annotate list_organisms.py @ 6:b6062d33cf13 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json

from webapollo import WAAuth, WebApolloInstance, accessible_organisms

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance')
    WAAuth(parser)
    parser.add_argument('email', help='User Email')
    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)

    gx_user = wa.users.assertOrCreateUser(args.email)

    all_orgs = wa.organisms.findAllOrganisms()

    orgs = accessible_organisms(gx_user, all_orgs)

    print(json.dumps(orgs, indent=2))