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GianlucaFicarelliGianlucaFicarelli
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Merge remote-tracking branch 'origin/main' into scientific-ion-channel
* origin/main: Add external data source and url (#327)
2 parents e478c64 + 9b85336 commit 93cea86

23 files changed

+1351
-27
lines changed

‎alembic/versions/20250820_105353_34a01809b4d4_add_external_url_and_scientific_.py

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"""Add external_url and scientific_artifact_external_url_link
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Revision ID: 34a01809b4d4
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Revises: 781c7a2474de
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Create Date: 2025-08-20 10:53:53.943089
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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 = "34a01809b4d4"
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down_revision: Union[str, None] = "781c7a2474de"
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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("channelpedia", "modeldb", "icgenealogy", name="externalsource").create(op.get_bind())
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op.create_table(
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"external_url",
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sa.Column(
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"source",
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postgresql.ENUM(
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"channelpedia", "modeldb", "icgenealogy", name="externalsource", create_type=False
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),
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nullable=False,
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),
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sa.Column("url", sa.String(), nullable=False),
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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.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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["created_by_id"], ["agent.id"], name=op.f("fk_external_url_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_external_url_updated_by_id_agent")
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_external_url")),
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)
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op.create_index(
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op.f("ix_external_url_created_by_id"), "external_url", ["created_by_id"], unique=False
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)
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op.create_index(
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op.f("ix_external_url_creation_date"), "external_url", ["creation_date"], unique=False
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)
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op.create_index(
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"ix_external_url_description_vector",
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"external_url",
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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_external_url_name"), "external_url", ["name"], unique=False)
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op.create_index(
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op.f("ix_external_url_updated_by_id"), "external_url", ["updated_by_id"], unique=False
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)
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op.create_index(op.f("ix_external_url_url"), "external_url", ["url"], unique=True)
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op.create_table(
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"scientific_artifact_external_url_link",
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sa.Column("external_url_id", sa.Uuid(), nullable=False),
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sa.Column("scientific_artifact_id", sa.Uuid(), nullable=False),
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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"],
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["agent.id"],
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name=op.f("fk_scientific_artifact_external_url_link_created_by_id_agent"),
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),
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sa.ForeignKeyConstraint(
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["external_url_id"],
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["external_url.id"],
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name=op.f("fk_scientific_artifact_external_url_link_external_url_id_external_url"),
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),
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sa.ForeignKeyConstraint(
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["scientific_artifact_id"],
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["scientific_artifact.id"],
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name=op.f(
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"fk_scientific_artifact_external_url_link_scientific_artifact_id_scientific_artifact"
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),
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),
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sa.ForeignKeyConstraint(
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["updated_by_id"],
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["agent.id"],
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name=op.f("fk_scientific_artifact_external_url_link_updated_by_id_agent"),
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),
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sa.PrimaryKeyConstraint("id", name=op.f("pk_scientific_artifact_external_url_link")),
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sa.UniqueConstraint(
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"external_url_id",
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"scientific_artifact_id",
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name="uq_scientific_artifact_external_url_link",
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),
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)
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op.create_index(
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op.f("ix_scientific_artifact_external_url_link_created_by_id"),
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"scientific_artifact_external_url_link",
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["created_by_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_scientific_artifact_external_url_link_creation_date"),
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"scientific_artifact_external_url_link",
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["creation_date"],
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unique=False,
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)
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op.create_index(
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op.f("ix_scientific_artifact_external_url_link_external_url_id"),
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"scientific_artifact_external_url_link",
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["external_url_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_scientific_artifact_external_url_link_scientific_artifact_id"),
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"scientific_artifact_external_url_link",
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["scientific_artifact_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_scientific_artifact_external_url_link_updated_by_id"),
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"scientific_artifact_external_url_link",
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["updated_by_id"],
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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_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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"publication",
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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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"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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"publication",
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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(
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op.f("ix_scientific_artifact_external_url_link_updated_by_id"),
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table_name="scientific_artifact_external_url_link",
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)
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op.drop_index(
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op.f("ix_scientific_artifact_external_url_link_scientific_artifact_id"),
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table_name="scientific_artifact_external_url_link",
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)
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op.drop_index(
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op.f("ix_scientific_artifact_external_url_link_external_url_id"),
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table_name="scientific_artifact_external_url_link",
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)
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op.drop_index(
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op.f("ix_scientific_artifact_external_url_link_creation_date"),
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table_name="scientific_artifact_external_url_link",
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)
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op.drop_index(
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op.f("ix_scientific_artifact_external_url_link_created_by_id"),
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table_name="scientific_artifact_external_url_link",
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)
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op.drop_table("scientific_artifact_external_url_link")
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op.drop_index(op.f("ix_external_url_url"), table_name="external_url")
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op.drop_index(op.f("ix_external_url_updated_by_id"), table_name="external_url")
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op.drop_index(op.f("ix_external_url_name"), table_name="external_url")
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op.drop_index(
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"ix_external_url_description_vector", table_name="external_url", postgresql_using="gin"
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)
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op.drop_index(op.f("ix_external_url_creation_date"), table_name="external_url")
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op.drop_index(op.f("ix_external_url_created_by_id"), table_name="external_url")
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op.drop_table("external_url")
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sa.Enum("channelpedia", "modeldb", "icgenealogy", name="externalsource").drop(op.get_bind())
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# ### end Alembic commands ###

‎alembic/versions/20250820_105425_80139d43afaf_add_triggers_for_external_url.py

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"""Add triggers for external_url
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Revision ID: 80139d43afaf
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Revises: 34a01809b4d4
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Create Date: 2025-08-20 10:54:25.908534
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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 = "80139d43afaf"
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down_revision: Union[str, None] = "34a01809b4d4"
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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_external_url_external_url_description_vector = PGTrigger(
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schema="public",
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signature="external_url_description_vector",
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on_entity="public.external_url",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON external_url\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_external_url_external_url_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_external_url_external_url_description_vector = PGTrigger(
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schema="public",
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signature="external_url_description_vector",
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on_entity="public.external_url",
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is_constraint=False,
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definition="BEFORE INSERT OR UPDATE ON external_url\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_external_url_external_url_description_vector)
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# ### end Alembic commands ###

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