feat: add dark/light mode toggle with localStorage persistence

- Enable Tailwind "class" dark mode strategy
- Use CSS custom properties for theme colors (bg, text, border)
- Add ThemeProvider context with toggle and localStorage persistence
- Add Sun/Moon toggle button in the header navigation
- Inline script in index.html prevents FOUC on page load
- All pages (Layout, Login, Register, ProtectedRoute) support both modes
- Default theme follows system preference (prefers-color-scheme)

Closes leeworks-agents/SPARC#33

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

.env.example

@@ -1,21 +1,42 @@
 # SPARC Configuration
 
+# ---- Application Environment ----
+# Set to "production" or "staging" in deployed environments.
+# The API will refuse to start with the default JWT secret unless APP_ENV=development.
+APP_ENV=development
+
+# ---- API Keys ----
+
 # SerpAPI key for patent search
 API_KEY=your_serpapi_key_here
 
 # OpenRouter API key for LLM analysis
 OPENROUTER_API_KEY=your_openrouter_key_here
 
-# Database configuration
-# All messages are stored in the database for persistence and caching
-DATABASE_URL=postgresql://postgres:postgres@localhost:5432/sparc
+# ---- Database ----
 
-# Cache configuration
-# When USE_CACHE=true: check database for cached responses before making API calls
-# When USE_CACHE=false: always make fresh API calls (still stores results in database)
-# Default: true
-USE_CACHE=true
+# PostgreSQL credentials (used by docker-compose)
+POSTGRES_USER=postgres
+POSTGRES_PASSWORD=change-me-to-a-secure-password
+POSTGRES_DB=sparc
 
-# JWT Secret for authentication
+# Full database URL (must match the credentials above)
+DATABASE_URL=postgresql://postgres:change-me-to-a-secure-password@localhost:5432/sparc
+
+# ---- Authentication ----
+
+# JWT Secret for signing tokens
 # IMPORTANT: Change this to a secure random string in production
 JWT_SECRET=your-secure-jwt-secret-change-in-production
+
+# ---- CORS ----
+
+# Comma-separated list of allowed origins for CORS
+# Defaults to http://localhost:3000,http://localhost:5173 when unset
+# CORS_ORIGINS=https://sparc.example.com,https://app.example.com
+
+# ---- Cache ----
+
+# When USE_CACHE=true: check database for cached responses before making API calls
+# When USE_CACHE=false: always make fresh API calls (still stores results in database)
+USE_CACHE=true

.gitea/workflows/build.yaml

@@ -9,7 +9,43 @@ on:
   workflow_dispatch:
 
 jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install system dependencies
+        shell: sh
+        run: |
+          apk add --no-cache git python3 py3-pip gcc musl-dev libpq-dev python3-dev
+
+      - name: Checkout code
+        shell: sh
+        run: |
+          git clone http://gitea.gitea.svc.cluster.local/${{ gitea.repository }}.git .
+          git checkout ${{ gitea.sha }}
+
+      - name: Install Python dependencies
+        shell: sh
+        run: |
+          pip3 install --break-system-packages -r requirements.txt ruff
+
+      - name: Run ruff linter
+        shell: sh
+        run: |
+          ruff check SPARC/ tests/
+
+      - name: Run pytest
+        shell: sh
+        env:
+          DATABASE_URL: "sqlite://"
+          API_KEY: "test-key"
+          OPENROUTER_API_KEY: "test-key"
+          JWT_SECRET: "test-secret-for-ci"
+          APP_ENV: "development"
+        run: |
+          python3 -m pytest tests/ -v --tb=short -x
+
   build-api:
+    needs: test
     runs-on: ubuntu-latest
     steps:
       - name: Install dependencies
@@ -81,6 +117,7 @@ jobs:
           echo "API image available at ${{ steps.tags.outputs.IMAGE_TAG }}"
 
   build-frontend:
+    needs: test
     runs-on: ubuntu-latest
     steps:
       - name: Install dependencies

.gitea/workflows/test.yaml

@@ -0,0 +1,46 @@
+name: Test and Lint
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install system dependencies
+        shell: sh
+        run: |
+          apk add --no-cache git python3 py3-pip gcc musl-dev libpq-dev python3-dev
+
+      - name: Checkout code
+        shell: sh
+        run: |
+          git clone http://gitea.gitea.svc.cluster.local/${{ gitea.repository }}.git .
+          git checkout ${{ gitea.sha }}
+
+      - name: Install Python dependencies
+        shell: sh
+        run: |
+          pip3 install --break-system-packages -r requirements.txt ruff
+
+      - name: Run ruff linter
+        shell: sh
+        run: |
+          ruff check SPARC/ tests/
+
+      - name: Run pytest
+        shell: sh
+        env:
+          DATABASE_URL: "sqlite://"
+          API_KEY: "test-key"
+          OPENROUTER_API_KEY: "test-key"
+          JWT_SECRET: "test-secret-for-ci"
+          APP_ENV: "development"
+        run: |
+          python3 -m pytest tests/ -v --tb=short -x

README.md

@@ -54,6 +54,21 @@ docker-compose up -d
 # - API Docs: http://localhost:8000/docs
 ```
 
+#### Patent PDF Storage
+
+The API stores downloaded patent PDFs in a `patents/` directory. In Docker,
+this is mounted as a bind mount (`./patents:/app/patents`) so that PDFs persist
+across container restarts.
+
+If you deploy to a different environment, ensure the `patents/` directory is a
+persistent volume. Without it, PDFs will be re-downloaded on every analysis.
+
+```yaml
+# docker-compose.yml excerpt
+volumes:
+  - ./patents:/app/patents
+```
+
 ### NixOS
 
 ```bash

SPARC/__init__.py

@@ -1,3 +1,4 @@
-from .types import Patents, Patent
+from .types import Patent as Patent
+from .types import Patents as Patents
 
-all = ["Patents", "Patent"]
+__all__ = ["Patents", "Patent"]

SPARC/analyzer.py

@@ -5,14 +5,17 @@ to provide company performance estimation based on patent portfolios.
 """
 
 import hashlib
+import logging
 from concurrent.futures import ThreadPoolExecutor, as_completed
 from typing import Callable
 
 from SPARC import config
+
+logger = logging.getLogger(__name__)
 from SPARC.database import DatabaseClient
-from SPARC.serp_api import SERP
 from SPARC.llm import LLMAnalyzer
-from SPARC.types import Patent, Patents, CompanyAnalysisResult, BatchAnalysisResult
+from SPARC.serp_api import SERP
+from SPARC.types import BatchAnalysisResult, CompanyAnalysisResult, Patent, Patents
 
 
 class CompanyAnalyzer:
@@ -52,13 +55,13 @@ class CompanyAnalyzer:
             query_hash = hashlib.sha256(company_name.lower().encode()).hexdigest()
             cached_ids = self.db.get_cached_serp_query(query_hash)
             if cached_ids is not None:
-                print(f"Using cached SERP results for {company_name} ({len(cached_ids)} patents)")
+                logger.info("Using cached SERP results for %s (%d patents)", company_name, len(cached_ids))
                 patents = Patents(patents=[
                     Patent(patent_id=pid, pdf_link="")
                     for pid in cached_ids
                 ])
             else:
-                print(f"Retrieving patents for {company_name}...")
+                logger.info("Retrieving patents for %s...", company_name)
                 patents = SERP.query(company_name)
                 # Cache the SERP results
                 if patents.patents:
@@ -66,12 +69,13 @@ class CompanyAnalyzer:
                         company_name=company_name,
                         query_hash=query_hash,
                         patent_ids=[p.patent_id for p in patents.patents],
+                        ttl_hours=config.serp_cache_ttl_hours,
                     )
 
         if not patents.patents:
             return f"No patents found for {company_name}"
 
-        print(f"Found {len(patents.patents)} patents. Processing...")
+        logger.info("Found %d patents. Processing...", len(patents.patents))
 
         # Download, parse, and minimize patents in parallel
         processed_patents = []
@@ -87,12 +91,12 @@ class CompanyAnalyzer:
                     if result:
                         processed_patents.append(result)
                 except Exception as e:
-                    print(f"Warning: Failed to process {patent.patent_id}: {e}")
+                    logger.warning("Failed to process %s: %s", patent.patent_id, e)
 
         if not processed_patents:
             return f"Failed to process any patents for {company_name}"
 
-        print(f"Analyzing portfolio with LLM...")
+        logger.info("Analyzing portfolio with LLM...")
 
