-Ui deployement

.dockerignore

@@ -0,0 +1,24 @@
+# Frontend build artifacts / deps (rebuilt inside the image)
+frontend/node_modules
+frontend/dist
+
+# Python caches / envs
+**/__pycache__
+*.pyc
+rag_env
+.venv
+venv
+
+# Legacy Streamlit UI (superseded by the React frontend; not run in the container)
+app.py
+ui/
+
+# Local runtime data (mounted via Azure Files in prod)
+uploaded_reports
+
+# Repo/tooling noise
+.git
+.gitattributes
+image.png
+README.md
+azure

.env

@@ -0,0 +1 @@
+GEMINI_API_KEY=AIzaSyD6LIwVuyNnAF7oe5jzwoN5mAc6Z6FXjFY

.gitignore

@@ -0,0 +1,16 @@
+# Python
+__pycache__/
+*.pyc
+.venv/
+venv/
+rag_env/
+
+# Node / frontend
+frontend/node_modules/
+frontend/dist/
+
+# Local runtime data
+uploaded_reports/
+
+# OS
+.DS_Store

Dockerfile

@@ -1,20 +1,41 @@
-FROM python:3.13.5-slim
+# ── Stage 1: build the React frontend ───────────────────────────────────────
+FROM node:20-slim AS frontend
+WORKDIR /app/frontend
+COPY frontend/package.json frontend/package-lock.json* ./
+RUN npm ci
+COPY frontend/ ./
+RUN npm run build            # emits /app/frontend/dist
 
+# ── Stage 2: python runtime (FastAPI serves API + built SPA) ─────────────────
+FROM python:3.11-slim AS runtime
 WORKDIR /app
 
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    curl \
-    git \
+# Build deps for faiss / paddle / native wheels
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        build-essential curl libgl1 libglib2.0-0 libgomp1 \
     && rm -rf /var/lib/apt/lists/*
 
+# Python deps first (better layer caching)
 COPY requirements.txt ./
+RUN pip install "torch>=2.3" --index-url https://download.pytorch.org/whl/cpu && \
+    pip install -r requirements.txt
+
+
+# App code + the base vector DB
 COPY src/ ./src/
+COPY backend/ ./backend/
+COPY output/ ./output/
 
-RUN pip3 install -r requirements.txt
+# Built frontend from stage 1
+COPY --from=frontend /app/frontend/dist ./frontend/dist
 
-EXPOSE 8501
+ENV CUDA_VISIBLE_DEVICES="" \
+    DB_PATH=output/biomedbert_vector_db \
+    UPLOAD_DIR=uploaded_reports \
+    PORT=8000
 
-HEALTHCHECK CMD curl --fail http://localhost:8501/_stcore/health
+EXPOSE 8000
+HEALTHCHECK --interval=30s --timeout=5s --start-period=90s \
+    CMD curl -fsS http://localhost:8000/api/health || exit 1
 
-ENTRYPOINT ["streamlit", "run", "src/streamlit_app.py", "--server.port=8501", "--server.address=0.0.0.0"]
+CMD ["sh", "-c", "uvicorn backend.main:app --host 0.0.0.0 --port ${PORT}"]

app.yaml

@@ -0,0 +1,268 @@
+id: /subscriptions/c5763c41-1363-4244-8f55-befc04bc3fdc/resourceGroups/patho-rag/providers/Microsoft.App/containerapps/pathorag
+identity:
+  principalId: a2dd65f8-ce7c-42ac-982e-d42dbe6dbe14
+  tenantId: 61f3e3b8-9b52-433a-a4eb-c67334ce54d5
+  type: SystemAssigned
+location: France Central
+name: pathorag
+properties:
+  configuration:
+    activeRevisionsMode: Single
+    dapr: null
+    identitySettings: []
+    ingress:
+      additionalPortMappings: null
+      allowInsecure: false
+      clientCertificateMode: null
+      corsPolicy: null
+      customDomains: null
+      exposedPort: 0
+      external: true
+      fqdn: pathorag.agreeablebeach-ed9dda6b.francecentral.azurecontainerapps.io
+      ipSecurityRestrictions: null
+      stickySessions: null
+      targetPort: 8000
+      targetPortHttpScheme: null
+      traffic:
+      - latestRevision: true
+        weight: 100
+      transport: Auto
+    maxInactiveRevisions: null
+    registries:
+    - identity: system
+      passwordSecretRef: ''
+      server: pathoragacr.azurecr.io
+      username: ''
+    revisionTransitionThreshold: null
+    runtime: null
+    secrets:
+    - name: google-api-key
+    service: null
+    targetLabel: ''
+  customDomainVerificationId: 8B0174A32E63E74188290E5173041F60F4E8386B5C95F7487A60CD2B2BC53587
+  delegatedIdentities: []
+  environmentId: /subscriptions/c5763c41-1363-4244-8f55-befc04bc3fdc/resourceGroups/lidc-rg/providers/Microsoft.App/managedEnvironments/managedEnvironment-lidcrg-a5f0
+  eventStreamEndpoint: https://francecentral.azurecontainerapps.dev/subscriptions/c5763c41-1363-4244-8f55-befc04bc3fdc/resourceGroups/patho-rag/containerApps/pathorag/eventstream
+  latestReadyRevisionName: pathorag--0000001
+  latestRevisionFqdn: pathorag--0000001.agreeablebeach-ed9dda6b.francecentral.azurecontainerapps.io
+  latestRevisionName: pathorag--0000001
+  managedEnvironmentId: /subscriptions/c5763c41-1363-4244-8f55-befc04bc3fdc/resourceGroups/lidc-rg/providers/Microsoft.App/managedEnvironments/managedEnvironment-lidcrg-a5f0
+  outboundIpAddresses:
+  - 20.74.16.183
+  - 20.74.94.128
+  - 20.74.94.150
+  - 20.74.93.40
+  - 98.66.249.192
+  - 98.66.250.10
+  - 98.66.248.181
+  - 98.66.249.135
+  - 98.66.248.214
+  - 98.66.250.141
+  - 20.19.239.83
+  - 172.189.12.75
+  - 172.189.174.219
+  - 4.178.216.19
+  - 172.189.173.164
+  - 4.178.14.102
+  - 20.216.214.144
+  - 20.19.159.158
+  - 20.216.214.132
+  - 172.189.28.145
+  - 40.66.62.27
+  - 4.251.149.121
+  - 20.19.159.161
+  - 4.176.16.39
+  - 172.189.105.120
+  - 40.66.63.35
+  - 4.233.27.154
+  - 4.176.16.32
+  - 4.233.27.155
+  - 172.189.165.195
+  - 172.189.15.42
+  - 4.233.27.160
+  - 20.19.232.87
+  - 172.189.15.26
+  - 172.189.28.153
+  - 172.189.14.215
+  - 4.251.149.128
+  - 172.189.158.145
+  - 172.189.107.176
+  - 4.176.46.125
+  - 172.189.28.148
+  - 4.176.16.37
+  - 4.176.16.44
+  - 4.176.46.141
+  - 20.216.214.197
+  - 172.189.28.156
+  - 172.189.14.226
+  - 4.251.149.135
+  - 20.19.236.225
+  - 172.189.14.230
+  - 4.178.14.133
+  - 20.19.159.180
+  - 4.176.46.129
+  - 172.189.107.188
+  - 20.216.221.212
+  - 4.233.27.166
+  - 4.176.46.151
+  - 20.216.214.182
+  - 4.251.201.207
+  - 20.216.214.169
+  - 20.216.221.231
+  - 4.251.201.192
+  - 172.189.14.240
+  - 4.176.46.122
+  - 4.178.14.148
+  - 4.176.46.177
+  - 4.176.46.173
+  - 4.251.149.136
+  - 4.233.27.161
+  - 172.189.107.190
+  - 172.189.165.198
+  - 172.189.28.167
+  - 172.189.28.164
+  - 20.19.159.183
+  - 20.216.221.229
+  - 4.178.14.135
+  - 20.19.232.86
+  - 20.216.221.203
+  - 20.216.214.158
+  - 20.216.221.205
+  - 20.40.148.255
+  - 4.211.69.69
+  - 4.251.202.168
+  - 4.251.186.182
+  - 4.178.14.42
+  - 4.251.138.82
+  - 172.189.13.56
+  - 4.211.69.75
+  - 172.189.46.179
+  - 20.216.196.172
+  - 20.216.214.129
+  - 4.251.201.171
+  - 51.103.5.3
+  - 20.199.32.9
+  - 172.189.158.203
+  - 51.11.233.150
+  - 172.189.14.180
+  - 172.189.27.233
+  - 20.74.47.218
+  - 172.189.28.133
+  - 20.216.216.188
+  - 20.216.216.219
+  - 20.216.217.5
+  - 20.216.216.182
+  - 98.66.242.126
+  - 98.66.242.144
+  - 98.66.242.209
+  - 98.66.242.230
+  - 98.66.242.239
+  - 98.66.242.232
+  - 172.189.12.72
+  - 20.19.223.96
+  - 20.19.220.136
+  - 20.19.221.135
+  - 4.233.16.221
+  - 4.176.46.82
+  - 4.251.201.180
+  - 20.74.96.18
+  - 172.189.14.188
+  - 20.19.207.214
+  - 4.251.149.8
+  - 4.233.27.143
+  - 20.216.221.100
+  - 20.19.207.234
+  - 4.233.27.148
+  - 20.19.207.210
+  - 4.233.28.23
+  - 20.216.221.171
+  - 172.189.28.136
+  - 4.233.27.142
+  - 20.216.221.185
+  - 20.216.221.177
+  - 4.178.14.70
+  - 172.189.159.19
+  - 20.19.159.153
+  - 4.178.14.41
+  - 172.189.107.169
+  - 20.19.159.143
+  - 4.176.46.112
+  - 172.189.107.149
+  - 172.189.165.187
+  - 4.176.16.0
+  - 172.189.165.182
+  - 4.176.16.27
+  - 4.251.149.91
+  - 4.176.16.14
+  - 172.189.158.226
+  - 4.178.13.255
+  - 4.178.14.18
+  - 4.178.14.63
+  - 4.178.14.36
+  - 172.189.14.208
+  - 172.189.158.239
+  - 20.19.159.41
+  - 20.216.221.200
+  - 4.176.16.21
+  - 20.19.207.222
+  - 4.233.27.244
+  - 172.189.158.230
+  - 4.176.46.94
+  - 4.251.149.99
+  - 4.251.149.50
+  - 4.251.149.109
+  - 4.251.201.186
+  - 172.189.107.139
+  - 20.216.214.131
+  - 172.189.28.140
+  - 172.189.14.205
+  - 20.19.159.140
+  - 172.189.28.143
+  - 172.189.28.135
+  - 20.19.159.136
+  - 172.189.158.223
+  - 40.66.60.105
+  - 4.233.26.37
+  - 4.178.14.2
+  - 20.216.221.164
+  - 172.189.105.174
+  - 4.233.27.134
+  - 20.216.219.52
+  - 172.189.44.67
+  patchingMode: Automatic
+  provisioningState: Succeeded
+  runningStatus: Running
+  template:
+    containers:
+    - env:
+      - name: GOOGLE_API_KEY
+        secretRef: google-api-key
+      image: pathoragacr.azurecr.io/pathorag:latest
+      imageType: ContainerImage
+      name: pathorag
+      resources:
+        cpu: 2.0
+        ephemeralStorage: 8Gi
+        memory: 4Gi
+    customMetricsSettings: null
+    initContainers: null
+    revisionSuffix: ''
+    scale:
+      cooldownPeriod: 300
+      maxReplicas: 3
+      minReplicas: 1
+      pollingInterval: 30
+      rules: null
+    serviceBinds: null
+    terminationGracePeriodSeconds: null
+    volumes: null
+  workloadProfileName: Consumption
+resourceGroup: patho-rag
+systemData:
+  createdAt: '2026-07-10T20:52:23.0352323'
+  createdBy: surya-prakash.selva@student-cs.fr
+  createdByType: User
+  lastModifiedAt: '2026-07-10T20:52:42.5113595'
+  lastModifiedBy: surya-prakash.selva@student-cs.fr
+  lastModifiedByType: User
+type: Microsoft.App/containerApps

