Add recording_arrays relationship to Simulation

alembic/versions/20260728_232749_7bb31ca36dbe_add_simulation_recording_arrays.py

@@ -0,0 +1,55 @@
+"""Add simulation recording_arrays
+
+Revision ID: 7bb31ca36dbe
+Revises: 79dbeada57f3
+Create Date: 2026-07-28 23:27:49.412975
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "7bb31ca36dbe"
+down_revision: Union[str, None] = "79dbeada57f3"
+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(
+        "simulatable_extracellular_recording_array__simulation",
+        sa.Column("simulatable_extracellular_recording_array_id", sa.Uuid(), nullable=False),
+        sa.Column("simulation_id", sa.Uuid(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["simulatable_extracellular_recording_array_id"],
+            ["simulatable_extracellular_recording_array.id"],
+            name=op.f(
+                "fk_simulatable_extracellular_recording_array__simulation_simulatable_extracellular_recording_array_id_simulatable_extracellular_recording_array"
+            ),
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["simulation_id"],
+            ["simulation.id"],
+            name=op.f(
+                "fk_simulatable_extracellular_recording_array__simulation_simulation_id_simulation"
+            ),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint(
+            "simulatable_extracellular_recording_array_id",
+            "simulation_id",
+            name=op.f("pk_simulatable_extracellular_recording_array__simulation"),
+        ),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("simulatable_extracellular_recording_array__simulation")
+    # ### end Alembic commands ###

app/db/model.py

@@ -1654,6 +1654,21 @@ class SimulationCampaign(
     }
 
 
+class SimulatableExtracellularRecordingArrayToSimulation(Base):
+    __tablename__ = "simulatable_extracellular_recording_array__simulation"
+
+    simulatable_extracellular_recording_array_id: Mapped[uuid.UUID] = mapped_column(
+        ForeignKey(
+            f"{EntityType.simulatable_extracellular_recording_array}.id", ondelete="CASCADE"
+        ),
+        primary_key=True,
+    )
+    simulation_id: Mapped[uuid.UUID] = mapped_column(
+        ForeignKey(f"{EntityType.simulation}.id", ondelete="CASCADE"),
+        primary_key=True,
+    )
+
+
 class Simulation(Entity, NameDescriptionVectorMixin):
     """Represents a simulation entity in the database.
 
@@ -1669,6 +1684,7 @@ class Simulation(Entity, NameDescriptionVectorMixin):
         entity (Entity): The entity this simulation is associated with.
         number_neurons (int): Number of neurons to be simulated
         scan_parameters (JSON_DICT): Scan parameters for the simulation.
+        recording_arrays: Simulatable extracellular recording arrays used by this simulation.
     """
 
     __tablename__ = EntityType.simulation.value
@@ -1693,6 +1709,13 @@ class Simulation(Entity, NameDescriptionVectorMixin):
         nullable=False,
         server_default="{}",
     )
+    recording_arrays: Mapped[list["SimulatableExtracellularRecordingArray"]] = relationship(
+        "SimulatableExtracellularRecordingArray",
+        primaryjoin=(
+            "Simulation.id == SimulatableExtracellularRecordingArrayToSimulation.simulation_id"
+        ),
+        secondary="simulatable_extracellular_recording_array__simulation",
+    )
 
     __mapper_args__ = {  # ruff:ignore[mutable-class-default]
         "polymorphic_identity": __tablename__,

app/queries/constants.py

@@ -8,6 +8,8 @@
     IonChannelModelingCampaign,
     IonChannelModelToEModel,
     IonChannelRecordingToIonChannelModelingCampaign,
+    SimulatableExtracellularRecordingArrayToSimulation,
+    Simulation,
     SkeletonizationCampaign,
     TaskConfig,
     Usage,
@@ -73,4 +75,16 @@
             "nested_id_getter": lambda *, items: [item.id for item in items],
         },
     },
+    Simulation: {
+        "recording_arrays": {
+            "relationship_name": "recording_arrays",
+            "db_model_factory": lambda *, parent_id, child_id: (
+                SimulatableExtracellularRecordingArrayToSimulation(
+                    simulation_id=parent_id,
+                    simulatable_extracellular_recording_array_id=child_id,
+                )
+            ),
+            "nested_id_getter": lambda *, items: [item.id for item in items],
+        },
+    },
 }

app/schemas/simulation.py

@@ -5,8 +5,11 @@
     NameDescriptionMixin,
 )
 from app.schemas.brain_region import BrainRegionCreateMixin, BrainRegionReadMixin
-from app.schemas.entity import EntityCreate, EntityRead, NestedEntityRead
+from app.schemas.entity import EntityCreate, EntityRead, NestedEntityCreate, NestedEntityRead
 from app.schemas.me_model import NestedMEModel
+from app.schemas.simulatable_extracellular_recording_array import (
+    NestedSimulatableExtracellularRecordingArrayRead,
+)
 from app.schemas.synaptome import NestedSynaptome
 from app.schemas.utils import make_update_schema
 
@@ -79,7 +82,7 @@ class SimulationBaseMixin(NameDescriptionMixin):
 
 
 class SimulationCreate(SimulationBaseMixin, EntityCreate):
-    pass
+    recording_arrays: list[NestedEntityCreate] = []  # ruff:ignore[mutable-class-default]
 