         # Analyze the full portfolio with LLM
         analysis = self.llm_analyzer.analyze_patent_portfolio(
@@ -104,21 +108,34 @@ class CompanyAnalyzer:
     def analyze_single_patent(self, patent_id: str, company_name: str) -> str:
         """Analyze a single patent by ID.
 
-        Useful for focused analysis of specific innovations.
+        Prerequisite:
+            The patent PDF must already exist at ``patents/{patent_id}.pdf``
+            before calling this method. PDFs are downloaded automatically when
+            using the batch analysis pipeline (``analyze_company`` or the
+            ``/analyze/batch`` API endpoint). For standalone usage, download
+            the PDF manually or call ``SERP.save_patents()`` first.
 
         Args:
-          patent_id: Publication ID of the patent
+          patent_id: Publication ID of the patent (e.g. "US-11234567-B2")
           company_name: Name of the company (for context)
 
         Returns:
           Analysis of the specific patent's innovation quality
+
+        Raises:
+          FileNotFoundError: If the patent PDF is not found at the expected path.
         """
-        # Note: This simplified version assumes the patent PDF is already downloaded
-        # A more complete implementation would support direct patent ID lookup
-        print(f"Analyzing patent {patent_id} for {company_name}...")
+        import os
+        logger.info("Analyzing patent %s for %s...", patent_id, company_name)
 
         patent_path = f"patents/{patent_id}.pdf"
 
+        if not os.path.exists(patent_path):
+            raise FileNotFoundError(
+                f"Patent PDF not found at '{patent_path}'. "
+                f"Download the PDF first using SERP.save_patents() or the batch analysis pipeline."
+            )
+
         try:
             sections = SERP.parse_patent_pdf(patent_path)
             minimized_content = SERP.minimize_patent_for_llm(sections)
@@ -129,6 +146,8 @@ class CompanyAnalyzer:
 
             return analysis
 
+        except FileNotFoundError:
+            raise
         except Exception as e:
             return f"Failed to analyze patent {patent_id}: {e}"
 
@@ -169,7 +188,7 @@ class CompanyAnalyzer:
 
             return {"patent_id": patent.patent_id, "content": minimized_content}
         except Exception as e:
-            print(f"Warning: Failed to process {patent.patent_id}: {e}")
+            logger.warning("Failed to process %s: %s", patent.patent_id, e)
             return None
 
     def _analyze_company_safe(self, company_name: str) -> CompanyAnalysisResult:
@@ -240,7 +259,7 @@ class CompanyAnalyzer:
         results: list[CompanyAnalysisResult] = []
         total = len(companies)
 
-        print(f"Starting batch analysis of {total} companies...")
+        logger.info("Starting batch analysis of %d companies...", total)
 
         with ThreadPoolExecutor(max_workers=max_workers) as executor:
             future_to_company = {
@@ -257,8 +276,8 @@ class CompanyAnalyzer:
                     result = future.result()
                     results.append(result)
 
-                    status = "✓" if result.success else "✗"
-                    print(f"[{completed}/{total}] {status} {company}")
+                    status = "OK" if result.success else "FAIL"
+                    logger.info("[%d/%d] %s %s", completed, total, status, company)
 
                     if progress_callback:
                         progress_callback(company, completed, total)
@@ -273,12 +292,12 @@ class CompanyAnalyzer:
                             error=str(e),
                         )
                     )
-                    print(f"[{completed}/{total}] ✗ {company}: {e}")
+                    logger.error("[%d/%d] FAIL %s: %s", completed, total, company, e)
 
         successful = sum(1 for r in results if r.success)
         failed = total - successful
 
-        print(f"\nBatch complete: {successful} succeeded, {failed} failed")
+        logger.info("Batch complete: %d succeeded, %d failed", successful, failed)
 
         return BatchAnalysisResult(
             results=results,
@@ -304,20 +323,20 @@ class CompanyAnalyzer:
         results: list[CompanyAnalysisResult] = []
         total = len(companies)
 
-        print(f"Starting sequential analysis of {total} companies...")
+        logger.info("Starting sequential analysis of %d companies...", total)
 
         for idx, company in enumerate(companies, 1):
-            print(f"\n[{idx}/{total}] Analyzing {company}...")
+            logger.info("[%d/%d] Analyzing %s...", idx, total, company)
             result = self._analyze_company_safe(company)
             results.append(result)
 
-            status = "✓" if result.success else "✗"
-            print(f"[{idx}/{total}] {status} {company}")
+            status = "OK" if result.success else "FAIL"
+            logger.info("[%d/%d] %s %s", idx, total, status, company)
 
         successful = sum(1 for r in results if r.success)
         failed = total - successful
 
-        print(f"\nBatch complete: {successful} succeeded, {failed} failed")
+        logger.info("Batch complete: %d succeeded, %d failed", successful, failed)
 
         return BatchAnalysisResult(
             results=results,

SPARC/api.py

@@ -7,20 +7,27 @@ from contextlib import asynccontextmanager
 from datetime import datetime
 from typing import Annotated, List
 
-from fastapi import BackgroundTasks, Depends, FastAPI, HTTPException, Query
+from fastapi import BackgroundTasks, Depends, FastAPI, HTTPException, Query, Request
 from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import JSONResponse
 from pydantic import BaseModel, EmailStr, Field
+from slowapi import Limiter
+from slowapi.errors import RateLimitExceeded
+from slowapi.util import get_remote_address
 
 from SPARC import config
 from SPARC.analyzer import CompanyAnalyzer
 from SPARC.auth import (
     TokenResponse,
     UserResponse,
+    check_jwt_secret,
+    close_db_client,
     create_tokens,
     decode_token,
     get_current_admin,
     get_current_user,
     get_db_client,
+    init_db_client,
 )
 from SPARC.types import BatchAnalysisResult, CompanyAnalysisResult
 
@@ -114,8 +121,7 @@ class AnalyticsResponse(BaseModel):
     period_days: int
 
 
-# In-memory job storage (for demo; production would use Redis/DB)
-_jobs: dict[str, JobStatus] = {}
+# Job counter for generating unique IDs (the actual state is in PostgreSQL)
 _job_counter = 0
 
 
@@ -148,12 +154,25 @@ _analyzer: CompanyAnalyzer | None = None
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
-    """Initialize resources on startup."""
+    """Initialize resources on startup, clean up on shutdown."""
     global _analyzer
+    check_jwt_secret()
+    init_db_client()
     _analyzer = CompanyAnalyzer()
+    # Mark any jobs that were running/pending before the restart as failed
+    from SPARC.database import DatabaseClient
+    _db = DatabaseClient(config.database_url)
+    _db.connect()
+    _db.initialize_schema()
+    stale = _db.mark_stale_jobs_failed()
+    if stale:
+        import logging
+        logging.getLogger(__name__).warning("Marked %d stale jobs as failed on startup", stale)
+    _db.close()
     yield
-    # Cleanup if needed
+    # Cleanup
     _analyzer = None
+    close_db_client()
 
 
 app = FastAPI(
@@ -164,10 +183,26 @@ app = FastAPI(
     root_path=config.root_path,
 )
 
+# Rate limiter (in-memory storage, suitable for single-instance deployments)
+limiter = Limiter(key_func=get_remote_address)
+app.state.limiter = limiter
+
+
+@app.exception_handler(RateLimitExceeded)
+async def rate_limit_handler(request: Request, exc: RateLimitExceeded):
+    """Return 429 with Retry-After header when rate limit is exceeded."""
+    retry_after = getattr(exc, "retry_after", 60)
+    return JSONResponse(
+        status_code=429,
+        content={"detail": "Rate limit exceeded. Please try again later."},
+        headers={"Retry-After": str(retry_after)},
+    )
+
+
 # Add CORS middleware for React frontend
 app.add_middleware(
     CORSMiddleware,
-    allow_origins=["http://localhost:3000", "http://localhost:5173"],
+    allow_origins=config.cors_origins,
     allow_credentials=True,
     allow_methods=["*"],
     allow_headers=["*"],
@@ -178,7 +213,8 @@ app.add_middleware(
 
 
 @app.post("/auth/register", response_model=UserResponse, tags=["Auth"])
-async def register(request: RegisterRequest):
+@limiter.limit("5/minute")
+async def register(request: Request, body: RegisterRequest):
     """Register a new user.
 