azure/deploy.md

@@ -0,0 +1,98 @@
+# Deploying to Azure Container Apps
+
+Single Docker image: FastAPI (`backend/main.py`) serves both the `/api/*` routes
+and the built React SPA at `/`. These steps build the image in Azure Container
+Registry (ACR) and run it on Azure Container Apps (ACA).
+
+## Prerequisites
+
+- `az` CLI logged in (`az login`) with a subscription selected.
+- A resource group, e.g. `az group create -n patho-rag -l eastus`.
+- Your `GOOGLE_API_KEY` for Gemini.
+- **Vector DB present locally**: `output/biomedbert_vector_db/{faiss.index,metadata.pkl}`
+  are tracked with git-LFS. Run `git lfs pull` so the image bakes real files,
+  not LFS pointer stubs (otherwise the app boots "degraded").
+
+## 1. Create an ACR and build the image
+
+```bash
+az acr create -g patho-rag -n pathoragacr --sku Basic
+az acr build -r pathoragacr -t pathorag:latest .   # builds Dockerfile in the cloud
+```
+
+## 2. Create the Container Apps environment
+
+```bash
+az extension add --name containerapp --upgrade
+az containerapp env create -g patho-rag -n patho-env -l eastus
+```
+
+## 3. Create the app
+
+```bash
+az containerapp create \
+  -g patho-rag -n pathorag \
+  --environment patho-env \
+  --image pathoragacr.azurecr.io/pathorag:latest \
+  --registry-server pathoragacr.azurecr.io \
+  --target-port 8000 --ingress external \
+  --min-replicas 1 --max-replicas 3 \
+  --cpu 2 --memory 4Gi \
+  --secrets google-api-key=<YOUR_GEMINI_KEY> \
+  --env-vars GOOGLE_API_KEY=secretref:google-api-key
+```
+
+- `--min-replicas 1` avoids scale-to-zero so the models stay warm (cold start
+  reloads BiomedBERT + cross-encoder + PaddleOCR, which is slow).
+- Bump `--cpu/--memory` if OCR/embedding is heavy; torch + paddle want headroom.
+
+The public URL is the app's FQDN:
+
+```bash
+az containerapp show -g patho-rag -n pathorag --query properties.configuration.ingress.fqdn -o tsv
+```
+
+## 4. Persist uploads + index across restarts (important)
+
+The container filesystem is **ephemeral** — uploaded PDFs and the FAISS index
+updates from new documents are lost on restart/redeploy unless mounted.
+
+1. Create a storage account + file share, and register it with the ACA env:
+
+```bash
+az storage account create -g patho-rag -n pathoragstore --sku Standard_LRS
+az storage share create --account-name pathoragstore -n ragdata
+az containerapp env storage set -g patho-rag -n patho-env \
+  --storage-name ragdata --azure-file-account-name pathoragstore \
+  --azure-file-account-key <KEY> --azure-file-share-name ragdata \
+  --access-mode ReadWrite
+```
+
+2. Mount it into the app (via `az containerapp update --yaml` volume/volumeMounts)
+   at both `uploaded_reports/` and `output/biomedbert_vector_db/`, and seed the
+   share with the initial `output/biomedbert_vector_db/` contents so the base
+   corpus is available on first boot.
+
+## 5. Model cache (optional, faster cold starts)
+
+BiomedBERT, the cross-encoder, and PaddleOCR weights download on first use. To
+avoid re-downloading on every new replica, either bake a warm cache into the
+image (pre-download during `docker build`) or point `HF_HOME` / the paddle cache
+dir at the mounted Azure Files share.
+
+## Update / redeploy
+
+```bash
+az acr build -r pathoragacr -t pathorag:latest .
+az containerapp update -g patho-rag -n pathorag \
+  --image pathoragacr.azurecr.io/pathorag:latest
+```
+
+## Smoke test
+
+- Open the FQDN → the SPA loads.
+- `GET /api/health` → `{"status":"ok","num_documents":N}`.
+- Ask a question → answer streams token-by-token with citations.
+- Upload a PDF → progress bar → the doc becomes selectable and highlights work.
+- Restart a replica → previously uploaded docs still present (confirms the mount).
+```

backend/main.py

@@ -0,0 +1,130 @@
+"""FastAPI app for the Pathology RAG system.
+
+Serves a streaming chat API over the existing RAG pipeline and (in the
+container) the built React SPA from the same origin.
+"""
+
+import os
+import json
+from pathlib import Path
+from contextlib import asynccontextmanager
+
+from fastapi import FastAPI, UploadFile, File, HTTPException
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import FileResponse
+from fastapi.staticfiles import StaticFiles
+from sse_starlette.sse import EventSourceResponse
+
+from .schemas import (
+    ChatRequest, ReportsResponse, HealthResponse, UploadStartResponse,
+)
+from .rag_service import service, UPLOAD_DIR
+
+FRONTEND_DIST = Path(__file__).resolve().parent.parent / "frontend" / "dist"
+
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    # Load the (expensive) pipeline once at startup.
+    service.load()
+    yield
+
+
+app = FastAPI(title="Pathology RAG API", lifespan=lifespan)
+
+# Permissive CORS only matters for local dev (Vite on :5173 → API on :8000).
+# In the container the SPA is same-origin so this is a no-op.
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["*"],
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+async def _sse(threaded_stream):
+    """Adapt a ThreadedEventStream ({"event","data":dict}) to the dict shape
+    EventSourceResponse expects ({"event", "data": <json str>})."""
+    async for item in threaded_stream:
+        yield {"event": item["event"], "data": json.dumps(item["data"])}
+
+
+# ── API ─────────────────────────────────────────────────────────────────────
+@app.get("/api/health", response_model=HealthResponse)
+async def health():
+    if service.ready:
+        return HealthResponse(status="ok", num_documents=len(service.get_reports()))
+    return HealthResponse(status="degraded", num_documents=0, detail=service.load_error)
+
+
+@app.get("/api/reports", response_model=ReportsResponse)
+async def reports():
+    return ReportsResponse(reports=service.get_reports())
+
+
+@app.post("/api/chat")
+async def chat(req: ChatRequest):
+    if not service.ready:
+        raise HTTPException(503, detail=f"Pipeline not ready: {service.load_error}")
+
+    history = [m.model_dump() for m in req.history] if req.history else None
+    producer = service.make_chat_producer(
+        question=req.question,
+        report_name=req.report_name,
+        report_names=req.report_names,
+        top_k=req.top_k,
+        history=history,
+    )
+    from .rag_service import ThreadedEventStream
+    stream = ThreadedEventStream()
+    stream.run(producer)
+    return EventSourceResponse(_sse(stream))
+
+
+@app.post("/api/upload", response_model=UploadStartResponse)
+async def upload(file: UploadFile = File(...)):
+    if not service.ready:
+        raise HTTPException(503, detail=f"Pipeline not ready: {service.load_error}")
+    if not file.filename.lower().endswith(".pdf"):
+        raise HTTPException(400, detail="Only PDF files are supported.")
+
+    upload_dir = Path(UPLOAD_DIR)
+    upload_dir.mkdir(exist_ok=True)
+    # Strip any path components from the client-supplied name.
+    safe_name = Path(file.filename).name
+    dest = upload_dir / safe_name
+    dest.write_bytes(await file.read())
+
+    job_id = service.start_upload(str(dest))
+    return UploadStartResponse(job_id=job_id, filename=safe_name)
+
+
+@app.get("/api/upload/{job_id}/events")
+async def upload_events(job_id: str):
+    stream = service.get_job(job_id)
+    if stream is None:
+        raise HTTPException(404, detail="Unknown or expired upload job.")
+
+    async def gen():
+        async for evt in _sse(stream):
+            yield evt
+        service.pop_job(job_id)
+
+    return EventSourceResponse(gen())
+
+
+@app.get("/api/pdf/{name}")
+async def get_pdf(name: str):
+    """Serve a raw uploaded PDF for the viewer. `name` may be the report stem
+    or the full file name; path components are stripped to prevent traversal."""
+    stem = Path(name).name
+    upload_dir = Path(UPLOAD_DIR)
+    candidate = upload_dir / (stem if stem.lower().endswith(".pdf") else f"{stem}.pdf")
+    if not candidate.exists():
+        raise HTTPException(404, detail="PDF not found.")
+    return FileResponse(str(candidate), media_type="application/pdf")
+
+
+# ── Static SPA (only when a build exists; in dev Vite serves the frontend) ──
+if FRONTEND_DIST.exists():
+    app.mount("/", StaticFiles(directory=str(FRONTEND_DIST), html=True), name="spa")

backend/rag_service.py

@@ -0,0 +1,204 @@
+"""Service layer around the existing RAG pipeline.
+
+Wraps `CompleteRAGPipeline` (retrieval + streaming generation) and
+`DynamicRAGUpdater` (OCR upload + index update), and provides a small
+thread→async bridge so the blocking ML work streams cleanly over SSE
+without blocking the event loop.
+"""
+
+import os
+import sys
+import uuid
+import queue
+import asyncio
+import threading
+from pathlib import Path
+from typing import Dict, List, Optional, Callable
+
+# Reuse the existing, working RAG code in src/
+sys.path.append(str(Path(__file__).resolve().parent.parent / "src"))
+
+DB_PATH = os.getenv("DB_PATH", "output/biomedbert_vector_db")
+EMBEDDING_MODEL = os.getenv(
+    "EMBEDDING_MODEL",
+    "microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext",
+)
+UPLOAD_DIR = os.getenv("UPLOAD_DIR", "uploaded_reports")
+
+
+# ────────────────────────────────────────────────────────────────────────────
+# Thread → async SSE bridge
+# ────────────────────────────────────────────────────────────────────────────
+class ThreadedEventStream:
+    """Runs a blocking `producer(emit)` in a daemon thread and exposes an async
+    iterator of the events it emits. The producer calls `emit({"event","data"})`
+    for each event; iteration ends when the producer returns (or raises, which
+    is surfaced as a final error event)."""
+
+    _DONE = object()
+
+    def __init__(self):
+        self._q: "queue.Queue" = queue.Queue()
+
+    def run(self, producer: Callable[[Callable[[dict], None]], None]):
+        def worker():
+            try:
+                producer(self._q.put)
+            except Exception as exc:  # noqa: BLE001 - surface to the client
+                self._q.put({"event": "error", "data": {"message": str(exc)}})
+            finally:
+                self._q.put(self._DONE)
+
+        threading.Thread(target=worker, daemon=True).start()
+
+    async def __aiter__(self):
+        while True:
+            try:
+                item = self._q.get_nowait()
+            except queue.Empty:
+                await asyncio.sleep(0.05)
+                continue
+            if item is self._DONE:
+                break
+            yield item
+
+
+class RagService:
+    def __init__(self):
+        self.pipeline = None
+        self._updater = None
+        self._ocr_engine = None
+        self.load_error: Optional[str] = None
+        self._jobs: Dict[str, ThreadedEventStream] = {}
+        self._job_files: Dict[str, str] = {}
+
+    # ── lifecycle ──────────────────────────────────────────────────────────
+    def load(self):
+        """Load the pipeline once at startup. Failures (missing API key / DB)
+        are captured so the app can still serve the frontend and report a
+        degraded health status instead of crashing."""
+        try:
+            from retriever import CompleteRAGPipeline
+            self.pipeline = CompleteRAGPipeline(
+                faiss_db_path=DB_PATH,
+                embedding_model=EMBEDDING_MODEL,
+            )
+            self.load_error = None
+        except Exception as exc:  # noqa: BLE001
+            import traceback
+            self.pipeline = None
+            self.load_error = str(exc)
+            # Print the full traceback so the real failing import shows up in
+            # container logs instead of just the top-level message.
+            print("=== PIPELINE LOAD FAILED ===", flush=True)
+            traceback.print_exc()
+
+    @property
+    def ready(self) -> bool:
+        return self.pipeline is not None
+
+    def _get_updater(self):
+        """Lazily build the OCR-based updater on first upload, reusing the
+        pipeline's already-loaded embedder so only one embedding model lives
+        in memory (same pattern the Streamlit app used)."""
+        if self._updater is None:
+            from paddleocr import PaddleOCR
+            from document_processor import DynamicRAGUpdater
+            if self._ocr_engine is None:
+                # PaddleOCR 3.x API (see document_processor for rationale).
+                self._ocr_engine = PaddleOCR(
+                    lang="en",
+                    use_doc_orientation_classify=False,
+                    use_doc_unwarping=False,
+                    use_textline_orientation=False,
+                )
+            self._updater = DynamicRAGUpdater(
+                vector_db_path=DB_PATH,
+                upload_dir=UPLOAD_DIR,
+                ocr_engine=self._ocr_engine,
+                embedder=self.pipeline.query_processor.model,
+            )
+        return self._updater
+
+    # ── reads ───────────────────────��──────────────────────────────────────
+    def get_reports(self) -> List[str]:
+        if not self.ready:
+            return []
+        return self.pipeline.get_available_reports()
+
+    # ── retrieval + streaming generation ────────────────────────────────────
+    @staticmethod
+    def _sources_payload(top_chunks: List[Dict]) -> List[dict]:
+        out = []
+        for i, src in enumerate(top_chunks, 1):
+            chunk = src["chunk"]
+            out.append({
+                "index": i,
+                "filename": chunk.get("filename", "unknown"),
+                "page": chunk.get("page"),
+                "line_bboxes": chunk.get("line_bboxes", []),
+                "text": chunk.get("text", ""),
+                "score": float(src.get("ce_score", src.get("score", 0.0))),
+            })
+        return out
+
+    def make_chat_producer(
+        self,
+        question: str,
+        report_name: Optional[str],
+        report_names: Optional[List[str]],
+        top_k: int,
+        history: Optional[List[dict]],
+    ):
+        """Returns a producer(emit) that: retrieves → emits `sources` →
+        streams `token` deltas → emits `done`."""
+
+        def producer(emit: Callable[[dict], None]):
+            top_chunks = self.pipeline.retrieve(
+                question,
+                report_name=report_name,
+                report_names=report_names,
+                top_k=top_k,
+            )
+            emit({"event": "sources", "data": {"sources": self._sources_payload(top_chunks)}})
+
+            if not top_chunks:
+                emit({"event": "token", "data": {"text": "No relevant information found for this question."}})
+                emit({"event": "done", "data": {"num_sources": 0}})
+                return
+
+            for delta in self.pipeline.llm.generate_stream(question, top_chunks, history):
+                emit({"event": "token", "data": {"text": delta}})
+
+            emit({"event": "done", "data": {"num_sources": len(top_chunks)}})
+
+        return producer
+
+    # ── upload as a background job with progress SSE ─────────────────────────
+    def start_upload(self, pdf_path: str) -> str:
+        job_id = uuid.uuid4().hex
+        stream = ThreadedEventStream()
+
+        def producer(emit: Callable[[dict], None]):
+            def cb(stage: str, detail: dict):
+                emit({"event": "progress", "data": {"stage": stage, **(detail or {})}})
+
+            updater = self._get_updater()
+            stats = updater.process_and_add_pdf(pdf_path, progress_callback=cb)
+            self.pipeline.reload_index()
+            emit({"event": "complete", "data": stats})
+
+        stream.run(producer)
+        self._jobs[job_id] = stream
+        self._job_files[job_id] = pdf_path
+        return job_id
+
+    def get_job(self, job_id: str) -> Optional[ThreadedEventStream]:
+        return self._jobs.get(job_id)
+
+    def pop_job(self, job_id: str):
+        self._jobs.pop(job_id, None)
+        self._job_files.pop(job_id, None)
+
+
+service = RagService()

backend/schemas.py

@@ -0,0 +1,41 @@
+"""Pydantic request/response models for the Pathology RAG API."""
+
+from typing import List, Optional
+from pydantic import BaseModel
+
+
+class ChatMessage(BaseModel):
+    role: str  # "user" | "assistant"
+    content: str
+
+
+class ChatRequest(BaseModel):
+    question: str
+    report_name: Optional[str] = None        # single-document scope (Document Chat)
+    report_names: Optional[List[str]] = None  # multi-document scope (Global Search)
+    top_k: int = 5
+    history: Optional[List[ChatMessage]] = None
+
+
+class SourceOut(BaseModel):
+    index: int
+    filename: str
+    page: Optional[int] = None
+    line_bboxes: List[List[float]] = []
+    text: str
+    score: float
+
+
+class ReportsResponse(BaseModel):
+    reports: List[str]
+
+
+class HealthResponse(BaseModel):
+    status: str            # "ok" | "degraded"
+    num_documents: int
+    detail: Optional[str] = None
+
+
+class UploadStartResponse(BaseModel):
+    job_id: str
+    filename: str

frontend/.gitignore

@@ -0,0 +1,4 @@
+node_modules
+dist
+*.local
+.DS_Store

frontend/index.html

@@ -0,0 +1,18 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Pathology RAG</title>
+    <link rel="preconnect" href="https://fonts.googleapis.com" />
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
+    <link
+      href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&display=swap"
+      rel="stylesheet"
+    />
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/src/main.tsx"></script>
+  </body>
+</html>

frontend/package.json

@@ -0,0 +1,33 @@
+{
+  "name": "pathology-rag-frontend",
+  "private": true,
+  "version": "1.0.0",
+  "type": "module",
+  "scripts": {
+    "dev": "vite",
+    "build": "tsc -b && vite build",
+    "preview": "vite preview"
+  },
+  "dependencies": {
+    "@tanstack/react-query": "^5.51.0",
+    "class-variance-authority": "^0.7.0",
+    "clsx": "^2.1.1",
+    "lucide-react": "^0.412.0",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "react-markdown": "^9.0.1",
+    "react-pdf": "^9.1.1",
+    "tailwind-merge": "^2.4.0"
+  },
+  "devDependencies": {
+    "@types/node": "^20.19.43",
+    "@types/react": "^18.3.3",
+    "@types/react-dom": "^18.3.0",
+    "@vitejs/plugin-react": "^4.3.1",
+    "autoprefixer": "^10.4.19",
+    "postcss": "^8.4.40",
+    "tailwindcss": "^3.4.7",
+    "typescript": "^5.5.4",
+    "vite": "^5.3.5"
+  }
+}

frontend/postcss.config.js

@@ -0,0 +1,6 @@
+export default {
+  plugins: {
+    tailwindcss: {},
+    autoprefixer: {},
+  },
+};

frontend/src/App.tsx

@@ -0,0 +1,31 @@
+import { useState } from "react";
+import { useQuery } from "@tanstack/react-query";
+import { AlertTriangle } from "lucide-react";
+import { getHealth } from "@/lib/api";
+import { Sidebar, type View } from "@/components/Sidebar";
+import { DocumentChat } from "@/views/DocumentChat";
+import { GlobalSearch } from "@/views/GlobalSearch";
+
+export default function App() {
+  const [view, setView] = useState<View>("document");
+  const { data: health } = useQuery({ queryKey: ["health"], queryFn: getHealth });
+
+  return (
+    <div className="flex h-screen overflow-hidden">
+      <Sidebar view={view} onView={setView} />
+      <main className="flex min-w-0 flex-1 flex-col">
+        {health?.status === "degraded" && (
+          <div className="flex items-center gap-2 border-b border-amber-500/30 bg-amber-500/10 px-4 py-2 text-xs text-amber-600 dark:text-amber-400">
+            <AlertTriangle className="h-4 w-4 shrink-0" />
+            <span className="truncate">
+              Backend not fully ready: {health.detail ?? "pipeline unavailable"}
+            </span>
+          </div>
+        )}
+        <div className="min-h-0 flex-1">
+          {view === "document" ? <DocumentChat /> : <GlobalSearch />}
+        </div>
+      </main>
+    </div>
+  );
+}

