Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into testing

* Fix conflicts

1 files changed, 17 insertions, 20 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 2a83a1cd..3f06e7f9 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
@@ -132,8 +129,8 @@ else
         export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
     fi
     while IFS=":" read -ra PPATH; do
-	for PPart in "${PPATH[@]}"; do
-	    if [ ! -d $PPart ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+	for PPART in "${PPATH[@]}"; do
+	    if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi
 	done
     done <<< "$PYTHONPATH"
     if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi