From ae46efda7ec0e42997bec93a1ffacc29366d190b Mon Sep 17 00:00:00 2001
From: John Nduli
Date: Tue, 11 Jun 2024 09:24:42 +0300
Subject: fix: use current_app's logger to log db errors

---
 gn3/api/correlation.py | 2 +-
 gn3/api/heatmaps.py    | 2 +-
 gn3/api/menu.py        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index eb4cc7d..c77dd93 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -64,7 +64,7 @@ def compute_lit_corr(species=None, gene_id=None):
     might be needed for actual computing of the correlation results
     """
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(current_app.config["SQL_URI"], logger=current_app.logger) as conn:
         target_traits_gene_ids = request.get_json()
         target_trait_gene_list = list(target_traits_gene_ids.items())
 
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
index 632c54a..172d555 100644
--- a/gn3/api/heatmaps.py
+++ b/gn3/api/heatmaps.py
@@ -24,7 +24,7 @@ def clustered_heatmaps():
         return jsonify({
             "message": "You need to provide at least two trait names."
         }), 400
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(current_app.config["SQL_URI"], logger=current_app.logger) as conn:
         def parse_trait_fullname(trait):
             name_parts = trait.split(":")
             return f"{name_parts[1]}::{name_parts[0]}"
diff --git a/gn3/api/menu.py b/gn3/api/menu.py
index 58b761e..377ac6b 100644
--- a/gn3/api/menu.py
+++ b/gn3/api/menu.py
@@ -10,5 +10,5 @@ menu = Blueprint("menu", __name__)
 @menu.route("/generate/json")
 def generate_json():
     """Get the menu in the JSON format"""
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(current_app.config["SQL_URI"], logger=current_app.logger) as conn:
         return jsonify(gen_dropdown_json(conn))
-- 
cgit v1.2.3