feat(helm-charts): Remove SNOMED archive and include stubbed SNOMED files instead

Author: jocelyneholdbrook

cogstack-cohorter/WebAPP/.dockerignore

@@ -3,5 +3,3 @@ client/node_modules/
 client-react/node_modules/
 server/node_modules/
 
-server/data/
-!server/data/snomed_terms_data.tar.gz

cogstack-cohorter/WebAPP/Dockerfile

@@ -5,11 +5,6 @@ COPY . .
 RUN cd /usr/src/app/client-react && npm install && npm run build
 RUN cd /usr/src/app/server && npm install
 
-# Bundle the demo SNOMED data archive so random/demo mode works with no volume mount.
-# Kept separate from server/data/ so a runtime volume mount doesn't shadow it.
-RUN mkdir -p /usr/src/app/server/data-bundled
-RUN cp /usr/src/app/server/data/snomed_terms_data.tar.gz /usr/src/app/server/data-bundled/
-
 COPY entrypoint.sh /entrypoint.sh
 RUN sed -i 's/\r$//' /entrypoint.sh && chmod +x /entrypoint.sh
 

cogstack-cohorter/WebAPP/entrypoint.sh

@@ -2,21 +2,15 @@
 set -e
 
 DATA_DIR=/usr/src/app/server/data
-BUNDLED_ARCHIVE=/usr/src/app/server/data-bundled/snomed_terms_data.tar.gz
 
-# ── Step 1: extract bundled SNOMED data if not already present ────────────────
-if [ ! -f "$DATA_DIR/snomed_terms.json" ]; then
-    echo "[webapp] Extracting bundled SNOMED data..."
-    tar xzvf "$BUNDLED_ARCHIVE" -C "$DATA_DIR"
-fi
+# Ensure the writable data directory exists (may be an emptyDir or PVC mount).
+mkdir -p "$DATA_DIR"
 
-# ── Step 2 (optional): generate random patient data ───────────────────────────
-# Runs only on first startup — skipped if patient data files already exist.
-# Set RANDOM_DATA=false and supply real MIMIC-IV shaped data via volume mount.
+# ── Generate random patient data on first startup (random/demo mode) ──────────
 if [ "${RANDOM_DATA}" = "true" ] && [ ! -f "$DATA_DIR/ptt2age.json" ]; then
     echo "[webapp] Generating random demo patient data..."
     node --max-old-space-size=32768 /usr/src/app/server/gen_random_data.js
 fi
 
-# ── Step 3: start the server ──────────────────────────────────────────────────
+# ── Start the server ──────────────────────────────────────────────────────────
 exec node --max-old-space-size=32768 server.js

cogstack-cohorter/WebAPP/server/data/cui_pt2ch_example.json

@@ -3,7 +3,7 @@
 // node --max-old-space-size=32768 gen_random_data.js
 console.log('Generating random data')
 const fs = require('fs');
-const snomed_terms = require('./data/snomed_terms.json');
+const snomed_terms = require('./data/snomed_example.json');
 
 // Returns a random integer between min (inclusive) and max (inclusive).
 function random_int(min, max) {

cogstack-cohorter/WebAPP/server/data/snomed_example.json

@@ -33,9 +33,15 @@ const NL2DSL_SERVER = process.env.NL2DSL_SERVER || "http://localhost:3002/api/co
 let port = process.env.PORT || 3000;
 console.log('Loading data...');
 
-// index all the snomed concepts
-const snomed_terms = require('./data/snomed_terms.json');
-const cui_pt2ch = require('./data/cui_pt2ch.json');
+// In random/demo mode use the example subset baked into the image.
+// In production mode use the full SNOMED files supplied via volume mount.
+const isRandomMode = (process.env.RANDOM_DATA || 'true') === 'true';
+const snomed_terms = isRandomMode
+    ? require('./data/snomed_example.json')
+    : require('./data/snomed_terms.json');
+const cui_pt2ch = isRandomMode
+    ? require('./data/cui_pt2ch_example.json')
+    : require('./data/cui_pt2ch.json');
 
 // for admin login
 const admin_pwd = process.env.PASSWORD || 'admin_pass';

cogstack-cohorter/WebAPP/server/gen_random_data.js

@@ -1,7 +1,4 @@
 # CI smoke-test overrides.
-# RANDOM_DATA=true is already the default — the image's bundled demo SNOMED data
-# is used automatically, so no data mount or init container is needed here.
-# Persistence is disabled so no PVC is provisioned during the test.
 webapp:
   persistence:
     enabled: false