Add filters for circuit in simulation campaign (#311)

Author: bilalesi

app/filters/circuit.py

@@ -1,12 +1,28 @@
 import uuid
 from typing import Annotated
 
+from fastapi_filter import with_prefix
+
 from app.db.model import Circuit
 from app.dependencies.filter import FilterDepends
-from app.filters.common import NameFilterMixin
+from app.filters.base import CustomFilter
+from app.filters.common import IdFilterMixin, NameFilterMixin
 from app.filters.scientific_artifact import ScientificArtifactFilter
 
 
+class NestedCircuitFilter(IdFilterMixin, NameFilterMixin, CustomFilter):
+    """Circuit filter with limited fields for nesting."""
+
+    scale: str | None = None
+    scale__in: list[str] | None = None
+
+    build_category: str | None = None
+    build_category__in: list[str] | None = None
+
+    class Constants(CustomFilter.Constants):
+        model = Circuit
+
+
 class CircuitFilter(ScientificArtifactFilter, NameFilterMixin):
     atlas_id: uuid.UUID | None = None
     root_circuit_id: uuid.UUID | None = None
@@ -39,3 +55,4 @@ class Constants(ScientificArtifactFilter.Constants):
 
 
 CircuitFilterDep = Annotated[CircuitFilter, FilterDepends(CircuitFilter)]
+NestedCircuitFilterDep = FilterDepends(with_prefix("circuit", NestedCircuitFilter))

app/filters/simulation.py

@@ -6,6 +6,7 @@
 from app.db.model import Simulation
 from app.dependencies.filter import FilterDepends
 from app.filters.base import CustomFilter
+from app.filters.circuit import NestedCircuitFilter, NestedCircuitFilterDep
 from app.filters.common import (
     ContributionFilterMixin,
     CreationFilterMixin,
@@ -18,6 +19,7 @@
 class SimulationFilterBase(NameFilterMixin, IdFilterMixin, CustomFilter):
     entity_id: uuid.UUID | None = None
     entity_id__in: list[uuid.UUID] | None = None
+    circuit: Annotated[NestedCircuitFilter | None, NestedCircuitFilterDep] = None
 
 
 class NestedSimulationFilter(SimulationFilterBase):

app/queries/factory.py

@@ -3,6 +3,7 @@
 from app.db.model import (
     Agent,
     BrainRegion,
+    Circuit,
     Contribution,
     EModel,
     Entity,
@@ -72,6 +73,7 @@ def _get_alias[T: type[Identifiable]](db_cls: T, name: str | None = None) -> T:
     simulation_alias = _get_alias(Simulation)
     used_alias = _get_alias(Entity, "used")
     generated_alias = _get_alias(Entity, "generated")
+    circuit_alias = _get_alias(Circuit)
 
     name_to_facet_query_params: dict[str, FacetQueryParams] = {
         "agent": {
@@ -111,6 +113,7 @@ def _get_alias[T: type[Identifiable]](db_cls: T, name: str | None = None) -> T:
         "pre_region": {"id": pre_region_alias.id, "label": pre_region_alias.name},
         "post_region": {"id": post_region_alias.id, "label": post_region_alias.name},
         "simulation": {"id": simulation_alias.id, "label": simulation_alias.name},
+        "simulation.circuit": {"id": circuit_alias.id, "label": circuit_alias.name},
     }
     filter_joins = {
         "species": lambda q: q.join(Species, db_model_class.species_id == Species.id),
@@ -180,6 +183,9 @@ def _get_alias[T: type[Identifiable]](db_cls: T, name: str | None = None) -> T:
         "simulation": lambda q: q.outerjoin(
             simulation_alias, db_model_class.id == simulation_alias.simulation_campaign_id
         ),
+        "simulation.circuit": lambda q: q.join(
+            circuit_alias, simulation_alias.entity_id == circuit_alias.id
+        ),
         "used": lambda q: q.outerjoin(
             Usage, db_model_class.id == Usage.usage_activity_id
         ).outerjoin(used_alias, Usage.usage_entity_id == used_alias.id),

