Mercurial > repos > gga > apollo_export
comparison list_organisms.py @ 0:b4a85d0c85b8 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
---|---|
date | Mon, 11 Sep 2017 05:47:07 -0400 |
parents | |
children | 950fb2bf116d |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:b4a85d0c85b8 |
---|---|
1 #!/usr/bin/env python | |
2 from __future__ import print_function | |
3 | |
4 import argparse | |
5 import json | |
6 | |
7 from webapollo import AssertUser, WAAuth, WebApolloInstance, accessible_organisms | |
8 | |
9 if __name__ == '__main__': | |
10 parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance') | |
11 WAAuth(parser) | |
12 parser.add_argument('email', help='User Email') | |
13 args = parser.parse_args() | |
14 | |
15 wa = WebApolloInstance(args.apollo, args.username, args.password) | |
16 | |
17 gx_user = AssertUser(wa.users.loadUsers(email=args.email)) | |
18 all_orgs = wa.organisms.findAllOrganisms() | |
19 | |
20 orgs = accessible_organisms(gx_user, all_orgs) | |
21 | |
22 print(json.dumps(orgs, indent=2)) |