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-rwxr-xr-xbin/genenetwork233
-rw-r--r--wqflask/utility/tools.py15
-rw-r--r--wqflask/wqflask/__init__.py4
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,