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https://github.com/galaxyproject/galaxy.git
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531 lines
31 KiB
Python
Executable File
531 lines
31 KiB
Python
Executable File
#!/usr/bin/env python
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import os, sys, logging
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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log = logging.getLogger()
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log.setLevel( 10 )
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log.addHandler( logging.StreamHandler( sys.stdout ) )
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "SQLAlchemy >= 0.4" )
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import time, ConfigParser, shutil
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from datetime import datetime, timedelta
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from time import strftime
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from optparse import OptionParser
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import galaxy.config
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import galaxy.model.mapping
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import sqlalchemy as sa
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from galaxy.model.orm import and_, eagerload
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from galaxy.objectstore import build_object_store_from_config
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from galaxy.exceptions import ObjectNotFound
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assert sys.version_info[:2] >= ( 2, 4 )
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def main():
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"""
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Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities
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of handling library datasets is mostly contained in the delete_datasets() method in this script.
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Assume we have 1 library dataset with: LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset
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At this point, we have the following database column values:
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LibraryDatasetDatasetAssociation deleted: False
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LibraryDataset deleted: False, purged: False
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Dataset deleted: False purged: False
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1. A user deletes the assumed dataset above from a data library via a UI menu option.
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This action results in the following database column values (changes from previous step marked with *):
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LibraryDatasetDatasetAssociation deleted: False
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LibraryDataset deleted: True*, purged: False
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Dataset deleted: False, purged: False
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2. After the number of days configured for the delete_datasets() method (option -6 below) have passed, execution
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of the delete_datasets() method results in the following database column values (changes from previous step marked with *):
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LibraryDatasetDatasetAssociation deleted: True*
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LibraryDataset deleted: True, purged: True*
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Dataset deleted: True*, purged: False
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3. After the number of days configured for the purge_datasets() method (option -3 below) have passed, execution
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of the purge_datasets() method results in the following database column values (changes from previous step marked with *):
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LibraryDatasetDatasetAssociation deleted: True
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LibraryDataset deleted: True, purged: True
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Dataset deleted: True, purged: True* (dataset file removed from disk if -r flag is used)
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This scenario is about as simple as it gets. Keep in mind that a Dataset object can have many HistoryDatasetAssociations
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and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations.
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Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects,
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and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.
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"""
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usage = "usage: %prog [options] galaxy.ini"
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parser = OptionParser(usage=usage)
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parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 )
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parser.add_option( "-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False )
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parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False )
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parser.add_option( "-f", "--force_retry", action="store_true", dest="force_retry", help="performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been", default=False )
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parser.add_option( "-1", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets" )
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parser.add_option( "-2", "--purge_histories", action="store_true", dest="purge_histories", default=False, help="purge deleted histories" )
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parser.add_option( "-3", "--purge_datasets", action="store_true", dest="purge_datasets", default=False, help="purge deleted datasets" )
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parser.add_option( "-4", "--purge_libraries", action="store_true", dest="purge_libraries", default=False, help="purge deleted libraries" )
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parser.add_option( "-5", "--purge_folders", action="store_true", dest="purge_folders", default=False, help="purge deleted library folders" )
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parser.add_option( "-6", "--delete_datasets", action="store_true", dest="delete_datasets", default=False, help="mark deletable datasets as deleted and purge associated dataset instances" )
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( options, args ) = parser.parse_args()
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if len(args) != 1 :
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parser.print_help()
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sys.exit()
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ini_file = args[0]
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if not ( options.purge_folders ^ options.delete_userless_histories ^ \
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options.purge_libraries ^ options.purge_histories ^ \
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options.purge_datasets ^ options.delete_datasets ):
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parser.print_help()
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sys.exit(0)
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if options.remove_from_disk and options.info_only:
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parser.error( "remove_from_disk and info_only are mutually exclusive" )
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config_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
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config_parser.read( ini_file )
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config_dict = {}
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for key, value in config_parser.items( "app:main" ):
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config_dict[key] = value
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config = galaxy.config.Configuration( **config_dict )
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app = CleanupDatasetsApplication( config )
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cutoff_time = datetime.utcnow() - timedelta( days=options.days )
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now = strftime( "%Y-%m-%d %H:%M:%S" )
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print "##########################################"
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print "\n# %s - Handling stuff older than %i days" % ( now, options.days )
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if options.info_only:
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print "# Displaying info only ( --info_only )\n"
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elif options.remove_from_disk:
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print "Datasets will be removed from disk.\n"
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else:
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print "Datasets will NOT be removed from disk.\n"
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if options.delete_userless_histories:
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delete_userless_histories( app, cutoff_time, info_only = options.info_only, force_retry = options.force_retry )
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elif options.purge_histories:
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purge_histories( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
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elif options.purge_datasets:
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purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
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elif options.purge_libraries:
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purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
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elif options.purge_folders:
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purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
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elif options.delete_datasets:
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delete_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry )
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app.shutdown()
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sys.exit(0)
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def delete_userless_histories( app, cutoff_time, info_only = False, force_retry = False ):
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# Deletes userless histories whose update_time value is older than the cutoff_time.
