details: http://www.bx.psu.edu/hg/galaxy/rev/2257980c5a58 changeset: 2761:2257980c5a58 user: Greg Von Kuster greg@bx.psu.edu date: Thu Sep 24 12:21:41 2009 -0400 description: Performance improvements in delete_datasets method in cleanup_datasets script ( hopefully enough ).
1 file(s) affected in this change:
scripts/cleanup_datasets/cleanup_datasets.py
diffs (82 lines):
diff -r 3e194c33f219 -r 2257980c5a58 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu Sep 24 11:55:55 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu Sep 24 12:21:41 2009 -0400 @@ -204,32 +204,42 @@
def delete_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ): # Marks datasets as deleted if associated items are all deleted. - print '# The following datasets have been marked deleted' + print "######### Starting delete_datasets #########\n" start = time.clock() if force_retry: - datasets = app.model.Dataset.filter( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ).all() + app.model.Dataset.filter( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ).all() - else: - datasets = app.model.Dataset.filter( and_( app.model.HistoryDatasetAssociation.table.c.deleted==True, - app.model.Dataset.table.c.deleted == False, - app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ) ).all() - datasets = datasets + app.model.Dataset.filter( and_( app.model.LibraryDatasetDatasetAssociation.table.c.deleted==True, - app.model.Dataset.table.c.deleted == False, - app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ) ).all() + history_datasets = app.model.Dataset.options( eagerload( "history_associations" ) ) \ + .filter( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time ).all() + library_datasets = app.model.Dataset.options( eagerload( "library_associations" ) ) \ + .filter( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time ).all() + else: + history_datasets = app.model.Dataset.filter_by( deleted = False ) \ + .options( eagerload( "history_associations" ) ) \ + .filter( and_( app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time, + app.model.HistoryDatasetAssociation.table.c.deleted==True ) ).all() + library_datasets = app.model.Dataset.filter_by( deleted = False ) \ + .options( eagerload( "library_associations" ) ) \ + .filter( and_( app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time, + app.model.LibraryDatasetDatasetAssociation.table.c.deleted==True ) ).all() + print "Time to query history and library datasets: ", time.clock() - start, "\n" + print "Processing ", len( history_datasets ), " history datasets and ", len( library_datasets ), " library datasets...\n\n" + datasets = history_datasets + library_datasets skip = [] deleted_dataset_count = 0 deleted_instance_count = 0 for dataset in datasets: + print "Processing dataset id:", dataset.id, "\n" if dataset.id not in skip and _dataset_is_deletable( dataset ): deleted_dataset_count += 1 - print "Dataset:", dataset.id for dataset_instance in dataset.history_associations + dataset.library_associations: - print "\tAssociated Dataset instance:", dataset_instance.__class__.__name__, dataset_instance.id - _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children = True, info_only = info_only ) + print "Associated Dataset instance: ", dataset_instance.__class__.__name__, dataset_instance.id, "\n" + _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) deleted_instance_count += 1 skip.append( dataset.id ) - print - print '# Examined %d datasets, marked %d as deleted and purged %d dataset instances\n' % ( len( skip ), deleted_dataset_count, deleted_instance_count ) - print "Elapsed time: ", time.clock() - start, "\n" + print "Time to process dataset id: ", dataset.id, " - ", time.clock() - start, "\n\n" + print "Time to mark datasets deleted: ", time.clock() - start, "\n\n" + print "Examined %d datasets, marked %d as deleted and purged %d dataset instances\n" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) + print "Total elapsed time: ", time.clock() - start, "\n" + print "######### Finished delete_datasets #########\n"
def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ): # Purges deleted datasets whose update_time is older than cutoff_time. Files may or may @@ -262,15 +272,16 @@ print "Elapsed time: ", stop - start, "\n"
-def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children = True, info_only = False ): - #purging a dataset instance marks the instance as deleted, - #and marks the dataset as deleted if it is not associated with another DatsetInstance that is not deleted +def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=False, is_deletable=False ): + # A dataset_instance is either a HDA or an LDDA. Purging a dataset instance marks the instance as deleted, + # and marks the associated dataset as deleted if it is not associated with another active DatsetInstance. if not info_only: dataset_instance.mark_deleted( include_children = include_children ) dataset_instance.clear_associated_files() dataset_instance.flush() dataset_instance.dataset.refresh() - if _dataset_is_deletable( dataset_instance.dataset ): + if is_deletable or _dataset_is_deletable( dataset_instance.dataset ): + # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True _delete_dataset( dataset_instance.dataset, app, remove_from_disk, info_only = info_only ) #need to purge children here if include_children: