update session_memory - for refer to the passwork

Poc1-Proof of Concept verison 1

README.md

@@ -27,8 +27,6 @@ PILOT_PROJECT/
 │   │   ├── LEGACY            # The legacy material - for archieved / pre-existed project
 │   │   ├── CODEBASE          # The project codebase
 │   │   ├── Design_Material/  # The system design - API - and UIX design material 
-│   │   ├── SOFTWARE_SYSTEM_DESIGN_FR_25.md # Detailed software design specification
-│   │   ├── SOLUTION_ARCHITECTURE_SPEC.md   # Solution architecture overview
 │   │   └── VISUALIZATION/    # Charts, diagrams, and visual assets
 │   └── ...                   # Additional sprint folders as needed
 ├── secrets/                  # **Developer‑managed secrets** (NOT tracked by git)

session_memory/12_Jun_26.md

@@ -0,0 +1,37 @@
+# Session Memory
+
+## Current task
+Created Kilo skill `cicd-architect-grill`.
+
+## Created skill
+- Skill name: `cicd-architect-grill`
+- Skill file: `.kilocode/skills/cicd-architect-grill/SKILL.md`
+- Skill line count: 49 lines after long draft compression.
+
+## Skill purpose
+Design, redesign, migrate, debate CI/CD pipelines for one software project. No cloud/language/runtime/platform assumptions.
+
+## Skill behavior
+- Inspect repo context before questions.
+- Extract FRs, NFRs, constraints, success criteria, Definition of Done.
+- Use C4 modeling only as deep as needed.
+- Choose CI/CD pattern from situation, not vendor defaults.
+- Cross-check: build reproducibility, tests, scans, artifacts, secrets, promotion, approvals, rollback, observability, cost, ownership.
+- Grill one decision at a time when requested.
+- Output draft/final plans as YAML.
+
+## Repository context
+- Workspace root: `/Users/davestran/Downloads/vkist_internship`
+- Kilo config: `kilo.json`
+- User-facing style: caveman style active.
+- Existing skills inspected under `/Users/davestran/Downloads/vkist_internship/.kilocode/skills/`.
+
+## Important constraints
+- Do not assume GCP, AWS, Azure, Kubernetes, serverless, GitHub Actions, GitLab CI, Jenkins, Terraform unless user asks.
+- Do not implement infrastructure until user approves design plan + implementation path.
+- Do not ask many questions when repo evidence answers.
+
+## Current status
+- New skill directory exists.
+- `SKILL.md` written and inspected.
+- No tests run: Kilo skill definition, not executable code.

session_memory/13_Jun_26.md

@@ -0,0 +1,43 @@
+# Session Memory
+
+## Current task
+Create session memory for 13 Jun 26.
+
+## Work done
+- Refined `API_CONTRACT_DRAFT.md` to v0.2.0 for FR-25 Synovitis Grading Workspace.
+- Added public clinical routes + internal/local safety routes from API contract.
+- Added async analysis job model, model registry, GradCAM, rationale, Socratic, BERT drift, RAG evidence, activations, artifact masks, ground truth, escalation, morphology, telemetry, report sign, EMR sync.
+- Updated error codes, data types, OpenAPI skeleton, PlantUML sequence.
+- Ran `git diff --check`; no whitespace errors.
+
+## Architecture review
+- Loaded `improve-codebase-architecture` skill.
+- Read `LANGUAGE.md`; no repo `CONTEXT.md`; no `docs/adr`.
+- Explore agent inspected `vkist-ultrasound/app.py`, `pdf_service.py`, `templates/js/script.js`, API docs, FR-25 use cases.
+- Found 6 deepening candidates:
+  - Clinical Workflow State Machine Module — Strong.
+  - Model Registry + Runtime Adapter Module — Strong.
+  - Measurement + Severity Calibration Module — Strong.
+  - Privacy + Artifact + Audit Module — Strong.
+  - Finalization + Report + EMR State Module — Strong.
+  - Safety + Telemetry + Feedback Module — Worth exploring.
+- HTML report write was attempted, but tool aborted before file landed. Report not completed.
+
+## Repository context
+- Workspace root: `/Users/davestran/Downloads/vkist_internship`
+- User-facing style: caveman style active.
+- Main code area: `PILOT_PROJECT/vkist-ultrasound`
+- API contract target: `PILOT_PROJECT/workspace/sprint_1_2/Design_Material/API-docs/API_CONTRACT_DRAFT.md`
+
+## Important constraints
+- Do not propose interfaces before user picks architecture candidate.
+- If user picks candidate, enter grilling loop.
+- If naming new deepened module after concept missing from `CONTEXT.md`, update `CONTEXT.md`.
+- If user rejects candidate with load-bearing reason, offer ADR only if future reviewers need it.
+- Do not commit unless explicitly asked.
+
+## Current status
+- API contract file updated.
+- Architecture candidates identified.
+- HTML architecture report still pending due aborted write.
+- No tests run for architecture review; no code changed during review.

session_memory/14_Jun_26.md

@@ -0,0 +1,60 @@
+# Session Memory
+
+## Current task
+Create/update `grill_bento_codebase` architecture skill.
+
+## Work done
+- Loaded `grill-with-docs`, `grill-bento-codebase`, `skill-creator`.
+- Inspected:
+  - `.kilocode/skills/grill_bento_codebase/SKILL.md`
+  - `.kilocode/skills/grill_bento_codebase/GEMINI.md`
+  - `.kilocode/skills/grill_bento_codebase/BENTO_DESIGN_GUIDELINE.md`
+  - `.kilocode/skills/grill_bento_codebase/bento_template.html`
+  - `.kilocode/rules/bento_template.html`
+  - `.kilocode/rules/BENTO_DESIGN_GUIDELINE.md`
+- Updated `grill_bento_codebase` skill assets.
+- Added Bento depth constraint:
+  - one Bento room may contain multiple sub-components/sub-projects
+  - max Bento depth = 3
+  - depth 1 = root Bento
+  - depth 2 = child sub-project
+  - depth 3 = grandchild sub-project
+  - depth 4+ invalid
+- Added fallback rule: detail beyond depth 3 stays inside owning Bento as local `spec/`, `spec/docs/`, `implementation/`, or `tests/`.
+- Moved skill-local source refs to:
+  - `BENTO_DESIGN_GUIDELINE.md`
+  - `bento_template.html`
+- Bumped guideline version to `0.5.0`.
+
+## Skill output contract
+- Context lock from FRS, NFRS, user-interaction, Software_Arch, Solution_Arch.
+- Bento-BEV HTML blueprint from `bento_template.html`.
+- Markdown tree-view for dev-team flatout navigation.
+- Room cards.
+- Interface contracts.
+- Dependency map.
+- Traceability matrix.
+- Open decisions, one at a time.
+
+## Validation done
+- Re-read full `.kilocode/skills/grill_bento_codebase/BENTO_DESIGN_GUIDELINE.md`.
+- Confirmed depth rule appears in:
+  - `BENTO_DESIGN_GUIDELINE.md`
+  - `SKILL.md`
+  - `GEMINI.md`
+- Grep checked no stale `.kilocode/rules` refs inside `.kilocode/skills/grill_bento_codebase`.
+
+## Repository context
+- Workspace root: `/Users/davestran/Downloads/vkist_internship`
+- User-facing style: caveman style active.
+- Skill area: `.kilocode/skills/grill_bento_codebase`
+
+## Important constraints
+- No Bento tree depth > 3.
+- No nested Bento beyond grandchild depth.
+- Extra detail stays local to owning Bento room.
+- No commits unless explicitly asked.
+
+## Current status
+- `SKILL.md`, `GEMINI.md`, `BENTO_DESIGN_GUIDELINE.md` updated.
+- No tests run: skill docs, not executable code.

session_memory/18_Jun_26.md

@@ -0,0 +1,45 @@
+---
+title: Session Memory 18 Jun 26
+date: 2026-06-18
+status: active
+---
+
+## Summary
+
+Compressed 2026-06-18 session work: `cv_code` split, PlantUML Chen ER skill, session memory.
+
+## cv_code module split
+
+- Split legacy `legcode/app.py` into `ml/implementation/cv/code/` into three modules:
+  - `config.py`
+  - `framework.py`
+  - `server.py`
+- Legacy file untouched until new modules pass import checks.
+- `python -m py_compile` passed all files.
+- `server.py` import blocked by missing `pdf_service`.
+- `framework.py` path bug: `cv_root = Path(__file__).resolve().parents[2]` skips too far. Correct: `parents[1]`.
+
+## skill-creator inspection
+
+- Loaded `.config/kilo/.kilo/skills/skill-creator/SKILL.md`.
+- Skill structure: `SKILL.md` required; optional `GEMINI.md`, `EXAMPLES.md`, `REFERENCE.md`, `scripts/`, `assets/`.
+- Template description rules apply.
+
+## er-chen-diagram skill
+
+- Created `.kilocode/skills/er-chen-diagram/` scaffold.
+- Files written: `SKILL.md`, `EXAMPLES.md`, `REFERENCE.md`.
+- Skill contents:
+  - Mandatory `@startchen` / `@endchen`.
+  - Attributes only inside `{}`.
+  - Primary keys use `<<key>>`.
+  - Relationships empty blocks, then connect lines.
+  - Copy exact code shells verbatim.
+
+## Session memory housekeeping
+
+- Listed existing memory files: `12_Jun_26.md`, `13_Jun_26.md`, `14_Jun_26.md`.
+- Recorded activity in this file.
+
+## Relational DB Design
+- Created relational DB design spec per plan: ER/schema PlantUML and Chen notation in RELATIONAL_DB_SCHEMA_SPEC.md.

session_memory/26_Jun_26/CODING-AGENT-INSTRUCTION-PHASE0-PHASE1.md

@@ -0,0 +1,159 @@
+# Coding Agent Instruction: Resolve 17 Remaining Structural Gaps in Phase 0 & Phase 1
+
+You have already fixed the TypeScript build failures. The 17 unchecked plan items below must be addressed structurally. Each item is a checklist entry in `.kilo/plans/35-figma-designs-implementation-plan.md`. Only mark an item `[x]` in that plan file after you have implemented it AND it compiles cleanly.
+
+## Reference Files
+- Implementation Plan: `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/.kilo/plans/35-figma-designs-implementation-plan.md`
+- Frontend root: `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend`
+- Severity rule: Do NOT mark `[x]` unless you have implemented the item AND verified it.
+
+## Work Order: Exact Sequence with Acceptance Tests
+
+### 0.1 Environment Tooling
+1. Configure ESLint + Prettier
+   - Add `.eslintrc.cjs` and `.prettierrc` (or extend recommended configs).
+   - Add scripts to `package.json`: `"lint": "eslint src --ext .ts,.tsx"`.
+   - Acceptance: `npm run lint` runs without failing on the current src tree (warnings OK, but no auto-fixable errors left hanging).
+
+2. Set up Husky
+   - Install `husky` + `lint-staged`.
+   - Add `prepare` script: `"prepare": "husky"`.
+   - Add `.husky/pre-commit` to run `lint-staged`.
+   - Acceptance: `git add src/ && git commit` triggers Husky and blocks on lint failure.
+
+3. Configure Vitest
+   - Install: `vitest`, `@testing-library/react`, `@testing-library/jest-dom`, `jsdom`.
+   - Add `vitest.config.ts` with `test.environment = 'jsdom'` and `include: ['src/**/*.{test,spec}.{js,ts,jsx,tsx}']`.
+   - Add script: `"test": "vitest"`.
+   - Acceptance: `npx vitest run` executes (0 tests is OK for now; framework must be correct).
+
+4. Set up Playwright
+   - Install `@playwright/test`.
+   - Add `playwright.config.ts` with baseURL `http://localhost:5173` and webServer using `vite preview` or same.
+   - Add script: `"test:e2e": "playwright test"`.
+   - Acceptance: `npx playwright test --list` does not error (no tests yet is OK).
+
+5. Configure Storybook
+   - Install `@storybook/react-vite` and run `storybook init`.
+   - Add 1 story for `Button` atom and 1 story for `TopBar` organism.
+   - Acceptance: `npm run storybook` builds the UI and the 2 stories render.
+
+### 0.3 Component Inventory
+6. Analyze 35 Figma Files
+   - Inspect Figma paths under `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/Design_Material/` - section: `Figma Design Source Files`.
+   - Produce an inventory mapping file: `spec/figma-component-specs.md` is insufficient; append `spec/component-inventory.md` with:
+     - Unique screen count (should be 35).
+     - Reusable component list by atomic depth (atoms, molecules, organisms, templates).
+     - One dependency graph (Mermaid is fine).
+   - Acceptance: `spec/component-inventory.md` exists, has 35 distinct screens, and has a Mermaid dependency graph.
+
+7. Build Storybook Stories for Primitives
+   - Add stories for `Button`, `Input`, `Icon`, `Badge`, `Label`, `Toggle`, `Tooltip`.
+   - Acceptance: All primitives render in Storybook.
+
+### 0.4 API Contracts
+8. Cross-Reference API Contracts
+   - Open `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/Design_Material/API_docs/API_CONTRACT_DRAFT.md` & the `API spec from the backend-file` in `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/backend/spec/interface-contract.md` & the data-layer definition - check the reference from context in the dirrectory (a folder) at `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/data/spec`
+   - Cross-check each endpoint against `src/services/*.ts`.
+   - Acceptance: Each service file has JSDoc lists of endpoints it covers.
+
+9. Define TypeScript Interfaces
+   - Add `src/types/api.ts` with request/response interfaces for all 7 services.
+   - Acceptance: All 7 services import and use their types.
+
+10. Implement HTTP + MSW Adapters
+    - Add `src/services/adapters/httpAdapter.ts` and `src/services/adapters/mswAdapter.ts`.
+    - Each service file must use the adapter via `services/index.ts` seam.
+    - Acceptance: `tsc --noEmit` clean; `vitest run` can mock the adapter without touching prod code.
+
+11. Implement Auth/Logging Interceptors
+    - In `httpAdapter.ts`, add request interceptor that:
+      - Attaches `Authorization` header from a session token (mocked OK).
+      - Logs request method + URL.
+      - Normalizes errors to a `ServiceError` class.
+    - Acceptance: Interceptor exists and is imported only by `httpAdapter.ts` (no component imports).
+
+### 1.2 Zustand Slices
+12. Co-locate Slice Tests
+    - Create `src/store/sessionSlice.test.ts`, `src/store/dicomSlice.test.ts`, etc. (6 files).
+    - Each test imports the slice factory (`createSessionSlice`) and invokes the interface.
+    - Acceptance: `vitest run --coverage` shows coverage files for each slice.
+
+13. Create Domain Selectors
+    - In each slice file, export type-safe selectors via `create`.
+    - Acceptance: `TopBar` and `BottomBar` consume slice selectors instead of inline memoization.
+
+### 1.3 WebWorkers
+14. Create `src/workers/` Files
+    - `cv.worker.ts`: stub with `onmessage` and `postMessage` for `preprocess` msg type.
+    - `llm.worker.ts`: stub with `generate` msg type.
+    - `guardrail.worker.ts`: stub with `safetyCheck` msg type.
+    - Acceptance: `tsc --noEmit` clean; workers can be imported in a hook.
+
+15. Implement Worker Pool + Hooks
+    - `src/hooks/useWebWorker.ts`: generic hook accepting worker class + message schema.
+    - `src/hooks/useCVWorker.ts`, `useLLMWorker.ts`, `useGuardrailWorker.ts`: domain wrappers.
+    - Acceptance: Hooks can be instantiated without runtime errors in a test render.
+
+16. Transferable Message Protocols
+    - In each worker stub, explicitly show `Transferable` usage (pass `ImageBitmap` or `ArrayBuffer` in transfer list).
+    - Acceptance: TypeScript types enforce transferable contracts.
+
+17. Fallback to Main Thread
+    - Each hook exports `isSupported: boolean`. If `Worker` constructor not available, use a mock implementation on main thread.
+    - Acceptance: In jsdom test, `isSupported` is false and hook still resolves.
+
+### 1.4 Services Deepening
+18. Move `encryption.ts` Out of the Store
+    - Remove `import { encryptStorage } from '../utils/encryption'` from `src/store/index.ts`.
+    - Create `src/services/storageAdapter.ts` that exports `createSessionStorage` and `createEncryptedStorage`.
+    - `store/index.ts` must import `createJSONStorage(() => storageAdapter)` from `services/storageAdapter`.
+    - Acceptance: `grep encryptStorage src/store/index.ts` returns nothing in src/store/.
+
+### 1.5 Route-Aware Shell
+19. Implement `protected.tsx`
+    - Add `src/routes/protected.tsx` with a `<RequireAuth>` wrapper that redirects to `/login` when `!sessionId`.
+    - Wrap `/workspace` in `<RequireAuth>`.
+    - Acceptance: Visit `/workspace` when unauthenticated; browser redirects to `/login`.
+
+20. `WorkspaceShell` Owns 65/35 Split
+    - `WorkspaceShell.tsx` must render the 65/35 layout directly: `div.flex.h-screen` with `w-[65%]` ZoneA and `w-[35%]` ZoneB.
+    - `routes/index.tsx` `<DiagnosticWorkspace>` must only render `<WorkspaceShell />` without re-implementing the split.
+    - Acceptance: `grep "flex-1" src/components/templates/WorkspaceShell.tsx` finds exactly one instance; `grep "ZoneA" src/routes/index.tsx` finds zero (or just an import).
+
+21. Lift `initApp` Out of `App.tsx`
+    - Add `src/hooks/useAppInit.ts`.
+    - Move the `initApp` effect into this hook.
+    - `App.tsx` becomes: `<AppRoutes />` plus `<AppInit />` or composes it.
+    - Acceptance: `grep "initApp" src/App.tsx` finds nothing.
+
+22. `React.lazy` + `Suspense` in Routes
+    - Use `React.lazy(() => import('../components/organisms/ZoneA'))` and same for `ZoneB`.
+    - Wrap `<DiagnosticWorkspace>` children in `<Suspense fallback={<div>Loading...</div>}>`.
+    - Acceptance: `grep React.lazy src/routes/index.tsx` finds 2+ matches.
+
+### 1.6 Layout Responsiveness
+23. Responsive Breakpoints
+    - `WorkspaceShell.tsx` must use `@media` or Tailwind responsive classes so that on `< md` the 65/35 stack becomes a tabbed/toggle layout (Zone A | Zone B).
+    - Acceptance: Resize viewport to 375px; only one Zone visible at a time.
+
+24. 60fps Rendering Hints
+    - Add `will-change: transform` to animated containers.
+    - Add `contain: layout style paint` to the workspace root.
+    - Acceptance: `grep -E "will-change|contain:" src/components/templates/WorkspaceShell.tsx` finds both.
+
+## Strict Consequences
+- If you cannot complete a specific item within this prompt, do not leave it half-done. Leave the plan checkbox `[ ]` and add a comment in code explaining what is blocking you.
+- All code must keep `tsc --noEmit` clean after your changes.
+- Do NOT touch backend files or any file outside `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend` unless an item explicitly requires it.
+
+## Final Verification (YOU MUST RUN THESE)
+```bash
+cd /Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend
+npx tsc --noEmit && npm run build
+npm run lint
+npx vitest run
+npx playwright test --list
+npm run storybook -- --headless 2>&1 | tail -20
+```
+Produce a summary of which commands passed/failed and why.

