feat(cogstack-cohorter): Make OAuth2 Paths Configurable At Runtime

cogstack-cohorter/.env.example

@@ -30,7 +30,7 @@ NPM_TOKEN=ghp_your_token_here
 # DEFAULT_USER_NAME=Local User
 # DEFAULT_USER_EMAIL=
 # DEFAULT_USER_ID=local
-# DEFAULT_USER_GROUPS=          # comma-separated, e.g. "cohorter-users,role:admin"
+# DEFAULT_USER_GROUPS=cohorter-users
 
 # ── Other runtime options ─────────────────────────────────────────────────────
 

cogstack-cohorter/WebAPP/Dockerfile

@@ -1,14 +1,4 @@
 FROM node:20
-
-ARG VITE_OAUTH2_USERINFO_PATH
-ARG VITE_OAUTH2_LOGIN_PATH
-ARG VITE_OAUTH2_LOGOUT_PATH
-
-# VITE_* vars must be ENV (not just ARG) for Vite to pick them up at build time.
-ENV VITE_OAUTH2_USERINFO_PATH=${VITE_OAUTH2_USERINFO_PATH}
-ENV VITE_OAUTH2_LOGIN_PATH=${VITE_OAUTH2_LOGIN_PATH}
-ENV VITE_OAUTH2_LOGOUT_PATH=${VITE_OAUTH2_LOGOUT_PATH}
-
 WORKDIR /usr/src/app/client-react
 COPY client-react/package*.json ./
 RUN --mount=type=secret,id=npm_token,required=true \

cogstack-cohorter/WebAPP/README.md

@@ -46,6 +46,39 @@ Please make sure to have the six data files ready in the `server/data/` folder b
 
 The recommended way to run the full stack (webapp + NL2DSL + MedCAT + Ollama) is via `docker-compose` from the `cogstack-cohorter/` root — see the root-level README and `.env.example` for details. The `NPM_TOKEN` is passed as a BuildKit secret; set it in the `.env` file before building.
 
+### Environment variables
+
+The webapp is configured entirely through environment variables — no rebuild is required to change settings.
+
+#### Server (Express backend)
+
+| Variable | Default                             | Description |
+|---|-------------------------------------|---|
+| `PORT` | `3000`                              | Port the Express server listens on |
+| `NL2DSL_SERVER` | `http://localhost:3002/api/compile` | URL of the NL2DSL service |
+| `RANDOM_DATA` | `true`                              | `true` → generate and serve synthetic demo data; `false` → load real data from `server/data/` |
+| `PASSWORD` | `admin_pass`                        | Password for the admin export panel |
+| `DEFAULT_USER_NAME` | `Local User`                        | Display name shown in the header when no oauth2-proxy is deployed |
+| `DEFAULT_USER_EMAIL` | _(empty)_                           | Email shown in the user panel when no oauth2-proxy is deployed |
+| `DEFAULT_USER_ID` | `local`                             | Opaque user ID returned by `/oauth2/userinfo` when no oauth2-proxy is deployed |
+| `DEFAULT_USER_GROUPS` | `cohorter-users`                    | Comma-separated groups returned by `/oauth2/userinfo` when no oauth2-proxy is deployed |
+
+#### Frontend runtime config (written to `config.js` at container startup)
+
+At startup `entrypoint.sh` writes `/config.js` into the pre-built static assets folder. `index.html` loads this file before the React bundle, so the values are available as `window.__RUNTIME_CONFIG__` without a rebuild.
+
+These variables are only needed when **oauth2-proxy is deployed in front of the app**. The defaults work correctly for standalone deployments — the Express server handles `/oauth2/userinfo` itself and returns the `DEFAULT_USER_*` values above.
+
+| Variable | Default | Description |
+|---|---|---|
+| `OAUTH2_USERINFO_PATH` | `/oauth2/userinfo` | Path the `UserSection` component fetches to get the logged-in user's info. With oauth2-proxy this is intercepted by oauth2-proxy before reaching Express. Without oauth2-proxy it hits the Express fallback endpoint. |
+| `OAUTH2_LOGIN_PATH` | `/oauth2/sign_in` | Path the header's "Sign in" button links to |
+| `OAUTH2_LOGOUT_PATH` | `/oauth2/sign_out?rd=/` | Path the header's "Sign out" button links to |
+
+When deploying with oauth2-proxy, the defaults are correct and no override is needed unless the oauth2-proxy is mounted at a non-standard prefix.
+
+In Kubernetes these are set as env vars on the webapp container (via helm `cogstack-cohorter.webapp.env`) and are picked up automatically on the next pod restart.
+
 ### Run using Docker with random data
 
