后端初始化结构

web/ws/backend/.env.example

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+# 项目信息
+PROJECT_NAME=PBMDB API
+VERSION=1.0.0
+API_V1_STR=/api/v1
+
+# 数据库配置
+DATABASE_URL=postgresql://webws_admin:your_password_here@postgres:5432/webws_database
+
+# 安全配置
+SECRET_KEY=your-secret-key-here-change-in-production-use-at-least-32-chars
+ACCESS_TOKEN_EXPIRE_MINUTES=10080
+
+# CORS 配置
+ALLOWED_ORIGINS=https://amiap.hzau.edu.cn,http://localhost:3000
+
+# 文件上传配置
+MAX_UPLOAD_SIZE=104857600
+UPLOAD_DIR=/app/uploads
+
+# 分页配置
+DEFAULT_PAGE_SIZE=20
+MAX_PAGE_SIZE=100

web/ws/backend/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+venv/
+env/
+ENV/
+*.egg-info/
+dist/
+build/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# 环境变量
+.env
+
+# 数据库
+*.db
+*.sqlite3
+
+# 上传文件
+uploads/
+*.log
+
+# 测试
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Alembic
+alembic/versions/*.pyc

web/ws/backend/CONTRIBUTING.md

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+# 开发指南
+
+## 快速开始
+
+### 本地开发
+
+```bash
+# 1. 进入后端目录
+cd /vol1/1000/docker_server/traefik/web/ws/backend
+
+# 2. 使用启动脚本（自动创建虚拟环境、安装依赖）
+./start.sh
+
+# 或者手动启动
+python3 -m venv venv
+source venv/bin/activate
+pip install -r requirements.txt
+uvicorn app.main:app --reload --host 0.0.0.0 --port 8000
+```
+
+访问：
+- API 文档: http://localhost:8000/docs
+- 健康检查: http://localhost:8000/health
+
+### Docker 开发
+
+```bash
+cd /vol1/1000/docker_server/traefik/web/ws
+
+# 构建镜像
+docker compose build backend
+
+# 启动服务
+docker compose up -d backend
+
+# 查看日志
+docker compose logs -f backend
+
+# 进入容器
+docker compose exec backend bash
+```
+
+## 开发流程
+
+### 1. 添加新的 API 端点
+
+**示例：添加实验数据 API**
+
+```bash
+# 1. 创建端点文件
+touch app/api/v1/endpoints/experiments.py
+```
+
+```python
+# app/api/v1/endpoints/experiments.py
+from fastapi import APIRouter
+
+router = APIRouter()
+
+@router.get("/")
+async def get_experiments():
+    """获取实验列表"""
+    return {"experiments": []}
+
+@router.get("/{experiment_id}")
+async def get_experiment(experiment_id: str):
+    """获取实验详情"""
+    return {"id": experiment_id}
+```
+
+```python
+# 2. 在 app/api/v1/router.py 中注册
+from app.api.v1.endpoints import experiments
+
+api_router.include_router(
+    experiments.router, 
+    prefix="/experiments", 
+    tags=["experiments"]
+)
+```
+
+### 2. 添加数据模型
+
+```bash
+# 创建模型文件
+touch app/models/experiment.py
+```
+
+```python
+# app/models/experiment.py
+from sqlalchemy import Column, String, Integer, DateTime
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()
+
+class Experiment(Base):
+    __tablename__ = "experiments"
+    
+    id = Column(Integer, primary_key=True)
+    name = Column(String(200))
+    description = Column(String(1000))
+    created_at = Column(DateTime)
+```
+
+### 3. 添加 Pydantic 模式
+
+```bash
+# 创建模式文件
+touch app/schemas/experiment.py
+```
+
+```python
+# app/schemas/experiment.py
+from pydantic import BaseModel
+from datetime import datetime
+from typing import Optional
+
+class ExperimentBase(BaseModel):
+    name: str
+    description: Optional[str] = None
+
+class ExperimentCreate(ExperimentBase):
+    pass
+
+class ExperimentResponse(ExperimentBase):
+    id: int
+    created_at: datetime
+    
+    class Config:
+        from_attributes = True
+```
+
+### 4. 添加业务逻辑
+
+```bash
+# 创建服务文件
+touch app/services/experiment_service.py
+```
+
+```python
+# app/services/experiment_service.py
+from sqlalchemy.orm import Session
+from app.models.experiment import Experiment
+from app.schemas.experiment import ExperimentCreate
+
+async def create_experiment(db: Session, data: ExperimentCreate):
+    """创建实验"""
+    experiment = Experiment(**data.dict())
+    db.add(experiment)
+    db.commit()
+    db.refresh(experiment)
+    return experiment
+```
+
+## 代码规范
+
+### Python 风格
+
+- 遵循 PEP 8 规范
+- 使用类型提示
+- 函数添加文档字符串
+
+```python
+async def get_strain_detail(strain_id: str) -> dict:
+    """
+    获取菌种详情
+    
+    Args:
+        strain_id: 菌种 ID
+        
+    Returns:
+        dict: 菌种详细信息
+        
+    Raises:
+        HTTPException: 菌种不存在时
+    """
+    pass
+```
+
+### 命名规范
+
+- 文件名：`snake_case.py`
+- 类名：`PascalCase`
+- 函数名：`snake_case`
+- 常量：`UPPER_CASE`
+
+### 目录组织
+
+```
+app/
+├── api/v1/endpoints/    # 按功能模块组织
+│   ├── strains.py       # 菌种相关
+│   ├── genes.py         # 基因相关
+│   └── upload.py        # 上传相关
+├── models/              # 数据库模型
+├── schemas/             # 数据验证模式
+└── services/            # 业务逻辑
+```
+
+## 测试
+
+### 单元测试
+
+```bash
+# 安装测试依赖
+pip install pytest pytest-asyncio httpx
+
+# 运行测试
+pytest
+```
+
+### API 测试
+
+```bash
+# 使用测试脚本
+./test_api.sh
+
+# 或使用 curl
+curl http://localhost:8000/health
+```
+
+## 数据库迁移
+
+```bash
+# 安装 alembic
+pip install alembic
+
+# 初始化
+alembic init alembic
+
+# 创建迁移
+alembic revision --autogenerate -m "Add experiments table"
+
+# 执行迁移
+alembic upgrade head
+
+# 回滚
+alembic downgrade -1
+```
+
+## 调试技巧
+
+### 1. 日志输出
+
+```python
+import logging
+
+logger = logging.getLogger(__name__)
+
+@router.get("/debug")
+async def debug_endpoint():
+    logger.info("Debug endpoint called")
+    logger.debug(f"Data: {data}")
+    return {"status": "ok"}
+```
+
+### 2. 断点调试
+
+```python
+# 使用 pdb
+import pdb; pdb.set_trace()
+
+# 或使用 breakpoint()
+breakpoint()
+```
+
+### 3. 查看 SQL 查询
+
+```python
+# 在配置中启用 SQL 日志
+DATABASE_URL = "postgresql://...?echo=true"
+```
+
+## 常见问题
+
+### Q: 导入错误？
+
+确保在项目根目录运行，并使用正确的 Python 路径：
+
+```bash
+export PYTHONPATH=/vol1/1000/docker_server/traefik/web/ws/backend:$PYTHONPATH
+```
+
+### Q: 数据库连接失败？
+
+检查 `.env` 文件中的 `DATABASE_URL` 配置。
+
+### Q: CORS 错误？
+
+在 `app/core/config.py` 中添加允许的源。
+
+## 部署检查清单
+
+- [ ] 修改生产环境 `SECRET_KEY`
+- [ ] 配置正确的 `DATABASE_URL`
+- [ ] 更新 `ALLOWED_ORIGINS`
+- [ ] 运行数据库迁移
+- [ ] 测试所有 API 端点
+- [ ] 配置日志记录
+- [ ] 设置监控和告警
+- [ ] 备份数据库
+
+## 贡献流程
+
+1. 创建功能分支
+2. 开发并测试
+3. 提交代码（commit message 规范）
+4. 提交 Pull Request
+5. Code Review
+6. 合并到主分支
+
+## 联系方式
+
+如有问题，请联系开发团队。

web/ws/backend/Dockerfile

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+# FastAPI 后端 Dockerfile
+FROM python:3.11-slim
+
+# 设置工作目录
+WORKDIR /app
+
+# 安装系统依赖
+RUN apt-get update && apt-get install -y \
+    gcc \
+    postgresql-client \
+    && rm -rf /var/lib/apt/lists/*
+
+# 复制依赖文件
+COPY requirements.txt .
+
+# 安装 Python 依赖
+RUN pip install --no-cache-dir -r requirements.txt
+
+# 复制应用代码
+COPY app/ ./app/
+
+# 创建上传目录
+RUN mkdir -p /app/uploads
+
+# 暴露端口
+EXPOSE 8000
+
+# 健康检查
+HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
+    CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" || exit 1
+
+# 启动命令
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"]

