From aa4d213692cb27a903fe1593e2dd3387e638b350 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 15 Jun 2023 14:40:37 +0300
Subject: Configs: Introduce Blueprints. Refactor configs in webqtlConfig.

* Introduce flask Blueprints to help with decoupling the various
  modules from the `wqflask/__init__.py` module
* Refactor settings: Create a function
  `base.webqtlConfig.init_app(...)` to handle setting up the
  configurations on the app correctly. Call this function at app
  creation time.
* Move configuration utility functions from `utility.tools` module to
  `utility.configuration` module.
* Use the `get_setting(...)` function to retrieve configuration
  settings from the application.
---
 wqflask/base/data_set/utils.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask/base/data_set/utils.py')

diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 703fee04..465538af 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -6,9 +6,9 @@ import json
 import hashlib
 from typing import List
 
+from flask import current_app as app
 
-from utility.tools import SQL_URI
-from base.webqtlConfig import TMPDIR
+from utility.configuration import get_setting
 from wqflask.database import parse_db_url, database_connection
 
 def geno_mrna_confidentiality(ob):
@@ -27,7 +27,7 @@ def query_table_timestamp(dataset_type: str):
 
     # computation data and actions
     with database_connection() as conn, conn.cursor() as cursor:
-        fetch_db_name = parse_db_url(SQL_URI)
+        fetch_db_name = parse_db_url(get_setting("SQL_URI"))
         cursor.execute(
             "SELECT UPDATE_TIME FROM "
             "information_schema.tables "
@@ -57,7 +57,7 @@ def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List
     samplelist_as_str = ",".join(samplelist)
 
     file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
-    file_path = os.path.join(TMPDIR, f"{file_name}.json")
+    file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
 
     with open(file_path, "w") as file_handler:
         json.dump(query_results, file_handler)
@@ -70,7 +70,7 @@ def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List)
     samplelist_as_str = ",".join(samplelist)
 
     file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
-    file_path = os.path.join(TMPDIR, f"{file_name}.json")
+    file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
     try:
         with open(file_path, "r") as file_handler:
 
-- 
cgit v1.2.3