Merge branch 'develop' into GEN_1067_warn_for_unchanged_mutations

Sage-Bionetworks · Mar 14, 2024 · b636835 · b636835
2 parents 672a695 + 9c10710
commit b636835
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/genie/extract.py b/genie/extract.py
@@ -4,6 +4,7 @@
 """
 
 import logging
+import sys
 from typing import List, Optional
 
 import synapseclient
@@ -13,6 +14,9 @@
 from genie import process_functions
 
 logger = logging.getLogger(__name__)
+stdout_handler = logging.StreamHandler(stream=sys.stdout)
+stdout_handler.setLevel(logging.INFO)
+logger.addHandler(stdout_handler)
 
 
 def get_center_input_files(
@@ -54,6 +58,7 @@ def get_center_input_files(
             if name.endswith(".vcf") and process != "mutation":
                 continue
 
+            logger.info(f"GETTING FILE {name} ({ent_synid})")
             ent = syn.get(ent_synid, downloadFile=downloadFile)
 
             # HACK: Clinical file can come as two files.