From 9c107104454e06c7bd3327a7205a5671a4ef9c84 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Wed, 13 Mar 2024 10:00:14 -0700
Subject: [PATCH] [GEN-1191] Add file logging (#552)

* add logging for getting files

* explicitly set logging at INFO level

* add stream for logger

* add stream handler to write to stdout

* add note
---
 genie/extract.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/genie/extract.py b/genie/extract.py
index 763fcfcd..7ea84225 100644
--- 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.