Add external data source

alembic/versions/20250820_105353_34a01809b4d4_add_external_url_and_scientific_.py

@@ -0,0 +1,276 @@
+"""Add external_url and scientific_artifact_external_url_link
+
+Revision ID: 34a01809b4d4
+Revises: 781c7a2474de
+Create Date: 2025-08-20 10:53:53.943089
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from alembic_postgresql_enum import TableReference
+from sqlalchemy.dialects import postgresql
+
+from sqlalchemy import Text
+import app.db.types
+
+# revision identifiers, used by Alembic.
+revision: str = "34a01809b4d4"
+down_revision: Union[str, None] = "781c7a2474de"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    sa.Enum("channelpedia", "modeldb", "icgenealogy", name="externalsource").create(op.get_bind())
+    op.create_table(
+        "external_url",
+        sa.Column(
+            "source",
+            postgresql.ENUM(
+                "channelpedia", "modeldb", "icgenealogy", name="externalsource", create_type=False
+            ),
+            nullable=False,
+        ),
+        sa.Column("url", sa.String(), nullable=False),
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column("created_by_id", sa.Uuid(), nullable=False),
+        sa.Column("updated_by_id", sa.Uuid(), nullable=False),
+        sa.Column(
+            "creation_date",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column(
+            "update_date",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column("name", sa.String(), nullable=False),
+        sa.Column("description", sa.String(), nullable=False),
+        sa.Column("description_vector", postgresql.TSVECTOR(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["created_by_id"], ["agent.id"], name=op.f("fk_external_url_created_by_id_agent")
+        ),
+        sa.ForeignKeyConstraint(
+            ["updated_by_id"], ["agent.id"], name=op.f("fk_external_url_updated_by_id_agent")
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_external_url")),
+    )
+    op.create_index(
+        op.f("ix_external_url_created_by_id"), "external_url", ["created_by_id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_external_url_creation_date"), "external_url", ["creation_date"], unique=False
+    )
+    op.create_index(
+        "ix_external_url_description_vector",
+        "external_url",
+        ["description_vector"],
+        unique=False,
+        postgresql_using="gin",
+    )
+    op.create_index(op.f("ix_external_url_name"), "external_url", ["name"], unique=False)
+    op.create_index(
+        op.f("ix_external_url_updated_by_id"), "external_url", ["updated_by_id"], unique=False
+    )
+    op.create_index(op.f("ix_external_url_url"), "external_url", ["url"], unique=True)
+    op.create_table(
+        "scientific_artifact_external_url_link",
+        sa.Column("external_url_id", sa.Uuid(), nullable=False),
+        sa.Column("scientific_artifact_id", sa.Uuid(), nullable=False),
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column("created_by_id", sa.Uuid(), nullable=False),
+        sa.Column("updated_by_id", sa.Uuid(), nullable=False),
+        sa.Column(
+            "creation_date",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column(
+            "update_date",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["created_by_id"],
+            ["agent.id"],
+            name=op.f("fk_scientific_artifact_external_url_link_created_by_id_agent"),
+        ),
+        sa.ForeignKeyConstraint(
+            ["external_url_id"],
+            ["external_url.id"],
+            name=op.f("fk_scientific_artifact_external_url_link_external_url_id_external_url"),
+        ),
+        sa.ForeignKeyConstraint(
+            ["scientific_artifact_id"],
+            ["scientific_artifact.id"],
+            name=op.f(
+                "fk_scientific_artifact_external_url_link_scientific_artifact_id_scientific_artifact"
+            ),
+        ),
+        sa.ForeignKeyConstraint(
+            ["updated_by_id"],
+            ["agent.id"],
+            name=op.f("fk_scientific_artifact_external_url_link_updated_by_id_agent"),
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_scientific_artifact_external_url_link")),
+        sa.UniqueConstraint(
+            "external_url_id",
+            "scientific_artifact_id",
+            name="uq_scientific_artifact_external_url_link",
+        ),
+    )
+    op.create_index(
+        op.f("ix_scientific_artifact_external_url_link_created_by_id"),
+        "scientific_artifact_external_url_link",
+        ["created_by_id"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_scientific_artifact_external_url_link_creation_date"),
+        "scientific_artifact_external_url_link",
+        ["creation_date"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_scientific_artifact_external_url_link_external_url_id"),
+        "scientific_artifact_external_url_link",
+        ["external_url_id"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_scientific_artifact_external_url_link_scientific_artifact_id"),
+        "scientific_artifact_external_url_link",
+        ["scientific_artifact_id"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_scientific_artifact_external_url_link_updated_by_id"),