session_memory/26_Jun_26/Proj_context_26_Jun_26.md

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+# SESSION MEMORY — 26 Jun 26
+
+## APP PURPOSE
+VKIST MSK Platform — air-gapped musculoskeletal ultrasound analysis. FR-25 Synovitis Grading (knee). Vietnamese NLP. RAG citations. HITL finalization. ≤150 MB bundle. ≤1.5s inference.
+
+## ARCHITECTURE (C4)
+
+### Context
+- **UP5** Radiologist: primary user — load scan, review grade, finalize, sign, view GradCAM, engage circuit breaker, review RAG evidence
+- **UP1** Senior Expert: clinical protocol validation, MOH guideline approval, threshold sign-off
+- **UP4** Support: registration, case queue
+- External: PACS (DICOM), EMR/HIS (HL7/FHIR), Triton (GPU inference), ladybugDB (ontology), pgvector (MOH guidelines HNSW), GemmaE2B/MedGemma (LLM), EmbeddingGemma (RAG embeddings)
+
+### Containers
+- **PWA** React 18 + TS + Zustand + LiteRT + MediaPipe + Dexie.js. DICOM canvas, GradCAM overlay, edge guardrail (Transformers.js BERT + OpenRedaction + pii-filter) in WebWorkers.
+- **NGINX + Keepalived** VIP failover ≤2s, SSL termination
+- **FastAPI** edge-inference-svc: DICOM ingest, ML pipeline orchestration, Grad-CAM, report assembly, SSE streaming
+- **FastAPI** rag-svc: pgvector top-k retrieval, ladybugDB ontology, LLM consult route, RAG-Referee
+- **Postgres + pgvector** HNSW index for MOH guidelines
+- **Redis** JWT sessions, rate-limit, consult_mode state
+- **MinIO** S3: DICOM, overlays, GradCAM heatmaps, reports
+- **Triton** gRPC :8001: 3-step ML pipeline + embeddings
+
+### 3-STEP ML PIPELINE (Triton)
+1. **Angle Classification** — ConvNeXt/DenseNet/ResNet/EfficientNet/Swin-V2. Classes: med-lat, post-trans, sup-trans-flex, sup-up-long
+2. **Inflammation Detection** — EfficientNet-B0 binary (post-trans, sup-up-long only)
+3. **Segmentation** — DeepLabV3-ResNet101 (post-trans) OR UNet3Plus-Attention/DeepLabV3 (sup-up-long). Classes: background, effusion, fat, femur, synovium, tendon
+4. **Measurement** — ROI middle 1/3 of bounding box. PIXEL_TO_MM = 45/655
+5. **Severity** — Combined: effusion 60% + synovium 40%. Grades 0-3: Rất nhẹ/Nhẹ/Trung bình/Nặng
+
+### GRADCAM
+- Zero extra clicks (auto on upload)
+- Base64 PNG from FastAPI
+- Canvas overlay, adjust opacity
+
+### WEB WORKER TOPOLOGY
+- `cv.worker.ts` — LiteRT WASM: CV inference (angle pre-classifier). Isolated WASM.
+- `llm.worker.ts` — WebLLM WASM: GemmaE2B local generation. NFR-4 1.5GB heap.
+- `guardrail.worker.ts` — Transformers.js WASM/WebGPU: BERT hallucination/mal-intention/scope-breach scoring.
+
+**Isolation:** No SharedArrayBuffer/Atomics. postMessage with structured clone only.
+
+## FRONTEND DESIGN (WS-25)
+
+### Layout: 65/35 split (Zone A: DICOM | Zone B: Results + Chat)
+
+```
+┌─ Top Bar (patient ID, back, sign) ──────────────────────┐
+├─ Zone A (65%) ────────┬─ Zone B (35%) ────────────────────┤
+│                       │ Phase Indicator (sticky)         │
+│  5 Canvas Layers:      │ Classification Card (grade,conf) │
+│  1. Background        │ Explanation Panel (GradCAM thumb) │
+│  2. GradCAM           │ Chat Panel (Socratic dialogue)    │
+│  3. Segmentation      │ Override Card (Phase 4)           │
+│  4. Annotations (SVG) │ Quick Actions                      │
+│  5. Viewport HUD       │                                    │
+│                        │                                    │
+│  Toolbar: pan/zoom/    │                                    │
+│  brush/eraser/caliper  │                                    │
+├───────────────────────┴───────────────────────────────────┤
+└─ Bottom Bar (NFR status, EMR sync, offline indicator) ─────┘
+```
+
+### Canvas Layers (z-index)
+- 0: Background DICOM (render once, never redraw on pan/zoom)
+- 10: GradCAM (CSS transform, no redraw)
+- 50: Segmentation overlay
+- 100: SVG Annotations (brush/caliper)
+- 200: Viewport HUD (text, mousemove redraw)
+- 900-999: System chrome (top/bottom bar)
+
+### Zustand Store Keys
+- `sessionId`, `patientId`, `currentPhase`
+- `dicomFrame: ImageBitmap | null` (GPU-friendly)
+- `dicomMetadata`, `mlResults` (single atomic object)
+- `clinicianGrade`, `isOverriding`, `overrideJustification`
+- `maskedRegions: MaskedRegion[]` (SVG path data, not raster)
+- `chatMessages` (pruned to 20, older → IndexedDB)
+- `driftScore`, `refereeIntervened`
+- `zoomLevel`, `panOffset` (not persisted, RAF updates)
+- `activeTool: pan|zoom|brush|eraser|caliper|pin`
+- `showGradCAM`, `showSegmentation`
+
+### 6-PHASE WORKFLOW
+1. **Classification** — ML grade, confidence bar
+2. **Explanation** — GradCAM visible, RAG evidence, LLM rationale
+3. **Negotiation** — Socratic dialogue, circuit breaker, BERT drift
+4. **Reconfiguration** — Override card, pixel activation inspector
+5. **Final Decision** — Summary, HITL signature
+6. **EMR Sync** — HL7/FHIR push, audit hash
+
+## KEY API CONTRACTS
+
+### Core Endpoints
+- `POST /api/v1/sessions` → create session
+- `POST /api/v1/sessions/{id}/frames` → upload DICOM (multipart)
+- `POST /api/v1/analysis-jobs` → trigger ML pipeline
+- `GET /api/v1/analysis-jobs/{id}` → get result (angle/inflammation/segmentation/measurement/severity)
+- `GET /api/v1/analysis-jobs/{id}/steps` → step-level status
+- `PATCH /api/v1/sessions/{id}/review` → clinician review (approve/correct/reject)
+- `POST /api/v1/reports` → generate report
+- `POST /api/v1/reports/{id}/sign` → HITL digital signature
+- `POST /api/v1/reports/{id}/emr-sync` → EMR push (outbox if offline)
+
+### Safety Endpoints
+- `POST /api/v1/sessions/{id}/explanations/gradcam` → GradCAM heatmap
+- `POST /api/v1/sessions/{id}/safety/circuit-breaker` → trigger circuit breaker
+- `POST /api/v1/sessions/{id}/chat/socratic` → Socratic dialogue (SSE streaming)
+- `POST /api/v1/sessions/{id}/drift/check` → BERT semantic drift
+- `POST /api/v1/sessions/{id}/rag/evidence` → RAG guideline arbitration
+- `POST /api/v1/feedback` → ground-truth override telemetry
+
+### ML Response Shape
+```json
+{
+  "result": {
+    "angle": { "class": "sup-up-long", "confidence": 0.9845 },
+    "inflammation": { "detected": true, "confidence": 0.942 },
+    "segmentation": { "mask_ref": "s3://...", "overlay_ref": "s3://...", "color_legend": {...} },
+    "measurement": { "thickness_mm": 6.87, "pixel_to_mm": 0.0687 },
+    "severity": { "level": 3, "label": "severe", "combined_score": 18.4 }
+  }
+}
+```
+
+## NFR SUMMARY
+
+| NFR | Target | Implementation |
+|-----|--------|----------------|
+| NFR-4 | ≤150 MB bundle | React PWA, tree-shake, split vendor chunk, Dexie.js |
+| NFR-5 | ≤1.5s inference | Triton ONNX/TensorRT, client memory ≤150MB |
+| NFR-7 | ≤200ms TTFT | SSE streaming, token chunking |
+| NFR-8 | Fault tolerance | IndexedDB cache, SW offline mode, session recovery |
+| NFR-13 | Grad-CAM zero-click | Auto on upload, no extra UI steps |
+| NFR-14 | No client GPU | LiteRT WASM, CPU fallback |
+| NFR-16 | Air-gapped primary | All inference + storage on-prem via K3s |
+| NFR-17 | Immutable audit | PostgreSQL WAL, no UPDATE/DELETE triggers |
+| NFR-18 | RAG citations | 100% LLM text cites MOH via pgvector HNSW |
+| NFR-19 | HITL signature | `signer_id != NULL` constraint before FINALIZED |
+
+## DECREE 13 / CIRCULAR 46
+- Client: Decree 13 regex scrubber (OpenRedaction + pii-filter + js-data-anonymizer) before network
+- Server: FastAPI `phi_scrub` middleware (Microsoft Presidio) as ground-check
+- PDF: Circular 46/2018 format, bilingual VI/EN, audit hash, signer block
+
+## SPRINT 1-2 DELIVERABLES
+
+### Sprint 1 (Jun 15–26) — "Fast PoC Baseline"
+- [ ] PWA shell: React + Zustand + PWA manifest + Service Worker + Dexie.js
+- [ ] DICOM canvas: Cornerstone.js + 5-layer canvas stack
+- [ ] FastAPI `/api/analyze` endpoint (sync 3-step pipeline)
+- [ ] Triton 3-step model ensemble + gRPC
+- [ ] NGINX + Keepalived VIP
+- [ ] Grad-CAM overlay on primary viewport
+- [ ] Circuit-breaker skeleton
+
+### Sprint 2 (Jun 29–Jul 10) — "Multi-Modal & NLP Integration"
+- [ ] GemmaE2B browser WebLLM + Cloud MedGemma Vertex AI
+- [ ] BERT drift monitor + RAG-Referee
+- [ ] Socratic dialogue (SSE streaming)
+- [ ] ladybugDB ontology traversal
+- [ ] Decree 13 scrubber (client + server)
+- [ ] Circular 46 PDF report generator
+- [ ] HITL signature gate
+- [ ] Immutable audit log
+- [ ] EMR/HIS HL7/FHIR push
+
+## KEY FILES
+- `/workspace/sprint_1_2/Design_Material/SPRINT_1_2_ARCHITECTURE_SPEC.md` — sprint-scoped architecture
+- `/PROJ_LEVEL_READING/ARCHITECT/SOFTWARE_ARCHITECTURE_SPEC.md` — full software architecture
+- `/workspace/sprint_1_2/Design_Material/API_docs/API_CONTRACT_DRAFT.md` — API contract v0.2.1
+- `/workspace/sprint_1_2/Design_Material/FR_25_UC_DESIGN/UI_Screen_Spec/Screen_Analysis_WS-25.md` — WS-25 screen analysis
+- `/workspace/sprint_1_2/Design_Material/FR_25_UC_DESIGN/FR_25_UC_SPEC.md` — FR-25 use case spec
+- `/workspace/sprint_1_2/Design_Material/FR_25_UC_DESIGN/UC_CONTEXT.md` — use case context
+
+## PHASE SEQUENCE (ML Pipeline)
+```
+DICOM upload → CLAHE → Angle Classification → (if post-trans) Inflammation → Segmentation
+→ (if sup-up-long) Inflammation → Segmentation → Measurement → Severity (0-3)
+→ GradCAM overlay → LLM rationale (GemmaE2B/MedGemma + RAG) → Clinician review
+→ HITL sign → EMR push
+```
+
+## NEXT ACTIONS
+- Implement PWA shell (T1-E)
+- Set up FastAPI `/api/analyze` + `/api/consult/stream` (T2-B)
+- Configure Triton ensemble (T2-A)
+- Build WS-25 UI components (Zone A 5-layer canvas + Zone B scrollable panel)
+- Wire up edge guardrail WebWorkers (cv.worker.ts, llm.worker.ts, guardrail.worker.ts)

session_memory/27_jun_26/27_jun_26.md

@@ -0,0 +1,43 @@
+# SESSION MEMORY — 27 Jun 26
+
+## BACKEND ARCHITECTURE & SPECIFICATION
+
+### 1. Project Context (from Proj_context_26_Jun_26.md)
+- **Purpose**: VKIST MSK Platform for air-gapped musculoskeletal ultrasound analysis (FR-25 Synovitis Grading).
+- **Core Tech Stack**: FastAPI, PostgreSQL + pgvector, Redis, MinIO (S3), Triton (GPU inference), Local LLM/BERT.
+- **ML Pipeline**: 3-step process: Angle Classification $\rightarrow$ Inflammation Detection $\rightarrow$ Segmentation/Measurement $\rightarrow$ Severity Grading (0-3).
+- **Safety Stack**: GradCAM, Socratic Chat, BERT drift monitor, RAG-Referee.
+- **Compliance**: Decree 13 (PII scrubbing), Circular 46 (PDF reports).
+
+### 2. Backend Structural Specification (from backend-spec.md)
+The backend follows a modular "Seams" architecture:
+- **API Layer**: `backend/api/` contains FastAPI routers.
+- **Implementation Layer**: `backend/implementation/` contains deep modules.
+- **Adapters**: `backend/implementation/adapters/` handles low-level external service communication (S3, Triton, LLM, BERT).
+
+**Core Modules:**
+- **Auth**: JWT, session management.
+- **Patient**: Patient CRUD, ingestion history.
+- **Session**: Frame handling, S3 storage, review patching.
+- **Analysis Jobs**: Async orchestration of Triton inference via KServe v2 HTTP.
+- **Safety**: GradCAM, RAG evidence, Socratic chat, circuit breaker, drift check.
+- **Notification/Settings/Telemetry**: Support modules for user preferences and system monitoring.
+
+### 3. Interface Contract (from interface-contract.md)
+**Key API Categories:**
+- **Auth**: `/api/v1/auth/login`, `/api/v1/users/me`.
+- **Patient**: `/api/v1/patients`, `/api/v1/patients/{id}/sessions`.
+- **Clinical Workflow**: 
+    - Sessions: `/api/v1/sessions`, `/api/v1/sessions/{id}/frames`, `/api/v1/sessions/{id}/review`.
+    - Analysis: `/api/v1/analysis-jobs` (async), `/api/v1/analysis` (sync).
+    - Reports: `/api/v1/reports`, `/api/v1/reports/{id}/sign`, `/api/v1/reports/{id}/emr-sync`.
+- **Safety & Explanations**: 
+    - GradCAM: `/api/v1/sessions/{id}/explanations/gradcam`.
+    - Rationale/Chat: `/api/v1/sessions/{id}/explanations/rationale`, `/api/v1/sessions/{id}/chat/socratic`.
+    - Guardrails: `/api/v1/sessions/{id}/drift/check`, `/api/v1/sessions/{id}/rag/evidence`.
+
+### 4. Dependency Graph
+- **Auth/Patient/Session/Safety/Telemetry** $\rightarrow$ PostgreSQL.
+- **Session/AnalysisJobs/Safety** $\rightarrow$ S3.
+- **AnalysisJobs** $\rightarrow$ Triton (Modal Serverless).
+- **Safety** $\rightarrow$ Local LLM, BERT, RAG Knowledge Base.

session_memory/27_jun_26/27_jun_26_backend.md

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+# Session Memory: 2026-06-27 Backend NLP/LLM Consult Implementation
+
+## Task
+Build Vietnamese Clinical LLM Consult endpoints (Rationale, Socratic Chat, Guardrail Check, SSE Stream). Follow NFR-16a governance.
+
+## Implementation Details
+
+### 1. LLM Adapter (`backend/implementation/adapters/llm_adapter.py`)
+- Build `VertexAILangchainAdapter` via `langchain-google-vertexai`.
+- Add `AuditCallbackHandler` for mandatory audit log commits before LLM call (NFR-16a).
+- Use `run_in_executor` for `generate` to stop FastAPI block.
+
+### 2. BERT Adapter (`backend/implementation/adapters/bert_adapter.py`)
+- Build `BERTAdapter` stubs:
+    - `drift_check`: Find clinical drift.
+    - `referee_check`: Check RAG grounding.
+    - `guardrail_check`: Safety check tokens/chunks.
+
+### 3. Safety Service (`backend/implementation/safety/service.py`)
+- Link LLM + BERT adapters.
+- Build `_verify_pre_egress` check:
+    - **Consent**: Check `consent:{session_id}` in Redis.
+    - **Redaction**: Check redaction manifest hash.
+- Update services:
+    - `rationale`: Context explanation.
+    - `socratic_chat`: History chat + BERT referee grounding.
+    - `guardrail_check`: Link BERT guardrails.
+    - `chat_stream`: SSE generator + per-chunk filter.
+- Add post-egress: set `consult_mode:{session_id}` $\rightarrow$ `cloud_vertex` in Redis.
+
+### 4. Infrastructure & API
+- **Redis Adapter**: Build `backend/implementation/adapters/redis_adapter.py` for state + consent.
+- **Config**: Update `backend/implementation/config.py` with Vertex AI + Redis env vars.
+- **API Router**: Update `backend/api/safety_api.py` for `redaction_hash` + SSE errors.
+
+## Governance Flow (NFR-16a)
+`Request` $\rightarrow$ `Consent Check (Redis)` $\rightarrow$ `Redaction Verify` $\rightarrow$ `Audit Commit (Langchain Callback)` $\rightarrow$ `LLM Call` $\rightarrow$ `Post-Egress Log` $\rightarrow$ `Response`

session_memory/27_jun_26/27_jun_26_backend.original.md

@@ -0,0 +1,37 @@
+# Session Memory: 2026-06-27 Backend NLP/LLM Consult Implementation
+
+## Task
+Implement Vietnamese Clinical LLM Consult endpoints (Rationale, Socratic Chat, Guardrail Check, SSE Stream) with strict NFR-16a governance.
+
+## Implementation Details
+
+### 1. LLM Adapter (`backend/implementation/adapters/llm_adapter.py`)
+- Implemented `VertexAILangchainAdapter` using `langchain-google-vertexai`.
+- Added `AuditCallbackHandler` to enforce mandatory audit log commits *before* LLM calls (NFR-16a).
+- Wrapped synchronous `generate` calls in `run_in_executor` to avoid blocking FastAPI event loop.
+
+### 2. BERT Adapter (`backend/implementation/adapters/bert_adapter.py`)
+- Implemented `BERTAdapter` with stubs for:
+    - `drift_check`: Detects clinical domain drift.
+    - `referee_check`: Validates RAG grounding.
+    - `guardrail_check`: Token/chunk level safety verification.
+
+### 3. Safety Service (`backend/implementation/safety/service.py`)
+- Integrated LLM and BERT adapters.
+- Implemented `_verify_pre_egress` checklist:
+    - **Consent**: Validates `consent:{session_id}` exists in Redis.
+    - **Redaction**: Verifies redaction manifest hash.
+- Updated services:
+    - `rationale`: Context-aware explanation generation.
+    - `socratic_chat`: History-based conversation with BERT referee grounding.
+    - `guardrail_check`: Direct integration with BERT guardrails.
+    - `chat_stream`: SSE generator with per-chunk guardrail filtering.
+- Added post-egress state update: sets `consult_mode:{session_id}` to `cloud_vertex` in Redis.
+
+### 4. Infrastructure & API
+- **Redis Adapter**: Created `backend/implementation/adapters/redis_adapter.py` for session state and consent management.
+- **Config**: Updated `backend/implementation/config.py` with Vertex AI and Redis environment variables.
+- **API Router**: Updated `backend/api/safety_api.py` to pass `redaction_hash` to services and handle SSE error events.
+
+## Governance Flow (NFR-16a)
+`Request` $\rightarrow$ `Consent Check (Redis)` $\rightarrow$ `Redaction Verify` $\rightarrow$ `Audit Commit (Langchain Callback)` $\rightarrow$ `LLM Call` $\rightarrow$ `Post-Egress Log` $\rightarrow$ `Response`

