feat: update biological material schema and routers

src/model/biological_material.py

@@ -1,28 +1,47 @@
+from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, Optional
 from uuid import UUID
 
 from litestar.dto import dto_field
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+from src.model.base import BaseDataclass
 from src.model.variable import Variable
 
 __all__ = ("BiologicalMaterial",)
 
 
 if TYPE_CHECKING:
     from src.model.method import Method
+    from src.model.vocabulary import Vocabulary
 
 
 class BiologicalMaterial(Variable):
     __tablename__: str = "biological_material_table"  # type: ignore[assignment]
     __mapper_args__ = {"polymorphic_identity": "biological_material"}
 
     id: Mapped[UUID] = mapped_column(ForeignKey("variable_table.id"), primary_key=True, info=dto_field("read-only"))
-    biological_location: Mapped[str | None]
+    title: Mapped[str] = mapped_column(nullable=False)
+    organism_id: Mapped[UUID] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
+    organism: Mapped["Vocabulary"] = relationship(
+        "Vocabulary", lazy=None, info=dto_field("read-only"), back_populates="organism"
+    )
+    genus: Mapped[str | None]
+    species: Mapped[str | None]
+    infraspecific_name: Mapped[str | None]
+
+    biological_material_latitude: Mapped[str | None]
+    biological_material_longitude: Mapped[str | None]
+    biological_material_altitude: Mapped[str | None]
+    biological_material_coordinates_uncertainty: Mapped[str | None]
+
     material_source_id: Mapped[str | None]
     material_source_doi: Mapped[str | None]
-    material_source_location: Mapped[str | None]
+    material_source_latitude: Mapped[str | None]
+    material_source_longitude: Mapped[str | None]
+    material_source_altitude: Mapped[str | None]
+    material_source_coordinates_uncertainty: Mapped[str | None]
     material_source_description: Mapped[str | None]
 
     # Relationship
@@ -34,3 +53,24 @@ class BiologicalMaterial(Variable):
         lazy=None,
         info=dto_field("read-only"),
     )
+
+
+@dataclass(kw_only=True)
+class BiologicalMaterialDataclass(BaseDataclass):
+    title: str
+    organism_id: UUID | None = field(default=None)
+    genus: str | None = field(default=None)
+    species: str | None = field(default=None)
+    infraspecific_name: str | None = field(default=None)
+    biological_material_latitude: str | None = field(default=None)
+    biological_material_longitude: str | None = field(default=None)
+    biological_material_altitude: str | None = field(default=None)
+    biological_material_coordinates_uncertainty: str | None = field(default=None)
+    material_source_id: str | None = field(default=None)
+    material_source_doi: str | None = field(default=None)
+    material_source_latitude: str | None = field(default=None)
+    material_source_longitude: str | None = field(default=None)
+    material_source_altitude: str | None = field(default=None)
+    material_source_coordinates_uncertainty: str | None = field(default=None)
+    material_source_description: str | None = field(default=None)
+    preprocessing_method_id: UUID | None = field(default=None)

src/router/biological_material.py

@@ -1,14 +1,23 @@
-from src.model import BiologicalMaterial
-from src.router.base import BaseController
+from litestar.dto import DataclassDTO, DTOConfig
+
+from src.model.biological_material import BiologicalMaterial, BiologicalMaterialDataclass
+from src.model.study import Study
+from src.router.base import DataclassController
 from src.router.utils.dto import DTOGenerator
 
 __all__ = ("BiologicalMaterialController",)
 
 
-BiologicalMaterialDTO = DTOGenerator[BiologicalMaterial](read_kwargs={"max_nested_depth": 1})
+class BiologicalMaterialDTO(DataclassDTO[BiologicalMaterialDataclass]):
+    config = DTOConfig(rename_strategy="camel")
+
+
+BiologicalMaterialReturnDTO = DTOGenerator[BiologicalMaterial]()
 
 
-class BiologicalMaterialController(BaseController[BiologicalMaterial]):
-    path = "/biological_material"
-    dto = BiologicalMaterialDTO.write_dto
-    return_dto = BiologicalMaterialDTO.read_dto
+class BiologicalMaterialController(DataclassController[BiologicalMaterial, BiologicalMaterialDataclass]):
+    path = "/biologicalMaterial"
+    dto = BiologicalMaterialDTO
+    return_dto = BiologicalMaterialDTO
+    attr_map = {"studies": ("study_id", Study)}
+    selectinload_attrs = [BiologicalMaterial.studies]