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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/get_studies_details.py	Wed Sep 28 06:03:30 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 studies 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 studies details')
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('get_studies', 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 studies')
+    studies = kb.get_objects(kb.Study)
+    logger.info('Retrieved {} studies'.format(len(studies)))
+    records = []
+    for s in studies:
+        enr = kb.get_enrolled(s)
+        rec = {'label': s.label,
+               'description': s.description,
+               'enrolled': len(enr)}
+        records.append(rec)
+          
+    with open(args.out_file, 'w') as outfile:
+        writer = csv.DictWriter(outfile, ['label', 'description', 'enrolled'],
+                                delimiter='\t')
+        # writer.writeheader()
+        writer.writerows(sorted(records, key=lambda key: key['label']))
+
+if __name__ == '__main__':
+    main(sys.argv[1:])