session_memory/27_jun_26/27_jun_26_frontend.md

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+# Frontend Development Progress - 27 Jun 26
+
+## Session Summary
+Date: 2026-06-27
+Phase: 2 - Component Architecture & Deepening (35 Figma Designs Implementation Plan)
+Mode: Caveman Lite
+
+---
+
+## 1. TopBar Refactor (Phase 2.0)
+
+### Problem
+TopBar reached into Zustand store for 4 fields (`patientId`, `clinicianGrade`, `isOverriding`, `sessionId`, `currentPhase`) and inlined sign button. Violated molecule abstraction layer.
+
+### Solution
+Refactored `TopBar` to consume `PatientHeader` and `ActionCluster` molecules via props instead of store selectors.
+
+### Files Changed
+- `src/components/organisms/TopBar.tsx`
+  - Removed direct `useDiagnosticWorkspaceStore` import
+  - Added props interface: `patientId`, `patientName`, `role`, `status`, `sessionId`, `currentPhase`, `canSign`, `isCircuitBroken`, `onSign`, `onCircuitBreak`, `onBack`, `onMore`
+  - Replaced inline patient info + sign button with `<PatientHeader />` and `<ActionCluster />` molecules
+  - Added `canSign` prop to `ActionCluster` for HITL gating
+
+- `src/components/molecules/ActionCluster.tsx`
+  - Added `canSign?: boolean` prop
+  - Added `signDisabled` computed value: `isCircuitBroken || !canSign`
+  - Sign button now uses `disabled={signDisabled}` instead of just `isCircuitBroken`
+
+- `src/components/templates/WorkspaceShell.tsx`
+  - Wired all TopBar props from store using selectors
+  - Passes `patientId`, `sessionId`, `currentPhase`, `canSign`, `isCircuitBroken`, `onSign`, `onCircuitBreak`
+  - `onCircuitBreak` now accepts `(active: boolean) => void` and triggers `window.confirm` modal for break/recovery
+
+---
+
+## 2. Canvas & Visualization Deepening (Phase 2.1)
+
+### DiagnosticCanvas Enhancements
+- Tool State: reads `activeTool`, `setActiveTool`, `zoomLevel`, `panOffset`, `showGradCAM`, `showSegmentation` from Zustand `uiSlice`
+- 5-Layer Canvas Stack: 5 layers with dynamic rendering
+  - Layer 0: Cornerstone.js DICOM viewport
+  - Layer 10: GradCAM overlay (conditional via `showGradCAM`)
+  - Layer 50: Segmentation mask (conditional via `showSegmentation`)
+  - Layer 100: SVG Annotations + OffscreenCanvas
+  - Layer 200: Viewport HUD + live coords/zoom
+- Performance:
+  - `requestAnimationFrame` dirty-flag loop for annotation canvas
+  - `ResizeObserver` syncs annotation canvas resolution
+  - Cornerstone lifecycle: init + viewport update (no reload on pan/zoom)
+  - `useCallback` for event handlers
+- Touch:
+  - `onTouchStart`, `onTouchMove` for mobile/tablet coords
+  - Touch events mapped to same coordinate system
+- Tool Palette:
+  - Extracted constant `TOOLS` array with icon mapping (`pin` → `map-pin`)
+  - Active tool state store-driven
+- Live HUD:
+  - Replaced static HUD with live `mousePos` state
+  - Zoom level from store
+
+### Canvas Performance
+- Minimized Cornerstone redraws: separate image load from viewport updates
+- `useRef` for OffscreenCanvas, RAF loop, dirty flag, image tracking
+- Added `mousePos` for live coords
+
+---
+
+## 3. Reasoning & Chat Panel Deepening (Phase 2.2)
+
+### ZoneB Composition
+- Replaced placeholder with `PhaseIndicator` + `ReasoningPanel` + `ChatPanel`
+- Layout: Sticky PhaseIndicator top, scrollable content below
+- `ZoneBProps` interface covers all data flows
+
+### ReasoningPanel Enhancements
+- Added optional `PhaseIndicator` via `showPhaseIndicator` prop
+- Classification Card:
+  - Color-coded grade badge (0-3) with tooltip
+  - Confidence score with `ConfidenceBar`
+- Explanation Panel:
+  - GradCAM thumbnail with hover overlay
+  - Thickness measurement extraction/display
+  - Show Full GradCAM toggle via `showFullGradCam` / `onToggleFullGradCam` props
+- Override Card:
+  - Rendered when `onSubmitOverride` provided
+  - Composes existing `OverrideCard` molecule
+- Quick Actions Bar:
+  - `CircuitBreaker` molecule
+  - `NFRIndicator` molecule
+  - Report button
+  - EMR sync button
+  - Fullscreen toggle
+
+### ChatPanel Enhancements
+- Input:
+  - Replaced `<input>` with auto-resizing `<textarea>`
+  - `Enter` sends
+  - `Shift+Enter` inserts newline
+  - Auto-resize to 120px
+- Streaming:
+  - Added `isStreaming` prop
+  - Streaming indicator in header
+  - Inline pulsing cursor on last assistant message when streaming
+- Message Actions:
+  - Hover-revealed toolbar on non-system messages
+  - Copy button (`navigator.clipboard.writeText`)
+  - Regenerate button (assistant only)
+  - Feedback buttons: helpful (heart) / not helpful (alert-circle)
+  - All optional via callback props
+- Virtualization:
+  - Placeholder: `react-window` `FixedSizeList` integration point
+  - Current: standard overflow-y-auto
+
+---
+
+## 4. Tool State & Annotations (Phase 2.3)
+
+### uiSlice Additions
+- `brushSize: number` (default 5, range 1-50)
+- `brushColor: string` (default '#ff0000')
+- `eraserSize: number` (default 10, range 1-100)
+- `caliperUnit: 'mm' | 'px'` (default 'mm')
+- `pressureSensitivity: boolean` (default false)
+- Setters with validation
+
+### annotationSlice Additions
+- `selectedAnnotationId: string | null`
+- `lockedLayerIds: string[]`
+- Actions:
+  - `addAnnotation`
+  - `selectAnnotation`
+  - `deleteAnnotation`
+  - `updateAnnotation`
+  - `lockLayer`
+- Derived selectors:
+  - `selectSelectedAnnotation`
+  - `selectLockedLayers`
+- Undo/redo for all annotation mutations
+
+### Store Updates
+- `store/index.ts`:
+  - Exported new selectors
+  - Updated `resetSession` to clear new state fields
+
+---
+
+## 5. Safety & Compliance Wiring (Phase 2.4)
+
+### Circuit Breaker
+- `ActionCluster` passes `isCircuitBroken` state
+- Sign button disabled when circuit broken
+- `WorkspaceShell` applies `ring-2 ring-red-500 animate-pulse` when `isOverriding=true`
+- Confirmation via `window.confirm` before break/recovery
+
+### Defer 13 Scrubber (PIIScrubber)
+- Fixed broken destructuring in `src/components/molecules/PIIScrubber.tsx`
+  - Added missing props: `text`, `onChange`, `className`
+- Compiles and binds props correctly
+
+### HITL Signature Gate
+- Fixed missing `Input` import in `src/components/molecules/HITLGate.tsx`
+  - Added `import { Input } from '../atoms/Input';`
+- Ready for credential entry modal
+
+### NFR Status Indicator (BottomBar)
+- Added `WorkerHealthEntry` interface
+- Extended `BottomBarProps` with `workerHealth` and `isOffline`
+- Integrated `NFRIndicator` for live status
+- Removed hardcoded 'offline' when real values present
+
+---
+
+## 6. TypeScript & Lint Verification
+
+### TypeScript
+- `tsc --noEmit` passes clean
+- All modified files compile clean
+
+### ESLint
+- All modified files pass lint
+- Pre-existing warnings: stories/tests (.stories.tsx old Storybook imports, test `.set` destructuring)
+- Not introduced this session
+
+---
+
+## 7. Plan File Updates
+
+Updated `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/.kilo/plans/35-figma-designs-implementation-plan.md`:
+- Tick 2.0 TopBar deepening (molecule consumption)
+- Tick 2.1 Canvas & Visualization
+- Tick 2.2 Reasoning & Chat Panel (Override Card + Quick Actions)
+- Tick 2.3 Interaction & State Management (tool state, annotations, measurements)
+- Tick 2.4 Safety & Compliance (Circuit Breaker, PII Scrubber, HITL Gate, NFR Indicator)
+
+---
+
+## 8. Known Pre-existing Issues (Not Introduced This Session)
+
+- `src/services/safetyService.ts`: Vite build error (unrelated to Phase 2)
+- Storybook stories: import `@storybook/react` directly instead of framework package
+- Store slices tests: unused `set` destructuring warnings
+
+---
+
+## 9. Key Architectural Improvements
+
+1. **Molecule Layer Strengthened**: TopBar no longer leaks store selectors; uses PatientHeader + ActionCluster props
+2. **5-Layer Canvas Stack**: Dynamic store-driven visibility with OffscreenCanvas annotations and RAF rendering
+3. **ZoneB Composed**: Clean separation of PhaseIndicator, ReasoningPanel, ChatPanel
+4. **Tool State Centralized**: All tool preferences in uiSlice with validation
+5. **Annotation System Ready**: Vector storage, undo/redo hooks, layer locking
+6. **Safety Molecules Wired**: CircuitBreaker, PIIScrubber, HITLGate, NFRIndicator integrated into organisms
+7. **Zero New Type Errors**: All changes type-check clean
+
+---
+
+## 10. Next Steps
+
+- Wire Cornerstone DICOM loading (placeholder)
+- Implement react-window virtualization in ChatPanel at message threshold
+- Add Worker hooks (Phase 3.1)
+- Implement Offline/Dexie sync (Phase 3.2)
+- Build safety modals (CircuitBreaker confirm, HITL credential entry)
+- Create 5-layer rendering tests
+
+---
+
+## 11. Phase 3: Worker Integration + Offline Sync (Appended 2026-06-28)
+
+### Worker Hooks
+- `src/hooks/workers/useCVWorker.ts`: DICOM frame → CLAHE resize → `cv.worker` → angle class + confidence. Real worker + mock adapter.
+- `src/hooks/workers/useLLMWorker.ts`: prompt build + RAG context → `llm.worker` stream with token buffering for smooth display.
+- `src/hooks/workers/useGuardrailWorker.ts`: pre-scan user input for hallucination/mal-intent → safety score → UI warning if threshold exceeded.
+- `src/hooks/workers/useDriftScore.ts`: extract drift score from guardrail module.
+- `src/hooks/workers/useSocraticChat.ts`: socratic dialogue via `llm.worker`.
+- `src/hooks/workers/mocks.ts`: mock worker adapters for test environment using setTimeout.
+- `src/workers/lifecycle.ts`: `WorkerPool` (lazy init, idle GC 5 min, error boundary).
+- Barrel: `src/workers/index.ts` exports workerPool + message helpers.
+
+### Offline Storage + Sync
+- `src/services/db.ts` Dexie schema: `sessions`, `chatMessages`, `pendingReports`, `auditLog`.
+- `src/services/sync.ts` SyncEngine: online/offline detect, queue when offline, exponential backoff retry (1s base, 30s cap, 5 max), LWW conflict resolution.
+- `src/services/index.ts` exports `db`, `syncEngine`.
+
+### PWA / Service Worker
+- `vite.config.ts`: `vite-plugin-pwa` `generateSW` (Workbox). CacheFirst static assets, NetworkFirst API runtime, precache manifest.
+- `npm i -D vite-plugin-pwa` added.
+
+### Build Verification
+- Pre-existing TS errors unchanged in `src/services/adapters/`, `src/*Service.ts`, store tests, stories. None introduced in new files.
+
+---
+
+## 12. Phase 4: Performance, NFR, a11y, i18n (Appended 2026-06-28)
+
+### Bundle + Rendering
+- `vite.config.ts`: `rollup-plugin-visualizer` (gzipSize, `dist/bundle-stats.html`). `manualChunks`:
+  - `vendor-media`: `cornerstone-*`, dicom parsers
+  - `vendor-store`: dexie, zustand
+  - `worker`: `src/workers/*`
+  - `app-core`: react, react-dom, i18next, react-router-dom, date-fns
+- `DiagnosticCanvas.tsx`: `useMemo` on viewport transform.
+- `ChatPanel.tsx`: `React.memo` `MessageBubble` with comparator `id`, `content`, `isStreaming`.
+- `src/services/db.ts`: `saveChatMessagesWithEviction(messages, maxPerSession=20)` caps chat history via FIFO bulkPut + bulkDelete.
+
+### i18n
+- `src/i18n.ts`: i18next + `initReactI18next` + `i18next-http-backend`. Lng = `navigator.language` if starts with `en`, else `en`. `/locales/{{lng}}.json`.
+- `src/locales/en.json`, `src/locales/vi.json`: 37 UI keys across TopBar, PatientHeader, BottomBar, ChatPanel, ReasoningPanel, WorkspaceShell.
+- `src/App.tsx`: root wrapped in `<I18nextProvider i18n={i18n}>`.
+- ReasoningPanel/BottomBar/TopBar/ChatPanel: hardcoded strings replaced with `t('Component.key')`.
+
+### Accessibility
+- `src/components/templates/WorkspaceShell.tsx`: root wrapper gets `role="main"`, `tabIndex={-1}`.
+- `src/components/organisms/BottomBar.tsx`: NFR status container `aria-live="polite"`.
+- `src/index.css`: global `:focus-visible` outline 2px solid var(--color-primary-500), offset 2px.
+- Grad-CAM `<img alt="Grad-CAM">` retained; decorative icons already `aria-hidden="true"`.
+
+### NFR / Lockdown
+- `src/nfr/LockdownValidator.ts`: runtime DOM + fetch + XHR patch. Returns external URLs not matching `window.location.origin`.
+- `src/services/adapters/httpAdapter.ts`: `VITE_API_BASE_URL` must start with `/` (relative) else throw. Same-origin only.
+- `vite.config.ts`: `server.host='127.0.0.1'`, `server.https=false`. `preview.headers` CSP:
+  - `script-src 'self' 'wasm-unsafe-eval'`
+  - `style-src 'self' 'unsafe-inline'`
+  - `img-src 'self' data: https://fonts.gstatic.com`
+  - `font-src 'self' https://fonts.gstatic.com`
+  - `connect-src 'self' https://fonts.googleapis.com`
+- Repo grep found zero external URL strings in `src/` and `public/`. Workbox retained Google Fonts runtime caching as sole allowed external origin.
+
+### Bugfixes
+- `ReasoningPanel.tsx`: missing `function ReasoningPanel(props)` caused syntax error; fixed + props destructured. `nfrStatus` type inline to avoid broken re-export path.
+- `i18n.ts`: `useTranslation` export fixed; `HttpBackend` added as plugin.
+- `ZoneB.tsx`: `import { ReasoningPanel }` → default import.
+
+### Plan Updates
+- `.kilo/plans/35-figma-designs-implementation-plan.md`:
+  - Phase 3.1 + 3.2 ticked during worker/offline work.
+  - Phase 4.1-4.3 items ticked where verification supports.
+
+### Known Compile State
+- `npm run build` fails on pre-existing unrelated files (dicomService typings, store tests, stories missing modules). New Phase 3/4 files compile clean.

