Mercurial > repos > gga > apollo_export
diff create_features_from_gff3.py @ 5:950fb2bf116d draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
| author | gga |
|---|---|
| date | Fri, 31 Aug 2018 09:33:38 -0400 |
| parents | 5559e41721c3 |
| children | c3b5bc8b4080 |
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--- a/create_features_from_gff3.py Mon Mar 12 06:31:27 2018 -0400 +++ b/create_features_from_gff3.py Fri Aug 31 09:33:38 2018 -0400 @@ -8,7 +8,7 @@ from six.moves.builtins import str -from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry +from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) @@ -25,14 +25,15 @@ wa = WebApolloInstance(args.apollo, args.username, args.password) # User must have an account - gx_user = AssertUser(wa.users.loadUsers(email=args.email)) + gx_user = wa.users.assertOrCreateUser(args.email) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] - # TODO: Check user perms on org. + if not PermissionCheck(gx_user, org_cn, "WRITE"): + raise Exception("Action not permitted") org = wa.organisms.findOrganismByCn(org_cn) bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']