Add update endpoints for service admins

app/db/utils.py

@@ -76,8 +76,10 @@ def load_db_model_from_pydantic[I: DeclarativeBase](
     created_by_id: uuid.UUID | None,
     updated_by_id: uuid.UUID | None,
     ignore_attributes: set[str] | None = None,
+    *,
+    exclude_defaults: bool = False,
 ) -> I:
-    data = json_model.model_dump(by_alias=True)
+    data = json_model.model_dump(by_alias=True, exclude_defaults=exclude_defaults)
 
     if created_by_id or updated_by_id:
         data["created_by_id"] = created_by_id

app/queries/common.py

@@ -31,6 +31,7 @@
 from app.schemas.activity import ActivityCreate, ActivityUpdate
 from app.schemas.auth import UserContext, UserContextWithProjectId, UserProfile
 from app.schemas.types import ListResponse, PaginationResponse
+from app.schemas.utils import NOT_SET
 from app.utils.uuid import create_uuid
 
 
@@ -354,15 +355,17 @@ def router_update_one[T: BaseModel, I: Identifiable](
     id_: uuid.UUID,
     db: Session,
     db_model_class: type[I],
-    user_context: UserContext,
+    user_context: UserContext | None,
     json_model: BaseModel,
     response_schema_class: type[T],
     apply_operations: ApplyOperations | None = None,
 ):
     query = (
         sa.select(db_model_class).where(db_model_class.id == id_).with_for_update(of=db_model_class)
     )
-    if id_model_class := get_declaring_class(db_model_class, "authorized_project_id"):
+    if user_context and (
+        id_model_class := get_declaring_class(db_model_class, "authorized_project_id")
+    ):
         query = constrain_to_private_entities(query, user_context, db_model_class=id_model_class)
     if apply_operations:
         query = apply_operations(query)
@@ -427,13 +430,15 @@ def router_update_activity_one[T: BaseModel, I: Activity](
     id_: uuid.UUID,
     db: Session,
     db_model_class: type[I],
-    user_context: UserContext | UserContextWithProjectId,
+    user_context: UserContext | UserContextWithProjectId | None,
     json_model: ActivityUpdate,
     response_schema_class: type[T],
     apply_operations: ApplyOperations | None = None,
 ) -> T:
     query = sa.select(db_model_class).where(db_model_class.id == id_)
-    if id_model_class := get_declaring_class(db_model_class, "authorized_project_id"):
+    if user_context and (
+        id_model_class := get_declaring_class(db_model_class, "authorized_project_id")
+    ):
         query = constrain_to_accessible_entities(
             query, user_context.project_id, db_model_class=id_model_class
         )
@@ -446,21 +451,24 @@ def router_update_activity_one[T: BaseModel, I: Activity](
     update_data = json_model.model_dump(
         exclude_unset=True,
         exclude_none=True,
-        exclude_defaults=True,
         exclude={"used_ids", "generated_ids"},
+        exclude_defaults=True,  # ignore NOT_SET default values
     )
 
     for key, value in update_data.items():
         setattr(obj, key, value)
 
-    if generated_ids := json_model.generated_ids:
+    # ignore NOT_SET values
+    generated_ids = json_model.generated_ids if json_model.generated_ids != NOT_SET else []
+
+    if generated_ids:
         if obj.generated:
             raise HTTPException(
                 status_code=404,
                 detail="It is forbidden to update generated_ids if they exist.",
             )
 
-        if (
+        if user_context and (
             unaccessible_entities := db.execute(
                 select_unauthorized_entities(generated_ids, user_context.project_id)
             )

app/routers/brain_region.py

@@ -1,11 +1,21 @@
 from fastapi import APIRouter
 
 import app.service.brain_region
+from app.routers.admin import router as admin_router
+
+ROUTE = "brain-region"
 
 router = APIRouter(
-    prefix="/brain-region",
-    tags=["brain-region"],
+    prefix=f"/{ROUTE}",
+    tags=[ROUTE],
 )
 
 read_many = router.get("")(app.service.brain_region.read_many)
 read_one = router.get("/{id_}")(app.service.brain_region.read_one)
+create_one = router.post("")(app.service.brain_region.create_one)
+update_one = router.patch("/{id_}")(app.service.brain_region.update_one)
+
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.brain_region.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.brain_region.admin_update_one
+)

app/routers/calibration.py

@@ -17,3 +17,4 @@
 update_one = router.patch("/{id_}")(app.service.calibration.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.calibration.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.calibration.admin_update_one)

