init: 初始化 dpb 桃育种系统代码库
前后端 + 后端 FastAPI 全量源码、部署脚本与文档。
This commit is contained in:
34047007@qq.com
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import urllib.parse
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from typing import Annotated
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from fastapi import APIRouter, Body, Depends, File, Path, Query, UploadFile
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from fastapi.responses import JSONResponse, StreamingResponse
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.common.response import ResponseSchema, StreamResponse, SuccessResponse
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from app.core.base_schema import AuthSchema, PageResultSchema, PaginationQueryParam, ImportResultSchema
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from app.core.dependencies import AuthPermission, db_getter
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from app.core.router_class import OperationLogRoute
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from app.utils.common_util import bytes2file_response
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from .schema import (
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MarkerCreateSchema,
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MarkerOutSchema,
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MarkerQueryParam,
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MarkerUpdateSchema,
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)
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from .service import MarkerService
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MarkerRouter = APIRouter(route_class=OperationLogRoute, prefix="/marker", tags=["分子标记"])
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@MarkerRouter.get("/detail/{id}", summary="获取分子标记详情", response_model=ResponseSchema[MarkerOutSchema])
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async def get_marker__detail_controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:detail"]))],
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id: Annotated[int, Path(description="标记ID")],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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result_dict = await service.detail(id=id)
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return SuccessResponse(data=result_dict, msg="获取分子标记详情成功")
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@MarkerRouter.get("/list", summary="分页查询分子标记", response_model=ResponseSchema[PageResultSchema[MarkerOutSchema]])
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async def get_marker__list_controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:query"]))],
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page: Annotated[PaginationQueryParam, Depends()],
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search: Annotated[MarkerQueryParam, Query()],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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result_dict = await service.page(
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page_no=page.page_no,
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page_size=page.page_size,
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search=search,
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order_by=page.order_by,
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)
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return SuccessResponse(data=result_dict, msg="查询分子标记列表成功")
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@MarkerRouter.get("/options", summary="分子标记下拉选项")
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async def get_marker__options_controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:query"]))],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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options = await service.list_options()
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return SuccessResponse(data=options, msg="获取分子标记选项成功")
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@MarkerRouter.post("/create", summary="创建分子标记", response_model=ResponseSchema[MarkerOutSchema])
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async def create_marker__controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:create"]))],
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data: Annotated[MarkerCreateSchema, Body(description="创建参数")],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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result_dict = await service.create(data=data)
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return SuccessResponse(data=result_dict, msg="创建分子标记成功")
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@MarkerRouter.put("/update/{id}", summary="修改分子标记", response_model=ResponseSchema[MarkerOutSchema])
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async def update_marker__controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:update"]))],
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id: Annotated[int, Path(description="标记ID")],
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data: Annotated[MarkerUpdateSchema, Body(description="修改参数")],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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result_dict = await service.update(id=id, data=data)
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return SuccessResponse(data=result_dict, msg="修改分子标记成功")
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@MarkerRouter.delete("/delete", summary="删除分子标记", response_model=ResponseSchema[None])
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async def delete_marker__controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:delete"]))],
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ids: Annotated[list[int], Body(description="ID列表")],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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await service.delete(ids=ids)
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return SuccessResponse(msg="删除分子标记成功")
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@MarkerRouter.post("/export", summary="导出分子标记")
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async def export_marker__controller(
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:export"]))],
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search: Annotated[MarkerQueryParam, Query()],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> StreamingResponse:
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service = MarkerService(auth, db)
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result_dict_list = await service.get_list(search=search)
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export_result = MarkerService.batch_export(obj_list=[item.model_dump() for item in result_dict_list])
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return StreamResponse(
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data=bytes2file_response(export_result),
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media_type="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
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headers={"Content-Disposition": f"attachment; filename={urllib.parse.quote('分子标记.xlsx')}"},
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)
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@MarkerRouter.post("/import", summary="导入分子标记", response_model=ResponseSchema[ImportResultSchema])
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async def import_marker__controller(
