Mercurial > repos > eric-rasche > apollo
comparison list_organisms.py @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
parents | d4ae83dedb14 |
children | f9a6e151b3b4 |
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4:23ead6905145 | 5:7610987e0c48 |
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2 import json | 2 import json |
3 import argparse | 3 import argparse |
4 from webapollo import WAAuth, WebApolloInstance, AssertUser, accessible_organisms | 4 from webapollo import WAAuth, WebApolloInstance, AssertUser, accessible_organisms |
5 | 5 |
6 if __name__ == '__main__': | 6 if __name__ == '__main__': |
7 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') | 7 parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance') |
8 WAAuth(parser) | 8 WAAuth(parser) |
9 parser.add_argument('email', help='User Email') | 9 parser.add_argument('email', help='User Email') |
10 args = parser.parse_args() | 10 args = parser.parse_args() |
11 | 11 |
12 wa = WebApolloInstance(args.apollo, args.username, args.password) | 12 wa = WebApolloInstance(args.apollo, args.username, args.password) |
14 gx_user = AssertUser(wa.users.loadUsers(email=args.email)) | 14 gx_user = AssertUser(wa.users.loadUsers(email=args.email)) |
15 all_orgs = wa.organisms.findAllOrganisms() | 15 all_orgs = wa.organisms.findAllOrganisms() |
16 | 16 |
17 orgs = accessible_organisms(gx_user, all_orgs) | 17 orgs = accessible_organisms(gx_user, all_orgs) |
18 | 18 |
19 print json.dumps(orgs, indent=2) | 19 print(json.dumps(orgs, indent=2)) |