     The first registered user automatically becomes an admin.
@@ -190,8 +226,8 @@ async def register(request: RegisterRequest):
     role = "admin" if user_count == 0 else "user"
 
     user = db.create_user(
-        email=request.email,
-        password=request.password,
+        email=body.email,
+        password=body.password,
         role=role,
     )
 
@@ -210,11 +246,12 @@ async def register(request: RegisterRequest):
 
 
 @app.post("/auth/login", response_model=TokenResponse, tags=["Auth"])
-async def login(request: LoginRequest):
+@limiter.limit("10/minute")
+async def login(request: Request, body: LoginRequest):
     """Authenticate user and return JWT tokens."""
     db = get_db_client()
 
-    user = db.authenticate_user(request.email, request.password)
+    user = db.authenticate_user(body.email, body.password)
 
     if not user:
         raise HTTPException(
@@ -422,20 +459,52 @@ async def analyze_companies_batch(
     return _convert_batch_result(result)
 
 
+def _get_job_db() -> "DatabaseClient":
+    """Get a DatabaseClient for job persistence."""
+    from SPARC.database import DatabaseClient
+    db = DatabaseClient(config.database_url)
+    return db
+
+
+def _job_row_to_status(row: dict) -> JobStatus:
+    """Convert a database job row to a JobStatus model."""
+    import json as _json
+    result = None
+    if row.get("result_json"):
+        result_data = row["result_json"]
+        if isinstance(result_data, str):
+            result_data = _json.loads(result_data)
+        result = BatchAnalysisResponse(**result_data)
+    return JobStatus(
+        job_id=row["job_id"],
+        status=row["status"],
+        progress=row["progress"],
+        total_companies=row["total_companies"],
+        completed_companies=row["completed_companies"],
+        result=result,
+        error=row.get("error"),
+    )
+
+
 def _run_batch_job(job_id: str, companies: list[str], max_workers: int):
     """Background task for batch analysis."""
-    global _jobs, _analyzer
+    import json as _json
+    global _analyzer
+
+    db = _get_job_db()
 
     if not _analyzer:
-        _jobs[job_id].status = "failed"
-        _jobs[job_id].error = "Analyzer not initialized"
+        db.update_job(job_id, status="failed", error="Analyzer not initialized")
         return
 
-    _jobs[job_id].status = "running"
+    db.update_job(job_id, status="running")
 
     def progress_callback(company: str, completed: int, total: int):
-        _jobs[job_id].completed_companies = completed
-        _jobs[job_id].progress = int((completed / total) * 100)
+        db.update_job(
+            job_id,
+            completed_companies=completed,
+            progress=int((completed / total) * 100),
+        )
 
     try:
         result = _analyzer.analyze_companies(
@@ -443,12 +512,15 @@ def _run_batch_job(job_id: str, companies: list[str], max_workers: int):
             max_workers=max_workers,
             progress_callback=progress_callback,
         )
-        _jobs[job_id].status = "completed"
-        _jobs[job_id].progress = 100
-        _jobs[job_id].result = _convert_batch_result(result)
+        batch_response = _convert_batch_result(result)
+        db.update_job(
+            job_id,
+            status="completed",
+            progress=100,
+            result_json=_json.dumps(batch_response.model_dump(), default=str),
+        )
     except Exception as e:
-        _jobs[job_id].status = "failed"
-        _jobs[job_id].error = str(e)
+        db.update_job(job_id, status="failed", error=str(e))
 
 
 @app.post("/analyze/batch/async", response_model=JobStatus, tags=["Analysis"])
@@ -473,19 +545,14 @@ async def analyze_companies_async(
     _job_counter += 1
     job_id = f"job_{_job_counter}_{datetime.now().strftime('%Y%m%d%H%M%S')}"
 
-    _jobs[job_id] = JobStatus(
-        job_id=job_id,
-        status="pending",
-        progress=0,
-        total_companies=len(request.companies),
-        completed_companies=0,
-    )
+    db = _get_job_db()
+    job_row = db.create_job(job_id=job_id, total_companies=len(request.companies))
 
     background_tasks.add_task(
         _run_batch_job, job_id, request.companies, request.max_workers
     )
 
-    return _jobs[job_id]
+    return _job_row_to_status(job_row)
 
 
 @app.get("/jobs/{job_id}", response_model=JobStatus, tags=["Jobs"])
@@ -501,10 +568,13 @@ async def get_job_status(
     Returns:
         Current job status including progress and results when complete
     """
-    if job_id not in _jobs:
+    db = _get_job_db()
+    job_row = db.get_job(job_id)
+
+    if not job_row:
         raise HTTPException(status_code=404, detail=f"Job {job_id} not found")
 
-    return _jobs[job_id]
+    return _job_row_to_status(job_row)
 
 
 @app.get("/jobs", response_model=list[JobStatus], tags=["Jobs"])
@@ -525,12 +595,6 @@ async def list_jobs(
     Returns:
         List of job statuses
     """
-    jobs = list(_jobs.values())
-
-    if status:
-        jobs = [j for j in jobs if j.status == status]
-
-    # Return most recent first
-    jobs.sort(key=lambda j: j.job_id, reverse=True)
-
-    return jobs[:limit]
+    db = _get_job_db()
+    job_rows = db.list_jobs(status=status, limit=limit)
+    return [_job_row_to_status(row) for row in job_rows]

SPARC/auth.py

@@ -13,11 +13,25 @@ from SPARC import config
 from SPARC.database import DatabaseClient
 
 # JWT Configuration
-JWT_SECRET = os.getenv("JWT_SECRET", "sparc-secret-key-change-in-production")
+_DEFAULT_JWT_SECRET = "sparc-secret-key-change-in-production"
+JWT_SECRET = os.getenv("JWT_SECRET", _DEFAULT_JWT_SECRET)
 JWT_ALGORITHM = "HS256"
 ACCESS_TOKEN_EXPIRE_MINUTES = 30
 REFRESH_TOKEN_EXPIRE_DAYS = 7
 
+
+def check_jwt_secret() -> None:
+    """Refuse to start with the default JWT secret in non-development environments.
+
+    Raises:
+        RuntimeError: If JWT_SECRET is the default value and APP_ENV is not 'development'.
+    """
+    if JWT_SECRET == _DEFAULT_JWT_SECRET and config.app_env != "development":
+        raise RuntimeError(
+            f"FATAL: JWT_SECRET is set to the default value and APP_ENV={config.app_env!r}. "
+            "Set a secure JWT_SECRET environment variable before running in non-development environments."
+        )
+
 security = HTTPBearer()
 
 
@@ -132,11 +146,36 @@ def decode_token(token: str) -> Optional[TokenPayload]:
         return None
 
 
+# Shared database client singleton, initialized at startup via init_db_client()
+_db_client: DatabaseClient | None = None
+
+
+def init_db_client() -> None:
+    """Initialize the shared database client. Call once at app startup."""
+    global _db_client
+    _db_client = DatabaseClient(config.database_url)
+    _db_client.connect()
+
+
+def close_db_client() -> None:
+    """Close the shared database client. Call at app shutdown."""
+    global _db_client
+    if _db_client:
+        _db_client.close()
+        _db_client = None
+
+
 def get_db_client() -> DatabaseClient:
-    """Get database client for auth operations."""
-    client = DatabaseClient(config.database_url)
-    client.connect()
-    return client
+    """Get the shared pooled database client for auth operations.
+
+    Returns the module-level singleton DatabaseClient. If not yet initialized
+    (e.g., during tests), creates a new instance as a fallback.
+    """
+    global _db_client
+    if _db_client is None:
+        _db_client = DatabaseClient(config.database_url)
+        _db_client.connect()
+    return _db_client
 
 
 async def get_current_user(

SPARC/config.py

@@ -2,11 +2,20 @@
 
 Loads environment variables from .env file for API keys and other secrets.
 """
-from dotenv import load_dotenv
+import logging
 import os
 
+from dotenv import load_dotenv
+
 load_dotenv()
 
+# Logging configuration
+log_level = os.getenv("LOG_LEVEL", "INFO").upper()
+logging.basicConfig(
+    level=getattr(logging, log_level, logging.INFO),
+    format="%(asctime)s %(levelname)s %(name)s %(message)s",
+)
+
 # SerpAPI key for patent search
 api_key = os.getenv("API_KEY")
 
@@ -30,6 +39,25 @@ use_database = os.getenv("USE_DATABASE", "false").lower() in ("true", "1", "yes"
 patent_search_days = int(os.getenv("PATENT_SEARCH_DAYS", "90"))
 patent_thread_workers = int(os.getenv("PATENT_THREAD_WORKERS", "5"))
 