web/ws/backend/README.md

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+# FastAPI 后端项目
+
+PBMDB (Plant Beneficial Microbe Database) 农业有益微生物综合信息数据库后端 API 服务。
+
+## 📁 项目结构
+
+```
+backend/
+├── app/
+│   ├── __init__.py
+│   ├── main.py              # FastAPI 应用入口
+│   ├── api/
+│   │   ├── __init__.py
+│   │   └── v1/
+│   │       ├── __init__.py
+│   │       ├── router.py    # API 路由汇总
+│   │       └── endpoints/
+│   │           ├── __init__.py
+│   │           ├── strains.py      # 菌种资源 API
+│   │           ├── genomes.py      # 基因组学数据 API
+│   │           ├── genes.py        # 基因资源 API
+│   │           ├── upload.py       # 数据汇交上传 API
+│   │           └── analysis.py     # 智能分析 API
+│   ├── core/
+│   │   ├── __init__.py
+│   │   ├── config.py        # 应用配置
+│   │   └── security.py      # 认证安全
+│   ├── models/              # SQLAlchemy 数据模型
+│   │   └── __init__.py
+│   ├── schemas/             # Pydantic 数据模式
+│   │   └── __init__.py
+│   └── services/            # 业务逻辑层
+│       └── __init__.py
+├── requirements.txt         # Python 依赖
+├── Dockerfile              # Docker 构建文件
+├── .env.example           # 环境变量示例
+└── README.md              # 本文件
+```
+
+## 🚀 技术栈
+
+- **FastAPI**: 现代、高性能 Python Web 框架
+- **Uvicorn**: ASGI 服务器
+- **SQLAlchemy**: ORM 数据库工具
+- **PostgreSQL**: 关系型数据库
+- **Pydantic**: 数据验证和设置管理
+
+## 🎯 核心功能模块
+
+### 1. 菌种资源 (`/api/v1/strains`)
+- 菌种列表查询（分类、搜索、分页）
+- 菌种详情展示
+- 菌种分类树
+
+### 2. 基因组学数据 (`/api/v1/genomes`)
+- 基因组数据列表（基因组学/转录组学/其他组学）
+- 基因组详情
+- 物种分类树
+
+### 3. 基因资源 (`/api/v1/genes`)
+- 基因列表查询（功能分类）
+- 基因详情
+- 功能基因分类
+
+### 4. 数据汇交 (`/api/v1/upload`)
+- 基因组数据上传
+- 宏基因组数据上传
+- 原始测序数据上传
+- 上传口令验证
+- 上传状态查询
+
+### 5. 智能分析 (`/api/v1/analysis`)
+- 智能问答（基于知识图谱）
+- 基因挖掘（序列比对）
+- 菌株评估
+- 知识图谱查询
+- 分析任务状态查询
+
+## ⚙️ 环境配置
+
+### 1. 创建环境变量文件
+
+```bash
+cd /vol1/1000/docker_server/traefik/web/ws/backend
+cp .env.example .env
+```
+
+编辑 `.env` 文件：
+
+```bash
+# 项目信息
+PROJECT_NAME=PBMDB API
+VERSION=1.0.0
+
+# 数据库配置
+DATABASE_URL=postgresql://webws_admin:your_password@postgres:5432/webws_database
+
+# 安全配置
+SECRET_KEY=your-secret-key-here-change-in-production
+
+# CORS 配置
+ALLOWED_ORIGINS=https://amiap.hzau.edu.cn,http://localhost:3000
+
+# 文件上传配置
+MAX_UPLOAD_SIZE=104857600
+UPLOAD_DIR=/app/uploads
+```
+
+## 🏃 本地开发
+
+### 使用虚拟环境
+
+```bash
+cd /vol1/1000/docker_server/traefik/web/ws/backend
+
+# 创建虚拟环境
+python3 -m venv venv
+source venv/bin/activate
+
+# 安装依赖
+pip install -r requirements.txt
+
+# 运行开发服务器
+uvicorn app.main:app --reload --host 0.0.0.0 --port 8000
+```
+
+访问：
+- API 文档: http://localhost:8000/docs
+- ReDoc 文档: http://localhost:8000/redoc
+- 健康检查: http://localhost:8000/health
+
+## 🐳 Docker 部署
+
+### 1. 更新 docker-compose.yml
+
+在 `/vol1/1000/docker_server/traefik/web/ws/docker-compose.yml` 中添加后端服务：
+
+```yaml
+services:
+  # ... 现有服务 ...
+  
+  backend:
+    build: ./backend
+    container_name: webws-backend
+    restart: unless-stopped
+    environment:
+      - DATABASE_URL=postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}
+    volumes:
