1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/b2f7abd50f6a/ changeset: b2f7abd50f6a user: greg date: 2011-07-13 15:39:02 summary: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed. affected #: 1 file (514 bytes)

--- a/scripts/cleanup_datasets/cleanup_datasets.py Tue Jul 12 18:14:56 2011 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 13 09:39:02 2011 -0400 @@ -310,17 +310,21 @@ dataset_ids.extend( [ row.id for row in history_dataset_ids_query.execute() ] ) # Process each of the Dataset objects for dataset_id in dataset_ids: + dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) + if dataset.id in skip: + continue + skip.append( dataset.id ) print "######### Processing dataset id:", dataset_id - dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) - if dataset.id not in skip and _dataset_is_deletable( dataset ): - deleted_dataset_count += 1 - for dataset_instance in dataset.history_associations + dataset.library_associations: - # Mark each associated HDA as deleted - _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 ) + if not _dataset_is_deletable( dataset ): + print "Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)" + continue + deleted_dataset_count += 1 + for dataset_instance in dataset.history_associations + dataset.library_associations: + # Mark each associated HDA as deleted + _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) + deleted_instance_count += 1 stop = time.time() - print "Examined %d datasets, marked %d as deleted and purged %d dataset instances" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) + print "Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) print "Total elapsed time: ", stop - start print "##########################################"

@@ -396,8 +400,13 @@ .filter( app.model.MetadataFile.table.c.lda_id==ldda.id ): metadata_files.append( metadata_file ) for metadata_file in metadata_files: - print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id - if not info_only: + op_description = "marked as deleted" + if remove_from_disk: + op_description = op_description + " and purged from disk" + if info_only: + print "The following metadata files attached to associations of Dataset '%s' will be %s (without 'info_only' mode):" % ( dataset.id, op_description ) + else: + print "The following metadata files attached to associations of Dataset '%s' have been %s:" % ( dataset.id, op_description ) if remove_from_disk: try: print "Removing disk file ", metadata_file.file_name

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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