details: http://www.bx.psu.edu/hg/galaxy/rev/3e391f7192f6 changeset: 1570:3e391f7192f6 user: Nate Coraor nate@bx.psu.edu date: Wed Oct 22 14:37:28 2008 -0400 description: Record a useful info message when a job fails to run because inputs are deleted. And clarify log messages.
1 file(s) affected in this change:
lib/galaxy/jobs/__init__.py
diffs (66 lines):
diff -r df07d0c2830f -r 3e391f7192f6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Oct 22 14:27:57 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Wed Oct 22 14:37:28 2008 -0400 @@ -15,7 +15,7 @@ log = logging.getLogger( __name__ )
# States for running a job. These are NOT the same as data states -JOB_WAIT, JOB_ERROR, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'error', 'ok', 'ready', 'deleted' +JOB_WAIT, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted'
class Sleeper( object ): """ @@ -163,8 +163,10 @@ if job_state == JOB_WAIT: if not self.track_jobs_in_database: new_waiting.append( job ) - elif job_state == JOB_ERROR: - log.info( "job %d ended with an error" % job.job_id ) + elif job_state == JOB_INPUT_ERROR: + log.info( "job %d unable to run: one or more inputs in error state" % job.job_id ) + elif job_state == JOB_INPUT_DELETED: + log.info( "job %d unable to run: one or more inputs deleted" % job.job_id ) elif job_state == JOB_READY: # If special queuing is enabled, put the ready jobs in the special queue if self.use_policy : @@ -320,6 +322,7 @@ dataset.flush() job.state = model.Job.states.ERROR job.command_line = self.command_line + job.info = message # If the failure is due to a Galaxy framework exception, save # the traceback if exception: @@ -356,12 +359,13 @@
def check_if_ready_to_run( self ): """ - Check if a job is ready to run by verifying that each of its input + Check if a job is ready to run by verifying that each of its input datasets is ready (specifically in the OK state). If any input dataset - has an error, fail the job and return JOB_ERROR. If all input datasets - are in OK state, return JOB_READY indicating that the job can be - dispatched. Otherwise, return JOB_WAIT indicating that input datasets - are still being prepared. + has an error, fail the job and return JOB_INPUT_ERROR. If any input + dataset is deleted, fail the job and return JOB_INPUT_DELETED. If all + input datasets are in OK state, return JOB_READY indicating that the + job can be dispatched. Otherwise, return JOB_WAIT indicating that input + datasets are still being prepared. """ job = model.Job.get( self.job_id ) job.refresh() @@ -373,11 +377,11 @@ # don't run jobs for which the input dataset was deleted if idata.deleted == True: self.fail( "input data %d was deleted before this job ran" % idata.hid ) - return JOB_ERROR + return JOB_INPUT_DELETED # an error in the input data causes us to bail immediately elif idata.state == idata.states.ERROR: self.fail( "error in input data %d" % idata.hid ) - return JOB_ERROR + return JOB_INPUT_ERROR elif idata.state != idata.states.OK: # need to requeue return JOB_WAIT