+      - ./backend/uploads:/app/uploads
+    networks:
+      - frontend
+    depends_on:
+      - postgres
+    labels:
+      - "traefik.enable=true"
+      
+      # HTTP 路由 - 重定向到 HTTPS
+      - "traefik.http.routers.webws-api-http.rule=Host(`amiap.hzau.edu.cn`) && PathPrefix(`/ABM/api`)"
+      - "traefik.http.routers.webws-api-http.entrypoints=web"
+      - "traefik.http.routers.webws-api-http.priority=100"
+      - "traefik.http.routers.webws-api-http.middlewares=redirect-to-https"
+      
+      # HTTPS 路由
+      - "traefik.http.routers.webws-api-https.rule=Host(`amiap.hzau.edu.cn`) && PathPrefix(`/ABM/api`)"
+      - "traefik.http.routers.webws-api-https.entrypoints=websecure"
+      - "traefik.http.routers.webws-api-https.priority=100"
+      - "traefik.http.routers.webws-api-https.tls.certresolver=myresolver"
+      
+      # StripPrefix 中间件（移除 /ABM/api 前缀）
+      - "traefik.http.routers.webws-api-https.middlewares=api-stripprefix"
+      - "traefik.http.middlewares.api-stripprefix.stripprefix.prefixes=/ABM/api"
+      
+      - "traefik.http.services.webws-api.loadbalancer.server.port=8000"
+```
+
+### 2. 构建并启动
+
+```bash
+cd /vol1/1000/docker_server/traefik/web/ws
+
+# 构建镜像
+docker compose build backend
+
+# 启动服务
+docker compose up -d backend
+
+# 查看日志
+docker compose logs -f backend
+```
+
+## 📡 API 访问地址
+
+部署后，API 通过以下地址访问：
+
+- **外部访问**: https://amiap.hzau.edu.cn/ABM/api/
+- **API 文档**: https://amiap.hzau.edu.cn/ABM/api/docs
+- **容器间访问**: http://webws-backend:8000/
+
+## 🔧 路由说明
+
+### URL 路径处理
+
+由于使用了 Traefik `StripPrefix` 中间件，路径会自动处理：
+
+**用户访问**: `https://amiap.hzau.edu.cn/ABM/api/strains/`
+**FastAPI 接收**: `/api/v1/strains/` (已移除 `/ABM/api`)
+
+### 路由优先级
+
+```
+Priority 100: /ABM/api/** → 后端 API 服务
+Priority 47:  /ABM/**     → Nginx 静态文件服务
+```
+
+不会产生冲突，Traefik 优先匹配更高优先级和更具体的路径。
+
+## 📊 数据库迁移
+
+### 使用 Alembic
+
+```bash
+# 进入容器
+docker compose exec backend bash
+
+# 初始化迁移（首次）
+alembic init alembic
+
+# 创建迁移
+alembic revision --autogenerate -m "Initial migration"
+
+# 执行迁移
+alembic upgrade head
+```
+
+## 🧪 测试 API
+
+### 使用 curl
+
+```bash
+# 健康检查
+curl https://amiap.hzau.edu.cn/ABM/api/health
+
+# 获取菌种列表
+curl https://amiap.hzau.edu.cn/ABM/api/api/v1/strains/
+
+# 获取基因组数据
+curl https://amiap.hzau.edu.cn/ABM/api/api/v1/genomes/
+```
+
+### 使用 Swagger UI
+
+访问 https://amiap.hzau.edu.cn/ABM/api/docs 进行交互式测试。
+
+## 📝 开发指南
+
+### 添加新的 API 端点
+
+1. 在 `app/api/v1/endpoints/` 下创建新文件
+2. 定义路由和处理函数
+3. 在 `app/api/v1/router.py` 中注册路由
+
+### 添加数据模型
+
+1. 在 `app/models/` 下创建 SQLAlchemy 模型
+2. 在 `app/schemas/` 下创建 Pydantic 模式
+3. 运行数据库迁移
+
+### 添加业务逻辑
+
+在 `app/services/` 下创建服务层代码，保持控制器简洁。
+
+## 🔒 安全注意事项
+
+1. **生产环境**必须修改 `SECRET_KEY`
+2. 使用环境变量管理敏感信息
+3. 启用 HTTPS（已配置）
+4. 实现完整的认证系统（待实现）
+5. 添加请求频率限制
+
+## 🚀 性能优化
+
+1. 使用数据库连接池
+2. 启用查询缓存（Redis）
+3. 异步文件处理
+4. 压缩响应数据
+5. CDN 加速静态资源
+
+## 📚 相关文档
+
+- [FastAPI 官方文档](https://fastapi.tiangolo.com/)
+- [Pydantic 文档](https://docs.pydantic.dev/)
+- [SQLAlchemy 文档](https://docs.sqlalchemy.org/)
+- [Uvicorn 文档](https://www.uvicorn.org/)
+
+## 📞 联系方式
+
+如有问题，请联系项目维护团队。

