Merge remote-tracking branch 'origin/main' into improve_filter_query

* origin/main:
  Add synaptome assets label (#176)
  Make EModel read_one/read_many schemas consistent (#177)

Author: GianlucaFicarelli

alembic/versions/20250519_133645_4da94988fa4f_default_migration_message.py

@@ -0,0 +1,64 @@
+"""Default migration message
+
+Revision ID: 4da94988fa4f
+Revises: 19e6c28114fa
+Create Date: 2025-05-19 13:36:45.039741
+
+"""
+
+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 = "4da94988fa4f"
+down_revision: Union[str, None] = "19e6c28114fa"
+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.sync_enum_values(
+        enum_schema="public",
+        enum_name="assetlabel",
+        new_values=[
+            "neurolucida",
+            "swc",
+            "hdf5",
+            "cell_composition_summary",
+            "cell_composition_volumes",
+            "single_neuron_synaptome_config",
+            "single_neuron_synaptome_simulation_io_result",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="asset", column_name="label")
+        ],
+        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="assetlabel",
+        new_values=[
+            "neurolucida",
+            "swc",
+            "hdf5",
+            "cell_composition_summary",
+            "cell_composition_volumes",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="asset", column_name="label")
+        ],
+        enum_values_to_rename=[],
+    )
+    # ### end Alembic commands ###

app/db/types.py

@@ -187,6 +187,8 @@ class AssetLabel(StrEnum):
     hdf5 = auto()
     cell_composition_summary = auto()
     cell_composition_volumes = auto()
+    single_neuron_synaptome_config = auto()
+    single_neuron_synaptome_simulation_io_result = auto()
 
 
 ALLOWED_ASSET_LABELS_PER_ENTITY = {
@@ -199,4 +201,8 @@ class AssetLabel(StrEnum):
         AssetLabel.cell_composition_summary,
         AssetLabel.cell_composition_volumes,
     },
+    EntityType.single_neuron_synaptome: {AssetLabel.single_neuron_synaptome_config},
+    EntityType.single_neuron_synaptome_simulation: {
+        AssetLabel.single_neuron_synaptome_simulation_io_result
+    },
 }

app/schemas/ion_channel_model.py

@@ -8,6 +8,7 @@
     AuthorizationOptionalPublicMixin,
     BrainRegionRead,
     CreationMixin,
+    EntityTypeMixin,
     IdentifiableMixin,
     SpeciesRead,
     StrainRead,
@@ -49,7 +50,7 @@ class IonChannelModelCreate(IonChannelModelBase, AuthorizationOptionalPublicMixi
 
 
 class IonChannelModelRead(
-    IonChannelModelBase, CreationMixin, IdentifiableMixin, AuthorizationMixin
+    IonChannelModelBase, CreationMixin, IdentifiableMixin, AuthorizationMixin, EntityTypeMixin
 ):
     species: SpeciesRead
     strain: StrainRead | None

app/service/emodel.py

@@ -46,6 +46,11 @@ def _load(select: sa.Select[tuple[EModel]]):
         selectinload(EModel.contributions).joinedload(Contribution.role),
         joinedload(EModel.mtypes),
         joinedload(EModel.etypes),
+        selectinload(EModel.assets),
+        selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.species),
+        selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.strain),
+        selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.brain_region),
+        selectinload(EModel.ion_channel_models).selectinload(IonChannelModel.assets),
         raiseload("*"),
     )
 
@@ -55,23 +60,13 @@ def read_one(
     db: SessionDep,
     id_: uuid.UUID,
 ) -> EModelReadExpanded:
-    def _load_expanded(select: sa.Select[tuple[EModel]]):
-        return _load(select).options(
-            selectinload(EModel.assets),
-            selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.species),
-            selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.strain),
-            selectinload(EModel.ion_channel_models).joinedload(IonChannelModel.brain_region),
-            selectinload(EModel.ion_channel_models).selectinload(IonChannelModel.assets),
-            raiseload("*"),
-        )
-
     return router_read_one(
         id_=id_,
         db=db,
         db_model_class=EModel,
         authorized_project_id=user_context.project_id,
         response_schema_class=EModelReadExpanded,
-        apply_operations=_load_expanded,
+        apply_operations=_load,
     )
 
 
@@ -99,10 +94,12 @@ def read_many(
     with_search: SearchDep,
     facets: FacetsDep,
     in_brain_region: InBrainRegionDep,
-) -> ListResponse[EModelRead]:
+) -> ListResponse[EModelReadExpanded]:
     morphology_alias = aliased(ReconstructionMorphology, flat=True)
+    ion_channel_model_alias = aliased(IonChannelModel, flat=True)
     aliases: Aliases = {
         ReconstructionMorphology: morphology_alias,
+        IonChannelModel: ion_channel_model_alias,
     }
 
     name_to_facet_query_params: dict[str, FacetQueryParams] = {
@@ -149,7 +146,7 @@ def read_many(
         apply_filter_query_operations=None,
         apply_data_query_operations=_load,
         pagination_request=pagination_request,
-        response_schema_class=EModelRead,
+        response_schema_class=EModelReadExpanded,
         name_to_facet_query_params=name_to_facet_query_params,
         filter_model=emodel_filter,
         filter_joins=filter_joins,

tests/test_emodel.py

@@ -78,7 +78,7 @@ def test_query_emodel(client: TestClient, create_emodel_ids: CreateIds):
     assert len(data) == 11
 
     assert "assets" in data[0]
-    assert "ion_channel_models" not in data[0]
+    assert "ion_channel_models" in data[0]
 
 
 def test_emodels_sorted(client: TestClient, create_emodel_ids: CreateIds):