Add sync option to keep classifications definitions up-to-date.

Dockerfile

@@ -13,7 +13,8 @@ RUN apt-get update && apt-get -y install \
     jq \
     git \
     unzip \
-    tzdata
+    tzdata \
+    wget
 
 # Install Pip libs
 RUN pip install \

manifest.json

@@ -1,23 +1,28 @@
 {
   "name": "pfile-mr-classifier",
   "label": "CNI: GE P-File Classifier",
-  "description": "Extracts GE P-File headers and generates JSON metadata (.metadata.json) which is saved in Flywheel on the P-File's info object. This gear also attempts to determine the P-Files classification.",
+  "description": "Extracts GE P-File header and generates JSON metadata (.metadata.json) which is saved in Flywheel on the P-File's info object. This gear also attempts to determine the P-File's classification (measurement, intent, etc.).",
   "maintainer": "Michael Perry <[email protected]>",
   "author": "Michael Perry <[email protected]>",
   "url": "https://cni.stanford.edu",
   "source": "https://github.com/cni/pfile-mr-classifier",
   "cite": "pfile-tools: GE P-File Utilities (https://github.com/njvack/pfile-tools)",
   "license": "BSD-2-Clause",
   "flywheel": "0",
-  "version": "1.0.0",
+  "version": "1.1.0",
   "custom": {
-    "docker-image": "stanfordcni/pfile-mr-classifier:1.0.0"
+    "docker-image": "stanfordcni/pfile-mr-classifier:1.1.0"
   },
   "config": {
     "timezone": {
-      "description": "Time Zone to which all timestamps should be localized. This will set the default time zone in the Gear and thus localize the timestamps to that time zone. Examples: 'America/Los_Angeles', 'America/New_York'. [default = 'America/Los_Angeles'].",
+      "description": "Time Zone to which all timestamps should be localized. This will set the default time zone in the Gear and thus localize the timestamps to that time zone. Examples: 'UTC', 'America/Los_Angeles', 'America/New_York'. [default = 'America/Los_Angeles'].",
       "type": "string",
       "default": "America/Los_Angeles"
+    },
+    "sync": {
+      "description": "Synchronize classification definitions with the latest known updates found at scitran-apps/dicom-mr-classifier [default = true].",
+      "type": "boolean",
+      "default": true
     }
   },
   "inputs": {

run

@@ -34,6 +34,16 @@ echo "$TZ" > /etc/timezone && ln -snf /usr/share/zoneinfo/"$TZ" /etc/localtime
 dpkg-reconfigure -f noninteractive tzdata
 
 
+if [[ ${config_sync} == "true" ]]; then
+  echo -e "$CONTAINER  Syncing classification code from scitran-apps/dicom-mr-classifier/master..."
+  wget --quiet -O ${FLYWHEEL_BASE}/classification_from_label.py \
+      https://raw.githubusercontent.com/scitran-apps/dicom-mr-classifier/master/classification_from_label.py
+  chmod +x ${FLYWHEEL_BASE}/classification_from_label.py
+else
+  echo -e "$CONTAINER  Not syncing classification code. Using built-in version..."
+fi
+
+
 ##############################################################################
 # Check I/O directories and Generate metadata
 
@@ -57,7 +67,7 @@ if [[ -f $input_file ]]; then
   # Generate the header from the zip file and export to csv
   echo -e "${CONTAINER}  Extracting header from $input_file"
   header_file=/tmp/pfile_header
-  unzip -p "$input_file" "*/P*.7.gz" | head -c 1000000 | gunzip > $header_file
+  unzip -p "$input_file" "*/P*.7.gz" | head -c 1000000 | gunzip > $header_file 2>/dev/null
   /opt/pfile-tools/pfile_tools/scripts/dump_pfile_header.py $header_file --separator=, > $header_file.csv
 
   if [[ ! -f "$header_file".csv ]]; then
@@ -66,7 +76,7 @@ if [[ -f $input_file ]]; then
   fi
 
   # Generate the metadata
-  echo -e "${CONTAINER}  Generating metadata"
+  echo -e "${CONTAINER}  Generating metadata..."
   PYHONPATH=$PYTHONPATH:/flywheel/v0/ python $FLYWHEEL_BASE/pfile-mr-classifier.py \
     "${input_file}" \
     "${header_file}" \