[galaxy-commits] galaxy-dist commit 6358247a4559: Job running: When finishing jobs, don't flush until all datasets have finished processing. Otherwise, the terminal job state is set once the first dataset is processed, and if the runner restarts, remaining datasets will not be processed.

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor nate@bx.psu.edu # Date 1282333327 14400 # Node ID 6358247a4559c9ec757484e16c618a831711fbc9 # Parent 8242280e5c74d1fb60daa12f2ddb37cc06bc7e75 Job running: When finishing jobs, don't flush until all datasets have finished processing. Otherwise, the terminal job state is set once the first dataset is processed, and if the runner restarts, remaining datasets will not be processed.

--- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -523,7 +523,6 @@ class JobWrapper( object ): if dataset.ext == 'auto': dataset.extension = 'txt' self.sa_session.add( dataset ) - self.sa_session.flush() if context['stderr']: dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR else: @@ -535,6 +534,10 @@ class JobWrapper( object ): # panel stops checking for updates. So allow the # self.sa_session.flush() at the bottom of this method set # the state instead. + + # Flush all the dataset and job changes above. Dataset state changes + # will now be seen by the user. + self.sa_session.flush()

# Save stdout and stderr if len( stdout ) > 32768: