From 286027a1c07c0bf6ca113715f87ee7f1380d09e0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 16 Jun 2023 12:57:16 +0300
Subject: configs: Fix issues caught by mechanical-rob tests

---
 wqflask/base/data_set/utils.py | 2 +-
 wqflask/base/trait.py          | 6 +++---
 wqflask/base/webqtlConfig.py   | 1 +
 3 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 465538af..11391d69 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -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(get_setting("SQL_URI"))
+        fetch_db_name = parse_db_url(get_setting(app, "SQL_URI"))
         cursor.execute(
             "SELECT UPDATE_TIME FROM "
             "information_schema.tables "
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 70afa2cc..3a52e889 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -172,13 +172,13 @@ class GeneralTrait:
         alias = 'Not available'
         if self.symbol:
             human_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.upper())
             mouse_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.capitalize())
             other_response = requests.get(
-                get_setting("GN2_BASE_URL") + "gn3/gene/aliases/" +
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" +
                 self.symbol.lower())
 
             if human_response and mouse_response and other_response:
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 296bd314..600c6800 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -93,6 +93,7 @@ def init_app(app):
         TEMPDIR, child)
     WEBQTL_TMPDIR = mkdir_with_temp_dir("/gn2/")
     app.config["WEBQTL_TMPDIR"] = WEBQTL_TMPDIR
+    app.config["TMPDIR"] = WEBQTL_TMPDIR
     app.config["WEBQTL_CACHEDIR"] = mkdir_with_temp_dir(
         f"{WEBQTL_TMPDIR}cache/")
 
-- 
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