view update_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
from webapollo import WebApolloInstance

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('organismId', help='Organism ID #')
    parser.add_argument('email', help='User Email')

    parser.add_argument('--commonName', help='Organism Common Name')
    parser.add_argument('--jbrowse', help='JBrowse Data Directory')
    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)
    data = wa.organisms.updateOrganismInfo(
        args.organismId,
        args.commonName,
        args.jbrowse,
        # mandatory
        blatdb=args.blatdb,
        genus=args.genus,
        species=args.species,
        public=args.public
    )
    # Need to filter data
    wanted_data = [x for x in data if str(x['id']) == str(args.organismId)]
    print json.dumps(wanted_data, indent=2)