Add update endpoints for users

app/db/auth.py

@@ -7,6 +7,7 @@
 from sqlalchemy.orm import Query
 
 from app.db.model import Entity
+from app.schemas.auth import UserContext
 
 
 def constrain_to_accessible_entities[Q: Query | Select](
@@ -25,6 +26,22 @@ def constrain_to_accessible_entities[Q: Query | Select](
     return query
 
 
+def constrain_to_private_entities[Q: Query | Select](
+    query: Q,
+    user_context: UserContext,
+    db_model_class: Any = Entity,
+) -> Q:
+    """Ensure a query is filtered to private rows that are viewable by the user."""
+    return query.where(
+        and_(
+            db_model_class.authorized_public == false(),
+            db_model_class.authorized_project_id.in_(user_context.user_project_ids)
+            if user_context.user_project_ids
+            else false(),
+        )
+    )
+
+
 def constrain_entity_query_to_project[Q: Query | Select | Delete](query: Q, project_id: UUID4) -> Q:
     """Ensure a query is filtered to rows in the user's project."""
     return query.where(Entity.authorized_project_id == project_id)

app/queries/common.py

@@ -7,6 +7,7 @@
 
 from app.db.auth import (
     constrain_to_accessible_entities,
+    constrain_to_private_entities,
     select_unauthorized_entities,
 )
 from app.db.model import Activity, Agent, Generation, Identifiable, Person, Usage
@@ -329,6 +330,39 @@ def router_read_many[T: BaseModel, I: Identifiable](  # noqa: PLR0913
     )
 
 
+def router_update_one[T: BaseModel, I: Identifiable](
+    *,
+    id_: uuid.UUID,
+    db: Session,
+    db_model_class: type[I],
+    user_context: UserContext,
+    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"):
+        query = constrain_to_private_entities(query, user_context, db_model_class=id_model_class)
+    if apply_operations:
+        query = apply_operations(query)
+
+    with ensure_result(error_message=f"{db_model_class.__name__} not found"):
+        obj = db.execute(query).unique().scalar_one()
+
+    # remove attributes with NOT_SET sentinel and leave only user set ones
+    update_data = json_model.model_dump(exclude_defaults=True)
+
+    for key, value in update_data.items():
+        setattr(obj, key, value)
+
+    db.flush()
+    db.refresh(obj)
+
+    return response_schema_class.model_validate(obj)
+
+
 def router_delete_one[T: BaseModel, I: Identifiable](
     *,
     id_: uuid.UUID,

app/routers/circuit.py

@@ -12,3 +12,4 @@
 read_many = router.get("")(app.service.circuit.read_many)
 read_one = router.get("/{id_}")(app.service.circuit.read_one)
 create_one = router.post("")(app.service.circuit.create_one)
+update_one = router.patch("/{id_}")(app.service.circuit.update_one)

app/routers/electrical_cell_recording.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.electrical_cell_recording.read_many)
 read_one = router.get("/{id_}")(app.service.electrical_cell_recording.read_one)
 create_one = router.post("")(app.service.electrical_cell_recording.create_one)
+update_one = router.patch("/{id_}")(app.service.electrical_cell_recording.update_one)

app/routers/electrical_recording_stimulus.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.electrical_recording_stimulus.read_many)
 read_one = router.get("/{id_}")(app.service.electrical_recording_stimulus.read_one)
 create_one = router.post("")(app.service.electrical_recording_stimulus.create_one)
+update_one = router.patch("/{id_}")(app.service.electrical_recording_stimulus.update_one)

app/routers/emodel.py

@@ -11,3 +11,4 @@
 read_many = router.get("")(app.service.emodel.read_many)
 read_one = router.get("/{id_}")(app.service.emodel.read_one)
 create_one = router.post("")(app.service.emodel.create_one)
+update_one = router.patch("/{id_}")(app.service.emodel.update_one)

app/routers/experimental_bouton_density.py

@@ -8,5 +8,6 @@
 )
 
 read_many = router.get("")(app.service.experimental_bouton_density.read_many)
-read_onw = router.get("/{id_}")(app.service.experimental_bouton_density.read_one)
+read_one = router.get("/{id_}")(app.service.experimental_bouton_density.read_one)
 create_one = router.post("")(app.service.experimental_bouton_density.create_one)
+update_one = router.patch("/{id_}")(app.service.experimental_bouton_density.update_one)