web/ws/backend/app/api/v1/endpoints/analysis.py

@@ -0,0 +1,112 @@
+"""
+智能分析 API
+"""
+from typing import Optional
+from fastapi import APIRouter, BackgroundTasks, HTTPException
+from pydantic import BaseModel
+
+router = APIRouter()
+
+
+class QuestionRequest(BaseModel):
+    """智能问答请求"""
+    question: str
+    context: Optional[str] = None
+
+
+class GeneMiningRequest(BaseModel):
+    """基因挖掘请求"""
+    sequence: str
+    algorithm: str = "blast"
+    parameters: Optional[dict] = None
+
+
+class StrainEvaluationRequest(BaseModel):
+    """菌株评估请求"""
+    strain_id: str
+    evaluation_type: str  # growth/resistance/etc
+
+
+@router.post("/qa")
+async def intelligent_qa(request: QuestionRequest):
+    """
+    智能问答
+    
+    基于知识图谱的智能问答系统
+    """
+    # TODO: 集成 AI 模型进行问答
+    return {
+        "question": request.question,
+        "answer": "This is a placeholder answer. AI integration pending.",
+        "confidence": 0.0
+    }
+
+
+@router.post("/gene-mining")
+async def gene_mining(
+    background_tasks: BackgroundTasks,
+    request: GeneMiningRequest
+):
+    """
+    基因挖掘
+    
+    通过序列比对等方法挖掘功能基因
+    """
+    # TODO: 实现基因挖掘算法
+    # background_tasks.add_task(run_gene_mining, request)
+    
+    return {
+        "status": "processing",
+        "task_id": "task_123",
+        "message": "Gene mining task started"
+    }
+
+
+@router.post("/strain-evaluation")
+async def strain_evaluation(
+    background_tasks: BackgroundTasks,
+    request: StrainEvaluationRequest
+):
+    """
+    菌株评估
+    
+    评估菌株的各项指标和应用潜力
+    """
+    # TODO: 实现菌株评估逻辑
+    return {
+        "status": "processing",
+        "task_id": "task_456",
+        "message": "Strain evaluation started"
+    }
+
+
+@router.get("/knowledge-graph")
+async def get_knowledge_graph(
+    entity: Optional[str] = None,
+    relationship: Optional[str] = None,
+):
+    """
+    知识图谱查询
+    
+    查询微生物知识图谱
+    """
+    # TODO: 实现知识图谱查询
+    return {
+        "nodes": [],
+        "edges": [],
+        "message": "Knowledge graph feature pending"
+    }
+
+
+@router.get("/task/{task_id}")
+async def get_analysis_task_status(task_id: str):
+    """
+    查询分析任务状态
+    """
+    # TODO: 从数据库或缓存查询任务状态
+    return {
+        "task_id": task_id,
+        "status": "completed",
+        "progress": 100,
+        "result": None
+    }

web/ws/backend/app/api/v1/endpoints/genes.py

@@ -0,0 +1,56 @@
+"""
+基因资源 API
+"""
+from typing import List, Optional
+from fastapi import APIRouter, Query, HTTPException
+
+router = APIRouter()
+
+
+@router.get("/")
+async def get_genes(
+    skip: int = Query(0, ge=0),
+    limit: int = Query(20, ge=1, le=100),
+    function_type: Optional[str] = None,
+    search: Optional[str] = None,
+):
+    """
+    获取基因列表
+    
+    - **skip**: 跳过记录数
+    - **limit**: 返回记录数
+    - **function_type**: 功能类型 (抗逆/促生/杀虫/抗病/其他)
+    - **search**: 搜索关键词
+    """
+    # TODO: 实现数据库查询
+    return {
+        "total": 0,
+        "items": [],
+        "skip": skip,
+        "limit": limit
+    }
+
+
+@router.get("/{gene_id}")
+async def get_gene_detail(gene_id: str):
+    """
+    获取基因详情
+    """
+    # TODO: 从数据库查询基因详细信息
+    raise HTTPException(status_code=404, detail="Gene not found")
+
+
+@router.get("/functions/categories")
+async def get_gene_functions():
+    """
+    获取基因功能分类
+    """
+    return {
+        "categories": [
+            {"id": 1, "name": "抗逆基因", "count": 0},
+            {"id": 2, "name": "促生基因", "count": 0},
+            {"id": 3, "name": "杀虫基因", "count": 0},
+            {"id": 4, "name": "抗病基因", "count": 0},
+            {"id": 5, "name": "其他功能基因", "count": 0},
+        ]
+    }

