From 70f95632f9bb754de1a40f8137f364e5bbcf6c43 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 29 Sep 2025 19:59:49 -0400
Subject: [PATCH 1/9] feat: add backend infrastructure foundation

Creates the base infrastructure layer for BRC Analytics backend:
- FastAPI application with health and cache endpoints
- Redis caching service with TTL management
- Docker Compose setup (backend + redis + nginx)
- nginx reverse proxy configuration
- uv for dependency management
- Ruff formatting for Python code
- E2E health check tests

This branch serves as the foundation for feature branches to build upon.
---
 .gitignore                       |   5 +
 backend/.dockerignore            |  35 +++
 backend/.env.example             |  14 ++
 backend/Dockerfile               |  46 ++++
 backend/README.md                |  99 ++++++++
 backend/app/__init__.py          |   1 +
 backend/app/api/__init__.py      |   1 +
 backend/app/api/v1/__init__.py   |   1 +
 backend/app/api/v1/cache.py      |  31 +++
 backend/app/api/v1/health.py     |  16 ++
 backend/app/core/__init__.py     |   1 +
 backend/app/core/cache.py        | 118 ++++++++++
 backend/app/core/config.py       |  34 +++
 backend/app/core/dependencies.py |  16 ++
 backend/app/main.py              |  31 +++
 backend/app/services/__init__.py |   1 +
 backend/pyproject.toml           |  32 +++
 backend/ruff.toml                |  12 +
 backend/uv.lock                  | 372 +++++++++++++++++++++++++++++++
 docker-compose.yml               |  58 +++++
 nginx.conf                       |  66 ++++++
 playwright.config.ts             |  39 ++++
 pyproject.toml                   |   1 +
 scripts/format-python.sh         |   4 +-
 tests/e2e/03-api-health.spec.ts  |  45 ++++
 25 files changed, 1077 insertions(+), 2 deletions(-)
 create mode 100644 backend/.dockerignore
 create mode 100644 backend/.env.example
 create mode 100644 backend/Dockerfile
 create mode 100644 backend/README.md
 create mode 100644 backend/app/__init__.py
 create mode 100644 backend/app/api/__init__.py
 create mode 100644 backend/app/api/v1/__init__.py
 create mode 100644 backend/app/api/v1/cache.py
 create mode 100644 backend/app/api/v1/health.py
 create mode 100644 backend/app/core/__init__.py
 create mode 100644 backend/app/core/cache.py
 create mode 100644 backend/app/core/config.py
 create mode 100644 backend/app/core/dependencies.py
 create mode 100644 backend/app/main.py
 create mode 100644 backend/app/services/__init__.py
 create mode 100644 backend/pyproject.toml
 create mode 100644 backend/ruff.toml
 create mode 100644 backend/uv.lock
 create mode 100644 docker-compose.yml
 create mode 100644 nginx.conf
 create mode 100644 playwright.config.ts
 create mode 100644 tests/e2e/03-api-health.spec.ts

diff --git a/.gitignore b/.gitignore
index fa70ebdbd..1c26dcfcf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,7 @@ npm-debug.log*
 /.env*.local
 /.env.development
 /.env.production
+backend/.env
 
 # typescript
 *.tsbuildinfo
@@ -32,6 +33,10 @@ npm-debug.log*
 # Build Dir
 /out
 
+# Playwright test artifacts
+/test-results
+/tests/screenshots
+
 # python
 venv
 __pycache__
diff --git a/backend/.dockerignore b/backend/.dockerignore
new file mode 100644
index 000000000..34842948c
--- /dev/null
+++ b/backend/.dockerignore
@@ -0,0 +1,35 @@
+# Python
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+.pytest_cache
+.mypy_cache
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Git
+.git
+.gitignore
+
+# Documentation
+*.md
+docs/
+
+# Tests
+tests/
\ No newline at end of file
diff --git a/backend/.env.example b/backend/.env.example
new file mode 100644
index 000000000..f786a7588
--- /dev/null
+++ b/backend/.env.example
@@ -0,0 +1,14 @@
+# Redis Configuration
+REDIS_URL=redis://redis:6379/0
+
+# Database Configuration (for future use)
+DATABASE_URL=postgresql://user:pass@localhost/dbname
+
+# Application Configuration
+CORS_ORIGINS=http://localhost:3000,http://localhost
+LOG_LEVEL=INFO
+ENVIRONMENT=development
+
+# Rate Limiting
+RATE_LIMIT_REQUESTS=100
+RATE_LIMIT_WINDOW=60
\ No newline at end of file
diff --git a/backend/Dockerfile b/backend/Dockerfile
new file mode 100644
index 000000000..def55cdcf
--- /dev/null
+++ b/backend/Dockerfile
@@ -0,0 +1,46 @@
+# Multi-stage build for uv-based Python application
+FROM python:3.12-slim as builder
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+WORKDIR /app
+
+# Copy dependency files
+COPY pyproject.toml uv.lock ./
+
+# Install dependencies into .venv
+RUN uv sync --frozen --no-install-project
+
+# Production stage
+FROM python:3.12-slim as runtime
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy uv for runtime
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Create non-root user
+RUN useradd --create-home --shell /bin/bash app
+
+WORKDIR /app
+
+# Copy virtual environment from builder
+COPY --from=builder /app/.venv /app/.venv
+
+# Add venv to PATH
+ENV PATH="/app/.venv/bin:$PATH"
+
+# Copy application code
+COPY . .
+
+# Change ownership
+RUN chown -R app:app /app
+USER app
+
+EXPOSE 8000
+
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"]
\ No newline at end of file
diff --git a/backend/README.md b/backend/README.md
new file mode 100644
index 000000000..6f5a8d441
--- /dev/null
+++ b/backend/README.md
@@ -0,0 +1,99 @@
+# BRC Analytics Backend
+
+FastAPI backend infrastructure for BRC Analytics.
+
+## Features
+
+- FastAPI REST API
+- Redis caching with TTL support
+- Health check endpoints
+- Docker deployment with nginx reverse proxy
+- uv for dependency management
+
+## Quick Start
+
+### Development (Local)
+
+```bash
+cd backend
+uv sync
+uv run uvicorn app.main:app --reload
+```
+
+API documentation: http://localhost:8000/api/docs
+
+### Production (Docker)
+
+```bash
+# Create environment file
+cp backend/.env.example backend/.env
+# Edit backend/.env if needed (defaults work for local development)
+
+# Start all services (nginx + backend + redis)
+docker compose up -d
+
+# Check service health
+curl http://localhost/api/v1/health
+
+# View logs
+docker compose logs -f backend
+
+# Rebuild after code changes
+docker compose up -d --build
+
+# Stop all services
+docker compose down
+```
+
+Services:
+
+- nginx: http://localhost (reverse proxy)
+- backend API: http://localhost:8000 (direct access)
+- API docs: http://localhost/api/docs
+- redis: localhost:6379
+
+## API Endpoints
+
+### Health & Monitoring
+
+- `GET /api/v1/health` - Overall service health status
+- `GET /api/v1/cache/health` - Redis cache connectivity check
+
+### Documentation
+
+- `GET /api/docs` - Interactive Swagger UI
+- `GET /api/redoc` - ReDoc API documentation
+
+## Configuration
+
+Environment variables (see `.env.example`):
+
+```bash
+# Redis
+REDIS_URL=redis://localhost:6379/0
+
+# Application
+CORS_ORIGINS=http://localhost:3000,http://localhost
+LOG_LEVEL=INFO
+```
+
+## Testing
+
+```bash
+# Run e2e tests
+npm run test:e2e
+
+# Or with Playwright directly
+npx playwright test tests/e2e/03-api-health.spec.ts
+```
+
+## Architecture
+
+```
+nginx (port 80)
+  ├── /api/* → FastAPI backend (port 8000)
+  └── /* → Next.js static files
+
+FastAPI backend
+  └── Redis cache (port 6379)
+```
diff --git a/backend/app/__init__.py b/backend/app/__init__.py
new file mode 100644
index 000000000..4c10750f2
--- /dev/null
+++ b/backend/app/__init__.py
@@ -0,0 +1 @@
+# BRC Analytics Backend
diff --git a/backend/app/api/__init__.py b/backend/app/api/__init__.py
new file mode 100644
index 000000000..28b07eff6
--- /dev/null
+++ b/backend/app/api/__init__.py
@@ -0,0 +1 @@
+# API package
diff --git a/backend/app/api/v1/__init__.py b/backend/app/api/v1/__init__.py
new file mode 100644
index 000000000..6c2f33cb2
--- /dev/null
+++ b/backend/app/api/v1/__init__.py
@@ -0,0 +1 @@
+# API v1 package
diff --git a/backend/app/api/v1/cache.py b/backend/app/api/v1/cache.py
new file mode 100644
index 000000000..82d8a30c7
--- /dev/null
+++ b/backend/app/api/v1/cache.py
@@ -0,0 +1,31 @@
+from fastapi import APIRouter, Depends, HTTPException
+
+from app.core.cache import CacheService
+from app.core.dependencies import get_cache_service
+
+router = APIRouter()
+
+
+@router.get("/health")
+async def cache_health(cache: CacheService = Depends(get_cache_service)):
+    """Check if cache service is healthy"""
+    try:
+        # Try to set and get a test value
+        test_key = "health_check"
+        test_value = "ok"
+
+        await cache.set(test_key, test_value, ttl=60)
+        result = await cache.get(test_key)
+        await cache.delete(test_key)
+
+        if result == test_value:
+            return {"status": "healthy", "cache": "connected"}
+        else:
+            raise HTTPException(
+                status_code=503, detail="Cache service not responding correctly"
+            )
+
+    except Exception as e:
+        raise HTTPException(
+            status_code=503, detail=f"Cache service unhealthy: {str(e)}"
+        )
diff --git a/backend/app/api/v1/health.py b/backend/app/api/v1/health.py
new file mode 100644
index 000000000..53bfd9ea5
--- /dev/null
+++ b/backend/app/api/v1/health.py
@@ -0,0 +1,16 @@
+from datetime import datetime
+
+from fastapi import APIRouter
+
+router = APIRouter()
+
+
+@router.get("/health")
+async def health_check():
+    """Health check endpoint for monitoring system status"""
+    return {
+        "status": "healthy",
+        "version": "1.0.0",
+        "timestamp": datetime.utcnow().isoformat(),
+        "service": "BRC Analytics API",
+    }
diff --git a/backend/app/core/__init__.py b/backend/app/core/__init__.py
new file mode 100644
index 000000000..d61a2551c
--- /dev/null
+++ b/backend/app/core/__init__.py
@@ -0,0 +1 @@
+# Core package
diff --git a/backend/app/core/cache.py b/backend/app/core/cache.py
new file mode 100644
index 000000000..bcec835b5
--- /dev/null
+++ b/backend/app/core/cache.py
@@ -0,0 +1,118 @@
+import hashlib
+import json
+import logging
+from datetime import timedelta
+from typing import Any, Dict, Optional
+
+import redis.asyncio as redis
+
+logger = logging.getLogger(__name__)
+
+
+class CacheService:
+    """Redis-based cache service with TTL support and key management"""
+
+    def __init__(self, redis_url: str):
+        self.redis = redis.from_url(redis_url, decode_responses=True)
+
+    async def get(self, key: str) -> Optional[Any]:
+        """Get a value from cache by key"""
+        try:
+            value = await self.redis.get(key)
+            if value:
+                return json.loads(value)
+            return None
+        except (redis.RedisError, json.JSONDecodeError) as e:
+            logger.error(f"Cache get error for key {key}: {e}")
+            return None
+
+    async def set(self, key: str, value: Any, ttl: int = 3600) -> bool:
+        """Set a value in cache with TTL (time to live) in seconds"""
+        try:
+            serialized_value = json.dumps(value, default=str)
+            await self.redis.setex(key, ttl, serialized_value)
+            return True
+        except (redis.RedisError, TypeError) as e:
+            logger.error(f"Cache set error for key {key}: {e}")
+            return False
+
+    async def delete(self, key: str) -> bool:
+        """Delete a key from cache"""
+        try:
+            result = await self.redis.delete(key)
+            return result > 0
+        except redis.RedisError as e:
+            logger.error(f"Cache delete error for key {key}: {e}")
+            return False
+
+    async def exists(self, key: str) -> bool:
+        """Check if key exists in cache"""
+        try:
+            return await self.redis.exists(key) > 0
+        except redis.RedisError as e:
+            logger.error(f"Cache exists error for key {key}: {e}")
+            return False
+
+    async def get_ttl(self, key: str) -> int:
+        """Get remaining TTL for a key (-1 if no TTL, -2 if key doesn't exist)"""
+        try:
+            return await self.redis.ttl(key)
+        except redis.RedisError as e:
+            logger.error(f"Cache TTL error for key {key}: {e}")
+            return -2
+
+    async def clear_pattern(self, pattern: str) -> int:
+        """Clear all keys matching a pattern"""
+        try:
+            keys = await self.redis.keys(pattern)
+            if keys:
+                return await self.redis.delete(*keys)
+            return 0
+        except redis.RedisError as e:
+            logger.error(f"Cache clear pattern error for {pattern}: {e}")
+            return 0
+
+    async def get_stats(self) -> Dict[str, Any]:
+        """Get cache statistics"""
+        try:
+            info = await self.redis.info()
+            return {
+                "hits": info.get("keyspace_hits", 0),
+                "misses": info.get("keyspace_misses", 0),
+                "hit_rate": self._calculate_hit_rate(info),
+                "memory_used": info.get("used_memory_human", "0B"),
+                "memory_used_bytes": info.get("used_memory", 0),
+                "keys_count": await self.redis.dbsize(),
+                "connected_clients": info.get("connected_clients", 0),
+            }
+        except redis.RedisError as e:
+            logger.error(f"Cache stats error: {e}")
+            return {}
+
+    def _calculate_hit_rate(self, info: Dict) -> float:
+        """Calculate cache hit rate from Redis info"""
+        hits = info.get("keyspace_hits", 0)
+        misses = info.get("keyspace_misses", 0)
+        total = hits + misses
+        return (hits / total) if total > 0 else 0.0
+
+    def make_key(self, prefix: str, params: Dict[str, Any]) -> str:
+        """Generate a cache key from prefix and parameters"""
+        # Sort parameters for consistent keys
+        param_str = json.dumps(params, sort_keys=True, default=str)
+        hash_val = hashlib.md5(param_str.encode()).hexdigest()[:16]
+        return f"{prefix}:{hash_val}"
+
+    async def close(self):
+        """Close Redis connection"""
+        await self.redis.close()
+
+
+# Cache TTL constants (in seconds)
+class CacheTTL:
+    FIVE_MINUTES = 300
+    ONE_HOUR = 3600
+    SIX_HOURS = 21600
+    ONE_DAY = 86400
+    ONE_WEEK = 604800
+    THIRTY_DAYS = 2592000
diff --git a/backend/app/core/config.py b/backend/app/core/config.py
new file mode 100644
index 000000000..eaa875b06
--- /dev/null
+++ b/backend/app/core/config.py
@@ -0,0 +1,34 @@
+import os
+from functools import lru_cache
+from typing import List
+
+
+class Settings:
+    """Application settings loaded from environment variables"""
+
+    # Redis settings
+    REDIS_URL: str = os.getenv("REDIS_URL", "redis://localhost:6379/0")
+
+    # Database settings (for future use)
+    DATABASE_URL: str = os.getenv("DATABASE_URL", "")
+
+    # CORS settings
+    CORS_ORIGINS: List[str] = os.getenv("CORS_ORIGINS", "http://localhost:3000").split(
+        ","
+    )
+
+    # Logging
+    LOG_LEVEL: str = os.getenv("LOG_LEVEL", "INFO")
+
+    # Environment
+    ENVIRONMENT: str = os.getenv("ENVIRONMENT", "development")
+
+    # Rate limiting
+    RATE_LIMIT_REQUESTS: int = int(os.getenv("RATE_LIMIT_REQUESTS", "100"))
+    RATE_LIMIT_WINDOW: int = int(os.getenv("RATE_LIMIT_WINDOW", "60"))  # seconds
+
+
+@lru_cache()
+def get_settings() -> Settings:
+    """Get cached settings instance"""
+    return Settings()
diff --git a/backend/app/core/dependencies.py b/backend/app/core/dependencies.py
new file mode 100644
index 000000000..b49924b6b
--- /dev/null
+++ b/backend/app/core/dependencies.py
@@ -0,0 +1,16 @@
+from functools import lru_cache
+
+from app.core.cache import CacheService
+from app.core.config import get_settings
+
+# Global cache service instance
+_cache_service = None
+
+
+async def get_cache_service() -> CacheService:
+    """Dependency to get cache service instance"""
+    global _cache_service
+    if _cache_service is None:
+        settings = get_settings()
+        _cache_service = CacheService(settings.REDIS_URL)
+    return _cache_service
diff --git a/backend/app/main.py b/backend/app/main.py
new file mode 100644
index 000000000..0beec7e0f
--- /dev/null
+++ b/backend/app/main.py
@@ -0,0 +1,31 @@
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+
+from app.api.v1 import cache, health
+from app.core.config import get_settings
+
+settings = get_settings()
+
+app = FastAPI(
+    title="BRC Analytics API",
+    version="1.0.0",
+    docs_url="/api/docs",
+    redoc_url="/api/redoc",
+)
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=settings.CORS_ORIGINS,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+# Include routers
+app.include_router(health.router, prefix="/api/v1", tags=["health"])
+app.include_router(cache.router, prefix="/api/v1/cache", tags=["cache"])
+
+
+@app.get("/")
+async def root():
+    return {"message": "BRC Analytics API", "version": "1.0.0"}
diff --git a/backend/app/services/__init__.py b/backend/app/services/__init__.py
new file mode 100644
index 000000000..a70b3029a
--- /dev/null
+++ b/backend/app/services/__init__.py
@@ -0,0 +1 @@
+# Services package
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
new file mode 100644
index 000000000..c9474e351
--- /dev/null
+++ b/backend/pyproject.toml
@@ -0,0 +1,32 @@
+[project]
+name = "brc-analytics-backend"
+version = "0.1.0"
+description = "FastAPI backend infrastructure for BRC Analytics"
+authors = [
+    {name = "BRC Team"}
+]
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "fastapi>=0.116.1",
+    "uvicorn>=0.35.0",
+    "redis>=6.4.0",
+    "httpx>=0.28.1",
+    "pydantic>=2.11.7",
+    "python-dotenv>=1.1.1"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.4.1",
+    "pytest-asyncio>=1.1.0",
+    "ruff>=0.13.0"
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["app"]
+
diff --git a/backend/ruff.toml b/backend/ruff.toml
new file mode 100644
index 000000000..bf02cb1b1
--- /dev/null
+++ b/backend/ruff.toml
@@ -0,0 +1,12 @@
+# Ruff configuration for backend
+# This prevents ruff from trying to parse poetry's pyproject.toml
+target-version = "py312"
+line-length = 88
+
+[format]
+quote-style = "double"
+indent-style = "space"
+
+[lint]
+select = ["E", "F", "I", "B"]
+fixable = ["ALL"]
diff --git a/backend/uv.lock b/backend/uv.lock
new file mode 100644
index 000000000..a96f5410f
--- /dev/null
+++ b/backend/uv.lock
@@ -0,0 +1,372 @@
+version = 1
+revision = 3
+requires-python = ">=3.12"
+
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/ee/67/531ea369ba64dcff5ec9c3402f9f51bf748cec26dde048a2f973a4eea7f5/annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89", size = 16081, upload-time = "2024-05-20T21:33:25.928Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643, upload-time = "2024-05-20T21:33:24.1Z" },
+]
+
+[[package]]
+name = "anyio"
+version = "4.11.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "idna" },
+    { name = "sniffio" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/c6/78/7d432127c41b50bccba979505f272c16cbcadcc33645d5fa3a738110ae75/anyio-4.11.0.tar.gz", hash = "sha256:82a8d0b81e318cc5ce71a5f1f8b5c4e63619620b63141ef8c995fa0db95a57c4", size = 219094, upload-time = "2025-09-23T09:19:12.58Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/15/b3/9b1a8074496371342ec1e796a96f99c82c945a339cd81a8e73de28b4cf9e/anyio-4.11.0-py3-none-any.whl", hash = "sha256:0287e96f4d26d4149305414d4e3bc32f0dcd0862365a4bddea19d7a1ec38c4fc", size = 109097, upload-time = "2025-09-23T09:19:10.601Z" },
+]
+
+[[package]]
+name = "brc-analytics-backend"
+version = "0.1.0"
+source = { editable = "." }
+dependencies = [
+    { name = "fastapi" },
+    { name = "httpx" },
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+[[package]]
+name = "starlette"
+version = "0.48.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "anyio" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
+]
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+wheels = [
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+name = "typing-extensions"
+version = "4.15.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/72/94/1a15dd82efb362ac84269196e94cf00f187f7ed21c242792a923cdb1c61f/typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466", size = 109391, upload-time = "2025-08-25T13:49:26.313Z" }
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+[[package]]
+name = "typing-inspection"
+version = "0.4.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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+]
+sdist = { url = "https://files.pythonhosted.org/packages/55/e3/70399cb7dd41c10ac53367ae42139cf4b1ca5f36bb3dc6c9d33acdb43655/typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464", size = 75949, upload-time = "2025-10-01T02:14:41.687Z" }
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+[[package]]
+name = "uvicorn"
+version = "0.37.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "click" },
+    { name = "h11" },
+]
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+wheels = [
+    { url = "https://files.pythonhosted.org/packages/85/cd/584a2ceb5532af99dd09e50919e3615ba99aa127e9850eafe5f31ddfdb9a/uvicorn-0.37.0-py3-none-any.whl", hash = "sha256:913b2b88672343739927ce381ff9e2ad62541f9f8289664fa1d1d3803fa2ce6c", size = 67976, upload-time = "2025-09-23T13:33:45.842Z" },
+]
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 000000000..5998b6b52
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,58 @@
+services:
+  nginx:
+    image: nginx:alpine
+    ports:
+      - "80:80"
+    volumes:
+      - ./nginx.conf:/etc/nginx/conf.d/default.conf
+      - ./out:/usr/share/nginx/html
+    depends_on:
+      backend:
+        condition: service_healthy
+    restart: unless-stopped
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:80/api/v1/health"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+
+  backend:
+    build:
+      context: ./backend
+      dockerfile: Dockerfile
+    ports:
+      - "8000:8000"
+    env_file:
+      - ./backend/.env
+    environment:
+      # Only override what needs Docker networking
+      REDIS_URL: redis://redis:6379/0
+    depends_on:
+      redis:
+        condition: service_healthy
+    restart: unless-stopped
+    extra_hosts:
+      - "host.docker.internal:host-gateway"
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:8000/api/v1/health"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+
+  redis:
+    image: redis:7-alpine
+    ports:
+      - "6379:6379"
+    command: redis-server --appendonly yes --maxmemory 256mb --maxmemory-policy allkeys-lru
+    volumes:
+      - redis_data:/data
+    restart: unless-stopped
+    healthcheck:
+      test: ["CMD", "redis-cli", "ping"]
+      interval: 15s
+      timeout: 5s
+      retries: 3
+      start_period: 10s
+
+volumes:
+  redis_data:
diff --git a/nginx.conf b/nginx.conf
new file mode 100644
index 000000000..d4371d099
--- /dev/null
+++ b/nginx.conf
@@ -0,0 +1,66 @@
+upstream backend {
+    server backend:8000;
+}
+
+server {
+    listen 80;
+    server_name localhost;
+
+    # Gzip compression
+    gzip on;
+    gzip_vary on;
+    gzip_min_length 1024;
+    gzip_types
+        application/json
+        application/javascript
+        text/css
+        text/javascript
+        text/plain
+        text/xml;
+
+    # Security headers
+    add_header X-Content-Type-Options nosniff;
+    add_header X-Frame-Options DENY;
+    add_header X-XSS-Protection "1; mode=block";
+
+    # API routes - proxy to FastAPI backend
+    location /api {
+        proxy_pass http://backend;
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection 'upgrade';
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+        proxy_cache_bypass $http_upgrade;
+        proxy_read_timeout 300;
+        proxy_connect_timeout 300;
+        proxy_send_timeout 300;
+    }
+
+    # Static files - serve Next.js build output
+    location / {
+        root /usr/share/nginx/html;
+        try_files $uri $uri.html $uri/ /index.html;
+        
+        # Cache static assets
+        location ~* \.(css|js|jpg|jpeg|png|gif|ico|svg|woff|woff2|ttf|eot)$ {
+            expires 1y;
+            add_header Cache-Control "public, immutable";
+        }
+        
+        # Cache HTML files for a shorter period
+        location ~* \.html$ {
+            expires 1h;
+            add_header Cache-Control "public";
+        }
+    }
+
+    # Health check endpoint
+    location /health {
+        access_log off;
+        return 200 "healthy\n";
+        add_header Content-Type text/plain;
+    }
+}
\ No newline at end of file
diff --git a/playwright.config.ts b/playwright.config.ts
new file mode 100644
index 000000000..a6b16332d
--- /dev/null
+++ b/playwright.config.ts
@@ -0,0 +1,39 @@
+import { defineConfig, devices } from "@playwright/test";
+
+/**
+ * Playwright configuration for BRC Analytics tests
+ */
+export default defineConfig({
+  forbidOnly: !!process.env.CI,
+  fullyParallel: false,
+  projects: [
+    {
+      name: "chromium",
+      use: { ...devices["Desktop Chrome"] },
+    },
+  ],
+  reporter: "html",
+  retries: process.env.CI ? 2 : 0,
+  testDir: "./tests/e2e",
+  use: {
+    baseURL: "http://localhost:3000",
+    screenshot: "only-on-failure",
+    trace: "on-first-retry",
+    video: "retain-on-failure",
+  },
+  webServer: [
+    {
+      command: "npm run dev",
+      reuseExistingServer: true,
+      timeout: 120 * 1000,
+      url: "http://localhost:3000",
+    },
+    {
+      command: "docker-compose up",
+      reuseExistingServer: true,
+      timeout: 120 * 1000,
+      url: "http://localhost:8000/api/v1/health",
+    },
+  ],
+  workers: 1,
+});
diff --git a/pyproject.toml b/pyproject.toml
index d2cd8cad6..e69f26a1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,7 @@
 target-version = "py38"
 line-length = 88
 indent-width = 4
+extend-exclude = ["backend/pyproject.toml", "backend/poetry.lock"]
 
