pediatric-ai-scribe-v3/docs/developer-guide.md

Developer guide

How the codebase is organized, how the main subsystems work, and where to extend them.

Layout

server.js                        Express entry, middleware stack, route mount
Dockerfile                       node:24-alpine, argon2 native compile deps
docker-compose.yml               app + postgres services

migrations/                      node-pg-migrate versioned schema changes
scripts/
  maintenance.js                 REINDEX / drift CLI
  release.sh                     semver bump + tag + push
  import-milestones.js           one-off seed import

src/
  db/
    database.js                  pool, baseline init, query helpers
    migrate.js                   programmatic node-pg-migrate runner
  middleware/
    auth.js                      JWT + session-table validation + sliding idle
    logging.js                   request log
  utils/
    ai.js                        callAI() multi-provider router + model whitelist
    models.js                    built-in model registry
    prompts.js                   templates (DB-overridable)
    promptSafe.js                <UNTRUSTED_*> wrapping + INJECTION_GUARD
    crypto.js                    AES-256-GCM (PHI at rest)
    passwords.js                 argon2id + bcrypt fallback + rehash
    sessions.js                  token hash, UA parse, session id
    platform.js                  isMobileClient()
    redact.js                    PHI redactor for audit details
    auditQueue.js                batched audit/api/access writer
    fileType.js                  magic-byte upload verifier
    errors.js                    generic 500 responder
    logger.js                    audit + api + access + Loki shipper
    notify.js                    ntfy push
    transcribe.js, tts.js        LiteLLM STT / TTS routes
  routes/                        Express routers for auth, AI workflows, education, logs, and user data

public/
  index.html                     SPA shell, version-stamped asset refs
  sw.js                          cache shell, network-first API
  manifest.json                  PWA
  js/                            vanilla JS modules (no bundler)
  components/                    per-tab HTML fragments loaded on demand
  css/styles.css
  template-guide.md              downloadable user template guide

mobile/                          Capacitor 6 wrapper (Android + iOS)
.github/workflows/               CI (auto-version, APK, docker)

Backend

Middleware stack (server.js)

request
  → helmet            CSP, HSTS, X-Content-Type-Options
  → CORS              fail-closed in prod if APP_URL/CORS_ORIGINS missing
  → cookieParser
  → express.json      10 MB cap
  → rate limiters     200/min general; 10/15min login; 20/15min sensitive
  → static            public/ with per-filetype Cache-Control; ?v=BUILD_ID cache-busts HTML on deploy
  → route handlers
  → 404 fallback      serves index.html for SPA routes

On boot:

• APP_VERSION read from package.json, printed + returned by /api/health/detailed.
• BUILD_ID = full Git HEAD SHA (worktrees and packed refs supported), or the validated image-baked revision. Unversioned development builds report unknown; no random SHA is invented.
• JWT_SECRET / DATA_ENCRYPTION_KEY fail-fast if missing in production.
• initDatabase() → runMigrations() → collation drift check.
• SIGTERM / SIGINT handler drains the audit queue and closes the pool.

DB helpers (src/db/database.js)

await db.get(sql, params);     // first row or null
await db.all(sql, params);     // array of rows
await db.run(sql, params);     // { lastInsertRowid, changes }
await db.query(sql, params);   // raw pg result
await db.getSetting(key);      // app_settings value (2 min cache)
await db.setSetting(key, v);   // writes + invalidates cache
db.pool                        // pg.Pool instance for transactions

SQL uses ? placeholders (auto-converted to $1, $2, ...) OR native $N. INSERTs without explicit RETURNING get RETURNING id appended.

Auth middleware (src/middleware/auth.js)

var { authMiddleware, adminMiddleware, moderatorMiddleware } = require('../middleware/auth');
router.post('/thing', authMiddleware, handler);            // requires auth
router.post('/admin-thing', authMiddleware, adminMiddleware, handler);

Sets req.user with { id, email, name, role, totp_enabled, disabled } and req.sessionId.

AI (src/utils/ai.js)

var { callAI } = require('../utils/ai');
var result = await callAI([
  { role: 'system', content: PROMPTS.hpiEncounter + INJECTION_GUARD },
  { role: 'user',   content: wrapUserText('transcript', transcript) }
], { model, maxTokens: 4000 });
// result = { content, model, usage }

Throws { code: 'model_not_permitted' } if the requested model isn't in the active allowlist.

