From 058f6592d8815a64544f6721a9984b89ea92522a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 19 Feb 2022 03:21:27 +0300
Subject: 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.
---
 gn3/computations/partial_correlations.py | 11 ++++++++---
 gn3/db/partial_correlations.py           |  3 ++-
 2 files changed, 10 insertions(+), 4 deletions(-)

(limited to 'gn3')

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())
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