view add_organism.py @ 2:c8e16c8eff98 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 6944305517dcccad3e6b37f8aba0b43ccb004540

#!/usr/bin/env python
import json
import argparse
import time
from webapollo import WebApolloInstance
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    parser.add_argument('apollo', help='Complete Apollo URL')
    parser.add_argument('username', help='WA Admin Username')
    parser.add_argument('password', help='WA Admin Password')

    parser.add_argument('cn', help='Organism Common Name')
    parser.add_argument('jbrowse', help='JBrowse Data Directory')
    parser.add_argument('email', help='User Email')
    parser.add_argument('--blatdb', help='BlatDB Directory')
    parser.add_argument('--genus', help='Organism Genus')
    parser.add_argument('--species', help='Organism Species')
    parser.add_argument('--public', action='store_true', help='Make organism public')

    args = parser.parse_args()


    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    gx_user = wa.users.loadUsers(email=args.email)
    if len(gx_user) == 0:
        raise Exception("Unknown user. Please register first")

    log.info("Adding Organism")
    orgs = wa.organisms.addOrganism(
        args.cn,
        args.jbrowse,
        blatdb=args.blatdb,
        genus=args.genus,
        species=args.species,
        public=args.public
    )
    log.info("Success: %s", orgs[0]['id'])

    # Must sleep before we're ready to handle
    time.sleep(1)
    log.info("Updating permissions for %s on %s", gx_user[0], args.cn)
    data = wa.users.updateOrganismPermission(
        gx_user[0], args.cn,
        write=True,
        export=True,
        read=True,
    )

    print json.dumps([org for org in orgs if org['commonName'] == args.cn], indent=2)