diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 15a32ea200a..5525e04246e 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -176,11 +176,17 @@ class JobQueue( object ):
self.dispatcher.put( job )
log.debug( "job %d dispatched" % job.job_id)
elif job_state == JOB_DELETED:
- log.debug( "job %d deleted by user while still queued" % job.job_id )
+ msg = "job %d deleted by user while still queued" % job.job_id
+ job.info = msg
+ log.debug( msg )
else:
- log.error( "unknown job state '%s' for job %d" % ( job_state, job.job_id ))
- except:
- log.exception( "failure running job %d" % job.job_id )
+ msg = "unknown job state '%s' for job %d" % ( job_state, job.job_id )
+ job.info = msg
+ log.error( msg )
+ except Exception, e:
+ msg = "failure running job %d: %s" % ( job.job_id, str( e ) )
+ job.info = msg
+ log.exception( msg )
# Update the waiting list
self.waiting = new_waiting
# If special (e.g. fair) scheduling is enabled, dispatch all jobs
@@ -194,9 +200,10 @@ class JobQueue( object ):
except Empty:
# squeue is empty, so stop dispatching
break
- except: # if something else breaks while dispatching
- job.fail( "failure dispatching job" )
- log.exception( "failure running job %d" % sjob.job_id )
+ except Exception, e: # if something else breaks while dispatching
+ msg = "failure running job %d: %s" % ( sjob.job_id, str( e ) )
+ job.fail( msg )
+ log.exception( msg )
def put( self, job_id, tool ):
"""Add a job to the queue (by job identifier)"""
@@ -301,7 +308,7 @@ class JobWrapper( object ):
self.extra_filenames = extra_filenames
return extra_filenames
- def fail( self, message, exception=False ):
+ def fail( self, message, state=None, exception=False ):
"""
Indicate job failure by setting state and message on all output
datasets.
@@ -309,25 +316,26 @@ class JobWrapper( object ):
job = model.Job.get( self.job_id )
job.refresh()
# if the job was deleted, don't fail it
- if job.state == job.states.DELETED:
- self.cleanup()
- return
- for dataset_assoc in job.output_datasets:
- dataset = dataset_assoc.dataset
- dataset.refresh()
- dataset.state = dataset.states.ERROR
- dataset.blurb = 'tool error'
- dataset.info = message
- dataset.set_size()
- 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:
- job.traceback = traceback.format_exc()
- job.flush()
+ if not job.state == job.states.DELETED:
+ for dataset_assoc in job.output_datasets:
+ dataset = dataset_assoc.dataset
+ dataset.refresh()
+ dataset.state = dataset.states.ERROR
+ dataset.blurb = 'tool error'
+ dataset.info = message
+ dataset.set_size()
+ dataset.flush()
+ if state is not None:
+ job.state = state
+ else:
+ 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:
+ job.traceback = traceback.format_exc()
+ job.flush()
+ # If the job was deleted, just clean up
self.cleanup()
def change_state( self, state, info = False ):
@@ -371,16 +379,19 @@ class JobWrapper( object ):
job.refresh()
for dataset_assoc in job.input_datasets:
idata = dataset_assoc.dataset
- if not idata: continue
+ if not idata:
+ continue
idata.refresh()
idata.dataset.refresh() #we need to refresh the base Dataset, since that is where 'state' is stored
# 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 )
+ if idata.deleted:
+ msg = "input data %d was deleted before this job started" % idata.hid
+ self.fail( msg, state=JOB_INPUT_DELETED )
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 )
+ msg = "input data %d is in an error state" % idata.hid
+ self.fail( msg, state=JOB_INPUT_ERROR )
return JOB_INPUT_ERROR
elif idata.state != idata.states.OK:
# need to requeue
@@ -467,8 +478,8 @@ class JobWrapper( object ):
os.remove( fname )
if self.working_directory is not None:
os.rmdir( self.working_directory )
- except:
- log.exception( "Unable to cleanup job %s" % self.job_id )
+ except Exception, e:
+ log.exception( "Unable to cleanup job %s, exception: %s" % ( str( self.job_id ), str( e ) ) )
def get_command_line( self ):
return self.command_line
@@ -617,7 +628,7 @@ class JobStopQueue( object ):
job = model.Job.get( job_id )
job.refresh()
job.state = job.states.DELETED
- job.info = "Job deleted by user before it completed."
+ job.info = "Job output deleted by user before job completed."
job.flush()
for dataset_assoc in job.output_datasets:
dataset = dataset_assoc.dataset
@@ -630,7 +641,7 @@ class JobStopQueue( object ):
dataset.deleted = True
dataset.blurb = 'deleted'
dataset.peek = 'Job deleted'
- dataset.info = 'Job deleted by user before it completed'
+ dataset.info = 'Job output deleted by user before job completed'
dataset.flush()
def put( self, job ):
diff --git a/templates/dataset/errors.tmpl b/templates/dataset/errors.tmpl
index 31f5356846a..4746869cc08 100644
--- a/templates/dataset/errors.tmpl
+++ b/templates/dataset/errors.tmpl
@@ -1,79 +1,69 @@
+
+ Dataset generation errors
+
+
+
+
-
-Dataset generation errors
-
-
-
-
+
+
Dataset generation errors
+
Dataset $dataset.hid: $dataset.display_name
-
-
-
Dataset generation errors
-
-
Dataset $dataset.hid: $dataset.display_name
-
- #if $dataset.creating_job_associations
-
- #set job = $dataset.creating_job_associations[0].job
-
- #if job.traceback
- The Galaxy framework encountered the following error while attempting
- to run the tool:
+ #if $dataset.creating_job_associations
+ #set job = $dataset.creating_job_associations[0].job
+ #if job.traceback
+ The Galaxy framework encountered the following error while attempting to run the tool:
+
${job.traceback}
+ #end if
+ #if $job.stderr or $job.info
+ Tool execution generated the following error message:
+ #if $job.stderr
+
${job.stderr}
+ #elif $job.info
+
${job.info}
+ #end if
+ #else
+ Tool execution did not generate any error messages.
+ #end if
+ #if $job.stdout
+ The tool produced the following additional output:
+
${job.stdout}
+ #end if
+ #else
+ The tool did not create any additional job / error info.
+ #end if
-
${job.traceback}
-
- #end if
-
- #if $job.stderr
- Tool execution generated the following error message:
-
${job.stderr}
- #else
- Tool execution did not generate any error messages.
- #end if
-
- #if $job.stdout
- The tool produced the following additional output:
-
${job.stdout}
- #end if
-
- #else
-
- The tool did not create any additional job / error info.
-
- #end if
-
-
Report this error to the Galaxy Team
-
-
The Galaxy team regularly reviews errors that occur in the application.
- However, if you would like to provide additional information (such as
- what you were trying to do when the error occurred) and a contact e-mail
- address, we will be better able to investigate your problem and get back
- to you.
-
-
-
Error Report
-
-
-
-
-
-
+
Report this error to the Galaxy Team
+
+ The Galaxy team regularly reviews errors that occur in the application.
+ However, if you would like to provide additional information (such as
+ what you were trying to do when the error occurred) and a contact e-mail
+ address, we will be better able to investigate your problem and get back
+ to you.
+