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authorFrederick Muriuki Muriithi2023-04-06 12:31:05 +0300
committerFrederick Muriuki Muriithi2023-04-06 12:31:05 +0300
commit17abad9300e4a96a14f94da486ef8307f7d27e06 (patch)
tree38fe3bfd36be9a821adfc67b83fbbd587ceb8b5e /tests/integration
parent3d873435f0d464864d4d691d6be4db40931fac05 (diff)
downloadgenenetwork3-17abad9300e4a96a14f94da486ef8307f7d27e06.tar.gz
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
Diffstat (limited to 'tests/integration')
-rw-r--r--tests/integration/conftest.py9
-rw-r--r--tests/integration/test_correlation.py10
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",