mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
65 lines
2.2 KiB
Python
65 lines
2.2 KiB
Python
#!/usr/bin/env python
|
|
from __future__ import print_function
|
|
|
|
import os
|
|
import sys
|
|
from optparse import OptionParser
|
|
|
|
from six.moves.configparser import ConfigParser
|
|
|
|
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
|
|
|
|
import galaxy.config
|
|
from galaxy.model import mapping
|
|
from galaxy.objectstore import build_object_store_from_config
|
|
default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'config/galaxy.ini'))
|
|
|
|
parser = OptionParser()
|
|
parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=default_config)
|
|
(options, args) = parser.parse_args()
|
|
|
|
|
|
def init():
|
|
options.config = os.path.abspath(options.config)
|
|
|
|
config_parser = ConfigParser(dict(here=os.getcwd(),
|
|
database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
|
|
config_parser.read(options.config)
|
|
|
|
config_dict = {}
|
|
for key, value in config_parser.items("app:main"):
|
|
config_dict[key] = value
|
|
|
|
config = galaxy.config.Configuration(**config_dict)
|
|
|
|
object_store = build_object_store_from_config(config)
|
|
return (mapping.init(config.file_path, config.database_connection, create_tables=False, object_store=object_store),
|
|
object_store)
|
|
|
|
|
|
if __name__ == '__main__':
|
|
print('Loading Galaxy model...')
|
|
model, object_store = init()
|
|
sa_session = model.context.current
|
|
|
|
set = 0
|
|
dataset_count = sa_session.query(model.Dataset).count()
|
|
print('Processing %i datasets...' % dataset_count)
|
|
percent = 0
|
|
print('Completed %i%%' % percent, end=' ')
|
|
sys.stdout.flush()
|
|
for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
|
|
if dataset.total_size is None:
|
|
dataset.set_total_size()
|
|
set += 1
|
|
if not set % 1000:
|
|
sa_session.flush()
|
|
new_percent = int(float(i) / dataset_count * 100)
|
|
if new_percent != percent:
|
|
percent = new_percent
|
|
print('\rCompleted %i%%' % percent, end=' ')
|
|
sys.stdout.flush()
|
|
sa_session.flush()
|
|
print('\rCompleted 100%')
|
|
object_store.shutdown()
|