web/ws/backend/app/api/v1/endpoints/genomes.py

@@ -0,0 +1,51 @@
+"""
+基因组学数据 API
+"""
+from typing import List, Optional
+from fastapi import APIRouter, Query, HTTPException
+
+router = APIRouter()
+
+
+@router.get("/")
+async def get_genomes(
+    skip: int = Query(0, ge=0),
+    limit: int = Query(20, ge=1, le=100),
+    data_type: Optional[str] = None,
+    species: Optional[str] = None,
+):
+    """
+    获取基因组数据列表
+    
+    - **skip**: 跳过记录数
+    - **limit**: 返回记录数
+    - **data_type**: 数据类型 (基因组学/转录组学/其他组学)
+    - **species**: 物种名称
+    """
+    # TODO: 实现数据库查询
+    return {
+        "total": 0,
+        "items": [],
+        "skip": skip,
+        "limit": limit
+    }
+
+
+@router.get("/{genome_id}")
+async def get_genome_detail(genome_id: str):
+    """
+    获取基因组详情
+    """
+    # TODO: 从数据库查询基因组详细信息
+    raise HTTPException(status_code=404, detail="Genome not found")
+
+
+@router.get("/species/tree")
+async def get_species_tree():
+    """
+    获取物种分类树
+    """
+    # TODO: 返回物种分类树结构
+    return {
+        "tree": []
+    }

web/ws/backend/app/api/v1/endpoints/strains.py

@@ -0,0 +1,56 @@
+"""
+菌种资源 API
+"""
+from typing import List, Optional
+from fastapi import APIRouter, Query, HTTPException
+
+router = APIRouter()
+
+
+@router.get("/")
+async def get_strains(
+    skip: int = Query(0, ge=0),
+    limit: int = Query(20, ge=1, le=100),
+    category: Optional[str] = None,
+    search: Optional[str] = None,
+):
+    """
+    获取菌种列表
+    
+    - **skip**: 跳过记录数
+    - **limit**: 返回记录数
+    - **category**: 菌种分类 (抗逆/促生/杀虫/抗病/食药用)
+    - **search**: 搜索关键词
+    """
+    # TODO: 实现数据库查询
+    return {
+        "total": 0,
+        "items": [],
+        "skip": skip,
+        "limit": limit
+    }
+
+
+@router.get("/{strain_id}")
+async def get_strain_detail(strain_id: str):
+    """
+    获取菌种详情
+    """
+    # TODO: 从数据库查询菌种详细信息
+    raise HTTPException(status_code=404, detail="Strain not found")
+
+
+@router.get("/categories/tree")
+async def get_strain_categories():
+    """
+    获取菌种分类树
+    """
+    return {
+        "categories": [
+            {"id": 1, "name": "抗逆微生物", "count": 0},
+            {"id": 2, "name": "促生微生物", "count": 0},
+            {"id": 3, "name": "杀虫微生物", "count": 0},
+            {"id": 4, "name": "抗病微生物", "count": 0},
+            {"id": 5, "name": "食药用微生物", "count": 0},
+        ]
+    }

web/ws/backend/app/api/v1/endpoints/upload.py

@@ -0,0 +1,107 @@
+"""
+数据汇交上传 API
+"""
+from typing import Optional
+from fastapi import APIRouter, UploadFile, File, Form, HTTPException, BackgroundTasks
+from app.core.security import verify_upload_key
+
+router = APIRouter()
+
+
+@router.post("/verify-key")
+async def verify_key(key: str = Form(...)):
+    """
+    验证上传口令
+    """
+    is_valid = await verify_upload_key(key)
+    if not is_valid:
+        raise HTTPException(status_code=401, detail="Invalid upload key")
+    return {"status": "success", "message": "Key verified"}
+
+
+@router.post("/genome")
+async def upload_genome_data(
+    background_tasks: BackgroundTasks,
+    project_id: str = Form(...),
+    submitter_name: str = Form(...),
+    submitter_email: str = Form(...),
+    upload_key: str = Form(...),
+    file: Optional[UploadFile] = File(None),
+):
+    """
+    上传基因组数据
+    
+    支持逐条提交和批量上传
+    """
+    # 验证口令
+    if not await verify_upload_key(upload_key):
+        raise HTTPException(status_code=401, detail="Invalid upload key")
+    
+    # TODO: 处理文件上传
+    if file:
+        # 异步保存文件
+        filename = file.filename
+        # background_tasks.add_task(save_file, file, filename)
+    
+    # TODO: 保存到数据库
+    return {
+        "status": "success",
+        "message": "Data uploaded successfully",
+        "project_id": project_id
+    }
+
+
+@router.post("/metagenome")
+async def upload_metagenome_data(
+    background_tasks: BackgroundTasks,
+    project_id: str = Form(...),
+    submitter_name: str = Form(...),
+    upload_key: str = Form(...),
+    file: Optional[UploadFile] = File(None),
+):
+    """
+    上传宏基因组数据
+    """
+    if not await verify_upload_key(upload_key):
+        raise HTTPException(status_code=401, detail="Invalid upload key")
+    
+    # TODO: 实现宏基因组数据上传逻辑
+    return {
+        "status": "success",
+        "message": "Metagenome data uploaded",
+        "project_id": project_id
+    }
+
+
+@router.post("/raw-data")
+async def upload_raw_data(
+    background_tasks: BackgroundTasks,
+    project_id: str = Form(...),
+    upload_key: str = Form(...),
+    file: UploadFile = File(...),
+):
+    """
+    上传原始测序数据
+    """
+    if not await verify_upload_key(upload_key):
+        raise HTTPException(status_code=401, detail="Invalid upload key")
+    
+    # TODO: 实现原始数据上传逻辑
+    return {
+        "status": "success",
+        "message": "Raw data uploaded",
+        "filename": file.filename
+    }
+
+
+@router.get("/status/{upload_id}")
+async def get_upload_status(upload_id: str):
+    """
+    查询上传状态
+    """
+    # TODO: 从数据库查询上传状态
+    return {
+        "upload_id": upload_id,
+        "status": "processing",
+        "progress": 50
+    }

