1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75739a5f696e/ Changeset: 75739a5f696e User: davebgx Date: 2015-01-30 17:17:01+00:00 Summary: Add script to update the paths to tool config files in installed repositories' metadata. Affected #: 1 file diff -r 3618b7a91e23096ecf7ce5842c1e16c749251a4d -r 75739a5f696e57362238ec5c022a17963dd31929 scripts/update_shed_config_path.py --- /dev/null +++ b/scripts/update_shed_config_path.py @@ -0,0 +1,80 @@ +import os +import argparse +import ConfigParser +import sys +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +import logging +import galaxy.model.tool_shed_install +import galaxy.model.tool_shed_install.mapping as mapping +from galaxy.model.orm import * +from galaxy import eggs +eggs.require('sqlalchemy') +import sqlalchemy + +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.''' + dialect_to_egg = { + "sqlite" : "pysqlite>=2", + "postgres" : "psycopg2", + "postgresql" : "psycopg2", + "mysql" : "MySQL_python" + } + dialect = ( database_connection.split( ':', 1 ) )[0] + try: + egg = dialect_to_egg[ dialect ] + try: + eggs.require( egg ) + print( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) + except: + # If the module is in the path elsewhere (i.e. non-egg), it'll still load. + print( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) + except KeyError: + # Let this go, it could possibly work with db's we don't support. + print( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) + + # Initialize the database connection. + engine = create_engine( database_connection ) + meta = MetaData( bind=engine ) + install_session = 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 ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.