Mercurial > repos > gga > apollo_feat_from_gff3
diff list_organisms.py @ 10:5d1cf95ade8a draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author | gga |
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date | Mon, 02 Dec 2019 05:51:05 -0500 |
parents | cc098732daf6 |
children |
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--- a/list_organisms.py Mon Jul 29 10:11:02 2019 -0400 +++ b/list_organisms.py Mon Dec 02 05:51:05 2019 -0500 @@ -4,19 +4,23 @@ import argparse import json -from webapollo import WAAuth, WebApolloInstance, accessible_organisms +from apollo import accessible_organisms + +from arrow.apollo import get_apollo_instance + +from webapollo import UserObj, handle_credentials if __name__ == '__main__': parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance') - WAAuth(parser) parser.add_argument('email', help='User Email') args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) - all_orgs = wa.organisms.findAllOrganisms() + all_orgs = wa.organisms.get_organisms() orgs = accessible_organisms(gx_user, all_orgs)