1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c5d7d2bd7928/ Changeset: c5d7d2bd7928 Branch: next-stable User: natefoo Date: 2013-03-26 20:40:36 Summary: Fix setting of external metadata broken by refactoring job preparation. Affected #: 7 files
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -95,35 +95,43 @@ """ raise NotImplementedError()
- # Runners must override the job handling methods - def queue_job(self, job_wrapper): + def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True): """Some sanity checks that all runners' queue_job() methods are likely to want to do """ job_id = job_wrapper.get_id_tag() job_state = job_wrapper.get_state() job_wrapper.is_ready = False + job_wrapper.runner_command_line = None
# Make sure the job hasn't been deleted if job_state == model.Job.states.DELETED: log.debug( "(%s) Job deleted by user before it entered the %s queue" % ( job_id, self.runner_name ) ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): job_wrapper.cleanup() - return + return False elif job_state != model.Job.states.QUEUED: log.info( "(%d) Job is in state %s, skipping execution" % ( job_id, job_state ) ) # cleanup may not be safe in all states - return + return False
# Prepare the job try: job_wrapper.prepare() - job_wrapper.runner_command_line = self.build_command_line( job_wrapper ) + job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) except: log.exception("(%s) Failure preparing job" % job_id) job_wrapper.fail( "failure preparing job", exception=True ) - return + return False
- job_wrapper.is_ready = True + if not job_wrapper.runner_command_line: + job_wrapper.finish( '', '' ) + return False + + return True + + # Runners must override the job handling methods + def queue_job(self, job_wrapper): + raise NotImplementedError()
def stop_job(self, job): raise NotImplementedError()
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -75,12 +75,11 @@
def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( ShellJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return
- # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line
# Get shell and job execution interface
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -58,12 +58,11 @@
def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( CondorJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return
- # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line
# get configured job destination
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -105,14 +105,13 @@
def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( DRMAAJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return
- # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line - + # get configured job destination job_destination = job_wrapper.job_destination
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -35,15 +35,14 @@ self._init_worker_threads()
def queue_job( self, job_wrapper ): - # Superclass method has some basic sanity checks - super( LocalJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return
stderr = stdout = '' exit_code = 0
- # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line
job_id = job_wrapper.get_id_tag()
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -222,12 +222,11 @@
def queue_job( self, job_wrapper ): """Create PBS script for a job and submit it to the PBS queue""" - # Superclass method has some basic sanity checks - super( PBSJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=not( self.app.config.pbs_stage_path ) ): return
- # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line
job_destination = job_wrapper.job_destination
diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -26,12 +26,14 @@ self._init_worker_threads()
def queue_job( self, job_wrapper ): - super( TaskedJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return
+ # command line has been added to the wrapper by prepare_job() + command_line = job_wrapper.runner_command_line + stderr = stdout = '' - command_line = job_wrapper.runner_command_line
# Persist the destination job_wrapper.set_job_destination(job_wrapper.job_destination)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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