534 lines
26 KiB
Python
534 lines
26 KiB
Python
from typing import Any
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from datetime import datetime
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from fastapi import UploadFile
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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 app.utils.dict_util import DictLabelResolver, dict_value_to_label
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from app.utils.number_gen import NumberGenService
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from .crud import BreedingCrossCombinationCRUD
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from .model import CrossCombinationModel
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from .schema import (
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CrossCombinationCreateSchema,
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CrossCombinationOutSchema,
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CrossCombinationQueryParam,
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CrossCombinationUpdateSchema,
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)
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from app.api.v1.module_bre.target.crud import BreedingTargetCRUD
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from app.api.v1.module_bre.germplasm.crud import BreedingGermplasmCRUD
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from app.core.base_crud import assert_dict_values, assert_no_children, assert_parents_exist
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from app.api.v1.module_bre.germplasm.model import BreedingGermplasmModel
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from app.api.v1.module_bre.pedigree.model import PedigreeModel
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from app.api.v1.module_bre.planting.model import PlantingModel
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from app.api.v1.module_bre.pollination.model import PollinationModel
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from app.api.v1.module_bre.seed_treatment.model import SeedTreatmentModel
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from app.api.v1.module_bre.seedling.model import SeedlingModel
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from app.api.v1.module_bre.selection_result.model import SelectionResultModel
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from app.api.v1.module_bre.target.model import TargetModel
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from app.api.v1.module_bre.trait_observation.model import TraitObservationModel
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from app.api.v1.module_bre.tree_evaluation.model import TreeEvaluationModel
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from app.api.v1.module_bre.tree.model import TreeModel
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from app.api.v1.module_bre.tree_photo.model import TreePhotoModel
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# 交配设计取值（与统计引擎 combining.solve 分支一致；不入 sys_dict，同 selection_index.method 模式）
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_COMBINING_DESIGNS = {"full_diallel", "partial_diallel", "line_tester", "nciii"}
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_DESIGN_LABELS = {
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"full_diallel": "完全双列",
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"partial_diallel": "部分双列",
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"line_tester": "line×tester (NCII)",
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"nciii": "NCIII 测交",
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}
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_DESIGN_FROM_LABEL = {v: k for k, v in _DESIGN_LABELS.items()}
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_SF_ALLELES = {"sf"}
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def _parse_s_alleles(raw: str | None) -> set[str] | None:
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"""解析 S-等位基因串（如 "S1/S3"、"S1,S2 S3"）→ 归一化等位集合；空白/无数据返回 None。
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大小写归一（S1/s1）；"Sf"/"sf" 为自交亲和功能缺失等位，单独标记含 sf。
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"""
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if raw is None or not str(raw).strip():
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return None
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parts = [p.strip() for p in str(raw).replace("/", ",").replace(";", ",").replace(" ", ",").split(",")]
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codes = {p.lower() for p in parts if p}
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return codes or None
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def _s_compat_check(female_s: str | None, male_s: str | None) -> tuple[str, str | None]:
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"""桃配子体型自交不亲和(S-RNase) 交配兼容性判定。
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规则：任一亲本携带 Sf（自交亲和等位，SI 功能缺失）→ 完全兼容；
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否则按共享 S 等位数：0=完全兼容，1=半兼容(花粉半数不亲和,坐果率降)，
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2=完全不相容（配了不结）。缺 S 数据 → 不校验(None)。
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返回 (状态, 文案)：状态 full/half/none/unknown。
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"""
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f_set, m_set = _parse_s_alleles(female_s), _parse_s_alleles(male_s)
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if f_set is None or m_set is None:
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return "unknown", None