+# LLM model to use via OpenRouter (e.g. "anthropic/claude-3.5-sonnet", "openai/gpt-4o")
+model = os.getenv("MODEL", "anthropic/claude-3.5-sonnet")
+
+# SERP cache TTL in hours (how long cached search results are considered fresh)
+serp_cache_ttl_hours = int(os.getenv("SERP_CACHE_TTL_HOURS", "24"))
+
 # Root path for running behind a reverse proxy (e.g., "/api" when served at /api/)
 # This ensures OpenAPI docs work correctly when accessed via the proxy
 root_path = os.getenv("ROOT_PATH", "")
+
+# Application environment: "development", "staging", or "production"
+# Used for safety checks (e.g., refusing default JWT secret in production)
+app_env = os.getenv("APP_ENV", "development")
+
+# CORS allowed origins (comma-separated)
+# Defaults to localhost dev origins when unset
+_cors_origins_raw = os.getenv("CORS_ORIGINS", "")
+cors_origins: list[str] = (
+    [o.strip() for o in _cors_origins_raw.split(",") if o.strip()]
+    if _cors_origins_raw
+    else ["http://localhost:3000", "http://localhost:5173"]
+)

SPARC/database.py

@@ -1,14 +1,15 @@
 """Database client for storing and retrieving LLM messages and user authentication."""
 
 import contextlib
-import psycopg2
-from psycopg2.pool import ThreadedConnectionPool
-from psycopg2.extras import RealDictCursor
-from typing import Dict, List, Optional
-from datetime import datetime, timedelta
-import json
 import hashlib
+import json
+from datetime import datetime, timedelta
+from typing import Dict, List, Optional
+
 import bcrypt
+import psycopg2
+from psycopg2.extras import RealDictCursor
+from psycopg2.pool import ThreadedConnectionPool
 
 
 class DatabaseClient:
@@ -171,6 +172,26 @@ class DatabaseClient:
                 ON serp_queries(query_hash)
             """)
 
+            # Create jobs table for persisting async batch job state
+            cursor.execute("""
+                CREATE TABLE IF NOT EXISTS jobs (
+                    job_id VARCHAR(128) PRIMARY KEY,
+                    status VARCHAR(20) NOT NULL DEFAULT 'pending',
+                    progress INTEGER NOT NULL DEFAULT 0,
+                    total_companies INTEGER NOT NULL DEFAULT 0,
+                    completed_companies INTEGER NOT NULL DEFAULT 0,
+                    result_json JSONB,
+                    error TEXT,
+                    created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+                    updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+                )
+            """)
+
+            cursor.execute("""
+                CREATE INDEX IF NOT EXISTS idx_jobs_status
+                ON jobs(status)
+            """)
+
             self.conn.commit()
 
     @staticmethod
@@ -201,8 +222,6 @@ class DatabaseClient:
         Returns:
             Cached message dict if found, None otherwise
         """
-        self.connect()
-
         prompt_hash = self.hash_prompt(prompt)
 
         query = """
@@ -225,7 +244,8 @@ class DatabaseClient:
 
         query += " ORDER BY timestamp DESC LIMIT 1"
 
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(query, params)
                 result = cursor.fetchone()
                 return dict(result) if result else None
@@ -256,11 +276,10 @@ class DatabaseClient:
         Returns:
             The ID of the inserted record
         """
-        self.connect()
-
         prompt_hash = self.hash_prompt(prompt)
 
-        with self.conn.cursor() as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor() as cursor:
                 cursor.execute(
                     """
                     INSERT INTO llm_messages
@@ -282,7 +301,7 @@ class DatabaseClient:
                 )
 
                 message_id = cursor.fetchone()[0]
-            self.conn.commit()
+            conn.commit()
 
             return message_id
 
@@ -304,8 +323,6 @@ class DatabaseClient:
         Returns:
             List of message dictionaries
         """
-        self.connect()
-
         query = "SELECT * FROM llm_messages WHERE 1=1"
         params = []
 
@@ -320,7 +337,8 @@ class DatabaseClient:
         query += " ORDER BY timestamp DESC LIMIT %s OFFSET %s"
         params.extend([limit, offset])
 
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(query, params)
                 return [dict(row) for row in cursor.fetchall()]
 
@@ -333,9 +351,8 @@ class DatabaseClient:
         Returns:
             Dictionary with analytics data
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 # Total messages
                 cursor.execute(
                     """
@@ -462,6 +479,131 @@ class DatabaseClient:
                 )
             conn.commit()
 
+    # Job Persistence Methods
+
+    def create_job(
+        self,
+        job_id: str,
+        total_companies: int,
+    ) -> Dict:
+        """Create a new job record.
+
+        Args:
+            job_id: Unique job identifier
+            total_companies: Number of companies in the batch
+
+        Returns:
+            Job dict
+        """
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
+                cursor.execute(
+                    """
+                    INSERT INTO jobs (job_id, status, progress, total_companies, completed_companies)
+                    VALUES (%s, 'pending', 0, %s, 0)
+                    RETURNING *
+                    """,
+                    (job_id, total_companies),
+                )
+                job = cursor.fetchone()
+            conn.commit()
+            return dict(job)
+
+    def update_job(
+        self,
+        job_id: str,
+        status: Optional[str] = None,
+        progress: Optional[int] = None,
+        completed_companies: Optional[int] = None,
+        result_json: Optional[str] = None,
+        error: Optional[str] = None,
+    ) -> Optional[Dict]:
+        """Update a job's state.
+
+        Only non-None fields are updated.
+        """
+        updates = []
+        params = []
+        if status is not None:
+            updates.append("status = %s")
+            params.append(status)
+        if progress is not None:
+            updates.append("progress = %s")
+            params.append(progress)
+        if completed_companies is not None:
+            updates.append("completed_companies = %s")
+            params.append(completed_companies)
+        if result_json is not None:
+            updates.append("result_json = %s")
+            params.append(result_json)
+        if error is not None:
+            updates.append("error = %s")
+            params.append(error)
+
+        if not updates:
+            return self.get_job(job_id)
+
+        updates.append("updated_at = CURRENT_TIMESTAMP")
+        params.append(job_id)
+
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
+                cursor.execute(
+                    f"UPDATE jobs SET {', '.join(updates)} WHERE job_id = %s RETURNING *",
+                    params,
+                )
+                job = cursor.fetchone()
+            conn.commit()
+            return dict(job) if job else None
+
+    def get_job(self, job_id: str) -> Optional[Dict]:
+        """Get a job by ID."""
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
+                cursor.execute("SELECT * FROM jobs WHERE job_id = %s", (job_id,))
+                job = cursor.fetchone()
+                return dict(job) if job else None
+
+    def list_jobs(
+        self,
+        status: Optional[str] = None,
+        limit: int = 10,
+    ) -> List[Dict]:
+        """List jobs, optionally filtered by status."""
+        query = "SELECT * FROM jobs"
+        params: list = []
+        if status:
+            query += " WHERE status = %s"
+            params.append(status)
+        query += " ORDER BY created_at DESC LIMIT %s"
+        params.append(limit)
+
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
+                cursor.execute(query, params)
+                return [dict(row) for row in cursor.fetchall()]
+
+    def mark_stale_jobs_failed(self) -> int:
+        """Mark any jobs in 'running' or 'pending' state as 'failed'.
+
+        Called at startup to clean up jobs that were interrupted by a restart.
+
+        Returns:
+            Number of jobs marked as failed.
+        """
+        with self.get_conn() as conn:
+            with conn.cursor() as cursor:
+                cursor.execute(
+                    """
+                    UPDATE jobs SET status = 'failed', error = 'Interrupted by server restart',
+                    updated_at = CURRENT_TIMESTAMP
+                    WHERE status IN ('running', 'pending')
+                    """
+                )
+                count = cursor.rowcount
+            conn.commit()
+            return count
+
     # User Authentication Methods
 
