validation result model (#171)

* Add validation result model

* Fix migration, update tests, filters, service

---------

Co-authored-by: Jean-Denis Courcol <[email protected]>
Co-authored-by: Eleftherios Zisis <[email protected]>

Author: 3 people

alembic/versions/20250521_131802_9730c55381f3_default_migration_message.py

@@ -0,0 +1,113 @@
+"""Default migration message
+
+Revision ID: 9730c55381f3
+Revises: b8490e92310f
+Create Date: 2025-05-21 13:18:02.105223
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from alembic_postgresql_enum import TableReference
+
+from sqlalchemy import Text
+import app.db.types
+
+# revision identifiers, used by Alembic.
+revision: str = "9730c55381f3"
+down_revision: Union[str, None] = "b8490e92310f"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "validation_result",
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column("passed", sa.Boolean(), nullable=False),
+        sa.Column("name", sa.String(), nullable=False),
+        sa.Column("validated_entity_id", sa.Uuid(), nullable=False),
+        sa.ForeignKeyConstraint(["id"], ["entity.id"], name=op.f("fk_validation_result_id_entity")),
+        sa.ForeignKeyConstraint(
+            ["validated_entity_id"],
+            ["entity.id"],
+            name=op.f("fk_validation_result_validated_entity_id_entity"),
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_validation_result")),
+    )
+    op.create_index(op.f("ix_validation_result_name"), "validation_result", ["name"], unique=False)
+    op.create_index(
+        op.f("ix_validation_result_validated_entity_id"),
+        "validation_result",
+        ["validated_entity_id"],
+        unique=False,
+    )
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "emodel",
+            "cell_composition",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "memodel",
+            "mesh",
+            "me_type_density",
+            "reconstruction_morphology",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "ion_channel_model",
+            "subject",
+            "validation_result",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "emodel",
+            "cell_composition",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "memodel",
+            "mesh",
+            "me_type_density",
+            "reconstruction_morphology",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "ion_channel_model",
+            "subject",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+    op.drop_index(op.f("ix_validation_result_validated_entity_id"), table_name="validation_result")
+    op.drop_index(op.f("ix_validation_result_name"), table_name="validation_result")
+    op.drop_table("validation_result")
+    # ### end Alembic commands ###

app/db/model.py

@@ -821,6 +821,26 @@ class IonChannelModelToEModel(Base):
     )
 
 
+class ValidationResult(Entity):
+    __tablename__ = EntityType.validation_result.value
+    id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), primary_key=True)
+    passed: Mapped[bool] = mapped_column(default=False)
+
+    name: Mapped[str] = mapped_column(index=True)
+
+    validated_entity_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), index=True)
+    validated_entity: Mapped[Entity] = relationship(
+        "Entity",
+        uselist=False,
+        foreign_keys=[validated_entity_id],
+    )
+
+    __mapper_args__ = {  # noqa: RUF012
+        "polymorphic_identity": __tablename__,
+        "inherit_condition": id == Entity.id,
+    }
+
+
 class Asset(Identifiable):
     """Asset table."""
 

app/db/types.py

@@ -66,6 +66,7 @@ class EntityType(StrEnum):
     single_neuron_synaptome_simulation = auto()
     ion_channel_model = auto()
     subject = auto()
+    validation_result = auto()
 
 
 class AgentType(StrEnum):

app/filters/validation_result.py

@@ -0,0 +1,25 @@
+import uuid
+from typing import Annotated
+
+from fastapi_filter import FilterDepends
+
+from app.db.model import ValidationResult
+from app.filters.base import CustomFilter
+from app.filters.common import EntityFilterMixin
+
+
+class ValidationResultFilter(
+    CustomFilter,
+    EntityFilterMixin,
+):
+    passed: bool | None = None
+    validated_entity_id: uuid.UUID | None = None
+
+    order_by: list[str] = ["name"]  # noqa: RUF012
+
+    class Constants(CustomFilter.Constants):
+        model = ValidationResult
+        ordering_model_fields = ["name"]  # noqa: RUF012
+
+
+ValidationResultFilterDep = Annotated[ValidationResultFilter, FilterDepends(ValidationResultFilter)]

app/routers/__init__.py

@@ -31,6 +31,7 @@
     species,
     strain,
     subject,
+    validation_result,
 )
 
