Migrating objects: chore(postgresql): checkpoint safe runtime reduction baseline

.backend_reload_marker

@@ -0,0 +1 @@
+reloadMarker=1780572679.3509667

alembic/env.py

@@ -36,6 +36,7 @@
     tag_model,
     protocol_tag_assignment_model,
     protocol_step_model,
+    scipion_object_model,
 )
 
 target_metadata = Base.metadata

alembic/versions/1f8e5b400102_add_scipion_object_persistence_models.py

@@ -0,0 +1,249 @@
+"""add scipion object persistence models
+
+Revision ID: 1f8e5b400102
+Revises: 6806b9a72a6e
+Create Date: 2026-06-19 11:10:02.296385
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+
+# revision identifiers, used by Alembic.
+revision: str = "1f8e5b400102"
+down_revision: Union[str, None] = "6806b9a72a6e"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "scipion_object_types",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("className", sa.Text(), nullable=False),
+        sa.Column("moduleName", sa.Text(), nullable=True),
+        sa.Column("baseClassName", sa.Text(), nullable=True),
+        sa.Column("mapperKind", sa.Text(), server_default="tree", nullable=False),
+        sa.Column(
+            "schema",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), nullable=True),
+        sa.CheckConstraint("\"mapperKind\" IN ('tree', 'flat_set', 'scalar', 'pointer')", name="ck_scipion_object_types_mapper_kind"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("className"),
+    )
+    op.create_index("idx_scipion_object_types_className", "scipion_object_types", ["className"])
+    op.create_index("idx_scipion_object_types_mapperKind", "scipion_object_types", ["mapperKind"])
+    op.create_index(
+        "idx_scipion_object_types_schema_gin",
+        "scipion_object_types",
+        ["schema"],
+        postgresql_using="gin",
+    )
+    op.create_index(op.f("ix_scipion_object_types_id"), "scipion_object_types", ["id"])
+
+    op.create_table(
+        "scipion_object_type_properties",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("typeId", sa.Integer(), nullable=False),
+        sa.Column("propertyPath", sa.Text(), nullable=False),
+        sa.Column("className", sa.Text(), nullable=True),
+        sa.Column("valueKind", sa.Text(), nullable=True),
+        sa.Column("isPointer", sa.Boolean(), server_default="false", nullable=False),
+        sa.Column("isNested", sa.Boolean(), server_default="false", nullable=False),
+        sa.Column(
+            "schema",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), nullable=True),
+        sa.ForeignKeyConstraint(["typeId"], ["scipion_object_types.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("typeId", "propertyPath", name="ux_scipion_object_type_properties_type_path"),
+    )
+    op.create_index("idx_scipion_object_type_properties_path", "scipion_object_type_properties", ["propertyPath"])
+    op.create_index(
+        "idx_scipion_object_type_properties_schema_gin",
+        "scipion_object_type_properties",
+        ["schema"],
+        postgresql_using="gin",
+    )
+    op.create_index(op.f("ix_scipion_object_type_properties_id"), "scipion_object_type_properties", ["id"])
+
+    op.create_table(
+        "scipion_objects",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("projectId", sa.Integer(), nullable=False),
+        sa.Column("protocolDbId", sa.Integer(), nullable=True),
+        sa.Column("scipionObjId", sa.Integer(), nullable=False),
+        sa.Column("parentObjectId", sa.Integer(), nullable=True),
+        sa.Column("name", sa.Text(), nullable=True),
+        sa.Column("path", sa.Text(), nullable=False),
+        sa.Column("className", sa.Text(), nullable=False),
+        sa.Column("value", sa.Text(), nullable=True),
+        sa.Column("label", sa.Text(), nullable=True),
+        sa.Column("comment", sa.Text(), nullable=True),
+        sa.Column("creation", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "metadata",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), nullable=True),
+        sa.ForeignKeyConstraint(["parentObjectId"], ["scipion_objects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["projectId"], ["projects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["protocolDbId"], ["protocols.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("projectId", "protocolDbId", "path", name="ux_scipion_objects_project_protocol_path"),
+        sa.UniqueConstraint(
+            "projectId",
+            "protocolDbId",
+            "scipionObjId",
+            name="ux_scipion_objects_project_protocol_obj",
+        ),
+    )
+    op.create_index("idx_scipion_objects_metadata_gin", "scipion_objects", ["metadata"], postgresql_using="gin")
+    op.create_index("idx_scipion_objects_parent", "scipion_objects", ["parentObjectId"])
+    op.create_index("idx_scipion_objects_project_class", "scipion_objects", ["projectId", "className"])
+    op.create_index("idx_scipion_objects_project_protocol", "scipion_objects", ["projectId", "protocolDbId"])
+    op.create_index(op.f("ix_scipion_objects_id"), "scipion_objects", ["id"])
+
+    op.create_table(
+        "scipion_object_relations",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("projectId", sa.Integer(), nullable=False),
+        sa.Column("creatorObjectId", sa.Integer(), nullable=False),
+        sa.Column("parentObjectId", sa.Integer(), nullable=False),
+        sa.Column("childObjectId", sa.Integer(), nullable=False),
+        sa.Column("name", sa.Text(), nullable=False),
+        sa.Column("parentExtended", sa.Text(), nullable=True),
