1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/2626e0f79dc2/ changeset: r5030:2626e0f79dc2 user: greg date: 2011-02-09 21:42:09 summary: Add a purged column to the LibraryDataset table - a LibraryDataset is marked purged when all associated LibraryDatasetDatasetAssociations are marked deleted. Fix the cleanup_datasets.py script to more correclty handle the lifecycle of LibraryDatasets. affected #: 4 files (4.3 KB)

--- a/lib/galaxy/model/__init__.py Wed Feb 09 13:24:35 2011 -0500 +++ b/lib/galaxy/model/__init__.py Wed Feb 09 15:42:09 2011 -0500 @@ -1106,14 +1106,6 @@ name = property( get_name, set_name ) def display_name( self ): self.library_dataset_dataset_association.display_name() - def get_purged( self ): - return self.library_dataset_dataset_association.dataset.purged - def set_purged( self, purged ): - if purged: - raise Exception( "Not implemented" ) - if not purged and self.purged: - raise Exception( "Cannot unpurge once purged" ) - purged = property( get_purged, set_purged ) def get_api_value( self, view='collection' ): # Since this class is a proxy to rather complex attributes we want to # display in other objects, we can't use the simpler method used by

--- a/lib/galaxy/model/mapping.py Wed Feb 09 13:24:35 2011 -0500 +++ b/lib/galaxy/model/mapping.py Wed Feb 09 15:42:09 2011 -0500 @@ -255,7 +255,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), key="_name", index=True ), #when not None/null this will supercede display in library (but not when imported into user's history?) Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "purged", Boolean, index=True, default=False ) )

LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata, Column( "id", Integer, primary_key=True ),

--- a/scripts/cleanup_datasets/cleanup_datasets.py Wed Feb 09 13:24:35 2011 -0500 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Feb 09 15:42:09 2011 -0500 @@ -22,6 +22,43 @@ assert sys.version_info[:2] >= ( 2, 4 )