Prompts (src/utils/prompts.js)

Flat PROMPTS object. Any template can be overridden live by writing a prompt.{name} row in app_settings. Admin Panel's Prompt Editor is the UX for that.

Settings (src/utils/config.js)

var v = await config.get('feature.read_aloud', 'false');   // key, default
await config.set('registration_enabled', 'true');

2-minute in-memory cache. Writes invalidate immediately.

Logger (src/utils/logger.js)

logger.audit(userId, 'action', 'details', req, { category: 'auth' });
logger.apiCall(userId, endpoint, { model, tokensInput, tokensOutput, duration });
logger.access(userId, 'login', req, true);
logger.error('scope', err.message);

Writes go to the database (batched), the daily JSONL file, and Loki (if configured).

Frontend

No framework, no bundler, no build step. public/index.html is the only document. Modules communicate through window.* globals and CustomEvent on document.

Tab system

app.js owns activateTab(name):

1. Fetch /components/{name}.html (browser-cached for 1 h, bust by ?v=BUILD_ID that the server injects).
2. Inject into .app-body.
3. Dispatch CustomEvent('tabChanged', { detail: { tab: name } }).
4. Feature modules (soap.js, encounters.js, etc.) listen for their own tab name and initialize DOM references inside the just-injected fragment.

Auth model (client)

auth.js branches on isNativeApp():

• Web — no localStorage token; relies on the ped_auth httpOnly cookie set by the server. /api/auth/me on boot verifies the session; failed verification shows the login screen.
• Mobile — token lives in capacitor-secure-storage-plugin (iOS Keychain / Android EncryptedSharedPreferences). getAuthHeaders() emits Authorization: Bearer <token>.

authFetch.js wraps window.fetch to catch 401 on authenticated /api/* requests and force re-login. BroadcastChannel('pedscribe-auth') propagates logout to sibling tabs.

Module load order

Fixed in index.html:

secureStorage → authFetch → auth → (feature modules)

All <script defer>. Dependencies enforced by declaration order.

Adding things

A new AI endpoint

1. Create src/routes/myFeature.js:

   var express = require('express');
   var router = express.Router();
   var { callAI } = require('../utils/ai');
   var { authMiddleware } = require('../middleware/auth');
   var PROMPTS = require('../utils/prompts');
   var { wrapUserText, INJECTION_GUARD } = require('../utils/promptSafe');
   var logger = require('../utils/logger');
   
   router.post('/my-feature', authMiddleware, async (req, res) => {
     try {
       var { transcript, model } = req.body;
       var result = await callAI([
         { role: 'system', content: PROMPTS.myFeature + INJECTION_GUARD },
         { role: 'user',   content: wrapUserText('transcript', transcript) }
       ], { model });
       res.json({ success: true, text: result.content });
       logger.audit(req.user.id, 'generate_my_feature', 'Generated', req, { category: 'clinical' });
     } catch (err) {
       res.status(500).json({ error: 'Request failed' });
     }
   });
   module.exports = router;
   

2. Mount in server.js:

   app.use('/api', require('./src/routes/myFeature'));
   

3. Add the template to src/utils/prompts.js.

4. Add a component under public/components/myfeature.html.

5. Add public/js/myFeature.js with a tabChanged listener.

6. Register the tab button in public/index.html.

A new table / column

New changes go in a migration file. See docs/migrations.md.

docker exec -w /app pediatric-ai-scribe npm run migrate:new -- add_my_table
# edit the generated file

A new setting

1. Optional — add a default in the defaults array inside initDatabase() (only needed if the app should seed it on fresh installs).
2. Read at runtime: await db.getSetting('my_key').
3. Admin-editable automatically through PUT /api/admin/config which accepts arbitrary keys.

Physician Templates And Preferences

1. Settings saves user templates/preferences through /api/memories into user_memories.
2. New rows encrypt name and content with the shared enc1: string format.
3. GET /api/memories/context decrypts rows and returns only AI-context categories: physical_exam, ros, encounter_format, family_history, assessment_plan, template_soap, template_hpi, template_wellvisit, template_sickvisit, and template_ed.
4. custom rows remain visible in settings but are not included in prompt context.
5. Legacy correction_* rows from the removed correction-learning feature are filtered out rather than deleted.

