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Initial implementation of brain-atlas endpoints
See #168 for the specification. Briefly; a `BrainAtlas` is an named entity that has an asset `annotation.nrrd` attached to it. It is associated with a particular `BrainRegionHierarchy` In addition, `BrainAtlasRegion` gives metadata for all the regions within a `BrainAtlas`; * their volume in the `annotation.nrrd` if they are a leaf, -1 otherwise. * an attached asset with the .obj mesh
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‎alembic/versions/20250523_085631_f750b8010fb9_brainatlas.py‎

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"""brainatlas
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Revision ID: f750b8010fb9
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Revises: 719dc38efbd6
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Create Date: 2025-05-23 08:56:31.033885
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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 alembic_utils.pg_trigger import PGTrigger
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from sqlalchemy import text as sql_text
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from sqlalchemy.dialects import postgresql
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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 = "f750b8010fb9"
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down_revision: Union[str, None] = "719dc38efbd6"
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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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"brain_atlas_region",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column("volume", sa.Float(), nullable=True),
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sa.Column("leaf_region", sa.Boolean(), nullable=False),
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sa.Column("brain_atlas_id", sa.Uuid(), nullable=False),
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sa.Column("brain_region_id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["brain_atlas_id"],
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["brain_atlas.id"],
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name=op.f("fk_brain_atlas_region_brain_atlas_id_brain_atlas"),
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),
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sa.ForeignKeyConstraint(
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["brain_region_id"],
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["brain_region.id"],
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name=op.f("fk_brain_atlas_region_brain_region_id_brain_region"),
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),
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sa.ForeignKeyConstraint(
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["id"], ["entity.id"], name=op.f("fk_brain_atlas_region_id_entity")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_brain_atlas_region")),
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)
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op.create_index(
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op.f("ix_brain_atlas_region_brain_atlas_id"),
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"brain_atlas_region",
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["brain_atlas_id"],
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unique=False,
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)
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op.create_index(
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op.f("ix_brain_atlas_region_brain_region_id"),
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"brain_atlas_region",
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["brain_region_id"],
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unique=False,
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)
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op.drop_index("ix_mesh_brain_region_id", table_name="mesh")
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op.drop_index("ix_mesh_description_vector", table_name="mesh", postgresql_using="gin")
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op.drop_index("ix_mesh_name", table_name="mesh")
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op.drop_table("mesh")
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op.add_column("brain_atlas", sa.Column("hierarchy_id", sa.Uuid(), nullable=False))
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op.drop_index("ix_brain_atlas_brain_region_id", table_name="brain_atlas")
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op.create_index(
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op.f("ix_brain_atlas_hierarchy_id"), "brain_atlas", ["hierarchy_id"], unique=False
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)
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op.drop_constraint(
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"fk_brain_atlas_brain_region_id_brain_region", "brain_atlas", type_="foreignkey"
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)
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op.create_foreign_key(
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op.f("fk_brain_atlas_hierarchy_id_brain_region_hierarchy"),
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"brain_atlas",
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"brain_region_hierarchy",
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["hierarchy_id"],
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["id"],
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)
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op.drop_column("brain_atlas", "brain_region_id")
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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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# ### 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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public_mesh_mesh_description_vector = PGTrigger(
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schema="public",
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signature="mesh_description_vector",
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on_entity="public.mesh",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON public.mesh FOR EACH ROW EXECUTE FUNCTION tsvector_update_trigger('description_vector', 'pg_catalog.english', 'description', 'name')",
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)
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op.create_entity(public_mesh_mesh_description_vector)
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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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"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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"brain_atlas", sa.Column("brain_region_id", sa.UUID(), autoincrement=False, nullable=False)
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)
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op.drop_constraint(
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op.f("fk_brain_atlas_hierarchy_id_brain_region_hierarchy"),
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"brain_atlas",
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type_="foreignkey",
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)
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op.create_foreign_key(
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"fk_brain_atlas_brain_region_id_brain_region",
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"brain_atlas",
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"brain_region",
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["brain_region_id"],
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["id"],
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)
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op.drop_index(op.f("ix_brain_atlas_hierarchy_id"), table_name="brain_atlas")
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op.create_index(
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"ix_brain_atlas_brain_region_id", "brain_atlas", ["brain_region_id"], unique=False
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)
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op.drop_column("brain_atlas", "hierarchy_id")
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op.create_table(
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"mesh",
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sa.Column("id", sa.UUID(), autoincrement=False, nullable=False),
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sa.Column("brain_region_id", sa.UUID(), autoincrement=False, nullable=False),
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sa.Column("name", sa.VARCHAR(), autoincrement=False, nullable=False),
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sa.Column("description", sa.VARCHAR(), autoincrement=False, nullable=False),
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sa.Column("description_vector", postgresql.TSVECTOR(), autoincrement=False, nullable=True),
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sa.ForeignKeyConstraint(
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["brain_region_id"], ["brain_region.id"], name="fk_mesh_brain_region_id_brain_region"
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),
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sa.ForeignKeyConstraint(["id"], ["entity.id"], name="fk_mesh_id_entity"),
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sa.PrimaryKeyConstraint("id", name="pk_mesh"),
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)
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op.create_index("ix_mesh_name", "mesh", ["name"], unique=False)
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op.create_index(
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"ix_mesh_description_vector",
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"mesh",
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["description_vector"],
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unique=False,
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postgresql_using="gin",
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)
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op.create_index("ix_mesh_brain_region_id", "mesh", ["brain_region_id"], unique=False)
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op.drop_index(op.f("ix_brain_atlas_region_brain_region_id"), table_name="brain_atlas_region")
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op.drop_index(op.f("ix_brain_atlas_region_brain_atlas_id"), table_name="brain_atlas_region")
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op.drop_table("brain_atlas_region")
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# ### end Alembic commands ###

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