+        sa.Column("childExtended", sa.Text(), nullable=True),
+        sa.Column(
+            "metadata",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("creation", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.ForeignKeyConstraint(["childObjectId"], ["scipion_objects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["creatorObjectId"], ["scipion_objects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["parentObjectId"], ["scipion_objects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["projectId"], ["projects.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_scipion_object_relations_child", "scipion_object_relations", ["childObjectId"])
+    op.create_index(
+        "idx_scipion_object_relations_metadata_gin",
+        "scipion_object_relations",
+        ["metadata"],
+        postgresql_using="gin",
+    )
+    op.create_index("idx_scipion_object_relations_parent", "scipion_object_relations", ["parentObjectId"])
+    op.create_index("idx_scipion_object_relations_project_name", "scipion_object_relations", ["projectId", "name"])
+    op.create_index(op.f("ix_scipion_object_relations_id"), "scipion_object_relations", ["id"])
+
+    op.create_table(
+        "scipion_sets",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("projectId", sa.Integer(), nullable=False),
+        sa.Column("protocolDbId", sa.Integer(), nullable=True),
+        sa.Column("objectId", sa.Integer(), nullable=True),
+        sa.Column("outputName", sa.Text(), nullable=False),
+        sa.Column("setClassName", sa.Text(), nullable=False),
+        sa.Column("itemClassName", sa.Text(), nullable=False),
+        sa.Column(
+            "properties",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), nullable=True),
+        sa.ForeignKeyConstraint(["objectId"], ["scipion_objects.id"], ondelete="SET NULL"),
+        sa.ForeignKeyConstraint(["projectId"], ["projects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["protocolDbId"], ["protocols.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("projectId", "protocolDbId", "outputName", name="ux_scipion_sets_project_protocol_output"),
+    )
+    op.create_index("idx_scipion_sets_project_protocol", "scipion_sets", ["projectId", "protocolDbId"])
+    op.create_index("idx_scipion_sets_properties_gin", "scipion_sets", ["properties"], postgresql_using="gin")
+    op.create_index(op.f("ix_scipion_sets_id"), "scipion_sets", ["id"])
+
+    op.create_table(
+        "scipion_set_columns",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("setId", sa.Integer(), nullable=False),
+        sa.Column("labelProperty", sa.Text(), nullable=False),
+        sa.Column("columnName", sa.Text(), nullable=False),
+        sa.Column("className", sa.Text(), nullable=True),
+        sa.Column("valueType", sa.Text(), nullable=True),
+        sa.Column("position", sa.Integer(), nullable=False),
+        sa.Column("indexed", sa.Boolean(), server_default="false", nullable=False),
+        sa.ForeignKeyConstraint(["setId"], ["scipion_sets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("setId", "columnName", name="ux_scipion_set_columns_set_column"),
+        sa.UniqueConstraint("setId", "labelProperty", name="ux_scipion_set_columns_set_label"),
+    )
+    op.create_index("idx_scipion_set_columns_label", "scipion_set_columns", ["labelProperty"])
+    op.create_index(op.f("ix_scipion_set_columns_id"), "scipion_set_columns", ["id"])
+
+    op.create_table(
+        "scipion_set_items",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("setId", sa.Integer(), nullable=False),
+        sa.Column("scipionItemId", sa.Integer(), nullable=False),
+        sa.Column("enabled", sa.Boolean(), server_default="true", nullable=False),
+        sa.Column("label", sa.Text(), nullable=True),
+        sa.Column("comment", sa.Text(), nullable=True),
+        sa.Column("creation", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "values",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), nullable=True),
+        sa.ForeignKeyConstraint(["setId"], ["scipion_sets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("setId", "scipionItemId", name="ux_scipion_set_items_set_item"),
+    )
+    op.create_index("idx_scipion_set_items_set", "scipion_set_items", ["setId"])
+    op.create_index("idx_scipion_set_items_values_gin", "scipion_set_items", ["values"], postgresql_using="gin")
+    op.create_index(op.f("ix_scipion_set_items_id"), "scipion_set_items", ["id"])
+
+    op.create_table(
+        "scipion_set_properties",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("setId", sa.Integer(), nullable=False),
+        sa.Column("key", sa.Text(), nullable=False),
+        sa.Column("value", sa.Text(), nullable=True),
+        sa.ForeignKeyConstraint(["setId"], ["scipion_sets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("setId", "key", name="ux_scipion_set_properties_set_key"),
+    )
+    op.create_index("idx_scipion_set_properties_key", "scipion_set_properties", ["key"])
+    op.create_index(op.f("ix_scipion_set_properties_id"), "scipion_set_properties", ["id"])
+
+
+def downgrade() -> None:
+    op.drop_table("scipion_set_properties")
+    op.drop_table("scipion_set_items")
+    op.drop_table("scipion_set_columns")
+    op.drop_table("scipion_sets")
+    op.drop_table("scipion_object_relations")
+    op.drop_table("scipion_objects")
+    op.drop_table("scipion_object_type_properties")
+    op.drop_table("scipion_object_types")

