From 083350466aa6cfdc5d20597f2c77c2b4f1b307b3 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Tue, 5 Mar 2024 22:23:49 -0800
Subject: [PATCH 1/5] add logging for getting files

---
 genie/extract.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/genie/extract.py b/genie/extract.py
index 763fcfcd..85e277df 100644
--- a/genie/extract.py
+++ b/genie/extract.py
@@ -54,6 +54,7 @@ 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.

From 7945ca68a75ec48cc6bd771cd1d8eed06318ecfd Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Tue, 5 Mar 2024 22:58:41 -0800
Subject: [PATCH 2/5] explicitly set logging at INFO level

---
 genie/extract.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/genie/extract.py b/genie/extract.py
index 85e277df..51ddfbbd 100644
--- a/genie/extract.py
+++ b/genie/extract.py
@@ -12,6 +12,7 @@
 
 from genie import process_functions
 
+logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 

From 0f5952d253f5f32b114ff35938ee0c9e5b7630f0 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Wed, 6 Mar 2024 01:45:32 -0800
Subject: [PATCH 3/5] add stream for logger

---
 genie/extract.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/genie/extract.py b/genie/extract.py
index 51ddfbbd..7eb1e24e 100644
--- a/genie/extract.py
+++ b/genie/extract.py
@@ -4,6 +4,7 @@
 """
 
 import logging
+import sys
 from typing import List, Optional
 
 import synapseclient
@@ -12,7 +13,7 @@
 
 from genie import process_functions
 
-logging.basicConfig(level=logging.INFO)
+logging.basicConfig(level=logging.INFO, stream=sys.stdout)
 logger = logging.getLogger(__name__)
 
 

From 32a1dac5b3b77a4f0695c30cf30f9e1b72a31da7 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Fri, 8 Mar 2024 12:55:07 -0800
Subject: [PATCH 4/5] add stream handler to write to stdout

---
 genie/extract.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/genie/extract.py b/genie/extract.py
index 7eb1e24e..1086a94c 100644
--- a/genie/extract.py
+++ b/genie/extract.py
@@ -13,8 +13,10 @@
 
 from genie import process_functions
 
-logging.basicConfig(level=logging.INFO, stream=sys.stdout)
 logger = logging.getLogger(__name__)
+stdout_handler = logging.StreamHandler(sys.stdout)
+stdout_handler.setLevel(logging.INFO)
+logger.addHandler(stdout_handler)
 
 
 def get_center_input_files(

From 39b381ff3a263efdf211feec2a47fa2344379169 Mon Sep 17 00:00:00 2001
From: rxu17 <26471741+rxu17@users.noreply.github.com>
Date: Fri, 8 Mar 2024 13:22:44 -0800
Subject: [PATCH 5/5] add note

---
 genie/extract.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/genie/extract.py b/genie/extract.py
index 1086a94c..7ea84225 100644
--- a/genie/extract.py
+++ b/genie/extract.py
@@ -14,7 +14,7 @@
 from genie import process_functions
 
 logger = logging.getLogger(__name__)
-stdout_handler = logging.StreamHandler(sys.stdout)
+stdout_handler = logging.StreamHandler(stream=sys.stdout)
 stdout_handler.setLevel(logging.INFO)
 logger.addHandler(stdout_handler)