diff options
Diffstat (limited to 'tests/integration')
| -rw-r--r-- | tests/integration/conftest.py | 4 | ||||
| -rw-r--r-- | tests/integration/test_correlation.py | 4 | ||||
| -rw-r--r-- | tests/integration/test_partial_correlations.py | 61 |
3 files changed, 40 insertions, 29 deletions
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index e1d1c37..be927a4 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -19,4 +19,6 @@ def client(): 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] + conn = database_connector() + yield conn + conn.close() diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py index cf63c17..d52ab01 100644 --- a/tests/integration/test_correlation.py +++ b/tests/integration/test_correlation.py @@ -71,7 +71,9 @@ class CorrelationIntegrationTest(TestCase): mock_compute_corr.return_value = [] - database_connector.return_value = (mock.Mock(), mock.Mock()) + database_connector.return_value = mock.Mock() + database_connector.return_value.__enter__ = mock.Mock() + database_connector.return_value.__exit__ = mock.Mock() post_data = {"1426678_at": "68031", "1426679_at": "68036", diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py index 7f9ff30..d249b42 100644 --- a/tests/integration/test_partial_correlations.py +++ b/tests/integration/test_partial_correlations.py @@ -1,4 +1,6 @@ """Test partial correlations""" +from unittest import mock + import pytest from gn3.computations.partial_correlations import partial_correlations_entry @@ -97,43 +99,46 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data): @pytest.mark.parametrize( "post_data", ({# ProbeSet - "primary_trait": {"dataset": "a_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Publish - "primary_trait": {"dataset": "a_Publish_dataset", "name": "a_name"}, + "primary_trait": { + "dataset": "a_Publish_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Geno - "primary_trait": {"dataset": "a_Geno_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_Geno_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Temp - "primary_trait": {"dataset": "a_Temp_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_Temp_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" })) -def test_partial_correlation_api_with_non_existent_primary_traits(client, post_data): +def test_partial_correlation_api_with_non_existent_primary_traits( + client, post_data, mocker): """ Check that the system responds appropriately in the case where the user makes a request with a non-existent primary trait. """ + mocker.patch("gn3.api.correlation.redis.Redis", mock.MagicMock()) response = client.post("/api/correlation/partial", json=post_data) assert ( - response.status_code == 404 and response.is_json and - response.json.get("status") != "error") + response.status_code == 200 and response.is_json and + response.json.get("status") == "success") @pytest.mark.integration_test @pytest.mark.slow @@ -141,41 +146,43 @@ def test_partial_correlation_api_with_non_existent_primary_traits(client, post_d "post_data", ({# ProbeSet "primary_trait": { - "dataset": "UCLA_BXDBXH_CARTILAGE_V2", "name": "ILM103710672"}, + "dataset": "UCLA_BXDBXH_CARTILAGE_V2", + "trait_name": "ILM103710672"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Publish - "primary_trait": {"dataset": "BXDPublish", "name": "BXD_12557"}, + "primary_trait": {"dataset": "BXDPublish", "trait_name": "BXD_12557"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Geno - "primary_trait": {"dataset": "AKXDGeno", "name": "D4Mit16"}, + "primary_trait": {"dataset": "AKXDGeno", "trait_name": "D4Mit16"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" } # Temp -- the data in the database for these is ephemeral, making it # difficult to test for this )) -def test_partial_correlation_api_with_non_existent_control_traits(client, post_data): +def test_partial_correlation_api_with_non_existent_control_traits(client, post_data, mocker): """ Check that the system responds appropriately in the case where the user makes a request with a non-existent control traits. The code repetition here is on purpose - valuing clarity over succinctness. """ + mocker.patch("gn3.api.correlation.redis.Redis", mock.MagicMock()) response = client.post("/api/correlation/partial", json=post_data) assert ( - response.status_code == 404 and response.is_json and - response.json.get("status") != "error") + response.status_code == 200 and response.is_json and + response.json.get("status") == "success") @pytest.mark.integration_test @pytest.mark.slow |