diff options
Diffstat (limited to 'tests/integration')
| -rw-r--r-- | tests/integration/conftest.py | 10 | ||||
| -rw-r--r-- | tests/integration/test_partial_correlations.py | 41 |
2 files changed, 50 insertions, 1 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] diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py index ff6d771..7f9ff30 100644 --- a/tests/integration/test_partial_correlations.py +++ b/tests/integration/test_partial_correlations.py @@ -1,7 +1,7 @@ """Test partial correlations""" import pytest -from tests.integration.conftest import client +from gn3.computations.partial_correlations import partial_correlations_entry @pytest.mark.integration_test @pytest.mark.parametrize( @@ -176,3 +176,42 @@ def test_partial_correlation_api_with_non_existent_control_traits(client, post_d assert ( response.status_code == 404 and response.is_json and response.json.get("status") != "error") + +@pytest.mark.integration_test +@pytest.mark.slow +@pytest.mark.parametrize( + "primary,controls,method,target", ( + (# Probeset + "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672", ( + "UCLA_BXDBXH_CARTILAGE_V2::nonExisting01", + "UCLA_BXDBXH_CARTILAGE_V2::nonExisting02", + "UCLA_BXDBXH_CARTILAGE_V2::ILM380019"), + "Genetic Correlation, Pearson's r", "BXDPublish"), + (# Publish + "BXDPublish::17937", ( + "BXDPublish::17940", + "BXDPublish::nonExisting03"), + "Genetic Correlation, Spearman's rho", "BXDPublish"), + (# Geno + "AKXDGeno::D4Mit16", ( + "AKXDGeno::D1Mit170", + "AKXDGeno::nonExisting04", + "AKXDGeno::D1Mit135", + "AKXDGeno::nonExisting05", + "AKXDGeno::nonExisting06"), + "SGO Literature Correlation", "BXDPublish") + ) + # Temp -- the data in the database for these is ephemeral, making it + # difficult to test for these without a temp database with the temp + # traits data set to something we are in control of + ) +def test_part_corr_api_with_mix_of_existing_and_non_existing_control_traits( + db_conn, primary, controls, method, target): + """ + Check that calling the function with a mix of existing and missing control + traits raises an warning. + """ + criteria = 10 + with pytest.warns(UserWarning): + partial_correlations_entry( + db_conn, primary, controls, method, criteria, target) |