Fix tool migrations with config file changes, do everything from

manage_db.sh.

scripts/manage_tools.py

@@ -1,39 +0,0 @@
-from __future__ import print_function
-
-import logging
-import os.path
-import sys
-from ConfigParser import SafeConfigParser
-
-from migrate.versioning.shell import main
-
-sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
-
-from galaxy.model.orm.scripts import read_config_file_arg
-from galaxy.util.properties import load_app_properties
-
-log = logging.getLogger(__name__)
-
-config_file = read_config_file_arg(sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini')
-if not os.path.exists(config_file):
-    print("Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file)
-    sys.exit(1)
-repo = 'lib/tool_shed/galaxy_install/migrate'
-
-properties = load_app_properties(config_file=config_file)
-cp = SafeConfigParser()
-cp.read(config_file)
-
-if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ:
-    # Running functional tests.
-    db_url = os.environ['GALAXY_TEST_DBURI']
-elif "install_database_connection" in properties:
-    db_url = properties["install_database_connection"]
-elif "database_connection" in properties:
-    db_url = properties["database_connection"]
-elif "database_file" in properties:
-    db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties["database_file"]
-else:
-    db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
-
-main(repository=repo, url=db_url)