Test partial correlations endpoint with non-existent primary traits

Test that the partial correlations endpoint responds with an appropriate
"not-found" message and the corresponding 404 status code in the case where a
request is made and the primary trait requested for does not exist in the
database.

Summary of the changes in each file:
* gn3/api/correlation.py: generalise the building of the response
* gn3/computations/partial_correlations.py: return with a "not-found" if the
  primary trait does not exist in the database
* gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions
  in the case that the primary trait did not exist
* pytest.ini: register a `slow` pytest marker
* tests/integration/test_partial_correlations.py: Add a new test to check for
  an appropriate 404 response in case of a primary trait that does not exist
  in the database.

1 files changed, 50 insertions, 1 deletions

diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py
index 5b520e0..17ea539 100644
--- a/tests/integration/test_partial_correlations.py
+++ b/tests/integration/test_partial_correlations.py
@@ -83,8 +83,57 @@ from tests.integration.conftest import client
             "target_db": None
         }))
 def test_partial_correlation_api_with_missing_request_data(client, post_data):
-    "Test /api/correlations/partial"
+    """
+    Test /api/correlations/partial endpoint with various expected request data
+    missing.
+    """
     response = client.post("/api/correlation/partial", json=post_data)
     assert (
         response.status_code == 400 and response.is_json and
         response.json.get("status") == "error")
+
+
+@pytest.mark.integration_test
+@pytest.mark.slow
+@pytest.mark.parametrize(
+    "post_data",
+    ({# ProbeSet
+        "primary_trait": {"dataset": "a_dataset", "name": "a_name"},
+        "control_traits": [
+            {"dataset": "a_dataset", "name": "a_name"},
+            {"dataset": "a_dataset2", "name": "a_name2"}],
+        "method": "a_method",
+        "target_db": "a_db"
+    }, {# Publish
+        "primary_trait": {"dataset": "a_Publish_dataset", "name": "a_name"},
+        "control_traits": [
+            {"dataset": "a_dataset", "name": "a_name"},
+            {"dataset": "a_dataset2", "name": "a_name2"}],
+        "method": "a_method",
+        "target_db": "a_db"
+    }, {# Geno
+        "primary_trait": {"dataset": "a_Geno_dataset", "name": "a_name"},
+        "control_traits": [
+            {"dataset": "a_dataset", "name": "a_name"},
+            {"dataset": "a_dataset2", "name": "a_name2"}],
+        "method": "a_method",
+        "target_db": "a_db"
+    }, {# Temp -- Fails due to missing table. Remove this sample if it is
+        # confirmed that the deletion of the database table is on purpose, and
+        # that Temp traits are no longer a thing
+        "primary_trait": {"dataset": "a_Temp_dataset", "name": "a_name"},
+        "control_traits": [
+            {"dataset": "a_dataset", "name": "a_name"},
+            {"dataset": "a_dataset2", "name": "a_name2"}],
+        "method": "a_method",
+        "target_db": "a_db"
+    }))
+def test_partial_correlation_api_with_non_existent_traits(client, post_data):
+    """
+    Check that the system responds appropriately in the case where the user
+    makes a request with a non-existent primary trait.
+    """
+    response = client.post("/api/correlation/partial", json=post_data)
+    assert (
+        response.status_code == 404 and response.is_json and
+        response.json.get("status") != "error")