frontend/src/components/ChatInput.tsx

@@ -0,0 +1,77 @@
+import { useRef, useState, type KeyboardEvent } from "react";
+import { ArrowUp, Square } from "lucide-react";
+import { cn } from "@/lib/utils";
+
+export function ChatInput({
+  onSend,
+  onStop,
+  busy,
+  disabled,
+  placeholder,
+}: {
+  onSend: (text: string) => void;
+  onStop?: () => void;
+  busy?: boolean;
+  disabled?: boolean;
+  placeholder?: string;
+}) {
+  const [text, setText] = useState("");
+  const ref = useRef<HTMLTextAreaElement>(null);
+
+  const submit = () => {
+    const t = text.trim();
+    if (!t || busy || disabled) return;
+    onSend(t);
+    setText("");
+    if (ref.current) ref.current.style.height = "auto";
+  };
+
+  const onKey = (e: KeyboardEvent<HTMLTextAreaElement>) => {
+    if (e.key === "Enter" && !e.shiftKey) {
+      e.preventDefault();
+      submit();
+    }
+  };
+
+  return (
+    <div
+      className={cn(
+        "flex items-end gap-2 rounded-2xl border border-border bg-card p-2 shadow-sm transition-colors focus-within:border-primary/60",
+        disabled && "opacity-60",
+      )}
+    >
+      <textarea
+        ref={ref}
+        value={text}
+        rows={1}
+        disabled={disabled}
+        placeholder={placeholder ?? "Ask a question…"}
+        onChange={(e) => {
+          setText(e.target.value);
+          e.target.style.height = "auto";
+          e.target.style.height = Math.min(e.target.scrollHeight, 200) + "px";
+        }}
+        onKeyDown={onKey}
+        className="max-h-[200px] flex-1 resize-none bg-transparent px-3 py-2 text-sm outline-none placeholder:text-muted-foreground"
+      />
+      {busy ? (
+        <button
+          onClick={onStop}
+          className="flex h-9 w-9 shrink-0 items-center justify-center rounded-xl bg-muted text-foreground hover:bg-accent"
+          title="Stop"
+        >
+          <Square className="h-4 w-4" />
+        </button>
+      ) : (
+        <button
+          onClick={submit}
+          disabled={!text.trim() || disabled}
+          className="flex h-9 w-9 shrink-0 items-center justify-center rounded-xl bg-primary text-primary-foreground transition-opacity hover:opacity-90 disabled:opacity-40"
+          title="Send"
+        >
+          <ArrowUp className="h-4 w-4" />
+        </button>
+      )}
+    </div>
+  );
+}

frontend/src/components/ChatThread.tsx

@@ -0,0 +1,35 @@
+import { useEffect, useRef } from "react";
+import { MessageBubble, type Message } from "./MessageBubble";
+
+export function ChatThread({
+  messages,
+  onCitation,
+  renderExtra,
+  empty,
+}: {
+  messages: Message[];
+  onCitation?: (message: Message, index: number) => void;
+  renderExtra?: (message: Message) => React.ReactNode;
+  empty?: React.ReactNode;
+}) {
+  const endRef = useRef<HTMLDivElement>(null);
+
+  useEffect(() => {
+    endRef.current?.scrollIntoView({ behavior: "smooth", block: "end" });
+  }, [messages]);
+
+  if (messages.length === 0 && empty) {
+    return <div className="flex flex-1 items-center justify-center p-6">{empty}</div>;
+  }
+
+  return (
+    <div className="flex-1 space-y-5 overflow-y-auto px-1 py-4">
+      {messages.map((m) => (
+        <MessageBubble key={m.id} message={m} onCitation={(idx) => onCitation?.(m, idx)}>
+          {renderExtra?.(m)}
+        </MessageBubble>
+      ))}
+      <div ref={endRef} />
+    </div>
+  );
+}

frontend/src/components/ExamplePrompts.tsx

@@ -0,0 +1,32 @@
+import { Sparkles } from "lucide-react";
+
+export function ExamplePrompts({
+  title,
+  prompts,
+  onPick,
+}: {
+  title: string;
+  prompts: string[];
+  onPick: (p: string) => void;
+}) {
+  return (
+    <div className="max-w-md text-center">
+      <div className="mx-auto mb-3 flex h-11 w-11 items-center justify-center rounded-xl bg-primary/10 text-primary">
+        <Sparkles className="h-5 w-5" />
+      </div>
+      <h2 className="mb-1 text-lg font-semibold">{title}</h2>
+      <p className="mb-4 text-sm text-muted-foreground">Try one of these to get started</p>
+      <div className="flex flex-col gap-2">
+        {prompts.map((p) => (
+          <button
+            key={p}
+            onClick={() => onPick(p)}
+            className="rounded-lg border border-border bg-card px-3 py-2 text-left text-sm transition-colors hover:border-primary/60 hover:bg-muted"
+          >
+            {p}
+          </button>
+        ))}
+      </div>
+    </div>
+  );
+}

frontend/src/components/MessageBubble.tsx

@@ -0,0 +1,91 @@
+import ReactMarkdown from "react-markdown";
+import { Microscope, User } from "lucide-react";
+import { cn } from "@/lib/utils";
+import type { Source } from "@/lib/api";
+
+export interface Message {
+  id: string;
+  role: "user" | "assistant";
+  content: string;
+  sources?: Source[];
+  streaming?: boolean;
+}
+
+/** Turn `[3]` reference markers into markdown links (#cite-3) so we can render
+ *  them as interactive citation chips via the `a` component override. */
+function withCitationLinks(text: string): string {
+  return text.replace(/\[(\d+)\]/g, "[$1](#cite-$1)");
+}
+
+export function MessageBubble({
+  message,
+  onCitation,
+  children,
+}: {
+  message: Message;
+  onCitation?: (index: number) => void;
+  children?: React.ReactNode;
+}) {
+  const isUser = message.role === "user";
+
+  return (
+    <div className={cn("flex gap-3 animate-fade-in", isUser && "flex-row-reverse")}>
+      <div
+        className={cn(
+          "flex h-8 w-8 shrink-0 items-center justify-center rounded-lg",
+          isUser ? "bg-muted text-foreground" : "bg-primary text-primary-foreground",
+        )}
+      >
+        {isUser ? <User className="h-4 w-4" /> : <Microscope className="h-4 w-4" />}
+      </div>
+
+      <div className={cn("min-w-0 max-w-[85%] space-y-2", isUser && "flex flex-col items-end")}>
+        <div
+          className={cn(
+            "rounded-2xl px-4 py-2.5 text-sm",
+            isUser
+              ? "bg-primary text-primary-foreground"
+              : "border border-border bg-card text-card-foreground",
+          )}
+        >
+          {isUser ? (
+            <span className="whitespace-pre-wrap">{message.content}</span>
+          ) : (
+            <div className="markdown">
+              <ReactMarkdown
+                components={{
+                  a: ({ href, children: c }) => {
+                    const m = href?.match(/^#cite-(\d+)$/);
+                    if (m) {
+                      const idx = Number(m[1]);
+                      return (
+                        <button
+                          onClick={() => onCitation?.(idx)}
+                          className="mx-0.5 inline-flex h-5 min-w-5 items-center justify-center rounded-md bg-primary/15 px-1 align-middle text-xs font-semibold text-primary hover:bg-primary/25"
+                          title={`Jump to source ${idx}`}
+                        >
+                          {idx}
+                        </button>
+                      );
+                    }
+                    return (
+                      <a href={href} target="_blank" rel="noreferrer" className="text-primary underline">
+                        {c}
+                      </a>
+                    );
+                  },
+                }}
+              >
+                {withCitationLinks(message.content) || "​"}
+              </ReactMarkdown>
+              {message.streaming && (
+                <span className="ml-0.5 inline-block h-4 w-1.5 translate-y-0.5 animate-pulse rounded-sm bg-primary" />
+              )}
+            </div>
+          )}
+        </div>
+        {children}
+      </div>
+    </div>
+  );
+}

frontend/src/components/PdfViewer.tsx

@@ -0,0 +1,131 @@
+import { useEffect, useMemo, useRef, useState } from "react";
+import { Document, Page, pdfjs } from "react-pdf";
+import { ChevronLeft, ChevronRight, ZoomIn, ZoomOut, Loader2 } from "lucide-react";
+import { pdfUrl } from "@/lib/api";
+import { Button } from "@/components/ui/button";
+
+// pdf.js worker (bundled by Vite)
+pdfjs.GlobalWorkerOptions.workerSrc = new URL(
+  "pdfjs-dist/build/pdf.worker.min.mjs",
+  import.meta.url,
+).toString();
+
+export function PdfViewer({
+  filename,
+  page,
+  highlights,
+  onPageChange,
+}: {
+  filename: string | null;
+  page: number;
+  highlights: number[][];
+  onPageChange: (p: number) => void;
+}) {
+  const containerRef = useRef<HTMLDivElement>(null);
+  const [containerWidth, setContainerWidth] = useState(600);
+  const [numPages, setNumPages] = useState(0);
+  const [zoom, setZoom] = useState(1);
+  const [renderScale, setRenderScale] = useState(1); // px per PDF point
+
+  useEffect(() => {
+    if (!containerRef.current) return;
+    const el = containerRef.current;
+    const ro = new ResizeObserver(() => setContainerWidth(el.clientWidth - 32));
+    ro.observe(el);
+    setContainerWidth(el.clientWidth - 32);
+    return () => ro.disconnect();
+  }, []);
+
+  const file = useMemo(() => (filename ? pdfUrl(filename) : null), [filename]);
+  const pageWidth = Math.max(200, containerWidth * zoom);
+
+  if (!file) {
+    return (
+      <div className="flex h-full items-center justify-center rounded-xl border-2 border-dashed border-border text-sm text-muted-foreground">
+        Upload or select a document to preview it here
+      </div>
+    );
+  }
+
+  return (
+    <div className="flex h-full flex-col rounded-xl border border-border bg-muted/30">
+      {/* toolbar */}
+      <div className="flex items-center gap-1 border-b border-border px-3 py-2">
+        <Button
+          variant="ghost"
+          size="icon"
+          disabled={page <= 1}
+          onClick={() => onPageChange(page - 1)}
+        >
+          <ChevronLeft className="h-4 w-4" />
+        </Button>
+        <span className="min-w-[90px] text-center text-xs text-muted-foreground">
+          Page {page} / {numPages || "…"}
+        </span>
+        <Button
+          variant="ghost"
+          size="icon"
+          disabled={numPages > 0 && page >= numPages}
+          onClick={() => onPageChange(page + 1)}
+        >
+          <ChevronRight className="h-4 w-4" />
+        </Button>
+        <div className="ml-auto flex items-center gap-1">
+          <Button variant="ghost" size="icon" onClick={() => setZoom((z) => Math.max(0.6, z - 0.15))}>
+            <ZoomOut className="h-4 w-4" />
+          </Button>
+          <span className="w-10 text-center text-xs text-muted-foreground">{Math.round(zoom * 100)}%</span>
+          <Button variant="ghost" size="icon" onClick={() => setZoom((z) => Math.min(2.5, z + 0.15))}>
+            <ZoomIn className="h-4 w-4" />
+          </Button>
+        </div>
+      </div>
+
+      {/* page */}
+      <div ref={containerRef} className="flex-1 overflow-auto p-4">
+        <Document
+          file={file}
+          onLoadSuccess={(pdf) => setNumPages(pdf.numPages)}
+          loading={
+            <div className="flex h-40 items-center justify-center text-muted-foreground">
+              <Loader2 className="mr-2 h-4 w-4 animate-spin" /> Loading document…
+            </div>
+          }
+          error={
+            <div className="flex h-40 items-center justify-center text-sm text-red-500">
+              Failed to load PDF.
+            </div>
+          }
+          className="flex justify-center"
+        >
+          <div className="relative shadow-lg" style={{ width: pageWidth }}>
+            <Page
+              pageNumber={page}
+              width={pageWidth}
+              renderTextLayer={false}
+              renderAnnotationLayer={false}
+              onLoadSuccess={(p) => setRenderScale(pageWidth / p.originalWidth)}
+            />
+            {/* highlight overlay (PDF points → pixels via renderScale) */}
+            <div className="pointer-events-none absolute inset-0">
+              {highlights.map((b, i) => (
+                <div
+                  key={i}
+                  className="absolute rounded-sm animate-pulse-ring"
+                  style={{
+                    left: b[0] * renderScale,
+                    top: b[1] * renderScale,
+                    width: (b[2] - b[0]) * renderScale,
+                    height: (b[3] - b[1]) * renderScale,
+                    background: "hsl(var(--highlight) / 0.38)",
+                    outline: "1px solid hsl(var(--highlight) / 0.8)",
+                  }}
+                />
+              ))}
+            </div>
+          </div>
+        </Document>
+      </div>
+    </div>
+  );
+}

