changeset 9:8a882207b3bf draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/updater/discard_from_collection.py	Mon Sep 26 09:26:34 2016 -0400
@@ -0,0 +1,91 @@
+import csv, argparse, sys, os
+
+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
+
+COLLECTION_TYPES = {'VesselsCollection' : 'VesselsCollectionItem',
+                    'DataCollection'    : 'DataCollectionItem'}
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='remove elements from a Vessels or Data Collection')
+    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
+    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
+                        help='logger level', 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('-I', '--ifile', type=str, required=True,
+                        help='list of collection items that will be removed')
+    parser.add_argument('--collection_type', type=str, required=True,
+                        choices=COLLECTION_TYPES.keys(),
+                        help='type of the collection')
+    parser.add_argument('--collection_label', type=str, required=True,
+                        help='label of the collection')
+
+    return parser
+
+def load_collection(coll_type, coll_label, kb):
+    query = 'SELECT coll FROM %s coll WHERE coll.label = :coll_label' % coll_type
+    coll = kb.find_all_by_query(query, {'coll_label' : coll_label})
+    return coll[0] if len(coll) > 0 else None
+
+def load_collection_items(collection, coll_type, kb):
+    if COLLECTION_TYPES[coll_type] == 'VesselsCollectionItem':
+        citems = kb.get_vessels_collection_items(collection)
+    elif COLLECTION_TYPES[coll_type] == 'DataCollectionItem':
+        citems =  kb.get_data_collection_items(collection)
+    else:
+        raise ValueError('Unknown data collection type %s' % COLLECTION_TYPES[coll_type])
+    ci_map = {}
+    for ci in citems:
+        ci_map[ci.id] = ci
+    return ci_map
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('discard_from_collection', 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('Loading collection %s from %s' % (args.collection_label,
+                                                    args.collection_type))
+    coll = load_collection(args.collection_type, args.collection_label, kb)
+    if not coll:
+        msg = 'No %s found with label %s' % (args.collection_type,
+                                             args.collection_label)
+        logger.error(msg)
+        sys.exit(msg)
+    logger.info('Loading items from collection')
+    coll_items = load_collection_items(coll, args.collection_type, kb)
+    logger.info('Fetched %d elements' % len(coll_items))
+
+    with open(args.ifile) as infile:
+        reader = csv.DictReader(infile, delimiter='\t')
+        to_be_deleted = [row['collection_item'] for row in reader]
+    logger.info('Found %d items to be deleted' % len(to_be_deleted))
+
+    for tbd in to_be_deleted:
+        try:
+            kb.delete(coll_items[tbd])
+            logger.info('%s with ID %s deleted' % (COLLECTION_TYPES[args.collection_type],
+                                                   tbd))
+        except KeyError, ke:
+            logger.warning('No %s related to ID %s' % (COLLECTION_TYPES[args.collection_type],
+                                                       ke))
+    logger.info('Job completed')
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])