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# The purge history script will handle marking DatasetInstances as deleted.
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# Nothing is removed from disk yet.
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history_count = 0
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start = time.time()
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if force_retry:
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histories = app.sa_session.query( app.model.History ) \
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.filter( and_( app.model.History.table.c.user_id==None,
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app.model.History.table.c.update_time < cutoff_time ) )
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else:
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histories = app.sa_session.query( app.model.History ) \
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.filter( and_( app.model.History.table.c.user_id==None,
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app.model.History.table.c.deleted==False,
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app.model.History.table.c.update_time < cutoff_time ) )
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for history in histories:
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if not info_only:
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print "Deleting history id ", history.id
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history.deleted = True
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app.sa_session.add( history )
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app.sa_session.flush()
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history_count += 1
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stop = time.time()
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print "Deleted %d histories" % history_count
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print "Elapsed time: ", stop - start
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print "##########################################"
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def purge_histories( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
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# Purges deleted histories whose update_time is older than the cutoff_time.
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# The dataset associations of each history are also marked as deleted.
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# The Purge Dataset method will purge each Dataset as necessary
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# history.purged == True simply means that it can no longer be undeleted
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# i.e. all associated datasets are marked as deleted
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history_count = 0
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start = time.time()
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if force_retry:
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histories = app.sa_session.query( app.model.History ) \
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.filter( and_( app.model.History.table.c.deleted==True,
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app.model.History.table.c.update_time < cutoff_time ) ) \
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.options( eagerload( 'datasets' ) )
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else:
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histories = app.sa_session.query( app.model.History ) \
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.filter( and_( app.model.History.table.c.deleted==True,
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app.model.History.table.c.purged==False,
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app.model.History.table.c.update_time < cutoff_time ) ) \
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.options( eagerload( 'datasets' ) )
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for history in histories:
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print ("### Processing history id %d (%s)" % (history.id, history.name)).encode('utf-8')
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for dataset_assoc in history.datasets:
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_purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
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if not info_only:
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# TODO: should the Delete DefaultHistoryPermissions be deleted here? This was incorrectly
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# done in the _list_delete() method of the history controller, so copied it here. Not sure
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# if we should ever delete info like this from the db though, so commented out for now...
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#for dhp in history.default_permissions:
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# dhp.delete()
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print "Purging history id ", history.id
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history.purged = True
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app.sa_session.add( history )
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app.sa_session.flush()
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else:
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print "History id %d will be purged (without 'info_only' mode)" % history.id
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history_count += 1
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stop = time.time()
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print 'Purged %d histories.' % history_count
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print "Elapsed time: ", stop - start
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print "##########################################"
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def purge_libraries( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
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# Purges deleted libraries whose update_time is older than the cutoff_time.
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# The dataset associations of each library are also marked as deleted.
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# The Purge Dataset method will purge each Dataset as necessary
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# library.purged == True simply means that it can no longer be undeleted
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# i.e. all associated LibraryDatasets/folders are marked as deleted
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library_count = 0
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start = time.time()
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if force_retry:
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libraries = app.sa_session.query( app.model.Library ) \
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.filter( and_( app.model.Library.table.c.deleted==True,
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app.model.Library.table.c.update_time < cutoff_time ) )
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else:
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libraries = app.sa_session.query( app.model.Library ) \
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.filter( and_( app.model.Library.table.c.deleted==True,
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app.model.Library.table.c.purged==False,
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app.model.Library.table.c.update_time < cutoff_time ) )
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for library in libraries:
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_purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only )
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if not info_only:
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print "Purging library id ", library.id
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library.purged = True
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app.sa_session.add( library )
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app.sa_session.flush()
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library_count += 1
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stop = time.time()
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print '# Purged %d libraries .' % library_count
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print "Elapsed time: ", stop - start
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print "##########################################"
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def purge_folders( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
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# Purges deleted folders whose update_time is older than the cutoff_time.