frontend/src/components/ReportPicker.tsx

@@ -0,0 +1,83 @@
+import { Check, ChevronDown, X } from "lucide-react";
+import { useState } from "react";
+import { cn } from "@/lib/utils";
+
+export function ReportPicker({
+  reports,
+  selected,
+  onChange,
+}: {
+  reports: string[];
+  selected: string[];
+  onChange: (next: string[]) => void;
+}) {
+  const [open, setOpen] = useState(false);
+
+  const toggle = (r: string) =>
+    onChange(selected.includes(r) ? selected.filter((x) => x !== r) : [...selected, r]);
+
+  return (
+    <div className="relative">
+      <button
+        onClick={() => setOpen((o) => !o)}
+        className="flex w-full items-center gap-2 rounded-lg border border-border bg-card px-3 py-2 text-sm"
+      >
+        <span className="text-muted-foreground">Scope:</span>
+        <span className="flex-1 truncate text-left">
+          {selected.length === 0 ? "All documents" : `${selected.length} selected`}
+        </span>
+        <ChevronDown className="h-4 w-4 text-muted-foreground" />
+      </button>
+
+      {selected.length > 0 && (
+        <div className="mt-2 flex flex-wrap gap-1.5">
+          {selected.map((r) => (
+            <span
+              key={r}
+              className="inline-flex items-center gap-1 rounded-full bg-primary/12 px-2 py-0.5 text-xs text-primary"
+            >
+              {r}
+              <button onClick={() => toggle(r)}>
+                <X className="h-3 w-3" />
+              </button>
+            </span>
+          ))}
+        </div>
+      )}
+
+      {open && (
+        <>
+          <div className="fixed inset-0 z-10" onClick={() => setOpen(false)} />
+          <div className="absolute z-20 mt-1 max-h-72 w-full overflow-auto rounded-lg border border-border bg-card p-1 shadow-lg">
+            {reports.length === 0 && (
+              <div className="px-3 py-2 text-xs text-muted-foreground">No documents indexed.</div>
+            )}
+            {reports.map((r) => {
+              const on = selected.includes(r);
+              return (
+                <button
+                  key={r}
+                  onClick={() => toggle(r)}
+                  className={cn(
+                    "flex w-full items-center gap-2 rounded-md px-2.5 py-1.5 text-left text-sm hover:bg-muted",
+                    on && "text-primary",
+                  )}
+                >
+                  <span
+                    className={cn(
+                      "flex h-4 w-4 items-center justify-center rounded border",
+                      on ? "border-primary bg-primary text-primary-foreground" : "border-border",
+                    )}
+                  >
+                    {on && <Check className="h-3 w-3" />}
+                  </span>
+                  <span className="truncate">{r}</span>
+                </button>
+              );
+            })}
+          </div>
+        </>
+      )}
+    </div>
+  );
+}

frontend/src/components/Sidebar.tsx

@@ -0,0 +1,64 @@
+import { FileText, Globe, Microscope } from "lucide-react";
+import { useQuery } from "@tanstack/react-query";
+import { getReports } from "@/lib/api";
+import { cn } from "@/lib/utils";
+import { ThemeToggle } from "./ThemeToggle";
+
+export type View = "document" | "global";
+
+const NAV: { id: View; label: string; icon: typeof FileText; desc: string }[] = [
+  { id: "document", label: "Document Chat", icon: FileText, desc: "Chat with one report" },
+  { id: "global", label: "Global Search", icon: Globe, desc: "Search across reports" },
+];
+
+export function Sidebar({ view, onView }: { view: View; onView: (v: View) => void }) {
+  const { data: reports } = useQuery({ queryKey: ["reports"], queryFn: getReports });
+
+  return (
+    <aside className="flex w-64 shrink-0 flex-col border-r border-border bg-card/50 backdrop-blur">
+      <div className="flex items-center gap-2.5 px-5 py-5">
+        <div className="flex h-9 w-9 items-center justify-center rounded-lg bg-primary text-primary-foreground">
+          <Microscope className="h-5 w-5" />
+        </div>
+        <div>
+          <div className="text-sm font-semibold leading-tight">Pathology RAG</div>
+          <div className="text-xs text-muted-foreground">Clinical document AI</div>
+        </div>
+      </div>
+
+      <nav className="flex flex-col gap-1 px-3">
+        {NAV.map((item) => {
+          const Icon = item.icon;
+          const active = view === item.id;
+          return (
+            <button
+              key={item.id}
+              onClick={() => onView(item.id)}
+              className={cn(
+                "group flex items-start gap-3 rounded-lg px-3 py-2.5 text-left transition-colors",
+                active ? "bg-primary/10 text-primary" : "hover:bg-muted text-foreground",
+              )}
+            >
+              <Icon className={cn("mt-0.5 h-4 w-4", active ? "text-primary" : "text-muted-foreground")} />
+              <span>
+                <span className="block text-sm font-medium">{item.label}</span>
+                <span className="block text-xs text-muted-foreground">{item.desc}</span>
+              </span>
+            </button>
+          );
+        })}
+      </nav>
+
+      <div className="mt-auto space-y-3 px-5 py-5">
+        <div className="rounded-lg border border-border bg-background/60 px-3 py-2.5">
+          <div className="text-xs text-muted-foreground">Documents indexed</div>
+          <div className="text-lg font-semibold">{reports?.length ?? "—"}</div>
+        </div>
+        <div className="flex items-center justify-between">
+          <span className="text-xs text-muted-foreground">Appearance</span>
+          <ThemeToggle />
+        </div>
+      </div>
+    </aside>
+  );
+}

frontend/src/components/SourceCard.tsx

@@ -0,0 +1,38 @@
+import { FileText } from "lucide-react";
+import { cn } from "@/lib/utils";
+import type { Source } from "@/lib/api";
+
+export function SourceCard({
+  source,
+  onClick,
+  active,
+}: {
+  source: Source;
+  onClick?: () => void;
+  active?: boolean;
+}) {
+  return (
+    <button
+      onClick={onClick}
+      className={cn(
+        "w-full rounded-lg border bg-card px-3 py-2.5 text-left transition-colors",
+        active ? "border-primary ring-1 ring-primary" : "border-border hover:border-primary/60",
+      )}
+    >
+      <div className="mb-1 flex items-center gap-2 text-xs">
+        <span className="flex h-5 w-5 items-center justify-center rounded bg-primary/15 font-semibold text-primary">
+          {source.index}
+        </span>
+        <FileText className="h-3.5 w-3.5 text-muted-foreground" />
+        <span className="truncate font-medium">{source.filename}</span>
+        {source.page != null && (
+          <span className="rounded-full bg-muted px-2 py-0.5 text-[11px] text-muted-foreground">
+            page {source.page}
+          </span>
+        )}
+        <span className="ml-auto text-[11px] text-muted-foreground">{source.score.toFixed(3)}</span>
+      </div>
+      <p className="line-clamp-2 text-xs text-muted-foreground">{source.text}</p>
+    </button>
+  );
+}

frontend/src/components/ThemeToggle.tsx

@@ -0,0 +1,12 @@
+import { Moon, Sun } from "lucide-react";
+import { useTheme } from "@/lib/theme";
+import { Button } from "@/components/ui/button";
+
+export function ThemeToggle() {
+  const { theme, toggle } = useTheme();
+  return (
+    <Button variant="ghost" size="icon" onClick={toggle} title="Toggle theme" aria-label="Toggle theme">
+      {theme === "dark" ? <Sun className="h-4 w-4" /> : <Moon className="h-4 w-4" />}
+    </Button>
+  );
+}

