Add BrainRegionMesh

Author: eleftherioszisis

app/filters/brain_region_mesh.py

@@ -0,0 +1,18 @@
+from typing import Annotated
+
+from fastapi_filter import FilterDepends
+
+from app.db.model import Mesh as BrainRegionMesh
+from app.filters.base import CustomFilter
+from app.filters.common import BrainRegionFilterMixin, EntityFilterMixin
+
+
+class BrainRegionMeshFilter(CustomFilter, BrainRegionFilterMixin, EntityFilterMixin):
+    order_by: list[str] = ["-creation_date"]  # noqa: RUF012
+
+    class Constants(CustomFilter.Constants):
+        model = BrainRegionMesh
+        ordering_model_fields = ["creation_date", "update_date", "name"]  # noqa: RUF012
+
+
+BrainRegionMeshFilterDep = Annotated[BrainRegionMeshFilter, FilterDepends(BrainRegionMeshFilter)]

app/filters/common.py

@@ -140,9 +140,10 @@ class SubjectFilterMixin:
 
 
 class BrainRegionFilter(NameFilterMixin, CustomFilter):
-    # TODO: Use IdFilterMixin when brain region keys migrate from int to uuid
-    id: int | None = None
-    id__in: list[int] | None = None
+    id: uuid.UUID | None = None
+    id__in: list[uuid.UUID] | None = None
+    hierarchy_id: uuid.UUID | None = None
+    annotation_value: int | None = None
     acronym: str | None = None
     acronym__in: list[str] | None = None
     order_by: list[str] = ["name"]  # noqa: RUF012

app/routers/__init__.py

@@ -7,6 +7,7 @@
     asset,
     brain_region,
     brain_region_hierarchy,
+    brain_region_mesh,
     cell_composition,
     contribution,
     electrical_cell_recording,
@@ -38,6 +39,7 @@
     asset.router,
     brain_region.router,
     brain_region_hierarchy.router,
+    brain_region_mesh.router,
     cell_composition.router,
     contribution.router,
     electrical_cell_recording.router,

app/routers/brain_region_mesh.py

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

app/schemas/brain_region_mesh.py

@@ -0,0 +1,28 @@
+import uuid
+
+from pydantic import BaseModel, ConfigDict
+
+from app.schemas.base import (
+    AuthorizationMixin,
+    AuthorizationOptionalPublicMixin,
+    BrainRegionRead,
+    CreationMixin,
+    EntityTypeMixin,
+    IdentifiableMixin,
+)
+
+
+class BrainRegionMeshBase(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+    name: str
+    description: str
+
+
+class BrainRegionMeshCreate(BrainRegionMeshBase, AuthorizationOptionalPublicMixin):
+    brain_region_id: uuid.UUID
+
+
+class BrainRegionMeshRead(
+    BrainRegionMeshBase, CreationMixin, IdentifiableMixin, AuthorizationMixin, EntityTypeMixin
+):
+    brain_region: BrainRegionRead

