xena_dataset.py: Add logging functionality

ucscXena · Jun 17, 2019 · d95d4e4 · d95d4e4
1 parent ca957be
commit d95d4e4
Show file tree

Hide file tree

Showing 2 changed files with 59 additions and 53 deletions.
diff --git a/xena_gdc_etl/gdc2xena.py b/xena_gdc_etl/gdc2xena.py
@@ -59,9 +59,9 @@ def gdc2xena(root_dir, projects, xena_dtypes):
     counts = 0
     unfinished = {}
     total_projects = len(projects)
-    log_format = '%(asctime)-15s [%(levelname)s]: %(message)s'
+    log_format = '%(asctime)-15s %(name)s [%(levelname)s]: %(message)s'
     logging.basicConfig(
-        level=logging.WARNING,
+        level=logging.INFO,
         format=log_format,
         datefmt='%Y-%m-%d %H:%M:%S',
         filename=os.path.join(
@@ -100,9 +100,9 @@ def gdc2xena(root_dir, projects, xena_dtypes):
                     json.dump(unfinished, outfile)
                 msg = 'No {} data for cohort {}.'.format(dtype, project)
                 logger.warning(msg, exc_info=True)
-                print(msg)
+                logging.info(msg)
     logging.shutdown()
     end_time = timeit.default_timer()
     m, s = divmod(int(end_time - start_time), 60)
     h, m = divmod(m, 60)
-    print('Finish in {:d}:{:02d}:{:02d}.'.format(h, m, s))
+    logging.info('Finish in {:d}:{:02d}:{:02d}.'.format(h, m, s))