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file: Annotated[UploadFile, File(description="导入文件")],
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auth: Annotated[AuthSchema, Depends(AuthPermission(["module_bre:marker:import"]))],
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db: Annotated[AsyncSession, Depends(db_getter)],
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) -> JSONResponse:
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service = MarkerService(auth, db)
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batch_import_result = await service.batch_import(file=file, update_support=True)
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return SuccessResponse(data=batch_import_result, msg="导入分子标记成功")
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@MarkerRouter.post("/download/template", summary="获取分子标记导入模板", dependencies=[Depends(AuthPermission(["module_bre:marker:download"]))])
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async def download_marker__template_controller() -> StreamingResponse:
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import_template_result = MarkerService.import_template_download()
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return StreamResponse(
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data=bytes2file_response(import_template_result),
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media_type="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
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headers={
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"Content-Disposition": f"attachment; filename={urllib.parse.quote('分子标记导入模板.xlsx')}",
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"Access-Control-Expose-Headers": "Content-Disposition",
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},
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)
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@@ -0,0 +1,18 @@
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from typing import Any
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.core.base_crud import CRUDBase
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from app.core.base_schema import AuthSchema
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from .model import MarkerModel
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class BreedingMarkerCRUD(CRUDBase[MarkerModel, Any, Any]):
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"""分子标记 CRUD —— 直接复用 CRUDBase（已自动注入数据权限过滤）。"""
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def __init__(self, auth: AuthSchema, db: AsyncSession) -> None:
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super().__init__(MarkerModel, auth, db)
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marker_crud = BreedingMarkerCRUD
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@@ -0,0 +1,30 @@
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"""分子标记 数据模型"""
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from sqlalchemy import Index, Integer, String
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from sqlalchemy.orm import Mapped, mapped_column
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from app.core.base_model import MappedBase, ModelMixin, UserMixin
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class MarkerModel(ModelMixin, UserMixin, MappedBase):
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"""分子标记（§3.7；SSR/SNP，panel/assembly_version 供 GS 同版本）。"""
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__tablename__ = "bre_marker"
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marker_name: Mapped[str] = mapped_column(String(64), nullable=False, comment="标记名称(唯一)")
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chromosome: Mapped[str | None] = mapped_column(String(16), nullable=True, comment="染色体", default=None)
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position: Mapped[int | None] = mapped_column(Integer, nullable=True, comment="物理位置(bp)", default=None)
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marker_type: Mapped[str | None] = mapped_column(String(16), nullable=True, comment="标记类型(SSR/SNP/INDEL)", default=None)
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panel: Mapped[str | None] = mapped_column(String(32), nullable=True, comment="标记 panel", default=None)
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assembly_version: Mapped[str | None] = mapped_column(String(32), nullable=True, comment="参考基因组版本", default=None)
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remark: Mapped[str | None] = mapped_column(String(512), nullable=True, comment="备注", default=None)
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# 无 status 列：覆盖基类默认 ix_<表>_status_deleted 索引（与 DDL 一致）
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__table_args__ = (
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Index("ix_bre_marker_created_deleted", "created_time", "is_deleted"),
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)
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@@ -0,0 +1,54 @@
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"""分子标记 —— Pydantic 校验/序列化模型。"""
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from datetime import datetime
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from pydantic import BaseModel, ConfigDict, Field
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from app.core.base_schema import CommonSchema
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class MarkerBaseSchema(BaseModel):
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model_config = ConfigDict(from_attributes=True)
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marker_name: str = Field(..., description="标记名称(唯一)")
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chromosome: str | None = Field(default=None, description="染色体")
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position: int | None = Field(default=None, description="物理位置(bp)")
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marker_type: str | None = Field(default=None, description="标记类型(SSR/SNP/INDEL)")
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panel: str | None = Field(default=None, description="标记 panel")
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assembly_version: str | None = Field(default=None, description="参考基因组版本")
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remark: str | None = Field(default=None, description="备注")
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class MarkerCreateSchema(MarkerBaseSchema):
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pass
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class MarkerUpdateSchema(MarkerBaseSchema):
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marker_name: str | None = Field(default=None, description="标记名称(唯一)")
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chromosome: str | None = Field(default=None, description="染色体")
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position: int | None = Field(default=None, description="物理位置(bp)")
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marker_type: str | None = Field(default=None, description="标记类型(SSR/SNP/INDEL)")
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panel: str | None = Field(default=None, description="标记 panel")
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assembly_version: str | None = Field(default=None, description="参考基因组版本")
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remark: str | None = Field(default=None, description="备注")
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class MarkerOutSchema(MarkerBaseSchema):
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id: int