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if f_set & _SF_ALLELES or m_set & _SF_ALLELES:
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return "full", None
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shared = sorted(f_set & m_set)
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if len(shared) >= 2:
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return "none", f"S-等位基因完全不相容（共享 {'/'.join(shared)}），该组合无法坐果"
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if len(shared) == 1:
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return "half", f"S-等位基因半兼容（共享 {shared[0]}），约半数花粉不亲和，坐果率下降"
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return "full", None
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def _validate_design_type(design_type: str | None) -> str | None:
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if _is_blank(design_type):
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return None
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code = _DESIGN_FROM_LABEL.get(str(design_type).strip()) or str(design_type).strip()
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if code not in _COMBINING_DESIGNS:
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raise CustomException(
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msg=f"交配设计取值不合法: {design_type}（可用: {'、'.join(_DESIGN_LABELS.values())}）"
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)
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return code
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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_float(v: Any) -> float | 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 float(v)
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except (TypeError, ValueError):
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return None
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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(v))
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except (TypeError, ValueError):
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return None
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class CrossCombinationService:
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"""杂交组合 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 _attach_fk_labels(self, items: list[CrossCombinationOutSchema]) -> None:
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if not items:
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return
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crud = BreedingCrossCombinationCRUD(self.auth, self.db)
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bre_target_id_ids = {getattr(it, "bre_target_id") for it in items if getattr(it, "bre_target_id")}
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if bre_target_id_ids:
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refs = await BreedingTargetCRUD(self.auth, self.db).get_list(search={"id": ("in", list(bre_target_id_ids))})
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ref_map = {r.id: getattr(r, "target_name") for r in refs}
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for it in items:
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it.bre_target_name = ref_map.get(getattr(it, "bre_target_id"))
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female_parent_id_ids = {getattr(it, "female_parent_id") for it in items if getattr(it, "female_parent_id")}
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if female_parent_id_ids:
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refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(search={"id": ("in", list(female_parent_id_ids))})
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ref_map = {r.id: getattr(r, "cultivar_name") for r in refs}
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for it in items:
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it.female_parent_name = ref_map.get(getattr(it, "female_parent_id"))
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male_parent_id_ids = {getattr(it, "male_parent_id") for it in items if getattr(it, "male_parent_id")}
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if male_parent_id_ids:
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refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(search={"id": ("in", list(male_parent_id_ids))})
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ref_map = {r.id: getattr(r, "cultivar_name") for r in refs}
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for it in items:
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it.male_parent_name = ref_map.get(getattr(it, "male_parent_id"))
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parent_combination_id_ids = {getattr(it, "parent_combination_id") for it in items if getattr(it, "parent_combination_id")}
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if parent_combination_id_ids:
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refs = await BreedingCrossCombinationCRUD(self.auth, self.db).get_list(search={"id": ("in", list(parent_combination_id_ids))})
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ref_map = {r.id: getattr(r, "combination_code") for r in refs}
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for it in items:
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it.parent_combination_code = ref_map.get(getattr(it, "parent_combination_id"))
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async def detail(self, id: int) -> CrossCombinationOutSchema:
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obj = await BreedingCrossCombinationCRUD(self.auth, self.db).get(id=id)
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if not obj:
