From f914dc21577253f293b50b890ea0ac4bd2fd5d1b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 21 Feb 2022 09:07:31 +0300
Subject: Test partial corrs API with mix of existing and non-existing control
 traits

Test that the partial correlations endpoint handles a mix of existing and
non-existing control traits gracefully and issues a warning to the user.

Summary of changes:
* gn3/computations/partial_correlations.py: Issue a warning for all
  non-existing control traits
* gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables
  instead of comma-separated list of tables
* tests/integration/conftest.py: Add `db_conn` fixture to provide a database
  connection to the tests. This will probably be changed in the future to
  connect to a temporary database for tests.
* tests/integration/test_partial_correlations.py: Add test to check for
  correct behaviour with a mix of existing and non-existing control traits
---
 gn3/computations/partial_correlations.py | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'gn3/computations')

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 1cc969c..3633a59 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -628,6 +628,12 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
         return {
             "status": "not-found",
             "message": "None of the requested control traits were found."}
+    for trait in cntrl_traits:
+        if trait["haveinfo"] == False:
+            warnings.warn(
+                (f"Control traits {trait['trait_fullname']} was not found "
+                 "- continuing without it."),
+                category=UserWarning)
 
     group = primary_trait["db"]["group"]
     primary_trait_data = all_traits_data[primary_trait["trait_name"]]
-- 
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