import argparse
import ConfigParser
import os
import sys
from sqlalchemy import create_engine, MetaData
from sqlalchemy.orm import scoped_session, sessionmaker
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
import galaxy.model.tool_shed_install.mapping as mapping
def main( opts, session, model ):
'''
Find all tool shed repositories with the bad path and update with the correct path.
'''
for row in session.query( model.ToolShedRepository ).all():
if 'shed_config_filename' in row.metadata:
if row.metadata['shed_config_filename'] == opts.bad_filename:
row.metadata['shed_config_filename'] = opts.good_filename
session.add( row )
session.flush()
return 0
def create_database( config_file ):
parser = ConfigParser.SafeConfigParser()
parser.read( config_file )
# Determine which database connection to use.
database_connection = parser.get( 'app:main', 'install_database_connection' )
if database_connection is None:
database_connection = parser.get( 'app:main', 'database_connection' )
if database_connection is None:
database_connection = 'sqlite:///%s' % parser.get( 'app:main', 'database_file' )
if database_connection is None:
print 'Unable to determine correct database connection.'
exit(1)
'''Initialize the database file.'''
# Initialize the database connection.
engine = create_engine( database_connection )
MetaData( bind=engine )
install_session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
model = mapping.init( database_connection )
return install_session, model
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument( '--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file." )
parser.add_argument( '--from', dest='bad_filename', required=True, help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
parser.add_argument( '--to', dest='good_filename', required=True, help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
parser.add_argument( '--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there." )
opts = parser.parse_args()
if not os.path.exists( opts.good_filename ) and not opts.force:
print 'The file %s does not exist, use the --force option to proceed.' % opts.good_filename
exit(1)
session, model = create_database( opts.config_file )
exit( main( opts, session, model ) )