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raise CustomException(msg="该杂交组合不存在")
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out = CrossCombinationOutSchema.model_validate(obj)
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await self._attach_fk_labels([out])
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return out
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async def get_list(
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self,
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search: CrossCombinationQueryParam | None = None,
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order_by: list[dict[str, str]] | None = None,
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) -> list[CrossCombinationOutSchema]:
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obj_list = await BreedingCrossCombinationCRUD(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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outs = [CrossCombinationOutSchema.model_validate(obj) for obj in obj_list]
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await self._attach_fk_labels(outs)
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return outs
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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: CrossCombinationQueryParam | None = None,
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order_by: list[dict[str, str]] | None = None,
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) -> PageResultSchema[CrossCombinationOutSchema]:
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offset = (page_no - 1) * page_size
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result = await BreedingCrossCombinationCRUD(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=CrossCombinationOutSchema,
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)
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await self._attach_fk_labels(result.items)
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return result
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async def _check_s_compat(self, female_parent_id: int | None, male_parent_id: int | None) -> str | None:
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"""读亲本 S-等位基因做交配兼容性校验；完全不相容 → 409；半兼容返回警示文案。"""
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if not female_parent_id or not male_parent_id:
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return None
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refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(
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search={"id": ("in", [female_parent_id, male_parent_id])}
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)
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by_id = {g.id: g for g in refs}
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female_s = getattr(by_id.get(female_parent_id), "s_alleles", None)
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male_s = getattr(by_id.get(male_parent_id), "s_alleles", None)
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status, msg = _s_compat_check(female_s, male_s)
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if status == "none":
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raise CustomException(msg=msg)
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return msg if status == "half" else None
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async def _check_parent_roles(self, female_parent_id: int | None, male_parent_id: int | None) -> None:
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"""亲本校验：母本父本同质自交 → 409；已显式配置为单角色的种质不得用于另一角色。
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桃为两性花，绝大多数种质可双作；can_be_female/can_be_male 两列
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default=False 表示未配置，视为均可（不拦）。仅当某侧被显式标记为
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不可作（该侧 False、另一侧 True）时按数据错误拦截。
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"""
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if not female_parent_id or not male_parent_id:
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return
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refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(
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search={"id": ("in", [female_parent_id, male_parent_id])}
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)
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by_id = {g.id: g for g in refs}
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female = by_id.get(female_parent_id)
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male = by_id.get(male_parent_id)
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if female is None or male is None:
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return
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f_name = getattr(female, "cultivar_name", "母本") or "母本"
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m_name = getattr(male, "cultivar_name", "父本") or "父本"
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if female_parent_id == male_parent_id:
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raise CustomException(msg=f"母本与父本同为「{f_name}」，自交组合请确认")
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if female.can_be_male and not female.can_be_female:
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raise CustomException(msg=f"母本「{f_name}」已标记为仅可作父本，不能作母本")
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if male.can_be_female and not male.can_be_male:
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raise CustomException(msg=f"父本「{m_name}」已标记为仅可作母本，不能作父本")
