|
0
|
1 import csv, argparse, sys, os
|
|
|
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 COLLECTION_TYPES = {'VesselsCollection' : 'VesselsCollectionItem',
|
|
|
8 'DataCollection' : 'DataCollectionItem'}
|
|
|
9
|
|
|
10 def make_parser():
|
|
|
11 parser = argparse.ArgumentParser(description='remove elements from a Vessels or Data Collection')
|
|
|
12 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
|
|
|
13 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
|
|
|
14 help='logger level', default='INFO')
|
|
|
15 parser.add_argument('-H', '--host', type=str, help='omero hostname')
|
|
|
16 parser.add_argument('-U', '--user', type=str, help='omero user')
|
|
|
17 parser.add_argument('-P', '--passwd', type=str, help='omero password')
|
|
|
18 parser.add_argument('-I', '--ifile', type=str, required=True,
|
|
|
19 help='list of collection items that will be removed')
|
|
|
20 parser.add_argument('--collection_type', type=str, required=True,
|
|
|
21 choices=COLLECTION_TYPES.keys(),
|
|
|
22 help='type of the collection')
|
|
|
23 parser.add_argument('--collection_label', type=str, required=True,
|
|
|
24 help='label of the collection')
|
|
|
25
|
|
|
26 return parser
|
|
|
27
|
|
|
28 def load_collection(coll_type, coll_label, kb):
|
|
|
29 query = 'SELECT coll FROM %s coll WHERE coll.label = :coll_label' % coll_type
|
|
|
30 coll = kb.find_all_by_query(query, {'coll_label' : coll_label})
|
|
|
31 return coll[0] if len(coll) > 0 else None
|
|
|
32
|
|
|
33 def load_collection_items(collection, coll_type, kb):
|
|
|
34 if COLLECTION_TYPES[coll_type] == 'VesselsCollectionItem':
|
|
|
35 citems = kb.get_vessels_collection_items(collection)
|
|
|
36 elif COLLECTION_TYPES[coll_type] == 'DataCollectionItem':
|
|
|
37 citems = kb.get_data_collection_items(collection)
|
|
|
38 else:
|
|
|
39 raise ValueError('Unknown data collection type %s' % COLLECTION_TYPES[coll_type])
|
|
|
40 ci_map = {}
|
|
|
41 for ci in citems:
|
|
|
42 ci_map[ci.id] = ci
|
|
|
43 return ci_map
|
|
|
44
|
|
|
45
|
|
|
46 def main(argv):
|
|
|
47 parser = make_parser()
|
|
|
48 args = parser.parse_args(argv)
|
|
|
49
|
|
|
50 logger = get_logger('discard_from_collection', level=args.loglevel,
|
|
|
51 filename=args.logfile)
|
|
|
52
|
|
|
53 try:
|
|
|
54 host = args.host or vlu.ome_host()
|
|
|
55 user = args.user or vlu.ome_user()
|
|
|
56 passwd = args.passwd or vlu.ome_passwd()
|
|
|
57 except ValueError, ve:
|
|
|
58 logger.critical(ve)
|
|
|
59 sys.exit(ve)
|
|
|
60
|
|
|
61 kb = KB(driver='omero')(host, user, passwd)
|
|
|
62 logger.info('Loading collection %s from %s' % (args.collection_label,
|
|
|
63 args.collection_type))
|
|
|
64 coll = load_collection(args.collection_type, args.collection_label, kb)
|
|
|
65 if not coll:
|
|
|
66 msg = 'No %s found with label %s' % (args.collection_type,
|
|
|
67 args.collection_label)
|
|
|
68 logger.error(msg)
|
|
|
69 sys.exit(msg)
|
|
|
70 logger.info('Loading items from collection')
|
|
|
71 coll_items = load_collection_items(coll, args.collection_type, kb)
|
|
|
72 logger.info('Fetched %d elements' % len(coll_items))
|
|
|
73
|
|
|
74 with open(args.ifile) as infile:
|
|
|
75 reader = csv.DictReader(infile, delimiter='\t')
|
|
|
76 to_be_deleted = [row['collection_item'] for row in reader]
|
|
|
77 logger.info('Found %d items to be deleted' % len(to_be_deleted))
|
|
|
78
|
|
|
79 for tbd in to_be_deleted:
|
|
|
80 try:
|
|
|
81 kb.delete(coll_items[tbd])
|
|
|
82 logger.info('%s with ID %s deleted' % (COLLECTION_TYPES[args.collection_type],
|
|
|
83 tbd))
|
|
|
84 except KeyError, ke:
|
|
|
85 logger.warning('No %s related to ID %s' % (COLLECTION_TYPES[args.collection_type],
|
|
|
86 ke))
|
|
|
87 logger.info('Job completed')
|
|
|
88
|
|
|
89
|
|
|
90 if __name__ == '__main__':
|
|
|
91 main(sys.argv[1:])
|
