From 7f66bb029322a06b52359abf8836e158afaa6755 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 20 Jun 2022 11:17:11 +0300
Subject: Restrict partial correlation method choices

- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
  partial correlations
---
 gn3/commands.py                 | 2 +-
 scripts/partial_correlations.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/gn3/commands.py b/gn3/commands.py
index 41418b0..0a74b7d 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -69,7 +69,7 @@ def compose_pcorrs_command(
     """Compose the command to run partias correlations"""
     prefix_cmd = (
         f"{sys.executable}", "-m", "scripts.partial_correlations",
-        primary_trait, ",".join(control_traits), f'"{method}"')
+        primary_trait, ",".join(control_traits), method)
     if (
             kwargs.get("target_database") is not None
             and kwargs.get("target_traits") is None):
diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py
index de364dc..d28a17a 100644
--- a/scripts/partial_correlations.py
+++ b/scripts/partial_correlations.py
@@ -106,7 +106,8 @@ def process_cli_arguments():
     parser.add_argument(
         "method",
         help="The correlation method to use",
-        type=str)
+        type=str,
+        choices=("Pearson's r", "Spearman's rho"))
     against_db_parser(against_traits_parser(
         parser.add_subparsers(
             title="subcommands",
-- 
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