1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/0639c7b53077/ changeset: 0639c7b53077 user: dannon date: 2011-12-08 18:08:53 summary: Email action on job failure, resolves bb issue #600. Fail/cleanup logic condensation. affected #: 1 file

diff -r 5e211b535425ba3ea80723153043be21446230d7 -r 0639c7b530774aea53776cc207b39cee22a5499a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -443,7 +443,7 @@ job = self.get_job() self.sa_session.refresh( job ) # if the job was deleted, don't fail it - if not job.state == model.Job.states.DELETED: + if not job.state == job.states.DELETED: # Check if the failure is due to an exception if exception: # Save the traceback immediately in case we generate another @@ -474,15 +474,18 @@ dataset.extension = 'data' self.sa_session.add( dataset ) self.sa_session.flush() - job.state = model.Job.states.ERROR + job.state = job.states.ERROR job.command_line = self.command_line job.info = message self.sa_session.add( job ) self.sa_session.flush() + #Perform email action even on failure. + for pja in [x for x in job.post_job_actions if x.action_type == "EmailAction"]: + ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job) # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up if self.tool: self.tool.job_failed( self, message, exception ) - if self.app.config.cleanup_job == 'always': + if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED): self.cleanup()

def change_state( self, state, info = False ): @@ -525,14 +528,9 @@ self.sa_session.expunge_all() job = self.get_job() # if the job was deleted, don't finish it - if job.state == job.states.DELETED: - if self.app.config.cleanup_job in ( 'always', 'onsuccess' ): - self.cleanup() - return - elif job.state == job.states.ERROR: - # Job was deleted by an administrator - self.fail( job.info ) - return + if job.state == job.states.DELETED or job.state == job.states.ERROR: + #ERROR at this point means the job was deleted by an administrator. + return self.fail( job.info ) if stderr: job.state = job.states.ERROR else: @@ -555,8 +553,7 @@ if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0: log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) ) else: - self.fail( "Job %s's output dataset(s) could not be read" % job.id ) - return + return self.fail( "Job %s's output dataset(s) could not be read" % job.id ) job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) def in_directory( file, directory ):

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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