frontend/src/components/UploadPanel.tsx

@@ -0,0 +1,119 @@
+import { useCallback, useRef, useState } from "react";
+import { UploadCloud, Loader2, CheckCircle2 } from "lucide-react";
+import { uploadAndTrack, type UploadProgress } from "@/lib/api";
+import { cn } from "@/lib/utils";
+
+const STAGE_LABEL: Record<string, string> = {
+  ocr: "Reading pages (OCR)",
+  embedding: "Generating embeddings",
+  indexing: "Updating index",
+  done: "Finishing up",
+};
+
+export function UploadPanel({ onIndexed }: { onIndexed: (filename: string) => void }) {
+  const inputRef = useRef<HTMLInputElement>(null);
+  const [drag, setDrag] = useState(false);
+  const [busy, setBusy] = useState(false);
+  const [progress, setProgress] = useState<UploadProgress | null>(null);
+  const [doneName, setDoneName] = useState<string | null>(null);
+  const [error, setError] = useState<string | null>(null);
+
+  const handle = useCallback(
+    (file: File) => {
+      if (!file.name.toLowerCase().endsWith(".pdf")) {
+        setError("Please choose a PDF file.");
+        return;
+      }
+      setBusy(true);
+      setError(null);
+      setDoneName(null);
+      setProgress({ stage: "ocr" });
+      const stem = file.name.replace(/\.pdf$/i, "");
+      uploadAndTrack(
+        file,
+        (p) => setProgress(p),
+        () => {
+          setBusy(false);
+          setProgress(null);
+          setDoneName(stem);
+          onIndexed(stem);
+        },
+        (msg) => {
+          setBusy(false);
+          setProgress(null);
+          setError(msg);
+        },
+      );
+    },
+    [onIndexed],
+  );
+
+  return (
+    <div>
+      <div
+        onDragOver={(e) => {
+          e.preventDefault();
+          setDrag(true);
+        }}
+        onDragLeave={() => setDrag(false)}
+        onDrop={(e) => {
+          e.preventDefault();
+          setDrag(false);
+          if (e.dataTransfer.files[0]) handle(e.dataTransfer.files[0]);
+        }}
+        onClick={() => !busy && inputRef.current?.click()}
+        className={cn(
+          "flex cursor-pointer flex-col items-center gap-2 rounded-xl border-2 border-dashed px-4 py-6 text-center transition-colors",
+          drag ? "border-primary bg-primary/5" : "border-border hover:border-primary/50",
+          busy && "cursor-default opacity-80",
+        )}
+      >
+        {busy ? (
+          <>
+            <Loader2 className="h-6 w-6 animate-spin text-primary" />
+            <div className="text-sm font-medium">
+              {progress ? STAGE_LABEL[progress.stage] ?? "Processing" : "Processing"}
+              {progress?.page && progress?.total ? ` · page ${progress.page}/${progress.total}` : ""}
+            </div>
+            <ProgressBar progress={progress} />
+          </>
+        ) : doneName ? (
+          <>
+            <CheckCircle2 className="h-6 w-6 text-emerald-500" />
+            <div className="text-sm font-medium">Indexed “{doneName}”</div>
+            <div className="text-xs text-muted-foreground">Click to upload another</div>
+          </>
+        ) : (
+          <>
+            <UploadCloud className="h-6 w-6 text-muted-foreground" />
+            <div className="text-sm font-medium">Drop a pathology PDF or click to browse</div>
+            <div className="text-xs text-muted-foreground">OCR + embedding runs automatically</div>
+          </>
+        )}
+        <input
+          ref={inputRef}
+          type="file"
+          accept="application/pdf"
+          className="hidden"
+          onChange={(e) => e.target.files?.[0] && handle(e.target.files[0])}
+        />
+      </div>
+      {error && <p className="mt-2 text-xs text-red-500">{error}</p>}
+    </div>
+  );
+}
+
+function ProgressBar({ progress }: { progress: UploadProgress | null }) {
+  // Coarse stage-based fill; OCR uses page fraction when available.
+  let pct = 10;
+  if (progress?.stage === "ocr") {
+    pct = progress.page && progress.total ? 10 + (progress.page / progress.total) * 50 : 30;
+  } else if (progress?.stage === "embedding") pct = 70;
+  else if (progress?.stage === "indexing") pct = 88;
+  else if (progress?.stage === "done") pct = 96;
+  return (
+    <div className="mt-1 h-1.5 w-full overflow-hidden rounded-full bg-muted">
+      <div className="h-full rounded-full bg-primary transition-all duration-500" style={{ width: `${pct}%` }} />
+    </div>
+  );
+}

frontend/src/components/ui/button.tsx

@@ -0,0 +1,34 @@
+import { forwardRef } from "react";
+import { cva, type VariantProps } from "class-variance-authority";
+import { cn } from "@/lib/utils";
+
+const buttonVariants = cva(
+  "inline-flex items-center justify-center gap-2 whitespace-nowrap rounded-md text-sm font-medium transition-colors focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-ring disabled:pointer-events-none disabled:opacity-50",
+  {
+    variants: {
+      variant: {
+        default: "bg-primary text-primary-foreground hover:opacity-90 shadow-sm",
+        outline: "border border-border bg-transparent hover:bg-muted",
+        ghost: "hover:bg-muted",
+        subtle: "bg-muted text-foreground hover:bg-accent",
+      },
+      size: {
+        default: "h-10 px-4 py-2",
+        sm: "h-8 px-3 text-xs",
+        icon: "h-9 w-9",
+      },
+    },
+    defaultVariants: { variant: "default", size: "default" },
+  },
+);
+
+export interface ButtonProps
+  extends React.ButtonHTMLAttributes<HTMLButtonElement>,
+    VariantProps<typeof buttonVariants> {}
+
+export const Button = forwardRef<HTMLButtonElement, ButtonProps>(
+  ({ className, variant, size, ...props }, ref) => (
+    <button ref={ref} className={cn(buttonVariants({ variant, size, className }))} {...props} />
+  ),
+);
+Button.displayName = "Button";

frontend/src/index.css

@@ -0,0 +1,94 @@
+@tailwind base;
+@tailwind components;
+@tailwind utilities;
+
+@layer base {
+  :root {
+    --background: 210 40% 98%;
+    --foreground: 222 47% 11%;
+    --card: 0 0% 100%;
+    --card-foreground: 222 47% 11%;
+    --muted: 210 40% 94%;
+    --muted-foreground: 215 16% 47%;
+    --primary: 221 83% 53%;
+    --primary-foreground: 0 0% 100%;
+    --accent: 210 40% 92%;
+    --accent-foreground: 222 47% 11%;
+    --border: 214 32% 88%;
+    --input: 214 32% 88%;
+    --ring: 221 83% 53%;
+    --radius: 0.75rem;
+    --highlight: 45 93% 58%;
+  }
+
+  .dark {
+    --background: 222 47% 7%;
+    --foreground: 210 40% 96%;
+    --card: 222 40% 10%;
+    --card-foreground: 210 40% 96%;
+    --muted: 217 33% 16%;
+    --muted-foreground: 215 20% 65%;
+    --primary: 217 91% 60%;
+    --primary-foreground: 222 47% 11%;
+    --accent: 217 33% 18%;
+    --accent-foreground: 210 40% 96%;
+    --border: 217 33% 20%;
+    --input: 217 33% 20%;
+    --ring: 217 91% 60%;
+    --highlight: 45 93% 58%;
+  }
+
+  * {
+    border-color: hsl(var(--border));
+  }
+  html,
+  body,
+  #root {
+    height: 100%;
+  }
+  body {
+    background-color: hsl(var(--background));
+    color: hsl(var(--foreground));
+    font-family: Inter, system-ui, sans-serif;
+    -webkit-font-smoothing: antialiased;
+  }
+}
+
+/* Slim, theme-aware scrollbars */
+::-webkit-scrollbar {
+  width: 10px;
+  height: 10px;
+}
+::-webkit-scrollbar-thumb {
+  background: hsl(var(--border));
+  border-radius: 999px;
+}
+::-webkit-scrollbar-track {
+  background: transparent;
+}
+
+/* Markdown answer typography */
+.markdown p {
+  margin: 0 0 0.7rem;
+  line-height: 1.7;
+}
+.markdown p:last-child {
+  margin-bottom: 0;
+}
+.markdown ul,
+.markdown ol {
+  margin: 0 0 0.7rem 1.2rem;
+  list-style: revert;
+}
+.markdown li {
+  margin: 0.2rem 0;
+}
+.markdown strong {
+  font-weight: 600;
+}
+.markdown code {
+  background: hsl(var(--muted));
+  padding: 0.1rem 0.35rem;
+  border-radius: 6px;
+  font-size: 0.85em;
+}

frontend/src/lib/api.ts

@@ -0,0 +1,126 @@
+import { parseSSE } from "./sse";
+
+export interface Source {
+  index: number;
+  filename: string;
+  page: number | null;
+  line_bboxes: number[][];
+  text: string;
+  score: number;
+}
+
+export interface ChatTurn {
+  role: "user" | "assistant";
+  content: string;
+}
+
+export interface ChatRequest {
+  question: string;
+  report_name?: string | null;
+  report_names?: string[] | null;
+  top_k?: number;
+  history?: ChatTurn[];
+}
+
+export interface ChatCallbacks {
+  onSources?: (sources: Source[]) => void;
+  onToken?: (text: string) => void;
+  onDone?: (numSources: number) => void;
+  onError?: (message: string) => void;
+}
+
+export async function getReports(): Promise<string[]> {
+  const r = await fetch("/api/reports");
+  if (!r.ok) throw new Error("Failed to load reports");
+  return (await r.json()).reports as string[];
+}
+
+export interface Health {
+  status: "ok" | "degraded";
+  num_documents: number;
+  detail?: string | null;
+}
+
+export async function getHealth(): Promise<Health> {
+  const r = await fetch("/api/health");
+  return r.json();
+}
+
+/** Stream a chat answer. Resolves when the stream ends. */
+export async function streamChat(
+  req: ChatRequest,
+  cb: ChatCallbacks,
+  signal?: AbortSignal,
+): Promise<void> {
+  const resp = await fetch("/api/chat", {
+    method: "POST",
+    headers: { "Content-Type": "application/json" },
+    body: JSON.stringify(req),
+    signal,
+  });
+
+  if (!resp.ok) {
+    const detail = await resp.text().catch(() => "");
+    cb.onError?.(`Request failed (${resp.status}). ${detail}`);
+    return;
+  }
+
+  for await (const evt of parseSSE(resp)) {
+    const data = safeParse(evt.data);
+    if (evt.event === "sources") cb.onSources?.(data.sources ?? []);
+    else if (evt.event === "token") cb.onToken?.(data.text ?? "");
+    else if (evt.event === "done") cb.onDone?.(data.num_sources ?? 0);
+    else if (evt.event === "error") cb.onError?.(data.message ?? "Unknown error");
+  }
+}
+
+export interface UploadProgress {
+  stage: string; // ocr | embedding | indexing | done | complete
+  page?: number;
+  total?: number;
+  num_chunks?: number;
+  vectors_added?: number;
+}
+
+/** Upload a PDF, then stream OCR/embedding/indexing progress until complete. */
+export async function uploadAndTrack(
+  file: File,
+  onProgress: (p: UploadProgress) => void,
+  onComplete: (stats: Record<string, unknown>) => void,
+  onError: (message: string) => void,
+): Promise<void> {
+  const form = new FormData();
+  form.append("file", file);
+
+  const start = await fetch("/api/upload", { method: "POST", body: form });
+  if (!start.ok) {
+    onError(`Upload failed (${start.status}).`);
+    return;
+  }
+  const { job_id } = await start.json();
+
+  const events = await fetch(`/api/upload/${job_id}/events`);
+  if (!events.ok) {
+    onError("Failed to open progress stream.");
+    return;
+  }
+
+  for await (const evt of parseSSE(events)) {
+    const data = safeParse(evt.data);
+    if (evt.event === "progress") onProgress(data as UploadProgress);
+    else if (evt.event === "complete") onComplete(data);
+    else if (evt.event === "error") onError(data.message ?? "Processing failed");
+  }
+}
+
+export function pdfUrl(filename: string): string {
+  return `/api/pdf/${encodeURIComponent(filename)}`;
+}
+
+function safeParse(s: string): any {
+  try {
+    return JSON.parse(s);
+  } catch {
+    return {};
+  }
+}