 [tool.ruff.format]
 quote-style = "double"
diff --git a/scripts/format-python.sh b/scripts/format-python.sh
index 960f7ed55..93f7400bb 100755
--- a/scripts/format-python.sh
+++ b/scripts/format-python.sh
@@ -2,11 +2,11 @@
 
 # Format Python files using Ruff (Rust-based formatter)
 echo "Formatting Python files with Ruff..."
-ruff format catalog/
+ruff format catalog/ backend/
 
 # Sort imports with Ruff
 echo "Sorting imports with Ruff..."
-ruff check --select I --fix catalog/
+ruff check --select I --fix catalog/ backend/
 
 # Exit with Ruff's status code
 exit $?
\ No newline at end of file
diff --git a/tests/e2e/03-api-health.spec.ts b/tests/e2e/03-api-health.spec.ts
new file mode 100644
index 000000000..614c6743c
--- /dev/null
+++ b/tests/e2e/03-api-health.spec.ts
@@ -0,0 +1,45 @@
+import { test, expect } from "@playwright/test";
+
+test.describe("BRC Analytics - API Infrastructure", () => {
+  test("backend API should be healthy", async ({ request }) => {
+    // Check backend health endpoint
+    const response = await request.get("http://localhost:8000/api/v1/health");
+    expect(response.ok()).toBeTruthy();
+
+    const health = await response.json();
+    expect(health.status).toBe("healthy");
+    expect(health.service).toBe("BRC Analytics API");
+    console.log("Backend health:", health);
+  });
+
+  test("cache health check should work", async ({ request }) => {
+    // Check cache health endpoint
+    const response = await request.get(
+      "http://localhost:8000/api/v1/cache/health"
+    );
+    expect(response.ok()).toBeTruthy();
+
+    const health = await response.json();
+    expect(health.status).toBe("healthy");
+    expect(health.cache).toBe("connected");
+    console.log("Cache health:", health);
+  });
+
+  test("API documentation should be accessible", async ({ page }) => {
+    // Navigate to API docs
+    await page.goto("http://localhost:8000/api/docs");
+
+    // Check that Swagger UI loaded
+    await expect(page.locator(".swagger-ui")).toBeVisible({ timeout: 10000 });
+
+    // Check for API title
+    const title = page.locator(".title");
+    await expect(title).toContainText("BRC Analytics API");
+
+    // Screenshot the API docs
+    await page.screenshot({
+      fullPage: true,
+      path: "tests/screenshots/api-docs.png",
+    });
+  });
+});

From 91cf035e8bfe925e70709d0399eca391926e70fb Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 5 Oct 2025 12:40:50 -0400
Subject: [PATCH 2/9] feat: add version endpoint for API metadata

Adds GET /api/v1/version endpoint that returns:
- API version (from APP_VERSION env var)
- Environment (development/production)
- Service name

This provides a simple way for the frontend to display version info
and demonstrates the backend infrastructure is working.
---
 backend/README.md               |  1 +
 backend/app/api/v1/version.py   | 16 ++++++++++++++++
 backend/app/core/config.py      |  3 +++
 backend/app/main.py             |  3 ++-
 tests/e2e/03-api-health.spec.ts | 12 ++++++++++++
 5 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 backend/app/api/v1/version.py

diff --git a/backend/README.md b/backend/README.md
index 6f5a8d441..59dd36564 100644
--- a/backend/README.md
+++ b/backend/README.md
@@ -58,6 +58,7 @@ Services:
 
 - `GET /api/v1/health` - Overall service health status
 - `GET /api/v1/cache/health` - Redis cache connectivity check
+- `GET /api/v1/version` - API version and environment information
 
 ### Documentation
 
diff --git a/backend/app/api/v1/version.py b/backend/app/api/v1/version.py
new file mode 100644
index 000000000..45845f339
--- /dev/null
+++ b/backend/app/api/v1/version.py
@@ -0,0 +1,16 @@
+from fastapi import APIRouter
+
+from app.core.config import get_settings
+
+router = APIRouter()
+settings = get_settings()
+
+
+@router.get("")
+async def get_version():
+    """Get API version and build information"""
+    return {
+        "version": settings.APP_VERSION,
+        "environment": settings.ENVIRONMENT,
+        "service": "BRC Analytics API",
+    }
diff --git a/backend/app/core/config.py b/backend/app/core/config.py
index eaa875b06..97a07dfcb 100644
--- a/backend/app/core/config.py
+++ b/backend/app/core/config.py
@@ -6,6 +6,9 @@
 class Settings:
     """Application settings loaded from environment variables"""
 
+    # Application
+    APP_VERSION: str = os.getenv("APP_VERSION", "1.0.0")
+
     # Redis settings
     REDIS_URL: str = os.getenv("REDIS_URL", "redis://localhost:6379/0")
 
diff --git a/backend/app/main.py b/backend/app/main.py
index 0beec7e0f..c5639b909 100644
--- a/backend/app/main.py
+++ b/backend/app/main.py
@@ -1,7 +1,7 @@
 from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 
-from app.api.v1 import cache, health
+from app.api.v1 import cache, health, version
 from app.core.config import get_settings
 
 settings = get_settings()
@@ -24,6 +24,7 @@
 # Include routers
 app.include_router(health.router, prefix="/api/v1", tags=["health"])
 app.include_router(cache.router, prefix="/api/v1/cache", tags=["cache"])
+app.include_router(version.router, prefix="/api/v1/version", tags=["version"])
 
 
 @app.get("/")
diff --git a/tests/e2e/03-api-health.spec.ts b/tests/e2e/03-api-health.spec.ts
index 614c6743c..d226146fc 100644
--- a/tests/e2e/03-api-health.spec.ts
+++ b/tests/e2e/03-api-health.spec.ts
@@ -25,6 +25,18 @@ test.describe("BRC Analytics - API Infrastructure", () => {
     console.log("Cache health:", health);
   });
 
+  test("version endpoint should return version info", async ({ request }) => {
+    // Check version endpoint
+    const response = await request.get("http://localhost:8000/api/v1/version");
+    expect(response.ok()).toBeTruthy();
+
+    const version = await response.json();
+    expect(version.version).toBeTruthy();
+    expect(version.environment).toBeTruthy();
+    expect(version.service).toBe("BRC Analytics API");
+    console.log("API version:", version);
+  });
+
   test("API documentation should be accessible", async ({ page }) => {
     // Navigate to API docs
     await page.goto("http://localhost:8000/api/docs");

From 0a9362896c1d5b46c1d442b986f8dae3ec8b8af2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 5 Oct 2025 13:28:25 -0400
Subject: [PATCH 3/9] feat: sync backend version from package.json

Use APP_VERSION build arg to inject version from package.json into
backend container. Adds docker-build.sh script to automate this.
All endpoints now use settings.APP_VERSION instead of hardcoded values.
---
 backend/Dockerfile           | 4 ++++
 backend/README.md            | 3 +++
 backend/app/api/v1/health.py | 5 ++++-
 backend/app/core/config.py   | 2 +-
 backend/app/main.py          | 4 ++--
 docker-compose.yml           | 2 ++
 scripts/docker-build.sh      | 8 ++++++++
 7 files changed, 24 insertions(+), 4 deletions(-)
 create mode 100755 scripts/docker-build.sh

diff --git a/backend/Dockerfile b/backend/Dockerfile
index def55cdcf..2ac07f53c 100644
--- a/backend/Dockerfile
+++ b/backend/Dockerfile
@@ -15,6 +15,10 @@ RUN uv sync --frozen --no-install-project
 # Production stage
 FROM python:3.12-slim as runtime
 
+# Accept version as build argument
+ARG APP_VERSION=0.15.0
+ENV APP_VERSION=${APP_VERSION}
+
 # Install system dependencies
 RUN apt-get update && apt-get install -y \
     curl \
diff --git a/backend/README.md b/backend/README.md
index 59dd36564..0d8cb8ade 100644
--- a/backend/README.md
+++ b/backend/README.md
@@ -29,6 +29,9 @@ API documentation: http://localhost:8000/api/docs
 cp backend/.env.example backend/.env
 # Edit backend/.env if needed (defaults work for local development)
 
+# Build with version from package.json
+./scripts/docker-build.sh
+
 # Start all services (nginx + backend + redis)
 docker compose up -d
 
diff --git a/backend/app/api/v1/health.py b/backend/app/api/v1/health.py
index 53bfd9ea5..47ee9ecaa 100644
--- a/backend/app/api/v1/health.py
+++ b/backend/app/api/v1/health.py
@@ -2,7 +2,10 @@
 
 from fastapi import APIRouter
 
+from app.core.config import get_settings
+
 router = APIRouter()
+settings = get_settings()
 
 
 @router.get("/health")
@@ -10,7 +13,7 @@ async def health_check():
     """Health check endpoint for monitoring system status"""
     return {
         "status": "healthy",
-        "version": "1.0.0",
+        "version": settings.APP_VERSION,
         "timestamp": datetime.utcnow().isoformat(),
         "service": "BRC Analytics API",
     }
diff --git a/backend/app/core/config.py b/backend/app/core/config.py
index 97a07dfcb..ef69175e9 100644
--- a/backend/app/core/config.py
+++ b/backend/app/core/config.py
@@ -7,7 +7,7 @@ class Settings:
     """Application settings loaded from environment variables"""
 
     # Application
-    APP_VERSION: str = os.getenv("APP_VERSION", "1.0.0")
+    APP_VERSION: str = os.getenv("APP_VERSION", "0.15.0")
 
     # Redis settings
     REDIS_URL: str = os.getenv("REDIS_URL", "redis://localhost:6379/0")
diff --git a/backend/app/main.py b/backend/app/main.py
index c5639b909..3d8521463 100644
--- a/backend/app/main.py
+++ b/backend/app/main.py
@@ -8,7 +8,7 @@
 
 app = FastAPI(
     title="BRC Analytics API",
-    version="1.0.0",
+    version=settings.APP_VERSION,
     docs_url="/api/docs",
     redoc_url="/api/redoc",
 )
@@ -29,4 +29,4 @@
 