Route reference

File	Mount	Auth	Purpose
auth.js	/api/auth	Public	Register, login, 2FA, email verify, password reset, backup codes
oidc.js	/api/auth	Public	OIDC SSO (Authorization Code + PKCE)
sessions.js	/api/sessions	Auth	Active sessions list + revoke
hpi.js	/api	Auth	HPI from encounter or dictation
soap.js	/api	Auth	SOAP generation
chartReview.js	/api	Auth	Chart review / pre-charting
hospitalCourse.js	/api	Auth	Hospital course
wellVisit.js	/api	Auth	Well visit + SSHADESS
sickVisit.js	/api	Auth	Sick visit
milestones.js	/api	Auth	Developmental milestone narratives
refine.js	/api	Auth	Refine / shorten / clarify
transcribe.js	/api	Auth	LiteLLM STT
tts.js	/api	Auth	LiteLLM TTS
encounters.js	/api	Auth	Save / load / optimistic-lock encounters
memories.js	/api	Auth	Templates + prompt preferences
audioBackups.js	/api	Auth	Encrypted audio retry store
documents.js	/api	Auth	S3 documents (magic-byte checked)
userPreferences.js	/api	Auth	Per-user STT/TTS choice
nextcloud.js	/api	Auth	Encrypted WebDAV tokens
billing.js	/api	Auth	ICD-10 / CPT code suggestion
logs.js	/api	Auth	Usage + audit dump (admin-only endpoints gated further)
admin.js	/api/admin	Admin	User management
adminConfig.js	/api/admin	Admin	Settings, prompts, models, SMTP, OIDC
adminMilestones.js	/api/admin	Admin	Milestone data management
clinicalAssistant.js	/api	Auth	Grounded clinical answers over MCP retrieval
myResources.js	/api	Auth	Personal teaching material: generate, refine, export
notes.js	/api	Auth	Personal notes
edEncounters.js	/api	Auth	ED encounters: staged notes, consolidate, MDM finalize
dontMiss.js	/api	Auth	Don't-miss diagnosis suggestions
patientEducation.js	/api	Auth	Patient education handouts
peGuide.js	/api	Auth	Physical exam guide
diagrams.js	/api	Auth	Diagram rendering
generatedImages.js	/api, /api/admin	Auth	Image generation jobs and their stored output
extensions.js	/api	Auth	Browser-extension integration
adminDocs.js	/api/admin/docs	Admin	In-app rendering of this docs/ tree

Frontend JS module reference

File	Purpose
secureStorage.js	Platform-branched token storage (Keychain / localStorage)
authFetch.js	Global fetch wrapper (401 → logout + reload)
auth.js	Login / register / SSO / session management / Turnstile / backup-code modal
app.js	Tab navigation, model selector, audio recorder, transcription orchestration
liveEncounter.js	Live recording UI + live preview
soap.js, hpi.js (none — in liveEncounter), sickVisit.js, wellVisit.js, hospitalCourse.js, chartReview.js	Clinical tabs
milestones.js + milestonesData.js	Milestones tab
shadess.js	SSHADESS adolescent assessment
encounters.js	Save / load / resume with optimistic lock
memories.js	Physician templates and prompt preferences UI
speechRecognition.js	Explicit opt-in browser Web Speech support
voicePreferences.js	Per-user STT/TTS override
audioBackup.js	Server + IndexedDB backup retries
nextcloud.js	Connect / export
documents.js	S3 upload / download
calculators.js	Pediatric calculators (BP, BMI, growth, bilirubin, vitals, etc.)
accountBoundary.js	One verified account owner per JS realm; guards cross-account leakage
ed-encounters.js	ED encounter workflow: staged notes, consolidate, MDM finalize
voiceDictation.js	Dictation capture and voice-mode call UI
transcriptionSettings.js	Transcription provider and model picker
recordingModules.js	Shared recorder wiring reused by the clinical tabs
calc-math.js	Pure calculator math, kept separate so it can be tested directly
admin-docs.js	Documentation viewer inside the Admin panel
drugs-loader.js, ui-state.js	Small shared helpers
e2e-bootstrap.js	Test-only hook; inert unless the e2e harness sets it up
admin.js	Admin panel (users, settings, prompts, models)

Larger features live in their own directory rather than a single file: admin/, assistant/, bedside/, calculators/, notes/, and wellVisit/.

