diff galaxy-tools/biobank/tools/get_titerplates_details.py @ 3:43be74e62bfe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/get_titerplates_details.py	Thu Sep 22 08:57:04 2016 -0400
@@ -0,0 +1,59 @@
+'''
+'''
+
+import argparse, csv, sys
+
+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='retrieve titerplates details')
+    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 passwd')
+    parser.add_argument('--out_file', type=str, required=True,
+                        help='output file with titerplates details')
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('get_titerplates', 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 titerplates')
+    titps = kb.get_objects(kb.TiterPlate)
+    logger.info('Retrieved {} titerplates'.format(len(titps)))
+    records = []
+    for tp in titps:
+        if type(tp) == kb.TiterPlate:
+            rec = {'label': tp.label,
+                   'barcode': tp.barcode,
+                   'status': tp.status.enum_label()}
+            records.append(rec)
+  
+    with open(args.out_file, 'w') as outfile:
+        writer = csv.DictWriter(outfile, ['label', 'barcode', 'status'],
+                                delimiter='\t')
+        writer.writeheader()
+        writer.writerows(sorted(records, key=lambda key: key['label']))
+
+if __name__ == '__main__':
+    main(sys.argv[1:])