app/routers/circuit.py

@@ -18,3 +18,4 @@
 update_one = router.patch("/{id_}")(app.service.circuit.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.circuit.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.circuit.admin_update_one)

app/routers/electrical_cell_recording.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.electrical_cell_recording.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.electrical_cell_recording.admin_update_one
+)

app/routers/electrical_recording_stimulus.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.electrical_recording_stimulus.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.electrical_recording_stimulus.admin_update_one
+)

app/routers/em_cell_mesh.py

@@ -1,13 +1,21 @@
 from fastapi import APIRouter
 
 import app.service.em_cell_mesh
+from app.routers.admin import router as admin_router
+
+ROUTE = "em-cell-mesh"
 
 router = APIRouter(
-    prefix="/em-cell-mesh",
-    tags=["em-cell-mesh"],
+    prefix=f"/{ROUTE}",
+    tags=[ROUTE],
 )
 
 read_many = router.get("")(app.service.em_cell_mesh.read_many)
 read_one = router.get("/{id_}")(app.service.em_cell_mesh.read_one)
 create_one = router.post("")(app.service.em_cell_mesh.create_one)
 update_one = router.patch("/{id_}")(app.service.em_cell_mesh.update_one)
+
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.em_cell_mesh.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.em_cell_mesh.admin_update_one
+)

app/routers/emodel.py

@@ -17,3 +17,4 @@
 update_one = router.patch("/{id_}")(app.service.emodel.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.emodel.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.emodel.admin_update_one)

app/routers/etype.py

@@ -12,5 +12,8 @@
 
 read_many = router.get("")(app.service.etype.read_many)
 read_one = router.get("/{id_}")(app.service.etype.read_one)
+create_one = router.post("")(app.service.etype.create_one)
+update_one = router.patch("/{id_}")(app.service.etype.update_one)
 
-admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.etype.read_one)
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.etype.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.etype.admin_update_one)

app/routers/experimental_bouton_density.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.experimental_bouton_density.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.experimental_bouton_density.admin_update_one
+)

app/routers/experimental_neuron_density.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.experimental_neuron_density.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.experimental_neuron_density.admin_update_one
+)

app/routers/experimental_synapses_per_connection.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.experimental_synapses_per_connection.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.experimental_synapses_per_connection.admin_update_one
+)

app/routers/ion_channel.py

@@ -1,12 +1,19 @@
 from fastapi import APIRouter
 
 import app.service.ion_channel
+from app.routers.admin import router as admin_router
+
+ROUTE = "ion-channel"
 
 router = APIRouter(
-    prefix="/ion-channel",
-    tags=["ion-channel"],
+    prefix=f"/{ROUTE}",
+    tags=[ROUTE],
 )
 
 read_many = router.get("")(app.service.ion_channel.read_many)
 read_one = router.get("/{id_}")(app.service.ion_channel.read_one)
 create_one = router.post("")(app.service.ion_channel.create_one)
+update_one = router.patch("/{id_}")(app.service.ion_channel.update_one)
+
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.ion_channel.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.ion_channel.admin_update_one)

app/routers/ion_channel_model.py

@@ -16,3 +16,6 @@
 update_one = router.patch("/{id_}")(app.service.ion_channel_model.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.ion_channel_model.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.ion_channel_model.admin_update_one
+)

app/routers/ion_channel_recording.py

@@ -1,13 +1,23 @@
 from fastapi import APIRouter
 
 import app.service.ion_channel_recording
+from app.routers.admin import router as admin_router
+
+ROUTE = "ion-channel-recording"
 
 router = APIRouter(
-    prefix="/ion-channel-recording",
-    tags=["ion-channel-recording"],
+    prefix=f"/{ROUTE}",
+    tags=[ROUTE],
 )
 
 read_many = router.get("")(app.service.ion_channel_recording.read_many)
 read_one = router.get("/{id_}")(app.service.ion_channel_recording.read_one)
 create_one = router.post("")(app.service.ion_channel_recording.create_one)
 update_one = router.patch("/{id_}")(app.service.ion_channel_recording.update_one)
+
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
+    app.service.ion_channel_recording.admin_read_one
+)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.ion_channel_recording.admin_update_one
+)

app/routers/license.py

@@ -13,5 +13,7 @@
 read_many = router.get("")(app.service.license.read_many)
 read_one = router.get("/{id_}")(app.service.license.read_one)
 create_one = router.post("")(app.service.license.create_one)
+update_one = router.patch("/{id_}")(app.service.license.update_one)
 
-admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.license.read_one)
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.license.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.license.admin_update_one)

app/routers/measurement_annotation.py

@@ -14,7 +14,11 @@
 read_one = router.get("/{id_}")(app.service.measurement_annotation.read_one)
 create_one = router.post("")(app.service.measurement_annotation.create_one)
 delete_one = router.delete("/{id_}")(app.service.measurement_annotation.delete_one)
+update_one = router.patch("/{id_}")(app.service.measurement_annotation.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.measurement_annotation.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.measurement_annotation.admin_update_one
+)

app/routers/memodel.py

@@ -16,3 +16,4 @@
 update_one = router.patch("/{id_}")(app.service.memodel.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.memodel.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.memodel.admin_update_one)

app/routers/memodel_calibration_result.py

@@ -18,3 +18,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.memodel_calibration_result.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.memodel_calibration_result.admin_update_one
+)

app/routers/morphology.py

@@ -16,3 +16,4 @@
 update_one = router.patch("/{id_}")(app.service.morphology.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.morphology.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.morphology.admin_update_one)

app/routers/mtype.py

@@ -12,5 +12,8 @@
 
 read_many = router.get("")(app.service.mtype.read_many)
 read_one = router.get("/{id_}")(app.service.mtype.read_one)
+create_one = router.post("")(app.service.mtype.create_one)
+update_one = router.patch("/{id_}")(app.service.mtype.update_one)
 
-admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.mtype.read_one)
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.mtype.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.mtype.admin_update_one)

app/routers/publication.py

@@ -13,5 +13,7 @@
 read_one = router.get("/{id_}")(app.service.publication.read_one)
 read_many = router.get("")(app.service.publication.read_many)
 create_one = router.post("")(app.service.publication.create_one)
+update_one = router.patch("/{id_}")(app.service.publication.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.publication.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.publication.admin_update_one)

app/routers/role.py

@@ -13,5 +13,7 @@
 read_many = router.get("")(app.service.role.read_many)
 read_one = router.get("/{id_}")(app.service.role.read_one)
 create_one = router.post("")(app.service.role.create_one)
+update_one = router.patch("/{id_}")(app.service.role.update_one)
 
-admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.role.read_one)
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.role.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.role.admin_update_one)

app/routers/simulation.py

@@ -12,3 +12,4 @@
 update_one = router.patch("/{id_}")(app.service.simulation.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.simulation.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.simulation.admin_update_one)

app/routers/simulation_campaign.py

@@ -14,3 +14,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.simulation_campaign.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.simulation_campaign.admin_update_one
+)

app/routers/simulation_execution.py

@@ -15,3 +15,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.simulation_execution.admin_read_one
 )
+admin_update_one = admin_router.patch("/simulation-execution/{id_}")(
+    app.service.simulation_execution.admin_update_one
+)

app/routers/simulation_generation.py

@@ -15,3 +15,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.simulation_generation.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.simulation_generation.admin_update_one
+)

app/routers/simulation_result.py

@@ -12,3 +12,6 @@
 update_one = router.patch("/{id_}")(app.service.simulation_result.update_one)
 
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.simulation_result.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.simulation_result.admin_update_one
+)

app/routers/single_neuron_simulation.py

@@ -14,3 +14,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.single_neuron_simulation.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.single_neuron_simulation.admin_update_one
+)

app/routers/single_neuron_synaptome.py

@@ -14,3 +14,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.single_neuron_synaptome.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.single_neuron_synaptome.admin_update_one
+)

app/routers/single_neuron_synaptome_simulation.py

@@ -14,3 +14,6 @@
 admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(
     app.service.single_neuron_synaptome_simulation.admin_read_one
 )
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(
+    app.service.single_neuron_synaptome_simulation.admin_update_one
+)

app/routers/species.py

@@ -1,12 +1,19 @@
 from fastapi import APIRouter
 
 import app.service.species
+from app.routers.admin import router as admin_router
+
+ROUTE = "species"
 
 router = APIRouter(
-    prefix="/species",
-    tags=["species"],
+    prefix=f"/{ROUTE}",
+    tags=[ROUTE],
 )
 
 read_many = router.get("")(app.service.species.read_many)
 read_one = router.get("/{id_}")(app.service.species.read_one)
 create_one = router.post("")(app.service.species.create_one)
+update_one = router.patch("/{id_}")(app.service.species.update_one)
+
+admin_read_one = admin_router.get(f"/{ROUTE}/{{id_}}")(app.service.species.admin_read_one)
+admin_update_one = admin_router.patch(f"/{ROUTE}/{{id_}}")(app.service.species.admin_update_one)