1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b4111248390/ changeset: 2b4111248390 user: natefoo date: 2012-09-11 18:22:03 summary: Distributed object store fixes for pgcleanup.py. affected #: 1 file diff -r 63cd6402badaf98f26080e71b1f0ed49db30e3ab -r 2b4111248390ae6340f4bec54d0cff29f48665fb scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -31,6 +31,12 @@ log = logging.getLogger() +class MetadataFile(Bunch): + pass + +class Dataset(Bunch): + pass + class Cleanup(object): def __init__(self): self.options = None @@ -199,12 +205,13 @@ log.info("All changes committed") def _remove_metadata_file(self, id, object_store_id, action_name): - metadata_file = Bunch(id=id, object_store_id=object_store_id) + metadata_file = MetadataFile(id=id, object_store_id=object_store_id) try: filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) self._log('Removing from disk: %s' % filename, action_name) - except ObjectNotFound: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get MetadataFile %s filename: %s' % (id, e)) return if not self.options.dry_run: @@ -656,8 +663,6 @@ """ log.info('Marking purged all Datasets marked deleted that are older than the specified number of days.') - # TODO: force retry option - event_id = self._create_event(inspect.stack()[0][3]) sql = """ @@ -700,15 +705,16 @@ self._log('Marked Dataset purged: %s in Object Store: %s' % (tup[0], tup[1])) # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) - dataset = Bunch(id=tup[0], object_store_id=tup[1]) + dataset = Dataset(id=tup[0], object_store_id=tup[1]) try: filename = self.object_store.get_filename(dataset) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get Dataset %s filename: %s' % (tup[0], e)) continue try: extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError): extra_files_dir = None # don't check for existence of the dataset, it should exist Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.