app/routers/experimental_neuron_density.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.experimental_neuron_density.read_many)
 read_one = router.get("/{id_}")(app.service.experimental_neuron_density.read_one)
 create_one = router.post("")(app.service.experimental_neuron_density.create_one)
+update_one = router.patch("/{id_}")(app.service.experimental_neuron_density.update_one)

app/routers/experimental_synapses_per_connection.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.experimental_synapses_per_connection.read_many)
 read_one = router.get("/{id_}")(app.service.experimental_synapses_per_connection.read_one)
 create_one = router.post("")(app.service.experimental_synapses_per_connection.create_one)
+update_one = router.patch("/{id_}")(app.service.experimental_synapses_per_connection.update_one)

app/routers/ion_channel_model.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.ion_channel_model.read_many)
 read_one = router.get("/{id_}")(app.service.ion_channel_model.read_one)
 create_one = router.post("")(app.service.ion_channel_model.create_one)
+update_one = router.patch("/{id_}")(app.service.ion_channel_model.update_one)

app/routers/memodel.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.memodel.read_many)
 read_one = router.get("/{id_}")(app.service.memodel.read_one)
 create_one = router.post("")(app.service.memodel.create_one)
+update_one = router.patch("/{id_}")(app.service.memodel.update_one)

app/routers/memodel_calibration_result.py

@@ -6,6 +6,8 @@
     prefix="/memodel-calibration-result",
     tags=["memodel-calibration-result"],
 )
+
 read_many = router.get("")(app.service.memodel_calibration_result.read_many)
 read_one = router.get("/{id_}")(app.service.memodel_calibration_result.read_one)
 create_one = router.post("")(app.service.memodel_calibration_result.create_one)
+update_one = router.patch("/{id_}")(app.service.memodel_calibration_result.update_one)

app/routers/morphology.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.morphology.read_many)
 read_one = router.get("/{id_}")(app.service.morphology.read_one)
 create_one = router.post("")(app.service.morphology.create_one)
+update_one = router.patch("/{id_}")(app.service.morphology.update_one)

app/routers/simulation.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.simulation.read_many)
 read_one = router.get("/{id_}")(app.service.simulation.read_one)
 create_one = router.post("")(app.service.simulation.create_one)
+update_one = router.patch("/{id_}")(app.service.simulation.update_one)

app/routers/simulation_campaign.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.simulation_campaign.read_many)
 read_one = router.get("/{id_}")(app.service.simulation_campaign.read_one)
 create_one = router.post("")(app.service.simulation_campaign.create_one)
+update_one = router.patch("/{id_}")(app.service.simulation_campaign.update_one)

app/routers/simulation_result.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.simulation_result.read_many)
 read_one = router.get("/{id_}")(app.service.simulation_result.read_one)
 create_one = router.post("")(app.service.simulation_result.create_one)
+update_one = router.patch("/{id_}")(app.service.simulation_result.update_one)

app/routers/single_neuron_simulation.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.single_neuron_simulation.read_many)
 read_one = router.get("/{id_}")(app.service.single_neuron_simulation.read_one)
 create_one = router.post("")(app.service.single_neuron_simulation.create_one)
+update_one = router.patch("/{id_}")(app.service.single_neuron_simulation.update_one)

app/routers/single_neuron_synaptome.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.single_neuron_synaptome.read_many)
 read_one = router.get("/{id_}")(app.service.single_neuron_synaptome.read_one)
 create_one = router.post("")(app.service.single_neuron_synaptome.create_one)
+update_one = router.patch("/{id_}")(app.service.single_neuron_synaptome.update_one)

app/routers/single_neuron_synaptome_simulation.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.single_neuron_synaptome_simulation.read_many)
 read_one = router.get("/{id_}")(app.service.single_neuron_synaptome_simulation.read_one)
 create_one = router.post("")(app.service.single_neuron_synaptome_simulation.create_one)
+update_one = router.patch("/{id_}")(app.service.single_neuron_synaptome_simulation.update_one)

app/routers/subject.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.subject.read_many)
 read_one = router.get("/{id_}")(app.service.subject.read_one)
 create_one = router.post("")(app.service.subject.create_one)
+update_one = router.patch("/{id_}")(app.service.subject.update_one)

app/routers/validation_result.py

@@ -10,3 +10,4 @@
 read_many = router.get("")(app.service.validation_result.read_many)
 read_one = router.get("/{id_}")(app.service.validation_result.read_one)
 create_one = router.post("")(app.service.validation_result.create_one)
+update_one = router.patch("/{id_}")(app.service.validation_result.update_one)