app/service/simulation_campaign.py

@@ -6,6 +6,7 @@
 
 from app.db.model import (
     Agent,
+    Circuit,
     Simulation,
     SimulationCampaign,
 )
@@ -84,20 +85,22 @@ def read_many(
     created_by_alias = aliased(Agent, flat=True)
     updated_by_alias = aliased(Agent, flat=True)
     simulation_alias = aliased(Simulation, flat=True)
-
+    circuit_alias = aliased(Circuit, flat=True)
     aliases: Aliases = {
         Agent: {
             "contribution": agent_alias,
             "created_by": created_by_alias,
             "updated_by": updated_by_alias,
         },
         Simulation: simulation_alias,
+        Circuit: circuit_alias,
     }
     facet_keys = filter_keys = [
         "created_by",
         "updated_by",
         "contribution",
         "simulation",
+        "simulation.circuit",
     ]
     name_to_facet_query_params, filter_joins = query_params_factory(
         db_model_class=SimulationCampaign,

tests/test_simulation_campaign.py

@@ -1,6 +1,6 @@
 import pytest
 
-from app.db.model import Simulation, SimulationCampaign
+from app.db.model import Circuit, CircuitBuildCategory, CircuitScale, Simulation, SimulationCampaign
 from app.db.types import EntityType
 