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async def _gen_combination_code(self, cross_year: int | None) -> str:
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"""自动生成组合编号：YY + 3 位序号（如 26001、26002…），原子取号。"""
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year = cross_year or datetime.now().year
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prefix = f"{year % 100:02d}"
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async def _seed() -> int | None:
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crud = BreedingCrossCombinationCRUD(self.auth, self.db)
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objs = await crud.get_list(search={"combination_code": ("like", prefix)})
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max_seq = 0
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for o in objs:
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code = o.combination_code or ""
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if code.startswith(prefix) and code[len(prefix):].isdigit():
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max_seq = max(max_seq, int(code[len(prefix):]))
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return max_seq + 1
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seq = await NumberGenService(self.db).next_seq(f"combination:{year}", seed_fn=_seed)
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return f"{prefix}{seq:03d}"
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async def create(self, data: CrossCombinationCreateSchema) -> CrossCombinationOutSchema:
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fields = data.model_dump(exclude_none=True)
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if _is_blank(fields.get("combination_code")):
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fields["combination_code"] = await self._gen_combination_code(fields.get("cross_year"))
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code = _validate_design_type(fields.get("design_type") or "full_diallel")
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fields["design_type"] = code or "full_diallel"
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data = CrossCombinationCreateSchema(**fields)
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exist_obj = await BreedingCrossCombinationCRUD(self.auth, self.db).get(combination_code=data.combination_code)
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if exist_obj:
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raise CustomException(msg="创建失败，组合编号已存在")
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await assert_parents_exist(
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self.db,
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[
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(TargetModel, data.bre_target_id, '育种目标'),
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(BreedingGermplasmModel, data.female_parent_id, '母本种质'),
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(BreedingGermplasmModel, data.male_parent_id, '父本种质'),
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(CrossCombinationModel, data.parent_combination_id, '母本组合'),
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],
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)
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await assert_dict_values(
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self.db,
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[
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('cross_method', data.cross_method, '杂交方式'),
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('cross_type', data.cross_type, '杂交类型'),
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('breeding_stage', data.stage, '育种阶段'),
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],
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)
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await self._check_parent_roles(data.female_parent_id, data.male_parent_id)
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s_compat = await self._check_s_compat(data.female_parent_id, data.male_parent_id)
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obj = await BreedingCrossCombinationCRUD(self.auth, self.db).create(data=data)
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out = CrossCombinationOutSchema.model_validate(obj)
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out.s_compat = s_compat
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await self._attach_fk_labels([out])
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return out
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async def update(self, id: int, data: CrossCombinationUpdateSchema) -> CrossCombinationOutSchema:
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obj = await BreedingCrossCombinationCRUD(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，该杂交组合不存在")
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if data.combination_code is not None:
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exist_obj = await BreedingCrossCombinationCRUD(self.auth, self.db).get(combination_code=data.combination_code)
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if exist_obj and exist_obj.id != id:
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raise CustomException(msg="更新失败，组合编号重复")
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await assert_parents_exist(
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self.db,
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[
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(TargetModel, data.bre_target_id, '育种目标'),
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(BreedingGermplasmModel, data.female_parent_id, '母本种质'),
