me model calibration result proposal

alembic/versions/20250526_173512_8d1610d7c882_default_migration_message.py

@@ -0,0 +1,34 @@
+"""Default migration message
+
+Revision ID: 8d1610d7c882
+Revises: 634224e88212
+Create Date: 2025-05-26 17:35:12.743948
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+from sqlalchemy import Text
+import app.db.types
+
+# revision identifiers, used by Alembic.
+revision: str = "8d1610d7c882"
+down_revision: Union[str, None] = "634224e88212"
+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.drop_constraint("unique_person_name_1", "person", type_="unique")
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_unique_constraint("unique_person_name_1", "person", ["given_name", "family_name"])
+    # ### end Alembic commands ###

alembic/versions/20250526_222351_1589bff44728_default_migration_message.py

@@ -0,0 +1,138 @@
+"""Default migration message
+
+Revision ID: 1589bff44728
+Revises: 8d1610d7c882
+Create Date: 2025-05-26 22:23:51.082630
+
+"""
+
+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 = "1589bff44728"
+down_revision: Union[str, None] = "8d1610d7c882"
+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(
+        "memodel_calibration_result",
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column("holding_current", sa.Float(), nullable=False),
+        sa.Column("threshold_current", sa.Float(), nullable=False),
+        sa.Column("rin", sa.Float(), nullable=True),
+        sa.Column("calibrated_entity_id", sa.Uuid(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["calibrated_entity_id"],
+            ["memodel.id"],
+            name=op.f("fk_memodel_calibration_result_calibrated_entity_id_memodel"),
+        ),
+        sa.ForeignKeyConstraint(
+            ["id"], ["entity.id"], name=op.f("fk_memodel_calibration_result_id_entity")
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_memodel_calibration_result")),
+    )
+    op.create_index(
+        op.f("ix_memodel_calibration_result_calibrated_entity_id"),
+        "memodel_calibration_result",
+        ["calibrated_entity_id"],
+        unique=False,
+    )
+    op.drop_column("memodel", "holding_current")
+    op.drop_column("memodel", "threshold_current")
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "emodel",
+            "cell_composition",
+            "memodel_calibration_result",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "memodel",
+            "mesh",
+            "me_type_density",
+            "reconstruction_morphology",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "ion_channel_model",
+            "subject",
+            "validation_result",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        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="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "emodel",
+            "cell_composition",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "memodel",
+            "mesh",
+            "me_type_density",
+            "reconstruction_morphology",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "ion_channel_model",
+            "subject",
+            "validation_result",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+    op.add_column(
+        "memodel",
+        sa.Column(
+            "threshold_current",
+            sa.DOUBLE_PRECISION(precision=53),
+            autoincrement=False,
+            nullable=True,
+        ),
+    )
+    op.add_column(
+        "memodel",
+        sa.Column(
+            "holding_current", sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True
+        ),
+    )
+    op.drop_index(
+        op.f("ix_memodel_calibration_result_calibrated_entity_id"),
+        table_name="memodel_calibration_result",
+    )
+    op.drop_table("memodel_calibration_result")
+    # ### end Alembic commands ###

app/cli/import_data.py

@@ -49,6 +49,7 @@
     Measurement,
     MeasurementAnnotation,
     MEModel,
+    MEModelCalibrationResult,
     METypeDensity,
     MTypeClass,
     MTypeClassification,
@@ -901,13 +902,23 @@ def ingest(db, project_context, data_list, all_data_by_id, hierarchy_name: str):
                 strain_id=morphology.strain_id,
                 creation_date=createdAt,
                 update_date=updatedAt,
-                holding_current=data.get("holding_current"),
-                threshold_current=data.get("threshold_current"),
             )
 
             db.add(db_item)
             db.flush()
-
+            db_calibration = MEModelCalibrationResult(
+                calibrated_entity_id=db_item.id,
+                holding_current=data.get("holding_current", 0),
+                threshold_current=data.get("threshold_current", 0),
+                authorized_project_id=project_context.project_id,
+                authorized_public=AUTHORIZED_PUBLIC,
+                created_by_id=created_by_id,
+                updated_by_id=updated_by_id,
+                creation_date=createdAt,
+                update_date=updatedAt,
+            )
+            db.add(db_calibration)
+            db.flush()
             utils.import_contribution(data, db_item.id, db)
 
             for annotation in ensurelist(data.get("annotation", [])):

app/db/model.py

@@ -231,7 +231,6 @@ class Person(Agent):
         "polymorphic_identity": __tablename__,
         "polymorphic_load": "selectin",
     }
-    __table_args__ = (UniqueConstraint("given_name", "family_name", name="unique_person_name_1"),)
 
 
 class Organization(Agent):
@@ -483,13 +482,17 @@ class MEModel(
         "ReconstructionMorphology", foreign_keys=[morphology_id], uselist=False
     )
 
-    holding_current: Mapped[float | None]
-    threshold_current: Mapped[float | None]
-
     emodel_id: Mapped[uuid.UUID] = mapped_column(ForeignKey(f"{EntityType.emodel}.id"))
 
     emodel = relationship("EModel", foreign_keys=[emodel_id], uselist=False)
 
+    calibration_result = relationship(
+        "MEModelCalibrationResult",
+        uselist=False,
+        foreign_keys="MEModelCalibrationResult.calibrated_entity_id",
+        lazy="joined",
+    )
+
     __mapper_args__ = {"polymorphic_identity": __tablename__}  # noqa: RUF012
 