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# The dataset associations of each folder are also marked as deleted.
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# The Purge Dataset method will purge each Dataset as necessary
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# libraryFolder.purged == True simply means that it can no longer be undeleted
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# i.e. all associated LibraryDatasets/folders are marked as deleted
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folder_count = 0
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start = time.time()
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if force_retry:
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folders = app.sa_session.query( app.model.LibraryFolder ) \
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.filter( and_( app.model.LibraryFolder.table.c.deleted==True,
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app.model.LibraryFolder.table.c.update_time < cutoff_time ) )
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else:
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folders = app.sa_session.query( app.model.LibraryFolder ) \
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.filter( and_( app.model.LibraryFolder.table.c.deleted==True,
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app.model.LibraryFolder.table.c.purged==False,
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app.model.LibraryFolder.table.c.update_time < cutoff_time ) )
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for folder in folders:
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_purge_folder( folder, app, remove_from_disk, info_only = info_only )
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folder_count += 1
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stop = time.time()
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print '# Purged %d folders.' % folder_count
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print "Elapsed time: ", stop - start
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print "##########################################"
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def delete_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
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# Marks datasets as deleted if associated items are all deleted.
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start = time.time()
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if force_retry:
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history_dataset_ids_query = sa.select( ( app.model.Dataset.table.c.id,
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app.model.Dataset.table.c.state ),
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whereclause = app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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from_obj = [ sa.outerjoin( app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table ) ] )
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library_dataset_ids_query = sa.select( ( app.model.LibraryDataset.table.c.id,
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app.model.LibraryDataset.table.c.deleted ),
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whereclause = app.model.LibraryDataset.table.c.update_time < cutoff_time,
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from_obj = [ app.model.LibraryDataset.table ] )
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else:
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# We really only need the id column here, but sqlalchemy barfs when trying to select only 1 column
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history_dataset_ids_query = sa.select( ( app.model.Dataset.table.c.id,
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app.model.Dataset.table.c.state ),
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whereclause = and_( app.model.Dataset.table.c.deleted == False,
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app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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app.model.HistoryDatasetAssociation.table.c.deleted == True ),
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from_obj = [ sa.outerjoin( app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table ) ] )
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library_dataset_ids_query = sa.select( ( app.model.LibraryDataset.table.c.id,
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app.model.LibraryDataset.table.c.deleted ),
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whereclause = and_( app.model.LibraryDataset.table.c.deleted == True,
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app.model.LibraryDataset.table.c.purged == False,
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app.model.LibraryDataset.table.c.update_time < cutoff_time ),
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from_obj = [ app.model.LibraryDataset.table ] )
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deleted_dataset_count = 0
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deleted_instance_count = 0
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skip = []
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# Handle library datasets. This is a bit tricky, so here's some clarification. We have a list of all
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# LibraryDatasets that were marked deleted before our cutoff_time, but have not yet been marked purged.
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# A LibraryDataset object is marked purged when all of its LibraryDatasetDatasetAssociations have been
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# marked deleted. When a LibraryDataset has been marked purged, it can never be undeleted in the data
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# library. We have several steps to complete here. For each LibraryDataset, get its associated Dataset
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# and add it to our accrued list of Datasets for later processing. We mark as deleted all of its
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# LibraryDatasetDatasetAssociations. Then we mark the LibraryDataset as purged. We then process our
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# list of Datasets.