app/service/brain_region_mesh.py

@@ -0,0 +1,87 @@
+import uuid
+
+from sqlalchemy.orm import joinedload, raiseload, selectinload
+
+from app.db.model import BrainRegion, Mesh as BrainRegionMesh
+from app.dependencies.auth import UserContextDep, UserContextWithProjectIdDep
+from app.dependencies.common import (
+    FacetQueryParams,
+    FacetsDep,
+    InBrainRegionDep,
+    PaginationQuery,
+    SearchDep,
+)
+from app.dependencies.db import SessionDep
+from app.filters.brain_region_mesh import BrainRegionMeshFilterDep
+from app.queries import facets as fc
+from app.queries.common import router_create_one, router_read_many, router_read_one
+from app.schemas.brain_region_mesh import BrainRegionMeshCreate, BrainRegionMeshRead
+from app.schemas.types import ListResponse
+
+
+def read_one(
+    user_context: UserContextDep,
+    db: SessionDep,
+    id_: uuid.UUID,
+) -> BrainRegionMeshRead:
+    return router_read_one(
+        db=db,
+        id_=id_,
+        db_model_class=BrainRegionMesh,
+        authorized_project_id=user_context.project_id,
+        response_schema_class=BrainRegionMeshRead,
+        apply_operations=lambda q: q.options(
+            joinedload(BrainRegionMesh.brain_region),
+            joinedload(BrainRegionMesh.assets),
+            raiseload("*"),
+        ),
+    )
+
+
+def create_one(
+    user_context: UserContextWithProjectIdDep,
+    json_model: BrainRegionMeshCreate,
+    db: SessionDep,
+) -> BrainRegionMeshRead:
+    return router_create_one(
+        db=db,
+        json_model=json_model,
+        db_model_class=BrainRegionMesh,
+        authorized_project_id=user_context.project_id,
+        response_schema_class=BrainRegionMeshRead,
+    )
+
+
+def read_many(
+    user_context: UserContextDep,
+    db: SessionDep,
+    pagination_request: PaginationQuery,
+    filter_model: BrainRegionMeshFilterDep,
+    with_search: SearchDep,
+    in_brain_region: InBrainRegionDep,
+    facets: FacetsDep,
+) -> ListResponse[BrainRegionMeshRead]:
+    name_to_facet_query_params: dict[str, FacetQueryParams] = fc.brain_region
+    apply_filter_query = lambda query: (
+        query.join(BrainRegion, BrainRegionMesh.brain_region_id == BrainRegion.id)
+    )
+    apply_data_options = lambda query: (
+        query.options(joinedload(BrainRegionMesh.brain_region))
+        .options(selectinload(BrainRegionMesh.assets))
+        .options(raiseload("*"))
+    )
+    return router_read_many(
+        db=db,
+        filter_model=filter_model,
+        db_model_class=BrainRegionMesh,
+        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=apply_filter_query,
+        apply_data_query_operations=apply_data_options,
+        aliases={},
+        pagination_request=pagination_request,
+        response_schema_class=BrainRegionMeshRead,
+        authorized_project_id=user_context.project_id,
+    )

tests/test_brain_region_mesh.py

@@ -0,0 +1,103 @@
+import pytest
+
+from .utils import (
+    assert_request,
+    check_authorization,
+    check_missing,
+    check_pagination,
+)
+
+ROUTE = "/brain-region-mesh"
+
+
+@pytest.fixture
+def json_data(
+    brain_region_id,
+):
+    return {
+        "brain_region_id": str(brain_region_id),
+        "description": "my-description",
+        "name": "my-name",
+        "authorized_public": False,
+    }
+
+
+def _assert_read_response(data, json_data):
+    assert data["brain_region"]["id"] == json_data["brain_region_id"]
+    assert data["description"] == json_data["description"]
+    assert data["name"] == json_data["name"]
+    assert data["type"] == "mesh"
+
+
+@pytest.fixture
+def create_id(client, json_data):
+    def _create_id(**kwargs):
+        return assert_request(client.post, url=ROUTE, json=json_data | kwargs).json()["id"]
+
+    return _create_id
+
+
+@pytest.fixture
+def model_id(create_id):
+    return create_id()
+
+
+def test_create_one(client, json_data):
+    data = assert_request(client.post, url=ROUTE, json=json_data).json()
+    _assert_read_response(data, json_data)
+
+
+def test_read_one(client, model_id, json_data):
+    data = assert_request(client.get, url=f"{ROUTE}/{model_id}").json()
+    _assert_read_response(data, json_data)
+
+    data = assert_request(client.get, url=ROUTE).json()
+    assert len(data["data"]) == 1
+
+
+def test_missing(client):
+    check_missing(ROUTE, client)
+
+
+def test_authorization(
+    client_user_1,
+    client_user_2,
+    client_no_project,
+    json_data,
+):
+    check_authorization(ROUTE, client_user_1, client_user_2, client_no_project, json_data)
+
+
+def test_pagination(client, create_id):
+    check_pagination(ROUTE, client, create_id)
+
+
+def test_filtering(client, brain_region_id, brain_region_hierarchy_id, model_id):
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={"brain_region__id": str(model_id)},
+    ).json()["data"]
+
+    assert len(data) == 0
+
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={"brain_region__id": str(brain_region_id)},
+    ).json()["data"]
+
+    assert len(data) == 1
+    assert data[0]["brain_region"]["id"] == str(brain_region_id)
+
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={
+            "brain_region__name": "RedRegion",
+            "brain_region__hierarchy_id": str(brain_region_hierarchy_id),
+        },
+    ).json()["data"]
+
+    assert len(data) == 1
+    assert data[0]["brain_region"]["id"] == str(brain_region_id)