web/ws/backend/app/api/v1/router.py

@@ -0,0 +1,14 @@
+"""
+API v1 路由汇总
+"""
+from fastapi import APIRouter
+from app.api.v1.endpoints import strains, genomes, genes, upload, analysis
+
+api_router = APIRouter()
+
+# 注册各模块路由
+api_router.include_router(strains.router, prefix="/strains", tags=["strains"])
+api_router.include_router(genomes.router, prefix="/genomes", tags=["genomes"])
+api_router.include_router(genes.router, prefix="/genes", tags=["genes"])
+api_router.include_router(upload.router, prefix="/upload", tags=["upload"])
+api_router.include_router(analysis.router, prefix="/analysis", tags=["analysis"])

web/ws/backend/app/core/config.py

@@ -0,0 +1,43 @@
+"""
+应用配置
+"""
+from typing import List
+from pydantic_settings import BaseSettings
+from pydantic import AnyHttpUrl
+
+
+class Settings(BaseSettings):
+    """应用配置类"""
+    
+    # 项目信息
+    PROJECT_NAME: str = "PBMDB API"
+    VERSION: str = "1.0.0"
+    API_V1_STR: str = "/api/v1"
+    
+    # 数据库配置
+    DATABASE_URL: str = "postgresql://webws_admin:password@postgres:5432/webws_database"
+    
+    # CORS 配置
+    ALLOWED_ORIGINS: List[str] = [
+        "https://amiap.hzau.edu.cn",
+        "http://localhost:3000",  # 本地开发
+    ]
+    
+    # 安全配置
+    SECRET_KEY: str = "your-secret-key-here-change-in-production"
+    ACCESS_TOKEN_EXPIRE_MINUTES: int = 60 * 24 * 7  # 7 days
+    
+    # 文件上传配置
+    MAX_UPLOAD_SIZE: int = 1024 * 1024 * 100  # 100MB
+    UPLOAD_DIR: str = "/app/uploads"
+    
+    # 分页配置
+    DEFAULT_PAGE_SIZE: int = 20
+    MAX_PAGE_SIZE: int = 100
+    
+    class Config:
+        env_file = ".env"
+        case_sensitive = True
+
+
+settings = Settings()

web/ws/backend/app/core/security.py

@@ -0,0 +1,39 @@
+"""
+安全认证模块
+"""
+from datetime import datetime, timedelta
+from typing import Optional
+from fastapi import Depends, HTTPException, status
+from fastapi.security import HTTPBearer, HTTPAuthorizationCredentials
+
+
+security = HTTPBearer()
+
+
+async def verify_token(
+    credentials: HTTPAuthorizationCredentials = Depends(security)
+) -> dict:
+    """
+    验证 Token
+    """
+    token = credentials.credentials
+    # TODO: 实现 JWT token 验证逻辑
+    return {"user_id": "example"}
+
+
+async def verify_upload_key(key: str) -> bool:
+    """
+    验证上传口令
+    用于数据汇交功能
+    """
+    # TODO: 从数据库或配置中验证口令
+    valid_keys = ["temp_key_123"]  # 临时示例
+    return key in valid_keys
+
+
+def create_access_token(data: dict, expires_delta: Optional[timedelta] = None) -> str:
+    """
+    创建访问令牌
+    """
+    # TODO: 实现 JWT token 生成
+    return "temporary_token"