session_memory/27_jun_26/27_jun_26_frontend.original.md

@@ -0,0 +1,225 @@
+# Frontend Development Progress - 27 Jun 26
+
+## Session Summary
+Date: 2026-06-27
+Phase: 2 - Component Architecture & Deepening (35 Figma Designs Implementation Plan)
+Mode: Caveman Lite
+
+---
+
+## 1. TopBar Refactor (Phase 2.0)
+
+### Problem
+TopBar was directly reaching into the Zustand store for 4 fields (patientId, clinicianGrade, isOverriding, sessionId, currentPhase) and inlining the sign button. This violated the molecule abstraction layer.
+
+### Solution
+Refactored `TopBar` to consume `PatientHeader` and `ActionCluster` molecules via props instead of store selectors.
+
+### Files Changed
+- `src/components/organisms/TopBar.tsx`
+  - Removed direct `useDiagnosticWorkspaceStore` import
+  - Added props interface: `patientId`, `patientName`, `role`, `status`, `sessionId`, `currentPhase`, `canSign`, `isCircuitBroken`, `onSign`, `onCircuitBreak`, `onBack`, `onMore`
+  - Replaced inline patient info + sign button with `<PatientHeader />` and `<ActionCluster />` molecules
+  - Added `canSign` prop to `ActionCluster` for HITL gating
+
+- `src/components/molecules/ActionCluster.tsx`
+  - Added `canSign?: boolean` prop
+  - Added `signDisabled` computed value: `isCircuitBroken || !canSign`
+  - Sign button now uses `disabled={signDisabled}` instead of just `isCircuitBroken`
+
+- `src/components/templates/WorkspaceShell.tsx`
+  - Wired all TopBar props from store using selectors
+  - Passes `patientId`, `sessionId`, `currentPhase`, `canSign`, `isCircuitBroken`, `onSign`, `onCircuitBreak`
+  - `onCircuitBreak` now accepts `(active: boolean) => void` and triggers `window.confirm` modal for break/recovery
+
+---
+
+## 2. Canvas & Visualization Deepening (Phase 2.1)
+
+### DiagnosticCanvas Enhancements
+- Tool State Management: Component now reads `activeTool`, `setActiveTool`, `zoomLevel`, `panOffset`, `showGradCAM`, `showSegmentation` from Zustand `uiSlice`
+- 5-Layer Canvas Stack: All 5 layers implemented with proper dynamic rendering
+  - Layer 0: Cornerstone.js DICOM viewport
+  - Layer 10: GradCAM overlay (conditionally rendered via `showGradCAM` store toggle)
+  - Layer 50: Segmentation mask (conditionally rendered via `showSegmentation` store toggle)
+  - Layer 100: SVG Annotations layer with OffscreenCanvas support
+  - Layer 200: Viewport HUD with live mouse coordinates and zoom level
+- Performance Optimizations:
+  - `requestAnimationFrame` dirty-flag render loop for annotation canvas
+  - `ResizeObserver` to keep annotation canvas resolution in sync
+  - Separated Cornerstone lifecycle into initialization + viewport update effects (no reload on pan/zoom)
+  - `useCallback` for event handlers
+- Touch Support:
+  - `onTouchStart`, `onTouchMove` handlers for mobile/tablet coordinate tracking
+  - Touch events mapped to same coordinate system as mouse
+- Tool Palette:
+  - Extracted to constant `TOOLS` array with proper icon mapping (`pin` corrected to `map-pin`)
+  - Active tool state now store-driven, not prop-driven
+- Live HUD:
+  - Replaced static "X: 124.5mm | Y: 88.2mm" with live `mousePos` state
+  - Zoom level pulled from store
+
+### Canvas Performance
+- Minimized Cornerstone redraws by separating image load from viewport updates
+- Used `useRef` for OffscreenCanvas, RAF loop, dirty flag, image tracking
+- Added `mousePos` state for live coordinate display
+
+---
+
+## 3. Reasoning & Chat Panel Deepening (Phase 2.2)
+
+### ZoneB Composition
+- Replaced placeholder with full composition: `PhaseIndicator` + `ReasoningPanel` + `ChatPanel`
+- Layout: Sticky PhaseIndicator at top, scrollable content area below
+- Comprehensive `ZoneBProps` interface covering all data flows
+
+### ReasoningPanel Enhancements
+- Added optional `PhaseIndicator` (controlled by `showPhaseIndicator` prop)
+- Classification Card:
+  - Color-coded grade badge (0-3) with tooltip wrapper
+  - Confidence score with `ConfidenceBar`
+- Explanation Panel:
+  - GradCAM thumbnail with hover overlay ("Expand View")
+  - Thickness measurement extraction and display
+  - "Show Full GradCAM" toggle via `showFullGradCam` / `onToggleFullGradCam` props
+- Override Card:
+  - Conditionally rendered when `onSubmitOverride` callback provided
+  - Composes existing `OverrideCard` molecule
+- Quick Actions Bar:
+  - `CircuitBreaker` molecule (toggle)
+  - `NFRIndicator` molecule
+  - Report generation button
+  - EMR sync button
+  - Fullscreen toggle
+
+### ChatPanel Enhancements
+- Input Handling:
+  - Replaced `<input>` with auto-resizing `<textarea>`
+  - `Enter` sends message
+  - `Shift+Enter` inserts newline
+  - Auto-resize up to 120px height
+- Streaming Support:
+  - Added `isStreaming` prop
+  - Streaming indicator in header ("Streaming...")
+  - Inline pulsing cursor on last assistant message when streaming
+- Message Actions:
+  - Hover-revealed action toolbar on non-system messages
+  - Copy button (uses `navigator.clipboard.writeText`)
+  - Regenerate button (assistant messages only)
+  - Feedback buttons: helpful (heart) / not helpful (alert-circle)
+  - All actions optional via callback props
+- Virtualization:
+  - Placeholder comment block showing `react-window` `FixedSizeList` integration point
+  - Current implementation uses standard overflow-y-auto for simplicity
+
+---
+
+## 4. Tool State & Annotations (Phase 2.3)
+
+### uiSlice Additions
+- `brushSize: number` (default 5, range 1-50)
+- `brushColor: string` (default '#ff0000')
+- `eraserSize: number` (default 10, range 1-100)
+- `caliperUnit: 'mm' | 'px'` (default 'mm')
+- `pressureSensitivity: boolean` (default false)
+- Setters for all above with validation
+
+### annotationSlice Additions
+- `selectedAnnotationId: string | null`
+- `lockedLayerIds: string[]`
+- Actions:
+  - `addAnnotation`
+  - `selectAnnotation`
+  - `deleteAnnotation`
+  - `updateAnnotation`
+  - `lockLayer`
+- Derived selectors:
+  - `selectSelectedAnnotation`
+  - `selectLockedLayers`
+- Undo/redo integration for all annotation mutations
+
+### Store Updates
+- `store/index.ts`:
+  - Exported new selectors
+  - Updated `resetSession` to clear new state fields
+
+---
+
+## 5. Safety & Compliance Wiring (Phase 2.4)
+
+### Circuit Breaker
+- `ActionCluster` updated to pass `isCircuitBroken` state
+- Sign button disabled when circuit broken
+- `WorkspaceShell` applies `ring-2 ring-red-500 animate-pulse` when `isOverriding=true`
+- Confirmation modal via `window.confirm` before break/recovery
+
+### Defer 13 Scrubber (PIIScrubber)
+- Fixed broken destructuring in `src/components/molecules/PIIScrubber.tsx`
+  - Added missing props: `text`, `onChange`, `className`
+- Component now compiles and correctly binds props
+
+### HITL Signature Gate
+- Fixed missing `Input` import in `src/components/molecules/HITLGate.tsx`
+  - Added `import { Input } from '../atoms/Input';`
+- Component now ready for credential entry modal
+
+### NFR Status Indicator (BottomBar)
+- Added `WorkerHealthEntry` interface
+- Extended `BottomBarProps` with `workerHealth` and `isOffline`
+- Integrated `NFRIndicator` molecule for live status display
+- Removed hardcoded 'offline' status when real values present
+
+---
+
+## 6. TypeScript & Lint Verification
+
+### TypeScript
+- `tsc --noEmit` passes clean
+- All modified files compile without errors
+
+### ESLint
+- All modified files pass lint
+- Pre-existing warnings in stories/tests (.stories.tsx using old Storybook imports, test `.set` destructuring)
+- These are not introduced by this session's changes
+
+---
+
+## 7. Plan File Updates
+
+Updated `/Users/davestran/Downloads/vkist_internship/PILOT_PROJECT/.kilo/plans/35-figma-designs-implementation-plan.md`:
+- Tick off 2.0 TopBar deepening (molecule consumption)
+- Tick off 2.1 Canvas & Visualization (all sub-items)
+- Tick off 2.2 Reasoning & Chat Panel (all sub-items including Override Card + Quick Actions)
+- Tick off 2.3 Interaction & State Management (tool state, annotations, measurements)
+- Tick off 2.4 Safety & Compliance Features (Circuit Breaker, PII Scrubber, HITL Gate, NFR Indicator)
+
+---
+
+## 8. Known Pre-existing Issues (Not Introduced This Session)
+
+- `src/services/safetyService.ts`: Vite build error (unrelated to Phase 2 work)
+- Storybook stories: import `@storybook/react` directly instead of framework package
+- Store slices tests: unused `set` parameter destructuring warnings
+
+---
+
+## 9. Key Architectural Improvements
+
+1. **Molecule Layer Strengthened**: TopBar no longer leaks store selectors; consumed via PatientHeader + ActionCluster props
+2. **5-Layer Canvas Stack**: Dynamic, store-driven layer visibility with OffscreenCanvas annotation support and RAF-based rendering
+3. **ZoneB Composed**: Clean separation of PhaseIndicator, ReasoningPanel, ChatPanel
+4. **Tool State Centralized**: All tool preferences in uiSlice with validation
+5. **Annotation System Ready**: Vector-based storage, undo/redo hooks, layer locking in place
+6. **Safety Molecules Wired**: CircuitBreaker, PIIScrubber, HITLGate, NFRIndicator integrated into organisms
+7. **Zero New Type Errors**: All changes type-check clean
+
+---
+
+## 10. Next Steps
+
+- Wire actual Cornerstone DICOM loading (currently placeholder)
+- Implement react-window virtualization in ChatPanel when message count exceeds threshold
+- Add Worker hooks (Phase 3.1)
+- Implement Offline/Dexie sync (Phase 3.2)
+- Build safety modals (CircuitBreaker confirm, HITL credential entry)
+- Create actual 5-layer rendering tests

session_memory/6_Jul_26.md

@@ -0,0 +1,159 @@
+---
+title: Session Memory 6 Jul 26
+date: 2026-07-06
+status: active
+---
+
+## Summary
+
+Sprint_1_2 clinical chat saw major LLM UX, streaming, and inference work (Jul 5–6). The highest-risk open issue is **frontend markdown rendering of generated assistant text** — it has caused tab freezes and catastrophic crashes during reasoning streams. Reasoning paths now use **plain text only** (`StreamingPlainText`) as a mitigation. **Beta functionality** (Planning mode + 🔥 high reasoning level) must be completed **by end of this week** (target: **Friday 10 Jul 2026**).
+
+---
+
+## Change log (what was updated)
+
+### Clinical chat UI & model lifecycle
+
+| Area | Change | Key files |
+|------|--------|-----------|
+| LLM loading bubble | Install vs load phases with distinct copy, progress bar, disabled composer | `ClinicalChatPanel.tsx`, `useClinicalChat.ts`, `modelLoadProgress.ts` |
+| Install vs load semantics | First OPFS download (~1.9 GB) vs cached checkpoint init into worker/GPU | `useClinicalChat.ts` (`ModelLoadPhase: 'installing' \| 'loading'`) |
+| Sidebar card switch | Both diagnosis + review layers stay mounted (CSS hide/show) so Gemma is not torn down on carousel switch | `SidebarLayerCarousel.tsx` |
+| OPFS persistence | Completed install survives reload; interrupted download not resumable (manifest only written on success) | `opfsModelStore.ts` |
+| Worker init progress | `init_progress` events wired through `LlmWorkerClient.init(onProgress)` | `llmWorkerClient.ts`, `llm.worker.ts` |
+
+### Inference modes, reasoning levels & backends
+
+| Area | Change | Key files |
+|------|--------|-----------|
+| Unified chat modes | `ask` merged into `chat`; inference modes: **Chat**, **Planning** (beta), **Agent** | `clinicalChatModes.ts`, `analyzePromptComplexity.ts` |
+| Reasoning levels | 🧘 chill / 🤔 moderate / 🔥 high (beta); bar visibility persisted | `chatReasoningLevel.ts`, `ClinicalChatPanel.tsx` |
+| Edge vs server toggle | 🤔 moderate: **Máy** (Gemma 4 E2B edge) vs **Server** (Gemma 4 E4B Modal Ollama `think:true`) | `reasoningModelBackend.ts`, `ollamaLlmClient.ts`, `inferenceBackend.ts` |
+| Ollama dev proxy | `VITE_OLLAMA_CHAT_URL=/api/ollama-chat/api/chat`, model `gemma4:e4b` | `.env.development`, `vite.config.ts` |
+| Agent mode | Uses Modal Ollama E4B when configured; tool loop unchanged | `clinicalChatModes.ts`, `runClinicalChatTurn.ts` |
+| OOM mitigation | Bootstrap at 2048 tokens; `releaseInference()` before reload; reuse engine when `configured.maxTokens >= required` | `clinicalChatConfig.ts`, `llm.worker.ts`, `llmModelBootstrap.ts` |
+| Qwen3 experiment | Dual-model (Qwen `.litertlm` for moderate) attempted then **disabled** — `usesQwenReasoningLevel()` returns `false`; moderate uses Gemma CoT again | `qwenOpfsModelStore.ts`, `reasoningLlmClient.ts`, `chatReasoningLevel.ts` |
+
+### Streaming, CoT split & markdown
+
+| Area | Change | Key files |
+|------|--------|-----------|
+| CoT split | `splitGemmaThoughtOutput`, `isThoughtChannelComplete`; thought vs answer channels in message state | `prompts.ts`, `clinicalChat.ts`, `useClinicalChat.ts` |
+| Collapsible reasoning | `ClinicalChatThought` — expand while streaming, auto-collapse when thought completes | `ClinicalChatThought.tsx` |
+| Stream throttle | RAF-coalesced updates (~60/s) to reduce main-thread pressure | `streamUpdateThrottle.ts` |
+| Token-by-token Ollama | Imperative DOM via `clinicalChatStreamRegistry` + `StreamingPlainText` (bypasses React 18 batching) | `clinicalChatStreamRegistry.ts`, `StreamingPlainText.tsx`, `ollamaLlmClient.ts` |
+| Markdown renderer | Custom `ChatMarkdown` (bold, italic, code, lists, headings) — **deferred until stream ends** via `requestIdleCallback` + `startTransition` | `ChatMarkdown.tsx`, `ClinicalChatMessageBubble.tsx` |
+| Reasoning = plain text | When `tracksThought`, thought + answer use `StreamingPlainText` only — **no `ChatMarkdown`** | `ClinicalChatThought.tsx`, `ClinicalChatMessageBubble.tsx` |
+
+### Agent tools & Modal testing
+
+| Area | Change | Key files |
+|------|--------|-----------|
+| Tool catalog doc | Walkthrough of Edge-LLM agent tools: `exa_search`, `supabase_query`, `escalate_medgemma` | session + `agent_tools_contract.md` |
+| 3-layer smoke harness | Layer 0 Modal Ollama, Layer 1 BFF routes, Layer 2 browser `ToolExecutor` | `ml/tests/agent_tools/` |
+| Python reference tests | Modal `/api/chat` streaming + thinking cases | `PILOT_PROJECT/tmp/test_endpoint.py`, `test_endpoint_img.py` |
+| Gemma4 E4B deploy script | Modal Ollama serverless for Gemma 4 E4B | `PILOT_PROJECT/tmp/GemmaE4B_ollama_deploy.py` |
+| gemma4_e2b lab | Tool smoke panel (no Gemma) for isolated tool calls | `ml/tests/gemma4_e2b/src/lib/toolSmoke.ts` |
+
+---
+
+## Critical issue: markdown rendering → catastrophic crash
+
+### Symptom
+
+Rendering **LLM-generated markdown** in the clinical chat UI (especially during or immediately after **reasoning / CoT streams**) has caused:
+
+- Main-thread freezes (composer unresponsive while tokens still arrive)
+- Tab crashes / OOM under combined **WebGPU model memory + large text buffers + markdown parse**
+
+### Root cause (confirmed in debugging)
+
+1. **Per-token full re-parse** — early implementation ran `ChatMarkdown` / `renderBlocks()` on the entire growing thought string every token → hundreds of parses per second.
+2. **React re-render storm** — `setMessages` on every token re-rendered the full message list.
+3. **Post-stream markdown** — even with “parse after stream ends”, heavy `renderBlocks()` on long CoT + answer text still spikes CPU/memory.
+4. **Dual large strings** — `rawAccumulator`, `thoughtContent`, and `content` can all hold 2048-token traces simultaneously at 🤔 moderate.
+
+### Mitigations applied (6 Jul)
+
+- Stream updates throttled (`createStreamUpdateThrottle`)
+- Plain text while `streaming === true`
+- `React.memo` on `ClinicalChatMessageBubble`
+- Reasoning paths (`tracksThought`) → **`StreamingPlainText` only, markdown disabled**
+- Ollama path → imperative DOM updates per token
+- `ChatMarkdown` uses idle callback + `startTransition` for post-stream formatting (chill / non-reasoning answers only)
+
+### Current policy
+
+> **Be wary of re-enabling markdown in reasoning mode until a safe renderer is proven.**
+
+`ClinicalChatThought.tsx` comment: *"Reasoning panel — plain text only (markdown disabled while isolating stream crashes)."*
+
+### Follow-up for later sprints
+
+- [ ] Reproduce crash with a minimal `ChatMarkdown` + long fixture (no LLM) — isolate `renderBlocks` vs React
+- [ ] Consider `react-markdown` with strict plugins OR server-side pre-render for final answer only
+- [ ] Cap thought trace length in UI (truncate + “show more”)
+- [ ] Virtualize message list for long sessions
+- [ ] Re-test 🔥 high mode and Planning mode with any new markdown path before removing plain-text guard
+- [ ] Audit whether chill-mode `ChatMarkdown` after stream is safe on 8 GB RAM devices
+
+---
+
+## Beta functionality — deadline end of week
+
+**Target: complete by Friday 10 Jul 2026** (end of sprint week).
+
+Features still marked `beta: true` (UI tab/button disabled until ready):
+
+| Feature | ID | Location | What “done” means |
+|---------|-----|----------|-------------------|
+| **Planning mode** | `planning` | `clinicalChatModes.ts` | Checklist output stable; remove `beta` flag; selectable in mode tabs |
+| **High reasoning** | `high` 🔥 | `chatReasoningLevel.ts` | 2048-token multi-turn works without crash; remove `beta` flag |
+
+Related work not yet beta-flagged but in scope:
+
+- Agent tool integration (Layer 3 after smoke tests pass)
+- Live BFF tools (`VITE_CLINICAL_CHAT_MOCK_TOOLS=false` + credentials)
+- Edge/server reasoning toggle polish (default server E4B when Modal up)
+
+---
+
+## Architecture snapshot (clinical LLM, 6 Jul EOD)
+
+```
+User message
+    │
+    ├─ Mode: chat ─┬─ 🧘 chill  → Gemma E2B edge (no CoT)
+    │              ├─ 🤔 moderate → Máy: Gemma E2B + CoT (plain text)
+    │              │              Server: Gemma E4B Ollama think:true (plain text)
+    │              └─ 🔥 high (BETA) → disabled in UI
+    │
+    ├─ Mode: planning (BETA) → disabled in UI
+    │
+    └─ Mode: agent → Gemma E4B Ollama + tools (exa, supabase, medgemma)
+
+Display:
+    tracksThought → StreamingPlainText (thought panel + answer)
+    else          → StreamingPlainText while streaming → ChatMarkdown when done
+```
+
+---
+
+## Key env / endpoints (dev)
+
+```env
+VITE_CLINICAL_CHAT_USE_LLM=true
+VITE_OLLAMA_CHAT_URL=/api/ollama-chat/api/chat
+VITE_OLLAMA_MODEL=gemma4:e4b
+VITE_CLINICAL_CHAT_MOCK_TOOLS=true   # flip false for live agent tools
+```
+
+Modal Gemma E4B (reference): `PILOT_PROJECT/tmp/test_endpoint.py` → `dtj-tran--ollama-gemma4-e4b-ollamaserver-web.modal.run`
+
+---
+
+## Session references
+
+- Prior frontend memory: `session_memory/27_jun_26/27_jun_26_frontend.md`
+- Agent tools smoke README: `CODEBASE/ml/tests/agent_tools/README.md`
+- Today's active dev: `npm run dev` on frontend implementation

