From 406eb27859cca232a562c722cbbd37aca2e3be84 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 12:26:19 +0300
Subject: autopep8: Fix E301,E302,E303,E304,E305,E306

---
 etc/default_settings.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

(limited to 'etc')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 27522187..a194b10e 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -73,23 +73,24 @@ SMTP_PASSWORD = "UNKNOWN"
 
 # ---- Behavioural settings (defaults) note that logger and log levels can
 #      be overridden at the module level and with enviroment settings
-WEBSERVER_MODE  = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
+WEBSERVER_MODE = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
 WEBSERVER_BRANDING = None   # Set the branding (nyi)
 WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
-WEBSERVER_URL    = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
+WEBSERVER_URL = "http://localhost:" + str(SERVER_PORT) + "/" # external URL
 
-LOG_LEVEL       = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
+LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
 LOG_LEVEL_DEBUG = '0'       # logger.debugf log level (0-5, 5 = show all)
-LOG_SQL         = 'False'   # Log SQL/backend and GN_SERVER calls
+LOG_SQL = 'False'   # Log SQL/backend and GN_SERVER calls
 LOG_SQL_ALCHEMY = 'False'
-LOG_BENCH       = True      # Log bench marks
+LOG_BENCH = True      # Log bench marks
 
-USE_REDIS       = True      # REDIS caching (note that redis will be phased out)
-USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
-HOME            = os.environ['HOME']
+USE_REDIS = True      # REDIS caching (note that redis will be phased out)
+USE_GN_SERVER = 'False'   # Use GN_SERVER SQL calls
+HOME = os.environ['HOME']
 
 # ---- Default locations
-GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data files
+# base dir for all static data files
+GENENETWORK_FILES = HOME + "/genotype_files"
 
 # ---- Path overrides for Genenetwork - the defaults are normally
 #      picked up from Guix or in the HOME directory
@@ -98,7 +99,7 @@ GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data fil
 # PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
 
 # ---- Local path to JS libraries - for development modules (only)
-JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
+JS_GN_PATH = os.environ['HOME'] + "/genenetwork/javascript"
 
 # ---- GN2 Executables (overwrite for testing only)
 # PLINK_COMMAND = str.strip(os.popen("which plink2").read())
-- 
cgit v1.2.3


From 62f26b901e49effb0105e517093fd873815c470c Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 25 Sep 2021 05:22:23 +0300
Subject: Remove hard-coded URL; use configured URL

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* etc/default_settings.py: remove duplicate configuration variable
* wqflask/wqflask/collect.py: use the configured url for the API
  server

  Use the configured URL rather that the hard-coded URL that was used
  for testing out the clustered heatmap generation.
---
 etc/default_settings.py    | 1 -
 wqflask/wqflask/collect.py | 8 +++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'etc')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index a194b10e..023aa53b 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -25,7 +25,6 @@ import os
 import sys
 
 GN_VERSION = open("../etc/VERSION", "r").read()
-GN_SERVER_URL = "http://localhost:8880/" # REST API server
 
 # ---- MySQL
 
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 41ff47ae..3475ae5d 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -12,6 +12,7 @@ from flask import flash
 from wqflask import app
 from utility import hmac
 from utility.formatting import numify
+from utility.tools import GN_SERVER_URL
 from utility.redis_tools import get_redis_conn
 
 from base.trait import create_trait
@@ -218,9 +219,10 @@ def view_collection():
 
         json_version.append(jsonable(trait_ob))
 
-    collection_info = dict(trait_obs=trait_obs,
-                           uc=uc,
-                           heatmap_data_url="http://localhost:8080/api/heatmaps/clustered")
+    collection_info = dict(
+        trait_obs=trait_obs,
+        uc=uc,
+        heatmap_data_url=f"{GN_SERVER_URL}api/heatmaps/clustered")
 
     if "json" in params:
         return json.dumps(json_version)
-- 
cgit v1.2.3