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uuid: str
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marker_name: str | None = None
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chromosome: str | None = None
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position: int | None = None
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marker_type: str | None = None
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panel: str | None = None
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assembly_version: str | None = None
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remark: str | None = None
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created_time: datetime | None = None
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updated_time: datetime | None = None
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created_by: CommonSchema | None = None
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updated_by: CommonSchema | None = None
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class MarkerQueryParam(BaseModel):
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marker_name: str | None = Field(default=None, description="标记名称", json_schema_extra={"q": "like"})
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marker_type: str | None = Field(default=None, description="标记类型")
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panel: str | None = Field(default=None, description="标记 panel")
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@@ -0,0 +1,213 @@
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from typing import Any
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from fastapi import UploadFile
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from sqlalchemy import select
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.core.base_schema import AuthSchema, PageResultSchema, ImportResultSchema
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from app.core.exceptions import CustomException
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from app.core.logger import logger
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from app.utils.common_util import search_to_dict
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from app.utils.excel_util import ExcelUtil
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from .crud import BreedingMarkerCRUD
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from .model import MarkerModel
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from .schema import (
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MarkerCreateSchema,
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MarkerOutSchema,
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MarkerQueryParam,
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MarkerUpdateSchema,
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)
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def _is_blank(v: Any) -> bool:
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return v is None or (isinstance(v, str) and v.strip() == "")
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def _none_if_blank(v: Any) -> Any:
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if _is_blank(v):
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return None
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return str(v).strip() if isinstance(v, str) else v
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def _to_int(v: Any) -> int | None:
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if _is_blank(v):
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return None
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try:
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return int(float(str(v).strip()))
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except (TypeError, ValueError):
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return None
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class MarkerService:
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"""分子标记 模块服务层"""
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def __init__(self, auth: AuthSchema, db: AsyncSession) -> None:
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self.auth = auth
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self.db = db
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async def _check_name(self, name: str, exclude_id: int | None = None) -> None:
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if _is_blank(name):
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raise CustomException(msg="标记名称不能为空")
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result = await self.db.execute(
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select(MarkerModel.id).where(
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MarkerModel.marker_name == str(name).strip(),
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MarkerModel.is_deleted.is_(False),
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)
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)
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obj_id = result.scalar_one_or_none()
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if obj_id is not None and obj_id != exclude_id:
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raise CustomException(msg=f"标记名称 {name} 已存在", status_code=409)
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async def detail(self, id: int) -> MarkerOutSchema:
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obj = await BreedingMarkerCRUD(self.auth, self.db).get(id=id)
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if not obj:
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raise CustomException(msg="该标记不存在")
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return MarkerOutSchema.model_validate(obj)
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async def get_list(
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self,
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search: MarkerQueryParam | None = None,
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order_by: list[dict[str, str]] | None = None,
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) -> list[MarkerOutSchema]:
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obj_list = await BreedingMarkerCRUD(self.auth, self.db).get_list(
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search=search_to_dict(search), order_by=order_by
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)
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return [MarkerOutSchema.model_validate(obj) for obj in obj_list]
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async def page(
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self,
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page_no: int,
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page_size: int,
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search: MarkerQueryParam | None = None,
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order_by: list[dict[str, str]] | None = None,
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) -> PageResultSchema[MarkerOutSchema]:
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offset = (page_no - 1) * page_size
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return await BreedingMarkerCRUD(self.auth, self.db).page(
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offset=offset,
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limit=page_size,
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order_by=order_by or [{"id": "asc"}],
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search=search_to_dict(search, {}),