def main(): + """ + Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities + of handling library datasets is mostly contained in the delete_datasets() method in this script. + + Assume we have 1 library dataset with: LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset + At this point, we have the following database column values: + + LibraryDatasetDatasetAssociation deleted: False + LibraryDataset deleted: False, purged: False + Dataset deleted: False purged: False + + 1. A user deletes the assumed dataset above from a data library via a UI menu option. + This action results in the following database column values (changes from previous step marked with *): + + LibraryDatasetDatasetAssociation deleted: False + LibraryDataset deleted: True*, purged: False + Dataset deleted: False, purged: False + + 2. After the number of days configured for the delete_datasets() method (option -6 below) have passed, execution + of the delete_datasets() method results in the following database column values (changes from previous step marked with *): + + LibraryDatasetDatasetAssociation deleted: True* + LibraryDataset deleted: True, purged: True* + Dataset deleted: True*, purged: False + + 3. After the number of days configured for the purge_datasets() method (option -3 below) have passed, execution + of the purge_datasets() method results in the following database column values (changes from previous step marked with *): + + LibraryDatasetDatasetAssociation deleted: True + LibraryDataset deleted: True, purged: True + Dataset deleted: True, purged: True* (dataset file removed from disk if -r flag is used) + + This scenario is about as simple as it gets. Keep in mind that a Dataset object can have many HistoryDatasetAssociations + and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations. + Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects, + and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects. + """ parser = OptionParser() parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 ) parser.add_option( "-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False ) @@ -215,40 +252,70 @@ whereclause = app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time, from_obj = [ sa.outerjoin( app.model.Dataset.table, app.model.HistoryDatasetAssociation.table ) ] ) - library_dataset_ids_query = sa.select( ( app.model.Dataset.table.c.id, - app.model.Dataset.table.c.state ), - whereclause = app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time, - from_obj = [ sa.outerjoin( app.model.Dataset.table, - app.model.LibraryDatasetDatasetAssociation.table ) ] ) + library_dataset_ids_query = sa.select( ( app.model.LibraryDataset.table.c.id, + app.model.LibraryDataset.table.c.deleted ), + whereclause = app.model.LibraryDataset.table.c.update_time < cutoff_time, + from_obj = [ app.model.LibraryDataset.table ] ) else: # We really only need the id column here, but sqlalchemy barfs when trying to select only 1 column history_dataset_ids_query = sa.select( ( app.model.Dataset.table.c.id, app.model.Dataset.table.c.state ), - whereclause = sa.and_( app.model.Dataset.table.c.deleted == False, - app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time, - app.model.HistoryDatasetAssociation.table.c.deleted == True ), + whereclause = and_( app.model.Dataset.table.c.deleted == False, + app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time, + app.model.HistoryDatasetAssociation.table.c.deleted == True ), from_obj = [ sa.outerjoin( app.model.Dataset.table, app.model.HistoryDatasetAssociation.table ) ] ) - library_dataset_ids_query = sa.select( ( app.model.Dataset.table.c.id, - app.model.Dataset.table.c.state ), - whereclause = sa.and_( app.model.Dataset.table.c.deleted == False, - app.model.LibraryDatasetDatasetAssociation.table.c.update_time < cutoff_time, - app.model.LibraryDatasetDatasetAssociation.table.c.deleted == True ), - from_obj = [ sa.outerjoin( app.model.Dataset.table, - app.model.LibraryDatasetDatasetAssociation.table ) ] ) - history_dataset_ids = [ row.id for row in history_dataset_ids_query.execute() ] - library_dataset_ids = [ row.id for row in library_dataset_ids_query.execute() ] - dataset_ids = history_dataset_ids + library_dataset_ids - skip = [] + library_dataset_ids_query = sa.select( ( app.model.LibraryDataset.table.c.id, + app.model.LibraryDataset.table.c.deleted ), + whereclause = and_( app.model.LibraryDataset.table.c.deleted == True, + app.model.LibraryDataset.table.c.purged == False, + app.model.LibraryDataset.table.c.update_time < cutoff_time ), + from_obj = [ app.model.LibraryDataset.table ] ) deleted_dataset_count = 0 deleted_instance_count = 0 + skip = [] + # Handle library datasets. This is a bit tricky, so here's some clarification. We have a list of all + # LibraryDatasets that were marked deleted before our cutoff_time, but have not yet been marked purged. + # A LibraryDataset object is marked purged when all of it's LibraryDatasetDatasetAssociations have been + # marked deleted. When a LibraryDataset has been marked purged, it can never be undeleted in the data + # library. We have several steps to complete here. For each LibraryDataset, get it's associated Dataset + # and add it to our accrued list of Datasets for later processing. We mark as deleted all of it's + # LibraryDatasetDatasetAssociations. Then we mark the LibraryDataset as purged. We then process our + # list of Datasets. + library_dataset_ids = [ row.id for row in library_dataset_ids_query.execute() ] + dataset_ids = [] + for library_dataset_id in library_dataset_ids: + print "######### Processing LibraryDataset id:", library_dataset_id + # Get the LibraryDataset and the current LibraryDatasetDatasetAssociation objects + ld = app.sa_session.query( app.model.LibraryDataset ).get( library_dataset_id ) + ldda = ld.library_dataset_dataset_association + # Append the associated Dataset object's id to our list of dataset_ids + dataset_ids.append( ldda.dataset_id ) + # Mark all of the LibraryDataset's associated LibraryDatasetDatasetAssociation objects' as deleted + if not ldda.deleted: + ldda.deleted = True + app.sa_session.add( ldda ) + print "Marked associated LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id + for expired_ldda in ld.expired_datasets: + if not expired_ldda.deleted: + expired_ldda.deleted = True + app.sa_session.add( expired_ldda ) + print "Marked associated expired LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id + # Mark the LibraryDataset as purged + ld.purged = True + app.sa_session.add( ld ) + print "Marked LibraryDataset id %d as purged" % ld.id + app.sa_session.flush() + # Add all datasets associated with Histories to our list + 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: 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: - print "Associated Dataset instance: ", dataset_instance.__class__.__name__, dataset_instance.id + # 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 ) @@ -293,7 +360,7 @@ # 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: - print "Deleting dataset_instance ", str( dataset_instance ), " id ", dataset_instance.id + print "Marking as deleted: ", dataset_instance.__class__.__name__, " id ", dataset_instance.id dataset_instance.mark_deleted( include_children = include_children ) dataset_instance.clear_associated_files() app.sa_session.add( dataset_instance ) @@ -312,8 +379,8 @@ return not bool( dataset.active_history_associations or dataset.active_library_associations )

def _delete_dataset( dataset, app, remove_from_disk, info_only=False, is_deletable=False ): - #marks a base dataset as deleted, hdas/ldas associated with dataset can no longer be undeleted - #metadata files attached to associated dataset Instances is removed now + # Marks a base dataset as deleted, hdas/lddas associated with dataset can no longer be undeleted. + # Metadata files attached to associated dataset Instances is removed now. if not is_deletable and not _dataset_is_deletable( dataset ): print "This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % ( dataset.id ) else: @@ -324,9 +391,9 @@ for metadata_file in app.sa_session.query( app.model.MetadataFile ) \ .filter( app.model.MetadataFile.table.c.hda_id==hda.id ): metadata_files.append( metadata_file ) - for lda in dataset.library_associations: + for ldda in dataset.library_associations: for metadata_file in app.sa_session.query( app.model.MetadataFile ) \ - .filter( app.model.MetadataFile.table.c.lda_id==lda.id ): + .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

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

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