Handle JSON override files in startup script

1 files changed, 17 insertions, 7 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d926d6a1..872e9326 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,14 +1,19 @@
 #! /bin/bash
 #
-# This will run the GN2 server (with default settings if none supplied). Pass in
-# your own settings file, e.g.
+# This will run the GN2 server (with default settings if none
+# supplied). Pass in your own settings file, e.g.
 #
 #   ./bin/genenetwork2 ~/my_settings.py
 #
+# But better is to retain the defaults and override them with
+# JSON file (see the deploy docs).
+#
+#   ./bin/genenetwork2 ~/my_overrides.json
+#
 # To run a maintenance script with settings (instead of the webserver) add that with
 # a -c switch, e.g.
 #
-#   ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
+#   ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
 #
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
@@ -23,10 +28,11 @@ if [ -d $GN2_GUIX_PATH ]; then
 fi
 echo $GN2_BASE_PATH
 
-# Handle settings parameter
+# Handle settings parameter (can be .py or .json)
 settings=$1
-if [ -z $settings ]; then
-    # get default
+ext="${settings##*.}"
+if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
+    overrides=$settings
     settings=$GN2_BASE_PATH/etc/default_settings.py
 else
     shift
@@ -35,7 +41,11 @@ if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
 fi
-export WQFLASK_SETTINGS=$settings
+export WQFLASK_SETTINGS=$settings     # Python
+export WQFLASK_OVERRIDES=$overrides   # JSON
+
+echo WQFLASK_SETTINGS=$settings
+echo WQFLASK_OVERRIDES=$overrides
 
 # We may change this one:
 export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH