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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/exporter/export_titer_plates.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,67 @@
+import logging, csv, argparse, sys, os
+
+from bl.vl.kb import KnowledgeBase as KB
+import bl.vl.kb.drivers.omero.utils as vlu
+
+LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
+LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
+LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+
+CSV_FIELDS = ['label', 'barcode', 'rows', 'columns', 'plate_status']
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='dump all TiterPlate objects to a TSV file')
+    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')
+    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('--ofile', type=str, help='output file',
+                        required=True)
+    return parser
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    log_level = getattr(logging, args.loglevel)
+    kwargs = {'format' : LOG_FORMAT,
+              'datefmt' : LOG_DATEFMT,
+              'level' : log_level}
+    if args.logfile:
+        kwargs['filename'] = args.logfile
+    logging.basicConfig(**kwargs)
+    logger = logging.getLogger()
+
+    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)
+    logging.info('Loading TiterPlate objects')
+    plates = kb.get_objects(kb.TiterPlate)
+    logging.info('Loaded %d objects' % len(plates))
+
+    with open(args.ofile, 'w') as ofile:
+        writer = csv.DictWriter(ofile, CSV_FIELDS, delimiter='\t')
+        writer.writeheader()
+        for pl in plates:
+            logger.debug('Dumping plate %d/%d' % (plates.index(pl) + 1, 
+                                                  len(plates)))
+            writer.writerow({'label' : pl.label,
+                             'barcode' : pl.barcode,
+                             'rows' : pl.rows,
+                             'columns' : pl.columns,
+                             'plate_status' : pl.status.enum_label()})
+    logger.info('Job done')
+                            
+                             
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])