From 11d543eeca08fe0df4bf2be7222234fadb516a51 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 27 Sep 2024 14:31:50 -0500
Subject: Bug: Use absolute path in place of relative path

Prior to this commit, an assumption is made that the application is
invoked with the root of the repository being the current working
directory. If this assumption is not met, then the system will not
find the appropriate path.

This commit forces the use of an absolute path, which should help
avoid issues with misplaced relative paths.
---
 gn3/api/rqtl.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index c2d988a..e029d8d 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -1,5 +1,6 @@
 """Endpoints for running the rqtl cmd"""
 import os
+from pathlib import Path
 
 from flask import Blueprint
 from flask import current_app
@@ -42,7 +43,9 @@ run the rqtl_wrapper script and return the results as JSON
         os.mkdir(outdir)
 
     rqtl_cmd = generate_rqtl_cmd(
-        rqtl_wrapper_cmd='scripts/rqtl_wrapper.R',
+        rqtl_wrapper_cmd=str(
+            Path(__file__).absolute().parent.parent.parent.joinpath(
+                'scripts/rqtl_wrapper.R')),
         rqtl_wrapper_kwargs=rqtl_kwargs,
         rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
     )
-- 
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