     @staticmethod
@@ -505,12 +647,11 @@ class DatabaseClient:
         Returns:
             Created user dict or None if email exists
         """
-        self.connect()
-
         password_hash = self.hash_password(password)
 
         try:
-            with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+            with self.get_conn() as conn:
+                with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                     cursor.execute(
                         """
                         INSERT INTO users (email, password_hash, role)
@@ -520,10 +661,9 @@ class DatabaseClient:
                         (email, password_hash, role),
                     )
                     user = cursor.fetchone()
-                self.conn.commit()
+                conn.commit()
                 return dict(user) if user else None
         except psycopg2.errors.UniqueViolation:
-            self.conn.rollback()
             return None
 
     def authenticate_user(self, email: str, password: str) -> Optional[Dict]:
@@ -536,9 +676,8 @@ class DatabaseClient:
         Returns:
             User dict if authenticated, None otherwise
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(
                     "SELECT * FROM users WHERE email = %s",
                     (email,),
@@ -563,9 +702,8 @@ class DatabaseClient:
         Returns:
             User dict or None
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(
                     "SELECT id, email, role, created_at FROM users WHERE id = %s",
                     (user_id,),
@@ -582,9 +720,8 @@ class DatabaseClient:
         Returns:
             User dict or None
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(
                     "SELECT id, email, role, created_at FROM users WHERE email = %s",
                     (email,),
@@ -602,9 +739,8 @@ class DatabaseClient:
         Returns:
             List of user dicts
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(
                     """
                     SELECT id, email, role, created_at
@@ -626,9 +762,8 @@ class DatabaseClient:
         Returns:
             Updated user dict or None
         """
-        self.connect()
-
-        with self.conn.cursor(cursor_factory=RealDictCursor) as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor(cursor_factory=RealDictCursor) as cursor:
                 cursor.execute(
                     """
                     UPDATE users
@@ -639,7 +774,7 @@ class DatabaseClient:
                     (role, user_id),
                 )
                 user = cursor.fetchone()
-            self.conn.commit()
+            conn.commit()
             return dict(user) if user else None
 
     def delete_user(self, user_id: int) -> bool:
@@ -651,12 +786,11 @@ class DatabaseClient:
         Returns:
             True if deleted
         """
-        self.connect()
-
-        with self.conn.cursor() as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor() as cursor:
                 cursor.execute("DELETE FROM users WHERE id = %s", (user_id,))
                 deleted = cursor.rowcount > 0
-            self.conn.commit()
+            conn.commit()
             return deleted
 
     def get_user_count(self) -> int:
@@ -665,8 +799,7 @@ class DatabaseClient:
         Returns:
             Number of users
         """
-        self.connect()
-
-        with self.conn.cursor() as cursor:
+        with self.get_conn() as conn:
+            with conn.cursor() as cursor:
                 cursor.execute("SELECT COUNT(*) FROM users")
                 return cursor.fetchone()[0]

SPARC/llm.py

@@ -1,9 +1,14 @@
 """LLM integration for patent analysis using OpenRouter."""
 
+import logging
+from typing import Dict
+
 from openai import OpenAI
+
 from SPARC import config
 from SPARC.database import DatabaseClient
-from typing import Dict
+
+logger = logging.getLogger(__name__)
 
 
 class LLMAnalyzer:
@@ -20,7 +25,7 @@ class LLMAnalyzer:
         """
         self.test_mode = test_mode
         self.use_cache = use_cache if use_cache is not None else config.use_cache
-        self.model = "anthropic/claude-3.5-sonnet"
+        self.model = config.model
 
         # Always initialize database client for storage and caching
         self.db_client = DatabaseClient(config.database_url)
@@ -59,11 +64,7 @@ Patent Content:
 Provide a concise analysis (2-3 paragraphs) focusing on what this patent reveals about the company's technical direction and competitive advantage."""
 
         if self.test_mode:
-            print("=" * 80)
-            print("TEST MODE - Prompt that would be sent to LLM:")
-            print("=" * 80)
-            print(prompt)
-            print("=" * 80)
+            logger.debug("TEST MODE - Prompt that would be sent to LLM:\n%s", prompt)
             return "[TEST MODE - No API call made]"
 
         # Check cache first
@@ -165,7 +166,7 @@ Patent Portfolio:
 Provide a comprehensive analysis (4-5 paragraphs) with a final verdict on the company's innovation strength and performance outlook."""
 
         if self.test_mode:
-            print(prompt)
+            logger.debug("TEST MODE - Portfolio prompt:\n%s", prompt)
             return "[TEST MODE]"
 
         metadata = {

SPARC/serp_api.py

@@ -1,12 +1,15 @@
 import os
-import serpapi
-from SPARC import config
 import re
-import pdfplumber  # pip install pdfplumber
-import requests
 from datetime import datetime, timedelta
 from typing import Dict
-from SPARC.types import Patents, Patent
+
+import pdfplumber  # pip install pdfplumber
+import requests
+import serpapi
+
+from SPARC import config
+from SPARC.types import Patent, Patents
+
 
 class SERP:
   def query(company: str, days_back: int = None) -> Patents:

SPARC/types.py

@@ -4,7 +4,7 @@ from datetime import datetime
 
 @dataclass
 class Patent:
-    patent_id: int
+    patent_id: str
     pdf_link: str
     pdf_path: str | None = None
     summary: dict | None = None

docker-compose.yml

@@ -3,15 +3,15 @@ services:
     image: postgres:16-alpine
     container_name: sparc-postgres
     environment:
-      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: sparc
+      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_DB: ${POSTGRES_DB}
     ports:
       - "5432:5432"
     volumes:
       - postgres_data:/var/lib/postgresql/data
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready -U postgres"]
+      test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER}"]
       interval: 5s
       timeout: 5s
       retries: 5
@@ -22,7 +22,7 @@ services:
     container_name: sparc-init-db
     command: python scripts/init_database.py
     environment:
-      DATABASE_URL: postgresql://postgres:postgres@postgres:5432/sparc
+      DATABASE_URL: postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}
     depends_on:
       postgres:
         condition: service_healthy
@@ -35,9 +35,11 @@ services:
     environment:
       API_KEY: ${API_KEY}
       OPENROUTER_API_KEY: ${OPENROUTER_API_KEY}
-      DATABASE_URL: postgresql://postgres:postgres@postgres:5432/sparc
+      DATABASE_URL: postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}
       USE_CACHE: "true"
       JWT_SECRET: ${JWT_SECRET:-sparc-secret-key-change-in-production}
+      CORS_ORIGINS: ${CORS_ORIGINS:-}
+      APP_ENV: ${APP_ENV:-development}
       ROOT_PATH: /api
     ports:
       - "8000:8000"

frontend/index.html

@@ -7,6 +7,15 @@
     <title>SPARC Dashboard</title>
   </head>
   <body>
+    <script>
+      // Prevent FOUC: apply saved theme before first render
+      (function() {
+        var theme = localStorage.getItem('theme');
+        if (theme === 'dark' || (!theme && window.matchMedia('(prefers-color-scheme: dark)').matches)) {
+          document.documentElement.classList.add('dark');
+        }
+      })();
+    </script>
     <div id="root"></div>
     <script type="module" src="/src/main.tsx"></script>
   </body>

frontend/src/App.tsx

@@ -1,6 +1,7 @@
 import { BrowserRouter, Routes, Route, Navigate } from 'react-router-dom';
 import { QueryClient, QueryClientProvider } from '@tanstack/react-query';
 import { AuthProvider } from './context/AuthContext';
+import { ThemeProvider } from './context/ThemeContext';
 import { Layout } from './components/Layout';
 import { ProtectedRoute } from './components/ProtectedRoute';
 import { Login } from './pages/Login';
@@ -22,6 +23,7 @@ const queryClient = new QueryClient({
 
 function App() {
   return (
+    <ThemeProvider>
     <QueryClientProvider client={queryClient}>
       <AuthProvider>
         <BrowserRouter>
@@ -61,6 +63,7 @@ function App() {
         </BrowserRouter>
       </AuthProvider>
     </QueryClientProvider>
+    </ThemeProvider>
   );
 }
 

frontend/src/components/Layout.tsx

@@ -1,9 +1,11 @@
 import { Outlet, NavLink, useNavigate } from 'react-router-dom';
 import { useAuth } from '../context/AuthContext';
-import { Search, Layers, BarChart3, Info, Users, LogOut } from 'lucide-react';
+import { useTheme } from '../context/ThemeContext';
+import { Search, Layers, BarChart3, Info, Users, LogOut, Sun, Moon } from 'lucide-react';
 
 export function Layout() {
   const { user, isAdmin, logout } = useAuth();
+  const { theme, toggleTheme } = useTheme();
   const navigate = useNavigate();
 
   const handleLogout = () => {
@@ -23,7 +25,7 @@ export function Layout() {
   }
 
   return (
-    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-indigo-950">
+    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-slate-100 dark:to-indigo-950">
       {/* Header */}
       <header className="bg-bg-card/80 backdrop-blur-lg border-b border-primary/20">
         <div className="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8">
@@ -63,6 +65,13 @@ export function Layout() {
 
