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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/updater/update_parents.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,110 @@
+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:])