alembic/versions/2fc2cd4da2e2_add_protocol_input_refs.py

@@ -0,0 +1,89 @@
+"""add protocol input refs
+
+Revision ID: 2fc2cd4da2e2
+Revises: 33ffae69565b
+Create Date: 2026-06-22 12:06:28.813389
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '2fc2cd4da2e2'
+down_revision: Union[str, None] = '33ffae69565b'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "protocol_input_refs",
+        sa.Column("projectId", sa.Integer(), nullable=False),
+        sa.Column("protocolDbId", sa.Integer(), nullable=False),
+        sa.Column("protocolId", sa.Text(), nullable=False),
+        sa.Column("inputName", sa.Text(), nullable=False),
+        sa.Column("itemIndex", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("parentProtocolDbId", sa.Integer(), nullable=True),
+        sa.Column("parentProtocolId", sa.Text(), nullable=True),
+        sa.Column("parentOutputName", sa.Text(), nullable=True),
+        sa.Column("objectClassName", sa.Text(), nullable=True),
+        sa.Column("objectId", sa.Text(), nullable=True),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), server_default=sa.text("now()"), nullable=False),
+        sa.PrimaryKeyConstraint(
+            "projectId",
+            "protocolDbId",
+            "inputName",
+            "itemIndex",
+            name="protocol_input_refs_pkey",
+        ),
+        sa.ForeignKeyConstraint(
+            ["projectId"],
+            ["projects.id"],
+            name="protocol_input_refs_projectId_fkey",
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["projectId", "protocolDbId"],
+            ["protocols.projectId", "protocols.id"],
+            name="protocol_input_refs_protocolDbId_fkey",
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["projectId", "parentProtocolDbId"],
+            ["protocols.projectId", "protocols.id"],
+            name="protocol_input_refs_parentProtocolDbId_fkey",
+            ondelete="CASCADE",
+        ),
+    )
+
+    op.create_index(
+        "idx_protocol_input_refs_protocol",
+        "protocol_input_refs",
+        ["projectId", "protocolDbId"],
+        unique=False,
+    )
+
+    op.create_index(
+        "idx_protocol_input_refs_parent",
+        "protocol_input_refs",
+        ["projectId", "parentProtocolDbId", "parentOutputName"],
+        unique=False,
+    )
+
+    op.create_index(
+        "idx_protocol_input_refs_parent_protocol_id",
+        "protocol_input_refs",
+        ["projectId", "parentProtocolId", "parentOutputName"],
+        unique=False,
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_protocol_input_refs_parent_protocol_id", table_name="protocol_input_refs")
+    op.drop_index("idx_protocol_input_refs_parent", table_name="protocol_input_refs")
+    op.drop_index("idx_protocol_input_refs_protocol", table_name="protocol_input_refs")
+    op.drop_table("protocol_input_refs")