             {/* User menu */}
             <div className="flex items-center gap-4">
+              <button
+                onClick={toggleTheme}
+                className="p-2 rounded-lg text-text-secondary hover:text-text-primary hover:bg-bg-card-hover transition-all"
+                aria-label={theme === 'dark' ? 'Switch to light mode' : 'Switch to dark mode'}
+              >
+                {theme === 'dark' ? <Sun size={18} /> : <Moon size={18} />}
+              </button>
               <div className="text-right hidden sm:block">
                 <div className="text-sm font-medium text-text-primary">{user?.email}</div>
                 <div className="text-xs text-text-secondary capitalize">{user?.role}</div>

frontend/src/components/ProtectedRoute.tsx

@@ -12,7 +12,7 @@ export function ProtectedRoute({ children, requireAdmin = false }: ProtectedRout
 
   if (isLoading) {
     return (
-      <div className="min-h-screen bg-gradient-to-br from-bg-dark to-indigo-950 flex items-center justify-center">
+      <div className="min-h-screen bg-gradient-to-br from-bg-dark to-slate-100 dark:to-indigo-950 flex items-center justify-center">
         <div className="animate-spin rounded-full h-12 w-12 border-t-2 border-b-2 border-primary"></div>
       </div>
     );

frontend/src/context/ThemeContext.tsx

@@ -0,0 +1,48 @@
+import { createContext, useContext, useEffect, useState } from 'react';
+
+type Theme = 'light' | 'dark';
+
+interface ThemeContextType {
+  theme: Theme;
+  toggleTheme: () => void;
+}
+
+const ThemeContext = createContext<ThemeContextType | undefined>(undefined);
+
+function getInitialTheme(): 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: React.ReactNode }) {
+  const [theme, setTheme] = useState<Theme>(getInitialTheme);
+
+  useEffect(() => {
+    const root = document.documentElement;
+    if (theme === 'dark') {
+      root.classList.add('dark');
+    } else {
+      root.classList.remove('dark');
+    }
+    localStorage.setItem('theme', theme);
+  }, [theme]);
+
+  const toggleTheme = () => {
+    setTheme((prev) => (prev === 'dark' ? 'light' : 'dark'));
+  };
+
+  return (
+    <ThemeContext.Provider value={{ theme, toggleTheme }}>
+      {children}
+    </ThemeContext.Provider>
+  );
+}
+
+export function useTheme() {
+  const context = useContext(ThemeContext);
+  if (!context) {
+    throw new Error('useTheme must be used within a ThemeProvider');
+  }
+  return context;
+}

frontend/src/index.css

@@ -2,6 +2,26 @@
 @tailwind components;
 @tailwind utilities;
 
+/* Light mode (default) */
+:root {
+  --color-bg-dark: #f1f5f9;
+  --color-bg-card: #ffffff;
+  --color-bg-card-hover: #e2e8f0;
+  --color-text-primary: #0f172a;
+  --color-text-secondary: #475569;
+  --color-border: #cbd5e1;
+}
+
+/* Dark mode */
+.dark {
+  --color-bg-dark: #0f172a;
+  --color-bg-card: #1e293b;
+  --color-bg-card-hover: #334155;
+  --color-text-primary: #f8fafc;
+  --color-text-secondary: #94a3b8;
+  --color-border: #334155;
+}
+
 body {
   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
   -webkit-font-smoothing: antialiased;
@@ -15,7 +35,7 @@ body {
 }
 
 ::-webkit-scrollbar-track {
-  background: #1e293b;
+  background: var(--color-bg-card);
 }
 
 ::-webkit-scrollbar-thumb {
@@ -30,5 +50,5 @@ body {
 /* Selection */
 ::selection {
   background: rgba(99, 102, 241, 0.3);
-  color: #f8fafc;
+  color: var(--color-text-primary);
 }

frontend/src/pages/Login.tsx

@@ -31,7 +31,7 @@ export function Login() {
   };
 
   return (
-    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-indigo-950 flex items-center justify-center px-4">
+    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-slate-100 dark:to-indigo-950 flex items-center justify-center px-4">
       <div className="w-full max-w-md">
         {/* Brand */}
         <div className="text-center mb-8">

frontend/src/pages/Register.tsx

@@ -40,7 +40,7 @@ export function Register() {
   };
 
   return (
-    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-indigo-950 flex items-center justify-center px-4">
+    <div className="min-h-screen bg-gradient-to-br from-bg-dark to-slate-100 dark:to-indigo-950 flex items-center justify-center px-4">
       <div className="w-full max-w-md">
         {/* Brand */}
         <div className="text-center mb-8">

frontend/tailwind.config.js

@@ -4,6 +4,7 @@ export default {
     "./index.html",
     "./src/**/*.{js,ts,jsx,tsx}",
   ],
+  darkMode: 'class',
   theme: {
     extend: {
       colors: {
@@ -16,15 +17,15 @@ export default {
         warning: '#f59e0b',
         error: '#ef4444',
         bg: {
-          dark: '#0f172a',
-          card: '#1e293b',
-          'card-hover': '#334155',
+          dark: 'var(--color-bg-dark)',
+          card: 'var(--color-bg-card)',
+          'card-hover': 'var(--color-bg-card-hover)',
         },
         text: {
-          primary: '#f8fafc',
-          secondary: '#94a3b8',
+          primary: 'var(--color-text-primary)',
+          secondary: 'var(--color-text-secondary)',
         },
-        border: '#334155',
+        border: 'var(--color-border)',
       },
     },
   },

requirements.txt

@@ -14,3 +14,4 @@ numpy
 pandas
 bcrypt
 PyJWT
+slowapi

ruff.toml

@@ -0,0 +1,8 @@
+[lint]
+select = ["E", "F", "I"]
+ignore = [
+    "E501",  # line too long (handled by formatter)
+]
+
+[lint.per-file-ignores]
+"tests/*" = ["E402", "F841"]  # allow import not at top of file, unused vars (mocks) in tests

scripts/init_database.py

@@ -40,6 +40,9 @@ def main():
         print("\nTables created:")
         print("  - llm_messages: Stores all LLM prompts and responses")
         print("  - users: Stores user accounts")
+        print("  - jobs: Stores async batch job state")
+        print("  - patents: Patent PDF cache")
+        print("  - serp_queries: SERP query result cache")
         print("\nIndexes created:")
         print("  - idx_messages_timestamp: For time-based queries")
         print("  - idx_messages_company: For company-specific queries")

tests/test_analyzer.py

@@ -1,9 +1,11 @@
 """Tests for the high-level company analyzer orchestration."""
 
+from unittest.mock import MagicMock, Mock
+
 import pytest
-from unittest.mock import Mock, patch, call, MagicMock
+
 from SPARC.analyzer import CompanyAnalyzer
-from SPARC.types import Patent, Patents, CompanyAnalysisResult, BatchAnalysisResult
+from SPARC.types import BatchAnalysisResult, Patent, Patents
 
 
 @pytest.fixture(autouse=True)
@@ -24,7 +26,7 @@ class TestCompanyAnalyzer:
         """Test analyzer initialization with API key."""
         mock_llm = mocker.patch("SPARC.analyzer.LLMAnalyzer")
 
-        analyzer = CompanyAnalyzer(openrouter_api_key="test-key")
+        _analyzer = CompanyAnalyzer(openrouter_api_key="test-key")  # noqa: F841
 
         mock_llm.assert_called_once_with(api_key="test-key")
 

tests/test_api.py

@@ -1,12 +1,13 @@
 """Tests for FastAPI web service endpoints."""
 
-import pytest
 from datetime import datetime
-from unittest.mock import Mock, patch
+from unittest.mock import Mock
+
+import pytest
 from fastapi.testclient import TestClient
 
-from SPARC.api import app, _analyzer, _jobs
-from SPARC.types import CompanyAnalysisResult, BatchAnalysisResult
+from SPARC.api import app
+from SPARC.types import BatchAnalysisResult, CompanyAnalysisResult
 
