15 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ca59c76da865/ Changeset: ca59c76da865 Branch: next-stable User: natefoo Date: 2013-03-20 17:55:52 Summary: Fix for processing Torque's 'E' state in the CLI runner. Affected #: 1 file
diff -r 6a80f6558febba87a6e32b9533256543597e8d30 -r ca59c76da865a29e14dd77f9152d2ae46126f11d lib/galaxy/jobs/runners/cli_job/torque.py --- a/lib/galaxy/jobs/runners/cli_job/torque.py +++ b/lib/galaxy/jobs/runners/cli_job/torque.py @@ -128,5 +128,6 @@ return job_states.OK
def __get_job_state(self, state): - return { 'R' : job_states.RUNNING, + return { 'E' : job_states.RUNNING, + 'R' : job_states.RUNNING, 'Q' : job_states.QUEUED }.get(state, state)
https://bitbucket.org/galaxy/galaxy-central/commits/ea325de13398/ Changeset: ea325de13398 Branch: next-stable User: natefoo Date: 2013-03-20 17:56:13 Summary: Bugfixes for the pbs job runner and the move to job destinations. Affected #: 1 file
diff -r ca59c76da865a29e14dd77f9152d2ae46126f11d -r ea325de133988fd36eeda175fd8df45081be4412 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -141,6 +141,9 @@ def url_to_destination(self, url): """Convert a legacy URL to a job destination"""
+ if not url: + return + # Determine the the PBS server url_split = url.split("/") server = url_split[2] @@ -161,6 +164,9 @@ try: opts = url.split('/')[4].strip().lstrip('-').split(' -') assert opts != [''] + # stripping the - comes later (in parse_destination_params) + for i, opt in enumerate(opts): + opts[i] = '-' + opt except: opts = [] for opt in opts: @@ -210,6 +216,8 @@ return rval
def __get_pbs_server(self, job_destination_params): + if job_destination_params is None: + return None return job_destination_params['destination'].split('@')[-1]
def queue_job( self, job_wrapper ): @@ -600,9 +608,13 @@
try: pbs_server_name = self.__get_pbs_server( job.destination_params ) + if pbs_server_name is None: + log.debug("(%s) Job queued but no destination stored in job params, cannot delete" + % job_tag ) + return c = pbs.pbs_connect( pbs_server_name ) if c <= 0: - log.debug("%s Connection to PBS server for job delete failed" + log.debug("(%s) Connection to PBS server for job delete failed" % job_tag ) return pbs.pbs_deljob( c, job.get_job_runner_external_id(), '' )
https://bitbucket.org/galaxy/galaxy-central/commits/86668e4a72fc/ Changeset: 86668e4a72fc Branch: next-stable User: natefoo Date: 2013-03-20 18:11:18 Summary: Add cleanup when skipping a queued job that was deleted. Affected #: 1 file
diff -r ea325de133988fd36eeda175fd8df45081be4412 -r 86668e4a72fc11d5bf0161e567b9c6c082560e63 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -103,8 +103,14 @@ job_wrapper.is_ready = False
# Make sure the job hasn't been deleted - if job_state != model.Job.states.QUEUED: + 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 + 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
# Prepare the job
https://bitbucket.org/galaxy/galaxy-central/commits/ae19f508eaa9/ Changeset: ae19f508eaa9 Branch: next-stable User: natefoo Date: 2013-03-20 18:11:45 Summary: Have the PBS runner use the superclass convenience method for pre-queueing sanity checks. Affected #: 1 file
diff -r 86668e4a72fc11d5bf0161e567b9c6c082560e63 -r ae19f508eaa989a6d16ed59de1308ce8e05b0ad4 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -222,29 +222,16 @@
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( LocalJobRunner, self ).queue_job( job_wrapper ) + if not job_wrapper.is_ready: + return
- try: - job_wrapper.prepare() - command_line = self.build_command_line( job_wrapper, include_metadata=not( self.app.config.pbs_stage_path ) ) - except: - job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) - return + # command line has been added to the wrapper by the superclass queue_job() + command_line = job_wrapper.runner_command_line
job_destination = job_wrapper.job_destination
- # This is silly, why would we queue a job with no command line? - if not command_line: - job_wrapper.finish( '', '' ) - return - - # Check for deletion before we change state - if job_wrapper.get_state() == model.Job.states.DELETED: - log.debug( "Job %s deleted by user before it entered the PBS queue" % job_wrapper.job_id ) - if self.app.config.cleanup_job in ( "always", "onsuccess" ): - job_wrapper.cleanup() - return - # Determine the job's PBS destination (server/queue) and options from the job destination definition pbs_queue_name = None pbs_server_name = self.default_pbs_server
https://bitbucket.org/galaxy/galaxy-central/commits/d0fa91fc995e/ Changeset: d0fa91fc995e Branch: next-stable User: natefoo Date: 2013-03-21 18:58:32 Summary: Standardize some job state properties common to asynchronous runners in AsynchronousJobState. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/c4535b8d46d5/ Changeset: c4535b8d46d5 Branch: next-stable User: natefoo Date: 2013-03-21 18:59:21 Summary: Convert the CLI runner to use job destinations. Affected #: 2 files Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/929fd34026bf/ Changeset: 929fd34026bf Branch: next-stable User: natefoo Date: 2013-03-22 18:11:57 Summary: Fix URL->destination conversion of jobs running prior to upgrade to destinations. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/b4da62a0e089/ Changeset: b4da62a0e089 Branch: next-stable User: natefoo Date: 2013-03-22 18:13:05 Summary: Refactor common operations in to AsynchronousJobSate/AsynchronousJobRunner. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/67c5a41aaaf4/ Changeset: 67c5a41aaaf4 Branch: next-stable User: natefoo Date: 2013-03-22 18:14:25 Summary: Convert drmaa runner from URLs to destinations. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/88c55e8ae98e/ Changeset: 88c55e8ae98e Branch: next-stable User: natefoo Date: 2013-03-22 18:14:50 Summary: Convert condor runner from URLs to destinations. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/eb4183e82817/ Changeset: eb4183e82817 Branch: next-stable User: natefoo Date: 2013-03-22 22:58:55 Summary: Additional CLI runner fixes for destinations. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/1ea94ed3afa2/ Changeset: 1ea94ed3afa2 Branch: next-stable User: natefoo Date: 2013-03-22 23:04:52 Summary: Don't finish jobs that are deleted. Affected #: 3 files Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/99b5a77e9840/ Changeset: 99b5a77e9840 Branch: next-stable User: natefoo Date: 2013-03-22 23:07:40 Summary: Additional examples for the job configuration sample. Affected #: 1 file Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/c82a139db1c9/ Changeset: c82a139db1c9 Branch: next-stable User: natefoo Date: 2013-03-22 23:08:45 Summary: Merge. Affected #: 42 files Diff not available.
https://bitbucket.org/galaxy/galaxy-central/commits/e0da441ad10c/ Changeset: e0da441ad10c User: natefoo Date: 2013-03-22 23:09:33 Summary: Merge next-stable. Affected #: 8 files Diff not available.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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