Test partial corrs endpoint with non-existing control traits

Test that if the endpoint is queried and not a single one of the control
traits exists in the database, then the endpoint will respond with a
404 (not-found) status code.

Summary of changes:
* gn3/computations/partial_correlations.py: Check whether any control trait is
  found. If none is found, return "not-found" message.
* gn3/db/partial_correlations.py: Fix bug in Geno query.
* tests/integration/test_partial_correlations.py: Add test for non-existing
  control traits. Rename function to make it clearer what it is testing
  for. Remove obsoleted comments.

3 files changed, 54 insertions, 9 deletions

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 16cbbdb..1cc969c 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -621,14 +621,19 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
             "status": "not-found",
             "message": f"Could not find primary trait {primary_trait['trait_fullname']}"
         }
+    cntrl_traits = tuple(
+        trait for trait in all_traits
+        if trait["trait_fullname"] != primary_trait_name)
+    if not any(trait["haveinfo"] for trait in cntrl_traits):
+        return {
+            "status": "not-found",
+            "message": "None of the requested control traits were found."}
+
     group = primary_trait["db"]["group"]
     primary_trait_data = all_traits_data[primary_trait["trait_name"]]
     primary_samples, primary_values, _primary_variances = export_informative(
         primary_trait_data)
 
-    cntrl_traits = tuple(
-        trait for trait in all_traits
-        if trait["trait_fullname"] != primary_trait_name)
     cntrl_traits_data = tuple(
         data for trait_name, data in all_traits_data.items()
         if trait_name != primary_trait["trait_name"])
diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py
index caf8d35..0931f09 100644
--- a/gn3/db/partial_correlations.py
+++ b/gn3/db/partial_correlations.py
@@ -197,13 +197,14 @@ def geno_traits_data(conn, traits):
         "AND GenoXRef.DataId = GenoData.Id "
         "AND GenoData.StrainId = Strain.Id "
         "ORDER BY Strain.Name").format(
-            species_ids=sp_ids,
+            species_ids=", ".join(["%s"] * len(sp_ids)),
             trait_names=", ".join(["%s"] * len(traits)),
             dataset_names=", ".join(["%s"] * len(dataset_names)))
     if len(sp_ids) > 0 and len(dataset_names) > 0:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute(
                 query,
+                sp_ids +
                 tuple(trait["trait_name"] for trait in traits) +
                 tuple(dataset_names))
             return organise_trait_data_by_trait(cursor.fetchall())
diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py
index 17ea539..ff6d771 100644
--- a/tests/integration/test_partial_correlations.py
+++ b/tests/integration/test_partial_correlations.py
@@ -92,7 +92,6 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
         response.status_code == 400 and response.is_json and
         response.json.get("status") == "error")
 
-
 @pytest.mark.integration_test
 @pytest.mark.slow
 @pytest.mark.parametrize(
@@ -118,9 +117,7 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
             {"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
+    }, {# Temp
         "primary_trait": {"dataset": "a_Temp_dataset", "name": "a_name"},
         "control_traits": [
             {"dataset": "a_dataset", "name": "a_name"},
@@ -128,7 +125,7 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
         "method": "a_method",
         "target_db": "a_db"
     }))
-def test_partial_correlation_api_with_non_existent_traits(client, post_data):
+def test_partial_correlation_api_with_non_existent_primary_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.
@@ -137,3 +134,45 @@ def test_partial_correlation_api_with_non_existent_traits(client, post_data):
     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(
+    "post_data",
+    ({# ProbeSet
+        "primary_trait": {
+            "dataset": "UCLA_BXDBXH_CARTILAGE_V2", "name": "ILM103710672"},
+        "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": "BXDPublish", "name": "BXD_12557"},
+        "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": "AKXDGeno", "name": "D4Mit16"},
+        "control_traits": [
+            {"dataset": "a_dataset", "name": "a_name"},
+            {"dataset": "a_dataset2", "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):
+    """
+    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.
+    """
+    response = client.post("/api/correlation/partial", json=post_data)
+    assert (
+        response.status_code == 404 and response.is_json and
+        response.json.get("status") != "error")