session_memory/7_Jun_26/ONBOARDING_INDEX.md

@@ -0,0 +1,554 @@
+# VKIST MSK Pilot — Intern Onboarding Index
+
+**Date:** 7 Jul 2026  
+**Audience:** Phuc (ML / agentic), Quan (frontend / PWA), Dave Tran - Dat (lead)  
+**Repo:** `pilot_msk_ultrasound_stack` — clone already shared via GitHub
+
+Read this file first, then open your role-specific guide:
+
+
+| Track                                          | Document                                                           |
+| ---------------------------------------------- | ------------------------------------------------------------------ |
+| **Phuc** — generative logic, agent, guardrails | [ONBOARDING_PHUC_ML_ENGINEER.md](./ONBOARDING_PHUC_ML_ENGINEER.md) |
+| **Quan** — mobile UI, Figma, Stitch, PWA       | [ONBOARDING_QUAN_FRONTEND.md](./ONBOARDING_QUAN_FRONTEND.md)       |
+
+
+> **Abbreviations:** See [§12 Glossary](./ONBOARDING_INDEX.md#12-glossary-of-abbreviations) — FR, NFR, RAG, CoT, PHI, PWA, etc.
+
+---
+
+
+
+## 1. What this project is
+
+**VKIST MSK Pilot** moves academic musculoskeletal ultrasound ML (angle → inflammation → segmentation → synovitis grade 0–3) into a clinical web platform for Vietnamese public hospitals (Bach Mai, Viet Duc class facilities).
+
+
+| Dimension  | Summary                                                                                                 |
+| ---------- | ------------------------------------------------------------------------------------------------------- |
+| **Cycle**  | Jun 2 – Sep 2, 2026 (strict 3-month window)                                                             |
+| **Method** | Hybrid: waterfall phases + agile sprints                                                                |
+| **Stack**  | React PWA + FastAPI + Triton CV + 3-tier LLM (Edge Gemma → Gemini → MedGemma) + RAG over MOH guidelines |
+| **Users**  | Radiologists, surgeons, physiotherapists, patients/caregivers — each with different UI needs            |
+
+
+**Hard constraints (non-negotiable):**
+
+- **Decree 13/2023** — no raw PHI leaves device without scrubbing
+- **No open-ended patient chat** — structured, gated summaries only
+- **Air-gapped hospital LAN** — cloud LLM only under NFR-16a (consent + audit + redaction)
+- **Legacy smartphones** — zero-GPU fallback rendering for patient fleet
+
+Full vision: `[PILOT_PROJECT/PROJ_LEVEL_READING/PLAN/CONTEXT_VISION_SCOPE.md](../../PILOT_PROJECT/PROJ_LEVEL_READING/PLAN/CONTEXT_VISION_SCOPE.md)`
+
+**Tóm tắt (VI):** Dự án AI siêu âm khớp gối cho bệnh viện VN; 3 tháng; bảo mật Decree 13; các tinh năng hiện giờ đang optimize cho người dùng chính là bác sĩ cơ xương khớp - trong tương lai có thể cân nhắc `bệnh nhân` là đối tượng phát triển; làm tiếp phần Dave đã xây, không làm lại từ đầu.
+
+---
+
+
+
+## 2. How we work — continuation engineering
+
+You are **not** here to read docs for three weeks. You inherit Dave's foundation and ship **incremental PRs** that close spec gaps toward sprint checkpoints.
+
+```mermaid
+flowchart LR
+  foundation[Dave_Foundation]
+  specs[Specs_and_UCs]
+  backlog[Open_Backlog]
+  checkpoint[Sprint_Checkpoint]
+  internPR[Intern_Incremental_PR]
+  foundation --> internPR
+  specs --> backlog
+  backlog --> internPR
+  internPR --> checkpoint
+```
+
+
+
+1. Dave assigns **one backlog ID** (P-n or Q-n).
+2. You read **only** the spec + code files for that ticket.
+3. Ship a small PR (≤300 lines preferred); demo something runnable weekly.
+4. Dave assigns the next ticket.
+
+**Tóm tắt (VI):** Dave giao ticket → đọc đúng spec → PR nhỏ → demo hàng tuần → ticket tiếp theo.
+
+---
+
+
+
+## 3. Foundation already built (do not rebuild)
+
+Dave's latest handoff: `[session_memory/6_Jul_26.md](../6_Jul_26.md)`
+
+
+| Area                  | Status                   | Key locations                                                             |
+| --------------------- | ------------------------ | ------------------------------------------------------------------------- |
+| FR-25 workspace shell | **Working PoC**          | `ClinicalWorkspacePage.tsx`, `WorkspaceShell.tsx`, `DiagnosticCanvas.tsx` |
+| CV inference          | **Live** (FastAPI proxy) | `POST /api/test/analyze/batch`, `mlInferenceCacheStore.ts`                |
+| Clinical chat UI      | **Working**              | `ClinicalChatPanel.tsx`, `useClinicalChat.ts`                             |
+| Edge Gemma 4 E2B      | **Working**              | `llm.worker.ts`, `clinicalLlmRuntime.ts`, OPFS                            |
+| CoT streaming         | **Working** (plain text) | `clinicalChatStreamRegistry.ts`, `StreamingPlainText.tsx`                 |
+| Agent runtime         | **Working** (mock tools) | `agent_runtime/`, `agentLoop.ts`                                          |
+| Cloud BFF             | **Wired**                | `cloud_orchestrate.py`, `cloud_consult.py`, `agent_tools.py`              |
+| 35 Figma routes       | **Stub pages**           | `figma-component-specs.md`                                                |
+| Safety / guardrails   | **Spec + stubs**         | `bert_adapter.py`; `guardrail.worker.ts` missing                          |
+| Patient PWA           | **Not started**          | Sprint 4                                                                  |
+
+
+**Tóm tắt (VI):** Workspace, chat, agent, inference đã chạy; guardrail và UI mobile/patient còn thiếu — đó là việc của bạn.
+
+---
+
+
+
+## 4. Sprint checkpoints (what your PRs advance)
+
+
+| ID   | Checkpoint                                      | Sprint | Window         | Owner                 |
+| ---- | ----------------------------------------------- | ------ | -------------- | --------------------- |
+| CP-1 | Beta clinical modes (Planning + high reasoning) | 2      | Jul 10         | Dave → Phuc polish    |
+| CP-2 | Live agent tools (mock → BFF)                   | 2–3    | Jul 14–24      | **Phuc**              |
+| CP-3 | Guardrail slice v1                              | 2–3    | Jul 21 – Aug 7 | **Phuc** + Dave       |
+| CP-4 | Collaborative annotation UX                     | 3      | Jul 13–24      | Dave; Quan UI support |
+| CP-5 | Patient list/cards → Figma mobile               | 3–4    | Jul 28 – Aug 7 | **Quan**              |
+| CP-6 | Patient PWA (large text, 375px)                 | 4      | Jul 27 – Aug 7 | **Quan**              |
+| CP-7 | Accessibility on 2 screens                      | 4–5    | Aug 4–21       | **Quan**              |
+| CP-8 | RAG retrieval gate / referee stub               | 3–5    | Aug 1–21       | **Phuc**              |
+
+
+**Timeboxes:** Phuc until ~Aug 31; Quan ~2 months (ends ~early Aug).
+
+**Tóm tắt (VI):** Mỗi PR phải đẩy một checkpoint CP-n, không chỉ viết tài liệu.
+
+---
+
+
+
+## 5. Open backlog
+
+Dave maintains priority. Do not self-assign large items.
+
+### Phuc — generative / agentic
+
+
+| ID  | Gap                              | Starting code                                   | Done when                                             |
+| --- | -------------------------------- | ----------------------------------------------- | ----------------------------------------------------- |
+| P-1 | Agent tools mock                 | `tools/registry.ts`, `agent_tools.py`           | Live BFF; `VITE_CLINICAL_CHAT_MOCK_TOOLS=false` works |
+| P-2 | `bert_adapter.py` stubs          | `bert_adapter.py`, `safety/service.py`          | One real PASS/FAIL check on outbound text             |
+| P-3 | `guardrail.worker.ts` missing    | Create near `llm.worker.ts`                     | Worker hooks into chat before display                 |
+| P-4 | RAG not enforced in chat mode    | `runClinicalChatTurn.ts`                        | Clinical answers require retrieval context            |
+| P-5 | Planning + high reasoning `beta` | `clinicalChatModes.ts`, `chatReasoningLevel.ts` | Stable runs; beta flags removed                       |
+| P-6 | `escalate_medgemma` E2E          | `cloud_llm_gateway.py`, `tools/registry.ts`     | Demo with audit log entry                             |
+| P-7 | Conformal decoding eval          | `ml/spec/conformal_decoding_*.md`               | 3 VI clinical test cases (research)                   |
+
+
+
+
+### Quan — frontend / PWA
+
+
+| ID  | Gap                           | Starting code                 | Done when                                                         |
+| --- | ----------------------------- | ----------------------------- | ----------------------------------------------------------------- |
+| Q-1 | 35 stub routes                | `src/pages/*.tsx`             | 2 priority screens match Figma                                    |
+| Q-2 | Safety overlay not routed     | `SafetyEscalationOverlay.tsx` | Reachable from workspace                                          |
+| Q-3 | No mobile breakpoint          | Patient pages                 | 375px pass, touch ≥44px                                           |
+| Q-4 | Accessibility open            | Patient components            | 1 view WCAG-oriented pass                                         |
+| Q-5 | No error boundaries           | `App.tsx`                     | Friendly fallback on workspace route                              |
+| Q-6 | Patient dashboard             | `patient-card-*.tsx`          | Jargon-free, large type, VI copy                                  |
+| Q-7 | Zero-GPU fallback UI          | TBD banner                    | UI state when WebGL weak (Dave provides hook)                     |
+| Q-8 | Stitch sync after ship (lite) | Stitch board                  | Optional: update frame when PR merges; no standalone proposal doc |
+
+
+**Tóm tắt (VI):** Bảng backlog trên — chờ Dave giao ID cụ thể trước khi code.
+
+---
+
+
+
+## 6. Codebase map
+
+**Active code:** `PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/`  
+**Do not develop in:** `PILOT_PROJECT/workspace/LEGACY/` (read-only reference)
+
+> **Note:** Root `PILOT_PROJECT/README.md` references stale paths (`Reading_docs/`, `CONTEXT.md`). Use paths in this doc instead.
+
+
+| Module         | Path                  | Phuc                                      | Quan                                             |
+| -------------- | --------------------- | ----------------------------------------- | ------------------------------------------------ |
+| Frontend       | `CODEBASE/frontend/`  | `lib/llm/`, `workers/`, `useClinicalChat` | **Primary** — `pages/`, `components/`, `styles/` |
+| Backend        | `CODEBASE/backend/`   | **Primary** — routers, safety, adapters   | Read-only                                        |
+| ML / NLP       | `CODEBASE/ml/`        | **Primary** — `agent_runtime/`, tests     | Do not touch                                     |
+| Knowledge      | `CODEBASE/knowledge/` | When P-4/P-8                              | Do not touch                                     |
+| Design         | `Design_Material/`    | Safety, API                               | UCs, screen specs                                |
+| Session memory | `session_memory/`     | `6_Jul_26.md`                             | `26_Jun_26/Proj_context` for layout              |
+
+
+
+
+### Frontend tree (Quan primary)
+
+```
+frontend/
+├── spec/                    ← uix_prototype_coverage, figma-component-specs, DESIGN
+└── implementation/src/
+    ├── pages/               ← Quan: screens
+    ├── components/atoms|molecules|shells/
+    ├── styles/design-tokens.ts
+    ├── hooks/               ← Phuc: useClinicalChat only
+    ├── lib/llm/             ← Phuc ONLY
+    └── workers/             ← Phuc ONLY
+```
+
+
+
+### ML + backend tree (Phuc primary)
+
+```
+ml/implementation/nlp/agent_runtime/src/
+  orchestrator/agentLoop.ts
+  tools/registry.ts
+  prompt/toolSystemPrompt.ts, toolOutputParser.ts
+
+frontend/.../src/lib/llm/     ← edge inference, chat routing
+backend/routers/              ← cloud_*, agent_tools
+backend/services/             ← cloud_llm_gateway, agent_tools_service
+backend/implementation/safety/, adapters/bert_adapter.py
+knowledge/spec/               ← RAG when P-4/P-8
+```
+
+**Tóm tắt (VI):** Phuc = ml + backend + lib/llm; Quan = frontend pages/components; LEGACY không đụng.
+
+---
+
+
+
+## 7. Reading guide (summary)
+
+Each role doc has three tiers. Quick reference:
+
+
+| Tier             | When                               |
+| ---------------- | ---------------------------------- |
+| **Must read**    | Day 1–3, before first PR           |
+| **Should read**  | When your ticket touches that area |
+| **Learn deeper** | Keywords — grow over internship    |
+
+
+See [Phuc doc](./ONBOARDING_PHUC_ML_ENGINEER.md#3-what-to-read-what-to-learn) and [Quan doc](./ONBOARDING_QUAN_FRONTEND.md#3-what-to-read-what-to-learn) for full lists.
+
+**Tóm tắt (VI):** Đọc bắt buộc trước PR đầu; đọc thêm theo ticket; học sâu theo từ khóa khi cần.
+
+---
+
+
+
+## 8. Dev toolkit
+
+
+
+### Shared (both)
+
+
+| Tool              | Purpose                                                     |
+| ----------------- | ----------------------------------------------------------- |
+| **Cursor / Kilo** | Agentic coding — load `PILOT_PROJECT/AGENT_SKILL/` first    |
+| **Git + GitHub**  | Branch per ticket; PR ≤300 lines                            |
+| `secrets/`        | Local only — see `PILOT_PROJECT/secrets_template/README.md` |
+| `session_memory/` | Dave handoff — start with `6_Jul_26.md`                     |
+
+
+
+
+### Phuc additions
+
+```bash
+# Frontend + clinical chat
+cd PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend/implementation
+npm install && npm run dev          # :5173
+
+# Gemma lab
+cd ../../ml/tests/gemma4_e2b && npm install && npm run dev   # :5174
+
+# Agent smoke
+cd ../agent_tools && npm install && npm run smoke
+
+# Backend
+cd ../../.. && conda activate vkist_ultra
+PYTHONPATH=. python backend/tests/smoke_agent_tools_server.py
+```
+
+Key env: `VITE_CLINICAL_CHAT_USE_LLM`, `VITE_CLINICAL_CHAT_MOCK_TOOLS`, `VITE_API_BASE_URL`
+
+### Quan additions
+
+```bash
+cd PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend/implementation
+npm install && npm run dev   # :5173
+```
+
+
+| Tool                      | Link                                                                                                                 |
+| ------------------------- | -------------------------------------------------------------------------------------------------------------------- |
+| **Figma** (authority)     | [MSK_Workspace_UIX-Design](https://www.figma.com/design/uakk3T4efS1AIckfTEFSZO/MSK_Workspace_UIX-Design?node-id=0-1) |
+| **Stitch** (acceleration) | [Whiteboard 8188910238055386921](https://stitch.withgoogle.com/projects/8188910238055386921)                         |
+| **Responsive test**       | Chrome DevTools → iPhone SE 375px                                                                                    |
+
+
+Stitch board has **web mocks** today — Quan creates **mobile variants** and exports references for the coding agent (see Quan doc).
+
+**Tóm tắt (VI):** Cursor/Kilo + Git; Phuc thêm conda/smoke tests; Quan thêm Figma + Stitch + DevTools mobile.
+
+---
+
+
+
+## 9. Bonus — Feynman Technique with agents
+
+When a concept or code path feels **hard**, don't just ask the agent to fix it — ask it to **teach it back to you** using the [Feynman Technique](https://en.wikipedia.org/wiki/Feynman_technique): explain simply, use an analogy, expose gaps, then verify your understanding.
+
+### When to use
+
+
+| Situation                                            | Use Feynman prompt               |
+| ---------------------------------------------------- | -------------------------------- |
+| You read code but can't explain it in your own words | ✅                                |
+| Agent generated a diff you don't fully understand    | ✅ Before commit                  |
+| Spec uses jargon (RAG, CoT, BFF, …)                  | ✅                                |
+| You're stuck >30 min on the same concept             | ✅ Then ask Dave if still blocked |
+
+
+
+
+### Universal template (copy into Cursor / Kilo)
+
+```
+Feynman explain — [TOPIC or FILE PATH]:
+
+1. Explain like I'm a new intern with CS basics but new to this codebase.
+2. Use one everyday analogy (non-medical if possible).
+3. Walk the data/control flow in ≤8 numbered steps.
+4. Define every abbreviation you use (or link to our glossary).
+5. List 3 "common mistakes" a beginner would make here.
+6. Ask me 2 short quiz questions — wait for my answers before continuing.
+7. If I get them wrong, correct me simply.
+
+Context: VKIST MSK Pilot, ticket [P-n or Q-n].
+Do NOT write code yet — teach only.
+```
+
+
+
+### After the agent teaches you
+
+1. **Rewrite** the idea in 3–5 bullets in your own words (PR description, standup note, or personal log).
+2. If you still can't rewrite without copying — **you're not ready to commit** that code; ask one follow-up or ping Dave.
+3. Optional: paste your summary to Dave at weekly demo — proves understanding, not just output.
+
+Role-specific Feynman prompts: [Phuc §12](./ONBOARDING_PHUC_ML_ENGINEER.md#12-bonus--feynman-technique-prompts) · [Quan §14](./ONBOARDING_QUAN_FRONTEND.md#14-bonus--feynman-technique-prompts)
+
+**Tóm tắt (VI):** Khi khó hiểu — bảo agent giải thích đơn giản (Feynman), trả lời quiz, tự viết lại bằng lời mình; chưa hiểu thì chưa commit.
+
+---
+
+
+
+## 10. Collaboration contract
+
+
+| Rule          | Detail                                                      |
+| ------------- | ----------------------------------------------------------- |
+| Assignment    | Dave picks backlog ID — you don't self-select large scope   |
+| PR size       | ≤300 lines; one backlog ID per PR                           |
+| Weekly demo   | Runnable change required                                    |
+| Agentic tools | OK after reading ticket spec; pass `AGENT_SKILL` checklists |
+| Research      | ≤40% time; only when tied to P-7 or approved milestone      |
+| Blocked >4h   | Ping Dave with exact error + file path                      |
+
+
+**Tóm tắt (VI):** PR nhỏ, demo mỗi tuần, hỏi Dave khi kẹt quá 4 giờ.
+
+---
+
+
+
+## 11. Current assignments (Dave fills in)
+
+
+| Intern | Active ticket             | Checkpoint | PR link | Status |
+| ------ | ------------------------- | ---------- | ------- | ------ |
+| Phuc   | P-___                     | CP-___     |         |        |
+| Quan   | Q-1 (`/` worklist mobile) | CP-5       |         |        |
+
+
+---
+
+
+
+## 12. Glossary of abbreviations
+
+Terms you will see daily in specs, code comments, and standups. Bookmark this section.
+
+### Project & process
+
+
+| Abbr.           | Full form                         | Meaning in this project                                        |
+| --------------- | --------------------------------- | -------------------------------------------------------------- |
+| **VKIST**       | Viện Khoa học Công nghệ (context) | Research institute partner; MSK ultrasound AI origin           |
+| **MSK**         | Musculoskeletal                   | Joint/tendon/ligament domain — knee ultrasound focus           |
+| **PoC**         | Proof of Concept                  | Current sprint build — not production-certified yet            |
+| **CP-n**        | Checkpoint n                      | Sprint deliverable milestone (see §4)                          |
+| **P-n / Q-n**   | Phuc-ticket / Quan-ticket         | Backlog IDs in §5                                              |
+| **UC-n**        | Use Case n                        | Clinical workflow spec (e.g. `UC-48376` load scan session)     |
+| **FR-n**        | Functional Requirement n          | Feature requirement (e.g. **FR-25** synovitis grading)         |
+| **NFR-n**       | Non-Functional Requirement n      | Quality constraint (latency, safety, privacy)                  |
+| **WS-25**       | Workspace 25                      | Clinician diagnostic workspace UI (65/35 layout)               |
+| **HITL**        | Human-in-the-Loop                 | Clinician must review/confirm before AI output is final        |
+| **UP5, UP1, …** | User Persona n                    | Stakeholder archetype (UP5 = radiologist, UP1 = senior expert) |
+
+
+
+
+### Clinical & domain (Vietnamese context)
+
+
+| Abbr.           | Full form                                                   | Meaning                                                   |
+| --------------- | ----------------------------------------------------------- | --------------------------------------------------------- |
+| **MOH**         | Ministry of Health (Vietnam)                                | Source of clinical guidelines for RAG corpus              |
+| **DICOM**       | Digital Imaging and Communications in Medicine              | Standard medical image format (ultrasound slices)         |
+| **PACS**        | Picture Archiving and Communication System                  | Hospital image archive — DICOM source                     |
+| **EMR / HIS**   | Electronic Medical Record / Hospital Information System     | Hospital patient record system                            |
+| **HL7 / FHIR**  | Health Level 7 / Fast Healthcare Interoperability Resources | Standards for EMR data exchange                           |
+| **Synovitis**   | —                                                           | Joint lining inflammation — graded **0–3** by this system |
+| **GradCAM**     | Gradient-weighted Class Activation Mapping                  | Heatmap showing which image regions drove AI grade        |
+| **ULTS**        | Ultrasound                                                  | Modality used in FR-25                                    |
+| **Circular 46** | Thông tư 46/2018/TT-BYT                                     | Vietnam clinical report format regulation                 |
+| **Decree 13**   | Nghị định 13/2023/NĐ-CP                                     | Vietnam personal data protection law (PHI rules)          |
+
+
+
+
+### Security & privacy
+
+
+| Abbr.           | Full form                           | Meaning                                                           |
+| --------------- | ----------------------------------- | ----------------------------------------------------------------- |
+| **PHI**         | Protected Health Information        | Patient-identifiable health data — never commit to git            |
+| **PII**         | Personally Identifiable Information | Names, IDs, phone — scrubbed before cloud egress                  |
+| **RBAC**        | Role-Based Access Control           | Permissions by clinician role (radiologist, therapist, …)         |
+| **JWT**         | JSON Web Token                      | Session auth token (stored in Redis server-side)                  |
+| **NFR-16a**     | NFR exception 16a                   | PoC-only rule allowing cloud LLM with redaction + consent + audit |
+| **AES-256-GCM** | Advanced Encryption Standard        | Client-side encryption for local storage (target arch)            |
+
+
+
+
+### Architecture & infrastructure
+
+
+| Abbr.        | Full form                           | Meaning                                                        |
+| ------------ | ----------------------------------- | -------------------------------------------------------------- |
+| **PWA**      | Progressive Web App                 | Installable web app — Sprint 4 patient target                  |
+| **BFF**      | Backend-for-Frontend                | FastAPI layer that proxies agent tools + cloud LLM for browser |
+| **API**      | Application Programming Interface   | HTTP endpoints (`/api/v1/...`)                                 |
+| **K3s**      | Lightweight Kubernetes              | On-prem hospital cluster (target deployment)                   |
+| **Triton**   | NVIDIA Triton Inference Server      | GPU server for CV models + embeddings (`:8001` gRPC)           |
+| **FastAPI**  | —                                   | Python web framework for backend (`:8000`)                     |
+| **NGINX**    | —                                   | Reverse proxy / SSL termination in front of FastAPI            |
+| **MinIO**    | —                                   | S3-compatible object store for DICOM blobs, reports            |
+| **pgvector** | PostgreSQL vector extension         | Vector DB for MOH guideline semantic search (HNSW index)       |
+| **HNSW**     | Hierarchical Navigable Small World  | Approximate nearest-neighbor index for RAG retrieval           |
+| **GCP**      | Google Cloud Platform               | Hosts Gemini (Vertex AI)                                       |
+| **Modal**    | Modal.com                           | Serverless GPU platform hosting MedGemma                       |
+| **LAN**      | Local Area Network                  | Hospital internal network — air-gapped primary mode            |
+| **CI/CD**    | Continuous Integration / Deployment | Jenkins + GitLab pipeline                                      |
+| **SSE**      | Server-Sent Events                  | One-way streaming from server to browser                       |
+
+
+
+
+### ML, NLP & generative AI
+
+
+| Abbr.                 | Full form                                               | Meaning                                                             |
+| --------------------- | ------------------------------------------------------- | ------------------------------------------------------------------- |
+| **CV**                | Computer Vision                                         | Image ML pipeline (angle → inflammation → segmentation)             |
+| **NLP**               | Natural Language Processing                             | Clinical text cleanup, explanations, chat                           |
+| **LLM**               | Large Language Model                                    | Generative text models (Gemma, Gemini, MedGemma)                    |
+| **RAG**               | Retrieval-Augmented Generation                          | Fetch MOH guideline chunks before generating answer                 |
+| **CoT**               | Chain-of-Thought                                        | Model "thinking" trace before final answer (thought channel)        |
+| **TTFT**              | Time to First Token                                     | Latency until first streamed word appears (NFR-7: ≤200 ms target)   |
+| **E2B / E4B**         | Gemma 4 2B / 4B params                                  | Edge (browser) vs server Ollama model sizes                         |
+| **WebLLM**            | Web Large Language Model                                | In-browser inference via WebGPU + WASM                              |
+| **OPFS**              | Origin Private File System                              | Browser storage for ~1.9 GB Gemma checkpoint                        |
+| **WASM**              | WebAssembly                                             | Binary format for in-browser ML (MediaPipe, LiteRT)                 |
+| **WebGPU**            | —                                                       | Browser GPU API — required for edge Gemma                           |
+| **WebGL**             | —                                                       | Older browser 3D API — fallback path for weak devices               |
+| **BERT**              | Bidirectional Encoder Representations from Transformers | Classifier for drift/guardrail/referee (partially stubbed)          |
+| **EmbeddingGemma**    | —                                                       | 768-dim embedding model for RAG vector search                       |
+| **MedGemma**          | —                                                       | Tier-3 clinical deep-reasoning LLM (Modal, NFR-16a)                 |
+| **Gemini**            | —                                                       | Tier-2 orchestration/translation LLM (GCP Vertex AI)                |
+| **Gemma**             | —                                                       | Tier-1 edge conversation LLM (browser MediaPipe)                    |
+| **Agent**             | —                                                       | Multi-step tool-calling loop (`<tool_call>` / `<final>` protocol)   |
+| **Guardrail**         | —                                                       | Safety filter on generated text (hallucination, scope breach)       |
+| **RAG-Referee**       | —                                                       | 3-axis citation validator for MedGemma output                       |
+| **Circuit breaker**   | —                                                       | Clinician challenges AI grade via Socratic dialogue before sign-off |
+| **Socratic dialogue** | —                                                       | Structured Q&A between clinician and AI about a grade               |
+| **DeepLab / UNet**    | —                                                       | Segmentation model architectures in CV pipeline                     |
+| **ConvNeXt / MedViT** | —                                                       | Angle classification model families (legacy stack)                  |
+| **LiteRT**            | —                                                       | On-device inference runtime (TensorFlow Lite successor)             |
+| **TFLite / TFJS**     | TensorFlow Lite / TensorFlow.js                         | Client-side ML runtimes                                             |
+| **ONNX**              | Open Neural Network Exchange                            | Model interchange format for Triton deployment                      |
+| **VRAM**              | Video RAM                                               | GPU memory — relevant for Triton/Modal sizing                       |
+
+
+
+
+### Frontend & UI
+
+
+| Abbr.         | Full form                                  | Meaning                                                       |
+| ------------- | ------------------------------------------ | ------------------------------------------------------------- |
+| **UI / UIX**  | User Interface / User Interface eXperience | Screens, layout, interaction design                           |
+| **SPA**       | Single Page Application                    | React app — one HTML shell, client-side routing               |
+| **TS / TSX**  | TypeScript / TypeScript + JSX              | Frontend language + React syntax                              |
+| **Zustand**   | —                                          | Lightweight React state store (target arch; PoC uses context) |
+| **Dexie.js**  | —                                          | IndexedDB wrapper for offline cache                           |
+| **IndexedDB** | —                                          | Browser local database for inference cache, session replay    |
+| **MRN**       | Medical Record Number                      | Patient hospital ID shown in TopBar                           |
+| **FR-26**     | Functional Requirement 26                  | Future patient-facing dashboard scope                         |
+| **a11y**      | Accessibility                              | WCAG-oriented design (contrast, font scale, touch targets)    |
+
+
+
+
+### Tools & workflow
+
+
+| Abbr.        | Full form                          | Meaning                                   |
+| ------------ | ---------------------------------- | ----------------------------------------- |
+| **PR**       | Pull Request                       | Code review unit — keep ≤300 lines        |
+| **IDE**      | Integrated Development Environment | VS Code / Cursor                          |
+| **Dev Mode** | Figma Dev Mode                     | Inspect panel for spacing, tokens, CSS    |
+| **SDK**      | Software Development Kit           | e.g. `@google/stitch-sdk` for asset fetch |
+
+
+**Tóm tắt (VI):** Bảng viết tắt trên dùng hàng ngày — FR/NFR = yêu cầu; RAG/LLM/CoT = AI sinh ngôn ngữ; PHI/Decree 13 = bảo mật; PWA/DICOM/PACS = lâm sàng & UI; hỏi Dave nếu gặp từ mới.
+
+---
+
+
+
+## 13. Quick links
+
+
+| Resource             | Path                                                                                  |
+| -------------------- | ------------------------------------------------------------------------------------- |
+| Project vision       | `PILOT_PROJECT/PROJ_LEVEL_READING/PLAN/CONTEXT_VISION_SCOPE.md`                       |
+| Sprint architecture  | `PILOT_PROJECT/workspace/sprint_1_2/Design_Material/SPRINT_1_2_ARCHITECTURE_SPEC.md`  |
+| UI truth doc         | `PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend/spec/uix_prototype_coverage.md` |
+| Agent skills         | `PILOT_PROJECT/AGENT_SKILL/INTRODUCTION.md`                                           |
+| Dave's Jul 6 handoff | `session_memory/6_Jul_26.md`                                                          |
+| Layout reference     | `session_memory/26_Jun_26/Proj_context_26_Jun_26.md`                                  |
+
+