app/schemas/circuit.py

@@ -4,6 +4,7 @@
 
 from app.db.types import CircuitBuildCategory, CircuitScale
 from app.schemas.scientific_artifact import ScientificArtifactCreate, ScientificArtifactRead
+from app.schemas.utils import make_update_schema
 
 
 class CircuitBase(BaseModel):
@@ -34,3 +35,6 @@ class CircuitRead(CircuitBase, ScientificArtifactRead):
 
 class CircuitCreate(CircuitBase, ScientificArtifactCreate):
     pass
+
+
+CircuitUpdate = make_update_schema(CircuitCreate, "CircuitUpdate")  # pyright: ignore [reportInvalidTypeForm]

app/schemas/density.py

@@ -18,6 +18,7 @@
 )
 from app.schemas.contribution import ContributionReadWithoutEntityMixin
 from app.schemas.subject import SubjectReadMixin
+from app.schemas.utils import make_update_schema
 
 
 class MeasurementRead(BaseModel):
@@ -73,6 +74,19 @@ class ExperimentalSynapsesPerConnectionCreate(ExperimentalDensityCreate):
     post_region_id: uuid.UUID
 
 
+ExperimentalSynapsesPerConnectionUpdate = make_update_schema(
+    ExperimentalSynapsesPerConnectionCreate, "ExperimentalSynapsesPerConnectionUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+ExperimentalBoutonDensityUpdate = make_update_schema(
+    ExperimentalBoutonDensityCreate, "ExperimentalBoutonDensityUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+ExperimentalNeuronDensityUpdate = make_update_schema(
+    ExperimentalNeuronDensityCreate, "ExperimentalNeuronDensityUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+
 class ExperimentalNeuronDensityRead(ExperimentalDensityRead):
     mtypes: list[MTypeClassRead] | None
     etypes: list[ETypeClassRead] | None

app/schemas/electrical_cell_recording.py

@@ -14,6 +14,7 @@
     ScientificArtifactCreate,
     ScientificArtifactRead,
 )
+from app.schemas.utils import make_update_schema
 
 
 class ElectricalCellRecordingBase(BaseModel):
@@ -71,6 +72,11 @@ class ElectricalCellRecordingCreate(ElectricalCellRecordingBase, ScientificArtif
     pass
 
 
+ElectricalCellRecordingUpdate = make_update_schema(
+    ElectricalCellRecordingCreate, "ElectricalCellRecordingUpdate"
+)  # pyright : ignore [reportInvalidTypeForm]
+
+
 class ElectricalCellRecordingRead(
     ElectricalCellRecordingBase,
     ScientificArtifactRead,

app/schemas/electrical_recording_stimulus.py

@@ -14,6 +14,7 @@
     EntityTypeMixin,
     IdentifiableMixin,
 )
+from app.schemas.utils import make_update_schema
 
 
 class ElectricalRecordingStimulusBase(BaseModel):
@@ -46,3 +47,8 @@ class ElectricalRecordingStimulusCreate(
     ElectricalRecordingStimulusBase, AuthorizationOptionalPublicMixin
 ):
     pass
+
+
+ElectricalRecordingStimulusUpdate = make_update_schema(
+    ElectricalRecordingStimulusCreate, "ElectricalRecordingStimulusUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]

app/schemas/emodel.py

@@ -17,6 +17,7 @@
 from app.schemas.ion_channel_model import IonChannelModelWAssets
 from app.schemas.morphology import ReconstructionMorphologyBase
 from app.schemas.species import NestedSpeciesRead, NestedStrainRead
+from app.schemas.utils import make_update_schema
 
 
 class ExemplarMorphology(CreationMixin, ReconstructionMorphologyBase, IdentifiableMixin):
@@ -39,6 +40,9 @@ class EModelCreate(EModelBase, AuthorizationOptionalPublicMixin):
     exemplar_morphology_id: uuid.UUID
 
 
+EModelUpdate = make_update_schema(EModelCreate, "EModelUpdate")  # pyright: ignore [reportInvalidTypeForm]
+
+
 class EModelRead(
     EModelBase,
     CreationMixin,

app/schemas/ion_channel_model.py

@@ -8,6 +8,7 @@
     ScientificArtifactRead,
 )
 from app.schemas.subject import SubjectReadMixin
+from app.schemas.utils import make_update_schema
 
 
 class UseIon(BaseModel):
@@ -44,6 +45,9 @@ class IonChannelModelCreate(
     pass
 