 @app.get("/")
 async def root():
-    return {"message": "BRC Analytics API", "version": "1.0.0"}
+    return {"message": "BRC Analytics API", "version": settings.APP_VERSION}
diff --git a/docker-compose.yml b/docker-compose.yml
index 5998b6b52..eb0eced43 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -20,6 +20,8 @@ services:
     build:
       context: ./backend
       dockerfile: Dockerfile
+      args:
+        APP_VERSION: ${APP_VERSION:-0.15.0}
     ports:
       - "8000:8000"
     env_file:
diff --git a/scripts/docker-build.sh b/scripts/docker-build.sh
new file mode 100755
index 000000000..1c00d03df
--- /dev/null
+++ b/scripts/docker-build.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Build Docker images with version from package.json
+VERSION=$(node -p "require('./package.json').version")
+export APP_VERSION=$VERSION
+
+echo "Building with version: $VERSION"
+docker compose build "$@"

From 1a4024b1d344d6556740ca3245b4bc45177711c8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Oct 2025 10:14:53 -0400
Subject: [PATCH 4/9] feat: add version display in footer

---
 .gitignore                                    |  1 +
 .../Footer/components/Branding/branding.tsx   |  2 +
 .../VersionDisplay/versionDisplay.tsx         | 34 +++++++++++++++
 app/hooks/useBackendVersion.ts                | 24 +++++++++++
 site-config/brc-analytics/local/.env          |  1 +
 tests/e2e/04-version-display.spec.ts          | 42 +++++++++++++++++++
 6 files changed, 104 insertions(+)
 create mode 100644 app/components/Layout/components/Footer/components/Branding/components/VersionDisplay/versionDisplay.tsx
 create mode 100644 app/hooks/useBackendVersion.ts
 create mode 100644 tests/e2e/04-version-display.spec.ts

diff --git a/.gitignore b/.gitignore
index 1c26dcfcf..1c4efe3f9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,3 +40,4 @@ backend/.env
 # python
 venv
 __pycache__
+playwright-report/
diff --git a/app/components/Layout/components/Footer/components/Branding/branding.tsx b/app/components/Layout/components/Footer/components/Branding/branding.tsx
index c6e831789..52e0b0bd5 100644
--- a/app/components/Layout/components/Footer/components/Branding/branding.tsx
+++ b/app/components/Layout/components/Footer/components/Branding/branding.tsx
@@ -3,6 +3,7 @@ import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/c
 import { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
 import { Brands, FooterText, LargeBrand, SmallBrand } from "./branding.styles";
 import { TYPOGRAPHY_PROPS } from "@databiosphere/findable-ui/lib/styles/common/mui/typography";
+import { VersionDisplay } from "./components/VersionDisplay/versionDisplay";
 
 export const Branding = (): JSX.Element => {
   return (
@@ -54,6 +55,7 @@ export const Branding = (): JSX.Element => {
           url="https://www.niaid.nih.gov/research/bioinformatics-resource-centers"
         />
       </FooterText>
+      <VersionDisplay />
     </Brands>
   );
 };
diff --git a/app/components/Layout/components/Footer/components/Branding/components/VersionDisplay/versionDisplay.tsx b/app/components/Layout/components/Footer/components/Branding/components/VersionDisplay/versionDisplay.tsx
new file mode 100644
index 000000000..b66059c3c
--- /dev/null
+++ b/app/components/Layout/components/Footer/components/Branding/components/VersionDisplay/versionDisplay.tsx
@@ -0,0 +1,34 @@
+"use client";
+
+import { Typography } from "@mui/material";
+import { useEffect, useState } from "react";
+import { TYPOGRAPHY_PROPS } from "@databiosphere/findable-ui/lib/styles/common/mui/typography";
+
+const CLIENT_VERSION = process.env.NEXT_PUBLIC_VERSION || "0.15.0";
+const BACKEND_URL = process.env.NEXT_PUBLIC_BACKEND_URL || "";
+
+export const VersionDisplay = (): JSX.Element => {
+  const [backendVersion, setBackendVersion] = useState<string | null>(null);
+
+  useEffect(() => {
+    if (!BACKEND_URL) {
+      // No backend URL configured, skip fetching
+      return;
+    }
+
+    fetch(`${BACKEND_URL}/api/v1/version`)
+      .then((res) => res.json())
+      .then((data) => setBackendVersion(data.version))
+      .catch(() => setBackendVersion(null)); // Gracefully handle backend unavailable
+  }, []);
+
+  return (
+    <Typography
+      color={TYPOGRAPHY_PROPS.COLOR.INK_LIGHT}
+      variant={TYPOGRAPHY_PROPS.VARIANT.BODY_SMALL_400}
+    >
+      Client build: {CLIENT_VERSION}
+      {backendVersion && ` • Server revision: ${backendVersion}`}
+    </Typography>
+  );
+};
diff --git a/app/hooks/useBackendVersion.ts b/app/hooks/useBackendVersion.ts
new file mode 100644
index 000000000..bde3d8879
--- /dev/null
+++ b/app/hooks/useBackendVersion.ts
@@ -0,0 +1,24 @@
+import { useEffect, useState } from "react";
+
+interface BackendVersion {
+  environment: string;
+  service: string;
+  version: string;
+}
+
+/**
+ * Hook to fetch backend version with graceful fallback.
+ * @returns Backend version string or null if backend is unavailable.
+ */
+export function useBackendVersion(): string | null {
+  const [version, setVersion] = useState<string | null>(null);
+
+  useEffect(() => {
+    fetch("/api/v1/version")
+      .then((res) => res.json())
+      .then((data: BackendVersion) => setVersion(data.version))
+      .catch(() => setVersion(null)); // Gracefully handle backend unavailable
+  }, []);
+
+  return version;
+}
diff --git a/site-config/brc-analytics/local/.env b/site-config/brc-analytics/local/.env
index 11329b58f..6cf1791ef 100644
--- a/site-config/brc-analytics/local/.env
+++ b/site-config/brc-analytics/local/.env
@@ -1,3 +1,4 @@
 NEXT_PUBLIC_ENA_PROXY_DOMAIN="https://brc-analytics.dev.clevercanary.com"
 NEXT_PUBLIC_SITE_CONFIG='brc-analytics-local'
 NEXT_PUBLIC_GALAXY_ENV="TEST"
+NEXT_PUBLIC_BACKEND_URL="http://localhost:8000"
diff --git a/tests/e2e/04-version-display.spec.ts b/tests/e2e/04-version-display.spec.ts
new file mode 100644
index 000000000..6244a3dda
--- /dev/null
+++ b/tests/e2e/04-version-display.spec.ts
@@ -0,0 +1,42 @@
+import { expect, test } from "@playwright/test";
+
+test.describe("Version Display", () => {
+  test("should show client version and backend version in footer", async ({
+    page,
+  }) => {
+    await page.goto("http://localhost:3000");
+
+    // Wait for the footer to be visible
+    const footer = page.locator("footer");
+    await expect(footer).toBeVisible();
+
+    // Check for client version (always present)
+    await expect(footer).toContainText("Client build:");
+
+    // Check for backend version (should appear after API call)
+    await expect(footer).toContainText("Server revision:", { timeout: 5000 });
+
+    // Verify both show 0.15.0
+    const versionText = await footer.textContent();
+    console.log("Version display:", versionText);
+    expect(versionText).toMatch(/Client build:.*0\.15\.0/);
+    expect(versionText).toMatch(/Server revision:.*0\.15\.0/);
+  });
+
+  test("should gracefully handle backend unavailable", async ({ page }) => {
+    // Block the API call to simulate backend unavailable
+    await page.route("**/api/v1/version", (route) => route.abort("failed"));
+
+    await page.goto("http://localhost:3000");
+
+    const footer = page.locator("footer");
+    await expect(footer).toBeVisible();
+
+    // Should still show client version
+    await expect(footer).toContainText("Client build:");
+
+    // Should NOT show server revision
+    const versionText = await footer.textContent();
+    expect(versionText).not.toContain("Server revision:");
+  });
+});

From 5e8f468bb0f925f06d47dada387564d01762e7af Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Oct 2025 10:18:30 -0400
Subject: [PATCH 5/9] chore: remove unused useBackendVersion hook

---
 app/hooks/useBackendVersion.ts | 24 ------------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 app/hooks/useBackendVersion.ts

diff --git a/app/hooks/useBackendVersion.ts b/app/hooks/useBackendVersion.ts
deleted file mode 100644
index bde3d8879..000000000
--- a/app/hooks/useBackendVersion.ts
+++ /dev/null
@@ -1,24 +0,0 @@
-import { useEffect, useState } from "react";
-
-interface BackendVersion {
-  environment: string;
-  service: string;
-  version: string;
-}
-
-/**
- * Hook to fetch backend version with graceful fallback.
- * @returns Backend version string or null if backend is unavailable.
- */
-export function useBackendVersion(): string | null {
-  const [version, setVersion] = useState<string | null>(null);
-
-  useEffect(() => {
-    fetch("/api/v1/version")
-      .then((res) => res.json())
-      .then((data: BackendVersion) => setVersion(data.version))
-      .catch(() => setVersion(null)); // Gracefully handle backend unavailable
-  }, []);
-
-  return version;
-}

From e631bb156f2637ee7c23c164caa181569823030f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Oct 2025 10:45:04 -0400
Subject: [PATCH 6/9] chore: configure Jest to exclude e2e tests

---
 jest.config.js | 6 ++++++
 package.json   | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 jest.config.js

diff --git a/jest.config.js b/jest.config.js
new file mode 100644
index 000000000..ce5b87876
--- /dev/null
+++ b/jest.config.js
@@ -0,0 +1,6 @@
+// Jest was configured in 74d3967f (Sept 2024) but no Jest tests were ever written.
+// This config excludes Playwright e2e tests which Jest cannot parse.
+module.exports = {
+  testEnvironment: "jsdom",
+  testPathIgnorePatterns: ["/node_modules/", "/tests/e2e/"],
+};
diff --git a/package.json b/package.json
index 2d9e57314..ee2f90671 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "format": "prettier --write . --cache",
     "format:python": "./scripts/format-python.sh",
     "prepare": "husky",
-    "test": "jest --runInBand",
+    "test": "jest --runInBand --passWithNoTests",
     "build-brc-db": "esrun catalog/build/ts/build-catalog.ts",
     "build-ga2-db": "esrun catalog/ga2/build/ts/build-catalog.ts",
     "build-brc-from-ncbi": "python3 -m catalog.build.py.build_files_from_ncbi",

From 69dfb9b716a834ccf913ee5828ef4c3fa329ca16 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 29 Sep 2025 20:02:02 -0400
Subject: [PATCH 7/9] add galaxy job execution features

builds on backend-infrastructure to add:
- galaxy api integration via bioblend
- job submission and monitoring capabilities
- workflow execution
- job history tracking
- results retrieval
- frontend galaxy ui (galaxyjob components, galaxyjobview)
- react hooks for galaxy functionality
- e2e test coverage for galaxy integration
- galaxy configuration settings (api url, api key, tool ids)
- bioblend dependency for galaxy communication

this feature can be independently reviewed and tested
---
 .../GalaxyJobForm/galaxyJobForm.styles.ts     |  38 ++
 .../GalaxyJob/GalaxyJobForm/galaxyJobForm.tsx | 251 +++++++++
 .../GalaxyJobHistory/galaxyJobHistory.tsx     | 240 +++++++++
 .../GalaxyJobResults/galaxyJobResults.tsx     | 262 ++++++++++
 .../GalaxyJobStatus/galaxyJobStatus.tsx       | 420 +++++++++++++++
 app/components/GalaxyJob/galaxyJob.tsx        |  32 ++
 app/hooks/useGalaxyJob.ts                     | 494 ++++++++++++++++++
 .../GalaxyJobView/galaxyJobView.styles.ts     |  18 +
 app/views/GalaxyJobView/galaxyJobView.tsx     |  26 +
 backend/.env.example                          |   8 +
 backend/app/api/v1/galaxy.py                  | 253 +++++++++
 backend/app/core/config.py                    |   8 +
 backend/app/main.py                           |   3 +-
 backend/app/models/__init__.py                |   1 +
 backend/app/models/galaxy.py                  | 123 +++++
 backend/app/services/galaxy_service.py        | 340 ++++++++++++
 backend/pyproject.toml                        |   7 +-
 pages/galaxy-test/index.tsx                   |  22 +
 tests/e2e/09-galaxy-integration.spec.ts       | 337 ++++++++++++
 19 files changed, 2879 insertions(+), 4 deletions(-)
 create mode 100644 app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.styles.ts
 create mode 100644 app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.tsx
 create mode 100644 app/components/GalaxyJob/GalaxyJobHistory/galaxyJobHistory.tsx
 create mode 100644 app/components/GalaxyJob/GalaxyJobResults/galaxyJobResults.tsx
 create mode 100644 app/components/GalaxyJob/GalaxyJobStatus/galaxyJobStatus.tsx
 create mode 100644 app/components/GalaxyJob/galaxyJob.tsx
 create mode 100644 app/hooks/useGalaxyJob.ts
 create mode 100644 app/views/GalaxyJobView/galaxyJobView.styles.ts
 create mode 100644 app/views/GalaxyJobView/galaxyJobView.tsx
 create mode 100644 backend/app/api/v1/galaxy.py
 create mode 100644 backend/app/models/__init__.py
 create mode 100644 backend/app/models/galaxy.py
 create mode 100644 backend/app/services/galaxy_service.py
 create mode 100644 pages/galaxy-test/index.tsx
 create mode 100644 tests/e2e/09-galaxy-integration.spec.ts

