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jdcourcolJean-Denis CourcolJean-Denis Courcolmgeplfeleftherioszisis
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me model calibration result proposal (#188)
* me model calibration result proposal * make rin optional, remove holding/threshold current from MEModel * MEModelCalibrationResult schema * add filter and router * Remove unique constraint from Person (#199) * move calibrated_entity_id to base class * import calibration results * adding memodel to calibrationresult relationship * Add joinedload * Add nested created_by, updated_by loader * add test for the memodel to calibration relationship --------- Co-authored-by: Jean-Denis Courcol <courcol@mac.home> Co-authored-by: Jean-Denis Courcol <courcol@mac.lan> Co-authored-by: MikeG <mgevaert@openbraininstitute.org> Co-authored-by: Eleftherios Zisis <eleftherios.zisis@epfl.ch> Co-authored-by: Gil Arturo Barrios del Villar <gilarturo.barriosdelvillar@openbraininstitute.org>
1 parent 207f737 commit 6856995

17 files changed

+472
-34
lines changed

‎alembic/versions/20250526_222351_1589bff44728_default_migration_message.py‎

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"""Default migration message
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Revision ID: 1589bff44728
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Revises: 8d1610d7c882
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Create Date: 2025-05-26 22:23:51.082630
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"""
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from typing import Sequence, Union
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from alembic import op
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import sqlalchemy as sa
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from alembic_postgresql_enum import TableReference
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from sqlalchemy import Text
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import app.db.types
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# revision identifiers, used by Alembic.
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revision: str = "1589bff44728"
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down_revision: Union[str, None] = "8d1610d7c882"
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branch_labels: Union[str, Sequence[str], None] = None
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depends_on: Union[str, Sequence[str], None] = None
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def upgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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op.create_table(
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"memodel_calibration_result",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column("holding_current", sa.Float(), nullable=False),
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sa.Column("threshold_current", sa.Float(), nullable=False),
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sa.Column("rin", sa.Float(), nullable=True),
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sa.Column("calibrated_entity_id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["calibrated_entity_id"],
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["memodel.id"],
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name=op.f("fk_memodel_calibration_result_calibrated_entity_id_memodel"),
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),
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sa.ForeignKeyConstraint(
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["id"], ["entity.id"], name=op.f("fk_memodel_calibration_result_id_entity")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_memodel_calibration_result")),
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)
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op.create_index(
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op.f("ix_memodel_calibration_result_calibrated_entity_id"),
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"memodel_calibration_result",
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["calibrated_entity_id"],
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unique=False,
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)
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op.drop_column("memodel", "holding_current")
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op.drop_column("memodel", "threshold_current")
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op.sync_enum_values(
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enum_schema="public",
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enum_name="entitytype",
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new_values=[
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"analysis_software_source_code",
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"brain_atlas",
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"brain_atlas_region",
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"emodel",
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"cell_composition",
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"memodel_calibration_result",
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"experimental_bouton_density",
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"experimental_neuron_density",
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"experimental_synapses_per_connection",
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"memodel",
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"mesh",
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"me_type_density",
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"reconstruction_morphology",
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"electrical_cell_recording",
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"electrical_recording_stimulus",
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"single_neuron_simulation",
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"single_neuron_synaptome",
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"single_neuron_synaptome_simulation",
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"ion_channel_model",
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"subject",
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"validation_result",
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],
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affected_columns=[
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TableReference(table_schema="public", table_name="entity", column_name="type")
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],
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enum_values_to_rename=[],
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)
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# ### end Alembic commands ###
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def downgrade() -> None:
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# ### commands auto generated by Alembic - please adjust! ###
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op.sync_enum_values(
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enum_schema="public",
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enum_name="entitytype",
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new_values=[
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"analysis_software_source_code",
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"brain_atlas",
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"brain_atlas_region",
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"emodel",
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"cell_composition",
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"experimental_bouton_density",
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"experimental_neuron_density",
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"experimental_synapses_per_connection",
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"memodel",
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"mesh",
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"me_type_density",
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"reconstruction_morphology",
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"electrical_cell_recording",
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"electrical_recording_stimulus",
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"single_neuron_simulation",
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"single_neuron_synaptome",
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"single_neuron_synaptome_simulation",
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"ion_channel_model",
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"subject",
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"validation_result",
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],
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affected_columns=[
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TableReference(table_schema="public", table_name="entity", column_name="type")
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],
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enum_values_to_rename=[],
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)
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op.add_column(
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"memodel",
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sa.Column(
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"threshold_current",
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sa.DOUBLE_PRECISION(precision=53),
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autoincrement=False,
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nullable=True,
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),
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)
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op.add_column(
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"memodel",
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sa.Column(
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"holding_current", sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True
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),
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)
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op.drop_index(
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op.f("ix_memodel_calibration_result_calibrated_entity_id"),
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table_name="memodel_calibration_result",
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)
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op.drop_table("memodel_calibration_result")
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# ### end Alembic commands ###

