details: http://www.bx.psu.edu/hg/galaxy/rev/e7492f6c18ca changeset: 2366:e7492f6c18ca user: Greg Von Kuster greg@bx.psu.edu date: Fri Apr 24 13:03:57 2009 -0400 description: Deleting the cleanup_dataset migration script until it is fixed, keeps it from being pushed to public.
1 file(s) affected in this change:
lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
diffs (78 lines):
diff -r fb401a784261 -r e7492f6c18ca lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Thu Apr 23 12:42:05 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -import sys, logging, os, time - -log = logging.getLogger( __name__ ) -log.setLevel(logging.DEBUG) -handler = logging.StreamHandler( sys.stdout ) -format = "%(name)s %(levelname)s %(asctime)s %(message)s" -formatter = logging.Formatter( format ) -handler.setFormatter( formatter ) -log.addHandler( handler ) - -from migrate import migrate_engine -from sqlalchemy import and_ - -# load existing galaxy model, we are only changing data -import galaxy.model -from galaxy.model import mapping -model = mapping.init( galaxy.model.Dataset.file_path, str( migrate_engine.url ) ) - -def __guess_dataset_by_filename( filename ): - """Return a guessed dataset by filename""" - try: - fields = os.path.split( filename ) - if fields: - if fields[-1].startswith( 'dataset_' ) and fields[-1].endswith( '.dat' ): #dataset_%d.dat - return model.Dataset.get( int( fields[-1][ len( 'dataset_' ): -len( '.dat' ) ] ) ) - except: - pass #some parsing error, we can't guess Dataset - return None - -def upgrade(): - log.debug( "Fixing a discrepancy concerning deleted shared history items." ) - affected_items = 0 - start_time = time.time() - for dataset in model.Dataset.filter( and_( model.Dataset.c.deleted == True, model.Dataset.c.purged == False ) ).all(): - for dataset_instance in dataset.history_associations + dataset.library_associations: - if not dataset_instance.deleted: - dataset.deleted = False - if dataset.file_size in [ None, 0 ]: - dataset.set_size() #Restore filesize - affected_items += 1 - break - galaxy.model.mapping.Session.flush() - log.debug( "%i items affected, and restored." % ( affected_items ) ) - log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) - - #fix share before hda - log.debug( "Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs." ) - dataset_by_filename = {} - changed_associations = 0 - start_time = time.time() - for dataset in model.Dataset.filter( model.Dataset.external_filename.like( '%dataset_%.dat' ) ).all(): - if dataset.file_name in dataset_by_filename: - guessed_dataset = dataset_by_filename[ dataset.file_name ] - else: - guessed_dataset = __guess_dataset_by_filename( dataset.file_name ) - if guessed_dataset and dataset.file_name != guessed_dataset.file_name:#not os.path.samefile( dataset.file_name, guessed_dataset.file_name ): - guessed_dataset = None - dataset_by_filename[ dataset.file_name ] = guessed_dataset - - if guessed_dataset is not None and guessed_dataset.id != dataset.id: #could we have a self referential dataset? - for dataset_instance in dataset.history_associations + dataset.library_associations: - dataset_instance.dataset = guessed_dataset - changed_associations += 1 - #mark original Dataset as deleted and purged, it is no longer in use, but do not delete file_name contents - dataset.deleted = True - dataset.external_filename = "Dataset was result of share before HDA, and has been replaced: %s mapped to Dataset %s" % ( dataset.external_filename, guessed_dataset.id ) - dataset.purged = True #we don't really purge the file here, but we mark it as purged, since this dataset is now defunct - galaxy.model.mapping.Session.flush() - log.debug( "%i items affected, and restored." % ( changed_associations ) ) - log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) - -def downgrade(): - log.debug( "Downgrade is not possible." ) -