diff --git a/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.styles.ts b/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.styles.ts
new file mode 100644
index 000000000..9b09be9ee
--- /dev/null
+++ b/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.styles.ts
@@ -0,0 +1,38 @@
+import styled from "@emotion/styled";
+
+export const FormContainer = styled.div`
+  display: flex;
+  flex-direction: column;
+  gap: 24px;
+  max-width: 800px;
+  margin: 0 auto;
+`;
+
+export const FormSection = styled.div`
+  display: flex;
+  flex-direction: column;
+  gap: 16px;
+`;
+
+export const InputSection = styled.div`
+  display: flex;
+  gap: 16px;
+  align-items: center;
+
+  @media (max-width: 600px) {
+    flex-direction: column;
+    align-items: stretch;
+  }
+`;
+
+export const ControlSection = styled.div`
+  display: flex;
+  gap: 16px;
+  align-items: center;
+  margin-top: 16px;
+
+  @media (max-width: 600px) {
+    flex-direction: column;
+    align-items: stretch;
+  }
+`;
diff --git a/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.tsx b/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.tsx
new file mode 100644
index 000000000..aedae7c57
--- /dev/null
+++ b/app/components/GalaxyJob/GalaxyJobForm/galaxyJobForm.tsx
@@ -0,0 +1,251 @@
+import { useState } from "react";
+import {
+  Button,
+  TextField,
+  Typography,
+  Card,
+  CardContent,
+  Alert,
+  Chip,
+  Box,
+  Divider,
+} from "@mui/material";
+import { PlayArrow, Refresh, Stop } from "@mui/icons-material";
+import { useGalaxyJob } from "../../../hooks/useGalaxyJob";
+import { GalaxyJobStatus } from "../GalaxyJobStatus/galaxyJobStatus";
+import {
+  FormContainer,
+  FormSection,
+  InputSection,
+  ControlSection,
+} from "./galaxyJobForm.styles";
+
+interface GalaxyJobFormProps {
+  galaxyJobHook: ReturnType<typeof useGalaxyJob>;
+}
+
+// Sample data for testing
+const SAMPLE_DATA = `Sample_ID	Gene	Position	Ref	Alt	Depth	Quality	Effect
+S001	ACE2	23403	A	G	156	99	missense_variant
+S001	ORF1ab	14408	C	T	203	99	synonymous_variant
+S002	Spike	23012	G	A	178	98	missense_variant
+S002	Spike	23063	A	T	145	97	missense_variant
+S003	ORF8	28144	T	C	234	99	synonymous_variant
+S003	N	28881	G	A	189	99	missense_variant
+S004	Spike	22995	C	A	167	98	missense_variant
+S004	ORF3a	25563	G	T	201	99	missense_variant
+S005	M	26530	A	G	178	97	synonymous_variant
+S005	E	26256	C	T	156	96	synonymous_variant`;
+
+export const GalaxyJobForm = ({
+  galaxyJobHook,
+}: GalaxyJobFormProps): JSX.Element => {
+  const [tabularData, setTabularData] = useState(SAMPLE_DATA);
+  const [numLines, setNumLines] = useState(3);
+  const [filename, setFilename] = useState("variant_calls");
+
+  const {
+    // Loading and submission state
+    isPolling,
+    isSubmitting,
+
+    // Job state
+    jobId,
+    jobResults,
+    jobStatus,
+
+    // Error states
+    pollingError,
+    // Actions
+    reset,
+    resultsError,
+    stopPolling,
+    submissionError,
+    submitJob,
+  } = galaxyJobHook;
+
+  const handleSubmit = async (e: React.FormEvent): Promise<void> => {
+    e.preventDefault();
+
+    if (!tabularData.trim()) {
+      return;
+    }
+
+    await submitJob({
+      filename: filename || "test_data",
+      num_random_lines: numLines,
+      tabular_data: tabularData,
+    });
+  };
+
+  const handleReset = (): void => {
+    reset();
+    setTabularData(SAMPLE_DATA);
+    setNumLines(3);
+    setFilename("variant_calls");
+  };
+
+  const isJobInProgress = isSubmitting || isPolling;
+  const hasActiveJob = Boolean(jobId);
+
+  return (
+    <FormContainer>
+      <Typography variant="body1" color="textSecondary" paragraph>
+        Paste your genomic data below to search for patterns, variants, or
+        sequences of interest. Logan Search will analyze your data and return
+        matching results.
+      </Typography>
+
+      {/* Input Form */}
+      <Card>
+        <CardContent>
+          <form onSubmit={handleSubmit}>
+            <FormSection>
+              <Typography variant="h6" gutterBottom>
+                Input Data
+              </Typography>
+
+              <InputSection>
+                <TextField
+                  label="Filename"
+                  value={filename}
+                  onChange={(e) => setFilename(e.target.value)}
+                  fullWidth
+                  size="small"
+                  disabled={isJobInProgress}
+                />
+
+                <TextField
+                  label="Maximum results to return"
+                  type="number"
+                  value={numLines}
+                  onChange={(e) => setNumLines(parseInt(e.target.value) || 1)}
+                  inputProps={{ max: 100, min: 1 }}
+                  size="small"
+                  disabled={isJobInProgress}
+                />
+              </InputSection>
+
+              <TextField
+                label="Tabular Data (TSV format)"
+                multiline
+                rows={8}
+                value={tabularData}
+                onChange={(e) => setTabularData(e.target.value)}
+                fullWidth
+                disabled={isJobInProgress}
+                helperText="Enter tab-separated genomic data (e.g., variants, sequences, annotations)"
+                sx={{ mt: 2 }}
+              />
+
+              <ControlSection>
+                <Button
+                  type="submit"
+                  variant="contained"
+                  startIcon={<PlayArrow />}
+                  disabled={isJobInProgress || !tabularData.trim()}
+                  size="large"
+                >
+                  {isSubmitting ? "Searching..." : "Search"}
+                </Button>
+
+                {isPolling && (
+                  <Button
+                    onClick={stopPolling}
+                    variant="outlined"
+                    startIcon={<Stop />}
+                    color="warning"
+                  >
+                    Stop Polling
+                  </Button>
+                )}
+
+                {hasActiveJob && (
+                  <Button
+                    onClick={handleReset}
+                    variant="outlined"
+                    startIcon={<Refresh />}
+                    disabled={isJobInProgress}
+                  >
+                    Reset
+                  </Button>
+                )}
+              </ControlSection>
+            </FormSection>
+          </form>
+        </CardContent>
+      </Card>
+
+      {/* Errors */}
+      {submissionError && (
+        <Alert severity="error" onClose={() => {}}>
+          <strong>Submission Error:</strong> {submissionError}
+        </Alert>
+      )}
+
+      {pollingError && (
+        <Alert severity="warning">
+          <strong>Polling Error:</strong> {pollingError}
+        </Alert>
+      )}
+
+      {resultsError && (
+        <Alert severity="error">
+          <strong>Results Error:</strong> {resultsError}
+        </Alert>
+      )}
+
+      {/* Job Status and Results (consolidated) */}
+      {(jobId || jobStatus) && (
+        <>
+          <Divider sx={{ my: 3 }} />
+          <GalaxyJobStatus
+            jobId={jobId}
+            status={jobStatus}
+            results={jobResults?.results}
+            isPolling={isPolling}
+          />
+        </>
+      )}
+
+      {/* Instructions */}
+      <Card sx={{ bgcolor: "background.paper", mt: 4 }}>
+        <CardContent>
+          <Typography variant="h6" gutterBottom>
+            How it works
+          </Typography>
+          <Box component="ol" sx={{ pl: 2 }}>
+            <Box component="li" sx={{ mb: 1 }}>
+              Data is uploaded to Galaxy using the upload tool
+            </Box>
+            <Box component="li" sx={{ mb: 1 }}>
+              The &quot;Select random lines&quot; tool is executed on the
+              uploaded data
+            </Box>
+            <Box component="li" sx={{ mb: 1 }}>
+              Job status is polled every 2 seconds until completion
+            </Box>
+            <Box component="li" sx={{ mb: 1 }}>
+              Results are retrieved and displayed when the job finishes
+            </Box>
+          </Box>
+
+          <Box sx={{ mt: 2 }}>
+            <Typography variant="body2" color="textSecondary" component="span">
+              This demonstrates the complete Galaxy API workflow:
+            </Typography>
+            <Box sx={{ alignItems: "center", display: "inline-flex", ml: 1 }}>
+              <Chip label="Upload" size="small" sx={{ mx: 0.5 }} />
+              <span>→</span>
+              <Chip label="Execute Tool" size="small" sx={{ mx: 0.5 }} />
+              <span>→</span>
+              <Chip label="Poll Status" size="small" sx={{ mx: 0.5 }} />
+              <span>→</span>
+              <Chip label="Get Results" size="small" sx={{ mx: 0.5 }} />
+            </Box>
+          </Box>
+        </CardContent>
+      </Card>
+    </FormContainer>
+  );
+};
diff --git a/app/components/GalaxyJob/GalaxyJobHistory/galaxyJobHistory.tsx b/app/components/GalaxyJob/GalaxyJobHistory/galaxyJobHistory.tsx
new file mode 100644
index 000000000..55efae579
--- /dev/null
+++ b/app/components/GalaxyJob/GalaxyJobHistory/galaxyJobHistory.tsx
@@ -0,0 +1,240 @@
+import React from "react";
+import {
+  Accordion,
+  AccordionDetails,
+  AccordionSummary,
+  Box,
+  Button,
+  Chip,
+  Typography,
+} from "@mui/material";
+import { ExpandMore, Delete, History } from "@mui/icons-material";
+
+interface GalaxyJobHistoryItem {
+  completed_time?: string;
+  created_time: string;
+  filename?: string;
+  job_id: string;
+  num_random_lines: number;
+  results?: Record<string, string>;
+  status: string;
+  tabular_data: string;
+  updated_time?: string;
+}
+
+interface GalaxyJobHistoryProps {
+  jobHistory: GalaxyJobHistoryItem[];
+  onClearHistory: () => void;
+}
+
+const getStatusColor = (status: string): string => {
+  switch (status.toLowerCase()) {
+    case "ok":
+    case "completed":
+      return "success";
+    case "running":
+    case "queued":
+    case "submitted":
+      return "info";
+    case "paused":
+      return "warning";
+    case "error":
+    case "failed":
+      return "error";
+    default:
+      return "default";
+  }
+};
+
+const formatDate = (dateString: string): string => {
+  try {
+    const date = new Date(dateString);
+    return date.toLocaleString();
+  } catch {
+    return dateString;
+  }
+};
+
+const truncateText = (text: string, maxLength: number): string => {
+  return text.length > maxLength ? `${text.substring(0, maxLength)}...` : text;
+};
+
+export const GalaxyJobHistory: React.FC<GalaxyJobHistoryProps> = ({
+  jobHistory,
+  onClearHistory,
+}) => {
+  if (jobHistory.length === 0) {
+    return (
+      <Box sx={{ border: "1px dashed #ccc", borderRadius: 1, mt: 3, p: 2 }}>
+        <Typography variant="body2" color="textSecondary" align="center">
+          <History sx={{ mr: 1, verticalAlign: "middle" }} />
+          No job history yet. Submit a job to see it appear here.
+        </Typography>
+      </Box>
+    );
+  }
+
+  return (
+    <Box sx={{ mt: 3 }}>
+      <Box
+        sx={{
+          alignItems: "center",
+          display: "flex",
+          justifyContent: "space-between",
+          mb: 2,
+        }}
+      >
+        <Typography variant="h6" component="h2">
+          <History sx={{ mr: 1, verticalAlign: "middle" }} />
+          Job History ({jobHistory.length})
+        </Typography>
+        <Button
+          variant="outlined"
+          color="error"
+          size="small"
+          startIcon={<Delete />}
+          onClick={onClearHistory}
+        >
+          Clear History
+        </Button>
+      </Box>
+
+      <Box sx={{ maxHeight: "400px", overflowY: "auto" }}>
+        {jobHistory.map((job, index) => (
+          <Accordion key={job.job_id} sx={{ mb: 1 }}>
+            <AccordionSummary expandIcon={<ExpandMore />}>
+              <Box
+                sx={{
+                  alignItems: "center",
+                  display: "flex",
+                  justifyContent: "space-between",
+                  width: "100%",
+                }}
+              >
+                <Box>
+                  <Typography variant="subtitle2">
+                    Job {index + 1}: {job.job_id}
+                  </Typography>
+                  <Typography variant="body2" color="textSecondary">
+                    {formatDate(job.created_time)} • {job.num_random_lines}{" "}
+                    lines
+                    {job.filename && ` • ${job.filename}`}
+                  </Typography>
+                </Box>
+                <Chip
+                  label={job.status}
+                  color={
+                    getStatusColor(job.status) as
+                      | "default"
+                      | "error"
+                      | "info"
+                      | "success"
+                      | "warning"
+                  }
+                  size="small"
+                  sx={{ ml: 2 }}
+                />
+              </Box>
+            </AccordionSummary>
+            <AccordionDetails>
+              <Box>
+                <Typography variant="subtitle2" gutterBottom>
+                  Job Details:
+                </Typography>
+                <Typography variant="body2" sx={{ mb: 1 }}>
+                  <strong>Job ID:</strong> {job.job_id}
+                </Typography>
+                <Typography variant="body2" sx={{ mb: 1 }}>
+                  <strong>Created:</strong> {formatDate(job.created_time)}
+                </Typography>
+                {job.updated_time && (
+                  <Typography variant="body2" sx={{ mb: 1 }}>
+                    <strong>Updated:</strong> {formatDate(job.updated_time)}
+                  </Typography>
+                )}
+                {job.completed_time && (
+                  <Typography variant="body2" sx={{ mb: 1 }}>
+                    <strong>Completed:</strong> {formatDate(job.completed_time)}
+                  </Typography>
+                )}
+                <Typography variant="body2" sx={{ mb: 1 }}>
+                  <strong>Random Lines:</strong> {job.num_random_lines}
+                </Typography>
+                {job.filename && (
+                  <Typography variant="body2" sx={{ mb: 1 }}>
+                    <strong>Filename:</strong> {job.filename}
+                  </Typography>
+                )}
+                <Typography variant="subtitle2" sx={{ mb: 1, mt: 2 }}>
+                  Input Data:
+                </Typography>
+                <Box
+                  sx={{
+                    backgroundColor: "#f5f5f5",
+                    border: "1px solid #ddd",
+                    borderRadius: 1,
+                    maxHeight: "150px",
+                    overflowY: "auto",
+                    p: 1,
+                  }}
+                >
+                  <Typography
+                    variant="body2"
+                    component="pre"
+                    sx={{ fontFamily: "monospace", fontSize: "0.75rem" }}
+                  >
+                    {truncateText(job.tabular_data, 500)}
+                  </Typography>
+                </Box>
+
+                {job.results && (
+                  <>
+                    <Typography variant="subtitle2" sx={{ mb: 1, mt: 2 }}>
+                      Job Results:
+                    </Typography>
+                    {((): JSX.Element[] => {
+                      console.log(
+                        `📋 Displaying results for job ${job.job_id}:`,
+                        job.results
+                      );
+                      return Object.entries(job.results).map(
+                        ([name, content]) => (
+                          <Box key={name} sx={{ mb: 2 }}>
+                            <Typography variant="body2" sx={{ mb: 1 }}>
+                              <strong>{name}:</strong>
+                            </Typography>
+                            <Box
+                              sx={{
+                                backgroundColor: "#f0f8ff",
+                                border: "1px solid #4caf50",
+                                borderRadius: 1,
+                                maxHeight: "200px",
+                                overflowY: "auto",
+                                p: 1,
+                              }}
+                            >
+                              <Typography
+                                variant="body2"
+                                component="pre"
+                                sx={{
+                                  fontFamily: "monospace",
+                                  fontSize: "0.75rem",
+                                }}
+                              >
+                                {content}
+                              </Typography>
+                            </Box>
+                          </Box>
+                        )
+                      );
+                    })()}
+                  </>
+                )}
+              </Box>
+            </AccordionDetails>
+          </Accordion>
+        ))}
+      </Box>
+    </Box>
+  );
+};
diff --git a/app/components/GalaxyJob/GalaxyJobResults/galaxyJobResults.tsx b/app/components/GalaxyJob/GalaxyJobResults/galaxyJobResults.tsx
new file mode 100644
index 000000000..17fd163ac
--- /dev/null
+++ b/app/components/GalaxyJob/GalaxyJobResults/galaxyJobResults.tsx
@@ -0,0 +1,262 @@
+import {
+  Card,
+  CardContent,
+  Typography,
+  Box,
+  Accordion,
+  AccordionSummary,
+  AccordionDetails,
+  Chip,
+  Alert,
+  LinearProgress,
+  Divider,
+} from "@mui/material";
+import { ExpandMore, CheckCircle, Description } from "@mui/icons-material";
+
+interface GalaxyJobOutput {
+  dataset: {
+    file_ext: string;
+    file_size?: number;
+    id: string;
+    name: string;
+    state: string;
+  };
+  id: string;
+  name: string;
+}
+
+interface GalaxyJobResult {
+  completed_time?: string;
+  created_time: string;
+  job_id: string;
+  outputs: GalaxyJobOutput[];
+  processing_time?: string;
+  results: Record<string, string>;
+  status: string;
+}
+
+interface Props {
+  isLoading: boolean;
+  results: GalaxyJobResult | null;
+}
+
+const formatDateTime = (dateTime: string): string => {
+  try {
+    return new Date(dateTime).toLocaleString();
+  } catch {
+    return dateTime;
+  }
+};
+
+const formatFileSize = (bytes?: number): string => {
+  if (!bytes) return "Unknown size";
+  if (bytes < 1024) return `${bytes} B`;
+  if (bytes < 1024 * 1024) return `${Math.round(bytes / 1024)} KB`;
+  return `${Math.round(bytes / (1024 * 1024))} MB`;
+};
+
+const countLines = (content: string): number => {
+  return content.trim().split("\n").length;
+};
+
+export const GalaxyJobResults = ({
+  isLoading,
+  results,
+}: Props): JSX.Element => {
+  if (isLoading) {
+    return (
+      <Card>
+        <CardContent>
+          <Box display="flex" alignItems="center" gap={2}>
+            <LinearProgress sx={{ flexGrow: 1 }} />
+            <Typography variant="body2" color="textSecondary">
+              Loading results...
+            </Typography>
+          </Box>
+        </CardContent>
+      </Card>
+    );
+  }
+
+  if (!results) {
+    return <div />;
+  }
+
+  const processingTime =
+    results.completed_time && results.created_time
+      ? new Date(results.completed_time).getTime() -
+        new Date(results.created_time).getTime()
+      : null;
+
+  return (
+    <Card>
+      <CardContent>
+        <Box display="flex" alignItems="center" gap={1} mb={2}>
+          <CheckCircle color="success" />
+          <Typography variant="h6">Job Completed Successfully</Typography>
+        </Box>
+
+        {/* Summary Information */}
+        <Box sx={{ mb: 3 }}>
+          <Typography variant="body2" color="textSecondary" gutterBottom>
+            Job ID:{" "}
+            <span style={{ fontFamily: "monospace" }}>{results.job_id}</span>
+          </Typography>
+
+          <Box display="flex" gap={2} flexWrap="wrap" sx={{ mt: 1 }}>
+            <Chip
+              label={`Status: ${results.status}`}
+              color="success"
+              size="small"
+            />
+            <Chip
+              label={`${results.outputs.length} output(s)`}
+              variant="outlined"
+              size="small"
+            />
+            {processingTime && (
+              <Chip
+                label={`Processed in ${Math.round(processingTime / 1000)}s`}
+                variant="outlined"
+                size="small"
+              />
+            )}
+          </Box>
+
+          <Box sx={{ mt: 2 }}>
+            <Typography variant="body2" color="textSecondary">
+              Created: {formatDateTime(results.created_time)}
+            </Typography>
+            {results.completed_time && (
+              <Typography variant="body2" color="textSecondary">
+                Completed: {formatDateTime(results.completed_time)}
+              </Typography>
+            )}
+          </Box>
+        </Box>
+
+        {/* Results Section */}
+        {Object.keys(results.results).length > 0 && (
+          <>
+            <Divider sx={{ mb: 2 }} />
+            <Typography variant="h6" gutterBottom>
+              Output Results
+            </Typography>
+
+            {Object.entries(results.results).map(
+              ([outputName, content], index) => {
+                const output = results.outputs.find(
+                  (o) => o.name === outputName
+                );
+                const lineCount = countLines(content);
+
+                return (
+                  <Accordion key={index} sx={{ mb: 1 }}>
+                    <AccordionSummary expandIcon={<ExpandMore />}>
+                      <Box
+                        display="flex"
+                        alignItems="center"
+                        gap={1}
+                        width="100%"
+                      >
+                        <Description />
+                        <Typography variant="subtitle1">
+                          {outputName}
+                        </Typography>
+                        <Box sx={{ ml: "auto", mr: 1 }}>
+                          <Chip
+                            label={`${lineCount} lines`}
+                            size="small"
+                            variant="outlined"
+                          />
+                          {output && (
+                            <Chip
+                              label={formatFileSize(output.dataset.file_size)}
+                              size="small"
+                              variant="outlined"
+                              sx={{ ml: 1 }}
+                            />
+                          )}
+                        </Box>
+                      </Box>
+                    </AccordionSummary>
+                    <AccordionDetails>
+                      {output && (
+                        <Box sx={{ mb: 2 }}>
+                          <Typography variant="body2" color="textSecondary">
+                            Dataset: {output.dataset.name} (
+                            {output.dataset.file_ext})
+                          </Typography>
+                          <Typography variant="body2" color="textSecondary">
+                            State: {output.dataset.state}
+                          </Typography>
+                        </Box>
+                      )}
+
+                      <Box
+                        sx={{
+                          bgcolor: "grey.50",
+                          borderRadius: 1,
+                          maxHeight: "300px",
+                          overflow: "auto",
+                          p: 2,
+                        }}
+                      >
+                        <Typography
+                          variant="body2"
+                          component="pre"
+                          sx={{
+                            fontFamily: "monospace",
+                            fontSize: "0.75rem",
+                            margin: 0,
+                            whiteSpace: "pre-wrap",
+                          }}
+                        >
+                          {content}
+                        </Typography>
+                      </Box>
+
+                      {lineCount > 10 && (
+                        <Alert severity="info" sx={{ mt: 2 }}>
+                          This output contains {lineCount} lines. Only the first
+                          portion is shown above.
+                        </Alert>
+                      )}
+                    </AccordionDetails>
+                  </Accordion>
+                );
+              }
+            )}
+          </>
+        )}
+
+        {/* Empty Results */}
+        {Object.keys(results.results).length === 0 && (
+          <>
+            <Divider sx={{ mb: 2 }} />
+            <Alert severity="warning">
+              Job completed successfully but no output content was retrieved.
+              This might indicate an issue with result retrieval or the outputs
+              may be empty.
+            </Alert>
+          </>
+        )}
+
+        {/* Success Message */}
+        <Box sx={{ bgcolor: "success.light", borderRadius: 1, mt: 3, p: 2 }}>
+          <Typography variant="body2" color="success.contrastText">
+            <strong>✅ Integration Test Successful!</strong>
+            <br />
+            The Galaxy API integration is working correctly. Data was
+            successfully:
+          </Typography>
+          <Box component="ul" sx={{ mb: 0, mt: 1, pl: 3 }}>
+            <li>Uploaded to Galaxy</li>
+            <li>Processed with the &quot;Select random lines&quot; tool</li>
+            <li>Retrieved as results</li>
+          </Box>
+        </Box>
+      </CardContent>
+    </Card>
+  );
+};
diff --git a/app/components/GalaxyJob/GalaxyJobStatus/galaxyJobStatus.tsx b/app/components/GalaxyJob/GalaxyJobStatus/galaxyJobStatus.tsx
new file mode 100644
index 000000000..3a4872c07
--- /dev/null
+++ b/app/components/GalaxyJob/GalaxyJobStatus/galaxyJobStatus.tsx
@@ -0,0 +1,420 @@
+import {
+  Card,
+  CardContent,
+  Typography,
+  Chip,
+  LinearProgress,
+  Box,
+  Divider,
+  Accordion,
+  AccordionSummary,
+  AccordionDetails,
+  Alert,
+} from "@mui/material";
+import {
+  Schedule,
+  PlayArrow,
+  CheckCircle,
+  Error,
+  Pause,
+  Delete,
+  CloudUpload,
+  HourglassEmpty,
+  ExpandMore,
+  Description,
+} from "@mui/icons-material";
+
+interface GalaxyJobOutput {
+  dataset: {
+    file_ext: string;
+    file_size?: number;
+    id: string;
+    name: string;
+    state: string;
+  };
+  id: string;
+  name: string;
+}
+
+interface GalaxyJobStatus {
+  created_time: string;
+  exit_code?: number;
+  is_complete: boolean;
+  is_successful: boolean;
+  job_id: string;
+  outputs: GalaxyJobOutput[];
+  state: string;
+  stderr?: string;
+  stdout?: string;
+  updated_time: string;
+}
+
+interface Props {
+  isPolling: boolean;
+  jobId: string | null;
+  results?: Record<string, string> | null;
+  status: GalaxyJobStatus | null;
+}
+
+const getStateIcon = (state: string): JSX.Element => {
+  switch (state) {
+    case "new":
+      return <Schedule />;
+    case "upload":
+      return <CloudUpload />;
+    case "waiting":
+    case "queued":
+      return <HourglassEmpty />;
+    case "running":
+      return <PlayArrow />;
+    case "ok":
+      return <CheckCircle />;
+    case "error":
+      return <Error />;
+    case "paused":
+      return <Pause />;
+    case "deleted":
+    case "deleted_new":
+      return <Delete />;
+    default:
+      return <Schedule />;
+  }
+};
+
+const getStateColor = (
+  state: string
+):
+  | "default"
+  | "primary"
+  | "secondary"
+  | "error"
+  | "warning"
+  | "info"
+  | "success" => {
+  switch (state) {
+    case "ok":
+      return "success";
+    case "error":
+      return "error";
+    case "running":
+      return "primary";
+    case "waiting":
+    case "queued":
+      return "warning";
+    case "paused":
+      return "secondary";
+    case "deleted":
+    case "deleted_new":
+      return "error";
+    default:
+      return "default";
+  }
+};
+
+const formatDateTime = (dateTime: string): string => {
+  try {
+    return new Date(dateTime).toLocaleString();
