( e ) )
def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" @@ -440,6 +426,6 @@ # The expected output is a single line containing a single numeric value: # the DRMAA job-ID. If not the case, will throw an error. jobId = stdoutdata - return jobId; + return jobId
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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