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library_dataset_ids = [ row.id for row in library_dataset_ids_query.execute() ]
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dataset_ids = []
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for library_dataset_id in library_dataset_ids:
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print "######### Processing LibraryDataset id:", library_dataset_id
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# Get the LibraryDataset and the current LibraryDatasetDatasetAssociation objects
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ld = app.sa_session.query( app.model.LibraryDataset ).get( library_dataset_id )
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ldda = ld.library_dataset_dataset_association
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# Append the associated Dataset object's id to our list of dataset_ids
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dataset_ids.append( ldda.dataset_id )
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# Mark all of the LibraryDataset's associated LibraryDatasetDatasetAssociation objects' as deleted
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if not ldda.deleted:
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ldda.deleted = True
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app.sa_session.add( ldda )
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print "Marked associated LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id
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for expired_ldda in ld.expired_datasets:
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if not expired_ldda.deleted:
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expired_ldda.deleted = True
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app.sa_session.add( expired_ldda )
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print "Marked associated expired LibraryDatasetDatasetAssociation id %d as deleted" % ldda.id
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# Mark the LibraryDataset as purged
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ld.purged = True
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app.sa_session.add( ld )
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print "Marked LibraryDataset id %d as purged" % ld.id
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app.sa_session.flush()
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# Add all datasets associated with Histories to our list
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dataset_ids.extend( [ row.id for row in history_dataset_ids_query.execute() ] )
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# Process each of the Dataset objects
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for dataset_id in dataset_ids:
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dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id )
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if dataset.id in skip:
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continue
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skip.append( dataset.id )
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print "######### Processing dataset id:", dataset_id
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if not _dataset_is_deletable( dataset ):
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print "Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)"
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continue
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deleted_dataset_count += 1
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for dataset_instance in dataset.history_associations + dataset.library_associations:
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# Mark each associated HDA as deleted
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_purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True )
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deleted_instance_count += 1
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stop = time.time()
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print "Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % ( len( skip ), deleted_dataset_count, deleted_instance_count )
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print "Total elapsed time: ", stop - start
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print "##########################################"
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def purge_datasets( app, cutoff_time, remove_from_disk, info_only = False, force_retry = False ):
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# Purges deleted datasets whose update_time is older than cutoff_time. Files may or may
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# not be removed from disk.
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dataset_count = 0
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disk_space = 0
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start = time.time()
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if force_retry:
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datasets = app.sa_session.query( app.model.Dataset ) \
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.filter( and_( app.model.Dataset.table.c.deleted==True,
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app.model.Dataset.table.c.purgable==True,
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app.model.Dataset.table.c.update_time < cutoff_time ) )
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else:
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datasets = app.sa_session.query( app.model.Dataset ) \
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.filter( and_( app.model.Dataset.table.c.deleted==True,
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app.model.Dataset.table.c.purgable==True,
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app.model.Dataset.table.c.purged==False,
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app.model.Dataset.table.c.update_time < cutoff_time ) )
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for dataset in datasets:
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file_size = dataset.file_size
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_purge_dataset( app, dataset, remove_from_disk, info_only = info_only )
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dataset_count += 1
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try:
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disk_space += file_size
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except:
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pass
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stop = time.time()
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print 'Purged %d datasets' % dataset_count
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if remove_from_disk:
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print 'Freed disk space: ', disk_space
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print "Elapsed time: ", stop - start
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print "##########################################"
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def _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=False, is_deletable=False ):
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# A dataset_instance is either a HDA or an LDDA. Purging a dataset instance marks the instance as deleted,
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# and marks the associated dataset as deleted if it is not associated with another active DatsetInstance.
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if not info_only:
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print "Marking as deleted: %s id %d (for dataset id %d)" % \
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( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id )
|
|
dataset_instance.mark_deleted( include_children = include_children )
|
|
dataset_instance.clear_associated_files()
|
|
app.sa_session.add( dataset_instance )
|
|
app.sa_session.flush()
|
|
app.sa_session.refresh( dataset_instance.dataset )
|
|
else:
|
|
print "%s id %d (for dataset id %d) will be marked as deleted (without 'info_only' mode)" % \
|
|
( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id )
|
|
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, is_deletable=is_deletable )
|
|
else:
|
|
if info_only:
|
|
print "Not deleting dataset ", dataset_instance.dataset.id, " (will be possibly deleted without 'info_only' mode)"
|
|
else:
|
|
print "Not deleting dataset %d (shared between multiple histories/libraries, at least one not deleted)" % dataset_instance.dataset.id
|
|
#need to purge children here
|
|
if include_children:
|
|
for child in dataset_instance.children:
|
|
_purge_dataset_instance( child, app, remove_from_disk, include_children = include_children, info_only = info_only )
|
|
|
|
def _dataset_is_deletable( dataset ):
|
|
#a dataset is deletable when it no longer has any non-deleted associations
|
|
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/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:
|
|
# Mark all associated MetadataFiles as deleted and purged and remove them from disk
|
|
metadata_files = []
|
|
#lets create a list of metadata files, then perform actions on them
|
|
for hda in dataset.history_associations:
|
|
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 ldda in dataset.library_associations:
|
|
for metadata_file in app.sa_session.query( app.model.MetadataFile ) \
|
|
.filter( app.model.MetadataFile.table.c.lda_id==ldda.id ):
|
|
metadata_files.append( metadata_file )
|
|
for metadata_file in metadata_files:
|
|
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
|
|
os.unlink( metadata_file.file_name )
|
|
except Exception, e:
|
|
print "Error, exception: %s caught attempting to purge metadata file %s\n" %( str( e ), metadata_file.file_name )
|
|
metadata_file.purged = True
|
|
app.sa_session.add( metadata_file )
|
|
app.sa_session.flush()
|
|
metadata_file.deleted = True
|
|
app.sa_session.add( metadata_file )
|
|
app.sa_session.flush()
|
|
print "%s" % metadata_file.file_name
|
|
if not info_only:
|
|
print "Deleting dataset id", dataset.id
|
|
dataset.deleted = True
|
|
app.sa_session.add( dataset )
|
|
app.sa_session.flush()
|
|
else:
|
|
print "Dataset %i will be deleted (without 'info_only' mode)" % ( dataset.id )
|
|
|
|
def _purge_dataset( app, dataset, remove_from_disk, info_only = False ):
|
|
if dataset.deleted:
|
|
try:
|
|
if dataset.purgable and _dataset_is_deletable( dataset ):
|
|
if not info_only:
|
|
# Remove files from disk and update the database
|
|
if remove_from_disk:
