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

1 files changed, 3 insertions, 1 deletions

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