From 272b8b320a5698167dd1209be33cdc642542cc5f Mon Sep 17 00:00:00 2001
From: Michael Perry <lmperry@stanford.edu>
Date: Mon, 25 Jun 2018 12:20:02 -0700
Subject: [PATCH] add parse_config function + bump version

---
 manifest.json |  4 ++--
 run           | 23 +++++++++++++++--------
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/manifest.json b/manifest.json
index 1349604..82ba888 100644
--- a/manifest.json
+++ b/manifest.json
@@ -8,9 +8,9 @@
   "source": "https://github.com/scitran-apps/parrec-mr-classifier",
   "license": "Apache-2.0",
   "flywheel": "0",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "custom": {
-    "docker-image": "scitran/parrec-mr-classifier:1.1.0"
+    "docker-image": "scitran/parrec-mr-classifier:1.1.1"
   },
   "config": {
     "timezone": {
diff --git a/run b/run
index de05a50..b78320f 100755
--- a/run
+++ b/run
@@ -16,18 +16,24 @@ MANIFEST_FILE=$FLYWHEEL_BASE/manifest.json
 ##############################################################################
 # Parse configuration
 
-if [[ -f $CONFIG_FILE ]]; then
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value)"' $CONFIG_FILE)
-else
-  CONFIG_FILE=$MANIFEST_FILE
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value.default)"' $CONFIG_FILE)
-fi
+function parse_config {
+
+  CONFIG_FILE=$FLYWHEEL_BASE/config.json
+  MANIFEST_FILE=$FLYWHEEL_BASE/manifest.json
+
+  if [[ -f $CONFIG_FILE ]]; then
+    echo "$(cat $CONFIG_FILE | jq -r '.config.'$1)"
+  else
+    CONFIG_FILE=$MANIFEST_FILE
+    echo "$(cat $MANIFEST_FILE | jq -r '.config.'$1'.default')"
+  fi
+}
 
 
 ##############################################################################
 # Set Time Zone
 
-TZ="${config_timezone}"
+TZ="$(parse_config 'timezone')"
 echo "${CONTAINER}  Setting time zone to: $TZ"
 echo "$TZ" > /etc/timezone && ln -snf /usr/share/zoneinfo/"$TZ" /etc/localtime
 dpkg-reconfigure -f noninteractive tzdata
@@ -36,7 +42,8 @@ dpkg-reconfigure -f noninteractive tzdata
 ##############################################################################
 # Handle sync option
 
-if [[ ${config_sync} == "true" ]]; then
+SYNC=$(parse_config 'sync')
+if [[ ${SYNC} == "true" ]]; then
   echo -e "$CONTAINER  Syncing classification code from scitran-apps/dicom-mr-classifier/sync-classification-e4..."
   mv ${FLYWHEEL_BASE}/classification_from_label.py /tmp
   wget --quiet -O ${FLYWHEEL_BASE}/classification_from_label.py \