|
|
# TODO: should permissions on the dataset be deleted here?
|
|
print "Removing disk, file ", dataset.file_name
|
|
os.unlink( dataset.file_name )
|
|
# Remove associated extra files from disk if they exist
|
|
if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ):
|
|
shutil.rmtree( dataset.extra_files_path ) #we need to delete the directory and its contents; os.unlink would always fail on a directory
|
|
usage_users = []
|
|
for hda in dataset.history_associations:
|
|
if not hda.purged:
|
|
hda.purged = True
|
|
if hda.history.user is not None and hda.history.user not in usage_users:
|
|
usage_users.append( hda.history.user )
|
|
for user in usage_users:
|
|
user.total_disk_usage -= dataset.total_size
|
|
app.sa_session.add( user )
|
|
print "Purging dataset id", dataset.id
|
|
dataset.purged = True
|
|
app.sa_session.add( dataset )
|
|
app.sa_session.flush()
|
|
else:
|
|
print "Dataset %i will be purged (without 'info_only' mode)" % (dataset.id)
|
|
else:
|
|
print "This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name )
|
|
except OSError, exc:
|
|
print "Error, dataset file has already been removed: %s" % str( exc )
|
|
print "Purging dataset id", dataset.id
|
|
dataset.purged = True
|
|
app.sa_session.add( dataset )
|
|
app.sa_session.flush()
|
|
except ObjectNotFound:
|
|
print "Dataset %i cannot be found in the object store" % dataset.id
|
|
except Exception, exc:
|
|
print "Error attempting to purge data file: ", dataset.file_name, " error: ", str( exc )
|
|
else:
|
|
print "Error: '%s' has not previously been deleted, so it cannot be purged\n" % dataset.file_name
|
|
|
|
def _purge_folder( folder, app, remove_from_disk, info_only = False ):
|
|
"""Purges a folder and its contents, recursively"""
|
|
for ld in folder.datasets:
|
|
print "Deleting library dataset id ", ld.id
|
|
ld.deleted = True
|
|
for ldda in [ld.library_dataset_dataset_association] + ld.expired_datasets:
|
|
_purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable
|
|
for sub_folder in folder.folders:
|
|
_purge_folder( sub_folder, app, remove_from_disk, info_only = info_only )
|
|
if not info_only:
|
|
# TODO: should the folder permissions be deleted here?
|
|
print "Purging folder id ", folder.id
|
|
folder.purged = True
|
|
app.sa_session.add( folder )
|
|
app.sa_session.flush()
|
|
|
|
class CleanupDatasetsApplication( object ):
|
|
"""Encapsulates the state of a Universe application"""
|
|
def __init__( self, config ):
|
|
if config.database_connection is False:
|
|
config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
|
|
self.object_store = build_object_store_from_config( config )
|
|
# Setup the database engine and ORM
|
|
self.model = galaxy.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False, object_store=self.object_store )
|
|
@property
|
|
def sa_session( self ):
|
|
"""
|
|
Returns a SQLAlchemy session -- currently just gets the current
|
|
session from the threadlocal session context, but this is provided
|
|
to allow migration toward a more SQLAlchemy 0.4 style of use.
|
|
"""
|
|
return self.model.context.current
|
|
def shutdown( self ):
|
|
self.object_store.shutdown()
|
|
|
|
if __name__ == "__main__": main()
|