 
 SimulationUserUpdate = make_update_schema(SimulationCreate, "SimulationUserUpdate")  # pyright: ignore [reportInvalidTypeForm]
@@ -99,4 +102,4 @@ class SimulationRead(
     SimulationBaseMixin,
     EntityRead,
 ):
-    pass
+    recording_arrays: list[NestedSimulatableExtracellularRecordingArrayRead]

app/service/simulation.py

@@ -47,6 +47,7 @@ def _load(query: sa.Select):
         joinedload(Simulation.updated_by),
         selectinload(Simulation.assets),
         selectinload(Simulation.contributions),
+        selectinload(Simulation.recording_arrays),
         raiseload("*"),
     )
 

scripts/export/build_database_archive.sh

@@ -2,7 +2,7 @@
 # Automatically generated, do not edit!
 set -euo pipefail
 SCRIPT_VERSION="1"
-SCRIPT_DB_VERSION="79dbeada57f3"
+SCRIPT_DB_VERSION="7bb31ca36dbe"
 echo "DB dump (version $SCRIPT_VERSION for db version $SCRIPT_DB_VERSION)"
 
 
@@ -211,6 +211,8 @@ SET TRANSACTION READ ONLY;
 \copy (SELECT t0.* FROM scientific_artifact_publication_link AS t0 JOIN entity AS t1 ON t1.id=t0.scientific_artifact_id WHERE t1.authorized_public IS NOT false) TO '$DATA_DIR/scientific_artifact_publication_link.csv' WITH CSV HEADER;
 \echo Dumping table simulatable_extracellular_recording_array
 \copy (SELECT t0.* FROM simulatable_extracellular_recording_array AS t0 JOIN entity AS t1 ON t1.id=t0.id JOIN entity AS t2 ON t2.id=t0.circuit_id WHERE t1.authorized_public IS NOT false AND t2.authorized_public IS NOT false) TO '$DATA_DIR/simulatable_extracellular_recording_array.csv' WITH CSV HEADER;
+\echo Dumping table simulatable_extracellular_recording_array__simulation
+\copy (SELECT t0.* FROM simulatable_extracellular_recording_array__simulation AS t0 JOIN entity AS t1 ON t1.id=t0.simulatable_extracellular_recording_array_id JOIN entity AS t2 ON t2.id=t0.simulation_id WHERE t1.authorized_public IS NOT false AND t2.authorized_public IS NOT false) TO '$DATA_DIR/simulatable_extracellular_recording_array__simulation.csv' WITH CSV HEADER;
 \echo Dumping table simulation
 \copy (SELECT t0.* FROM simulation AS t0 JOIN entity AS t1 ON t1.id=t0.id JOIN entity AS t2 ON t2.id=t0.simulation_campaign_id JOIN entity AS t3 ON t3.id=t0.entity_id WHERE t1.authorized_public IS NOT false AND t2.authorized_public IS NOT false AND t3.authorized_public IS NOT false) TO '$DATA_DIR/simulation.csv' WITH CSV HEADER;
 \echo Dumping table simulation_campaign
@@ -265,7 +267,7 @@ install -m 755 /dev/stdin "$WORK_DIR/load.sh" <<'EOF_LOAD_SCRIPT'
 # Automatically generated, do not edit!
 set -euo pipefail
 SCRIPT_VERSION="1"
-SCRIPT_DB_VERSION="79dbeada57f3"
+SCRIPT_DB_VERSION="7bb31ca36dbe"
 echo "DB load (version $SCRIPT_VERSION for db version $SCRIPT_DB_VERSION)"
 
 

tests/test_simulation.py

@@ -1,7 +1,8 @@
 import pytest
 
 from app.db.model import Simulation, SimulationCampaign
-from app.db.types import EntityType
+from app.db.types import ElectrodeType, EntityType
+from app.types import EntityRoute
 
 from .utils import (
     PROJECT_ID,
@@ -50,6 +51,7 @@ def _assert_read_response(data, json_data):
     assert "authorized_public" in data
     assert "authorized_project_id" in data
     assert "assets" in data
+    assert "recording_arrays" in data
     assert data["name"] == json_data["name"]
     assert data["description"] == json_data["description"]
     assert data["type"] == EntityType.simulation
@@ -60,6 +62,28 @@ def _assert_read_response(data, json_data):
 def test_create_one(client, json_data):
     data = assert_request(client.post, url=ROUTE, json=json_data).json()
     _assert_read_response(data, json_data)
+    assert data["recording_arrays"] == []
+
+
+def test_create_one_with_recording_arrays(client, json_data, root_circuit):
+    array_route = f"/{EntityRoute.simulatable_extracellular_recording_array}"
+    arrays = [
+        assert_request(
+            client.post,
+            url=array_route,
+            json={
+                "name": f"array-{i}",
+                "description": f"array-description-{i}",
+                "electrode_type": ElectrodeType.custom,
+                "circuit_id": str(root_circuit.id),
+            },
+        ).json()
+        for i in range(2)
+    ]
+    payload = json_data | {"recording_arrays": [{"id": array["id"]} for array in arrays]}
+    data = assert_request(client.post, url=ROUTE, json=payload).json()
+    _assert_read_response(data, payload)
+    assert {array["id"] for array in data["recording_arrays"]} == {array["id"] for array in arrays}
 
 
 def test_update_one(clients, public_json_data):