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, 4 insertions, 2 deletions

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())