From cfb3ff04e921cda320d46bf4eaabf1610019e1c7 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 19 Mar 2018 13:06:13 +0000
Subject: - Disabled PYTHONPATH injection - fix Guix instead, see
 https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
 - Renamed WQFLASK_SETTINGS to GN2_SETTINGS

---
 bin/genenetwork2            | 33 +++++++++++++++------------------
 wqflask/utility/tools.py    | 15 +--------------
 wqflask/wqflask/__init__.py |  4 ++--
 3 files changed, 18 insertions(+), 34 deletions(-)

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 2a83a1cd..b9e0a02b 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -68,32 +68,29 @@ if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
     echo "Can not use $1 switch without default settings file"
     exit 1
 fi
-# Handle settings parameter (can be .py or .json)
-if [ ! -z $1 ]; then
-    settings=$(realpath "$1")
-    if [ ! -e $settings ]; then
-        settings=$GN2_BASE_DIR/etc/default_settings.py
-    else
-        shift
-    fi
-fi
 
-ext="${settings##*.}"
-if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
-    overrides=$settings
+settings=$1
+if [ -z $settings ]; then
+    settings=$GN2_BASE_DIR/etc/default_settings.py
 else
-    echo $settings
+    shift
 fi
+settings=$(realpath $settings)
+
+# ext="${settings##*.}"
+# if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
+#     overrides=$settings
+# else
+#     echo $settings
+# fi
 
 if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
 fi
-export WQFLASK_SETTINGS=$settings     # Python
-export WQFLASK_OVERRIDES=$overrides   # JSON
 
-echo WQFLASK_SETTINGS=$settings
-echo WQFLASK_OVERRIDES=$overrides
+export GN2_SETTINGS=$settings     # Python
+echo GN2_SETTINGS=$settings
 
 # This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead
 # if [ -z $ELASTICSEARCH_PROFILE ]; then
@@ -115,7 +112,7 @@ if [ -z $GN2_PROFILE ]; then
     read -p "PRESS [ENTER] TO CONTINUE..."
 else
     export PATH=$GN2_PROFILE/bin:$PATH
-    export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages${PYTHONPATH:+:}$PYTHONPATH"
+    export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
     export R_LIBS_SITE=$GN2_PROFILE/site-library
     export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0
     export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 8c9fed96..bae3a7f4 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -54,7 +54,7 @@ def get_setting(command_id,guess=None):
     # print("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
     if command is None or command == "":
-        command = OVERRIDES.get(command_id)
+        command = OVERRIDES.get(command_id) # currently not in use
         if command is None:
             # ---- Check whether setting exists in app
             command = value(app.config.get(command_id))
@@ -285,18 +285,5 @@ assert_dir(JS_TWITTER_POST_FETCHER_PATH)
 
 from six import string_types
 
-if os.environ.get('WQFLASK_OVERRIDES'):
-    jsonfn = get_setting('WQFLASK_OVERRIDES')
-    logger.info("WQFLASK_OVERRIDES: %s" % jsonfn)
-    with open(jsonfn) as data_file:
-        overrides = json.load(data_file)
-        for k in overrides:
-            cmd = overrides[k]
-            if isinstance(cmd, string_types):
-                OVERRIDES[k] = eval(cmd)
-            else:
-                OVERRIDES[k] = cmd
-            logger.debug(OVERRIDES)
-
 # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
 assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 2188ce17..bc8e9900 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -13,8 +13,8 @@ logging.basicConfig(level=logging.INFO)
 app = Flask(__name__)
 
 app.config.from_object('cfg.default_settings')   # Get the defaults from cfg.default_settings
-app.config.from_envvar('WQFLASK_SETTINGS')       # See http://flask.pocoo.org/docs/config/#configuring-from-files
-# Note we also use WQFLASK_OVERRIDES
+app.config.from_envvar('GN2_SETTINGS')       # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
 
 app.jinja_env.globals.update(
     undefined = jinja2.StrictUndefined,
-- 
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