mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Nicola Soranzo
101 lines
4.0 KiB
Python
Executable File
101 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env python
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import os
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import sys
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from ConfigParser import ConfigParser
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from optparse import OptionParser
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
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import galaxy.config
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from galaxy.model.util import pgcalc
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from galaxy.objectstore import build_object_store_from_config
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from galaxy.util import nice_size
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default_config = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, 'config/galaxy.ini') )
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parser = OptionParser()
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parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config )
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parser.add_option( '-u', '--username', dest='username', help='Username of user to update', default='all' )
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parser.add_option( '-e', '--email', dest='email', help='Email address of user to update', default='all' )
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parser.add_option( '--dry-run', dest='dryrun', help='Dry run (show changes but do not save to database)', action='store_true', default=False )
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( options, args ) = parser.parse_args()
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def init():
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options.config = os.path.abspath( options.config )
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if options.username == 'all':
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options.username = None
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if options.email == 'all':
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options.email = None
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config_parser = ConfigParser( dict( here=os.getcwd(),
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database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
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config_parser.read( options.config )
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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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object_store = build_object_store_from_config( config )
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from galaxy.model import mapping
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return (mapping.init( config.file_path, config.database_connection, create_tables=False, object_store=object_store ),
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object_store,
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config.database_connection.split(':')[0])
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def quotacheck( sa_session, users, engine ):
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sa_session.refresh( user )
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current = user.get_disk_usage()
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print user.username, '<' + user.email + '>:',
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if engine not in ( 'postgres', 'postgresql' ):
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new = user.calculate_disk_usage()
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sa_session.refresh( user )
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# usage changed while calculating, do it again
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if user.get_disk_usage() != current:
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print 'usage changed while calculating, trying again...'
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return quotacheck( sa_session, user, engine )
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else:
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new = pgcalc( sa_session, user.id, dryrun=options.dryrun )
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# yes, still a small race condition between here and the flush
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print 'old usage:', nice_size( current ), 'change:',
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if new in ( current, None ):
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print 'none'
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else:
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if new > current:
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print '+%s' % ( nice_size( new - current ) )
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else:
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print '-%s' % ( nice_size( current - new ) )
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if not options.dryrun and engine not in ( 'postgres', 'postgresql' ):
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user.set_disk_usage( new )
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sa_session.add( user )
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sa_session.flush()
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if __name__ == '__main__':
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print 'Loading Galaxy model...'
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model, object_store, engine = init()
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sa_session = model.context.current
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if not options.username and not options.email:
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user_count = sa_session.query( model.User ).count()
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print 'Processing %i users...' % user_count
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for i, user in enumerate( sa_session.query( model.User ).enable_eagerloads( False ).yield_per( 1000 ) ):
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print '%3i%%' % int( float(i) / user_count * 100 ),
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quotacheck( sa_session, user, engine )
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print '100% complete'
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object_store.shutdown()
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sys.exit( 0 )
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elif options.username:
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user = sa_session.query( model.User ).enable_eagerloads( False ).filter_by( username=options.username ).first()
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elif options.email:
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user = sa_session.query( model.User ).enable_eagerloads( False ).filter_by( email=options.email ).first()
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if not user:
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print 'User not found'
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sys.exit( 1 )
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object_store.shutdown()
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quotacheck( sa_session, user, engine )
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