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out_schema=MarkerOutSchema,
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)
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async def create(self, data: MarkerCreateSchema) -> MarkerOutSchema:
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await self._check_name(data.marker_name)
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obj = await BreedingMarkerCRUD(self.auth, self.db).create(data=data)
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return MarkerOutSchema.model_validate(obj)
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async def update(self, id: int, data: MarkerUpdateSchema) -> MarkerOutSchema:
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obj = await BreedingMarkerCRUD(self.auth, self.db).get(id=id)
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if not obj:
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raise CustomException(msg="更新失败，该标记不存在")
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if not _is_blank(data.marker_name):
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await self._check_name(data.marker_name, exclude_id=id)
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obj = await BreedingMarkerCRUD(self.auth, self.db).update(id=id, data=data)
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return MarkerOutSchema.model_validate(obj)
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async def delete(self, ids: list[int]) -> None:
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if not ids:
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raise CustomException(msg="删除失败，删除对象不能为空")
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objs = await BreedingMarkerCRUD(self.auth, self.db).get_list(search={"id": ("in", ids)})
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obj_map = {o.id: o for o in objs}
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for id_ in ids:
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if id_ not in obj_map:
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raise CustomException(msg="删除失败，该标记不存在")
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await BreedingMarkerCRUD(self.auth, self.db).delete(ids=ids)
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async def list_options(self) -> list[dict[str, Any]]:
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"""供前端下拉选择使用：返回 [{value, label}]。"""
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obj_list = await BreedingMarkerCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
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return [{"value": o.id, "label": o.marker_name} for o in obj_list]
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@staticmethod
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def batch_export(obj_list: list[dict[str, Any]]) -> bytes:
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mapping_dict = {
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"marker_name": "标记名称",
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"chromosome": "染色体",
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"position": "物理位置(bp)",
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"marker_type": "标记类型",
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"panel": "标记panel",
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"assembly_version": "参考基因组版本",
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"remark": "备注",
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"created_time": "创建时间",
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"created_by": "创建者",
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}
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data = [dict(item) for item in obj_list]
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for item in data:
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creator = item.get("created_by")
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item["created_by"] = creator.get("name", "未知") if isinstance(creator, dict) else "未知"
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return ExcelUtil.export_list2excel(list_data=data, mapping_dict=mapping_dict)
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async def batch_import(self, file: UploadFile, update_support: bool = False) -> ImportResultSchema:
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header_dict = {
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"标记名称": "marker_name",
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"染色体": "chromosome",
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"物理位置(bp)": "position",
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"标记类型": "marker_type",
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"标记panel": "panel",
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"参考基因组版本": "assembly_version",
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"备注": "remark",
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}
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try:
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contents = await file.read()
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rows = ExcelUtil.read_excel_to_dicts(contents)
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await file.close()
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if not rows:
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raise CustomException(msg="导入文件为空")
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missing_headers = [h for h in header_dict if h not in rows[0]]
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if missing_headers:
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raise CustomException(msg=f"导入文件缺少必要的列: {', '.join(missing_headers)}")
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error_msgs: list[str] = []
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success_count = 0
|
||||
crud = BreedingMarkerCRUD(self.auth, self.db)
|
||||
seen_names: set[str] = set()
|
||||
for i, row in enumerate(rows, start=1):
|
||||
try:
|
||||
name = row.get("marker_name")
|
||||
if _is_blank(name):
|
||||
raise CustomException(msg="标记名称不能为空")
|
||||
name = str(name).strip()
|
||||
if name in seen_names:
|
||||
raise CustomException(msg=f"文件内标记名称重复：{name}")
|
||||
seen_names.add(name)
|
||||
await self._check_name(name)
|
||||
fields = {
|
||||
"marker_name": name,
|
||||
"chromosome": _none_if_blank(row.get("chromosome")),
|
||||
"position": _to_int(row.get("position")),
|
||||
"marker_type": _none_if_blank(row.get("marker_type")),
|
||||
"panel": _none_if_blank(row.get("panel")),
|
||||
"assembly_version": _none_if_blank(row.get("assembly_version")),
|
||||
"remark": _none_if_blank(row.get("remark")),
|
||||
}
|
||||
await crud.create(data=MarkerCreateSchema(**fields))
|
||||
success_count += 1
|
||||
except Exception as e:
|
||||
error_msgs.append(f"第{i}行: {e!s}")
|
||||
continue
|
||||
return ImportResultSchema(
|
||||
valid_count=success_count,
|
||||
invalid_count=len(error_msgs),
|
||||
message_list=error_msgs,
|
||||
)
|
||||
except Exception as e:
|
||||
logger.error(f"批量导入分子标记失败: {e!s}")
|
||||
raise CustomException(msg=f"导入失败: {e!s}")
|
||||
|
||||
@staticmethod
|
||||
def import_template_download() -> bytes:
|
||||
header_list = [
|
||||
"标记名称",
|
||||
"染色体",
|
||||
"物理位置(bp)",
|
||||
"标记类型",
|
||||
"标记panel",
|
||||
"参考基因组版本",
|
||||
"备注",
|
||||
]
|
||||
return ExcelUtil.get_excel_template(
|
||||
header_list=header_list,
|
||||
selector_header_list=["标记类型"],
|
||||
option_list=[{"标记类型": ["SNP", "SSR", "INDEL", "InDel"]}],
|
||||
)
|
||||
Reference in New Issue
Block a user