From 83a7aa7533f8f4ecac049dc0e93aff6429e6e5ae Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 18 Feb 2022 07:17:50 +0300
Subject: 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.
---
 gn3/computations/partial_correlations.py | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'gn3/computations')

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 85e3c11..16cbbdb 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -616,6 +616,11 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
     primary_trait = tuple(
         trait for trait in all_traits
         if trait["trait_fullname"] == primary_trait_name)[0]
+    if not primary_trait["haveinfo"]:
+        return {
+            "status": "not-found",
+            "message": f"Could not find primary trait {primary_trait['trait_fullname']}"
+        }
     group = primary_trait["db"]["group"]
     primary_trait_data = all_traits_data[primary_trait["trait_name"]]
     primary_samples, primary_values, _primary_variances = export_informative(
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