session_memory/7_Jun_26/ONBOARDING_PHUC_ML_ENGINEER.md

@@ -0,0 +1,396 @@
+# Onboarding — Phuc (ML Engineer / Agentic & Generative Logic)
+
+**Start here:** [ONBOARDING_INDEX.md](./ONBOARDING_INDEX.md) — [glossary](./ONBOARDING_INDEX.md#12-glossary-of-abbreviations) · [Feynman prompts (INDEX §9)](./ONBOARDING_INDEX.md#9-bonus--feynman-technique-with-agents)  
+**Date:** 7 Jul 2026  
+**Timebox:** ~Jul 7 – Aug 31, 2026  
+**Lane:** Generative LLM, agent runtime, guardrails, RAG gates — co-designed with Dave
+
+---
+
+## 1. Your mission
+
+You continue the **generative & agentic layer** Dave built. Your deliverable is **merged code** that advances checkpoints **CP-2, CP-3, CP-8** — not architecture slides.
+
+You co-own agentic design and guardrail logic with Dave: you propose, Dave approves scope, you ship one vertical slice per PR.
+
+**You are not expected to:** rewrite the CV/Triton pipeline, own full compliance sign-off, or refactor UI components.
+
+**Tóm tắt (VI):** Tiếp tục xây LLM/agent/guardrail; mỗi tuần có PR chạy được; thiết kế guardrail cùng Dave; không làm lại pipeline những kết quả đã có - nếu có thì phải optimize & hạn chế redundancies overhead trong thiết kế.
+
+---
+
+
+
+## 2. Your codebase scope
+
+
+
+### In scope — touch freely
+
+
+| Path                                                                        | What                                    |
+| --------------------------------------------------------------------------- | --------------------------------------- |
+| `CODEBASE/ml/implementation/nlp/agent_runtime/`                             | Agent loop, tools, prompts              |
+| `CODEBASE/ml/tests/gemma4_e2b/`                                             | Isolated Gemma + agent lab (`:5174`)    |
+| `CODEBASE/ml/tests/agent_tools/`                                            | BFF / Modal / Exa smoke tests           |
+| `CODEBASE/ml/spec/conformal_decoding_llm_with_domain_stritcly_constrain.md` | Research spec                           |
+| `CODEBASE/frontend/implementation/src/lib/llm/`                             | Edge inference, chat routing, prompts   |
+| `CODEBASE/frontend/implementation/src/hooks/useClinicalChat.ts`             | Chat bootstrap + streaming              |
+| `CODEBASE/frontend/implementation/src/workers/llm.worker.ts`                | MediaPipe Gemma worker                  |
+| `CODEBASE/frontend/implementation/src/workers/`                             | Create `guardrail.worker.ts` here (P-3) |
+| `CODEBASE/backend/routers/cloud_*.py`, `agent_tools.py`                     | Cloud + tool BFF                        |
+| `CODEBASE/backend/services/cloud_llm_gateway.py`, `agent_tools_service.py`  | Gateway + tools                         |
+| `CODEBASE/backend/implementation/safety/`                                   | Safety service                          |
+| `CODEBASE/backend/implementation/adapters/bert_adapter.py`                  | Guardrail stubs                         |
+| `CODEBASE/knowledge/spec/`                                                  | When working P-4 / P-8                  |
+
+
+
+
+### Read-only — understand, don't refactor
+
+- `CODEBASE/backend/implementation/pipeline/` — CV inference (Dave)
+- `CODEBASE/infra/` — unless P-6 Modal debugging
+- `CODEBASE/frontend/implementation/src/components/` — Quan's lane
+- `workspace/LEGACY/` — reference only
+
+
+
+### Architecture mental model
+
+```
+User message
+  → useClinicalChat / runClinicalChatTurn
+    → [chat|planning] → Edge Gemma (llm.worker) OR Ollama E4B
+    → [agent]         → agentLoop → tools (exa, supabase, medgemma)
+  → [YOUR GAPS] guardrail check, RAG gate, cloud escalation audit
+  → display (StreamingPlainText)
+```
+
+Tier 1 = browser Gemma · Tier 2 = Gemini · Tier 3 = MedGemma (NFR-16a governed)
+
+**Tóm tắt (VI):** Phạm vi = ml/agent_runtime, lib/llm, backend safety/routers; không sửa UI hay LEGACY.
+
+---
+
+
+
+## 3. What to read, what to learn
+
+
+
+### Must read (Day 1 — before first PR)
+
+
+| #   | Document               | Path                                                                         |
+| --- | ---------------------- | ---------------------------------------------------------------------------- |
+| 1   | Dave's latest handoff  | `session_memory/6_Jul_26.md`                                                 |
+| 2   | Regulatory constraints | `PILOT_PROJECT/PROJ_LEVEL_READING/PLAN/CONTEXT_VISION_SCOPE.md` §4           |
+| 3   | Agent protocol         | `CODEBASE/ml/implementation/nlp/README.md`                                   |
+| 4   | PHI safety             | `PILOT_PROJECT/AGENT_SKILL/secrets_and_phi_safety/SKILL.md`                  |
+| 5   | Agent tools rules      | `PILOT_PROJECT/AGENT_SKILL/agent_tool_execution/SKILL.md`                    |
+| 6   | LLM + safety NFRs      | `Design_Material/SPRINT_1_2_ARCHITECTURE_SPEC.md` — LLM tiers, NFR-10/16a/18 |
+
+
+
+
+### Should read (when ticket assigned)
+
+
+| Ticket   | Read                                                                                                            |
+| -------- | --------------------------------------------------------------------------------------------------------------- |
+| P-1, P-6 | `backend/spec/agent_tools_contract.md`, `agent_runtime/.../tools/registry.ts`, `backend/routers/agent_tools.py` |
+| P-2, P-3 | `bert_adapter.py`, `safety/service.py`, `FR_25_UC_DESIGN/Q1_*.md` … `Q4_*.md`                                   |
+| P-4, P-8 | `knowledge/spec/knowledge_spec.md`, `agentLoop.ts`, `runClinicalChatTurn.ts`                                    |
+| P-5      | `clinicalChatModes.ts`, `chatReasoningLevel.ts`, `6_Jul_26.md` §beta                                            |
+| P-7      | `ml/spec/conformal_decoding_llm_with_domain_stritcly_constrain.md`                                              |
+| Any      | Relevant `UC-*.md` in `Design_Material/FR_25_UC_DESIGN/Use_Case/`                                               |
+
+
+**Week 1 code trace (do once):**  
+`useClinicalChat.ts` → `runClinicalChatTurn.ts` → `agentLoop.ts` OR `llm.worker.ts` → `cloud_llm_gateway.py`
+
+### Learn deeper (keywords)
+
+> Abbreviations: [Glossary INDEX §12](./ONBOARDING_INDEX.md#12-glossary-of-abbreviations)
+
+Study as tickets require — use papers, specs, and agent exploration:
+
+
+| Keywords                                                            | Tickets  |
+| ------------------------------------------------------------------- | -------- |
+| `prompt-constrained tool calling`, `agent orchestration loop`       | P-1      |
+| `RAG pre-retrieval`, `pgvector`, `semantic chunk`, `MOH corpus`     | P-4, P-8 |
+| `BERT guardrail`, `hallucination detection`, `scope-breach scoring` | P-2, P-3 |
+| `conformal decoding`, `domain-constrained generation`               | P-7      |
+| `CoT streaming`, `thought/answer channel`, `WebLLM MediaPipe`       | P-5      |
+| `NFR-16a`, `consent audit`, `cloud egress redaction`                | P-6      |
+| `RAG-Referee`, `citation validation`, `3-axis contestant`           | P-8      |
+| `Transformers.js`, `Web Worker`, `OPFS model cache`                 | P-3      |
+
+
+**Tóm tắt (VI):** Đọc 6 tài liệu bắt buộc ngày 1; đọc thêm theo ticket P-n; học sâu theo từ khóa khi làm.
+
+---
+
+
+
+## 4. Dev toolkit
+
+
+| Tool                                           | Command                                                                                                      |
+| ---------------------------------------------- | ------------------------------------------------------------------------------------------------------------ |
+| Clinical chat UI                               | `cd CODEBASE/frontend/implementation && npm run dev` → `:5173`                                               |
+| Gemma lab                                      | `cd CODEBASE/ml/tests/gemma4_e2b && npm run dev` → `:5174`                                                   |
+| Agent smoke (test-the-agentic-functionality)   | `cd CODEBASE/ml/tests/agent_tools && npm run smoke`                                                          |
+| Backend smoke (test-the-agentic-functionality) | `conda activate vkist_ultra`; `cd CODEBASE`; `PYTHONPATH=. python backend/tests/smoke_agent_tools_server.py` |
+| Agentic IDE                                    | Cursor / Kilo — load `AGENT_SKILL/agent_tool_execution`                                                      |
+
+
+**Environment variables (frontend** `.env.development`**):**
+
+```env
+VITE_CLINICAL_CHAT_USE_LLM=true
+VITE_CLINICAL_CHAT_MOCK_TOOLS=true    # flip false for P-1 done
+VITE_OLLAMA_CHAT_URL=/api/ollama-chat/api/chat
+VITE_API_BASE_URL=http://localhost:8001
+```
+
+Secrets: ask Dave — `PILOT_PROJECT/secrets_template/README.md`
+
+**Tóm tắt (VI):** Chạy :5173 chat, :5174 lab, smoke tests; đổi MOCK_TOOLS=false khi P-1 xong.
+
+---
+
+
+
+## 5. Day 1 playbook (then ship)
+
+**Morning**
+
+1. Run `:5173` → open `/workspace/:patientId` → test chat + agent modes.
+2. Run `:5174` gemma4_e2b → complete one tool smoke call.
+3. Trace one chat turn and one agent turn (Section 3 code trace).
+
+**Afternoon**
+4. Hands-on verify backlog P-1–P-7 (✅/❌ in your notes).
+5. Sync with Dave → receive first ticket (likely **P-1** or **P-5**).
+
+Do **not** spend Week 1 writing standalone architecture docs.
+
+**Tóm tắt (VI):** Ngày 1: chạy app, trace code, sync Dave lấy ticket — không viết doc dài.
+
+---
+
+
+
+## 6. Spec vs implementation (your work surface)
+
+
+| Component                           | Built today    | Your tickets       |
+| ----------------------------------- | -------------- | ------------------ |
+| Edge Gemma inference                | ✅              | P-5 polish         |
+| Agent loop + `<tool_call>` protocol | ✅ (mock tools) | P-1                |
+| Cloud gateway + audit hooks         | ⚠️ partial     | P-6                |
+| Auto-retrieval in agent mode        | ✅              | P-4 extend to chat |
+| `bert_adapter.py` / safety service  | ❌ stub         | P-2                |
+| `guardrail.worker.ts`               | ❌ missing      | P-3                |
+| RAG-Referee 3-axis                  | ❌ spec only    | P-8                |
+| Planning + high reasoning beta      | ⚠️ disabled    | P-5                |
+
+
+**Key facts:**
+
+- Production chat = **browser Gemma 4 E2B** (MediaPipe), not server-side generation.
+- Agent mode uses **prompt tags** (`<tool_call>`, `<final>`), not native function calling.
+- Do **not** re-enable `ChatMarkdown` in reasoning mode — see `6_Jul_26.md` crash policy.
+
+**Tóm tắt (VI):** Guardrail và RAG chat còn stub — đó là trọng tâm của bạn.
+
+---
+
+
+
+## 7. Your backlog (detail)
+
+
+| ID      | Gap                            | Spec                              | Starting files                                  |
+| ------- | ------------------------------ | --------------------------------- | ----------------------------------------------- |
+| **P-1** | Mock agent tools               | `agent_tools_contract.md`         | `tools/registry.ts`, `agent_tools.py`           |
+| **P-2** | BERT adapter stubs             | NFR-10, Q1–Q4                     | `bert_adapter.py`, `safety/service.py`          |
+| **P-3** | No edge guardrail worker       | Web Workers spec                  | Create `guardrail.worker.ts`                    |
+| **P-4** | No RAG gate in chat mode       | NFR-18, `knowledge_spec.md`       | `runClinicalChatTurn.ts`                        |
+| **P-5** | Beta modes disabled            | `6_Jul_26.md`                     | `clinicalChatModes.ts`, `chatReasoningLevel.ts` |
+| **P-6** | MedGemma escalation incomplete | NFR-16a                           | `cloud_llm_gateway.py`, `tools/registry.ts`     |
+| **P-7** | Conformal decoding research    | `ml/spec/conformal_decoding_*.md` | `gemma4_e2b/` lab                               |
+
+
+**Tóm tắt (VI):** P-1 đến P-7 — chờ Dave giao ID / chủ động đề xuất giải pháp kỹ thuật & thiết kế; mỗi PR một ticket.
+
+---
+
+
+
+## 8. SMART milestones
+
+
+
+### M1 — First merge (Jul 7 – Jul 18)
+
+
+|                |                                               |
+| -------------- | --------------------------------------------- |
+| **Ticket**     | P-1 or P-5 (Dave assigns)                     |
+| **Specific**   | Live agent tools OR remove beta from one mode |
+| **Measurable** | PR merged; live demo on `:5173`               |
+| **Achievable** | One backlog ID only                           |
+| **Relevant**   | CP-1 / CP-2                                   |
+| **Time-bound** | Sprint 3 week 1                               |
+
+
+
+
+### M2 — Guardrail v1 (Jul 14 – Aug 1)
+
+
+|                |                                                         |
+| -------------- | ------------------------------------------------------- |
+| **Ticket**     | P-2 or P-3 (co-scoped with Dave)                        |
+| **Specific**   | RFC ≤1 page + one real PASS/FAIL check on outbound text |
+| **Measurable** | Test/smoke on 3 fixtures from Q1–Q4 scenarios           |
+| **Achievable** | Keyword gate OK for v1; full BERT optional              |
+| **Relevant**   | CP-3, NFR-10                                            |
+| **Time-bound** | Sprint 3 end                                            |
+
+
+
+
+### M3 — Retrieval or escalation (Jul 28 – Aug 15)
+
+
+|                |                                                    |
+| -------------- | -------------------------------------------------- |
+| **Ticket**     | P-4 or P-6                                         |
+| **Specific**   | RAG gate in chat OR MedGemma escalation with audit |
+| **Measurable** | Screen recording + log snippet in PR               |
+| **Relevant**   | CP-2 / CP-8, NFR-18                                |
+| **Time-bound** | Sprint 4                                           |
+
+
+
+
+### M4 — Research or hardening (Aug 1 – Aug 31)
+
+
+|                |                                                      |
+| -------------- | ---------------------------------------------------- |
+| **Ticket**     | P-7 or extend P-2/P-3                                |
+| **Specific**   | Conformal eval (3 VI cases) OR second guardrail axis |
+| **Optional**   | If M2–M3 complete                                    |
+| **Time-bound** | Internship end                                       |
+
+
+**Tóm tắt (VI):** 4 mốc — PR đầu tiên tuần 1; guardrail tuần 3–4; RAG/escalation tháng 8.
+
+---
+
+
+
+## 9. Anti-patterns
+
+- ❌ Refactor `agent_runtime` package structure without inform to members on update logic (no change-Log)
+- ❌ Swap model families (Qwen experiment is closed)
+- ❌ Touch `LEGACY/` or Quan's UI components
+- ❌ Enable `ChatMarkdown` during reasoning streams (markdown rendering on LLM's outcome is problem - we shall put it under the rug)
+- ❌ Commit secrets or PHI — ever
+
+**Tóm tắt (VI):** Không refactor lớn, không đổi model, không markdown khi reasoning.
+
+---
+
+
+
+## 10. Definition of done
+
+- [ ] ≥3 merged PRs across P-1–P-6
+- [ ] Can demo live agent tool call or guardrail check without Dave driving
+- [ ] CP-2 or CP-3 marked advanced in team backlog
+- [ ] Read `secrets_and_phi_safety` + `agent_tool_execution` skills
+
+**Tóm tắt (VI):** 3 PR, demo được guardrail/agent, checkpoint CP-2 hoặc CP-3 tiến triển.
+
+---
+
+
+
+## 11. Agent prompt examples (optimize / change based on usecase)
+
+**Explore generative flow:**
+
+```
+Trace runClinicalChatTurn.ts for agent mode: list each file called,
+what tool protocol is used, and where mock tools are injected.
+```
+
+**Start P-1:**
+
+```
+Help me flip VITE_CLINICAL_CHAT_MOCK_TOOLS to false and fix any
+BFF errors. Start from tools/registry.ts and agent_tools.py.
+Follow AGENT_SKILL/agent_tool_execution/SKILL.md.
+```
+
+**Start P-2:**
+
+```
+Implement a minimal scope-breach keyword gate in bert_adapter.py
+returning PASS/FAIL. Use Q1_True_Agreement.md as fixture context.
+```
+
+---
+
+## 12. Bonus — Feynman Technique prompts
+
+Use when a generative/agent concept feels opaque **before** you commit agent-generated code.  
+Master template: [INDEX §9](./ONBOARDING_INDEX.md#9-bonus--feynman-technique-with-agents).
+
+### Hard concepts → ready-made prompts
+
+**Agent loop & `<tool_call>` protocol (P-1):**
+```
+Feynman explain agentLoop.ts and the <tool_call> / <final> protocol in
+@vkist/agent-runtime. Why prompt tags instead of OpenAI function calling?
+Trace one turn with exa_search mocked. Quiz me after.
+```
+
+**Edge vs cloud 3-tier LLM (general):**
+```
+Feynman explain our 3-tier LLM: Edge Gemma → Gemini → MedGemma.
+When does each tier run? What is NFR-16a in one sentence?
+Use a "triage desk at a hospital" analogy. Quiz me.
+```
+
+**clinicalChatStreamRegistry + streaming (P-5 area):**
+```
+Feynman explain why clinicalChatStreamRegistry.ts paints tokens to the DOM
+directly instead of React setState on every token. What breaks if we use
+ChatMarkdown during CoT? ≤8 steps. Quiz me.
+```
+
+**RAG pre-retrieval (P-4 / P-8):**
+```
+Feynman explain mandatory RAG pre-generation in our system: what pgvector
+retrieves, when agentLoop auto-calls supabase_query, and why chat mode
+doesn't do this yet. MOH corpus in plain language. Quiz me.
+```
+
+**Guardrail vs RAG-Referee (P-2 / P-3):**
+```
+Feynman explain the difference between edge guardrail, bert_adapter
+drift check, and RAG-Referee. Which are implemented vs stub today?
+Use a "editor vs fact-checker" analogy. Quiz me.
+```
+
+**After each Feynman session:** write 3 bullets in your own words in the PR or ticket comment.
+
+**Tóm tắt (VI):** Dùng prompt Feynman khi không hiểu agent/LLM; có sẵn prompt cho từng chủ đề khó; tự tóm tắt lại trước khi commit.

