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AurelienJaquierAurelienJaquier
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Add IonChannel and IonChannelRecording (#305)
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+1853
-34
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‎alembic/versions/20250910_145121_d58bc70ec10f_rename_table_electrical_cell_recording.py‎

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"""Rename table electrical_cell_recording to electrical_recording
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Revision ID: d58bc70ec10f
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Revises: 9df9950d73a0
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Create Date: 2025-09-10 14:51:21.492590
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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.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 = "d58bc70ec10f"
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down_revision: Union[str, None] = "9df9950d73a0"
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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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op.rename_table("electrical_cell_recording", "electrical_recording")
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op.execute("ALTER INDEX pk_electrical_cell_recording RENAME TO pk_electrical_recording")
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def downgrade() -> None:
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op.rename_table("electrical_recording", "electrical_cell_recording")
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op.execute("ALTER INDEX pk_electrical_recording RENAME TO pk_electrical_cell_recording")

‎alembic/versions/20250910_150438_b352b28dae67_add_ion_channel_and_ion_channel_.py‎

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"""Add ion_channel and ion_channel_recording
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Revision ID: b352b28dae67
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Revises: d58bc70ec10f
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Create Date: 2025-09-10 15:04:38.633137
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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.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 = "b352b28dae67"
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down_revision: Union[str, None] = "d58bc70ec10f"
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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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"ion_channel",
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sa.Column("label", sa.String(), nullable=False),
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sa.Column("gene", sa.String(), nullable=False),
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sa.Column("synonyms", sa.ARRAY(sa.VARCHAR()), nullable=False),
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sa.Column("name", sa.String(), nullable=False),
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sa.Column("description", sa.String(), nullable=False),
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sa.Column("description_vector", postgresql.TSVECTOR(), nullable=True),
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column("created_by_id", sa.Uuid(), nullable=False),
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sa.Column("updated_by_id", sa.Uuid(), nullable=False),
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sa.Column(
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"creation_date",
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sa.DateTime(timezone=True),
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server_default=sa.text("now()"),
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nullable=False,
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),
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sa.Column(
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"update_date",
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sa.DateTime(timezone=True),
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server_default=sa.text("now()"),
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nullable=False,
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),
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sa.ForeignKeyConstraint(
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["created_by_id"], ["agent.id"], name=op.f("fk_ion_channel_created_by_id_agent")
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),
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sa.ForeignKeyConstraint(
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["updated_by_id"], ["agent.id"], name=op.f("fk_ion_channel_updated_by_id_agent")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_ion_channel")),
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)
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op.create_index(
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op.f("ix_ion_channel_created_by_id"), "ion_channel", ["created_by_id"], unique=False
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)
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op.create_index(
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op.f("ix_ion_channel_creation_date"), "ion_channel", ["creation_date"], unique=False
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)
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op.create_index(
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"ix_ion_channel_description_vector",
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"ion_channel",
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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(op.f("ix_ion_channel_label"), "ion_channel", ["label"], unique=True)
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op.create_index(op.f("ix_ion_channel_name"), "ion_channel", ["name"], unique=False)
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op.create_index(
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op.f("ix_ion_channel_updated_by_id"), "ion_channel", ["updated_by_id"], unique=False
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)
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op.create_table(
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"electrical_cell_recording",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["id"],
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["electrical_recording.id"],
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name=op.f("fk_electrical_cell_recording_id_electrical_recording"),
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_electrical_cell_recording")),
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)
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op.create_table(
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"ion_channel_recording",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column("cell_line", sa.String(), nullable=False),
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sa.Column("ion_channel_id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["id"],
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["electrical_recording.id"],
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name=op.f("fk_ion_channel_recording_id_electrical_recording"),
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),
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sa.ForeignKeyConstraint(
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["ion_channel_id"],
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["ion_channel.id"],
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name=op.f("fk_ion_channel_recording_ion_channel_id_ion_channel"),
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_ion_channel_recording")),
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)
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op.create_index(
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op.f("ix_ion_channel_recording_ion_channel_id"),
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"ion_channel_recording",
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["ion_channel_id"],
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unique=False,
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)
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op.drop_index(
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op.f("ix_electrical_cell_recording_description_vector"),
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table_name="electrical_recording",
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postgresql_using="gin",
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)
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op.drop_index(op.f("ix_electrical_cell_recording_name"), table_name="electrical_recording")
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op.create_index(
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"ix_electrical_recording_description_vector",
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"electrical_recording",
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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(
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op.f("ix_electrical_recording_name"), "electrical_recording", ["name"], unique=False
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)
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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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"cell_composition",
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"electrical_cell_recording",
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"electrical_recording",
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"electrical_recording_stimulus",
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"emodel",
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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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"external_url",
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"ion_channel",
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"ion_channel_model",
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"ion_channel_recording",
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"memodel",
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"mesh",
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"memodel_calibration_result",
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"me_type_density",
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"reconstruction_morphology",
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"simulation",
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"simulation_campaign",
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"simulation_campaign_generation",
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"simulation_execution",
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"simulation_result",
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"scientific_artifact",
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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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"subject",
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"validation_result",
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"circuit",
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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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"cell_composition",
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"electrical_cell_recording",
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"electrical_recording_stimulus",
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"emodel",
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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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"external_url",
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"ion_channel_model",
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"memodel",
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"mesh",
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"memodel_calibration_result",
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"me_type_density",
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"reconstruction_morphology",
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"simulation",
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"simulation_campaign",
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"simulation_campaign_generation",
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"simulation_execution",
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"simulation_result",
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"scientific_artifact",
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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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"subject",
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"validation_result",
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"circuit",
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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.drop_index(op.f("ix_electrical_recording_name"), table_name="electrical_recording")
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op.drop_index(
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"ix_electrical_recording_description_vector",
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table_name="electrical_recording",
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postgresql_using="gin",
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)
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op.create_index(
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op.f("ix_electrical_cell_recording_name"), "electrical_recording", ["name"], unique=False
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)
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op.create_index(
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op.f("ix_electrical_cell_recording_description_vector"),
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"electrical_recording",
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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.drop_index(
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op.f("ix_ion_channel_recording_ion_channel_id"), table_name="ion_channel_recording"
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)
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op.drop_table("ion_channel_recording")
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op.drop_table("electrical_cell_recording")
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op.drop_index(op.f("ix_ion_channel_updated_by_id"), table_name="ion_channel")
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op.drop_index(op.f("ix_ion_channel_name"), table_name="ion_channel")
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op.drop_index(op.f("ix_ion_channel_label"), table_name="ion_channel")
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op.drop_index(
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"ix_ion_channel_description_vector", table_name="ion_channel", postgresql_using="gin"
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)
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op.drop_index(op.f("ix_ion_channel_creation_date"), table_name="ion_channel")
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op.drop_index(op.f("ix_ion_channel_created_by_id"), table_name="ion_channel")
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op.drop_table("ion_channel")
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# ### end Alembic commands ###

