|
0
|
1 import sys, csv, argparse, time, json
|
|
|
2
|
|
|
3 from bl.vl.kb import KnowledgeBase as KB
|
|
|
4 import bl.vl.utils.ome_utils as vlu
|
|
|
5 from bl.vl.utils import get_logger, LOG_LEVELS
|
|
|
6
|
|
|
7
|
|
|
8 def make_parser():
|
|
|
9 parser = argparse.ArgumentParser(description='update parents')
|
|
|
10 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
|
|
|
11 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
|
|
|
12 help='logging level (default=INFO)', default='INFO')
|
|
|
13 parser.add_argument('-H', '--host', type=str, help='omero hostname')
|
|
|
14 parser.add_argument('-U', '--user', type=str, help='omero user')
|
|
|
15 parser.add_argument('-P', '--passwd', type=str, help='omero password')
|
|
|
16 parser.add_argument('-O', '--operator', type=str, help='operator',
|
|
|
17 required=True)
|
|
|
18 parser.add_argument('--in_file', type=str, required=True,
|
|
|
19 help='input file with individual, father and mother')
|
|
|
20 return parser
|
|
|
21
|
|
|
22
|
|
|
23 def update_parents(individual, father, mother, operator, kb, logger):
|
|
|
24 backup = {}
|
|
|
25 logger.info('Updating parents for individual %s', individual.id)
|
|
|
26 if individual.father != father:
|
|
|
27 backup['father'] = individual.father.id if individual.father else None
|
|
|
28 logger.info('Setting father to %s (old value %s)' % (father.id if father else None,
|
|
|
29 backup['father']))
|
|
|
30 individual.father = father
|
|
|
31 if individual.mother != mother:
|
|
|
32 backup['mother'] = individual.mother.id if individual.mother else None
|
|
|
33 logger.info('Setting mother to %s (old value %s)' % (mother.id if mother else None,
|
|
|
34 backup['mother']))
|
|
|
35 individual.mother = mother
|
|
|
36 if len(backup.items()) > 0:
|
|
|
37 update_object(individual, backup, operator, kb, logger)
|
|
|
38 return individual
|
|
|
39 else:
|
|
|
40 logger.info('No update needed for individual %s' % individual.id)
|
|
|
41 return None
|
|
|
42
|
|
|
43
|
|
|
44 def update_object(obj, backup_values, operator, kb, logger):
|
|
|
45 logger.debug('Building ActionOnAction for object %s' % obj.id)
|
|
|
46 act_setup = build_action_setup('update-parents-%f' % time.time(),
|
|
|
47 backup_values, kb, logger)
|
|
|
48 aoa_conf = {
|
|
|
49 'setup': act_setup,
|
|
|
50 'actionCategory': kb.ActionCategory.UPDATE,
|
|
|
51 'operator': operator,
|
|
|
52 'target': obj.lastUpdate if obj.lastUpdate else obj.action,
|
|
|
53 'context': obj.action.context
|
|
|
54 }
|
|
|
55 logger.debug('Updating object with new ActionOnAction')
|
|
|
56 obj.lastUpdate = kb.factory.create(kb.ActionOnAction, aoa_conf)
|
|
|
57
|
|
|
58
|
|
|
59 def build_action_setup(label, backup, kb, logger):
|
|
|
60 logger.debug('Creating a new ActionSetup with label %s and backup %r' % (label,
|
|
|
61 backup))
|
|
|
62 conf = {
|
|
|
63 'label': label,
|
|
|
64 'conf': json.dumps({'backup': backup})
|
|
|
65 }
|
|
|
66 asetup = kb.factory.create(kb.ActionSetup, conf)
|
|
|
67 return asetup
|
|
|
68
|
|
|
69
|
|
|
70 def main(argv):
|
|
|
71 parser = make_parser()
|
|
|
72 args = parser.parse_args(argv)
|
|
|
73
|
|
|
74 logger = get_logger('update_parents', level=args.loglevel,
|
|
|
75 filename=args.logfile)
|
|
|
76
|
|
|
77 try:
|
|
|
78 host = args.host or vlu.ome_host()
|
|
|
79 user = args.user or vlu.ome_user()
|
|
|
80 passwd = args.passwd or vlu.ome_passwd()
|
|
|
81 except ValueError, ve:
|
|
|
82 logger.critical(ve)
|
|
|
83 sys.exit(ve)
|
|
|
84
|
|
|
85 kb = KB(driver='omero')(host, user, passwd)
|
|
|
86
|
|
|
87 logger.info('Retrieving individuals')
|
|
|
88 inds = kb.get_objects(kb.Individual)
|
|
|
89 logger.info('Retrieved %d individuals' % len(inds))
|
|
|
90 inds_lookup = {}
|
|
|
91 for i in inds:
|
|
|
92 inds_lookup[i.id] = i
|
|
|
93
|
|
|
94 with open(args.in_file) as in_file:
|
|
|
95 to_be_updated = []
|
|
|
96 reader = csv.DictReader(in_file, delimiter='\t')
|
|
|
97 for row in reader:
|
|
|
98 ind = inds_lookup[row['individual']]
|
|
|
99 father = inds_lookup[row['father']] if row['father'] != 'None' else None
|
|
|
100 mother = inds_lookup[row['mother']] if row['mother'] != 'None' else None
|
|
|
101 ind = update_parents(ind, father, mother, args.operator, kb, logger)
|
|
|
102 if ind:
|
|
|
103 to_be_updated.append(ind)
|
|
|
104
|
|
|
105 logger.info('%d individuals are going to be updated' % len(to_be_updated))
|
|
|
106 kb.save_array(to_be_updated)
|
|
|
107 logger.info('Update complete')
|
|
|
108
|
|
|
109 if __name__ == '__main__':
|
|
|
110 main(sys.argv[1:])
|
