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63 lines
2.2 KiB
Python
63 lines
2.2 KiB
Python
#!/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 import mapping
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from galaxy.objectstore import build_object_store_from_config
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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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( 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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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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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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if __name__ == '__main__':
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print 'Loading Galaxy model...'
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model, object_store = init()
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sa_session = model.context.current
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set = 0
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dataset_count = sa_session.query( model.Dataset ).count()
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print 'Processing %i datasets...' % dataset_count
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percent = 0
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print 'Completed %i%%' % percent,
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sys.stdout.flush()
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for i, dataset in enumerate( sa_session.query( model.Dataset ).enable_eagerloads( False ).yield_per( 1000 ) ):
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if dataset.total_size is None:
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dataset.set_total_size()
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set += 1
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if not set % 1000:
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sa_session.flush()
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new_percent = int( float(i) / dataset_count * 100 )
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if new_percent != percent:
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percent = new_percent
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print '\rCompleted %i%%' % percent,
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sys.stdout.flush()
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sa_session.flush()
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print 'Completed 100%%'
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object_store.shutdown()
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