From 05013c13710eccadb69746bf186eb672c2af69c4 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 22 Oct 2025 13:27:54 -0500
Subject: Fetch configs from app setting and pass them down

Fix the code to avoid using global variables holding configuration
variables to avoid the failures caused by action-at-a-distance effects
due to change of a value elsewhere.

This way, all code consistently receives the same configuration values
passed on from callers.

We pass on the following configuration settings:
* TMPDIR
* SQL_URI
* TEXTDIR
---
 gn3/api/correlation.py | 6 ++++--
 gn3/api/ctl.py         | 5 +++--
 gn3/api/wgcna.py       | 4 +++-
 3 files changed, 10 insertions(+), 5 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 6af96d7..3667a24 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -9,7 +9,6 @@ from flask import Blueprint
 from flask import request
 from flask import current_app
 
-from gn3.settings import SQL_URI
 from gn3.db_utils import database_connection
 from gn3.commands import run_sample_corr_cmd
 from gn3.responses.pcorrs_responses import build_response
@@ -144,7 +143,10 @@ def partial_correlation():
             cmd=command,
             job_queue=compute_job_queue(current_app),
             options={
-                "env": {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI},
+                "env": {
+                    "PYTHONPATH": ":".join(sys.path),
+                    "SQL_URI": current_app.config["SQL_URI"]
+                },
             },
             log_level=logging.getLevelName(
                 current_app.logger.getEffectiveLevel()).lower())
diff --git a/gn3/api/ctl.py b/gn3/api/ctl.py
index ac33d63..39c286f 100644
--- a/gn3/api/ctl.py
+++ b/gn3/api/ctl.py
@@ -2,7 +2,7 @@
 
 from flask import Blueprint
 from flask import request
-from flask import jsonify
+from flask import jsonify, current_app
 
 from gn3.computations.ctl import call_ctl_script
 
@@ -18,7 +18,8 @@ def run_ctl():
     """
     ctl_data = request.json
 
-    (cmd_results, response) = call_ctl_script(ctl_data)
+    (cmd_results, response) = call_ctl_script(
+        ctl_data, current_app.config["TMPDIR"])
     return (jsonify({
         "results": response
     }), 200) if response is not None else (jsonify({"error": str(cmd_results)}), 401)
diff --git a/gn3/api/wgcna.py b/gn3/api/wgcna.py
index fa044cf..5468a2e 100644
--- a/gn3/api/wgcna.py
+++ b/gn3/api/wgcna.py
@@ -17,7 +17,9 @@ def run_wgcna():
 
     wgcna_script = current_app.config["WGCNA_RSCRIPT"]
 
-    results = call_wgcna_script(wgcna_script, wgcna_data)
+    results = call_wgcna_script(wgcna_script,
+                                wgcna_data,
+                                current_app.config["TMPDIR"])
 
     if results.get("data") is None:
         return jsonify(results), 401
-- 
cgit 1.4.1