frontend/src/lib/sse.ts

@@ -0,0 +1,39 @@
+export interface SSEvent {
+  event: string;
+  data: string;
+}
+
+/**
+ * Parse a Server-Sent Events stream from a fetch Response body into an async
+ * iterator of {event, data}. Used for POST-based SSE where EventSource (GET
+ * only) can't be used.
+ */
+export async function* parseSSE(response: Response): AsyncGenerator<SSEvent> {
+  if (!response.body) throw new Error("Response has no body");
+  const reader = response.body.getReader();
+  const decoder = new TextDecoder();
+  let buffer = "";
+
+  while (true) {
+    const { done, value } = await reader.read();
+    if (done) break;
+    // Normalize CRLF (sse-starlette uses "\r\n" line endings) so a single
+    // "\n\n" boundary check works regardless of the server's separator.
+    buffer += decoder.decode(value, { stream: true }).replace(/\r\n/g, "\n");
+
+    let sep: number;
+    // Events are separated by a blank line.
+    while ((sep = buffer.indexOf("\n\n")) !== -1) {
+      const raw = buffer.slice(0, sep);
+      buffer = buffer.slice(sep + 2);
+
+      let event = "message";
+      const dataLines: string[] = [];
+      for (const line of raw.split("\n")) {
+        if (line.startsWith("event:")) event = line.slice(6).trim();
+        else if (line.startsWith("data:")) dataLines.push(line.slice(5).replace(/^ /, ""));
+      }
+      if (dataLines.length) yield { event, data: dataLines.join("\n") };
+    }
+  }
+}

frontend/src/lib/theme.tsx

@@ -0,0 +1,36 @@
+import { createContext, useContext, useEffect, useState, type ReactNode } from "react";
+
+type Theme = "light" | "dark";
+
+interface ThemeCtx {
+  theme: Theme;
+  toggle: () => void;
+}
+
+const Ctx = createContext<ThemeCtx | null>(null);
+
+function initialTheme(): Theme {
+  const stored = localStorage.getItem("theme");
+  if (stored === "light" || stored === "dark") return stored;
+  return window.matchMedia("(prefers-color-scheme: dark)").matches ? "dark" : "light";
+}
+
+export function ThemeProvider({ children }: { children: ReactNode }) {
+  const [theme, setTheme] = useState<Theme>(initialTheme);
+
+  useEffect(() => {
+    const root = document.documentElement;
+    root.classList.toggle("dark", theme === "dark");
+    localStorage.setItem("theme", theme);
+  }, [theme]);
+
+  const toggle = () => setTheme((t) => (t === "dark" ? "light" : "dark"));
+
+  return <Ctx.Provider value={{ theme, toggle }}>{children}</Ctx.Provider>;
+}
+
+export function useTheme() {
+  const ctx = useContext(Ctx);
+  if (!ctx) throw new Error("useTheme must be used within ThemeProvider");
+  return ctx;
+}

frontend/src/lib/useChat.ts

@@ -0,0 +1,82 @@
+import { useCallback, useRef, useState } from "react";
+import { streamChat, type Source, type ChatTurn } from "./api";
+import type { Message } from "@/components/MessageBubble";
+
+let idCounter = 0;
+const nextId = () => `m${++idCounter}`;
+
+export interface SendScope {
+  report_name?: string | null;
+  report_names?: string[] | null;
+  top_k?: number;
+}
+
+export function useChat(onSources?: (sources: Source[], forMessageId: string) => void) {
+  const [messages, setMessages] = useState<Message[]>([]);
+  const [busy, setBusy] = useState(false);
+  const abortRef = useRef<AbortController | null>(null);
+
+  const patch = (id: string, fn: (m: Message) => Message) =>
+    setMessages((prev) => prev.map((m) => (m.id === id ? fn(m) : m)));
+
+  const send = useCallback(
+    (text: string, scope: SendScope) => {
+      if (busy) return;
+      const history: ChatTurn[] = messages.map((m) => ({ role: m.role, content: m.content }));
+
+      const userMsg: Message = { id: nextId(), role: "user", content: text };
+      const botId = nextId();
+      const botMsg: Message = { id: botId, role: "assistant", content: "", streaming: true };
+      setMessages((prev) => [...prev, userMsg, botMsg]);
+      setBusy(true);
+
+      const ctrl = new AbortController();
+      abortRef.current = ctrl;
+
+      streamChat(
+        {
+          question: text,
+          report_name: scope.report_name ?? null,
+          report_names: scope.report_names ?? null,
+          top_k: scope.top_k ?? 5,
+          history,
+        },
+        {
+          onSources: (sources) => {
+            patch(botId, (m) => ({ ...m, sources }));
+            onSources?.(sources, botId);
+          },
+          onToken: (t) => patch(botId, (m) => ({ ...m, content: m.content + t })),
+          onDone: () => {
+            patch(botId, (m) => ({ ...m, streaming: false }));
+            setBusy(false);
+          },
+          onError: (msg) => {
+            patch(botId, (m) => ({
+              ...m,
+              streaming: false,
+              content: m.content || `⚠️ ${msg}`,
+            }));
+            setBusy(false);
+          },
+        },
+        ctrl.signal,
+      );
+    },
+    [busy, messages, onSources],
+  );
+
+  const stop = useCallback(() => {
+    abortRef.current?.abort();
+    setBusy(false);
+    setMessages((prev) => prev.map((m) => (m.streaming ? { ...m, streaming: false } : m)));
+  }, []);
+
+  const reset = useCallback(() => {
+    abortRef.current?.abort();
+    setMessages([]);
+    setBusy(false);
+  }, []);
+
+  return { messages, busy, send, stop, reset };
+}

frontend/src/lib/utils.ts

@@ -0,0 +1,6 @@
+import { clsx, type ClassValue } from "clsx";
+import { twMerge } from "tailwind-merge";
+
+export function cn(...inputs: ClassValue[]) {
+  return twMerge(clsx(inputs));
+}

frontend/src/main.tsx

@@ -0,0 +1,20 @@
+import React from "react";
+import ReactDOM from "react-dom/client";
+import { QueryClient, QueryClientProvider } from "@tanstack/react-query";
+import { ThemeProvider } from "./lib/theme";
+import App from "./App";
+import "./index.css";
+
+const queryClient = new QueryClient({
+  defaultOptions: { queries: { refetchOnWindowFocus: false } },
+});
+
+ReactDOM.createRoot(document.getElementById("root")!).render(
+  <React.StrictMode>
+    <QueryClientProvider client={queryClient}>
+      <ThemeProvider>
+        <App />
+      </ThemeProvider>
+    </QueryClientProvider>
+  </React.StrictMode>,
+);

frontend/src/views/DocumentChat.tsx

@@ -0,0 +1,117 @@
+import { useCallback, useEffect, useState } from "react";
+import { useQuery, useQueryClient } from "@tanstack/react-query";
+import { getReports, type Source } from "@/lib/api";
+import { useChat } from "@/lib/useChat";
+import { PdfViewer } from "@/components/PdfViewer";
+import { UploadPanel } from "@/components/UploadPanel";
+import { ChatThread } from "@/components/ChatThread";
+import { ChatInput } from "@/components/ChatInput";
+import { ExamplePrompts } from "@/components/ExamplePrompts";
+import type { Message } from "@/components/MessageBubble";
+
+const EXAMPLES = [
+  "What are the key abnormal findings?",
+  "What is the tumor grade and stage?",
+  "Summarize the ER / PR / HER2 receptor status.",
+];
+
+export function DocumentChat() {
+  const qc = useQueryClient();
+  const { data: reports } = useQuery({ queryKey: ["reports"], queryFn: getReports });
+  const [activeDoc, setActiveDoc] = useState<string | null>(null);
+  const [page, setPage] = useState(1);
+  const [highlights, setHighlights] = useState<number[][]>([]);
+
+  // Focus the viewer on the top source's page and highlight its lines.
+  const focusSources = useCallback((sources: Source[]) => {
+    const top = sources.find((s) => s.page != null);
+    if (!top || top.page == null) {
+      setHighlights([]);
+      return;
+    }
+    const boxes = sources
+      .filter((s) => s.page === top.page)
+      .flatMap((s) => s.line_bboxes);
+    setPage(top.page);
+    setHighlights(boxes);
+  }, []);
+
+  const { messages, busy, send, stop, reset } = useChat((sources) => focusSources(sources));
+
+  // When the active document changes, start a fresh conversation.
+  useEffect(() => {
+    reset();
+    setPage(1);
+    setHighlights([]);
+  }, [activeDoc, reset]);
+
+  const onCitation = (message: Message, index: number) => {
+    const src = message.sources?.find((s) => s.index === index);
+    if (src?.page != null) {
+      setPage(src.page);
+      setHighlights(src.line_bboxes);
+    }
+  };
+
+  const submit = (text: string) => {
+    if (!activeDoc) return;
+    send(text, { report_name: activeDoc });
+  };
+
+  return (
+    <div className="flex h-full gap-4 p-4">
+      {/* LEFT — document */}
+      <div className="flex w-[54%] flex-col gap-3">
+        <div className="flex items-center gap-2">
+          <select
+            value={activeDoc ?? ""}
+            onChange={(e) => setActiveDoc(e.target.value || null)}
+            className="flex-1 rounded-lg border border-border bg-card px-3 py-2 text-sm outline-none"
+          >
+            <option value="">Select a document…</option>
+            {reports?.map((r) => (
+              <option key={r} value={r}>
+                {r}
+              </option>
+            ))}
+          </select>
+        </div>
+        <div className="min-h-0 flex-1">
+          <PdfViewer filename={activeDoc} page={page} highlights={highlights} onPageChange={setPage} />
+        </div>
+        <UploadPanel
+          onIndexed={(name) => {
+            qc.invalidateQueries({ queryKey: ["reports"] });
+            setActiveDoc(name);
+          }}
+        />
+      </div>
+
+      {/* RIGHT — chat */}
+      <div className="flex min-w-0 flex-1 flex-col">
+        <ChatThread
+          messages={messages}
+          onCitation={onCitation}
+          empty={
+            activeDoc ? (
+              <ExamplePrompts title={`Ask about ${activeDoc}`} prompts={EXAMPLES} onPick={submit} />
+            ) : (
+              <div className="max-w-sm text-center text-sm text-muted-foreground">
+                Upload a pathology PDF or select an indexed document to start chatting with it.
+              </div>
+            )
+          }
+        />
+        <div className="pt-2">
+          <ChatInput
+            onSend={submit}
+            onStop={stop}
+            busy={busy}
+            disabled={!activeDoc}
+            placeholder={activeDoc ? "Ask about this document…" : "Select a document first"}
+          />
+        </div>
+      </div>
+    </div>
+  );
+}