 Set `RANDOM_DATA=true` in your `.env` file (or leave it unset — it defaults to `true`), then from the `cogstack-cohorter/` root:

cogstack-cohorter/WebAPP/client-react/index.html

@@ -36,6 +36,7 @@
   <body class="overflow-x-hidden">
     <noscript>You need to enable JavaScript to run this app.</noscript>
     <div id="root"></div>
+    <script src="/config.js" onerror="window.__RUNTIME_CONFIG__={}"></script>
     <script type="module" src="/src/main.jsx"></script>
   </body>
 </html>

cogstack-cohorter/WebAPP/client-react/src/App.jsx

@@ -10,10 +10,10 @@ import { LoadQueryDialog } from './LoadQueryDialog';
 // Fixed header height
 const HEADER_HEIGHT = 80;
 
-// OAuth2 proxy paths — configurable at build time via .env
-const USERINFO_PATH = import.meta.env.VITE_OAUTH2_USERINFO_PATH ?? '/oauth2/userinfo';
-const LOGIN_PATH    = import.meta.env.VITE_OAUTH2_LOGIN_PATH    ?? '/oauth2/sign_in';
-const LOGOUT_PATH   = import.meta.env.VITE_OAUTH2_LOGOUT_PATH   ?? '/oauth2/sign_out?rd=/';
+const runtimeConfig = (typeof window !== 'undefined' && window.__RUNTIME_CONFIG__) || {};
+const USERINFO_PATH = runtimeConfig.OAUTH2_USERINFO_PATH || '/oauth2/userinfo';
+const LOGIN_PATH    = runtimeConfig.OAUTH2_LOGIN_PATH    || '/oauth2/sign_in';
+const LOGOUT_PATH   = runtimeConfig.OAUTH2_LOGOUT_PATH   || '/oauth2/sign_out?rd=/';
 
 function App() {
   const rootRef  = useRef(null);

cogstack-cohorter/WebAPP/entrypoint.sh

@@ -18,5 +18,24 @@ if [ "${RANDOM_DATA}" = "true" ] && \
     node --max-old-space-size=32768 /usr/src/app/server/gen_random_data.js
 fi
 
+# ── Inject runtime config for the React app ──────────────────────────────────
+# Writes config.js into the pre-built dist folder so Express serves it
+# as /config.js.
+# Override any of these via OAUTH2_* env vars.
+#
+# Values are sanitised before being embedded in the JS string literal:
+# backslashes are escaped first, then double-quotes, preventing a
+# malformed env var from injecting arbitrary JavaScript.
+_js_escape() { printf '%s' "$1" | sed 's/\\/\\\\/g; s/"/\\"/g'; }
+
+CONFIG_JS=/usr/src/app/client-react/dist/config.js
+{
+  printf 'window.__RUNTIME_CONFIG__ = {\n'
+  printf '  OAUTH2_USERINFO_PATH: "%s",\n' "$(_js_escape "${OAUTH2_USERINFO_PATH:-/oauth2/userinfo}")"
+  printf '  OAUTH2_LOGIN_PATH:    "%s",\n' "$(_js_escape "${OAUTH2_LOGIN_PATH:-/oauth2/sign_in}")"
+  printf '  OAUTH2_LOGOUT_PATH:   "%s",\n' "$(_js_escape "${OAUTH2_LOGOUT_PATH:-/oauth2/sign_out?rd=/}")"
+  printf '};\n'
+} > "$CONFIG_JS"
+
 # ── Start the server ──────────────────────────────────────────────────────────
 exec node --max-old-space-size=32768 server.js

cogstack-cohorter/WebAPP/server/server.js

@@ -675,13 +675,9 @@ app.post('/compare_query', (req, res) => {
 //
 // During development (or when OAuth2 is not yet deployed) this returns a
 // configurable default user so the Header/UserSection renders correctly
-// without any real authentication.  Override the defaults via env vars:
-//   DEFAULT_USER_NAME  — displayed username  (default: "Local User")
-//   DEFAULT_USER_EMAIL — user email          (default: "")
-//   DEFAULT_USER_ID    — opaque user id      (default: "local")
-//   DEFAULT_USER_GROUPS — comma-separated groups (default: "")
+// without any real authentication.
 app.get("/oauth2/userinfo", (req, res) => {
-    const groups = process.env.DEFAULT_USER_GROUPS
+    const groups = process.env.DEFAULT_USER_GROUPS || 'cohorter-users'
         ? process.env.DEFAULT_USER_GROUPS.split(',').map(g => g.trim()).filter(Boolean)
         : [];
     res.status(200).json({

cogstack-cohorter/docker-compose.yml

@@ -79,7 +79,7 @@ services:
       DEFAULT_USER_EMAIL: "${DEFAULT_USER_EMAIL:-}"
       DEFAULT_USER_ID: "${DEFAULT_USER_ID:-local}"
       # Comma-separated list, e.g. "cohorter-users,role:admin"
-      DEFAULT_USER_GROUPS: "${DEFAULT_USER_GROUPS:-}"
+      DEFAULT_USER_GROUPS: "${DEFAULT_USER_GROUPS:-cohorter-users}"
     volumes:
       # Mount your data directory here. It should contain either:
       #   - snomed_terms_data.tar.gz (will be auto-extracted on startup), or