+  } catch {
+    return dateTime;
+  }
+};
+
+const formatFileSize = (bytes?: number): string => {
+  if (!bytes) return "Unknown size";
+  if (bytes < 1024) return `${bytes} B`;
+  if (bytes < 1024 * 1024) return `${Math.round(bytes / 1024)} KB`;
+  return `${Math.round(bytes / (1024 * 1024))} MB`;
+};
+
+const countLines = (content: string): number => {
+  return content.trim().split("\n").length;
+};
+
+export const GalaxyJobStatus = ({
+  isPolling,
+  jobId,
+  results,
+  status,
+}: Props): JSX.Element => {
+  if (!jobId) {
+    return <div />;
+  }
+
+  const isCompleted = status?.is_complete && status?.state === "ok";
+  const hasResults = results && Object.keys(results).length > 0;
+
+  return (
+    <Card>
+      <CardContent>
+        <Box display="flex" alignItems="center" gap={1} mb={2}>
+          {isCompleted ? (
+            <>
+              <CheckCircle color="success" />
+              <Typography variant="h6">Search Complete</Typography>
+            </>
+          ) : (
+            <Typography variant="h6">Logan Search Status</Typography>
+          )}
+        </Box>
+
+        <Box
+          sx={{
+            alignItems: "center",
+            display: "flex",
+            flexDirection: { sm: "row", xs: "column" },
+            gap: 2,
+          }}
+        >
+          <Box display="flex" alignItems="center" gap={1}>
+            <Typography variant="body2" color="textSecondary">
+              Job ID:
+            </Typography>
+            <Typography variant="body2" fontFamily="monospace">
+              {jobId}
+            </Typography>
+          </Box>
+
+          <Box>
+            <Box
+              display="flex"
+              alignItems="center"
+              gap={1}
+              justifyContent="flex-end"
+            >
+              {isPolling && (
+                <Chip
+                  label="Polling..."
+                  size="small"
+                  color="primary"
+                  variant="outlined"
+                />
+              )}
+            </Box>
+          </Box>
+        </Box>
+
+        {status && (
+          <>
+            <Box sx={{ mt: 2 }}>
+              <Box display="flex" alignItems="center" gap={1} mb={1}>
+                {getStateIcon(status.state)}
+                <Chip
+                  label={status.state.toUpperCase()}
+                  color={getStateColor(status.state)}
+                  size="small"
+                />
+                {!status.is_complete && (
+                  <LinearProgress sx={{ flexGrow: 1, ml: 2 }} />
+                )}
+              </Box>
+
+              <Box
+                sx={{
+                  display: "flex",
+                  flexDirection: { sm: "row", xs: "column" },
+                  gap: 2,
+                  mt: 1,
+                }}
+              >
+                <Typography variant="body2" color="textSecondary">
+                  Created: {formatDateTime(status.created_time)}
+                </Typography>
+                <Typography variant="body2" color="textSecondary">
+                  Updated: {formatDateTime(status.updated_time)}
+                </Typography>
+              </Box>
+
+              {status.outputs.length > 0 && (
+                <>
+                  <Divider sx={{ my: 2 }} />
+                  <Typography variant="subtitle2" gutterBottom>
+                    Outputs ({status.outputs.length})
+                  </Typography>
+                  {status.outputs.map((output) => (
+                    <Box key={output.id} sx={{ mb: 1 }}>
+                      <Typography variant="body2">
+                        <strong>{output.name}:</strong> {output.dataset.name}
+                        {output.dataset.file_size && (
+                          <>
+                            {" "}
+                            ({Math.round(output.dataset.file_size / 1024)} KB)
+                          </>
+                        )}
+                      </Typography>
+                      <Box display="flex" gap={1} mt={0.5}>
+                        <Chip
+                          label={output.dataset.state}
+                          size="small"
+                          variant="outlined"
+                        />
+                        <Chip
+                          label={output.dataset.file_ext}
+                          size="small"
+                          variant="outlined"
+                        />
+                      </Box>
+                    </Box>
+                  ))}
+                </>
+              )}
+
+              {/* Show stderr/stdout for debugging if job failed */}
+              {status.state === "error" && (status.stderr || status.stdout) && (
+                <>
+                  <Divider sx={{ my: 2 }} />
+                  <Typography variant="subtitle2" color="error" gutterBottom>
+                    Error Information
+                  </Typography>
+                  {status.stderr && (
+                    <Box
+                      sx={{
+                        bgcolor: "error.light",
+                        borderRadius: 1,
+                        mb: 1,
+                        p: 1,
+                      }}
+                    >
+                      <Typography variant="caption" color="error.contrastText">
+                        STDERR:
+                      </Typography>
+                      <Typography
+                        variant="body2"
+                        component="pre"
+                        sx={{ fontSize: "0.75rem", whiteSpace: "pre-wrap" }}
+                      >
+                        {status.stderr}
+                      </Typography>
+                    </Box>
+                  )}
+                  {status.stdout && (
+                    <Box sx={{ bgcolor: "grey.100", borderRadius: 1, p: 1 }}>
+                      <Typography variant="caption" color="textSecondary">
+                        STDOUT:
+                      </Typography>
+                      <Typography
+                        variant="body2"
+                        component="pre"
+                        sx={{ fontSize: "0.75rem", whiteSpace: "pre-wrap" }}
+                      >
+                        {status.stdout}
+                      </Typography>
+                    </Box>
+                  )}
+                </>
+              )}
+            </Box>
+          </>
+        )}
+
+        {/* Results Section - Show when job is completed successfully */}
+        {isCompleted && hasResults && (
+          <>
+            <Divider sx={{ my: 3 }} />
+            <Typography variant="h6" gutterBottom>
+              Search Results
+            </Typography>
+
+            {Object.entries(results!).map(([outputName, content], index) => {
+              const output = status!.outputs.find((o) => o.name === outputName);
+              const lineCount = countLines(content);
+
+              return (
+                <Accordion key={index} sx={{ mb: 1 }}>
+                  <AccordionSummary expandIcon={<ExpandMore />}>
+                    <Box
+                      display="flex"
+                      alignItems="center"
+                      gap={1}
+                      width="100%"
+                    >
+                      <Description />
+                      <Typography variant="subtitle1">{outputName}</Typography>
+                      <Box sx={{ ml: "auto", mr: 1 }}>
+                        <Chip
+                          label={`${lineCount} lines`}
+                          size="small"
+                          variant="outlined"
+                        />
+                        {output && (
+                          <Chip
+                            label={formatFileSize(output.dataset.file_size)}
+                            size="small"
+                            variant="outlined"
+                            sx={{ ml: 1 }}
+                          />
+                        )}
+                      </Box>
+                    </Box>
+                  </AccordionSummary>
+                  <AccordionDetails>
+                    {output && (
+                      <Box sx={{ mb: 2 }}>
+                        <Typography variant="body2" color="textSecondary">
+                          Dataset: {output.dataset.name} (
+                          {output.dataset.file_ext})
+                        </Typography>
+                        <Typography variant="body2" color="textSecondary">
+                          State: {output.dataset.state}
+                        </Typography>
+                      </Box>
+                    )}
+
+                    <Box
+                      sx={{
+                        bgcolor: "grey.50",
+                        borderRadius: 1,
+                        maxHeight: "300px",
+                        overflow: "auto",
+                        p: 2,
+                      }}
+                    >
+                      <Typography
+                        variant="body2"
+                        component="pre"
+                        sx={{
+                          fontFamily: "monospace",
+                          fontSize: "0.75rem",
+                          margin: 0,
+                          whiteSpace: "pre-wrap",
+                        }}
+                      >
+                        {content}
+                      </Typography>
+                    </Box>
+
+                    {lineCount > 10 && (
+                      <Alert severity="info" sx={{ mt: 2 }}>
+                        This output contains {lineCount} lines. Only the first
+                        portion is shown above.
+                      </Alert>
+                    )}
+                  </AccordionDetails>
+                </Accordion>
+              );
+            })}
+
+            {/* Success Message */}
+            <Box
+              sx={{ bgcolor: "success.light", borderRadius: 1, mt: 3, p: 2 }}
+            >
+              <Typography variant="body2" color="success.contrastText">
+                <strong>✅ Analysis Complete!</strong>
+                <br />
+                Your Logan Search analysis has completed successfully.
+              </Typography>
+            </Box>
+          </>
+        )}
+
+        {!status && (
+          <Box display="flex" alignItems="center" gap={1} sx={{ mt: 2 }}>
+            <LinearProgress sx={{ flexGrow: 1 }} />
+            <Typography variant="body2" color="textSecondary">
+              Waiting for job status...
+            </Typography>
+          </Box>
+        )}
+      </CardContent>
+    </Card>
+  );
+};
diff --git a/app/components/GalaxyJob/galaxyJob.tsx b/app/components/GalaxyJob/galaxyJob.tsx
new file mode 100644
index 000000000..f3b5d5d79
--- /dev/null
+++ b/app/components/GalaxyJob/galaxyJob.tsx
@@ -0,0 +1,32 @@
+import { Container, Typography, Box } from "@mui/material";
+import { useGalaxyJob } from "../../hooks/useGalaxyJob";
+import { GalaxyJobForm } from "./GalaxyJobForm/galaxyJobForm";
+import { GalaxyJobHistory } from "./GalaxyJobHistory/galaxyJobHistory";
+
+export const GalaxyJob = (): JSX.Element => {
+  const galaxyJobHook = useGalaxyJob();
+
+  return (
+    <Container maxWidth="lg">
+      <Box sx={{ py: 4 }}>
+        <Typography variant="h3" component="h1" gutterBottom align="center">
+          Logan Search
+        </Typography>
+        <Typography
+          variant="h6"
+          color="textSecondary"
+          align="center"
+          paragraph
+          sx={{ mb: 4 }}
+        >
+          Analyze genomic data using Logan Search powered by Galaxy
+        </Typography>
+        <GalaxyJobForm galaxyJobHook={galaxyJobHook} />
+        <GalaxyJobHistory
+          jobHistory={galaxyJobHook.jobHistory}
+          onClearHistory={galaxyJobHook.clearJobHistory}
+        />
+      </Box>
+    </Container>
+  );
+};
diff --git a/app/hooks/useGalaxyJob.ts b/app/hooks/useGalaxyJob.ts
new file mode 100644
index 000000000..2817ad388
--- /dev/null
+++ b/app/hooks/useGalaxyJob.ts
@@ -0,0 +1,494 @@
+import { useState, useCallback, useEffect } from "react";
+import ky from "ky";
+
+// Types based on our backend models
+interface GalaxyJobSubmission {
+  filename?: string;
+  num_random_lines: number;
+  tabular_data: string;
+}
+
+interface GalaxyJobResponse {
+  job_id: string;
+  message: string;
+  status: string;
+  upload_dataset_id: string;
+}
+
+interface GalaxyJobOutput {
+  dataset: {
+    file_ext: string;
+    file_size?: number;
+    id: string;
+    name: string;
+    state: string;
+  };
+  id: string;
+  name: string;
+}
+
+interface GalaxyJobStatus {
+  created_time: string;
+  exit_code?: number;
+  is_complete: boolean;
+  is_successful: boolean;
+  job_id: string;
+  outputs: GalaxyJobOutput[];
+  state: string;
+  stderr?: string;
+  stdout?: string;
+  updated_time: string;
+}
+
+interface GalaxyJobResult {
+  completed_time?: string;
+  created_time: string;
+  job_id: string;
+  outputs: GalaxyJobOutput[];
+  processing_time?: string;
+  results: Record<string, string>;
+  status: string;
+}
+
+// Job history item for localStorage
+interface GalaxyJobHistoryItem {
+  completed_time?: string;
+  created_time: string;
+  filename?: string;
+  job_id: string;
+  num_random_lines: number;
+  results?: Record<string, string>;
+  status: string;
+  tabular_data: string;
+  updated_time?: string;
+}
+
+// Hook state interface
+interface GalaxyJobState {
+  // Results retrieval state
+  isLoadingResults: boolean;
+  // Polling state
+  isPolling: boolean;
+  // Submission state
+  isSubmitting: boolean;
+
+  // Job tracking state
+  jobHistory: GalaxyJobHistoryItem[];
+  jobId: string | null;
+  jobResults: GalaxyJobResult | null;
+  jobStatus: GalaxyJobStatus | null;
+
+  // Error states
+  pollingError: string | null;
+  resultsError: string | null;
+  submissionError: string | null;
+}
+
+interface GalaxyJobActions {
+  clearJobHistory: () => void;
+  getResults: (jobId: string) => Promise<void>;
+  reset: () => void;
+  startPolling: (jobId: string) => void;
+  stopPolling: () => void;
+  submitJob: (submission: GalaxyJobSubmission) => Promise<void>;
+}
+
+const BACKEND_URL = "http://localhost:8000";
+const POLLING_INTERVAL = 2000; // 2 seconds
+const STORAGE_KEY = "galaxy_job_history";
+
+// localStorage utilities
+const loadJobHistory = (): GalaxyJobHistoryItem[] => {
+  if (typeof window === "undefined") return [];
+
+  try {
+    const stored = localStorage.getItem(STORAGE_KEY);
+    return stored ? JSON.parse(stored) : [];
+  } catch (error: unknown) {
+    console.error("Failed to load job history from localStorage:", error);
+    return [];
+  }
+};
+
+const saveJobHistory = (history: GalaxyJobHistoryItem[]): void => {
+  if (typeof window === "undefined") return;
+
+  try {
+    localStorage.setItem(STORAGE_KEY, JSON.stringify(history));
+  } catch (error: unknown) {
+    console.error("Failed to save job history to localStorage:", error);
+  }
+};
+
+const addJobToHistory = (job: GalaxyJobHistoryItem): void => {
+  const history = loadJobHistory();
+  // Add new job at the beginning (most recent first)
+  const updatedHistory = [
+    job,
+    ...history.filter((h) => h.job_id !== job.job_id),
+  ];
+  // Keep only the most recent 50 jobs
+  const trimmedHistory = updatedHistory.slice(0, 50);
+  saveJobHistory(trimmedHistory);
+};
+
+const updateJobInHistory = (
+  jobId: string,
+  updates: Partial<GalaxyJobHistoryItem>
+): void => {
+  console.log(`📝 Updating job ${jobId} in history with:`, updates);
+  const history = loadJobHistory();
+  const updatedHistory = history.map((job) =>
+    job.job_id === jobId ? { ...job, ...updates } : job
+  );
+  saveJobHistory(updatedHistory);
+  console.log(`✅ Job ${jobId} updated in history`);
+};
+
+export const useGalaxyJob = (): GalaxyJobState & GalaxyJobActions => {
+  const [state, setState] = useState<GalaxyJobState>(() => ({
+    isLoadingResults: false,
+    isPolling: false,
+    isSubmitting: false,
+    jobHistory: [],
+    jobId: null,
+    jobResults: null,
+    jobStatus: null,
+    pollingError: null,
+    resultsError: null,
+    submissionError: null,
+  }));
+
+  const [pollingIntervalId, setPollingIntervalId] =
+    useState<NodeJS.Timeout | null>(null);
+
+  // Load job history on mount (client-side only)
+  useEffect((): void => {
+    if (typeof window !== "undefined") {
+      const history = loadJobHistory();
+      setState((prev) => ({ ...prev, jobHistory: history }));
+    }
+  }, []);
+
+  // Submit job to Galaxy
+  const submitJob = useCallback(
+    async (submission: GalaxyJobSubmission): Promise<void> => {
+      setState((prev) => ({
+        ...prev,
+        isSubmitting: true,
+        jobId: null,
+        jobResults: null,
+        jobStatus: null,
+        submissionError: null,
+      }));
+
+      try {
+        const response = await ky
+          .post(`${BACKEND_URL}/api/v1/galaxy/submit-job`, {
+            json: submission,
+            timeout: 60000, // 60 seconds
+          })
+          .json<GalaxyJobResponse>();
+
+        // Create job history item
+        const historyItem: GalaxyJobHistoryItem = {
+          created_time: new Date().toISOString(),
+          filename: submission.filename,
+          job_id: response.job_id,
+          num_random_lines: submission.num_random_lines,
+          status: "submitted",
+          tabular_data: submission.tabular_data,
+        };
+
+        // Save to localStorage
+        addJobToHistory(historyItem);
+
+        // Update state with new job and refresh history
+        const updatedHistory = loadJobHistory();
+        setState((prev) => ({
+          ...prev,
+          isSubmitting: false,
+          jobHistory: updatedHistory,
+          jobId: response.job_id,
+        }));
+
+        // Will start polling via useEffect when jobId changes
+      } catch (error: unknown) {
+        let errorMessage = "Failed to submit job";
+        if (error && typeof error === "object" && "response" in error) {
+          const httpError = error as {
+            response: {
+              json: () => Promise<{ detail?: string }>;
+              status: number;
+              statusText: string;
+            };
+          };
+          try {
+            const errorData = await httpError.response.json();
+            errorMessage = errorData.detail || errorMessage;
+          } catch {
+            errorMessage = `HTTP ${httpError.response.status}: ${httpError.response.statusText}`;
+          }
+        } else if (error && typeof error === "object" && "message" in error) {
+          errorMessage = (error as Error).message || errorMessage;
+        }
+
+        setState((prev) => ({
+          ...prev,
+          isSubmitting: false,
+          submissionError: errorMessage,
+        }));
+      }
+    },
+    []
+  );
+
+  // Get job status
+  const getJobStatus = useCallback(
+    async (jobId: string): Promise<GalaxyJobStatus | null> => {
+      try {
+        const response = await ky
+          .get(`${BACKEND_URL}/api/v1/galaxy/jobs/${jobId}/status`, {
+            timeout: 30000,
+          })
+          .json<GalaxyJobStatus>();
+
+        return response;
+      } catch (error: unknown) {
+        console.error("Failed to get job status:", error);
+        return null;
+      }
+    },
+    []
+  );
+
+  // Get job results
+  const getResults = useCallback(async (jobId: string): Promise<void> => {
+    console.log(`🔍 Getting results for job ${jobId}`);
+    setState((prev) => ({
+      ...prev,
+      isLoadingResults: true,
+      resultsError: null,
+    }));
+
+    try {
+      const response = await ky
+        .get(`${BACKEND_URL}/api/v1/galaxy/jobs/${jobId}/results`, {
+          timeout: 30000,
+        })
+        .json<GalaxyJobResult>();
+
+      console.log(`✅ Got results for job ${jobId}:`, response);
+
+      setState((prev) => ({
+        ...prev,
+        isLoadingResults: false,
+        jobResults: response,
+      }));
+
+      // Save results to localStorage
+      console.log(`💾 Saving results to localStorage for job ${jobId}`);
+      updateJobInHistory(jobId, {
+        completed_time: response.completed_time,
+        results: response.results,
+        status: response.status,
+      });
+      console.log(`✅ Results saved to localStorage for job ${jobId}`);
+    } catch (error: unknown) {
+      let errorMessage = "Failed to get results";
+      if (error && typeof error === "object" && "response" in error) {
+        const httpError = error as {
+          response: {
+            json: () => Promise<{ detail?: string }>;
+            status: number;
+            statusText: string;
+          };
+        };
+        try {
+          const errorData = await httpError.response.json();
+          errorMessage = errorData.detail || errorMessage;
+        } catch {
+          errorMessage = `HTTP ${httpError.response.status}: ${httpError.response.statusText}`;
+        }
+      } else if (error && typeof error === "object" && "message" in error) {
+        errorMessage = (error as Error).message || errorMessage;
+      }
+
+      setState((prev) => ({
+        ...prev,
+        isLoadingResults: false,
+        resultsError: errorMessage,
+      }));
+    }
+  }, []);
+
+  // Start polling job status
+  const startPolling = useCallback(
+    (jobId: string): void => {
+      // Clear any existing polling
+      if (pollingIntervalId) {
+        clearInterval(pollingIntervalId);
+      }
+
+      setState((prev) => ({
+        ...prev,
+        isPolling: true,
+        pollingError: null,
+      }));
+
+      // Poll immediately
+      getJobStatus(jobId).then((status) => {
+        if (status) {
+          setState((prev) => ({ ...prev, jobStatus: status }));
+
+          // Update job status in history
+          updateJobInHistory(jobId, {
+            status: status.state,
+            updated_time: status.updated_time,
+          });
+
+          // If job is complete, stop polling and get results
+          if (status.is_complete) {
+            console.log(
+              `🏁 Job ${jobId} completed with status: ${status.state}, successful: ${status.is_successful}`
+            );
+            // Stop polling inline
+            if (pollingIntervalId) {
+              clearInterval(pollingIntervalId);
+              setPollingIntervalId(null);
+            }
+            setState((prev) => ({ ...prev, isPolling: false }));
+
+            if (status.is_successful) {
+              console.log(
+                `🚀 Job ${jobId} was successful, fetching results...`
+              );
+              // Get results for completed successful jobs
+              getResults(jobId);
+            } else {
+              console.log(
+                `❌ Job ${jobId} was not successful, skipping results fetch`
+              );
+            }
+          }
+        }
+      });
+
+      // Set up interval polling
+      const intervalId = setInterval(async () => {
+        const status = await getJobStatus(jobId);
+        if (status) {
+          setState((prev) => ({ ...prev, jobStatus: status }));
+
+          // Update job status in history
+          updateJobInHistory(jobId, {
+            status: status.state,
+            updated_time: status.updated_time,
+          });
+
+          // If job is complete, stop polling and get results
+          if (status.is_complete) {
+            console.log(
+              `🏁 Job ${jobId} completed in polling loop with status: ${status.state}, successful: ${status.is_successful}`
+            );
+            // Stop polling inline
+            clearInterval(intervalId);
+            setPollingIntervalId(null);
+            setState((prev) => ({ ...prev, isPolling: false }));
+
+            if (status.is_successful) {
+              console.log(
+                `🚀 Job ${jobId} was successful in polling loop, fetching results...`
+              );
+              // Get results for completed successful jobs
+              getResults(jobId);
+            } else {
+              console.log(
+                `❌ Job ${jobId} was not successful in polling loop, skipping results fetch`
+              );
+            }
+          }
+        } else {
+          setState((prev) => ({
+            ...prev,
+            pollingError: "Failed to get job status",
+          }));
+        }
+      }, POLLING_INTERVAL);
+
+      setPollingIntervalId(intervalId);
+    },
+    [pollingIntervalId, getJobStatus, getResults]
+  );
+
+  // Stop polling
+  const stopPolling = useCallback((): void => {
+    if (pollingIntervalId) {
+      clearInterval(pollingIntervalId);
+      setPollingIntervalId(null);
+    }
+    setState((prev) => ({
+      ...prev,
+      isPolling: false,
+    }));
+  }, [pollingIntervalId]);
+
+  // Clear job history
+  const clearJobHistory = useCallback((): void => {
+    if (typeof window !== "undefined") {
+      localStorage.removeItem(STORAGE_KEY);
+    }
+    setState((prev) => ({ ...prev, jobHistory: [] }));
+  }, []);
+
+  // Reset all state
+  const reset = useCallback((): void => {
+    if (pollingIntervalId) {
+      clearInterval(pollingIntervalId);
+      setPollingIntervalId(null);
+    }
+
+    const currentHistory = loadJobHistory();
+    setState({
+      isLoadingResults: false,
+      isPolling: false,
+      isSubmitting: false,
+      jobHistory: currentHistory,
+      jobId: null,
+      jobResults: null,
+      jobStatus: null,
+      pollingError: null,
+      resultsError: null,
+      submissionError: null,
+    });
+  }, [pollingIntervalId]);
+
+  // Auto-start polling when a new job is submitted
+  useEffect((): void => {
+    if (state.jobId && !state.isPolling && !state.jobResults) {
+      startPolling(state.jobId);
+    }
+  }, [state.jobId, state.isPolling, state.jobResults, startPolling]);
+
+  // Cleanup on unmount
+  useEffect((): (() => void) => {
+    return (): void => {
+      if (pollingIntervalId) {
+        clearInterval(pollingIntervalId);
+      }
+    };
+  }, [pollingIntervalId]);
+
+  return {
+    // State
+    ...state,
+
+    // Actions
+    clearJobHistory,
+    getResults,
+    reset,
+    startPolling,
+    stopPolling,
+    submitJob,
+  };
+};
diff --git a/app/views/GalaxyJobView/galaxyJobView.styles.ts b/app/views/GalaxyJobView/galaxyJobView.styles.ts
new file mode 100644
index 000000000..3bb6dadcb
--- /dev/null
+++ b/app/views/GalaxyJobView/galaxyJobView.styles.ts
@@ -0,0 +1,18 @@
+import styled from "@emotion/styled";
+import { GridPaperSection } from "@databiosphere/findable-ui/lib/components/common/Section/section.styles";
+
+export const TestSection = styled(GridPaperSection)`
+  && {
+    margin: 0 auto;
+    max-width: 1200px;
+    padding: 32px 20px;
+  }
+`;
+
+export const TestContainer = styled.div`
+  display: flex;
+  flex-direction: column;
+  gap: 24px;
+  margin: 0 auto;
+  max-width: 800px;
+`;
diff --git a/app/views/GalaxyJobView/galaxyJobView.tsx b/app/views/GalaxyJobView/galaxyJobView.tsx
new file mode 100644
index 000000000..5b89bbc2f
--- /dev/null
+++ b/app/views/GalaxyJobView/galaxyJobView.tsx
@@ -0,0 +1,26 @@
+import { Fragment } from "react";
+import { SectionHero } from "../../components/Layout/components/AppLayout/components/Section/components/SectionHero/sectionHero";
+import { GalaxyJob } from "../../components/GalaxyJob/galaxyJob";
+import { TestContainer, TestSection } from "./galaxyJobView.styles";
+
+const BREADCRUMBS = [
+  { path: "/", text: "Home" },
+  { path: "/galaxy-test", text: "Galaxy Integration Test" },
+];
+
+export const GalaxyJobView = (): JSX.Element => {
+  return (
+    <Fragment>
+      <SectionHero
+        breadcrumbs={BREADCRUMBS}
+        head="Galaxy Integration Test"
+        subHead="Test the Galaxy Jobs API integration by submitting data and tracking job execution"
+      />
+      <TestSection>
+        <TestContainer>
+          <GalaxyJob />
+        </TestContainer>
+      </TestSection>
+    </Fragment>
+  );
+};
diff --git a/backend/.env.example b/backend/.env.example
index f786a7588..14b7a7353 100644
--- a/backend/.env.example
+++ b/backend/.env.example
@@ -4,6 +4,14 @@ REDIS_URL=redis://redis:6379/0
 # Database Configuration (for future use)
 DATABASE_URL=postgresql://user:pass@localhost/dbname
 
+# Galaxy API Configuration
+GALAXY_API_URL=https://test.galaxyproject.org/api
+GALAXY_API_KEY=your_galaxy_service_account_key_here
+
+# Galaxy Tool IDs (can be customized if needed)
+GALAXY_UPLOAD_TOOL_ID=upload1
+GALAXY_RANDOM_LINES_TOOL_ID=random_lines1
+
 # Application Configuration
 CORS_ORIGINS=http://localhost:3000,http://localhost
 LOG_LEVEL=INFO
diff --git a/backend/app/api/v1/galaxy.py b/backend/app/api/v1/galaxy.py
new file mode 100644
index 000000000..fd5bd25be
--- /dev/null
+++ b/backend/app/api/v1/galaxy.py
@@ -0,0 +1,253 @@
+"""Galaxy API integration endpoints."""
+
+import logging
+from fastapi import APIRouter, Depends, HTTPException, BackgroundTasks
+from typing import Dict, Any
+
+from app.core.dependencies import get_cache_service
+from app.core.cache import CacheService
+from app.services.galaxy_service import GalaxyService
+from app.models.galaxy import (
+    GalaxyJobSubmission,
+    GalaxyJobResponse,
+    GalaxyJobStatus,
+    GalaxyJobResult,
+    GalaxyJobState
+)
+
+logger = logging.getLogger(__name__)
+router = APIRouter()
+
+
+async def get_galaxy_service(cache: CacheService = Depends(get_cache_service)) -> GalaxyService:
+    """Dependency to get Galaxy service instance."""
+    return GalaxyService(cache)
+
+
+@router.get("/health")
+async def galaxy_health(galaxy_service: GalaxyService = Depends(get_galaxy_service)):
+    """Check Galaxy service health and configuration."""
+    return {
+        "status": "healthy" if galaxy_service.is_available() else "unavailable",
+        "galaxy_configured": galaxy_service.is_available(),
+        "api_url": galaxy_service.settings.GALAXY_API_URL,
+        "upload_tool_id": galaxy_service.settings.GALAXY_UPLOAD_TOOL_ID,
+        "random_lines_tool_id": galaxy_service.settings.GALAXY_RANDOM_LINES_TOOL_ID
+    }
+
+
+@router.post("/submit-job", response_model=GalaxyJobResponse)
+async def submit_galaxy_job(
+    submission: GalaxyJobSubmission,
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """
+    Submit a job to Galaxy: upload tabular data and run random lines tool.
+    
+    Returns job ID for tracking the random lines tool execution.
+    """
+    try:
+        if not galaxy_service.is_available():
+            raise HTTPException(
+                status_code=503, 
+                detail="Galaxy service is not available. Please check configuration."
+            )
+        
+        # Validate input data
+        if not submission.tabular_data.strip():
+            raise HTTPException(
+                status_code=400,
+                detail="Tabular data cannot be empty"
+            )
+        
+        if submission.num_random_lines <= 0:
+            raise HTTPException(
+                status_code=400,
+                detail="Number of random lines must be greater than 0"
+            )
+        
+        # Check if data has multiple lines
+        lines = submission.tabular_data.strip().split('\n')
+        if len(lines) < submission.num_random_lines:
+            raise HTTPException(
+                status_code=400,
+                detail=f"Cannot select {submission.num_random_lines} lines from {len(lines)} lines of data"
+            )
+        
+        logger.info(f"Submitting Galaxy job with {len(lines)} lines of data, selecting {submission.num_random_lines} random lines")
+        
+        # Submit job to Galaxy
+        response = await galaxy_service.submit_job(submission)
+        
+        logger.info(f"Galaxy job submitted successfully: {response.job_id}")
+        return response
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        logger.error(f"Failed to submit Galaxy job: {str(e)}")
+        raise HTTPException(
+            status_code=500,
+            detail=f"Failed to submit job to Galaxy: {str(e)}"
+        )
+
+
+@router.get("/jobs/{job_id}/status", response_model=GalaxyJobStatus)
+async def get_job_status(
+    job_id: str,
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """Get the current status of a Galaxy job."""
+    try:
+        if not galaxy_service.is_available():
+            raise HTTPException(
+                status_code=503, 
+                detail="Galaxy service is not available"
+            )
+        
+        logger.debug(f"Getting status for job: {job_id}")
+        status = await galaxy_service.get_job_status(job_id)
+        
+        return status
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        logger.error(f"Failed to get job status for {job_id}: {str(e)}")
+        raise HTTPException(
+            status_code=500,
+            detail=f"Failed to get job status: {str(e)}"
+        )
+
+
+@router.get("/jobs/{job_id}/results", response_model=GalaxyJobResult)
+async def get_job_results(
+    job_id: str,
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """Get the complete results from a finished Galaxy job."""
+    try:
+        if not galaxy_service.is_available():
+            raise HTTPException(
+                status_code=503, 
+                detail="Galaxy service is not available"
+            )
+        
+        logger.debug(f"Getting results for job: {job_id}")
+        results = await galaxy_service.get_job_results(job_id)
+        
+        return results
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        # Check if it's a "job not complete" error
+        if "not yet complete" in str(e):
+            raise HTTPException(
+                status_code=202,  # Accepted but processing not complete
+                detail=str(e)
+            )
+        elif "failed" in str(e).lower():
+            raise HTTPException(
+                status_code=422,  # Unprocessable Entity - job failed
+                detail=str(e)
+            )
+        else:
+            logger.error(f"Failed to get job results for {job_id}: {str(e)}")
+            raise HTTPException(
+                status_code=500,
+                detail=f"Failed to get job results: {str(e)}"
+            )
+
+
+@router.get("/jobs/{job_id}", response_model=Dict[str, Any])
+async def get_job_details(
+    job_id: str,
+    include_results: bool = False,
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """
+    Get comprehensive job information including status and optionally results.
+    
+    This is a convenience endpoint that combines status and results.
+    """
+    try:
+        if not galaxy_service.is_available():
+            raise HTTPException(
+                status_code=503, 
+                detail="Galaxy service is not available"
+            )
+        
+        # Always get status
+        status = await galaxy_service.get_job_status(job_id)
+        
+        response = {
+            "job_id": job_id,
+            "status": status.dict()
+        }
+        
+        # Include results if requested and job is complete
+        if include_results and status.is_complete and status.is_successful:
+            try:
+                results = await galaxy_service.get_job_results(job_id)
+                response["results"] = results.dict()
+            except Exception as e:
+                logger.warning(f"Failed to get results for completed job {job_id}: {e}")
+                response["results_error"] = str(e)
+        
+        return response
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        logger.error(f"Failed to get job details for {job_id}: {str(e)}")
+        raise HTTPException(
+            status_code=500,
+            detail=f"Failed to get job details: {str(e)}"
+        )
+
+
+@router.delete("/jobs/{job_id}")
+async def cancel_job(
+    job_id: str,
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """Cancel a running Galaxy job (future implementation)."""
+    # Note: This would require implementing job cancellation in GalaxyService
+    # For now, just return a placeholder response
+    raise HTTPException(
+        status_code=501,
+        detail="Job cancellation not yet implemented"
+    )
+
+
+# Example endpoint for testing Galaxy connectivity
+@router.post("/test-connection")
+async def test_galaxy_connection(
+    galaxy_service: GalaxyService = Depends(get_galaxy_service)
+):
+    """Test connection to Galaxy API (admin/debug endpoint)."""
+    try:
+        if not galaxy_service.is_available():
+            return {
+                "status": "error",
+                "message": "Galaxy service not configured",
+                "configured": False
+            }
+        
+        # Try a simple API call to test connectivity
+        # This could be improved to actually test API access
+        return {
+            "status": "success",
+            "message": "Galaxy service is configured and available",
+            "configured": True,
+            "api_url": galaxy_service.settings.GALAXY_API_URL
+        }
+        
+    except Exception as e:
+        logger.error(f"Galaxy connection test failed: {e}")
+        return {
+            "status": "error", 
+            "message": f"Connection test failed: {str(e)}",
+            "configured": True
+        }
\ No newline at end of file
diff --git a/backend/app/core/config.py b/backend/app/core/config.py
index ef69175e9..59137e37a 100644
--- a/backend/app/core/config.py
+++ b/backend/app/core/config.py
@@ -15,6 +15,14 @@ class Settings:
     # Database settings (for future use)
     DATABASE_URL: str = os.getenv("DATABASE_URL", "")
 
+    # Galaxy API settings
+    GALAXY_API_URL: str = os.getenv("GALAXY_API_URL", "https://test.galaxyproject.org/api")
+    GALAXY_API_KEY: str = os.getenv("GALAXY_API_KEY", "")
+
+    # Galaxy Tool IDs
+    GALAXY_UPLOAD_TOOL_ID: str = os.getenv("GALAXY_UPLOAD_TOOL_ID", "upload1")
+    GALAXY_RANDOM_LINES_TOOL_ID: str = os.getenv("GALAXY_RANDOM_LINES_TOOL_ID", "random_lines1")
+
     # CORS settings
     CORS_ORIGINS: List[str] = os.getenv("CORS_ORIGINS", "http://localhost:3000").split(
         ","
diff --git a/backend/app/main.py b/backend/app/main.py
index 3d8521463..1558901f7 100644
--- a/backend/app/main.py
+++ b/backend/app/main.py
@@ -1,7 +1,7 @@
 from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 
-from app.api.v1 import cache, health, version
+from app.api.v1 import cache, galaxy, health, version
 from app.core.config import get_settings
 
 settings = get_settings()
@@ -25,6 +25,7 @@
 app.include_router(health.router, prefix="/api/v1", tags=["health"])
 app.include_router(cache.router, prefix="/api/v1/cache", tags=["cache"])
 app.include_router(version.router, prefix="/api/v1/version", tags=["version"])
+app.include_router(galaxy.router, prefix="/api/v1/galaxy", tags=["galaxy"])
 
 
 @app.get("/")
diff --git a/backend/app/models/__init__.py b/backend/app/models/__init__.py
new file mode 100644
index 000000000..4e0130476
--- /dev/null
+++ b/backend/app/models/__init__.py
@@ -0,0 +1 @@
+"""Data models for the BRC Analytics API"""
\ No newline at end of file
diff --git a/backend/app/models/galaxy.py b/backend/app/models/galaxy.py
new file mode 100644
index 000000000..3e943c12b
--- /dev/null
+++ b/backend/app/models/galaxy.py
@@ -0,0 +1,123 @@
+"""Galaxy API integration models."""
+
+from typing import Dict, List, Optional, Any
+from pydantic import BaseModel, Field
+from enum import Enum
+
+
+class GalaxyJobState(str, Enum):
+    """Galaxy job states as defined in the API."""
+    NEW = "new"
+    UPLOAD = "upload"
+    WAITING = "waiting"
+    QUEUED = "queued"
+    RUNNING = "running"
+    OK = "ok"
+    ERROR = "error"
+    PAUSED = "paused"
+    DELETED = "deleted"
+    DELETED_NEW = "deleted_new"
+
+
+class GalaxyJobSubmission(BaseModel):
+    """Request model for submitting a job to Galaxy."""
+    tabular_data: str = Field(..., description="Tabular data content (TSV format)")
+    num_random_lines: int = Field(default=10, ge=1, le=1000, description="Number of random lines to select")
+    filename: Optional[str] = Field(default="input_data", description="Name for the uploaded file")
+
+
+class GalaxyJobResponse(BaseModel):
+    """Response model for job submission."""
+    job_id: str = Field(..., description="Galaxy job ID for tracking")
+    upload_dataset_id: str = Field(..., description="ID of the uploaded dataset")
+    status: str = Field(default="submitted", description="Initial job status")
+    message: str = Field(default="Job submitted successfully")
+
+
+class GalaxyDataset(BaseModel):
+    """Model for Galaxy dataset information."""
+    id: str
+    name: str
+    state: str
+    file_ext: str
+    file_size: Optional[int] = None
+    created_time: Optional[str] = None
+    updated_time: Optional[str] = None
+
+
+class GalaxyJobOutput(BaseModel):
+    """Model for Galaxy job output information."""
+    id: str
+    name: str
+    dataset: GalaxyDataset
+
+
+class GalaxyJobDetails(BaseModel):
+    """Detailed information about a Galaxy job."""
+    id: str
+    tool_id: str
+    state: GalaxyJobState
+    created_time: str
+    updated_time: str
+    outputs: List[GalaxyJobOutput] = []
+    inputs: Dict[str, Any] = {}
+    stdout: Optional[str] = None
+    stderr: Optional[str] = None
+    exit_code: Optional[int] = None
+
+
+class GalaxyJobStatus(BaseModel):
+    """Status response for a Galaxy job."""
+    job_id: str
+    state: GalaxyJobState
+    created_time: str
+    updated_time: str
+    is_complete: bool = Field(default=False, description="Whether the job has finished (success or failure)")
+    is_successful: bool = Field(default=False, description="Whether the job completed successfully")
+    outputs: List[GalaxyJobOutput] = []
+    stdout: Optional[str] = None
+    stderr: Optional[str] = None
+    exit_code: Optional[int] = None
+
+
+class GalaxyJobResult(BaseModel):
+    """Final results from a completed Galaxy job."""
+    job_id: str
+    status: GalaxyJobState
+    outputs: List[GalaxyJobOutput]
+    results: Dict[str, str] = Field(default_factory=dict, description="Output dataset contents")
+    processing_time: Optional[str] = None
+    created_time: str
+    completed_time: Optional[str] = None
+
+
+class GalaxyAPIError(BaseModel):
+    """Model for Galaxy API errors."""
+    error: str
+    message: str
+    status_code: int
+    job_id: Optional[str] = None
+
+
+# Internal Galaxy API request/response models (for service layer)
+
+class GalaxyUploadRequest(BaseModel):
+    """Internal model for Galaxy upload tool request."""
+    tool_id: str
+    history_id: str
+    inputs: Dict[str, Any]
+
+
+class GalaxyToolRequest(BaseModel):
+    """Internal model for Galaxy tool execution request."""
+    tool_id: str
+    history_id: str
+    inputs: Dict[str, Any]
+
+
+class GalaxyAPIResponse(BaseModel):
+    """Generic Galaxy API response wrapper."""
+    success: bool = True
+    data: Optional[Dict[str, Any]] = None
+    error: Optional[str] = None
+    status_code: int = 200
\ No newline at end of file
diff --git a/backend/app/services/galaxy_service.py b/backend/app/services/galaxy_service.py
new file mode 100644
index 000000000..871a4404c
--- /dev/null
+++ b/backend/app/services/galaxy_service.py
@@ -0,0 +1,340 @@
+"""Galaxy API integration service using BioBLEND."""
+
+import asyncio
+import logging
+from typing import Dict, List, Optional, Any, Tuple
+from bioblend.galaxy import GalaxyInstance
+from bioblend.galaxy.histories import HistoryClient
+from bioblend.galaxy.tools import ToolClient
+from bioblend.galaxy.jobs import JobsClient
+from bioblend.galaxy.datasets import DatasetClient
+from app.core.config import get_settings
+from app.core.cache import CacheService, CacheTTL
+from app.models.galaxy import (
+    GalaxyJobSubmission,
+    GalaxyJobResponse,
+    GalaxyJobDetails,
+    GalaxyJobStatus,
+    GalaxyJobResult,
+    GalaxyJobState,
+    GalaxyJobOutput,
+    GalaxyDataset,
+    GalaxyAPIError,
+    GalaxyAPIResponse
+)
+
+logger = logging.getLogger(__name__)
+
+
+class GalaxyService:
+    """Service for interacting with Galaxy API using BioBLEND."""
+    
+    def __init__(self, cache: CacheService):
+        self.cache = cache
+        self.settings = get_settings()
+        
+        # Check if Galaxy is configured
+        if not self.settings.GALAXY_API_KEY:
+            logger.warning("Galaxy API key not configured - Galaxy features will be disabled")
+            self._galaxy_available = False
+            self.gi = None
+        else:
+            self._galaxy_available = True
+            # Initialize BioBLEND Galaxy instance
+            self.gi = GalaxyInstance(
+                url=self.settings.GALAXY_API_URL.replace('/api', ''),  # BioBLEND expects base URL without /api
+                key=self.settings.GALAXY_API_KEY
+            )
+            logger.info(f"Galaxy service initialized with BioBLEND for URL: {self.settings.GALAXY_API_URL}")
+        
+        # Shared BRC Analytics history
+        self._shared_history_id = None
+    
+    def is_available(self) -> bool:
+        """Check if Galaxy service is available."""
+        return self._galaxy_available and bool(self.settings.GALAXY_API_KEY)
+    
+    async def submit_job(self, submission: GalaxyJobSubmission) -> GalaxyJobResponse:
+        """
+        Submit a complete job: upload data and run the random lines tool.
+        
+        Returns job ID for tracking the random lines tool execution.
+        """
+        if not self.is_available():
+            raise Exception("Galaxy service not available - check API key configuration")
+        
+        logger.info(f"Submitting Galaxy job with {len(submission.tabular_data)} chars of data")
+        
+        try:
+            # Step 0: Get or create the shared BRC Analytics history
+            history_id = await self._get_or_create_shared_history()
+            
+            # Step 1: Upload the tabular data
+            upload_dataset_id = await self._upload_tabular_data(
+                submission.tabular_data, 
+                submission.filename,
+                history_id
+            )
+            
+            # Step 2: Run the random lines tool on the uploaded data
+            job_id = await self._run_random_lines_tool(
+                upload_dataset_id, 
+                submission.num_random_lines,
+                history_id
+            )
+            
+            return GalaxyJobResponse(
+                job_id=job_id,
+                upload_dataset_id=upload_dataset_id,
+                status="submitted",
+                message=f"Job {job_id} submitted successfully"
+            )
+            
+        except Exception as e:
+            logger.error(f"Failed to submit Galaxy job: {str(e)}")
+            raise Exception(f"Galaxy job submission failed: {str(e)}")
+    
+    async def get_job_status(self, job_id: str) -> GalaxyJobStatus:
+        """Get the current status of a Galaxy job using BioBLEND."""
+        if not self.is_available():
+            raise Exception("Galaxy service not available")
+        
+        # Check cache first
+        cache_key = self.cache.make_key("galaxy:job_status", {"job_id": job_id})
+        cached_status = await self.cache.get(cache_key)
+        
+        if cached_status and cached_status.get("state") in ["ok", "error"]:
+            # Job is complete, return cached result
+            return GalaxyJobStatus(**cached_status)
+        
+        try:
+            # Use BioBLEND to get job details
+            job_data = self.gi.jobs.show_job(job_id)
+            
+            # Debug: log the full job data response
+            logger.info(f"BioBLEND job {job_id} full response: {job_data}")
+            
+            # Parse job status
+            status = GalaxyJobStatus(
+                job_id=job_id,
+                state=GalaxyJobState(job_data["state"]),
+                created_time=job_data["create_time"],
+                updated_time=job_data["update_time"],
+                is_complete=job_data["state"] in ["ok", "error", "deleted"],
+                is_successful=job_data["state"] == "ok",
+                stdout=job_data.get("stdout"),
+                stderr=job_data.get("stderr"),
+                exit_code=job_data.get("exit_code")
+            )
+            
+            # Debug: log state changes
+            logger.info(f"BioBLEND Job {job_id} current state: {job_data['state']}, complete: {status.is_complete}, successful: {status.is_successful}")
+            
+            # If job is complete, get outputs
+            if status.is_complete:
+                status.outputs = await self._get_job_outputs(job_id)
+                # Cache completed job status for 1 hour
+                await self.cache.set(cache_key, status.dict(), CacheTTL.ONE_HOUR)
+            
+            return status
+                
+        except Exception as e:
+            logger.error(f"BioBLEND error getting job status: {e}")
+            raise Exception(f"Failed to get job status using BioBLEND: {str(e)}")
+    
+    async def get_job_results(self, job_id: str) -> GalaxyJobResult:
+        """Get the complete results from a finished Galaxy job."""
+        if not self.is_available():
+            raise Exception("Galaxy service not available")
+        
+        # Check cache first
+        cache_key = self.cache.make_key("galaxy:job_results", {"job_id": job_id})
+        cached_results = await self.cache.get(cache_key)
+        if cached_results:
+            return GalaxyJobResult(**cached_results)
+        
+        try:
+            # Get job status first
+            status = await self.get_job_status(job_id)
+            
+            if not status.is_complete:
+                raise Exception(f"Job {job_id} is not yet complete (state: {status.state})")
+            
+            if not status.is_successful:
+                raise Exception(f"Job {job_id} failed with state: {status.state}")
+            
+            # Get output contents
+            results = {}
+            for output in status.outputs:
+                try:
+                    content = await self._get_dataset_content(output.dataset.id)
+                    results[output.name] = content
+                except Exception as e:
+                    logger.warning(f"Failed to get content for output {output.name}: {e}")
+                    results[output.name] = f"Error retrieving content: {str(e)}"
+            
+            # Create result object
+            result = GalaxyJobResult(
+                job_id=job_id,
+                status=status.state,
+                outputs=status.outputs,
+                results=results,
+                created_time=status.created_time,
+                completed_time=status.updated_time
+            )
+            
+            # Cache results for 24 hours
+            await self.cache.set(cache_key, result.dict(), CacheTTL.ONE_DAY)
+            return result
+            
+        except Exception as e:
+            logger.error(f"Error getting job results: {e}")
+            raise Exception(f"Failed to get job results: {str(e)}")
+    
+    
+    async def _upload_tabular_data(self, data: str, filename: str, history_id: str) -> str:
+        """Upload tabular data to Galaxy using BioBLEND and return dataset ID."""
+        try:
+            # Use BioBLEND's paste_content method for uploading text data
+            upload_result = self.gi.tools.paste_content(
+                content=data,
+                history_id=history_id,
+                file_name=filename,
+                file_type='tabular'
+            )
+            
+            logger.info(f"BioBLEND upload response: {upload_result}")
+            
+            # Get the output dataset ID from the outputs
+            outputs = upload_result.get("outputs", [])
+            if not outputs:
+                raise Exception("No outputs returned from BioBLEND upload")
+            
+            dataset_id = outputs[0]["id"]
+            logger.info(f"Uploaded data to dataset: {dataset_id} using BioBLEND")
+            return dataset_id
+            
+        except Exception as e:
+            logger.error(f"BioBLEND upload failed: {e}")
+            raise Exception(f"Failed to upload data using BioBLEND: {str(e)}")
+    
+    async def _run_random_lines_tool(self, input_dataset_id: str, num_lines: int, history_id: str) -> str:
+        """Run the random lines tool using BioBLEND and return job ID."""
+        try:
+            tool_inputs = {
+                "input": {
+                    "src": "hda",
+                    "id": input_dataset_id
+                },
+                "num_lines": str(num_lines),
+                "seed_source|seed_source_selector": "no_seed"
+            }
+            
+            # Use BioBLEND to run the tool
+            tool_response = self.gi.tools.run_tool(
+                history_id=history_id,
+                tool_id=self.settings.GALAXY_RANDOM_LINES_TOOL_ID,
+                tool_inputs=tool_inputs
+            )
+            
+            logger.info(f"BioBLEND tool response: {tool_response}")
+            
+            # Get the job ID
+            jobs = tool_response.get("jobs", [])
+            if not jobs:
+                raise Exception("No jobs returned from BioBLEND tool execution")
+            
+            job_id = jobs[0]["id"]
+            logger.info(f"Started random lines tool with BioBLEND job ID: {job_id}")
+            return job_id
+            
+        except Exception as e:
+            logger.error(f"BioBLEND tool execution failed: {e}")
+            raise Exception(f"Failed to run random lines tool using BioBLEND: {str(e)}")
+    
+    async def _get_job_outputs(self, job_id: str) -> List[GalaxyJobOutput]:
+        """Get output information for a job using BioBLEND."""
+        try:
+            # Get job outputs using BioBLEND
+            job_details = self.gi.jobs.show_job(job_id)
+            outputs = []
+            
+            # Get outputs from job details
+            job_outputs = job_details.get("outputs", {})
+            
+            for output_name, output_data in job_outputs.items():
+                # Get dataset details using BioBLEND
+                dataset_details = self.gi.datasets.show_dataset(output_data["id"])
+                
+                dataset_info = GalaxyDataset(
+                    id=dataset_details["id"],
+                    name=dataset_details["name"],
+                    state=dataset_details["state"],
+                    file_ext=dataset_details.get("file_ext", "txt"),
+                    file_size=dataset_details.get("file_size"),
+                    created_time=dataset_details.get("created_time"),
+                    updated_time=dataset_details.get("updated_time")
+                )
+                
+                output = GalaxyJobOutput(
+                    id=dataset_details["id"],
+                    name=output_name,
+                    dataset=dataset_info
+                )
+                outputs.append(output)
+            
+            return outputs
+            
+        except Exception as e:
+            logger.error(f"BioBLEND error getting job outputs: {e}")
+            # Fallback to empty outputs list
+            return []
+    
+    async def _get_dataset_content(self, dataset_id: str) -> str:
+        """Get the actual content of a dataset using BioBLEND."""
+        try:
+            # Use BioBLEND to download dataset content
+            content = self.gi.datasets.download_dataset(dataset_id)
+            if isinstance(content, bytes):
+                return content.decode('utf-8')
+            return str(content)
+        
+        except Exception as e:
+            logger.error(f"BioBLEND error getting dataset content: {e}")
+            return f"Error retrieving dataset content: {str(e)}"
+    
+    async def _get_or_create_shared_history(self) -> str:
+        """Get or create the shared 'BRC ANALYTICS JOBS' history using BioBLEND."""
+        shared_history_name = "BRC ANALYTICS JOBS"
+        
+        if self._shared_history_id:
+            return self._shared_history_id
+        
+        try:
+            # Get all histories using BioBLEND
+            histories = self.gi.histories.get_histories()
+            
+            # Look for existing shared history
+            for history in histories:
+                if history.get("name") == shared_history_name:
+                    history_id = history["id"]
+                    logger.info(f"Using existing shared history: {history_id} ({shared_history_name})")
+                    self._shared_history_id = history_id
+                    return history_id
+            
+            # If we get here, the shared history doesn't exist, so create it
+            logger.info(f"Creating new shared history: {shared_history_name}")
+            new_history = self.gi.histories.create_history(name=shared_history_name)
+            history_id = new_history["id"]
+            logger.info(f"Created shared history: {history_id} ({shared_history_name})")
+            self._shared_history_id = history_id
+            return history_id
+                
+        except Exception as e:
+            logger.error(f"Error getting or creating shared history: {e}")
+            # Fallback to creating a new history with timestamp
+            import time
+            fallback_name = f"{shared_history_name} - {int(time.time())}"
+            logger.warning(f"Falling back to creating history: {fallback_name}")
+            fallback_history = self.gi.histories.create_history(name=fallback_name)
+            return fallback_history["id"]
\ No newline at end of file
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index c9474e351..71a2f5a97 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -8,12 +8,13 @@ authors = [
 readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
+    "bioblend>=1.4.0",
     "fastapi>=0.116.1",
-    "uvicorn>=0.35.0",
-    "redis>=6.4.0",
     "httpx>=0.28.1",
     "pydantic>=2.11.7",
-    "python-dotenv>=1.1.1"
+    "python-dotenv>=1.1.1",
+    "redis>=6.4.0",
+    "uvicorn>=0.35.0"
 ]
 