 
+IonChannelModelUpdate = make_update_schema(IonChannelModelCreate, "IonChannelModelUpdate")  # pyright: ignore [reportInvalidTypeForm]
+
+
 class IonChannelModelRead(
     IonChannelModelBase,
     NestedScientificArtifactRead,

app/schemas/me_model.py

@@ -18,6 +18,7 @@
 from app.schemas.memodel_calibration_result import MEModelCalibrationResultRead
 from app.schemas.morphology import ReconstructionMorphologyRead
 from app.schemas.species import NestedSpeciesRead, NestedStrainRead
+from app.schemas.utils import make_update_schema
 
 
 class MEModelBase(BaseModel):
@@ -41,6 +42,9 @@ class MEModelCreate(MEModelBase, AuthorizationOptionalPublicMixin):
     strain_id: uuid.UUID | None = None
 
 
+MEModelUpdate = make_update_schema(MEModelCreate, "MEModelUpdate")  # pyright: ignore [reportInvalidTypeForm]
+
+
 class MEModelRead(
     MEModelBase,
     CreationMixin,

app/schemas/memodel_calibration_result.py

@@ -9,6 +9,7 @@
     CreationMixin,
     IdentifiableMixin,
 )
+from app.schemas.utils import make_update_schema
 
 
 class MEModelCalibrationResultBase(BaseModel):
@@ -34,3 +35,8 @@ class MEModelCalibrationResultCreate(
     MEModelCalibrationResultBase, AuthorizationOptionalPublicMixin
 ):
     """Create model for MEModel calibration results."""
+
+
+MEModelCalibrationResultUpdate = make_update_schema(
+    MEModelCalibrationResultCreate, "MEModelCalibrationResultUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]

app/schemas/morphology.py

@@ -19,6 +19,7 @@
 from app.schemas.contribution import ContributionReadWithoutEntityMixin
 from app.schemas.measurement_annotation import MeasurementAnnotationRead
 from app.schemas.species import NestedSpeciesRead, NestedStrainRead
+from app.schemas.utils import make_update_schema
 
 
 class ReconstructionMorphologyBase(BaseModel):
@@ -40,6 +41,11 @@ class ReconstructionMorphologyCreate(
     legacy_id: list[str] | None = None
 
 
+ReconstructionMorphologyUpdate = make_update_schema(
+    ReconstructionMorphologyCreate, "ReconstructionMorphologyUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+
 class ReconstructionMorphologyRead(
     ReconstructionMorphologyBase,
     CreationMixin,

app/schemas/simulation.py

@@ -16,6 +16,7 @@
 )
 from app.schemas.me_model import NestedMEModel
 from app.schemas.synaptome import NestedSynaptome
+from app.schemas.utils import make_update_schema
 
 
 class SingleNeuronSimulationBase(BaseModel):
@@ -36,6 +37,11 @@ class SingleNeuronSimulationCreate(
     me_model_id: uuid.UUID
 
 
+SingleNeuronSimulationUpdate = make_update_schema(
+    SingleNeuronSimulationCreate, "SingleNeuronSimulationUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+
 class SingleNeuronSimulationRead(
     SingleNeuronSimulationBase,
     BrainRegionReadMixin,
@@ -57,6 +63,11 @@ class SingleNeuronSynaptomeSimulationCreate(
     synaptome_id: uuid.UUID
 
 
+SingleNeuronSynaptomeSimulationUpdate = make_update_schema(
+    SingleNeuronSynaptomeSimulationCreate, "SingleNeuronSynaptomeSimulationUpdate"
+)  # pyright: ignore [reportInvalidTypeForm]
+
+
 class SingleNeuronSynaptomeSimulationRead(
     SingleNeuronSimulationBase,
     BrainRegionReadMixin,
@@ -83,6 +94,9 @@ class SimulationCreate(SimulationBase, AuthorizationOptionalPublicMixin):
     pass
 
 
+SimulationUpdate = make_update_schema(SimulationCreate, "SimulationUpdate")  # pyright: ignore [reportInvalidTypeForm]
+
+
 class NestedSimulationRead(SimulationBase, EntityTypeMixin, IdentifiableMixin):
     pass