mirror of
https://github.com/galaxyproject/galaxy.git
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104 lines
4.0 KiB
Python
Executable File
104 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env python
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from __future__ import print_function
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import os
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import sys
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from optparse import OptionParser
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from six.moves.configparser import ConfigParser
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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 + '>:', end=' ')
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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:', end=' ')
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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), end=' ')
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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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