Unification of Galaxy configuration parsing for scripts/*

This commit is contained in:
John Chilton
2018-03-23 16:14:49 -04:00
parent 8fa8660b25
commit 5f3f792f6f
19 changed files with 537 additions and 382 deletions
+18 -21
View File
@@ -2,32 +2,36 @@
"""
Script to encode/decode the IDs that galaxy exposes to users and admins.
"""
import argparse
import logging
import os
import sys
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
from galaxy.model import mapping
from galaxy.model.orm.scripts import get_config
from galaxy.util.properties import load_app_properties
from galaxy.util.script import app_properties_from_args, populate_config_args
from galaxy.web.security import SecurityHelper
logging.basicConfig()
log = logging.getLogger(__name__)
# Get config file and load up SA session
config = get_config(sys.argv)
model = mapping.init('/tmp/', config['db_url'])
sa_session = model.context.current
parser = argparse.ArgumentParser()
parser.add_argument('action', metavar='ACTION', type=str,
default=None,
help='decode|encode')
parser.add_argument('value', metavar='VALUE', type=str,
default=None,
help='value to encode or decode')
populate_config_args(parser)
args = parser.parse_args()
# With the config file we can load the full app properties
app_properties = load_app_properties(ini_file=config['config_file'])
app_properties = app_properties_from_args(args)
helper = SecurityHelper(id_secret=app_properties.get('id_secret'))
# We need the ID secret for configuring the security helper to decrypt
# galaxysession cookies.
if "id_secret" not in app_properties:
log.warning('No ID_SECRET specified. Please set the "id_secret" in your galaxy.ini.')
log.warning('No ID_SECRET specified. Please set the "id_secret" in your galaxy.yml.')
id_secret = app_properties.get('id_secret', 'dangerous_default')
@@ -35,17 +39,10 @@ security_helper = SecurityHelper(id_secret=id_secret)
# And get access to the models
# Login manager to manage current_user functionality
if len(sys.argv) != 3:
sys.stdout.write("python %s (encode|decode) value\n" % sys.argv[0])
sys.exit(1)
action = sys.argv[1]
value = sys.argv[2]
if action == 'decode':
sys.stdout.write(security_helper.decode_guid(value.lstrip('F')))
elif action == 'encode':
sys.stdout.write(security_helper.encode_guid(value))
if args.action == 'decode':
sys.stdout.write(security_helper.decode_guid(args.value.lstrip('F')))
elif args.action == 'encode':
sys.stdout.write(security_helper.encode_guid(args.value))
else:
sys.stdout.write("Unknown argument")
sys.stdout.write('\n')