‎app/cli/import_data.py‎

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

‎app/db/model.py‎

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@@ -482,13 +482,17 @@ class MEModel(
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"ReconstructionMorphology", foreign_keys=[morphology_id], uselist=False
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)
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holding_current: Mapped[float | None]
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threshold_current: Mapped[float | None]
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emodel_id: Mapped[uuid.UUID] = mapped_column(ForeignKey(f"{EntityType.emodel}.id"))
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emodel = relationship("EModel", foreign_keys=[emodel_id], uselist=False)
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calibration_result = relationship(
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"MEModelCalibrationResult",
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uselist=False,
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foreign_keys="MEModelCalibrationResult.calibrated_entity_id",
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lazy="joined",
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)
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__mapper_args__ = {"polymorphic_identity": __tablename__} # noqa: RUF012
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}
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class MEModelCalibrationResult(Entity):
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__tablename__ = EntityType.memodel_calibration_result.value
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id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), primary_key=True)
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holding_current: Mapped[float]
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threshold_current: Mapped[float]
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rin: Mapped[float | None]
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calibrated_entity_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("memodel.id"), index=True)
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calibrated_entity: Mapped[Entity] = relationship(
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"MEModel",
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uselist=False,
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foreign_keys=[calibrated_entity_id],
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)
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__mapper_args__ = { # noqa: RUF012
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"polymorphic_identity": __tablename__,
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"inherit_condition": id == Entity.id,
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}
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class Asset(Identifiable):
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"""Asset table."""
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‎app/db/types.py‎

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brain_atlas_region = auto()
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emodel = auto()
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cell_composition = auto()
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memodel_calibration_result = auto()
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experimental_bouton_density = auto()
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experimental_neuron_density = auto()
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experimental_synapses_per_connection = auto()

‎app/filters/memodel_calibration_result.py‎

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

‎app/routers/__init__.py‎

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license,
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measurement_annotation,
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memodel,
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memodel_calibration_result,
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morphology,
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mtype,
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organization,
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license.router,
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measurement_annotation.router,
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memodel.router,
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memodel_calibration_result.router,
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morphology.router,
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mtype.router,
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organization.router,

‎app/routers/memodel_calibration_result.py‎

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from fastapi import APIRouter
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import app.service.memodel_calibration_result
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router = APIRouter(
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prefix="/memodel-calibration-result",
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tags=["memodel-calibration-result"],
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)
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read_many = router.get("")(app.service.memodel_calibration_result.read_many)
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read_one = router.get("/{id_}")(app.service.memodel_calibration_result.read_one)
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create_one = router.post("")(app.service.memodel_calibration_result.create_one)

‎app/schemas/me_model.py‎

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)
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from app.schemas.contribution import ContributionReadWithoutEntity
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from app.schemas.emodel import EModelRead
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from app.schemas.memodel_calibration_result import MEModelCalibrationResultRead
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from app.schemas.morphology import ReconstructionMorphologyRead
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name: str
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description: str
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validation_status: ValidationStatus = ValidationStatus.created
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holding_current: float | None = None
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threshold_current: float | None = None
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# To be used by entities who reference MEModel
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etypes: list[ETypeClassRead] | None
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morphology: ReconstructionMorphologyRead
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emodel: EModelRead
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calibration_result: MEModelCalibrationResultRead | None

‎app/schemas/memodel_calibration_result.py‎

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

‎app/service/memodel.py‎

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Contribution,
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EModel,
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MEModel,
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MEModelCalibrationResult,
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ReconstructionMorphology,
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)
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from app.dependencies.auth import UserContextDep, UserContextWithProjectIdDep
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joinedload(MEModel.etypes),
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joinedload(MEModel.created_by),
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joinedload(MEModel.updated_by),
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joinedload(MEModel.calibration_result).joinedload(MEModelCalibrationResult.created_by),
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joinedload(MEModel.calibration_result).joinedload(MEModelCalibrationResult.updated_by),
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raiseload("*"),
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)
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