 
@@ -832,6 +835,25 @@ class ValidationResult(Entity):
     }
 
 
+class MEModelCalibrationResult(Entity):
+    __tablename__ = EntityType.memodel_calibration_result.value
+    id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), primary_key=True)
+    holding_current: Mapped[float]
+    threshold_current: Mapped[float]
+    rin: Mapped[float | None]
+    calibrated_entity_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("memodel.id"), index=True)
+    calibrated_entity: Mapped[Entity] = relationship(
+        "MEModel",
+        uselist=False,
+        foreign_keys=[calibrated_entity_id],
+    )
+
+    __mapper_args__ = {  # noqa: RUF012
+        "polymorphic_identity": __tablename__,
+        "inherit_condition": id == Entity.id,
+    }
+
+
 class Asset(Identifiable):
     """Asset table."""
 

app/db/types.py

@@ -53,6 +53,7 @@ class EntityType(StrEnum):
     brain_atlas_region = auto()
     emodel = auto()
     cell_composition = auto()
+    memodel_calibration_result = auto()
     experimental_bouton_density = auto()
     experimental_neuron_density = auto()
     experimental_synapses_per_connection = auto()

app/filters/memodel_calibration_result.py

@@ -0,0 +1,27 @@
+import uuid
+from typing import Annotated
+
+from fastapi_filter import FilterDepends
+
+from app.db.model import MEModelCalibrationResult
+from app.filters.base import CustomFilter
+from app.filters.common import EntityFilterMixin
+
+
+class MEModelCalibrationResultFilter(
+    CustomFilter,
+    EntityFilterMixin,
+):
+    passed: bool | None = None
+    calibrated_entity_id: uuid.UUID | None = None
+
+    order_by: list[str] = ["calibrated_entity_id"]  # noqa: RUF012
+
+    class Constants(CustomFilter.Constants):
+        model = MEModelCalibrationResult
+        ordering_model_fields = ["calibrated_entity_id"]  # noqa: RUF012
+
+
+MEModelCalibrationResultFilterDep = Annotated[
+    MEModelCalibrationResultFilter, FilterDepends(MEModelCalibrationResultFilter)
+]

app/routers/__init__.py

@@ -20,6 +20,7 @@
     license,
     measurement_annotation,
     memodel,
+    memodel_calibration_result,
     morphology,
     mtype,
     organization,
@@ -54,6 +55,7 @@
     license.router,
     measurement_annotation.router,
     memodel.router,
+    memodel_calibration_result.router,
     morphology.router,
     mtype.router,
     organization.router,

app/routers/memodel_calibration_result.py

@@ -0,0 +1,11 @@
+from fastapi import APIRouter
+
+import app.service.memodel_calibration_result
+
+router = APIRouter(
+    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)

app/schemas/me_model.py

@@ -17,6 +17,7 @@
 )
 from app.schemas.contribution import ContributionReadWithoutEntity
 from app.schemas.emodel import EModelRead
+from app.schemas.memodel_calibration_result import MEModelCalibrationResultRead
 from app.schemas.morphology import ReconstructionMorphologyRead
 
 
@@ -25,8 +26,6 @@ class MEModelBase(BaseModel):
     name: str
     description: str
     validation_status: ValidationStatus = ValidationStatus.created
-    holding_current: float | None = None
-    threshold_current: float | None = None
 
 
 # To be used by entities who reference MEModel
@@ -59,3 +58,4 @@ class MEModelRead(
     etypes: list[ETypeClassRead] | None
     morphology: ReconstructionMorphologyRead
     emodel: EModelRead
+    calibration_result: MEModelCalibrationResultRead | None

app/schemas/memodel_calibration_result.py

@@ -0,0 +1,28 @@
+import uuid
+
+from pydantic import BaseModel
+
+from app.schemas.agent import CreatedByUpdatedByMixin
+from app.schemas.base import (
+    CreationMixin,
+    IdentifiableMixin,
+)
+
+
+class MEModelCalibrationResultBase(BaseModel):
+    """Base model for MEModel calibration results."""
+
+    holding_current: float
+    threshold_current: float
+    rin: float | None = None
+    calibrated_entity_id: uuid.UUID
+
+
+class MEModelCalibrationResultRead(
+    MEModelCalibrationResultBase, CreationMixin, IdentifiableMixin, CreatedByUpdatedByMixin
+):
+    """Read model for MEModel calibration results, including entity metadata."""
+
+
+class MEModelCalibrationResultCreate(MEModelCalibrationResultBase):
+    """Create model for MEModel calibration results."""

app/service/memodel.py

@@ -14,6 +14,7 @@
     Contribution,
     EModel,
     MEModel,
+    MEModelCalibrationResult,
     ReconstructionMorphology,
 )
 from app.dependencies.auth import UserContextDep, UserContextWithProjectIdDep
@@ -70,6 +71,8 @@ def _load(select: Select):
         joinedload(MEModel.etypes),
         joinedload(MEModel.created_by),
         joinedload(MEModel.updated_by),
+        joinedload(MEModel.calibration_result).joinedload(MEModelCalibrationResult.created_by),
+        joinedload(MEModel.calibration_result).joinedload(MEModelCalibrationResult.updated_by),
         raiseload("*"),
     )