1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/c8293bc4a964/ changeset: c8293bc4a964 user: natefoo date: 2012-09-28 20:30:10 summary: Allow Postgres users to update user disk usage with a fast wCTE rather than a slower computation in Python. affected #: 1 file

diff -r 8759493589092eb06138a75cf020f9cd8348106f -r c8293bc4a964863237fc069b4c1419a4674045e7 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -43,31 +43,58 @@

from galaxy.model import mapping

- return mapping.init( config.file_path, config.database_connection, create_tables = False, object_store = object_store ), object_store + return mapping.init( config.file_path, config.database_connection, create_tables = False, object_store = object_store ), object_store, config.database_connection.split(':')[0]

-def quotacheck( sa_session, users ): +def pgcalc( sa_session, id ): + sql = """ + UPDATE galaxy_user + SET disk_usage = (SELECT SUM(total_size) + FROM ( SELECT d.total_size + FROM history_dataset_association hda + JOIN history h ON h.id = hda.history_id + JOIN dataset d ON hda.dataset_id = d.id + WHERE h.user_id = :id + AND h.purged = false + AND hda.purged = false + AND d.purged = false + AND d.id NOT IN (SELECT dataset_id + FROM library_dataset_dataset_association) + GROUP BY d.id) sizes) + WHERE id = :id + RETURNING disk_usage; + """ + r = sa_session.execute(sql, {'id':id}) + new = r.fetchone()[0] + if options.dryrun: + sa_session.rollback() + return new + +def quotacheck( sa_session, users, engine ): sa_session.refresh( user ) current = user.get_disk_usage() print user.username, '<' + user.email + '> old usage:', str( current ) + ',', - new = user.calculate_disk_usage() - sa_session.refresh( user ) - # usage changed while calculating, do it again - if user.get_disk_usage() != current: - print 'usage changed while calculating, trying again...' - return quotacheck( sa_session, user ) + if engine != 'postgres': + new = user.calculate_disk_usage() + sa_session.refresh( user ) + # usage changed while calculating, do it again + if user.get_disk_usage() != current: + print 'usage changed while calculating, trying again...' + return quotacheck( sa_session, user, engine ) + else: + new = pgcalc( sa_session, user.id ) # yes, still a small race condition between here and the flush if new == current: print 'no change' else: print 'new usage:', new - if not options.dryrun: + if not options.dryrun and engine != 'postgres': user.set_disk_usage( new ) sa_session.add( user ) sa_session.flush()

if __name__ == '__main__': print 'Loading Galaxy model...' - model, object_store = init() + model, object_store, engine = init() sa_session = model.context.current

if not options.username and not options.email: @@ -75,7 +102,7 @@ print 'Processing %i users...' % user_count for i, user in enumerate( sa_session.query( model.User ).enable_eagerloads( False ).yield_per( 1000 ) ): print '%3i%%' % int( float(i) / user_count * 100 ), - quotacheck( sa_session, user ) + quotacheck( sa_session, user, engine ) print '100% complete' object_store.shutdown() sys.exit( 0 ) @@ -87,4 +114,4 @@ print 'User not found' sys.exit( 1 ) object_store.shutdown() - quotacheck( sa_session, user ) + quotacheck( sa_session, user, engine )

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

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