feat: update observed variable schema

Author: harryle95

src/model/method.py

@@ -12,7 +12,6 @@
 
 if TYPE_CHECKING:
     from src.model.device import Device
-    from src.model.observed_variable import ObservedVariable
     from src.model.vocabulary import Vocabulary
 
 
@@ -24,12 +23,8 @@ class Method(Base):
     # Relationships:
     method_reference_id: Mapped[UUID | None] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
     method_reference: Mapped[Optional["Vocabulary"]] = relationship(
-        back_populates="method", lazy=None, info=dto_field("read-only")
+        back_populates="method", lazy=None, info=dto_field("read-only"),
     )
 
     device_id: Mapped[UUID | None] = mapped_column(ForeignKey("device_table.id", ondelete="SET NULL"))
     device: Mapped[Optional["Device"]] = relationship(lazy=None, info=dto_field("read-only"))
-
-    observed_variable: Mapped[Optional["ObservedVariable"]] = relationship(
-        back_populates="method", lazy=None, info=dto_field("read-only")
-    )

src/model/observed_variable.py

@@ -1,25 +1,46 @@
+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.variable import Variable
+from src.model.variable import Variable, VariableDataclass
 
 __all__ = ("ObservedVariable",)
 
 
 if TYPE_CHECKING:
-    from src.model.method import Method
+    from src.model.vocabulary import Vocabulary
 
 
 class ObservedVariable(Variable):
     __tablename__: str = "observed_variable_table"  # type: ignore[assignment]
     __mapper_args__ = {"polymorphic_identity": "observed_variable"}
-
     id: Mapped[UUID] = mapped_column(ForeignKey("variable_table.id"), primary_key=True, info=dto_field("read-only"))
-    method_id: Mapped[UUID | None] = mapped_column(ForeignKey("method_table.id"))
-    method: Mapped[Optional["Method"]] = relationship(
-        back_populates="observed_variable", lazy=None, info=dto_field("read-only")
+
+    title: Mapped[str] = mapped_column(nullable=False)
+    variable_reference_id: Mapped[UUID | None] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
+    variable_reference: Mapped[Optional["Vocabulary"]] = relationship(
+        "Vocabulary",
+        lazy=None,
+        back_populates="variable_reference",
+        info=dto_field("read-only"),
+        foreign_keys=[variable_reference_id],
+    )
+    trait_reference_id: Mapped[UUID | None] = mapped_column(ForeignKey("vocabulary_table.id", ondelete="SET NULL"))
+    trait_reference: Mapped[Optional["Vocabulary"]] = relationship(
+        "Vocabulary",
+        lazy=None,
+        back_populates="trait_reference",
+        info=dto_field("read-only"),
+        foreign_keys=[trait_reference_id],
     )
+
+
+@dataclass(kw_only=True)
+class ObservedVariableDataclass(VariableDataclass):
+    title: str
+    variable_reference_id: UUID | None = field(default=None)
+    trait_reference_id: UUID | None = field(default=None)

src/model/vocabulary.py

@@ -18,6 +18,7 @@
     from src.model.facility import Facility
     from src.model.institution import Institution
     from src.model.method import Method
+    from src.model.observed_variable import ObservedVariable
 
     #     from src.model.observation_unit import ObservationUnit
     #     from src.model.sample import Sample
@@ -81,6 +82,18 @@ class Vocabulary(Base):
     organism: Mapped[list["BiologicalMaterial"]] = relationship(
         back_populates="organism", lazy=None, info=dto_field("private")
     )
+    variable_reference: Mapped[list["ObservedVariable"]] = relationship(
+        lazy=None,
+        back_populates="variable_reference",
+        info=dto_field("read-only"),
+        foreign_keys="[ObservedVariable.variable_reference_id]",
+    )
+    trait_reference: Mapped[list["ObservedVariable"]] = relationship(
+        lazy=None,
+        back_populates="trait_reference",
+        info=dto_field("read-only"),
+        foreign_keys="[ObservedVariable.trait_reference_id]",
+    )
     # observation_units: Mapped[list["ObservationUnit"]] = relationship(
     #     "ObservationUnit", back_populates="observation_unit_type", lazy="selectin", info=dto_field("read-only")
     # )

src/router/observed_variable.py

@@ -9,6 +9,6 @@
 
 
 class ObservedVariableController(BaseController[ObservedVariable]):
-    path = "/observed_variable"
+    path = "/observedVariable"
     dto = ObservedVariableDTO.write_dto
     return_dto = ObservedVariableDTO.read_dto