 [project.optional-dependencies]
diff --git a/pages/galaxy-test/index.tsx b/pages/galaxy-test/index.tsx
new file mode 100644
index 000000000..f90de14b9
--- /dev/null
+++ b/pages/galaxy-test/index.tsx
@@ -0,0 +1,22 @@
+import { GetStaticProps } from "next";
+import { StyledPagesMain } from "../../app/components/Layout/components/Main/main.styles";
+import { GalaxyJobView } from "../../app/views/GalaxyJobView/galaxyJobView";
+
+export const GalaxyJob = (): JSX.Element => {
+  return <GalaxyJobView />;
+};
+
+export const getStaticProps: GetStaticProps = async () => {
+  return {
+    props: {
+      pageTitle: "Galaxy Integration Test",
+      themeOptions: {
+        palette: { background: { default: "#FAFBFB" } }, // SMOKE_LIGHTEST
+      },
+    },
+  };
+};
+
+export default GalaxyJob;
+
+GalaxyJob.Main = StyledPagesMain;
diff --git a/tests/e2e/09-galaxy-integration.spec.ts b/tests/e2e/09-galaxy-integration.spec.ts
new file mode 100644
index 000000000..74a2d487e
--- /dev/null
+++ b/tests/e2e/09-galaxy-integration.spec.ts
@@ -0,0 +1,337 @@
+import { test, expect } from "@playwright/test";
+
+test.describe("BRC Analytics - Galaxy Integration", () => {
+  test("Galaxy service health check", async ({ request }) => {
+    // Check backend health first
+    const response = await request.get("http://localhost:8000/api/v1/health");
+    expect(response.ok()).toBeTruthy();
+
+    const health = await response.json();
+    console.log("Backend health:", health);
+
+    // Check Galaxy-specific health endpoint
+    const galaxyResponse = await request.get(
+      "http://localhost:8000/api/v1/galaxy/health"
+    );
+    expect(galaxyResponse.ok()).toBeTruthy();
+
+    const galaxyHealth = await galaxyResponse.json();
+    console.log("Galaxy health:", galaxyHealth);
+
+    expect(galaxyHealth.status).toBe("healthy");
+    expect(galaxyHealth.galaxy_configured).toBe(true);
+    expect(galaxyHealth.api_url).toMatch(
+      /galaxyproject\.org|host\.docker\.internal|localhost/
+    );
+
+    if (galaxyHealth.galaxy_configured) {
+      console.log("✅ Galaxy is configured and available");
+    } else {
+      console.log("⚠️ Galaxy is not configured - skipping Galaxy tests");
+    }
+  });
+
+  // eslint-disable-next-line sonarjs/cognitive-complexity -- Complex test that covers full Galaxy job lifecycle
+  test("Galaxy job submission and lifecycle", async ({ request }) => {
+    // First check if Galaxy is available
+    const healthResponse = await request.get(
+      "http://localhost:8000/api/v1/galaxy/health"
+    );
+    const health = await healthResponse.json();
+
+    if (!health.galaxy_configured) {
+      console.log("Skipping Galaxy test - service not configured");
+      // Skip remaining assertions if Galaxy is not configured
+      expect(health.galaxy_configured).toBe(false);
+      return;
+    }
+
+    // Test data for Galaxy job submission
+    const testData = `header1\theader2\theader3
+sample1\tvalue1\tdata1
+sample2\tvalue2\tdata2
+sample3\tvalue3\tdata3
+sample4\tvalue4\tdata4
+sample5\tvalue5\tdata5
+sample6\tvalue6\tdata6
+sample7\tvalue7\tdata7
+sample8\tvalue8\tdata8
+sample9\tvalue9\tdata9
+sample10\tvalue10\tdata10`;
+
+    // Step 1: Submit Galaxy job
+    console.log("🚀 Submitting Galaxy job...");
+    const submitResponse = await request.post(
+      "http://localhost:8000/api/v1/galaxy/submit-job",
+      {
+        data: {
+          filename: "e2e-test-data.tsv",
+          num_random_lines: 3,
+          tabular_data: testData,
+        },
+      }
+    );
+
+    expect(submitResponse.ok()).toBeTruthy();
+    const submitResult = await submitResponse.json();
+    console.log("Job submission result:", submitResult);
+
+    expect(submitResult).toHaveProperty("job_id");
+    expect(submitResult).toHaveProperty("upload_dataset_id");
+    expect(submitResult.status).toBe("submitted");
+    expect(submitResult.message).toContain("submitted successfully");
+
+    const jobId = submitResult.job_id;
+    console.log(`📝 Job ID: ${jobId}`);
+
+    // Step 2: Poll job status
+    console.log("⏳ Polling job status...");
+    let jobStatus;
+    let attempts = 0;
+    const maxAttempts = 30; // 5 minutes with 10-second intervals
+
+    do {
+      await new Promise((resolve) => setTimeout(resolve, 10000)); // Wait 10 seconds
+
+      const statusResponse = await request.get(
+        `http://localhost:8000/api/v1/galaxy/jobs/${jobId}/status`
+      );
+      expect(statusResponse.ok()).toBeTruthy();
+
+      jobStatus = await statusResponse.json();
+      console.log(
+        `📊 Job ${jobId} status: ${jobStatus.state} (attempt ${attempts + 1})`
+      );
+
+      expect(jobStatus).toHaveProperty("job_id", jobId);
+      expect(jobStatus).toHaveProperty("state");
+      expect(jobStatus).toHaveProperty("is_complete");
+      expect(jobStatus).toHaveProperty("is_successful");
+      expect(jobStatus).toHaveProperty("created_time");
+      expect(jobStatus).toHaveProperty("updated_time");
+
+      attempts++;
+    } while (!jobStatus.is_complete && attempts < maxAttempts);
+
+    if (!jobStatus.is_complete) {
+      console.log(`⚠️ Job did not complete within ${maxAttempts} attempts`);
+      console.log(`Final status: ${jobStatus.state}`);
+      // Don't fail the test for slow Galaxy infrastructure
+      return;
+    }
+
+    console.log(`✅ Job completed with state: ${jobStatus.state}`);
+
+    // Step 3: Get job results (if successful)
+    if (jobStatus.is_successful) {
+      console.log("📥 Retrieving job results...");
+      const resultsResponse = await request.get(
+        `http://localhost:8000/api/v1/galaxy/jobs/${jobId}/results`
+      );
+      expect(resultsResponse.ok()).toBeTruthy();
+
+      const results = await resultsResponse.json();
+      console.log("Job results:", results);
+
+      expect(results).toHaveProperty("job_id", jobId);
+      expect(results).toHaveProperty("status");
+      expect(results).toHaveProperty("outputs");
+      expect(results).toHaveProperty("results");
+      expect(results).toHaveProperty("created_time");
+      expect(results).toHaveProperty("completed_time");
+
+      // Verify that we got some output data
+      if (results.outputs && results.outputs.length > 0) {
+        console.log(`📊 Job produced ${results.outputs.length} output(s)`);
+
+        // Check that results contain actual data
+        const outputKeys = Object.keys(results.results);
+        expect(outputKeys.length).toBeGreaterThan(0);
+
+        // Verify the random lines output contains 3 lines as requested
+        for (const outputName of outputKeys) {
+          const outputContent = results.results[outputName];
+          if (
+            typeof outputContent === "string" &&
+            outputContent.includes("\t")
+          ) {
+            const lines = outputContent.trim().split("\n");
+            console.log(`📄 Output '${outputName}' has ${lines.length} lines`);
+
+            // Should have header + 3 random lines = 4 total lines
+            expect(lines.length).toBeLessThanOrEqual(4);
+            expect(lines.length).toBeGreaterThan(0);
+          }
+        }
+      }
+    } else {
+      console.log(`❌ Job failed with state: ${jobStatus.state}`);
+      if (jobStatus.stderr) {
+        console.log("Error output:", jobStatus.stderr);
+      }
+    }
+  });
+
+  test("Galaxy job error handling", async ({ request }) => {
+    // First check if Galaxy is available
+    const healthResponse = await request.get(
+      "http://localhost:8000/api/v1/galaxy/health"
+    );
+    const health = await healthResponse.json();
+
+    if (!health.galaxy_configured) {
+      console.log("Skipping Galaxy error test - service not configured");
+      // Skip remaining assertions if Galaxy is not configured
+      expect(health.galaxy_configured).toBe(false);
+      return;
+    }
+
+    // Test 1: Invalid job submission (empty data)
+    console.log("🧪 Testing error handling for empty data...");
+    const emptyDataResponse = await request.post(
+      "http://localhost:8000/api/v1/galaxy/submit-job",
+      {
+        data: {
+          filename: "empty.tsv",
+          num_random_lines: 5,
+          tabular_data: "",
+        },
+      }
+    );
+
+    // Should either reject or handle gracefully
+    if (!emptyDataResponse.ok()) {
+      const error = await emptyDataResponse.json();
+      console.log("Empty data error (expected):", error);
+      expect(emptyDataResponse.status()).toBeGreaterThanOrEqual(400);
+    } else {
+      console.log("Empty data was accepted (Galaxy may handle this)");
+    }
+
+    // Test 2: Non-existent job status
+    console.log("🧪 Testing error handling for non-existent job...");
+    const fakeJobResponse = await request.get(
+      "http://localhost:8000/api/v1/galaxy/jobs/fake-job-id-12345/status"
+    );
+
+    expect(fakeJobResponse.status()).toBeGreaterThanOrEqual(400);
+    const fakeJobError = await fakeJobResponse.json();
+    console.log("Fake job error (expected):", fakeJobError);
+
+    // Test 3: Invalid job results request
+    console.log("🧪 Testing error handling for non-existent job results...");
+    const fakeResultsResponse = await request.get(
+      "http://localhost:8000/api/v1/galaxy/jobs/fake-job-id-12345/results"
+    );
+
+    expect(fakeResultsResponse.status()).toBeGreaterThanOrEqual(400);
+    const fakeResultsError = await fakeResultsResponse.json();
+    console.log("Fake results error (expected):", fakeResultsError);
+  });
+
+  test("Galaxy frontend integration", async ({ page }) => {
+    // Navigate to Galaxy test page
+    console.log("🌐 Testing Galaxy frontend integration...");
+    await page.goto("http://localhost:3000/galaxy-test");
+
+    // Check that the page loads
+    await expect(page.locator("h1").first()).toContainText("Galaxy", {
+      timeout: 10000,
+    });
+
+    // Look for key UI elements
+    const form = page.locator("form");
+    const textArea = page.getByLabel("Tabular Data (TSV format)");
+    const submitButton = page.locator("button[type='submit']");
+
+    await expect(form).toBeVisible();
+    await expect(textArea).toBeVisible();
+    await expect(submitButton).toBeVisible();
+
+    // Check if there's a number input for random lines
+    const numberInput = page.locator("input[type='number']");
+    if (await numberInput.isVisible()) {
+      console.log("✅ Random lines input found");
+    }
+
+    // Check for job history section
+    const historySection = page.locator("text=Job History");
+    if (await historySection.isVisible()) {
+      console.log("✅ Job history section found");
+    }
+
+    // Take a screenshot of the Galaxy test page
+    await page.screenshot({
+      fullPage: true,
+      path: "tests/screenshots/galaxy-test-page.png",
+    });
+
+    console.log("📸 Screenshot saved: galaxy-test-page.png");
+  });
+
+  test("Galaxy frontend job submission simulation", async ({ page }) => {
+    // Navigate to Galaxy test page
+    await page.goto("http://localhost:3000/galaxy-test");
+
+    // Wait for page to load
+    await expect(page.locator("h1").first()).toContainText("Galaxy", {
+      timeout: 10000,
+    });
+
+    // Fill in test data
+    const testData = `gene_id\texpression\tfold_change
+GENE001\t123.45\t2.1
+GENE002\t67.89\t-1.5
+GENE003\t234.56\t3.2
+GENE004\t45.67\t-0.8
+GENE005\t156.78\t1.9`;
+
+    const textArea = page.getByLabel("Tabular Data (TSV format)");
+    await textArea.fill(testData);
+
+    // Set number of random lines
+    const numberInput = page.locator("input[type='number']");
+    if (await numberInput.isVisible()) {
+      await numberInput.fill("3");
+    }
+
+    // Take screenshot before submission
+    await page.screenshot({
+      path: "tests/screenshots/galaxy-test-before-submit.png",
+    });
+
+    // Submit the form (only if we can see the submit button)
+    const submitButton = page.locator("button[type='submit']");
+    if ((await submitButton.isVisible()) && (await submitButton.isEnabled())) {
+      console.log("🚀 Submitting test job via frontend...");
+
+      // Click submit
+      await submitButton.click();
+
+      // Wait a moment for the UI to respond
+      await page.waitForTimeout(2000);
+
+      // Look for success indicators
+      const successMessage = page.locator("text=submitted");
+      const jobIdDisplay = page.locator("text=Job ID");
+
+      if (
+        (await successMessage.isVisible()) ||
+        (await jobIdDisplay.isVisible())
+      ) {
+        console.log("✅ Job submission appears successful in UI");
+
+        // Take screenshot after submission
+        await page.screenshot({
+          path: "tests/screenshots/galaxy-test-after-submit.png",
+        });
+      } else {
+        console.log(
+          "ℹ️ No immediate success indicators found (may be loading)"
+        );
+      }
+    } else {
+      console.log("ℹ️ Submit button not available or disabled");
+    }
+  });
+});

From d5f276606d4becc4833a19413ba7e6b191ced19f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 29 Sep 2025 22:52:34 -0400
Subject: [PATCH 8/9] chore: update README for Galaxy branch and sync
 .gitignore

- Update README to describe Galaxy integration only (not LLM/ENA)
- Sync .gitignore from infrastructure branch
---
 backend/README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/backend/README.md b/backend/README.md
index 0d8cb8ade..5f64dedc3 100644
--- a/backend/README.md
+++ b/backend/README.md
@@ -1,6 +1,6 @@
 # BRC Analytics Backend
 
-FastAPI backend infrastructure for BRC Analytics.
+FastAPI backend infrastructure for BRC Analytics with Galaxy integration.
 
 ## Features
 
@@ -9,6 +9,7 @@ FastAPI backend infrastructure for BRC Analytics.
 - Health check endpoints
 - Docker deployment with nginx reverse proxy
 - uv for dependency management
+- Galaxy workflow execution via BioBLEND
 
 ## Quick Start
 

From 624e82e34f235e356b7da4951dcd27c1cb67718e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 3 Oct 2025 17:12:36 -0400
Subject: [PATCH 9/9] chore: regenerate uv.lock with bioblend dependencies

---
 backend/uv.lock | 491 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 491 insertions(+)

diff --git a/backend/uv.lock b/backend/uv.lock
index a96f5410f..f3282985f 100644
--- a/backend/uv.lock
+++ b/backend/uv.lock
@@ -2,6 +2,79 @@ version = 1
 revision = 3
 requires-python = ">=3.12"
 
+[[package]]
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+]
+
+[[package]]
+name = "aiohttp"
+version = "3.12.15"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "aiohappyeyeballs" },
+    { name = "aiosignal" },
+    { name = "attrs" },
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