web/ws/backend/app/main.py

@@ -0,0 +1,43 @@
+"""
+FastAPI 应用入口
+"""
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from app.core.config import settings
+from app.api.v1.router import api_router
+
+app = FastAPI(
+    title=settings.PROJECT_NAME,
+    version=settings.VERSION,
+    description="PBMDB (Plant Beneficial Microbe Database) API",
+    docs_url="/docs",
+    redoc_url="/redoc",
+)
+
+# CORS 配置
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=settings.ALLOWED_ORIGINS,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+# 注册路由
+app.include_router(api_router, prefix="/api/v1")
+
+
+@app.get("/")
+async def root():
+    """健康检查端点"""
+    return {
+        "status": "ok",
+        "message": "PBMDB API is running",
+        "version": settings.VERSION
+    }
+
+
+@app.get("/health")
+async def health_check():
+    """健康检查"""
+    return {"status": "healthy"}

web/ws/backend/manage.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    """Run administrative tasks."""
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'config.settings.base')
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError as exc:
+        raise ImportError(
+            "Couldn't import Django. Are you sure it's installed and "
+            "available on your PYTHONPATH environment variable? Did you "
+            "forget to activate a virtual environment?"
+        ) from exc
+    execute_from_command_line(sys.argv)
+
+
+if __name__ == '__main__':
+    main()

web/ws/backend/requirements.txt

@@ -0,0 +1,27 @@
+# FastAPI 核心
+fastapi>=0.104.0
+uvicorn[standard]>=0.24.0
+pydantic>=2.5.0
+pydantic-settings>=2.1.0
+
+# 数据库
+sqlalchemy>=2.0.0
+asyncpg>=0.29.0
+alembic>=1.13.0
+
+# 文件处理
+aiofiles>=23.2.0
+python-multipart>=0.0.6
+
+# 认证
+python-jose[cryptography]>=3.3.0
+passlib[bcrypt]>=1.7.4
+
+# 其他常用库
+python-dateutil>=2.8.2
+pytz>=2023.3
+
+# 可选：AI/ML 相关（按需取消注释）
+# transformers>=4.35.0
+# torch>=2.1.0
+# scikit-learn>=1.3.0

web/ws/backend/start.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+# FastAPI 开发服务器启动脚本
+
+set -e
+
+echo "=========================================="
+echo "启动 FastAPI 开发服务器"
+echo "=========================================="
+
+# 检查虚拟环境
+if [ ! -d "venv" ]; then
+    echo "创建虚拟环境..."
+    python3 -m venv venv
+fi
+
+# 激活虚拟环境
+echo "激活虚拟环境..."
+source venv/bin/activate
+
+# 安装依赖
+echo "安装依赖..."
+pip install -r requirements.txt
+
+# 检查环境变量
+if [ ! -f ".env" ]; then
+    echo "警告: .env 文件不存在，复制 .env.example..."
+    cp .env.example .env
+    echo "请编辑 .env 文件配置数据库等信息"
+fi
+
+# 启动服务器
+echo ""
+echo "=========================================="
+echo "启动服务器..."
+echo "=========================================="
+echo "API 文档: http://localhost:8000/docs"
+echo "健康检查: http://localhost:8000/health"
+echo "=========================================="
+echo ""
+
+uvicorn app.main:app --reload --host 0.0.0.0 --port 8000

web/ws/backend/test_api.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+# FastAPI API 测试脚本
+
+BASE_URL="https://amiap.hzau.edu.cn/ABM/api"
+
+echo "=========================================="
+echo "测试 PBMDB FastAPI 接口"
+echo "=========================================="
+
+echo -e "\n✓ 1. 健康检查..."
+curl -s "${BASE_URL}/health" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 2. 根路径..."
+curl -s "${BASE_URL}/" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 3. 获取菌种列表..."
+curl -s "${BASE_URL}/api/v1/strains/" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 4. 获取菌种分类..."
+curl -s "${BASE_URL}/api/v1/strains/categories/tree" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 5. 获取基因组列表..."
+curl -s "${BASE_URL}/api/v1/genomes/" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 6. 获取基因列表..."
+curl -s "${BASE_URL}/api/v1/genes/" | jq '.' || echo "Failed"
+
+echo -e "\n✓ 7. 获取基因功能分类..."
+curl -s "${BASE_URL}/api/v1/genes/functions/categories" | jq '.' || echo "Failed"
+
+echo -e "\n=========================================="
+echo "测试完成"
+echo "=========================================="
+echo "访问 API 文档: ${BASE_URL}/docs"
+echo "=========================================="