comparison galaxy-tools/biobank/updater/update_parents.py @ 0:ba6cf6ede027 draft default tip

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0:ba6cf6ede027

import sys, csv, argparse, time, json

from bl.vl.kb import KnowledgeBase as KB
import bl.vl.utils.ome_utils as vlu
from bl.vl.utils import get_logger, LOG_LEVELS


def make_parser():
    parser = argparse.ArgumentParser(description='update parents')
    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
                        help='logging level (default=INFO)', default='INFO')
    parser.add_argument('-H', '--host', type=str, help='omero hostname')
    parser.add_argument('-U', '--user', type=str, help='omero user')
    parser.add_argument('-P', '--passwd', type=str, help='omero password')
    parser.add_argument('-O', '--operator', type=str, help='operator',
                        required=True)
    parser.add_argument('--in_file', type=str, required=True,
                        help='input file with individual, father and mother')
    return parser


def update_parents(individual, father, mother, operator, kb, logger):
    backup = {}
    logger.info('Updating parents for individual %s', individual.id)
    if individual.father != father:
        backup['father'] = individual.father.id if individual.father else None
        logger.info('Setting father to %s (old value %s)' % (father.id if father else None,
                                                             backup['father']))
        individual.father = father
    if individual.mother != mother:
        backup['mother'] = individual.mother.id if individual.mother else None
        logger.info('Setting mother to %s (old value %s)' % (mother.id if mother else None,
                                                             backup['mother']))
        individual.mother = mother
    if len(backup.items()) > 0:
        update_object(individual, backup, operator, kb, logger)
        return individual
    else:
        logger.info('No update needed for individual %s' % individual.id)
        return None


def update_object(obj, backup_values, operator, kb, logger):
    logger.debug('Building ActionOnAction for object %s' % obj.id)
    act_setup = build_action_setup('update-parents-%f' % time.time(),
                                   backup_values, kb, logger)
    aoa_conf = {
        'setup': act_setup,
        'actionCategory': kb.ActionCategory.UPDATE,
        'operator': operator,
        'target': obj.lastUpdate if obj.lastUpdate else obj.action,
        'context': obj.action.context
        }
    logger.debug('Updating object with new ActionOnAction')
    obj.lastUpdate = kb.factory.create(kb.ActionOnAction, aoa_conf)


def build_action_setup(label, backup, kb, logger):
    logger.debug('Creating a new ActionSetup with label %s and backup %r' % (label,
                                                                             backup))
    conf = {
        'label': label,
        'conf': json.dumps({'backup': backup})
    }
    asetup = kb.factory.create(kb.ActionSetup, conf)
    return asetup


def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv)

    logger = get_logger('update_parents', level=args.loglevel,
                        filename=args.logfile)

    try:
        host = args.host or vlu.ome_host()
        user = args.user or vlu.ome_user()
        passwd = args.passwd or vlu.ome_passwd()
    except ValueError, ve:
        logger.critical(ve)
        sys.exit(ve)

    kb = KB(driver='omero')(host, user, passwd)

    logger.info('Retrieving individuals')
    inds = kb.get_objects(kb.Individual)
    logger.info('Retrieved %d individuals' % len(inds))
    inds_lookup = {}
    for i in inds:
        inds_lookup[i.id] = i

    with open(args.in_file) as in_file:
        to_be_updated = []
        reader = csv.DictReader(in_file, delimiter='\t')
        for row in reader:
            ind = inds_lookup[row['individual']]
            father = inds_lookup[row['father']] if row['father'] != 'None' else None
            mother = inds_lookup[row['mother']] if row['mother'] != 'None' else None
            ind = update_parents(ind, father, mother, args.operator, kb, logger)
            if ind:
                to_be_updated.append(ind)
                
    logger.info('%d individuals are going to be updated' % len(to_be_updated))
    kb.save_array(to_be_updated)
    logger.info('Update complete')

if __name__ == '__main__':
    main(sys.argv[1:])