details: http://www.bx.psu.edu/hg/galaxy/rev/dc5068efc3e7 changeset: 2480:dc5068efc3e7 user: Nate Coraor nate@bx.psu.edu date: Tue Jul 14 11:33:42 2009 -0400 description: Fix job recovery when a tool has been removed while the job is running

1 file(s) affected in this change:

lib/galaxy/jobs/__init__.py

diffs (24 lines):

diff -r 3f407d489ade -r dc5068efc3e7 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri May 22 14:46:17 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Jul 14 11:33:42 2009 -0400 @@ -119,10 +119,17 @@ """ model = self.app.model for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all(): - log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) - self.queue.put( ( job.id, job.tool_id ) ) + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + else: + log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) + self.queue.put( ( job.id, job.tool_id ) ) for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all(): - if job.job_runner_name is None: + if job.tool_id not in self.app.toolbox.tools_by_id: + log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) ) + JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator, or' ) + elif job.job_runner_name is None: log.debug( "no runner: %s is still in queued state, adding to the jobs queue" %job.id ) self.queue.put( ( job.id, job.tool_id ) ) else: