view list_organisms.py @ 3:bf2f5f6e11a9 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
author gga
date Wed, 20 Sep 2017 09:43:23 -0400
parents dc738069b5ac
children 0af4179e6758
line wrap: on
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#!/usr/bin/env python
from __future__ import print_function

import argparse
import json

from webapollo import AssertUser, 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 = AssertUser(wa.users.loadUsers(email=args.email))
    all_orgs = wa.organisms.findAllOrganisms()

    orgs = accessible_organisms(gx_user, all_orgs)

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