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GianlucaFicarelliGianlucaFicarelli
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Add generic campaign and config related activities
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‎alembic/versions/20260218_104617_c3208a1f2c6b_add_generic_campaign_models.py‎

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"""Add generic campaign models
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Revision ID: c3208a1f2c6b
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Revises: 523e523531a7
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Create Date: 2026-02-18 10:46:17.576165
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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 = "c3208a1f2c6b"
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down_revision: Union[str, None] = "523e523531a7"
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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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sa.Enum(
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"circuit_simulation",
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"circuit_extraction",
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"ion_channel_modeling",
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"skeletonization",
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"ion_channel_simulation",
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"em_synapse_mapping",
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name="tasktype",
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).create(op.get_bind())
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op.sync_enum_values(
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enum_schema="public",
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enum_name="activitytype",
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new_values=[
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"simulation_execution",
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"simulation_generation",
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"validation",
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"calibration",
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"analysis_notebook_execution",
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"ion_channel_modeling_execution",
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"ion_channel_modeling_config_generation",
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"circuit_extraction_config_generation",
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"circuit_extraction_execution",
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"skeletonization_execution",
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"skeletonization_config_generation",
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"config_generation",
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"config_execution",
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],
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affected_columns=[
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TableReference(table_schema="public", table_name="activity", column_name="type")
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],
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enum_values_to_rename=[],
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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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"cell_morphology",
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"cell_morphology_protocol",
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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_model",
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"ion_channel_modeling_campaign",
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"ion_channel_modeling_config",
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"ion_channel_recording",
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"memodel",
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"memodel_calibration_result",
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"me_type_density",
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"simulation",
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"simulation_campaign",
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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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"circuit_extraction_campaign",
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"circuit_extraction_config",
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"em_dense_reconstruction_dataset",
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"em_cell_mesh",
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"analysis_notebook_template",
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"analysis_notebook_environment",
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"analysis_notebook_result",
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"skeletonization_config",
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"skeletonization_campaign",
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"campaign",
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"item_config",
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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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TableReference(
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table_schema="public", table_name="measurement_label", column_name="entity_type"
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),
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],
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enum_values_to_rename=[],
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)
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op.create_table(
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"campaign",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column(
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"task_type",
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postgresql.ENUM(
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"circuit_simulation",
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"circuit_extraction",
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"ion_channel_modeling",
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"skeletonization",
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"ion_channel_simulation",
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"em_synapse_mapping",
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name="tasktype",
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create_type=False,
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),
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nullable=False,
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),
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sa.Column(
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"scan_parameters",
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postgresql.JSONB(astext_type=sa.Text()),
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server_default="{}",
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nullable=False,
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),
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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.ForeignKeyConstraint(["id"], ["entity.id"], name=op.f("fk_campaign_id_entity")),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_campaign")),
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)
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op.create_index(
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"ix_campaign_description_vector",
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"campaign",
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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_campaign_name"), "campaign", ["name"], unique=False)
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op.create_index(op.f("ix_campaign_task_type"), "campaign", ["task_type"], unique=False)
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op.create_table(
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"config_execution",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column(
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"executor",
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postgresql.ENUM(
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"single_node_job",
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"distributed_job",
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"jupyter_notebook",
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name="executortype",
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create_type=False,
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),
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nullable=True,
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),
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sa.Column("execution_id", sa.Uuid(), nullable=True),
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sa.ForeignKeyConstraint(
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["id"], ["activity.id"], name=op.f("fk_config_execution_id_activity")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_config_execution")),
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)
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op.create_table(
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"config_generation",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["id"], ["activity.id"], name=op.f("fk_config_generation_id_activity")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_config_generation")),
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)
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op.create_table(
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"entity__campaign",
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sa.Column("entity_id", sa.Uuid(), nullable=False),
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sa.Column("campaign_id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["campaign_id"],
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["campaign.id"],
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name=op.f("fk_entity__campaign_campaign_id_campaign"),
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ondelete="CASCADE",
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),
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sa.ForeignKeyConstraint(
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["entity_id"],
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["entity.id"],
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name=op.f("fk_entity__campaign_entity_id_entity"),