+        "scientific_artifact_external_url_link",
+        ["updated_by_id"],
+        unique=False,
+    )
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "cell_composition",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "emodel",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "external_url",
+            "ion_channel_model",
+            "memodel",
+            "mesh",
+            "memodel_calibration_result",
+            "me_type_density",
+            "publication",
+            "reconstruction_morphology",
+            "simulation",
+            "simulation_campaign",
+            "simulation_campaign_generation",
+            "simulation_execution",
+            "simulation_result",
+            "scientific_artifact",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "subject",
+            "validation_result",
+            "circuit",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.sync_enum_values(
+        enum_schema="public",
+        enum_name="entitytype",
+        new_values=[
+            "analysis_software_source_code",
+            "brain_atlas",
+            "brain_atlas_region",
+            "cell_composition",
+            "electrical_cell_recording",
+            "electrical_recording_stimulus",
+            "emodel",
+            "experimental_bouton_density",
+            "experimental_neuron_density",
+            "experimental_synapses_per_connection",
+            "ion_channel_model",
+            "memodel",
+            "mesh",
+            "memodel_calibration_result",
+            "me_type_density",
+            "publication",
+            "reconstruction_morphology",
+            "simulation",
+            "simulation_campaign",
+            "simulation_campaign_generation",
+            "simulation_execution",
+            "simulation_result",
+            "scientific_artifact",
+            "single_neuron_simulation",
+            "single_neuron_synaptome",
+            "single_neuron_synaptome_simulation",
+            "subject",
+            "validation_result",
+            "circuit",
+        ],
+        affected_columns=[
+            TableReference(table_schema="public", table_name="entity", column_name="type")
+        ],
+        enum_values_to_rename=[],
+    )
+    op.drop_index(
+        op.f("ix_scientific_artifact_external_url_link_updated_by_id"),
+        table_name="scientific_artifact_external_url_link",
+    )
+    op.drop_index(
+        op.f("ix_scientific_artifact_external_url_link_scientific_artifact_id"),
+        table_name="scientific_artifact_external_url_link",
+    )
+    op.drop_index(
+        op.f("ix_scientific_artifact_external_url_link_external_url_id"),
+        table_name="scientific_artifact_external_url_link",
+    )
+    op.drop_index(
+        op.f("ix_scientific_artifact_external_url_link_creation_date"),
+        table_name="scientific_artifact_external_url_link",
+    )
+    op.drop_index(
+        op.f("ix_scientific_artifact_external_url_link_created_by_id"),
+        table_name="scientific_artifact_external_url_link",
+    )
+    op.drop_table("scientific_artifact_external_url_link")
+    op.drop_index(op.f("ix_external_url_url"), table_name="external_url")
+    op.drop_index(op.f("ix_external_url_updated_by_id"), table_name="external_url")
+    op.drop_index(op.f("ix_external_url_name"), table_name="external_url")
+    op.drop_index(
+        "ix_external_url_description_vector", table_name="external_url", postgresql_using="gin"
+    )
+    op.drop_index(op.f("ix_external_url_creation_date"), table_name="external_url")
+    op.drop_index(op.f("ix_external_url_created_by_id"), table_name="external_url")
+    op.drop_table("external_url")
+    sa.Enum("channelpedia", "modeldb", "icgenealogy", name="externalsource").drop(op.get_bind())
+    # ### end Alembic commands ###

alembic/versions/20250820_105425_80139d43afaf_add_triggers_for_external_url.py

@@ -0,0 +1,51 @@
+"""Add triggers for external_url
+
+Revision ID: 80139d43afaf
+Revises: 34a01809b4d4
+Create Date: 2025-08-20 10:54:25.908534
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from alembic_utils.pg_trigger import PGTrigger
+from sqlalchemy import text as sql_text
+
+from sqlalchemy import Text
+import app.db.types
+
+# revision identifiers, used by Alembic.
+revision: str = "80139d43afaf"
+down_revision: Union[str, None] = "34a01809b4d4"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    public_external_url_external_url_description_vector = PGTrigger(
+        schema="public",
+        signature="external_url_description_vector",
+        on_entity="public.external_url",
+        is_constraint=False,
+        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)",
+    )
+    op.create_entity(public_external_url_external_url_description_vector)
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    public_external_url_external_url_description_vector = PGTrigger(
+        schema="public",
+        signature="external_url_description_vector",
+        on_entity="public.external_url",
+        is_constraint=False,
+        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)",
+    )
+    op.drop_entity(public_external_url_external_url_description_vector)
+
+    # ### end Alembic commands ###