details: http://www.bx.psu.edu/hg/galaxy/rev/20683fe3bfcb changeset: 1640:20683fe3bfcb user: Greg Von Kuster greg@bx.psu.edu date: Sun Nov 30 08:03:21 2008 -0500 description: Fixes, code cleanup in cleanup_datasets.py.
1 file(s) affected in this change:
scripts/cleanup_datasets/cleanup_datasets.py
diffs (141 lines):
diff -r bcd158679985 -r 20683fe3bfcb scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Mon Nov 24 11:46:45 2008 -0500 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Sun Nov 30 08:03:21 2008 -0500 @@ -9,12 +9,7 @@ new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path
-from galaxy import eggs -import galaxy.model.mapping -import pkg_resources - -pkg_resources.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy.orm import eagerload +from galaxy.model.orm import *
assert sys.version_info[:2] >= ( 2, 4 )
@@ -79,8 +74,10 @@ # Provide info about the histories and datasets that will be affected if the delete_userless_histories function is executed. history_count = 0 dataset_count = 0 - where = ( h.table.c.user_id==None ) & ( h.table.c.deleted==False ) & ( h.table.c.update_time < cutoff_time ) - histories = h.query().filter( where ).options( eagerload( 'active_datasets' ) ).all() + histories = h.filter( and_( h.table.c.user_id==None, + h.table.c.deleted==False, + h.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'active_datasets' ) ).all()
print '# The following datasets and associated userless histories will be deleted' start = time.clock() @@ -102,17 +99,18 @@ # The datasets associated with each history are also deleted. Nothing is removed from disk. history_count = 0 dataset_count = 0 - h_where = ( h.table.c.user_id==None ) & ( h.table.c.deleted==False ) & ( h.table.c.update_time < cutoff_time )
print '# The following datasets and associated userless histories have been deleted' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'active_datasets' ) ).all() + histories = h.filter( and_( h.table.c.user_id==None, + h.table.c.deleted==False, + h.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'active_datasets' ) ).all() for history in histories: for dataset_assoc in history.active_datasets: if not dataset_assoc.deleted: # Mark all datasets as deleted - d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ).all() + datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() for dataset in datasets: if not dataset.deleted: dataset.deleted = True @@ -136,17 +134,17 @@ history_count = 0 dataset_count = 0 disk_space = 0 - h_where = ( h.table.c.deleted==True ) & ( h.table.c.purged==False ) & ( h.table.c.update_time < cutoff_time ) - print '# The following datasets and associated deleted histories will be purged' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ).all() + histories = h.filter( and_( h.table.c.deleted==True, + h.table.c.purged==False, + h.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'datasets' ) ).all() for history in histories: for dataset_assoc in history.datasets: # Datasets can only be purged if their HistoryDatasetAssociation has been deleted. if dataset_assoc.deleted: - d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ).all() + datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() for dataset in datasets: if dataset.purgable and not dataset.purged: print "%s" % dataset.file_name @@ -169,17 +167,17 @@ disk_space = 0 file_size = 0 errors = False - h_where = ( h.table.c.deleted==True ) & ( h.table.c.purged==False ) & ( h.table.c.update_time < cutoff_time ) - print '# The following datasets and associated deleted histories have been purged' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ).all() + histories = h.filter( and_( h.table.c.deleted==True, + h.table.c.purged==False, + h.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'datasets' ) ).all() for history in histories: errors = False for dataset_assoc in history.datasets: if dataset_assoc.deleted: - d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ).all() + datasets = d.filter( d.table.c.id==dataset_assoc.dataset_id ).all() for dataset in datasets: if dataset.purgable and not dataset.purged: file_size = dataset.file_size @@ -221,11 +219,12 @@ # Provide info about the datasets that will be affected if the purge_datasets function is executed. dataset_count = 0 disk_space = 0 - where = ( d.table.c.deleted==True ) & ( d.table.c.purgable==True ) & ( d.table.c.purged==False ) & ( d.table.c.update_time < cutoff_time ) - print '# The following deleted datasets will be purged' start = time.clock() - datasets = d.query().filter( where ).all() + datasets = d.filter( and_( d.table.c.deleted==True, + d.table.c.purgable==True, + d.table.c.purged==False, + d.table.c.update_time < cutoff_time ) ).all() for dataset in datasets: print "%s" % dataset.file_name dataset_count += 1 @@ -243,11 +242,12 @@ dataset_count = 0 disk_space = 0 file_size = 0 - where = ( d.table.c.deleted==True ) & ( d.table.c.purgable==True ) & ( d.table.c.purged==False ) & ( d.table.c.update_time < cutoff_time ) - print '# The following deleted datasets have been purged' start = time.clock() - datasets = d.query().filter( where ).all() + datasets = d.filter( and_( d.table.c.deleted==True, + d.table.c.purgable==True, + d.table.c.purged==False, + d.table.c.update_time < cutoff_time ) ).all() for dataset in datasets: file_size = dataset.file_size if remove_from_disk: @@ -289,7 +289,8 @@ # See if the dataset has been shared if dataset.external_filename: # This check handles the pre-history_dataset_association approach to sharing. - shared_data = d.filter( and_( d.table.c.external_filename==dataset.external_filename, d.table.c.deleted==False ) ).all() + shared_data = d.filter( and_( d.table.c.external_filename==dataset.external_filename, + d.table.c.deleted==False ) ).all() if shared_data: purgable = False if purgable: