temdb 3.0.0__py3-none-any.whl

temdb/migrations/versions/20260721_44f75ed44d66_updated_at_nullable_no_server_default.py

@@ -0,0 +1,165 @@
+"""updated_at nullable, no server_default
+
+Revision ID: 44f75ed44d66
+Revises: bec991e0d0eb
+Create Date: 2026-07-21 15:07:38.694622
+
+"""
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "44f75ed44d66"
+down_revision: str | Sequence[str] | None = "bec991e0d0eb"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "acquisition_tasks",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    op.alter_column(
+        "acquisitions",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    op.alter_column(
+        "blocks", "updated_at", existing_type=postgresql.TIMESTAMP(timezone=True), server_default=None, nullable=True
+    )
+    op.alter_column(
+        "cutting_sessions",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    op.alter_column(
+        "datasets", "updated_at", existing_type=postgresql.TIMESTAMP(timezone=True), server_default=None, nullable=True
+    )
+    op.alter_column(
+        "lens_corrections",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    op.alter_column(
+        "microscopes",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    op.alter_column(
+        "rois", "updated_at", existing_type=postgresql.TIMESTAMP(timezone=True), server_default=None, nullable=True
+    )
+    op.alter_column(
+        "sections", "updated_at", existing_type=postgresql.TIMESTAMP(timezone=True), server_default=None, nullable=True
+    )
+    op.alter_column(
+        "specimens", "updated_at", existing_type=postgresql.TIMESTAMP(timezone=True), server_default=None, nullable=True
+    )
+    op.alter_column(
+        "substrates",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=None,
+        nullable=True,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "substrates",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "specimens",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "sections",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "rois",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "microscopes",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "lens_corrections",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "datasets",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "cutting_sessions",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "blocks",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "acquisitions",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    op.alter_column(
+        "acquisition_tasks",
+        "updated_at",
+        existing_type=postgresql.TIMESTAMP(timezone=True),
+        server_default=sa.text("now()"),
+        nullable=False,
+    )
+    # ### end Alembic commands ###

temdb/migrations/versions/20260721_bec991e0d0eb_dataset_status_server_default.py

@@ -0,0 +1,38 @@
+"""dataset.status server_default
+
+Revision ID: bec991e0d0eb
+Revises: ec4c96d0bf77
+Create Date: 2026-07-21 14:12:14.207627
+
+"""
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "bec991e0d0eb"
+down_revision: str | Sequence[str] | None = "ec4c96d0bf77"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "datasets",
+        "status",
+        existing_type=sa.VARCHAR(),
+        server_default=sa.text("'collecting'"),
+        existing_nullable=False,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column("datasets", "status", existing_type=sa.VARCHAR(), server_default=None, existing_nullable=False)
+    # ### end Alembic commands ###

temdb/migrations/versions/20260801_a1d2f3e4b5c6_add_sections_run_parameters.py

@@ -0,0 +1,67 @@
+"""add sections.run_parameters and migrate legacy nested payload
+
+Revision ID: a1d2f3e4b5c6
+Revises: 44f75ed44d66
+Create Date: 2026-08-01 00:00:00.000000
+
+"""
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "a1d2f3e4b5c6"
+down_revision: str | Sequence[str] | None = "44f75ed44d66"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    op.add_column("sections", sa.Column("run_parameters", postgresql.JSONB(astext_type=sa.Text()), nullable=True))
+
+    op.execute(
+        sa.text(
+            """
+            UPDATE sections
+            SET run_parameters = section_metrics->'run_parameters'
+            WHERE run_parameters IS NULL
+              AND section_metrics IS NOT NULL
+              AND section_metrics ? 'run_parameters'
+            """
+        )
+    )
+
+    op.execute(
+        sa.text(
+            """
+            UPDATE sections
+            SET section_metrics = section_metrics - 'run_parameters'
+            WHERE section_metrics IS NOT NULL
+              AND section_metrics ? 'run_parameters'
+            """
+        )
+    )
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    op.execute(
+        sa.text(
+            """
+            UPDATE sections
+            SET section_metrics = jsonb_set(
+                COALESCE(section_metrics, '{}'::jsonb),
+                '{run_parameters}',
+                run_parameters,
+                true
+            )
+            WHERE run_parameters IS NOT NULL
+            """
+        )
+    )
+
+    op.drop_column("sections", "run_parameters")

temdb/server/__init__.py

@@ -0,0 +1,3 @@
+from temdb.server.main import create_app
+
+__all__ = ["create_app"]