Update calls to `database_connection` function

Pass in the database URI at call time.

2 files changed, 4 insertions, 3 deletions

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 7d80b3fb..5d00d600 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -9,7 +9,7 @@ from utility.redis_tools import (get_redis_conn,
                                  get_resource_info,
                                  get_resource_id,
                                  add_resource)
-from utility.tools import GN_PROXY_URL
+from utility.tools import get_setting, GN_PROXY_URL
 
 Redis = get_redis_conn()
 
@@ -82,7 +82,7 @@ def add_new_resource(dataset, trait_id=None):
 
 
 def get_group_code(dataset):
-    with database_connection() as conn, conn.cursor() as cursor:
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
         cursor.execute(
             "SELECT InbredSetCode FROM InbredSet WHERE Name=%s",
             (dataset.group.name,)
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 0c0794dc..8b20bd74 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -3,6 +3,7 @@ from base.trait import create_trait
 from base.species import TheSpecies
 
 from utility import hmac
+from utility.tools import get_setting
 
 from wqflask.database import database_connection
 
@@ -51,7 +52,7 @@ def get_species_groups():
     """Group each species into a group"""
     _menu = {}
     species, group_name = None, None
-    with database_connection() as conn, conn.cursor() as cursor:
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
         cursor.execute(
             "SELECT s.MenuName, i.InbredSetName FROM InbredSet i "
             "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId "