Initial commit: BtToxin Pipeline project structure

.env.example

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+# Application
+APP_NAME=BtToxin Pipeline
+DEBUG=false
+
+# Database
+DATABASE_URL=postgresql://postgres:password@localhost:5432/bttoxin
+
+# Redis
+REDIS_URL=redis://localhost:6379/0
+
+# S3/MinIO
+S3_ENDPOINT=http://localhost:9000
+S3_ACCESS_KEY=minioadmin
+S3_SECRET_KEY=minioadmin
+S3_BUCKET=bttoxin-results
+
+# Docker
+DOCKER_IMAGE=quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0
+
+# NCBI
+NCBI_EMAIL=your_email@example.com

.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.so
+.Python
+venv/
+*.egg-info/
+
+# Node
+node_modules/
+dist/
+
+# System
+.DS_Store
+
+# Environment
+.env
+*.log
+
+# Data
+uploads/
+results/
+logs/
+tests/test_data/genomes/*.fna
+
+# IDE
+.vscode/
+.idea/
+*.swp

.woodpecker/test.yml

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+when:
+  event: [push, pull_request]
+
+steps:
+  prepare:
+    image: bttoxin-digger:latest
+    commands:
+      - echo "Preparing environment..."
+      - BtToxin_Digger --version
+
+  test:
+    image: python:3.10
+    commands:
+      - pip install pytest httpx
+      - pytest tests/

Makefile

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+.PHONY: help dev build test clean
+
+help:
+	@echo "BtToxin Pipeline Commands:"
+	@echo "  make dev       - Start development environment"
+	@echo "  make build     - Build Docker images"
+	@echo "  make test      - Run tests"
+	@echo "  make clean     - Clean up"
+
+dev:
+	docker compose -f config/docker-compose.yml up -d
+
+build:
+	docker compose -f config/docker-compose.yml build
+
+test:
+	cd backend && pytest
+
+clean:
+	docker compose -f config/docker-compose.yml down -v
+	rm -rf uploads/ results/ logs/

README.md

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+# BtToxin Pipeline
+
+Automated Bacillus thuringiensis toxin mining system with CI/CD integration.
+
+## Quick Start
+
+### Prerequisites
+
+- Docker / Podman
+- Python 3.10+
+- Node.js 18+
+
+### Development Setup
+```bash
+# 1. Clone and setup
+git clone <your-repo>
+cd bttoxin-pipeline
+
+# 2. Install dependencies
+cd backend && pip install -r requirements.txt
+cd ../frontend && npm install
+
+# 3. Start services
+docker compose -f config/docker-compose.yml up -d
+
+# 4. Run backend
+cd backend
+uvicorn app.main:app --reload
+
+# 5. Run frontend
+cd frontend
+npm run dev
+```
+
+## Architecture
+
+Frontend (Vue 3) → Backend (FastAPI) → Celery → Docker (BtToxin_Digger)
+                         ↓
+                   PostgreSQL + Redis
+                         ↓
+                      S3/MinIO
+
+## Documentation
+
+- [API Documentation](docs/api.md)
+- [Deployment Guide](docs/deployment.md)
+- [Usage Guide](docs/usage.md)
+
+## License
+
+MIT License

backend/app/__init__.py

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+"""BtToxin Pipeline Backend Application"""
+__version__ = "1.0.0"

backend/app/api/v1/jobs.py

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+"""任务管理 API"""
+from fastapi import APIRouter, Depends, HTTPException, UploadFile, File
+from sqlalchemy.orm import Session
+from typing import List
+from pathlib import Path
+import uuid
+import shutil
+
+from ...database import get_db
+from ...models.job import Job, JobStatus
+from ...schemas.job import JobResponse
+from ...workers.tasks import run_bttoxin_analysis
+from ...config import settings
+
+router = APIRouter()
+
+UPLOAD_DIR = Path(settings.UPLOAD_DIR)
+RESULTS_DIR = Path(settings.RESULTS_DIR)
+UPLOAD_DIR.mkdir(exist_ok=True)
+RESULTS_DIR.mkdir(exist_ok=True)
+
+@router.post("/create", response_model=JobResponse)
+async def create_job(
+    files: List[UploadFile] = File(...),
+    sequence_type: str = "nucl",
+    scaf_suffix: str = ".fna",
+    threads: int = 4,
+    db: Session = Depends(get_db)
+):
+    """创建新任务"""
+    job_id = str(uuid.uuid4())
+
+    job_input_dir = UPLOAD_DIR / job_id
+    job_output_dir = RESULTS_DIR / job_id
+    job_input_dir.mkdir(parents=True)
+    job_output_dir.mkdir(parents=True)
+
+    uploaded_files = []
+    for file in files:
+        file_path = job_input_dir / file.filename
+        with open(file_path, "wb") as buffer:
+            shutil.copyfileobj(file.file, buffer)
+        uploaded_files.append(file.filename)
+
+    job = Job(
+        id=job_id,
+        status=JobStatus.PENDING,
+        input_files=uploaded_files,
+        sequence_type=sequence_type,
+        scaf_suffix=scaf_suffix,
+        threads=threads
+    )
+
+    db.add(job)
+    db.commit()
+    db.refresh(job)
+
+    task = run_bttoxin_analysis.delay(
+        job_id=job_id,
+        input_dir=str(job_input_dir),
+        output_dir=str(job_output_dir),
+        sequence_type=sequence_type,
+        scaf_suffix=scaf_suffix,
+        threads=threads
+    )
+
+    job.celery_task_id = task.id
+    db.commit()
+
+    return job
+
+@router.get("/{job_id}", response_model=JobResponse)
+async def get_job(job_id: str, db: Session = Depends(get_db)):
+    """获取任务详情"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+    return job
+
+@router.get("/{job_id}/progress")
+async def get_job_progress(job_id: str, db: Session = Depends(get_db)):
+    """获取任务进度"""
+    job = db.query(Job).filter(Job.id == job_id).first()
+    if not job:
+        raise HTTPException(status_code=404, detail="Job not found")
+
+    if job.celery_task_id:
+        from ...core.celery_app import celery_app
+        task = celery_app.AsyncResult(job.celery_task_id)
+
+        return {
+            'job_id': job_id,
+            'status': job.status,
+            'celery_state': task.state,
+            'progress': task.info if task.state == 'PROGRESS' else None
+        }
+
+    return {'job_id': job_id, 'status': job.status}

backend/app/api/v1/results.py

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+"""结果查询 API"""
+from fastapi import APIRouter
+
+router = APIRouter()
+
+@router.get("/")
+async def results_info():
+    return {"message": "Results endpoint"}

backend/app/api/v1/upload.py

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+"""文件上传 API"""
+from fastapi import APIRouter
+
+router = APIRouter()
+
+@router.get("/")
+async def upload_info():
+    return {"message": "Upload endpoint"}

backend/app/config.py

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+"""应用配置"""
+from pydantic_settings import BaseSettings
+from typing import Optional
+
+class Settings(BaseSettings):
+    """应用设置"""
+
+    # 应用基础配置
+    APP_NAME: str = "BtToxin Pipeline"
+    APP_VERSION: str = "1.0.0"
+    DEBUG: bool = False
+
+    # API 配置
+    API_V1_STR: str = "/api/v1"
+
+    # 数据库
+    DATABASE_URL: str = "postgresql://postgres:password@localhost:5432/bttoxin"
+
+    # Redis
+    REDIS_URL: str = "redis://localhost:6379/0"
+
+    # S3/MinIO
+    S3_ENDPOINT: Optional[str] = None
+    S3_ACCESS_KEY: str = ""
+    S3_SECRET_KEY: str = ""
+    S3_BUCKET: str = "bttoxin-results"
+    S3_REGION: str = "us-east-1"
+
+    # Docker
+    DOCKER_IMAGE: str = "quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0"
+
+    # 文件路径
+    UPLOAD_DIR: str = "uploads"
+    RESULTS_DIR: str = "results"
+
+    # Celery
+    CELERY_BROKER_URL: str = "redis://localhost:6379/0"
+    CELERY_RESULT_BACKEND: str = "redis://localhost:6379/0"
+
+    # CORS
+    CORS_ORIGINS: list = ["http://localhost:3000", "http://localhost:5173"]
+
+    class Config:
+        env_file = ".env"
+        case_sensitive = True
+
+settings = Settings()

