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, 5 insertions, 6 deletions

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index d1f7b32..3229a0e 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -7,17 +7,16 @@ import subprocess
 from pathlib import Path
 
 
-from gn3.settings import TMPDIR
 from gn3.commands import run_cmd
 
 
-def dump_wgcna_data(request_data: dict):
+def dump_wgcna_data(request_data: dict, tmpdir: str):
     """function to dump request data to json file"""
     filename = f"{str(uuid.uuid4())}.json"
 
-    temp_file_path = os.path.join(TMPDIR, filename)
+    temp_file_path = os.path.join(tmpdir, filename)
 
-    request_data["TMPDIR"] = TMPDIR
+    request_data["TMPDIR"] = tmpdir
 
     with open(temp_file_path, "w", encoding="utf-8") as output_file:
         json.dump(request_data, output_file)
@@ -65,9 +64,9 @@ def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     return cmd
 
 
-def call_wgcna_script(rscript_path: str, request_data: dict):
+def call_wgcna_script(rscript_path: str, request_data: dict, tmpdir: str):
     """function to call wgcna script"""
-    generated_file = dump_wgcna_data(request_data)
+    generated_file = dump_wgcna_data(request_data, tmpdir)
     cmd = compose_wgcna_cmd(rscript_path, generated_file)
 
     # stream_cmd_output(request_data, cmd)  disable streaming of data