comparison list_organisms.py @ 10:dca2fb399ee6 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

9:d8bb1f9b85b2

from __future__ import print_function

import argparse
import json

from webapollo import WAAuth, WebApolloInstance, accessible_organisms

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)

    gx_user = wa.users.assertOrCreateUser(args.email)

    all_orgs = wa.organisms.findAllOrganisms()

    orgs = accessible_organisms(gx_user, all_orgs)

    print(json.dumps(orgs, indent=2))

10:dca2fb399ee6

from __future__ import print_function

import argparse
import json

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')
    parser.add_argument('email', help='User Email')
    args = parser.parse_args()

    wa = get_apollo_instance()

    gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
    handle_credentials(gx_user)

    all_orgs = wa.organisms.get_organisms()

    orgs = accessible_organisms(gx_user, all_orgs)

    print(json.dumps(orgs, indent=2))