‎alembic/versions/20250910_151320_b89af5e363b9_update_triggers.py‎

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"""Update triggers
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Revision ID: b89af5e363b9
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Revises: b352b28dae67
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Create Date: 2025-09-10 15:13:20.918399
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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_utils.pg_trigger import PGTrigger
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from sqlalchemy import text as sql_text
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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 = "b89af5e363b9"
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down_revision: Union[str, None] = "b352b28dae67"
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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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public_ion_channel_ion_channel_description_vector = PGTrigger(
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schema="public",
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signature="ion_channel_description_vector",
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on_entity="public.ion_channel",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON ion_channel\n FOR EACH ROW EXECUTE FUNCTION\n tsvector_update_trigger(description_vector, 'pg_catalog.english', description, name)",
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)
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op.create_entity(public_ion_channel_ion_channel_description_vector)
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public_electrical_recording_electrical_recording_description_vector = PGTrigger(
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schema="public",
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signature="electrical_recording_description_vector",
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on_entity="public.electrical_recording",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON electrical_recording\n FOR EACH ROW EXECUTE FUNCTION\n tsvector_update_trigger(description_vector, 'pg_catalog.english', description, name)",
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)
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op.create_entity(public_electrical_recording_electrical_recording_description_vector)
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public_electrical_recording_electrical_cell_recording_description_vector = PGTrigger(
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schema="public",
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signature="electrical_cell_recording_description_vector",
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on_entity="public.electrical_recording",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON public.electrical_recording FOR EACH ROW EXECUTE FUNCTION tsvector_update_trigger('description_vector', 'pg_catalog.english', 'description', 'name')",
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)
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op.drop_entity(public_electrical_recording_electrical_cell_recording_description_vector)
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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_electrical_recording_electrical_cell_recording_description_vector = PGTrigger(
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schema="public",
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signature="electrical_cell_recording_description_vector",
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on_entity="public.electrical_recording",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON public.electrical_recording 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_electrical_recording_electrical_cell_recording_description_vector)
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public_electrical_recording_electrical_recording_description_vector = PGTrigger(
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schema="public",
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signature="electrical_recording_description_vector",
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on_entity="public.electrical_recording",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON electrical_recording\n FOR EACH ROW EXECUTE FUNCTION\n tsvector_update_trigger(description_vector, 'pg_catalog.english', description, name)",
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)
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op.drop_entity(public_electrical_recording_electrical_recording_description_vector)
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public_ion_channel_ion_channel_description_vector = PGTrigger(
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schema="public",
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signature="ion_channel_description_vector",
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on_entity="public.ion_channel",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON ion_channel\n FOR EACH ROW EXECUTE FUNCTION\n tsvector_update_trigger(description_vector, 'pg_catalog.english', description, name)",
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)
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op.drop_entity(public_ion_channel_ion_channel_description_vector)
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# ### end Alembic commands ###

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