 
 @pytest.fixture

tests/test_auth.py

@@ -0,0 +1,302 @@
+"""Tests for JWT authentication flow: register, login, protected routes, refresh, admin access."""
+
+from datetime import datetime, timezone
+from unittest.mock import MagicMock, patch
+
+import pytest
+from fastapi.testclient import TestClient
+
+from SPARC.api import app
+from SPARC.auth import create_access_token, create_refresh_token
+
+
+@pytest.fixture
+def client():
+    """Create test client."""
+    return TestClient(app)
+
+
+@pytest.fixture(autouse=True)
+def mock_db(monkeypatch):
+    """Mock the database client used by auth endpoints.
+
+    Returns a MagicMock with all DB methods pre-configured.
+    """
+    db = MagicMock()
+
+    # Default: no users exist
+    db.get_user_count.return_value = 0
+    db.get_user_by_id.return_value = None
+    db.get_user_by_email.return_value = None
+    db.authenticate_user.return_value = None
+    db.create_user.return_value = None
+    db.get_all_users.return_value = []
+    db.update_user_role.return_value = None
+    db.delete_user.return_value = False
+
+    with patch("SPARC.api.get_db_client", return_value=db), \
+         patch("SPARC.auth.get_db_client", return_value=db):
+        yield db
+
+
+def _make_admin_user():
+    return {
+        "id": 1,
+        "email": "admin@test.com",
+        "role": "admin",
+        "created_at": datetime(2025, 1, 1, tzinfo=timezone.utc),
+    }
+
+
+def _make_regular_user():
+    return {
+        "id": 2,
+        "email": "user@test.com",
+        "role": "user",
+        "created_at": datetime(2025, 1, 1, tzinfo=timezone.utc),
+    }
+
+
+def _auth_header(user_dict):
+    """Create an Authorization header with a valid access token for the given user."""
+    token = create_access_token(user_dict["id"], user_dict["email"], user_dict["role"])
+    return {"Authorization": f"Bearer {token}"}
+
+
+class TestRegister:
+    """POST /auth/register"""
+
+    def test_register_first_user_becomes_admin(self, client, mock_db):
+        """First registered user should get admin role."""
+        mock_db.get_user_count.return_value = 0
+        mock_db.create_user.return_value = {
+            "id": 1,
+            "email": "admin@test.com",
+            "role": "admin",
+            "created_at": datetime(2025, 1, 1, tzinfo=timezone.utc),
+        }
+
+        response = client.post(
+            "/auth/register",
+            json={"email": "admin@test.com", "password": "securepass123"},
+        )
+
+        assert response.status_code == 200
+        data = response.json()
+        assert data["email"] == "admin@test.com"
+        assert data["role"] == "admin"
+        mock_db.create_user.assert_called_once_with(
+            email="admin@test.com", password="securepass123", role="admin"
+        )
+
+    def test_register_subsequent_user_gets_user_role(self, client, mock_db):
+        """Non-first user should get regular user role."""
+        mock_db.get_user_count.return_value = 1
+        mock_db.create_user.return_value = _make_regular_user()
+
+        response = client.post(
+            "/auth/register",
+            json={"email": "user@test.com", "password": "securepass123"},
+        )
+
+        assert response.status_code == 200
+        data = response.json()
+        assert data["role"] == "user"
+
+    def test_register_duplicate_email_returns_400(self, client, mock_db):
+        """Registering with an existing email should return 400."""
+        mock_db.get_user_count.return_value = 1
+        mock_db.create_user.return_value = None  # indicates duplicate
+
+        response = client.post(
+            "/auth/register",
+            json={"email": "existing@test.com", "password": "securepass123"},
+        )
+
+        assert response.status_code == 400
+        assert "already registered" in response.json()["detail"].lower()
+
+
+class TestLogin:
+    """POST /auth/login"""
+
+    def test_login_valid_credentials_returns_tokens(self, client, mock_db):
+        """Valid credentials should return access and refresh tokens."""
+        user = _make_regular_user()
+        mock_db.authenticate_user.return_value = user
+
+        response = client.post(
+            "/auth/login",
+            json={"email": "user@test.com", "password": "correctpassword"},
+        )
+
+        assert response.status_code == 200
+        data = response.json()
+        assert "access_token" in data
+        assert "refresh_token" in data
+        assert data["token_type"] == "bearer"
+
+    def test_login_invalid_credentials_returns_401(self, client, mock_db):
+        """Invalid credentials should return 401."""
+        mock_db.authenticate_user.return_value = None
+
+        response = client.post(
+            "/auth/login",
+            json={"email": "user@test.com", "password": "wrongpassword"},
+        )
+
+        assert response.status_code == 401
+        assert "invalid" in response.json()["detail"].lower()
+
+
+class TestGetMe:
+    """GET /auth/me"""
+
+    def test_valid_access_token_returns_user(self, client, mock_db):
+        """A valid access token should return the user's data."""
+        user = _make_regular_user()
+        mock_db.get_user_by_id.return_value = user
+
+        response = client.get("/auth/me", headers=_auth_header(user))
+
+        assert response.status_code == 200
+        data = response.json()
+        assert data["email"] == "user@test.com"
+        assert data["id"] == 2
+
+    def test_missing_token_returns_401(self, client):
+        """No token should return 401 (403 from HTTPBearer)."""
+        response = client.get("/auth/me")
+        assert response.status_code in (401, 403)
+
+    def test_expired_token_returns_401(self, client, mock_db):
+        """An expired token should return 401."""
+        # Create a token that has already expired
+        from datetime import timedelta
+
+        import jwt as pyjwt
+        from SPARC.auth import JWT_ALGORITHM, JWT_SECRET
+
+        payload = {
+            "sub": "1",
+            "email": "user@test.com",
+            "role": "user",
+            "exp": datetime.now(timezone.utc) - timedelta(hours=1),
+            "type": "access",
+        }
+        expired_token = pyjwt.encode(payload, JWT_SECRET, algorithm=JWT_ALGORITHM)
+
+        response = client.get(
+            "/auth/me", headers={"Authorization": f"Bearer {expired_token}"}
+        )
+        assert response.status_code == 401
+
+    def test_refresh_token_as_access_returns_401(self, client, mock_db):
+        """Using a refresh token as an access token should return 401."""
+        user = _make_regular_user()
+        refresh_token = create_refresh_token(user["id"], user["email"], user["role"])
+
+        response = client.get(
+            "/auth/me", headers={"Authorization": f"Bearer {refresh_token}"}
+        )
+        assert response.status_code == 401
+
+
+class TestRefreshToken:
+    """POST /auth/refresh"""
+
+    def test_valid_refresh_token_returns_new_tokens(self, client, mock_db):
+        """A valid refresh token should issue new access and refresh tokens."""
+        user = _make_regular_user()
+        mock_db.get_user_by_id.return_value = user
+        refresh = create_refresh_token(user["id"], user["email"], user["role"])
+
+        response = client.post(
+            "/auth/refresh", json={"refresh_token": refresh}
+        )
+
+        assert response.status_code == 200
+        data = response.json()
+        assert "access_token" in data
+        assert "refresh_token" in data
+
+    def test_invalid_refresh_token_returns_401(self, client, mock_db):
+        """An invalid refresh token should return 401."""
+        response = client.post(
+            "/auth/refresh", json={"refresh_token": "invalid-token-string"}
+        )
+        assert response.status_code == 401
+
+    def test_access_token_as_refresh_returns_401(self, client, mock_db):
+        """Using an access token as a refresh token should return 401."""
+        user = _make_regular_user()
+        access = create_access_token(user["id"], user["email"], user["role"])
+
+        response = client.post(
+            "/auth/refresh", json={"refresh_token": access}
+        )
+        assert response.status_code == 401
+
+
+class TestAdminUsers:
+    """GET /admin/users and PATCH /admin/users/{id}/role"""
+
+    def test_admin_can_list_users(self, client, mock_db):
+        """Admin token should allow listing users."""
+        admin = _make_admin_user()
+        mock_db.get_user_by_id.return_value = admin
+        mock_db.get_all_users.return_value = [admin, _make_regular_user()]
+
+        response = client.get("/admin/users", headers=_auth_header(admin))
+
+        assert response.status_code == 200
+        data = response.json()
+        assert len(data) == 2
+
+    def test_regular_user_cannot_list_users(self, client, mock_db):
+        """Regular user token should be rejected with 403."""
+        user = _make_regular_user()
+        mock_db.get_user_by_id.return_value = user
+
+        response = client.get("/admin/users", headers=_auth_header(user))
+
+        assert response.status_code == 403
+
+    def test_no_token_cannot_list_users(self, client):
+        """No token should be rejected."""
+        response = client.get("/admin/users")
+        assert response.status_code in (401, 403)
+
+    def test_admin_can_change_user_role(self, client, mock_db):
+        """Admin should be able to change another user's role."""
+        admin = _make_admin_user()
+        mock_db.get_user_by_id.return_value = admin
+        mock_db.update_user_role.return_value = {
+            "id": 2,
+            "email": "user@test.com",
+            "role": "admin",
+            "created_at": datetime(2025, 1, 1, tzinfo=timezone.utc),
+        }
+
+        response = client.patch(
+            "/admin/users/2/role",
+            json={"role": "admin"},
+            headers=_auth_header(admin),
+        )
+
+        assert response.status_code == 200
+        assert response.json()["role"] == "admin"
+
+    def test_admin_cannot_change_own_role(self, client, mock_db):
+        """Admin should not be able to change their own role."""
+        admin = _make_admin_user()
+        mock_db.get_user_by_id.return_value = admin
+
+        response = client.patch(
+            "/admin/users/1/role",
+            json={"role": "user"},
+            headers=_auth_header(admin),
+        )
+
+        assert response.status_code == 400
+        assert "own role" in response.json()["detail"].lower()

tests/test_llm.py

@@ -1,7 +1,9 @@
 """Tests for LLM analysis functionality."""
 