 from .utils import (
@@ -125,3 +125,235 @@ def test_filtering(client, models, simulation_json_data, person_id):
         client.get, url=ROUTE, params={"simulation__name": simulation_json_data["name"]}
     ).json()["data"]
     assert len(data) == 3
+
+
+@pytest.fixture
+def multiple_circuits(db, brain_atlas_id, subject_id, brain_region_id, license_id, person_id):
+    circuits_data = [
+        {
+            "name": "micro-circuit-1",
+            "description": "Micro Circuit 1",
+            "has_morphologies": True,
+            "has_point_neurons": False,
+            "has_electrical_cell_models": True,
+            "has_spines": False,
+            "number_neurons": 100,
+            "number_synapses": 1000,
+            "number_connections": 50,
+            "scale": CircuitScale.microcircuit,
+            "build_category": CircuitBuildCategory.computational_model,
+            "atlas_id": brain_atlas_id,
+            "subject_id": subject_id,
+            "brain_region_id": brain_region_id,
+            "license_id": license_id,
+            "authorized_public": False,
+            "created_by_id": person_id,
+            "updated_by_id": person_id,
+            "authorized_project_id": PROJECT_ID,
+        },
+        {
+            "name": "micro-circuit-2",
+            "description": "Micro Circuit 2",
+            "has_morphologies": False,
+            "has_point_neurons": True,
+            "has_electrical_cell_models": False,
+            "has_spines": True,
+            "number_neurons": 1000,
+            "number_synapses": 10000,
+            "number_connections": 200,
+            "scale": CircuitScale.microcircuit,
+            "build_category": CircuitBuildCategory.em_reconstruction,
+            "atlas_id": brain_atlas_id,
+            "subject_id": subject_id,
+            "brain_region_id": brain_region_id,
+            "license_id": license_id,
+            "authorized_public": False,
+            "created_by_id": person_id,
+            "updated_by_id": person_id,
+            "authorized_project_id": PROJECT_ID,
+        },
+        {
+            "name": "pair-circuit-1",
+            "description": "Pair Circuit 1",
+            "has_morphologies": True,
+            "has_point_neurons": True,
+            "has_electrical_cell_models": True,
+            "has_spines": True,
+            "number_neurons": 10000,
+            "number_synapses": 100000,
+            "number_connections": 500,
+            "scale": CircuitScale.pair,
+            "build_category": CircuitBuildCategory.computational_model,
+            "atlas_id": brain_atlas_id,
+            "subject_id": subject_id,
+            "brain_region_id": brain_region_id,
+            "license_id": license_id,
+            "authorized_public": False,
+            "created_by_id": person_id,
+            "updated_by_id": person_id,
+            "authorized_project_id": PROJECT_ID,
+        },
+    ]
+
+    circuits = [add_db(db, Circuit(**circuit_data)) for circuit_data in circuits_data]
+    return circuits
+
+
+@pytest.fixture
+def campaigns_with_different_circuits(
+    db, json_data, person_id, simulation_json_data, multiple_circuits
+):
+    campaigns = []
+
+    for i, circuit in enumerate(multiple_circuits):
+        campaign = add_db(
+            db,
+            MODEL(
+                **(
+                    json_data
+                    | {
+                        "name": f"campaign-circuit-{i}",
+                        "description": f"Campaign for circuit {i}",
+                        "created_by_id": person_id,
+                        "updated_by_id": person_id,
+                        "authorized_project_id": PROJECT_ID,
+                    }
+                )
+            ),
+        )
+        campaigns.append(campaign)
+
+        add_db(
+            db,
+            Simulation(
+                **simulation_json_data
+                | {
+                    "name": f"simulation-circuit-{i}",
+                    "simulation_campaign_id": campaign.id,
+                    "entity_id": circuit.id,
+                    "created_by_id": person_id,
+                    "updated_by_id": person_id,
+                    "authorized_project_id": PROJECT_ID,
+                }
+            ),
+        )
+
+    return campaigns
+
+
+def test_filter_by_circuit_id(client, campaigns_with_different_circuits, multiple_circuits):  # noqa: ARG001
+    first_circuit_id = str(multiple_circuits[0].id)
+    data = assert_request(client.get, url=ROUTE, params={"circuit__id": first_circuit_id}).json()[
+        "data"
+    ]
+
+    assert len(data) == 1
+    assert data[0]["name"] == "campaign-circuit-0"
+
+    second_circuit_id = str(multiple_circuits[1].id)
+    data = assert_request(client.get, url=ROUTE, params={"circuit__id": second_circuit_id}).json()[
+        "data"
+    ]
+
+    assert len(data) == 1
+    assert data[0]["name"] == "campaign-circuit-1"
+
+
+def test_filter_by_circuit_name(client, campaigns_with_different_circuits, multiple_circuits):  # noqa: ARG001
+    data = assert_request(
+        client.get, url=ROUTE, params={"circuit__name": "micro-circuit-1"}
+    ).json()["data"]
+
+    assert len(data) == 1
+    assert data[0]["name"] == "campaign-circuit-0"
+
+    data = assert_request(
+        client.get, url=ROUTE, params={"circuit__name__in": "micro-circuit-2"}
+    ).json()["data"]
+
+    assert len(data) == 1
+    assert data[0]["name"] == "campaign-circuit-1"
+
+
+def test_filter_by_circuit_scale(client, campaigns_with_different_circuits, multiple_circuits):  # noqa: ARG001
+    data = assert_request(
+        client.get, url=ROUTE, params={"circuit__scale": CircuitScale.microcircuit}
+    ).json()["data"]
+
+    assert len(data) == 2
+
+    data = assert_request(
+        client.get, url=ROUTE, params={"circuit__scale": CircuitScale.pair}
+    ).json()["data"]
+
+    assert len(data) == 1
+
+
+def test_filter_by_circuit_scale_empty(
+    client,
+    campaigns_with_different_circuits,  # noqa: ARG001
+    multiple_circuits,  # noqa: ARG001
+):
+    data = assert_request(
+        client.get, url=ROUTE, params={"circuit__scale": CircuitScale.small}
+    ).json()["data"]
+
+    assert len(data) == 0
+
+
+def test_filter_by_circuit_scale_in(client, campaigns_with_different_circuits, multiple_circuits):  # noqa: ARG001
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={"circuit__scale__in": [CircuitScale.microcircuit, CircuitScale.pair]},
+    ).json()["data"]
+
+    assert len(data) == 3
+    campaign_names = {campaign["name"] for campaign in data}
+    assert campaign_names == {"campaign-circuit-0", "campaign-circuit-1", "campaign-circuit-2"}
+
+
+def test_filter_by_circuit_build_category(
+    client,
+    campaigns_with_different_circuits,  # noqa: ARG001
+    multiple_circuits,  # noqa: ARG001
+):
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={"circuit__build_category": CircuitBuildCategory.computational_model},
+    ).json()["data"]
+
+    assert len(data) == 2
+    campaign_names = {campaign["name"] for campaign in data}
+    assert campaign_names == {"campaign-circuit-0", "campaign-circuit-2"}
+
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={"circuit__build_category": CircuitBuildCategory.em_reconstruction},
+    ).json()["data"]
+
+    assert len(data) == 1
+    assert data[0]["name"] == "campaign-circuit-1"
+
+
+def test_filter_by_circuit_build_category_in(
+    client,
+    campaigns_with_different_circuits,  # noqa: ARG001
+    multiple_circuits,  # noqa: ARG001
+):
+    data = assert_request(
+        client.get,
+        url=ROUTE,
+        params={
+            "circuit__build_category__in": [
+                CircuitBuildCategory.computational_model,
+                CircuitBuildCategory.em_reconstruction,
+            ],
+        },
+    ).json()["data"]
+
+    assert len(data) == 3
+    campaign_names = {campaign["name"] for campaign in data}
+    assert campaign_names == {"campaign-circuit-0", "campaign-circuit-1", "campaign-circuit-2"}