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(BreedingGermplasmModel, data.male_parent_id, '父本种质'),
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(CrossCombinationModel, data.parent_combination_id, '母本组合'),
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],
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)
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await assert_dict_values(
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self.db,
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[
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('cross_method', data.cross_method, '杂交方式'),
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('cross_type', data.cross_type, '杂交类型'),
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('breeding_stage', data.stage, '育种阶段'),
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],
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)
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if data.design_type is not None:
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data.design_type = _validate_design_type(data.design_type) or data.design_type
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eff_female = data.female_parent_id if data.female_parent_id is not None else obj.female_parent_id
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eff_male = data.male_parent_id if data.male_parent_id is not None else obj.male_parent_id
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await self._check_parent_roles(eff_female, eff_male)
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s_compat = await self._check_s_compat(eff_female, eff_male)
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obj = await BreedingCrossCombinationCRUD(self.auth, self.db).update(id=id, data=data)
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out = CrossCombinationOutSchema.model_validate(obj)
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out.s_compat = s_compat
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await self._attach_fk_labels([out])
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return out
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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 BreedingCrossCombinationCRUD(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，该杂交组合不存在")
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await assert_no_children(
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self.db,
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ids,
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[
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(PollinationModel, 'combination_id', '授粉'),
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(SeedTreatmentModel, 'combination_id', '种子处理'),
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(SeedlingModel, 'combination_id', '实生苗'),
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(PlantingModel, 'combination_id', '定植'),
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(TreeModel, 'combination_id', '单株'),
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(TreeEvaluationModel, 'combination_id', '单株评价'),
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(TreePhotoModel, 'combination_id', '单株照片'),
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(SelectionResultModel, 'combination_id', '选择结果'),
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(TraitObservationModel, 'combination_id', '性状观测'),
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(PedigreeModel, 'combination_id', '系谱'),
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],
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)
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await BreedingCrossCombinationCRUD(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, female_parent_id, male_parent_id}]。
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female/male 亲本 id 供单株表单选中组合后自动回填母本/父本。
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"""
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obj_list = await BreedingCrossCombinationCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
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return [
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{
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"value": o.id,
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"label": o.combination_code,
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"female_parent_id": o.female_parent_id,
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"male_parent_id": o.male_parent_id,
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}
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for o in obj_list
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]
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@staticmethod
|
||
def batch_export(obj_list: list[dict[str, Any]]) -> bytes:
|
||
mapping_dict = {
|
||
"combination_code": "组合编号",
|
||
"cross_year": "杂交年份",
|
||
"bre_target_name": "育种目标",
|
||
"female_parent_name": "母本",
|
||
"male_parent_name": "父本",
|
||
"parent_combination_code": "母本组合",
|
||
"cross_method": "杂交方式",
|
||
"cross_type": "杂交类型",
|
||
"design_type": "交配设计",
|
||
"reason": "组配理由",
|
||
"stage": "育种阶段",
|
||
"cross_date": "杂交日期",
|
||
"seed_count": "获种数",
|
||
"remark": "备注",
|
||
"created_time": "创建时间",
|
||
"created_by": "创建者",
|
||
}
|
||
data = [dict(item) for item in obj_list]
|
||
for item in data:
|
||
creator = item.get("created_by")
|
||
item["created_by"] = creator.get("name", "未知") if isinstance(creator, dict) else "未知"
|
||
item["cross_method"] = dict_value_to_label("cross_method", item.get("cross_method"))
|
||
item["cross_type"] = dict_value_to_label("cross_type", item.get("cross_type"))