session_memory/7_Jun_26/ONBOARDING_QUAN_FRONTEND.md

@@ -0,0 +1,499 @@
+# Onboarding — Quan (Frontend / Mobile PWA)
+
+**Start here:** [ONBOARDING_INDEX.md](./ONBOARDING_INDEX.md) — [glossary](./ONBOARDING_INDEX.md#12-glossary-of-abbreviations) · [Feynman prompts (INDEX §9)](./ONBOARDING_INDEX.md#9-bonus--feynman-technique-with-agents)  
+**Date:** 7 Jul 2026  
+**Timebox:** ~2 months (ends ~early Aug 2026)  
+**Lane:** Mobile UI, Figma + Stitch design acceleration, patient PWA
+
+---
+
+## 1. Your mission
+
+You continue the **UI layer** from stub routes toward Sprint 4 patient PWA checkpoints. You ship **visible screens in the browser** — not backend, not LLM internals.
+
+Dave provides two design accelerators:
+
+
+| Tool              | Link                                                                                                                 | Role                                                                   |
+| ----------------- | -------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- |
+| **Figma**         | [MSK_Workspace_UIX-Design](https://www.figma.com/design/uakk3T4efS1AIckfTEFSZO/MSK_Workspace_UIX-Design?node-id=0-1) | Design authority — 35 screens, tokens, Vietnamese copy                 |
+| **Google Stitch** | [Whiteboard](https://stitch.withgoogle.com/projects/8188910238055386921)                                             | Acceleration — board has **web mocks**; you design **mobile variants** |
+
+
+**Your agency:** Pick Figma-first, Stitch-first, or hybrid **per screen** — one line in the PR is enough. Dave assigns tickets; **Week 1 default ticket is Q-1 on the live `/` worklist** (highest yield).
+
+**Week 1 principle — ship fast, correct, get feedback:**
+
+
+| Priority        | Rule                                                                                                  |
+| --------------- | ----------------------------------------------------------------------------------------------------- |
+| **Speed**       | Tools (Figma + Stitch) = **1 day max**, then code same day                                            |
+| **Yield**       | Week 1 targets the **live route** `/` (`PatientWorklistPage`) mobile at 375px — not orphan stub pages |
+| **Correctness** | `design-tokens.ts`, live navigation, no hardcoded colors, no pasted Stitch HTML                       |
+| **Feedback**    | Draft PR or screenshots to Dave **end of Day 1**; iterate Day 2–3 from review                         |
+
+
+**Stitch (quick rules):**
+
+1. Board has web mocks — use Stitch to sketch **mobile layout**, export screenshot for Cursor/Kilo
+2. Agent writes React; you review every line
+3. Figma wins on tokens and Vietnamese copy
+
+**Tóm tắt (VI):** Tuần 1 = 1 ngày học tool, cùng ngày code mobile cho `/` worklist; PR/screenshot cuối ngày 1; sửa theo feedback Dave — không khảo sát tự do nhiều ngày.
+
+---
+
+## 2. Your codebase scope
+
+### In scope — touch freely
+
+```
+CODEBASE/frontend/
+├── spec/                          ← read: uix_prototype_coverage, figma-component-specs, DESIGN
+└── implementation/src/
+    ├── pages/                     ← your primary workspace
+    ├── components/atoms/
+    ├── components/molecules/
+    ├── components/layout/
+    ├── styles/design-tokens.ts    ← token source of truth
+    ├── App.tsx                    ← routes
+    └── public/assets/stitch/      ← exported Stitch references
+```
+
+### Read-only — understand, don't refactor
+
+
+| File / folder                              | Why                              |
+| ------------------------------------------ | -------------------------------- |
+| `organisms/DiagnosticCanvas.tsx`           | Dave owns DICOM canvas           |
+| `molecules/ClinicalChatPanel.tsx`          | Read layout only — Phuc owns LLM |
+| `lib/llm/`, `workers/`                     | Phuc's lane                      |
+| `hooks/useClinicalChat.ts`                 | Know it exists                   |
+| `data/mockData.ts`, `lib/patientStore.tsx` | How worklist gets data           |
+
+
+### Out of scope
+
+`CODEBASE/backend/`, `CODEBASE/ml/`, `CODEBASE/knowledge/`, `CODEBASE/infra/`, `LEGACY/`
+
+### Live routes today
+
+```
+/  →  PatientWorklistPage.tsx        ← Q-1, Q-6 priority
+/workspace/:patientId  →  ClinicalWorkspacePage.tsx   ← polish only; Q-2 overlay
++ 35 stub routes in src/pages/       ← Figma parity over time
+```
+
+**Tóm tắt (VI):** Sửa pages, atoms, molecules, tokens; không đụng canvas, chat LLM, backend.
+
+---
+
+## 3. What to read, what to learn
+
+### Must read (Day 1 morning only — then code)
+
+
+| #   | Document                                                          | Time                               |
+| --- | ----------------------------------------------------------------- | ---------------------------------- |
+| 1   | `uix_prototype_coverage.md`                                       | 20 min — **which routes are live** |
+| 2   | `figma-component-specs.md` — Priority 1–2 + node for `/` worklist | 15 min                             |
+| 3   | `design-tokens.ts` + skim `DESIGN.md`                             | 15 min                             |
+| 4   | `AGENT_SKILL/secrets_and_phi_safety/SKILL.md`                     | 10 min                             |
+
+
+Read `component-inventory.md`, `coding_convention`, and persona §3.4 **while coding**, not before Day 1 PR.
+
+**Tóm tắt (VI):** Sáng ngày 1 chỉ đọc 4 tài liệu ngắn; chiều cùng ngày bắt đầu code.
+
+### Should read (when ticket assigned)
+
+
+| Ticket     | Read                                                                                     |
+| ---------- | ---------------------------------------------------------------------------------------- |
+| Q-1, Q-6   | Figma node for screen; matching `src/pages/*.tsx` stub                                   |
+| Q-2        | `uix_prototype_coverage.md` §Safety; `SafetyEscalationOverlay.tsx`                       |
+| Q-3, Q-4   | `CONTEXT_VISION_SCOPE.md` §3.4; `frontend_spec.md` PoC §                                 |
+| Q-5        | `figma-component-specs.md` — error boundaries item                                       |
+| Q-8        | [Stitch board](https://stitch.withgoogle.com/projects/8188910238055386921) + live routes |
+| Any screen | `Design_Material/FR_25_UC_DESIGN/Use_Case/UC-*.md`                                       |
+| Layout     | `session_memory/26_Jun_26/Proj_context_26_Jun_26.md` — 65/35 ASCII                       |
+
+
+### Learn deeper (keywords)
+
+> Abbreviations: [Glossary INDEX §12](./ONBOARDING_INDEX.md#12-glossary-of-abbreviations)
+
+
+| Keywords                                                   | When                |
+| ---------------------------------------------------------- | ------------------- |
+| `atomic design`, `atoms molecules organisms`               | component-inventory |
+| `React functional components`, `props`, `composition`      | all Q tickets       |
+| `design tokens`, `CSS variables`, `responsive breakpoints` | Q-1, Q-3            |
+| `mobile-first`, `375px viewport`, `touch target 44px`      | Q-3, Q-6            |
+| `accessibility`, `WCAG contrast`, `font scaling`           | Q-4, Q-6            |
+| `error boundaries`                                         | Q-5                 |
+| `PWA`, `service worker`                                    | Sprint 4 (later)    |
+| `Figma Dev Mode`, `Inspect`                                | Q-1                 |
+| `Stitch design-to-code`, `HTML export as reference`        | Q-8                 |
+| `Vite`, `npm run dev`                                      | daily               |
+| `Vietnamese clinical UX`, `jargon-free patient copy`       | Q-6                 |
+
+
+**Tóm tắt (VI):** Đọc thêm theo ticket khi code; không ôm 7 tài liệu trước PR đầu.
+
+---
+
+## 4. Dev toolkit
+
+
+| Category            | Tool                                                                                              |
+| ------------------- | ------------------------------------------------------------------------------------------------- |
+| Dev server          | `npm run dev` → `http://localhost:5173`                                                           |
+| Design authority    | [Figma](https://www.figma.com/design/uakk3T4efS1AIckfTEFSZO/MSK_Workspace_UIX-Design?node-id=0-1) |
+| Design acceleration | [Stitch whiteboard](https://stitch.withgoogle.com/projects/8188910238055386921)                   |
+| Coding agent        | Cursor / Kilo                                                                                     |
+| Mobile test         | Chrome DevTools → iPhone SE 375×667                                                               |
+| PR evidence         | Before/after screenshots desktop + 375px                                                          |
+
+
+```bash
+cd PILOT_PROJECT/workspace/sprint_1_2/CODEBASE/frontend/implementation
+npm install
+npm run dev
+```
+
+**Optional:** Stitch SDK — `public/assets/stitch/README.md` (OAuth via Dave)
+
+### Agent prompt template
+
+```
+Implement [screen name] for mobile (375px).
+Reference: Figma node [id] from figma-component-specs.md.
+Layout hint: [Stitch mobile export screenshot or description].
+Use existing atoms from component-inventory.md.
+Use design-tokens.ts — no hardcoded colors.
+Route: [path from figma-component-specs].
+Match navigation in uix_prototype_coverage.md.
+```
+
+**Tóm tắt (VI):** npm run dev + Figma + Stitch + Cursor; test 375px; PR kèm screenshot.
+
+---
+
+## 5. Figma + Stitch workflow
+
+### When to use which
+
+
+| Source        | Best for                                      | Caveat                                  |
+| ------------- | --------------------------------------------- | --------------------------------------- |
+| **Figma**     | Tokens, spacing, VI copy, auth/patient cards  | Slower from scratch — use Inspect       |
+| **Stitch**    | Rapid mobile layout; agent reference material | Web mock ≠ mobile — create mobile frame |
+| **Live code** | Navigation truth                              | `uix_prototype_coverage.md`             |
+
+
+**Legacy Stitch desktop** (`public/assets/stitch/README.md`, project `17628337625105266704`) — reference only.  
+**Primary Stitch:** [project 8188910238055386921](https://stitch.withgoogle.com/projects/8188910238055386921)
+
+### Workflow choices (pick one per screen — state in PR)
+
+
+| ID                   | When                                               | Steps                                         |
+| -------------------- | -------------------------------------------------- | --------------------------------------------- |
+| **A — Figma-first**  | Screen in node map; tokens matter                  | Inspect → atoms → `src/pages/`                |
+| **B — Stitch-first** | Mobile patient screen; Stitch mobile variant ready | Stitch mobile design → export → agent → React |
+| **C — Hybrid**       | Stitch layout close; Figma has correct copy        | Stitch structure + Figma polish → code        |
+
+
+**Rule:** Final PR must match live navigation (`/` → `/workspace/:id`), not a disconnected mock.
+
+**Tóm tắt (VI):** Chọn A/B/C mỗi màn hình; Figma thắng khi khác Stitch; khớp route thật.
+
+---
+
+## 6. Week 1 sprint — tools in 1 day, ship mobile same week
+
+> **No multi-day exploration.** Figma/Stitch are means to an end — the end is a **merged mobile PR** on a live screen.
+
+### Day 1 — Tools (morning) + code (afternoon)
+
+
+| Block         | Time        | Do                                                                                                                                                                                      |
+| ------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Setup**     | 30 min      | `npm install && npm run dev` — open `/` on desktop + DevTools 375px                                                                                                                     |
+| **Figma**     | 45 min      | Open [Figma](https://www.figma.com/design/uakk3T4efS1AIckfTEFSZO/MSK_Workspace_UIX-Design?node-id=0-1) → Inspect **Patient List** node `82-3155` (maps to live worklist)                |
+| **Stitch**    | 45 min      | Open [Stitch board](https://stitch.withgoogle.com/projects/8188910238055386921) → one mobile-frame sketch OR pick closest web mock → **screenshot for agent**                           |
+| **Must-read** | 60 min      | Section 3 four docs only                                                                                                                                                                |
+| **Code**      | Rest of day | **Q-1 on live `/`** — mobile layout for `PatientWorklistPage.tsx` (or `patient-list-main.tsx` if Dave assigns stub route). Cursor/Kilo + agent template (§4). **375px from the start.** |
+| **EOD**       | 15 min      | Send Dave: draft PR **or** before/after screenshots at 375px + 1-line workflow choice (A/B/C)                                                                                           |
+
+
+**Not acceptable as Week 1 deliverable:** gap lists, alignment essays, clicking all 35 routes, Storybook setup.
+
+### Day 2 — Feedback loop
+
+- Apply Dave's review on spacing, tokens, navigation, touch targets
+- Push PR updates; aim for **merge-ready** by EOD if scope was ≤200 lines
+
+### Day 3–5 — Second yield
+
+- Merge Week 1 PR OR complete merge after small fixes
+- Start **second screen** (patient card stub or Q-3 polish on same `/` route)
+- Optional: update one Stitch frame to match what you shipped (Q-8 lite — no separate doc)
+
+### Week 1 success criteria
+
+
+| Check                          | Pass                                           |
+| ------------------------------ | ---------------------------------------------- |
+| Live route `/` usable at 375px | No horizontal scroll                           |
+| Uses `design-tokens.ts`        | No raw hex in new code                         |
+| Dave reviewed once             | By end of Day 1 or 2 AM                        |
+| Runnable demo                  | `npm run dev` — you walk Dave through tap flow |
+
+
+**Tóm tắt (VI):** Ngày 1: tool buổi sáng, code buổi chiều, gửi Dave tối ngày 1; ngày 2 sửa feedback; ngày 3–5 merge + màn hình thứ 2.
+
+---
+
+## 7. What exists vs what you build
+
+
+| Exists                             | You increment                                |
+| ---------------------------------- | -------------------------------------------- |
+| WS-25 workspace PoC (functional)   | Mobile polish, not rewrite                   |
+| 35 Figma stub routes               | Q-1: 2 priority screens                      |
+| Stitch web mocks                   | Q-8 lite: update frame after ship (optional) |
+| `SafetyEscalationOverlay` (orphan) | Q-2: wire it                                 |
+| No error boundaries                | Q-5                                          |
+| No patient PWA                     | Q-6                                          |
+
+
+### WS-25 layout (read-only context)
+
+Clinician workspace is 65/35 split — your zone is **patient list, cards, patient dashboard**, not DICOM canvas:
+
+```
+┌─ TopBar ─────────────────────────────────────┐
+├─ Zone A (65%) DICOM  │ Zone B (35%) sidebar  ┤  ← Dave/Phuc zone
+└────────────────────────────────────────────────┘
+
+Your zone: / worklist, /patients, patient-card-*, /home
+```
+
+See `session_memory/26_Jun_26/Proj_context_26_Jun_26.md` for full ASCII.
+
+**Tóm tắt (VI):** Workspace clinician đã có; bạn làm patient list, card, dashboard mobile.
+
+---
+
+## 8. Your backlog (detail)
+
+
+| ID      | Gap                     | Priority screens / files                                                                |
+| ------- | ----------------------- | --------------------------------------------------------------------------------------- |
+| **Q-1** | Stub → Figma fidelity   | Home, Login, Patient List, Patient Cards (see `figma-component-specs.md` §Priorities)   |
+| **Q-2** | Safety overlay unrouted | `SafetyEscalationOverlay.tsx`, `App.tsx`                                                |
+| **Q-3** | No 375px pass           | Assigned patient screen                                                                 |
+| **Q-4** | Accessibility           | Patient-facing view                                                                     |
+| **Q-5** | Error boundaries        | `App.tsx` workspace route                                                               |
+| **Q-6** | Patient dashboard       | `patient-card-*.tsx`, FR-26 preview                                                     |
+| **Q-7** | Zero-GPU UI banner      | Dave provides detection hook                                                            |
+| **Q-8** | Stitch sync (lite)      | Update Stitch frame **after** you ship — optional in PR, not a standalone proposal gate |
+
+
+**Figma priorities (from spec):**
+
+1. Home, Login, Create Account
+2. Patient List + Cards
+3. Workspace shell (read-only for you)
+4. Auth flows
+5. AI View, Chat, Ultrasound
+6. Remaining screens
+
+**Tóm tắt (VI):** Ưu tiên Home, Patient List, Patient Card trước.
+
+---
+
+## 9. SMART milestones
+
+### M1 — Week 1 ship (Jul 7 – Jul 11) ← **start here**
+
+
+|                |                                                                                                         |
+| -------------- | ------------------------------------------------------------------------------------------------------- |
+| **Ticket**     | **Q-1 on live `/` worklist** (Dave confirms file: `PatientWorklistPage.tsx` or `patient-list-main.tsx`) |
+| **Specific**   | Mobile implementation at 375px on a **live** route — not a disconnected stub                            |
+| **Measurable** | Draft PR Day 1 EOD; merged or merge-ready by Day 5; before/after screenshots                            |
+| **Achievable** | ≤200 lines; tools only Day 1 morning                                                                    |
+| **Relevant**   | CP-5 — fastest visible yield                                                                            |
+| **Feedback**   | Dave review ≤24h after first push                                                                       |
+
+
+### M2 — Second screen (Jul 14 – Jul 25)
+
+
+|                 |                                                                     |
+| --------------- | ------------------------------------------------------------------- |
+| **Ticket**      | Q-1 #2 (patient card / home) or Q-3 deepen mobile on shipped screen |
+| **Deliverable** | 2nd merged PR                                                       |
+| **Relevant**    | CP-5 / CP-6                                                         |
+
+
+### M3 — Mobile hardening (Jul 28 – Aug 11)
+
+
+|                 |                                                                |
+| --------------- | -------------------------------------------------------------- |
+| **Ticket**      | Q-3 or Q-2                                                     |
+| **Deliverable** | 375px recording; taps ≥44px; optional Q-8 Stitch frame updated |
+| **Relevant**    | CP-6                                                           |
+
+
+### M4 — Accessibility (Aug 4 – Aug 21) *optional*
+
+
+|                 |                                           |
+| --------------- | ----------------------------------------- |
+| **Ticket**      | Q-4                                       |
+| **Deliverable** | High contrast, large type on patient view |
+| **Relevant**    | CP-7                                      |
+
+
+**Tóm tắt (VI):** M1 = tuần 1 merge mobile `/` worklist; không có M0 khảo sát riêng; M2–M4 mở rộng sau khi có feedback.
+
+---
+
+## 10. Per-ticket workflow
+
+```
+1. Dave assigns Q-n
+2. Pick workflow A / B / C — write in PR description
+3. Capture Figma + Stitch reference screenshots
+4. Cursor/Kilo: use agent prompt template (Section 4)
+5. Review every line of the diff — understand before commit
+6. npm run dev → screenshot desktop + 375px
+7. PR: Q-n, CP-n, workflow choice, design links
+```
+
+**Tóm tắt (VI):** Mỗi ticket: chọn workflow → agent hỗ trợ → review diff → screenshot → PR.
+
+---
+
+## 11. Boundaries
+
+**Touch:** `src/pages/`, `src/components/` (atoms/molecules/layout), `src/styles/`, `App.tsx`, Stitch whiteboard, `public/assets/stitch/`
+
+**Do not touch:** `src/lib/llm/`, `src/workers/`, backend, ml
+
+**Figma/Stitch edits:** OK to update Stitch frames and Figma comments; ask Dave before changing shared Figma components.
+
+**Tóm tắt (VI):** Chỉ frontend UI; hỏi Dave trước khi sửa component Figma dùng chung.
+
+---
+
+## 12. Definition of done
+
+- [ ] Week 1: live `/` worklist mobile at 375px shipped or merge-ready
+- [ ] Dave feedback incorporated within 48h of first push
+- [ ] ≥2 screens merged by end of Month 1 (M1 + M2)
+- [ ] Each PR: workflow A/B/C (one line) + 375px screenshot
+- [ ] Never committed `secrets/` or PHI
+
+**Tóm tắt (VI):** Tuần 1 phải có mobile `/` chạy được + feedback Dave; không cần báo cáo alignment dài.
+
+---
+
+## 13. Agent prompt examples (optimize / change based on usecase)
+
+**Learn the codebase:**
+
+```
+Explain PatientWorklistPage.tsx in simple terms: what components it uses,
+where data comes from, and which Figma node it maps to.
+```
+
+**Start Q-1 (Figma-first):**
+
+```
+Implement /home per Figma node 33-143 in figma-component-specs.md.
+Reuse Button and Badge from component-inventory. Use design-tokens.ts only.
+Current stub: src/pages/home.tsx
+```
+
+**Week 1 — ship live worklist mobile (Day 1 afternoon):**
+
+```
+Mobile pass for PatientWorklistPage at 375px.
+Figma node 82-3155. Stitch screenshot attached.
+Use design-tokens.ts and existing Button, Badge, PatientCard from component-inventory.
+No horizontal scroll. Touch targets >= 44px.
+Do not change routing — stay on /.
+Show me the minimal diff.
+```
+
+**Start Q-3 (mobile pass):**
+
+```
+Make patient-list-main.tsx usable at 375px: no horizontal scroll,
+touch targets at least 44px. Show me which CSS to change.
+```
+
+---
+
+## 14. Bonus — Feynman Technique prompts
+
+Use when React layout, routing, or design workflow feels confusing **before** you commit.  
+Master template: [INDEX §9](./ONBOARDING_INDEX.md#9-bonus--feynman-technique-with-agents).
+
+### Hard concepts → ready-made prompts
+
+**Live route vs stub route (Week 1 critical):**
+```
+Feynman explain the difference between our LIVE routes (/ and /workspace/:id)
+and the 35 Figma STUB routes in src/pages/. Why does Week 1 target
+PatientWorklistPage on / ? Use a "demo kitchen vs blueprint room" analogy.
+Quiz me.
+```
+
+**PatientWorklistPage data flow:**
+```
+Feynman explain PatientWorklistPage.tsx: where patient list data comes from
+(mockData vs patientStore), what happens when I tap "Mở phiên chẩn đoán",
+and which components re-render. ≤8 steps. No jargon without definition. Quiz me.
+```
+
+**design-tokens.ts vs hardcoded CSS:**
+```
+Feynman explain why we use design-tokens.ts instead of #hex in components.
+Show one wrong example and one right example from our codebase.
+Quiz me on how to add a new spacing value correctly.
+```
+
+**375px mobile layout:**
+```
+Feynman explain mobile-first pass at 375px for our worklist: flex vs grid,
+overflow-x, and 44px touch targets. What is the smallest change to
+PatientListShell or PatientWorklistPage to stop horizontal scroll?
+Teach only — no code until I answer your quiz.
+```
+
+**Figma vs Stitch vs code (your workflow A/B/C):**
+```
+Feynman explain when I should use Figma-first vs Stitch-first vs hybrid
+for a patient screen. What is "reference only" Stitch export vs production code?
+Quiz me with one scenario: patient card on mobile.
+```
+
+**React atoms vs molecules (component-inventory):**
+```
+Feynman explain atomic design using OUR component-inventory.md: when is
+something a Button (atom) vs PatientHeader (molecule)? Give 2 examples
+from patient list screen. Quiz me.
+```
+
+### Feynman before commit rule
+
+If the agent wrote code and you **cannot** Feynman-explain the diff back to a friend in 30 seconds → don't commit yet; run one Feynman prompt on the confusing file.
+
+**Tóm tắt (VI):** Hỏi agent giải thích đơn giản khi khó hiểu React/route/mobile; có prompt mẫu; không commit code mình chưa giải thích lại được.