frontend/src/views/GlobalSearch.tsx

@@ -0,0 +1,86 @@
+import { useState } from "react";
+import { useQuery } from "@tanstack/react-query";
+import { X } from "lucide-react";
+import { getReports, type Source } from "@/lib/api";
+import { useChat } from "@/lib/useChat";
+import { ChatThread } from "@/components/ChatThread";
+import { ChatInput } from "@/components/ChatInput";
+import { ReportPicker } from "@/components/ReportPicker";
+import { SourceCard } from "@/components/SourceCard";
+import { PdfViewer } from "@/components/PdfViewer";
+import { ExamplePrompts } from "@/components/ExamplePrompts";
+
+const EXAMPLES = [
+  "What ER/PR/HER2 receptor patterns appear across reports?",
+  "Which reports mention lymph node involvement?",
+  "Summarize the most common diagnoses.",
+];
+
+interface Preview {
+  filename: string;
+  page: number;
+  highlights: number[][];
+}
+
+export function GlobalSearch() {
+  const { data: reports } = useQuery({ queryKey: ["reports"], queryFn: getReports });
+  const [selected, setSelected] = useState<string[]>([]);
+  const [preview, setPreview] = useState<Preview | null>(null);
+  const { messages, busy, send, stop } = useChat();
+
+  const submit = (text: string) =>
+    send(text, { report_names: selected.length ? selected : null });
+
+  const openSource = (s: Source) =>
+    setPreview({ filename: s.filename, page: s.page ?? 1, highlights: s.line_bboxes });
+
+  return (
+    <div className="mx-auto flex h-full w-full max-w-3xl flex-col p-4">
+      <div className="pb-3">
+        <ReportPicker reports={reports ?? []} selected={selected} onChange={setSelected} />
+      </div>
+
+      <ChatThread
+        messages={messages}
+        empty={<ExamplePrompts title="Search across all reports" prompts={EXAMPLES} onPick={submit} />}
+        renderExtra={(m) =>
+          m.role === "assistant" && m.sources && m.sources.length > 0 ? (
+            <div className="grid gap-2 sm:grid-cols-2">
+              {m.sources.map((s) => (
+                <SourceCard key={s.index} source={s} onClick={() => openSource(s)} />
+              ))}
+            </div>
+          ) : null
+        }
+      />
+
+      <div className="pt-2">
+        <ChatInput onSend={submit} onStop={stop} busy={busy} placeholder="Ask across your reports…" />
+      </div>
+
+      {preview && (
+        <div className="fixed inset-0 z-50 flex items-center justify-center bg-black/50 p-6" onClick={() => setPreview(null)}>
+          <div
+            className="flex h-[85vh] w-full max-w-3xl flex-col overflow-hidden rounded-xl border border-border bg-background"
+            onClick={(e) => e.stopPropagation()}
+          >
+            <div className="flex items-center justify-between border-b border-border px-4 py-2.5">
+              <span className="truncate text-sm font-medium">{preview.filename}</span>
+              <button onClick={() => setPreview(null)} className="rounded-md p-1 hover:bg-muted">
+                <X className="h-4 w-4" />
+              </button>
+            </div>
+            <div className="min-h-0 flex-1 p-3">
+              <PdfViewer
+                filename={preview.filename}
+                page={preview.page}
+                highlights={preview.highlights}
+                onPageChange={(p) => setPreview((prev) => (prev ? { ...prev, page: p, highlights: [] } : prev))}
+              />
+            </div>
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}

frontend/src/vite-env.d.ts

@@ -0,0 +1 @@
+/// <reference types="vite/client" />

frontend/tailwind.config.js

@@ -0,0 +1,55 @@
+/** @type {import('tailwindcss').Config} */
+export default {
+  darkMode: "class",
+  content: ["./index.html", "./src/**/*.{ts,tsx}"],
+  theme: {
+    extend: {
+      colors: {
+        border: "hsl(var(--border))",
+        input: "hsl(var(--input))",
+        ring: "hsl(var(--ring))",
+        background: "hsl(var(--background))",
+        foreground: "hsl(var(--foreground))",
+        muted: {
+          DEFAULT: "hsl(var(--muted))",
+          foreground: "hsl(var(--muted-foreground))",
+        },
+        card: {
+          DEFAULT: "hsl(var(--card))",
+          foreground: "hsl(var(--card-foreground))",
+        },
+        primary: {
+          DEFAULT: "hsl(var(--primary))",
+          foreground: "hsl(var(--primary-foreground))",
+        },
+        accent: {
+          DEFAULT: "hsl(var(--accent))",
+          foreground: "hsl(var(--accent-foreground))",
+        },
+      },
+      borderRadius: {
+        lg: "var(--radius)",
+        md: "calc(var(--radius) - 2px)",
+        sm: "calc(var(--radius) - 4px)",
+      },
+      fontFamily: {
+        sans: ["Inter", "system-ui", "sans-serif"],
+      },
+      keyframes: {
+        "fade-in": {
+          from: { opacity: "0", transform: "translateY(4px)" },
+          to: { opacity: "1", transform: "translateY(0)" },
+        },
+        "pulse-ring": {
+          "0%, 100%": { opacity: "0.55" },
+          "50%": { opacity: "0.9" },
+        },
+      },
+      animation: {
+        "fade-in": "fade-in 0.25s ease-out",
+        "pulse-ring": "pulse-ring 1.2s ease-in-out 2",
+      },
+    },
+  },
+  plugins: [],
+};

frontend/tsconfig.json

@@ -0,0 +1,23 @@
+{
+  "compilerOptions": {
+    "target": "ES2020",
+    "useDefineForClassFields": true,
+    "lib": ["ES2020", "DOM", "DOM.Iterable"],
+    "module": "ESNext",
+    "skipLibCheck": true,
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "resolveJsonModule": true,
+    "isolatedModules": true,
+    "noEmit": true,
+    "jsx": "react-jsx",
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noFallthroughCasesInSwitch": true,
+    "baseUrl": ".",
+    "paths": { "@/*": ["./src/*"] }
+  },
+  "include": ["src"],
+  "references": [{ "path": "./tsconfig.node.json" }]
+}

frontend/tsconfig.node.json

@@ -0,0 +1,11 @@
+{
+  "compilerOptions": {
+    "composite": true,
+    "skipLibCheck": true,
+    "module": "ESNext",
+    "moduleResolution": "bundler",
+    "allowSyntheticDefaultImports": true,
+    "strict": true
+  },
+  "include": ["vite.config.ts"]
+}

frontend/tsconfig.node.tsbuildinfo

@@ -0,0 +1 @@
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frontend/tsconfig.tsbuildinfo

@@ -0,0 +1 @@
+{"root":["./src/app.tsx","./src/main.tsx","./src/vite-env.d.ts","./src/components/chatinput.tsx","./src/components/chatthread.tsx","./src/components/exampleprompts.tsx","./src/components/messagebubble.tsx","./src/components/pdfviewer.tsx","./src/components/reportpicker.tsx","./src/components/sidebar.tsx","./src/components/sourcecard.tsx","./src/components/themetoggle.tsx","./src/components/uploadpanel.tsx","./src/components/ui/button.tsx","./src/lib/api.ts","./src/lib/sse.ts","./src/lib/theme.tsx","./src/lib/usechat.ts","./src/lib/utils.ts","./src/views/documentchat.tsx","./src/views/globalsearch.tsx"],"version":"5.9.3"}

frontend/vite.config.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("vite").UserConfig;
+export default _default;

frontend/vite.config.js

@@ -0,0 +1,20 @@
+import { defineConfig } from "vite";
+import react from "@vitejs/plugin-react";
+import path from "path";
+export default defineConfig({
+    plugins: [react()],
+    resolve: {
+        alias: { "@": path.resolve(__dirname, "./src") },
+    },
+    server: {
+        port: 5173,
+        // Dev-only: proxy API calls to the FastAPI backend so the SPA and API
+        // share an origin during development (mirrors the container in prod).
+        proxy: {
+            "/api": {
+                target: "http://localhost:8000",
+                changeOrigin: true,
+            },
+        },
+    },
+});

frontend/vite.config.ts

@@ -0,0 +1,21 @@
+import { defineConfig } from "vite";
+import react from "@vitejs/plugin-react";
+import path from "path";
+
+export default defineConfig({
+  plugins: [react()],
+  resolve: {
+    alias: { "@": path.resolve(__dirname, "./src") },
+  },
+  server: {
+    port: 5173,
+    // Dev-only: proxy API calls to the FastAPI backend so the SPA and API
+    // share an origin during development (mirrors the container in prod).
+    proxy: {
+      "/api": {
+        target: "http://localhost:8000",
+        changeOrigin: true,
+      },
+    },
+  },
+});

output/biomedbert_vector_db/faiss.index

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:13e528783241822262d42f011636618870f54d84c8cbbaffdf7a21fa92dd0d2f
-size 30584877
+oid sha256:bccf824362c2bc66295313f5c1d327c0409a9b9e86b6767fd9f46de9de9c39df
+size 30591021

output/biomedbert_vector_db/metadata.pkl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:1138cbbb3cd4e2cec0f626bb88d412b95e22a0cc77c4d291cb35f5757a86c925
-size 10202202
+oid sha256:b7cd713d5984a5bbee9eb14706f4e6a6daa7e2e13116c860ef3dbb369fd69275
+size 10205100

requirements.txt

@@ -1,15 +1,24 @@
-streamlit>=1.32.0
-jinja2
-
-numpy>=1.26.4
-
-torch>=2.3.0
-torchvision>=0.18.0
-torchaudio>=2.3.0
-
-transformers>=4.41.0
-sentence-transformers>=3.0.0
-accelerate>=0.30.0
+# ── Web API (React + FastAPI deployment) ──
+fastapi>=0.110.0
+uvicorn[standard]>=0.29.0
+python-multipart>=0.0.9
+sse-starlette>=2.0.0
+
+# numpy 2.3.x: matches the set paddlepaddle 3.x is happy with.
+numpy>=1.26,<2.4
+
+# ── ML / RAG stack ──
+# torch is installed separately in the Dockerfile from the CPU wheel index
+# (https://download.pytorch.org/whl/cpu) so we never pull the ~2GB CUDA build.
+# The transformers stack below is pinned to a known-good, mutually-compatible
+# set (verified importing cleanly locally) so a fresh container build can't
+# resolve an incompatible combination that breaks `PreTrainedModel` at import.
+transformers==4.57.3
+sentence-transformers==5.2.0
+huggingface-hub==0.36.0
+tokenizers==0.22.2
+safetensors==0.7.0
+accelerate==1.13.0
 
 faiss-cpu>=1.8.0
 rank-bm25
@@ -20,11 +29,13 @@ pandas
 scikit-learn
 tqdm
 
+# ── PDF + OCR ──
 pillow
-pdf2image
-pytesseract
 pymupdf
-paddlepaddle
-paddleocr
+# PaddleOCR 3.x — the OCR extraction code targets the 3.x predict() API
+# (rec_texts / dt_polys). Do not drop below 3.0.
+paddlepaddle>=3.0.0,<4.0.0
+paddleocr>=3.0.0,<4.0.0
 
-gradio>=4.0
+# Note: the legacy Streamlit UI (app.py / ui/) is not run in the container and
+# is excluded via .dockerignore; install `streamlit` separately to run it.