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ondelete="CASCADE",
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),
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sa.PrimaryKeyConstraint("entity_id", "campaign_id", name=op.f("pk_entity__campaign")),
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)
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op.create_table(
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"item_config",
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sa.Column("id", sa.Uuid(), nullable=False),
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sa.Column(
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"task_type",
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postgresql.ENUM(
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"circuit_simulation",
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"circuit_extraction",
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"ion_channel_modeling",
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"skeletonization",
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"ion_channel_simulation",
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"em_synapse_mapping",
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name="tasktype",
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create_type=False,
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),
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nullable=False,
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),
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sa.Column(
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"scan_parameters",
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postgresql.JSONB(astext_type=sa.Text()),
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server_default="{}",
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nullable=False,
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),
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sa.Column("campaign_id", sa.Uuid(), 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.ForeignKeyConstraint(
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["campaign_id"], ["campaign.id"], name=op.f("fk_item_config_campaign_id_campaign")
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),
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sa.ForeignKeyConstraint(["id"], ["entity.id"], name=op.f("fk_item_config_id_entity")),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_item_config")),
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)
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op.create_index(
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op.f("ix_item_config_campaign_id"), "item_config", ["campaign_id"], unique=False
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)
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op.create_index(
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"ix_item_config_description_vector",
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"item_config",
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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_item_config_name"), "item_config", ["name"], unique=False)
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op.create_index(op.f("ix_item_config_task_type"), "item_config", ["task_type"], unique=False)
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op.create_table(
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"entity__item_config",
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sa.Column("entity_id", sa.Uuid(), nullable=False),
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sa.Column("item_config_id", sa.Uuid(), nullable=False),
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sa.ForeignKeyConstraint(
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["entity_id"],
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["entity.id"],
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name=op.f("fk_entity__item_config_entity_id_entity"),
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ondelete="CASCADE",
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),
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sa.ForeignKeyConstraint(
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["item_config_id"],
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["item_config.id"],
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name=op.f("fk_entity__item_config_item_config_id_item_config"),
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ondelete="CASCADE",
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),
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sa.PrimaryKeyConstraint("entity_id", "item_config_id", name=op.f("pk_entity__item_config")),
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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.drop_table("entity__item_config")
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op.drop_index(op.f("ix_item_config_task_type"), table_name="item_config")
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op.drop_index(op.f("ix_item_config_name"), table_name="item_config")
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op.drop_index(
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"ix_item_config_description_vector", table_name="item_config", postgresql_using="gin"
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)
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op.drop_index(op.f("ix_item_config_campaign_id"), table_name="item_config")
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op.drop_table("item_config")
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op.drop_table("entity__campaign")
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op.drop_table("config_generation")
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op.drop_table("config_execution")
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op.drop_index(op.f("ix_campaign_task_type"), table_name="campaign")
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op.drop_index(op.f("ix_campaign_name"), table_name="campaign")
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op.drop_index("ix_campaign_description_vector", table_name="campaign", postgresql_using="gin")
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op.drop_table("campaign")
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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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"cell_morphology",
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"cell_morphology_protocol",
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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_model",
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"ion_channel_modeling_campaign",
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"ion_channel_modeling_config",
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"ion_channel_recording",
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"memodel",
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"memodel_calibration_result",
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"me_type_density",
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"simulation",
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"simulation_campaign",
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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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"circuit_extraction_campaign",
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"circuit_extraction_config",
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"em_dense_reconstruction_dataset",
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"em_cell_mesh",
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"analysis_notebook_template",
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"analysis_notebook_environment",
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"analysis_notebook_result",
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"skeletonization_config",
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"skeletonization_campaign",
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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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TableReference(
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table_schema="public", table_name="measurement_label", column_name="entity_type"
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),
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],
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enum_values_to_rename=[],
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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="activitytype",
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new_values=[
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"simulation_execution",
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"simulation_generation",
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"validation",
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"calibration",
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"analysis_notebook_execution",
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"ion_channel_modeling_execution",
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"ion_channel_modeling_config_generation",
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"circuit_extraction_config_generation",
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"circuit_extraction_execution",
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"skeletonization_execution",
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"skeletonization_config_generation",
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],
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affected_columns=[
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TableReference(table_schema="public", table_name="activity", column_name="type")
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],
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enum_values_to_rename=[],
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)
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sa.Enum(
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"circuit_simulation",
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"circuit_extraction",
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"ion_channel_modeling",
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"skeletonization",
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"ion_channel_simulation",
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"em_synapse_mapping",
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name="tasktype",
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).drop(op.get_bind())
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# ### end Alembic commands ###

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