From 8a84c4d6762446e5fdf9f9121f539c89419ae6a0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 22 Nov 2024 12:16:28 -0600
Subject: Use gn-libs code for db connection.

Use the code in gn-libs to connect to the database, rather than a
local module.
---
 uploader/genotypes/models.py | 7 ++++---
 uploader/genotypes/views.py  | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'uploader/genotypes')

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 44c98b1..4c3e634 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -4,8 +4,9 @@ from datetime import datetime
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
+from flask import current_app as app
 
-from uploader.db_utils import debug_query
+from gn_libs.mysqldb import debug_query
 
 def genocode_by_population(
         conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
@@ -38,7 +39,7 @@ def genotype_markers(
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, (species_id,))
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall())
 
 
@@ -64,7 +65,7 @@ def genotype_dataset(
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, _params)
-        debug_query(cursor)
+        debug_query(cursor, app.logger)
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py
index 0821eca..e6b1ba7 100644
--- a/uploader/genotypes/views.py
+++ b/uploader/genotypes/views.py
@@ -1,5 +1,6 @@
 """Views for the genotypes."""
 from MySQLdb.cursors import DictCursor
+from gn_libs.mysqldb import database_connection
 from flask import (flash,
                    request,
                    url_for,
@@ -11,7 +12,6 @@ from flask import (flash,
 from uploader.ui import make_template_renderer
 from uploader.oauth2.client import oauth2_post
 from uploader.authorisation import require_login
-from uploader.db_utils import database_connection
 from uploader.species.models import all_species, species_by_id
 from uploader.monadic_requests import make_either_error_handler
 from uploader.request_checks import with_species, with_population
-- 
cgit v1.2.3