root/galaxy-central/scripts/cleanup_datasets/update_dataset_size.py

#!/usr/bin/env python
"""
Updates dataset.size column.
Remember to backup your database before running.
"""

import sys, os, ConfigParser
import galaxy.app

assert sys.version_info[:2] >= ( 2, 4 )

def main():
    ini_file = sys.argv.pop(1)
    conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
    conf_parser.read( ini_file )
    configuration = {}
    for key, value in conf_parser.items( "app:main" ): 
        configuration[key] = value
    app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
    
    #Step through Datasets, determining size on disk for each.
    print "Determining the size of each dataset..."
    for row in app.model.Dataset.table.select().execute():
        purged = app.model.Dataset.get( row.id ).purged
        file_size = app.model.Dataset.get( row.id ).file_size
        if file_size is None and not purged:
            size_on_disk = app.model.Dataset.get( row.id ).get_size()
            print "Updating Dataset.%d with file_size: %d" %( row.id, size_on_disk )
            app.model.Dataset.table.update( app.model.Dataset.table.c.id == row.id ).execute( file_size=size_on_disk )
    app.shutdown()
    sys.exit(0)

if __name__ == "__main__":
    main()