backend/app/core/celery_app.py

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+"""Celery 配置"""
+from celery import Celery
+from ..config import settings
+
+celery_app = Celery(
+    "bttoxin_worker",
+    broker=settings.CELERY_BROKER_URL,
+    backend=settings.CELERY_RESULT_BACKEND,
+    include=['app.workers.tasks']
+)
+
+celery_app.conf.update(
+    task_serializer='json',
+    accept_content=['json'],
+    result_serializer='json',
+    timezone='UTC',
+    enable_utc=True,
+    task_track_started=True,
+    task_time_limit=7200,
+    worker_prefetch_multiplier=1,
+)

backend/app/core/docker_client.py

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+"""Docker 客户端管理"""
+import docker
+from typing import Dict, Any
+from pathlib import Path
+import logging
+
+logger = logging.getLogger(__name__)
+
+class DockerManager:
+    """Docker 容器管理器"""
+
+    def __init__(self, image: str = None):
+        from ..config import settings
+        self.client = docker.from_env()
+        self.image = image or settings.DOCKER_IMAGE
+
+    def ensure_image(self) -> bool:
+        """确保镜像存在"""
+        try:
+            self.client.images.get(self.image)
+            return True
+        except docker.errors.ImageNotFound:
+            logger.info(f"Pulling image {self.image}...")
+            self.client.images.pull(self.image)
+            return True
+
+    def run_bttoxin_digger(
+        self,
+        input_dir: Path,
+        output_dir: Path,
+        sequence_type: str = "nucl",
+        scaf_suffix: str = ".fna",
+        threads: int = 4
+    ) -> Dict[str, Any]:
+        """运行 BtToxin_Digger"""
+        self.ensure_image()
+
+        volumes = {
+            str(input_dir.absolute()): {'bind': '/data', 'mode': 'ro'},
+            str(output_dir.absolute()): {'bind': '/results', 'mode': 'rw'}
+        }
+
+        command = [
+            "/usr/local/env-execute", "BtToxin_Digger",
+            "--SeqPath", "/data",
+            "--SequenceType", sequence_type,
+            "--Scaf_suffix", scaf_suffix,
+            "--threads", str(threads)
+        ]
+
+        try:
+            container = self.client.containers.run(
+                self.image,
+                command=command,
+                volumes=volumes,
+                platform="linux/amd64",
+                detach=True,
+                remove=False
+            )
+
+            result = container.wait()
+            logs = container.logs().decode('utf-8')
+            container.remove()
+
+            return {
+                'success': result['StatusCode'] == 0,
+                'logs': logs,
+                'exit_code': result['StatusCode']
+            }
+        except Exception as e:
+            logger.error(f"Error: {e}")
+            return {'success': False, 'error': str(e)}

backend/app/database.py

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+"""数据库连接"""
+from sqlalchemy import create_engine
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import sessionmaker
+
+from .config import settings
+
+engine = create_engine(
+    settings.DATABASE_URL,
+    pool_pre_ping=True,
+    echo=settings.DEBUG
+)
+
+SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+Base = declarative_base()
+
+def get_db():
+    """获取数据库会话"""
+    db = SessionLocal()
+    try:
+        yield db
+    finally:
+        db.close()

backend/app/main.py

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+"""FastAPI 主应用"""
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from contextlib import asynccontextmanager
+
+from .config import settings
+from .api.v1 import jobs, upload, results
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    """应用生命周期管理"""
+    # 启动时
+    print("🚀 Starting BtToxin Pipeline API...")
+    yield
+    # 关闭时
+    print("👋 Shutting down BtToxin Pipeline API...")
+
+app = FastAPI(
+    title=settings.APP_NAME,
+    version=settings.APP_VERSION,
+    description="Automated Bacillus thuringiensis toxin mining pipeline",
+    lifespan=lifespan
+)
+
+# CORS
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=settings.CORS_ORIGINS,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+# 路由
+app.include_router(jobs.router, prefix=f"{settings.API_V1_STR}/jobs", tags=["jobs"])
+app.include_router(upload.router, prefix=f"{settings.API_V1_STR}/upload", tags=["upload"])
+app.include_router(results.router, prefix=f"{settings.API_V1_STR}/results", tags=["results"])
+
+@app.get("/")
+async def root():
+    return {
+        "name": settings.APP_NAME,
+        "version": settings.APP_VERSION,
+        "status": "healthy"
+    }
+
+@app.get("/health")
+async def health():
+    return {"status": "ok"}

backend/app/models/job.py

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+"""任务模型"""
+from sqlalchemy import Column, String, Integer, DateTime, JSON, Enum, Text
+from sqlalchemy.sql import func
+import enum
+
+from ..database import Base
+
+class JobStatus(str, enum.Enum):
+    PENDING = "pending"
+    RUNNING = "running"
+    COMPLETED = "completed"
+    FAILED = "failed"
+
+class Job(Base):
+    __tablename__ = "jobs"
+
+    id = Column(String, primary_key=True, index=True)
+    celery_task_id = Column(String, nullable=True)
+    status = Column(Enum(JobStatus), default=JobStatus.PENDING)
+
+    input_files = Column(JSON)
+    sequence_type = Column(String, default="nucl")
+    scaf_suffix = Column(String, default=".fna")
+    threads = Column(Integer, default=4)
+
+    result_url = Column(String, nullable=True)
+    logs = Column(Text, nullable=True)
+    error_message = Column(Text, nullable=True)
+
+    created_at = Column(DateTime(timezone=True), server_default=func.now())
+    updated_at = Column(DateTime(timezone=True), onupdate=func.now())
+    completed_at = Column(DateTime(timezone=True), nullable=True)

backend/app/schemas/job.py

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+"""任务 Schema"""
+from pydantic import BaseModel
+from typing import Optional, List
+from datetime import datetime
+from enum import Enum
+
+class JobStatus(str, Enum):
+    PENDING = "pending"
+    RUNNING = "running"
+    COMPLETED = "completed"
+    FAILED = "failed"
+
+class JobCreate(BaseModel):
+    input_files: List[str]
+    sequence_type: str = "nucl"
+    scaf_suffix: str = ".fna"
+    threads: int = 4
+
+class JobResponse(BaseModel):
+    id: str
+    status: JobStatus
+    input_files: List[str]
+    sequence_type: str
+    threads: int
+    result_url: Optional[str] = None
+    error_message: Optional[str] = None
+    created_at: datetime
+    completed_at: Optional[datetime] = None
+
+    class Config:
+        from_attributes = True

backend/app/workers/tasks.py

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+"""Celery 任务"""
+from celery import Task
+from pathlib import Path
+import shutil
+import logging
+
+from ..core.celery_app import celery_app
+from ..core.docker_client import DockerManager
+from ..database import SessionLocal
+from ..models.job import Job, JobStatus
+
+logger = logging.getLogger(__name__)
+
+@celery_app.task(bind=True)
+def run_bttoxin_analysis(
+    self,
+    job_id: str,
+    input_dir: str,
+    output_dir: str,
+    sequence_type: str = "nucl",
+    scaf_suffix: str = ".fna",
+    threads: int = 4
+):
+    """执行分析任务"""
+    db = SessionLocal()
+
+    try:
+        job = db.query(Job).filter(Job.id == job_id).first()
+        job.status = JobStatus.RUNNING
+        db.commit()
+
+        self.update_state(
+            state='PROGRESS',
+            meta={'current': 20, 'total': 100, 'status': 'Running analysis...'}
+        )
+
+        docker_manager = DockerManager()
+        result = docker_manager.run_bttoxin_digger(
+            input_dir=Path(input_dir),
+            output_dir=Path(output_dir),
+            sequence_type=sequence_type,
+            scaf_suffix=scaf_suffix,
+            threads=threads
+        )
+
+        if result['success']:
+            job.status = JobStatus.COMPLETED
+            job.logs = result.get('logs', '')
+        else:
+            job.status = JobStatus.FAILED
+            job.error_message = result.get('error', 'Analysis failed')
+
+        db.commit()
+
+        return {'job_id': job_id, 'status': job.status}
+
+    except Exception as e:
+        logger.error(f"Task failed: {e}")
+        job.status = JobStatus.FAILED
+        job.error_message = str(e)
+        db.commit()
+        raise
+    finally:
+        db.close()

backend/requirements.txt

@@ -0,0 +1,38 @@
+# Web 框架
+fastapi==0.115.5
+uvicorn[standard]==0.32.1
+python-multipart==0.0.20
+
+# 任务队列
+celery==5.4.0
+redis==5.2.1
+flower==2.0.1
+
+# 容器管理
+docker==7.1.0
+
+# 数据库
+sqlalchemy==2.0.36
+alembic==1.14.0
+psycopg2-binary==2.9.10
+
+# 对象存储
+boto3==1.35.78
+minio==7.2.11
+
+# 数据处理
+biopython==1.84
+pandas==2.2.3
+
+# 工具
+pydantic==2.10.4
+pydantic-settings==2.6.1
+python-dotenv==1.0.1
+aiofiles==24.1.0
+
+# 监控
+prometheus-client==0.21.0
+
+# 测试
+pytest==8.3.4
+httpx==0.28.1

config/docker-compose.yml

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+version: '3.8'
+
+services:
+  postgres:
+    image: postgres:15
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: password
+      POSTGRES_DB: bttoxin
+    ports:
+      - "5432:5432"
+    volumes:
+      - postgres_data:/var/lib/postgresql/data
+
+  redis:
+    image: redis:7-alpine
+    ports:
+      - "6379:6379"
+
+  minio:
+    image: minio/minio
+    command: server /data --console-address ":9001"
+    environment:
+      MINIO_ROOT_USER: minioadmin
+      MINIO_ROOT_PASSWORD: minioadmin
+    ports:
+      - "9000:9000"
+      - "9001:9001"
+    volumes:
+      - minio_data:/data
+
+  backend:
+    build:
+      context: ..
+      dockerfile: docker/worker/Dockerfile
+    command: uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload
+    ports:
+      - "8000:8000"
+    volumes:
+      - ../backend:/app
+      - /var/run/docker.sock:/var/run/docker.sock
+    environment:
+      DATABASE_URL: postgresql://postgres:password@postgres:5432/bttoxin
+      REDIS_URL: redis://redis:6379/0
+    depends_on:
+      - postgres
+      - redis
+
+  celery:
+    build:
+      context: ..
+      dockerfile: docker/worker/Dockerfile
+    command: celery -A app.core.celery_app worker --loglevel=info
+    volumes:
+      - ../backend:/app
+      - /var/run/docker.sock:/var/run/docker.sock
+    environment:
+      DATABASE_URL: postgresql://postgres:password@postgres:5432/bttoxin
+      REDIS_URL: redis://redis:6379/0
+    depends_on:
+      - postgres
+      - redis
+
+  frontend:
+    build:
+      context: ..
+      dockerfile: docker/frontend/Dockerfile
+    ports:
+      - "3000:80"
+    depends_on:
+      - backend
+
+volumes:
+  postgres_data:
+  minio_data:

docker/digger/Dockerfile

@@ -0,0 +1,46 @@
+# BtToxin_Digger Docker 镜像
+FROM continuumio/miniconda3:4.10.3
+
+LABEL maintainer="your-email@example.com" \
+      description="BtToxin_Digger for Pipeline" \
+      version="1.0.10"
+
+ENV LANG=C.UTF-8 \
+    PATH=/opt/conda/envs/bttoxin/bin:$PATH \
+    CONDA_DEFAULT_ENV=bttoxin \
+    PYTHONUNBUFFERED=1
+
+# 配置 conda
+RUN conda config --add channels defaults && \
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority flexible && \
+    conda install -n base -c conda-forge mamba -y
+
+# 安装 BtToxin_Digger
+RUN mamba install -y \
+    python=3.7.10 \
+    perl=5.26.2 && \
+    mamba install -y \
+    bttoxin_digger=1.0.10 && \
+    conda clean -afy
+
+# 安装额外工具
+RUN apt-get update && apt-get install -y \
+    curl wget jq git && \
+    rm -rf /var/lib/apt/lists/*
+
+# 创建工作目录
+RUN mkdir -p /workspace/input /workspace/output /workspace/logs
+
+WORKDIR /workspace
+
+# 复制入口脚本
+COPY entrypoint.sh /usr/local/bin/
+RUN chmod +x /usr/local/bin/entrypoint.sh
+
+HEALTHCHECK --interval=30s --timeout=10s --retries=3 \
+    CMD BtToxin_Digger --version || exit 1
+
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
+CMD ["--help"]

docker/digger/entrypoint.sh

@@ -0,0 +1,84 @@
+#!/bin/bash
+set -e
+
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+RED='\033[0;31m'
+NC='\033[0m'
+
+log_info() {
+    echo -e "${GREEN}[INFO]${NC} $1"
+}
+
+log_warn() {
+    echo -e "${YELLOW}[WARN]${NC} $1"
+}
+
+log_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+init() {
+    log_info "Initializing BtToxin_Digger environment..."
+
+    if ! BtToxin_Digger --version &>/dev/null; then
+        log_error "BtToxin_Digger not found!"
+        exit 1
+    fi
+
+    log_info "BtToxin_Digger $(BtToxin_Digger --version)"
+    log_info "Python $(python --version)"
+    log_info "Perl $(perl --version | head -2 | tail -1)"
+}
+
+update_db() {
+    log_info "Updating BtToxin_Digger database..."
+    if BtToxin_Digger --update-db; then
+        log_info "Database updated successfully"
+    else
+        log_warn "Database update failed, using existing database"
+    fi
+}
+
+run_analysis() {
+    log_info "Starting toxin mining analysis..."
+    log_info "Input: $INPUT_PATH"
+    log_info "Type: $SEQUENCE_TYPE"
+    log_info "Threads: $THREADS"
+
+    BtToxin_Digger \
+        --SeqPath "$INPUT_PATH" \
+        --SequenceType "$SEQUENCE_TYPE" \
+        --Scaf_suffix "$SCAF_SUFFIX" \
+        --threads "$THREADS" \
+        2>&1 | tee /workspace/logs/digger.log
+
+    if [ $? -eq 0 ]; then
+        log_info "Analysis completed successfully"
+    else
+        log_error "Analysis failed!"
+        exit 1
+    fi
+}
+
+main() {
+    INPUT_PATH="${INPUT_PATH:-/workspace/input}"
+    SEQUENCE_TYPE="${SEQUENCE_TYPE:-nucl}"
+    SCAF_SUFFIX="${SCAF_SUFFIX:-.fna}"
+    THREADS="${THREADS:-4}"
+    UPDATE_DB="${UPDATE_DB:-false}"
+
+    init
+
+    if [ "$UPDATE_DB" = "true" ]; then
+        update_db
+    fi
+
+    if [ $# -gt 0 ]; then
+        exec BtToxin_Digger "$@"
+    else
+        run_analysis
+    fi
+}
+
+main "$@"

docker/frontend/Dockerfile

@@ -0,0 +1,18 @@
+FROM node:18-alpine as builder
+
+WORKDIR /app
+
+COPY frontend/package*.json ./
+RUN npm ci
+
+COPY frontend/ .
+RUN npm run build
+
+FROM nginx:alpine
+
+COPY --from=builder /app/dist /usr/share/nginx/html
+COPY docker/frontend/nginx.conf /etc/nginx/conf.d/default.conf
+
+EXPOSE 80
+
+CMD ["nginx", "-g", "daemon off;"]

docker/frontend/nginx.conf

@@ -0,0 +1,24 @@
+server {
+    listen 80;
+    server_name localhost;
+    root /usr/share/nginx/html;
+    index index.html;
+
+    location / {
+        try_files $uri $uri/ /index.html;
+    }
+
+    location /api {
+        proxy_pass http://backend:8000;
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    }
+
+    location /ws {
+        proxy_pass http://backend:8000;
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+    }
+}

docker/worker/Dockerfile

@@ -0,0 +1,25 @@
+FROM python:3.10-slim
+
+WORKDIR /app
+
+# 安装系统依赖
+RUN apt-get update && apt-get install -y \
+    gcc \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# 安装 Docker CLI
+RUN curl -fsSL https://get.docker.com -o get-docker.sh && \
+    sh get-docker.sh && \
+    rm get-docker.sh
+
+# 复制依赖文件
+COPY backend/requirements.txt .
+
+# 安装 Python 依赖
+RUN pip install --no-cache-dir -r requirements.txt
+
+# 复制应用代码
+COPY backend/ .
+
+CMD ["celery", "-A", "app.core.celery_app", "worker", "--loglevel=info"]

frontend/index.html

@@ -0,0 +1,12 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>BtToxin Pipeline</title>
+</head>
+<body>
+  <div id="app"></div>
+  <script type="module" src="/src/main.js"></script>
+</body>
+</html>

frontend/package.json

@@ -0,0 +1,22 @@
+{
+  "name": "bttoxin-frontend",
+  "version": "1.0.0",
+  "type": "module",
+  "scripts": {
+    "dev": "vite",
+    "build": "vite build",
+    "preview": "vite preview"
+  },
+  "dependencies": {
+    "vue": "^3.5.13",
+    "vue-router": "^4.5.0",
+    "pinia": "^2.3.0",
+    "axios": "^1.7.9",
+    "naive-ui": "^2.40.1",
+    "@vicons/ionicons5": "^0.12.0"
+  },
+  "devDependencies": {
+    "@vitejs/plugin-vue": "^5.2.1",
+    "vite": "^6.0.5"
+  }
+}

frontend/src/App.vue

@@ -0,0 +1,41 @@
+<template>
+  <n-config-provider :theme="darkTheme">
+    <n-layout>
+      <n-layout-header bordered>
+        <n-space align="center" justify="space-between" style="padding: 16px">
+          <n-h2>BtToxin Pipeline</n-h2>
+          <n-menu mode="horizontal" :options="menuOptions" />
+        </n-space>
+      </n-layout-header>
+
+      <n-layout-content style="padding: 24px">
+        <router-view />
+      </n-layout-content>
+
+      <n-layout-footer bordered style="padding: 16px; text-align: center">
+        BtToxin Pipeline © 2025
+      </n-layout-footer>
+    </n-layout>
+  </n-config-provider>
+</template>
+
+<script setup>
+import { darkTheme } from 'naive-ui'
+import { h } from 'vue'
+import { RouterLink } from 'vue-router'
+
+const menuOptions = [
+  {
+    label: () => h(RouterLink, { to: '/' }, { default: () => 'Home' }),
+    key: 'home'
+  },
+  {
+    label: () => h(RouterLink, { to: '/upload' }, { default: () => 'Upload' }),
+    key: 'upload'
+  },
+  {
+    label: () => h(RouterLink, { to: '/jobs' }, { default: () => 'Jobs' }),
+    key: 'jobs'
+  }
+]
+</script>

frontend/src/main.js

@@ -0,0 +1,14 @@
+import { createApp } from 'vue'
+import { createPinia } from 'pinia'
+import naive from 'naive-ui'
+import App from './App.vue'
+import router from './router'
+
+const app = createApp(App)
+const pinia = createPinia()
+
+app.use(pinia)
+app.use(router)
+app.use(naive)
+
+app.mount('#app')

frontend/src/router.js

@@ -0,0 +1,31 @@
+import { createRouter, createWebHistory } from 'vue-router'
+
+const routes = [
+  {
+    path: '/',
+    name: 'Home',
+    component: () => import('./views/Home.vue')
+  },
+  {
+    path: '/upload',
+    name: 'Upload',
+    component: () => import('./views/Upload.vue')
+  },
+  {
+    path: '/jobs',
+    name: 'Jobs',
+    component: () => import('./views/Jobs.vue')
+  },
+  {
+    path: '/jobs/:id',
+    name: 'JobDetail',
+    component: () => import('./views/JobDetail.vue')
+  }
+]
+
+const router = createRouter({
+  history: createWebHistory(),
+  routes
+})
+
+export default router

frontend/src/services/api.js

@@ -0,0 +1,22 @@
+import axios from 'axios'
+
+const api = axios.create({
+  baseURL: '/api/v1',
+  timeout: 30000
+})
+
+export default {
+  createJob(formData) {
+    return api.post('/jobs/create', formData, {
+      headers: { 'Content-Type': 'multipart/form-data' }
+    })
+  },
+
+  getJob(jobId) {
+    return api.get(`/jobs/${jobId}`)
+  },
+
+  getJobProgress(jobId) {
+    return api.get(`/jobs/${jobId}/progress`)
+  }
+}

frontend/src/views/Home.vue

@@ -0,0 +1,7 @@
+<template>
+  <n-space vertical size="large">
+    <n-card title="Welcome to BtToxin Pipeline">
+      <p>Automated Bacillus thuringiensis toxin mining system</p>
+    </n-card>
+  </n-space>
+</template>

frontend/src/views/JobDetail.vue

@@ -0,0 +1,5 @@
+<template>
+  <n-card title="Job Details">
+    <p>Job ID: {{ $route.params.id }}</p>
+  </n-card>
+</template>

frontend/src/views/Jobs.vue

@@ -0,0 +1,5 @@
+<template>
+  <n-card title="Job List">
+    <n-empty description="No jobs yet" />
+  </n-card>
+</template>

frontend/src/views/Upload.vue

@@ -0,0 +1,7 @@
+<template>
+  <n-card title="Upload Genome Files">
+    <n-upload multiple>
+      <n-button>Select Files</n-button>
+    </n-upload>
+  </n-card>
+</template>

frontend/vite.config.js

@@ -0,0 +1,21 @@
+import { defineConfig } from 'vite'
+import vue from '@vitejs/plugin-vue'
+import { fileURLToPath, URL } from 'node:url'
+
+export default defineConfig({
+  plugins: [vue()],
+  resolve: {
+    alias: {
+      '@': fileURLToPath(new URL('./src', import.meta.url))
+    }
+  },
+  server: {
+    port: 3000,
+    proxy: {
+      '/api': {
+        target: 'http://localhost:8000',
+        changeOrigin: true
+      }
+    }
+  }
+})

scripts/download_bpprc_data.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+"""从 BPPRC/NCBI 下载测试数据"""
+import os
+import argparse
+from pathlib import Path
+from Bio import Entrez, SeqIO
+import logging
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+Entrez.email = "your_email@example.com"
+
+TEST_GENOMES = {
+    'Bacillus_thuringiensis_HD-73': 'NZ_CP004069.1',
+    'Bacillus_thuringiensis_YBT-1520': 'NZ_CP003889.1',
+    'Bacillus_thuringiensis_BMB171': 'NC_014171.1',
+}
+
+def download_genome(accession, output_file):
+    """下载基因组"""
+    try:
+        logger.info(f"Downloading {accession}...")
+        handle = Entrez.efetch(
+            db="nucleotide",
+            id=accession,
+            rettype="fasta",
+            retmode="text"
+        )
+
+        with open(output_file, 'w') as f:
+            f.write(handle.read())
+
+        handle.close()
+        logger.info(f"✓ Downloaded: {output_file}")
+        return True
+    except Exception as e:
+        logger.error(f"✗ Failed: {e}")
+        return False
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--output-dir', default='tests/test_data/genomes')
+    parser.add_argument('--email', required=True)
+    args = parser.parse_args()
+
+    Entrez.email = args.email
+    output_dir = Path(args.output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    for name, accession in TEST_GENOMES.items():
+        output_file = output_dir / f"{name}.fna"
+        download_genome(accession, output_file)
+
+if __name__ == '__main__':
+    main()