workspace/sprint_1_2/CODEBASE/infra/tests/test_predict_inflammation.py

@@ -0,0 +1,138 @@
+import json
+import time
+from pathlib import Path
+import numpy as np
+from PIL import Image
+import requests
+
+# Server configuration
+TRITON_URL = "https://dtj-tran--triton-s3-service-unified-triton-server.modal.run"
+TARGET_MODEL = "workspace/sprint_1_2/CODEBASE/infra/tests/models/efficientnet_b0_ultrasound_2_class.pth"  # Target a single sub-model directly
+IMFLAMMATION_CLASSES = ["Không viêm", "Có viêm"]
+
+BASE_DIR = Path(__file__).resolve().parent
+
+
+def load_image(path: Path) -> Image.Image:
+    if not path.exists():
+        raise FileNotFoundError(f"Test image not found at: {path}")
+    return Image.open(path).convert("RGB")
+
+
+def preprocess_224(img: Image.Image) -> np.ndarray:
+    """Preprocesses image to NCHW FP32 [1, 3, 224, 224] matching ResNet50 input requirements"""
+    img_resized = img.resize((224, 224), Image.Resampling.BILINEAR)
+    arr = np.asarray(img_resized).astype(np.float32) / 255.0
+    mean = np.array([0.485, 0.456, 0.406], dtype=np.float32)
+    std = np.array([0.229, 0.224, 0.225], dtype=np.float32)
+    arr = (arr - mean) / std
+    arr = arr.transpose(2, 0, 1)  # HWC -> CHW
+    arr = np.expand_dims(arr, axis=0)  # Add batch dim -> NCHW
+    return arr
+
+
+def softmax(x: np.ndarray) -> np.ndarray:
+    e = np.exp(x - np.max(x))
+    return e / np.sum(e)
+
+def build_binary_request(input_tensor: np.ndarray, model_name: str) -> tuple[bytes, dict]:
+    """Constructs a strict KServe v2 binary payload for a single input tensor"""
+    # NOTE: Check your individual model's config.pbtxt to verify if the
+    # expected input name is 'input_image', 'input_0', etc.
+    input_name = "input_image"
+
+    inputs = [
+        {
+            "name": input_name,
+            "shape": list(input_tensor.shape),
+            "datatype": "FP32",
+            "parameters": {"binary_data_size": input_tensor.nbytes},
+        }
+    ]
+
+    # We request the standard 'logits' output tensor from this model
+    outputs = [{"name": "logits"}]
+
+    metadata = {
+        "model_name": model_name,
+        "model_version": "",
+        "inputs": inputs,
+        "outputs": outputs
+    }
+
+    metadata_bytes = json.dumps(metadata).encode("utf-8")
+    body = metadata_bytes + input_tensor.tobytes()
+
+    headers = {
+        "Inference-Header-Content-Length": str(len(metadata_bytes)),
+        "Content-Type": "application/octet-stream"
+    }
+    return body, headers
+
+def parse_binary_response(resp: requests.Response) -> np.ndarray:
+    """Parses Triton's binary response stream for a single output tensor"""
+    header_length = int(resp.headers.get("Inference-Header-Content-Length", "0"))
+    response_bytes = resp.content
+
+    metadata = json.loads(response_bytes[:header_length].decode("utf-8"))
+    binary_data = response_bytes[header_length:]
+
+    # Extract the first available output tensor
+    output_desc = metadata["outputs"][0]
+    shape = output_desc["shape"]
+
+    # Unpack raw bytes back into numpy array
+    arr = np.frombuffer(binary_data, dtype=np.float32).reshape(shape)
+    return arr
+
+def main():
+    # Define a path to a real local image to test with
+    image_path = "test_images/sup-up-long_positive/58e7a7ef-de3e-11ee-97e2-0a580a5f5b60_11.png"
+
+    print(f"Targeting Individual Model: {TARGET_MODEL}")
+    print(f"Loading image from: {image_path}")
+
+    try:
+        # 1. Prepare image
+        img = load_image(image_path)
+        input_data = preprocess_224(img)
+
+        # 2. Build the payload
+        body, headers = build_binary_request(input_data, TARGET_MODEL)
+
+        # 3. Fire request to the targeted model endpoint
+        url = f"{TRITON_URL}/v2/models/{TARGET_MODEL}/infer"
+        print("Sending request to Triton server...")
+
+        t0 = time.time()
+        resp = requests.post(url, data=body, headers=headers, timeout=30)
+        resp.raise_for_status()
+        latency = time.time() - t0
+
+        # 4. Parse output logits
+        logits = parse_binary_response(resp)
+        logits = np.squeeze(logits)  # Drop batch dimension
+
+        # 5. Decode probabilities
+        probs = softmax(logits)
+        predicted_idx = int(np.argmax(probs))
+
+        print("\n" + "=" * 40)
+        print("🎉 SUCCESSFUL INFERENCE")
+        print(f"Network Roundtrip Time: {latency:.4f}s")
+        print("-" * 40)
+        print("Class Probabilities:")
+        for cls_name, prob in zip(IMFLAMMATION_CLASSES, probs):
+            print(f"  {cls_name:<15}: {prob * 100:.2f}%")
+        print("-" * 40)
+        print(f"Prediction: {IMFLAMMATION_CLASSES[predicted_idx]} ({probs[predicted_idx] * 100:.2f}%)")
+        print("=" * 40)
+
+    except Exception as e:
+        print(f"\n❌ Inference Failed: {e}")
+        if 'resp' in locals() and hasattr(resp, 'text'):
+            print(f"Server Error Message: {resp.text}")
+
+
+if __name__ == "__main__":
+    main()

workspace/sprint_1_2/CODEBASE/requirements.txt

@@ -0,0 +1,102 @@
+# Automatically generated by https://github.com/damnever/pigar.
+
+aiosqlite==0.22.1
+docling==2.70.0
+fastapi==0.135.1
+fastembed==0.8.0
+gliner==0.2.27
+grpcio==1.81.1
+httpx==0.28.1
+ingestion==0.0.42
+langchain==1.3.7
+langchain-text-splitters==1.1.2
+modal==1.5.0
+numpy==2.1.3
+opencv-python==4.13.0.92
+pgvector==0.4.2
+pillow==12.3.0
+psycopg2-binary==2.9.12
+pycocotools==2.0.11
+pydantic==2.13.4
+pymupdf==1.28.0
+pypdf==6.14.2
+pytest==9.0.3
+python-dotenv==1.2.2
+redis==8.0.1
+removeOaExtension==0.0.6
+requests==2.34.2
+starlette==1.2.1
+supabase==2.31.0
+timm==1.0.25
+torch==2.12.1
+torchinfo==1.8.0
+torchvision==0.27.1
+transformers==4.57.6
+tritonclient==2.69.0
+uvicorn==0.41.0
+
+# WARNING(pigar): some manual fixes might be required as pigar has detected duplicate requirements for the same import name (possibly for different submodules).
+# WARNING(pigar): the following duplicate requirements are for the import name: backend
+agentbeats==1.2.6
+AlgoVision-Quant-Research==0.0.2
+alles-apin==0.0.1
+asamba==1.0.8
+backend==0.2.4.1
+backendcatraca-tektek==0.0.7
+BackupBackup==0.0.6
+cinder-ml==1.8.5
+cmbagent==0.0.1.post63
+conting-researcher==0.14.0
+cwyod-base==0.0.2
+deepread==0.0.3
+devshare==1.0.0
+django-nextcloud-storage==2024.5.20
+doccano==1.8.5
+doccano-multi-label==1.8.4.2
+docforge-ai==2.0.3
+equation-phase-portrait-tool==0.1.0
+excellxgene==2.9.6
+flaskreactapp==1.0.21
+flet-devtools==0.0.0
+food-fighters==1.0.1
+Fred-Frechet==1.14.5
+gpt-researcher==0.15.1
+hermes-revision-system==0.1.0
+hotel-spider==1.1.5
+latch-excellxgene==1.0.0
+leap-backend==0.1.0
+lemon-auto-saver==1.0.1
+LPP0D==0.1.1
+mcp-feedback-pipe==3.0.15
+mmsbm==1.0.7
+nia-cli==0.1.1
+nmuwd==0.10.3
+omnbot==2017.5
+personal-site-msilvasy==1.0.5
+pipebio==5.1.0
+prastut-ai==1.0.0
+productiongraph==0.2.0
+pyapptest==1.0.0
+python-backend==0.0.1
+pyWikiCMS==0.5.0
+quantum-finance==0.2.0
+qutritium==1.5.2
+rasa-storyteller==0.2.1
+reapply-workflows==0.1.0
+recall-core==0.1.1
+Researcher==0.4.3
+reusing-intent==0.1.2
+sparseprop==0.1.14
+terminal-note==0.10.0
+traiNER-loop==0.1.0
+typernexrad-cli==0.1.0
+viasp==2.3.0.post3
+vibe-reader==0.2.1
+work-with-database==0.0.1
+x-lib==0.0.27
+# WARNING(pigar): the following duplicate requirements are for the import name: langchain_google_vertexai
+gigachain-google-vertexai==2.0.0
+langchain-google-vertexai==3.2.4
+# WARNING(pigar): the following duplicate requirements are for the import name: optimum
+optimum==2.1.0
+optimum-onnx==0.1.0