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 |
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| -1:000000000000 | 0:b4a85d0c85b8 |
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| 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)) |