|
||
item["design_type"] = _DESIGN_LABELS.get(item.get("design_type"), item.get("design_type"))
|
||
item["stage"] = dict_value_to_label("breeding_stage", item.get("stage"))
|
||
return ExcelUtil.export_list2excel(list_data=data, mapping_dict=mapping_dict)
|
||
|
||
async def batch_import(self, file: UploadFile, update_support: bool = False) -> ImportResultSchema:
|
||
header_dict = {
|
||
"组合编号": "combination_code",
|
||
"杂交年份": "cross_year",
|
||
"育种目标": "bre_target_id",
|
||
"母本": "female_parent_id",
|
||
"父本": "male_parent_id",
|
||
"母本组合": "parent_combination_id",
|
||
"杂交方式": "cross_method",
|
||
"杂交类型": "cross_type",
|
||
"交配设计": "design_type",
|
||
"组配理由": "reason",
|
||
"育种阶段": "stage",
|
||
"杂交日期": "cross_date",
|
||
"获种数": "seed_count",
|
||
"备注": "remark",
|
||
}
|
||
try:
|
||
contents = await file.read()
|
||
rows = ExcelUtil.read_excel_to_dicts(contents)
|
||
await file.close()
|
||
if not rows:
|
||
raise CustomException(msg="导入文件为空")
|
||
missing_headers = [h for h in header_dict if h not in rows[0]]
|
||
if missing_headers:
|
||
raise CustomException(msg=f"导入文件缺少必要的列: {', '.join(missing_headers)}")
|
||
bre_target_id_refs = await BreedingTargetCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
|
||
bre_target_id_map = {getattr(r, "target_name"): r.id for r in bre_target_id_refs}
|
||
female_parent_id_refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
|
||
female_parent_id_map = {getattr(r, "cultivar_name"): r.id for r in female_parent_id_refs}
|
||
male_parent_id_refs = await BreedingGermplasmCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
|
||
male_parent_id_map = {getattr(r, "cultivar_name"): r.id for r in male_parent_id_refs}
|
||
parent_combination_id_refs = await BreedingCrossCombinationCRUD(self.auth, self.db).get_list(order_by=[{"id": "asc"}])
|
||
parent_combination_id_map = {getattr(r, "combination_code"): r.id for r in parent_combination_id_refs}
|
||
mapped_rows = []
|
||
for row in rows:
|
||
mapped_rows.append({en: row.get(ch) for ch, en in header_dict.items()})
|
||
required_fields = ["combination_code", "bre_target_id"]
|
||
errors = []
|
||
for field in required_fields:
|
||
missing_indices = [i + 1 for i, r in enumerate(mapped_rows) if _is_blank(r.get(field))]
|
||
if missing_indices:
|
||
field_name = next(k for k, v in header_dict.items() if v == field)
|
||
rows_str = "、".join(str(i) for i in missing_indices)
|
||
errors.append(f"{field_name}不能为空，第{rows_str}行")
|
||
if errors:
|
||
raise CustomException(msg=f"导入失败，以下行缺少必要字段：\n{'; '.join(errors)}")
|
||
error_msgs: list[str] = []
|
||
success_count = 0
|
||
crud = BreedingCrossCombinationCRUD(self.auth, self.db)
|
||
resolver = DictLabelResolver(self.auth, self.db, ["cross_method", "cross_type", "breeding_stage"])
|
||
for i, row in enumerate(mapped_rows, start=1):
|
||
try:
|
||
bre_target_id_val = bre_target_id_map.get(str(row.get("bre_target_id")).strip()) if not _is_blank(row.get("bre_target_id")) else None
|
||
female_parent_id_val = female_parent_id_map.get(str(row.get("female_parent_id")).strip()) if not _is_blank(row.get("female_parent_id")) else None
|
||
male_parent_id_val = male_parent_id_map.get(str(row.get("male_parent_id")).strip()) if not _is_blank(row.get("male_parent_id")) else None
|
||
parent_combination_id_val = parent_combination_id_map.get(str(row.get("parent_combination_id")).strip()) if not _is_blank(row.get("parent_combination_id")) else None
|
||
fields = {
|
||
"combination_code": _none_if_blank(row.get("combination_code")),
|
||
"cross_year": _to_int(row.get("cross_year")),
|
||
"bre_target_id": bre_target_id_val,
|
||
"female_parent_id": female_parent_id_val,
|
||
"male_parent_id": male_parent_id_val,
|
||
"parent_combination_id": parent_combination_id_val,
|
||
"cross_method": await resolver.resolve("cross_method", row.get("cross_method")),
|
||
"cross_type": await resolver.resolve("cross_type", row.get("cross_type")),
|
||
"design_type": _validate_design_type(row.get("design_type")) or "full_diallel",
|
||
"reason": _none_if_blank(row.get("reason")),
|
||
"stage": await resolver.resolve("breeding_stage", row.get("stage")),
|
||
"cross_date": _none_if_blank(row.get("cross_date")),
|
||
"seed_count": _to_int(row.get("seed_count")),
|
||
"remark": _none_if_blank(row.get("remark")),
|
||
}
|
||
await self._check_parent_roles(female_parent_id_val, male_parent_id_val)
|
||
unique_kwargs = {"combination_code": fields["combination_code"]}
|
||
create_data = CrossCombinationCreateSchema(**fields)
|
||
exist_obj = await crud.get(**unique_kwargs)
|
||
if exist_obj:
|
||
if update_support:
|
||
await crud.update(id=exist_obj.id, data=CrossCombinationUpdateSchema(**fields))
|
||
success_count += 1
|
||
else:
|
||
error_msgs.append(f"第{i}行: 组合编号 {fields['combination_code']} 已存在")
|
||
else:
|
||
await crud.create(data=create_data)
|
||
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"批量导入杂交组合失败: {e!s}")
|
||
raise CustomException(msg=f"导入失败: {e!s}")
|
||
|
||
@staticmethod
|
||
def import_template_download() -> bytes:
|
||
header_list = [
|
||
"组合编号",
|
||
"杂交年份",
|
||
"育种目标",
|
||
"母本",
|
||
"父本",
|
||
"母本组合",
|
||
"杂交方式",
|
||
"杂交类型",
|
||
"交配设计",
|
||
"组配理由",
|
||
"育种阶段",
|
||
"杂交日期",
|
||
"获种数",
|
||
"备注",
|
||
]
|
||
selector_header_list = ["杂交方式", "杂交类型", "交配设计", "育种阶段"]
|
||
option_list = [
|
||
{"杂交方式": ["人工杂交", "自然授粉", "回交"]},
|
||
{"杂交类型": ["杂交", "自交", "开放"]},
|
||
{"交配设计": ["完全双列", "部分双列", "line×tester (NCII)", "NCIII 测交"]},
|
||
{"育种阶段": ["germplasm", "parent", "seedling", "sp", "ap", "line", "regional_trial", "released"]},
|
||
]
|
||
return ExcelUtil.get_excel_template(
|
||
header_list=header_list,
|
||
selector_header_list=selector_header_list,
|
||
option_list=option_list,
|
||
) |