Test partial corrs API with mix of existing and non-existing control traits

Test that the partial correlations endpoint handles a mix of existing and
non-existing control traits gracefully and issues a warning to the user.

Summary of changes:
* gn3/computations/partial_correlations.py: Issue a warning for all
  non-existing control traits
* gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables
  instead of comma-separated list of tables
* tests/integration/conftest.py: Add `db_conn` fixture to provide a database
  connection to the tests. This will probably be changed in the future to
  connect to a temporary database for tests.
* tests/integration/test_partial_correlations.py: Add test to check for
  correct behaviour with a mix of existing and non-existing control traits

1 files changed, 10 insertions, 0 deletions

diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
index be58d80..e1d1c37 100644
--- a/tests/integration/conftest.py
+++ b/tests/integration/conftest.py
@@ -1,12 +1,22 @@
+"""Module that holds fixtures for integration tests"""
 import pytest
 
 from gn3.app import create_app
+from gn3.db_utils import database_connector
 
 @pytest.fixture(scope="session")
 def client():
+    """Create a test client fixture for tests"""
     # Do some setup
     app = create_app()
     app.config.update({"TESTING": True})
     app.testing = True
     yield app.test_client()
     # Do some teardown/cleanup
+
+
+@pytest.fixture
+def db_conn():
+    """Create a db connection fixture for tests"""
+    ## Update this to use temp db once that is in place
+    return database_connector()[0]