+from unittest.mock import Mock
+
 import pytest
-from unittest.mock import Mock, MagicMock, patch
+
 from SPARC.llm import LLMAnalyzer
 
 

tests/test_rate_limit.py

@@ -0,0 +1,97 @@
+"""Tests for rate limiting on auth endpoints."""
+
+import pytest
+from unittest.mock import Mock, patch, MagicMock
+from fastapi.testclient import TestClient
+
+from SPARC.api import app
+
+
+@pytest.fixture
+def client():
+    """Create test client with rate limiter enabled."""
+    return TestClient(app)
+
+
+@pytest.fixture(autouse=True)
+def reset_limiter():
+    """Reset rate limiter storage between tests."""
+    from SPARC.api import limiter
+    limiter.reset()
+    yield
+
+
+class TestRateLimiting:
+    """Test rate limiting on login and register endpoints."""
+
+    @patch("SPARC.api.get_db_client")
+    def test_login_allows_requests_under_limit(self, mock_db_client, client):
+        """Login endpoint allows requests under the rate limit."""
+        mock_db = MagicMock()
+        mock_db.authenticate_user.return_value = None
+        mock_db_client.return_value = mock_db
+
+        # Should allow at least a few requests
+        for _ in range(5):
+            response = client.post(
+                "/auth/login",
+                json={"email": "test@example.com", "password": "password123"},
+            )
+            # 401 is expected (invalid credentials), not 429
+            assert response.status_code == 401
+
+    @patch("SPARC.api.get_db_client")
+    def test_login_rate_limited_after_threshold(self, mock_db_client, client):
+        """Login endpoint returns 429 after exceeding rate limit."""
+        mock_db = MagicMock()
+        mock_db.authenticate_user.return_value = None
+        mock_db_client.return_value = mock_db
+
+        # Send more than the limit (10/minute)
+        statuses = []
+        for _ in range(15):
+            response = client.post(
+                "/auth/login",
+                json={"email": "test@example.com", "password": "password123"},
+            )
+            statuses.append(response.status_code)
+
+        # At least one should be 429
+        assert 429 in statuses, f"Expected 429 in statuses but got: {set(statuses)}"
+
+    @patch("SPARC.api.get_db_client")
+    def test_register_rate_limited_after_threshold(self, mock_db_client, client):
+        """Register endpoint returns 429 after exceeding rate limit."""
+        mock_db = MagicMock()
+        mock_db.get_user_count.return_value = 1
+        mock_db.create_user.return_value = None  # triggers 400 (email exists)
+        mock_db_client.return_value = mock_db
+
+        # Send more than the limit (5/minute)
+        statuses = []
+        for _ in range(10):
+            response = client.post(
+                "/auth/register",
+                json={"email": "test@example.com", "password": "password123"},
+            )
+            statuses.append(response.status_code)
+
+        # At least one should be 429
+        assert 429 in statuses, f"Expected 429 in statuses but got: {set(statuses)}"
+
+    @patch("SPARC.api.get_db_client")
+    def test_rate_limit_returns_retry_after_header(self, mock_db_client, client):
+        """Rate limited responses include a Retry-After header."""
+        mock_db = MagicMock()
+        mock_db.authenticate_user.return_value = None
+        mock_db_client.return_value = mock_db
+
+        # Exhaust the limit
+        for _ in range(15):
+            response = client.post(
+                "/auth/login",
+                json={"email": "test@example.com", "password": "password123"},
+            )
+            if response.status_code == 429:
+                assert "Retry-After" in response.headers
+                break

tests/test_security.py

@@ -0,0 +1,116 @@
+"""Tests for security hardening: JWT secret startup check, CORS config, credential handling."""
+
+import os
+from unittest.mock import patch
+
+import pytest
+
+
+class TestJWTSecretStartupCheck:
+    """Test the startup guard that refuses default JWT secret in non-dev environments."""
+
+    def test_default_secret_in_production_raises(self):
+        """Starting with default secret and APP_ENV=production must raise RuntimeError."""
+        with patch.dict(os.environ, {"APP_ENV": "production"}):
+            # Reload config to pick up the new APP_ENV
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+
+            from SPARC.auth import _DEFAULT_JWT_SECRET, check_jwt_secret
+            # Patch JWT_SECRET to the default
+            with patch("SPARC.auth.JWT_SECRET", _DEFAULT_JWT_SECRET):
+                with pytest.raises(RuntimeError, match="FATAL.*JWT_SECRET"):
+                    check_jwt_secret()
+
+            # Restore config
+            with patch.dict(os.environ, {"APP_ENV": "development"}):
+                importlib.reload(SPARC.config)
+
+    def test_default_secret_in_development_succeeds(self):
+        """Starting with default secret and APP_ENV=development must not raise."""
+        with patch.dict(os.environ, {"APP_ENV": "development"}):
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+
+            from SPARC.auth import _DEFAULT_JWT_SECRET, check_jwt_secret
+            with patch("SPARC.auth.JWT_SECRET", _DEFAULT_JWT_SECRET):
+                # Should not raise
+                check_jwt_secret()
+
+            # Restore
+            importlib.reload(SPARC.config)
+
+    def test_custom_secret_in_production_succeeds(self):
+        """Starting with a custom secret in production must not raise."""
+        with patch.dict(os.environ, {"APP_ENV": "production"}):
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+
+            from SPARC.auth import check_jwt_secret
+            with patch("SPARC.auth.JWT_SECRET", "my-secure-random-secret-abc123"):
+                # Should not raise
+                check_jwt_secret()
+
+            with patch.dict(os.environ, {"APP_ENV": "development"}):
+                importlib.reload(SPARC.config)
+
+    def test_default_secret_unset_env_succeeds(self):
+        """When APP_ENV is unset (defaults to development), default secret is allowed."""
+        with patch.dict(os.environ, {}, clear=False):
+            # Remove APP_ENV if present
+            env = os.environ.copy()
+            env.pop("APP_ENV", None)
+            with patch.dict(os.environ, env, clear=True):
+                import importlib
+                import SPARC.config
+                importlib.reload(SPARC.config)
+
+                from SPARC.auth import _DEFAULT_JWT_SECRET, check_jwt_secret
+                with patch("SPARC.auth.JWT_SECRET", _DEFAULT_JWT_SECRET):
+                    # Should not raise (defaults to development)
+                    check_jwt_secret()
+
+                with patch.dict(os.environ, {"APP_ENV": "development"}):
+                    importlib.reload(SPARC.config)
+
+
+class TestCORSConfig:
+    """Test that CORS origins are configurable via environment variable."""
+
+    def test_default_cors_origins(self):
+        """When CORS_ORIGINS is unset, defaults to localhost origins."""
+        with patch.dict(os.environ, {"CORS_ORIGINS": ""}):
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+            assert SPARC.config.cors_origins == [
+                "http://localhost:3000",
+                "http://localhost:5173",
+            ]
+
+    def test_custom_cors_origins(self):
+        """Setting CORS_ORIGINS configures allowed origins."""
+        with patch.dict(os.environ, {"CORS_ORIGINS": "https://sparc.example.com,https://app.example.com"}):
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+            assert SPARC.config.cors_origins == [
+                "https://sparc.example.com",
+                "https://app.example.com",
+            ]
+            # Restore
+            with patch.dict(os.environ, {"CORS_ORIGINS": ""}):
+                importlib.reload(SPARC.config)
+
+    def test_single_cors_origin(self):
+        """A single origin without comma works correctly."""
+        with patch.dict(os.environ, {"CORS_ORIGINS": "https://sparc.example.com"}):
+            import importlib
+            import SPARC.config
+            importlib.reload(SPARC.config)
+            assert SPARC.config.cors_origins == ["https://sparc.example.com"]
+            with patch.dict(os.environ, {"CORS_ORIGINS": ""}):
+                importlib.reload(SPARC.config)

tests/test_serp_api.py

@@ -1,9 +1,8 @@
 """Tests for SERP API patent retrieval and parsing functionality."""
 
-import os
-import pytest
-from unittest.mock import patch, Mock
 from datetime import datetime, timedelta
+from unittest.mock import Mock
+
 from SPARC.serp_api import SERP
 from SPARC.types import Patent