from __future__ import print_function

import argparse
import os
import sys

from six.moves.configparser import SafeConfigParser
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 = 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))