Remove deprecated `gn3.db_utils.database_connector` function

Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.

Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils

2 files changed, 10 insertions, 9 deletions

diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
index c953d84..795c42d 100644
--- a/tests/integration/conftest.py
+++ b/tests/integration/conftest.py
@@ -4,7 +4,7 @@ import MySQLdb
 
 from gn3.app import create_app
 from gn3.chancy import random_string
-from gn3.db_utils import parse_db_url, database_connector
+from gn3.db_utils import parse_db_url, database_connection
 
 @pytest.fixture(scope="session")
 def client():
@@ -18,17 +18,18 @@ def client():
 
 
 @pytest.fixture(scope="session")
-def db_conn():
+def db_conn(client):
     """Create a db connection fixture for tests"""
     # 01) Generate random string to append to all test db artifacts for the session
+    live_db_uri = client.application.config["SQL_URI"]
     rand_str = random_string(15)
-    live_db_details = parse_db_url()
+    live_db_details = parse_db_url(live_db_uri)
     test_db_name = f"test_{live_db_details[3]}_{rand_str}"
     #
     # 02) Create new test db
     #     Use context manager to ensure the live connection is automatically
     #     closed on exit
-    with database_connector() as live_db_conn:
+    with database_connection(live_db_uri) as live_db_conn:
         with live_db_conn.cursor() as live_db_cursor:
             live_db_cursor.execute(f"CREATE DATABASE {test_db_name}")
             #
diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
index c1d518d..51769b5 100644
--- a/tests/integration/test_correlation.py
+++ b/tests/integration/test_correlation.py
@@ -65,15 +65,15 @@ class CorrelationIntegrationTest(TestCase):
 
     @pytest.mark.integration_test
     @mock.patch("gn3.api.correlation.compute_all_lit_correlation")
-    @mock.patch("gn3.api.correlation.database_connector")
-    def test_lit_correlation(self, database_connector, mock_compute_corr):
+    @mock.patch("gn3.api.correlation.database_connection")
+    def test_lit_correlation(self, database_connection, mock_compute_corr):
         """Test api/correlation/lit_corr/{species}/{gene_id}"""
 
         mock_compute_corr.return_value = []
 
-        database_connector.return_value = mock.Mock()
-        database_connector.return_value.__enter__ = mock.Mock()
-        database_connector.return_value.__exit__ = mock.Mock()
+        database_connection.return_value = mock.Mock()
+        database_connection.return_value.__enter__ = mock.Mock()
+        database_connection.return_value.__exit__ = mock.Mock()
 
         post_data = {"1426678_at": "68031",
                      "1426679_at": "68036",