Mercurial > repos > gga > apollo_export
diff create_or_update_organism.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 | 236155b4e5f9 |
children | db216690cbbf |
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--- a/create_or_update_organism.py Mon Mar 12 06:31:27 2018 -0400 +++ b/create_or_update_organism.py Fri Aug 31 09:33:38 2018 -0400 @@ -8,11 +8,10 @@ import sys import time -from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance +from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) - if __name__ == '__main__': parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') WAAuth(parser) @@ -33,8 +32,8 @@ if isinstance(org_cn, list): org_cn = org_cn[0] - # User must have an account - gx_user = AssertUser(wa.users.loadUsers(email=args.email)) + # User must have an account, if not, create it + gx_user = wa.users.assertOrCreateUser(args.email) log.info("Determining if add or update required") try: @@ -43,14 +42,9 @@ org = None if org: - has_perms = False old_directory = org['directory'] - for user_owned_organism in gx_user.organismPermissions: - if 'WRITE' in user_owned_organism['permissions']: - has_perms = True - break - if not has_perms: + if not PermissionCheck(gx_user, org_cn, "WRITE"): print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.") sys.exit(2)