 router = APIRouter()
@@ -47,6 +48,7 @@
     experimental_bouton_density.router,
     experimental_neuron_density.router,
     experimental_synapses_per_connection.router,
+    ion_channel_model.router,
     license.router,
     measurement_annotation.router,
     memodel.router,
@@ -61,7 +63,7 @@
     species.router,
     strain.router,
     subject.router,
-    ion_channel_model.router,
+    validation_result.router,
 ]
 for r in authenticated_routers:
     router.include_router(r, dependencies=[Depends(user_verified)])

app/routers/validation_result.py

@@ -0,0 +1,12 @@
+from fastapi import APIRouter
+
+import app.service.validation_result
+
+router = APIRouter(
+    prefix="/validation-result",
+    tags=["validation-result"],
+)
+
+read_many = router.get("")(app.service.validation_result.read_many)
+read_one = router.get("/{id_}")(app.service.validation_result.read_one)
+create_one = router.post("")(app.service.validation_result.create_one)

app/schemas/validation.py

@@ -0,0 +1,25 @@
+import uuid
+
+from pydantic import BaseModel
+
+from app.schemas.agent import CreatedByUpdatedByMixin
+from app.schemas.base import (
+    CreationMixin,
+    IdentifiableMixin,
+)
+
+
+class ValidationResultBase(BaseModel):
+    name: str
+    passed: bool
+    validated_entity_id: uuid.UUID
+
+
+class ValidationResultRead(
+    ValidationResultBase, CreationMixin, IdentifiableMixin, CreatedByUpdatedByMixin
+):
+    pass
+
+
+class ValidationResultCreate(ValidationResultBase):
+    pass

app/service/validation_result.py

@@ -0,0 +1,82 @@
+import uuid
+
+import sqlalchemy as sa
+from sqlalchemy.orm import joinedload
+
+from app.db.model import Subject, ValidationResult
+from app.dependencies.auth import UserContextDep, UserContextWithProjectIdDep
+from app.dependencies.common import (
+    FacetsDep,
+    InBrainRegionDep,
+    PaginationQuery,
+    SearchDep,
+)
+from app.dependencies.db import SessionDep
+from app.filters.validation_result import ValidationResultFilterDep
+from app.queries.common import router_create_one, router_read_many, router_read_one
+from app.schemas.types import ListResponse
+from app.schemas.validation import ValidationResultCreate, ValidationResultRead
+
+
+def _load(query: sa.Select):
+    return query.options(
+        joinedload(Subject.species),
+    )
+
+
+def read_one(
+    user_context: UserContextDep,
+    db: SessionDep,
+    id_: uuid.UUID,
+) -> ValidationResultRead:
+    return router_read_one(
+        db=db,
+        id_=id_,
+        db_model_class=ValidationResult,
+        authorized_project_id=user_context.project_id,
+        response_schema_class=ValidationResultRead,
+        apply_operations=_load,
+    )
+
+
+def create_one(
+    user_context: UserContextWithProjectIdDep,
+    json_model: ValidationResultCreate,
+    db: SessionDep,
+) -> ValidationResultRead:
+    return router_create_one(
+        db=db,
+        user_context=user_context,
+        db_model_class=ValidationResult,
+        json_model=json_model,
+        response_schema_class=ValidationResultRead,
+    )
+
+
+def read_many(
+    user_context: UserContextDep,
+    db: SessionDep,
+    pagination_request: PaginationQuery,
+    filter_model: ValidationResultFilterDep,
+    with_search: SearchDep,
+    facets: FacetsDep,
+    in_brain_region: InBrainRegionDep,
+) -> ListResponse[ValidationResultRead]:
+    aliases = {}
+    name_to_facet_query_params = {}
+    return router_read_many(
+        db=db,
+        filter_model=filter_model,
+        db_model_class=ValidationResult,
+        with_search=with_search,
+        with_in_brain_region=in_brain_region,
+        facets=facets,
+        name_to_facet_query_params=name_to_facet_query_params,
+        apply_filter_query_operations=None,
+        apply_data_query_operations=_load,
+        aliases=aliases,
+        pagination_request=pagination_request,
+        response_schema_class=ValidationResultRead,
+        authorized_project_id=user_context.project_id,
+        filter_joins=None,
+    )

tests/conftest.py

@@ -372,6 +372,20 @@ def mtype_class_id(db):
     )
 
 
+@pytest.fixture
+def validation_result_id(client, morphology_id):
+    return assert_request(
+        client.post,
+        url="/validation-result",
+        json={
+            "name": "test_validation_result",
+            "passed": True,
+            "validated_entity_id": str(morphology_id),
+            "authorized_public": False,
+        },
+    ).json()["id"]
+
+
 CreateIds = Callable[[int], list[str]]