From 6e86be5910d01b8d682e217c0e53e49cf709a237 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 27 Sep 2024 16:20:18 -0500
Subject: Bug: Use absolute paths in place of relative paths.

Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
---
 gn3/computations/ctl.py   | 2 +-
 gn3/computations/wgcna.py | 9 ++++++---
 2 files changed, 7 insertions(+), 4 deletions(-)

(limited to 'gn3')

diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py
index eb34656..f881410 100644
--- a/gn3/computations/ctl.py
+++ b/gn3/computations/ctl.py
@@ -13,7 +13,7 @@ def call_ctl_script(data):
     """function to call ctl script"""
     data["imgDir"] = TMPDIR
     temp_file_name = dump_wgcna_data(data)
-    cmd = compose_wgcna_cmd("scripts/ctl_analysis.R", temp_file_name)
+    cmd = compose_wgcna_cmd("ctl_analysis.R", temp_file_name)
 
     cmd_results = run_cmd(cmd)
     with open(temp_file_name, "r", encoding="utf-8") as outputfile:
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index a86c9ab..d1f7b32 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -1,10 +1,10 @@
 """module contains code to preprocess and call wgcna script"""
-
 import os
 import json
 import uuid
-import subprocess
 import base64
+import subprocess
+from pathlib import Path
 
 
 from gn3.settings import TMPDIR
@@ -58,7 +58,10 @@ def process_image(image_loc: str) -> bytes:
 def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     """function to componse wgcna cmd"""
     # (todo):issue relative paths to abs paths
-    cmd = f"Rscript scripts/{rscript_path} {temp_file_path}"
+    abs_rscript_path = str(
+        Path(__file__).absolute().parent.parent.parent.joinpath(
+            f"scripts/{rscript_path}"))
+    cmd = f"Rscript {abs_rscript_path} {temp_file_path}"
     return cmd
 
 
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