Common tasks

Change default temperature

Edit the default in callAI() in src/utils/ai.js. Per-call options.temperature overrides.

Override a prompt without deploying

Admin Panel → Prompts → pick the template → edit → save. Takes effect immediately; cache is invalidated on write.

Add a model to the dropdown

Admin Panel → Models → Add Custom Model. Exact provider ID, display name, cost string, category (free / fast / smart / premium). Appears immediately for all users.

Trace an AI call

docker compose logs -f pediatric-scribe | grep '\[AI\]'

Or:

SELECT endpoint, model_used, tokens_input, tokens_output, duration_ms, cost_estimate, error
FROM api_log
ORDER BY timestamp DESC
LIMIT 20;

Force a re-index

docker exec -w /app pediatric-ai-scribe npm run maint:reindex

Runs after any Postgres image upgrade if the startup drift check didn't catch it.

Local development

docker compose up -d postgres      # just the DB
npm ci
cp .env.example .env               # set JWT_SECRET, DATA_ENCRYPTION_KEY, provider credentials
node server.js

App binds http://localhost:3000. Without APP_URL, production-mode guards relax (open CORS, non-secure cookies) — never deploy like this.

Or run it the way production does, against the built image:

cp .env.example .env
./scripts/build-image.sh
docker compose up -d --no-build
curl -fsS http://127.0.0.1:3552/api/health

Use Node 24 to match the image. Tests run from the repository root with npm ci && npm test; node --check <file> is a fast syntax gate when you are touching a backend entrypoint.

Change workflow

1. Read the relevant route, utility, frontend module, and tests before editing.
2. Make the smallest correct change.
3. Add or update a regression test when changing clinical rendering, model routing, auth, settings, or source handling.
4. Run focused tests first if available.
5. Run npm test before deploy or commit.
6. Deploy with Docker only after tests pass.
7. Verify /api/health after deploy.

Changing the Clinical Assistant

Clinical Assistant changes should usually include tests because small rendering or prompt changes can affect clinical trust.

High-risk areas:

• citation linking,
• table rendering,
• source title cleanup,
• named-source provenance rules,
• image intent detection,
• MCP result normalization,
• provider/model selection.

When a real answer renders badly, save a de-identified example as a fixture or direct test input. Do not make broad global repairs that convert arbitrary numbers into citation links.

Frontend rendering rules

Use textContent for plain text. Use innerHTML only for static templates, sanitized markdown, or HTML built entirely from escaped values.

Safe patterns:

el.textContent = userText;
el.innerHTML = escapeHtml(userText).replace(/\n/g, '<br>');
el.innerHTML = sanitizeHtml(renderMarkdown(modelOutput));

Unsafe pattern:

el.innerHTML = modelOutput;

If a dynamic value enters an HTML string, escape it at the point of insertion. If it is an attribute value, escape quotes too.

Deployment checks

Deploy with scripts/deploy.sh, never with docker compose up by hand:

./scripts/build-image.sh
REV=$(git rev-parse HEAD)
scripts/deploy.sh "ped-ai-local:$REV" "$REV"

deploy.sh moves the PED_AI_IMAGE pin in .env, waits for health, then reads /api/build and rolls back if the container came up on a different revision. Running up by hand does none of that: /api/health passing proves a container is up, not that it is the one you built, and a pin left from an earlier deploy will happily start an older image while everything looks fine. See deployment.md for the full sequence.

To check by hand what is serving:

curl -fsS http://127.0.0.1:3552/api/build     # must equal `git rev-parse HEAD`
docker compose ps pediatric-scribe

If the browser still shows old frontend behavior after the revision checks out, force-refresh or check the injected BUILD_ID asset query string.

Documentation expectations

Keep docs close to operational truth. If a behavior changes, update the most specific doc in the same change. Prefer short, current docs over long historical explanations.