From 36f8421a8fe223189ab88ee1df3923719ffa4fc0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 24 May 2022 04:46:57 +0300
Subject: New script to compute partial correlations

* Add a new script to compute the partial correlations against:
  - a select list of traits, or
  - an entire dataset
  depending on the specified subcommand. This new script is meant to supercede
  the `scripts/partial_correlations.py` script.

* Fix the check for errors
* Reorganise the order of arguments for the
  `partial_correlations_with_target_traits` function: move the `method`
  argument before the `target_trait_names` argument so that the common
  arguments in the partial correlation computation functions share the same
  order.
---
 gn3/api/correlation.py                   | 4 ++--
 gn3/computations/partial_correlations.py | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

(limited to 'gn3')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 5f2d486..3aadcb9 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -148,8 +148,8 @@ def partial_correlation():
             trait_fullname(args["primary_trait"]),
             tuple(
                 trait_fullname(trait) for trait in args["control_traits"]),
+            args["method"],
             tuple(
-                trait_fullname(trait) for trait in args["target_traits"]),
-            args["method"])
+                trait_fullname(trait) for trait in args["target_traits"]))
 
     return build_response({"status": "success", "results": results})
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 530dd71..f316f67 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -681,7 +681,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
 
     check_res = check_for_common_errors(
         conn, primary_trait_name, control_trait_names, threshold)
-    if check_res.get("status") == "error":
+    if check_res.get("status") != "success":
         return check_res
 
     primary_trait = check_res["primary_trait"]
@@ -819,15 +819,15 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
 
 def partial_correlations_with_target_traits(
         conn: Any, primary_trait_name: str,
-        control_trait_names: Tuple[str, ...],
-        target_trait_names: Tuple[str, ...], method: str) -> dict:
+        control_trait_names: Tuple[str, ...], method: str,
+        target_trait_names: Tuple[str, ...]) -> dict:
     """
     Compute partial correlation against a specific selection of traits.
     """
     threshold = 0
     check_res = check_for_common_errors(
         conn, primary_trait_name, control_trait_names, threshold)
-    if check_res.get("status") == "error":
+    if check_res.get("status") != "success":
         return check_res
 
     target_traits = {
-- 
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