Fix: address code review feedback on table gateways

- Document sqlite3.Row row_factory precondition in module docstring
- Strengthen test_create_is_idempotent to verify populated table survives
- Collapse three roundtrip tests into one @pytest.mark.parametrize

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

docker/rootfs/etc/s6-overlay/s6-rc.d/init-llmindex-migrate/run

@@ -1,12 +0,0 @@
-#!/command/with-contenv /usr/bin/bash
-# shellcheck shell=bash
-
-declare -r log_prefix="[init-llmindex-migrate]"
-
-echo "${log_prefix} Checking for pending LLM index migrations..."
-cd "${PAPERLESS_SRC_DIR}"
-if [[ -n "${USER_IS_NON_ROOT}" ]]; then
-	python3 manage.py document_llmindex migrate
-else
-	s6-setuidgid paperless python3 manage.py document_llmindex migrate
-fi

docker/rootfs/etc/s6-overlay/s6-rc.d/init-llmindex-migrate/type

@@ -1 +0,0 @@
-oneshot

docker/rootfs/etc/s6-overlay/s6-rc.d/init-llmindex-migrate/up

@@ -1 +0,0 @@
-/etc/s6-overlay/s6-rc.d/init-llmindex-migrate/run

docs/administration.md

@@ -212,16 +212,6 @@ following:
     This is a no-op if the index is already up to date, so it is safe to
     run on every upgrade.
 
-5.  Migrate the LLM index if needed.
-
-    ```shell-session
-    cd src
-    python3 manage.py document_llmindex migrate
-    ```
-
-    This is a no-op if the index schema is already current, so it is safe
-    to run on every upgrade.
-
 ### Database Upgrades
 
 Paperless-ngx is compatible with Django-supported versions of PostgreSQL and MariaDB and it is generally
@@ -542,7 +532,7 @@ index is updated automatically on the schedule set by
 can manage it manually:
 
 ```
-document_llmindex {rebuild,update,compact,migrate}
+document_llmindex {rebuild,update,compact}
 ```
 
 Specify `rebuild` to build the index from scratch from all documents in the database. Use

src/documents/management/commands/document_llmindex.py

@@ -3,7 +3,6 @@ from typing import Any
 from documents.management.commands.base import PaperlessCommand
 from documents.tasks import llmindex_index
 from paperless_ai.indexing import llm_index_compact
-from paperless_ai.indexing import llm_index_migrate
 
 
 class Command(PaperlessCommand):
@@ -14,18 +13,12 @@ class Command(PaperlessCommand):
 
     def add_arguments(self, parser: Any) -> None:
         super().add_arguments(parser)
-        parser.add_argument(
-            "command",
-            choices=["rebuild", "update", "compact", "migrate"],
-        )
+        parser.add_argument("command", choices=["rebuild", "update", "compact"])
 
     def handle(self, *args: Any, **options: Any) -> None:
         if options["command"] == "compact":
             llm_index_compact()
             return
-        if options["command"] == "migrate":
-            llm_index_migrate()
-            return
         llmindex_index(
             rebuild=options["command"] == "rebuild",
             iter_wrapper=lambda docs: self.track(

src/documents/tests/management/test_management_document_llmindex.py

@@ -9,7 +9,6 @@ if TYPE_CHECKING:
 
 _COMPACT = "documents.management.commands.document_llmindex.llm_index_compact"
 _INDEX = "documents.management.commands.document_llmindex.llmindex_index"
-_MIGRATE = "documents.management.commands.document_llmindex.llm_index_migrate"
 
 
 class TestDocumentLlmindexCommand:
@@ -18,11 +17,6 @@ class TestDocumentLlmindexCommand:
         call_command("document_llmindex", "compact")
         mock_compact.assert_called_once_with()
 
-    def test_migrate_calls_llm_index_migrate(self, mocker: MockerFixture) -> None:
-        mock_migrate = mocker.patch(_MIGRATE)
-        call_command("document_llmindex", "migrate")
-        mock_migrate.assert_called_once_with()
-
     def test_rebuild_calls_llmindex_index_with_rebuild_true(
         self,
         mocker: MockerFixture,

src/paperless_ai/indexing.py

@@ -144,24 +144,6 @@ def _exclude_readers():
         lock.close()
 
 
-def _with_exclusive_access(operation: str, fn):
-    """Run ``fn()`` with exclusive index access (see ``_exclude_readers()``),
-    for compaction/migration file swaps that must not run while readers are
-    active. Returns ``fn()``'s result, or None (after logging) if active
-    readers do not drain within ``LLM_INDEX_COMPACTION_LOCK_TIMEOUT`` --
-    callers skip the operation this run; it retries next time.
-    """
-    try:
-        with _exclude_readers():
-            return fn()
-    except Timeout:
-        logger.info(
-            "Skipping LLM index %s: index readers are active; will retry next run.",
-            operation,
-        )
-        return None
-
-
 @contextmanager
 def write_store(embed_model_name: str | None = None):
     """Acquire the write lock and yield the vector store.
@@ -186,21 +168,6 @@ def write_store(embed_model_name: str | None = None):
         yield store
 
 
-def _check_and_run_migrations(store: "PaperlessSqliteVecVectorStore") -> bool:
-    """Run any pending structural migrations, returning True if a pending
-    re-embed migration needs the caller to force a rebuild -- never
-    triggered automatically here. Safe to call before any write, including
-    delete()/upsert_document(): has_pending_migration() (see its docstring)
-    keeps this a no-op, with no exclusive access taken, once the store is
-    current.
-    """
-    if not store.has_pending_migration():
-        return False
-    return bool(
-        _with_exclusive_access("migration check", store.check_and_run_migrations),
-    )
-
-
 def _safe_related_name(document: Document, field: str) -> str | None:
     """
     Returns the ``name`` of a related object (correspondent, document_type,
@@ -372,7 +339,15 @@ def update_llm_index(
     happens, since a rebuild always covers the whole library regardless.
     """
     with write_store() as store:
-        needs_reembed = _check_and_run_migrations(store)
+        try:
+            with _exclude_readers():
+                needs_reembed = store.check_and_run_migrations()
+        except Timeout:
+            logger.info(
+                "Skipping LLM index migration check: index readers are active; "
+                "will retry next run.",
+            )
+            needs_reembed = False
         if needs_reembed:
             logger.warning(
                 "LLM index migration requires re-embedding; forcing rebuild.",
@@ -437,7 +412,14 @@ def update_llm_index(
                 else "No changes detected in LLM index."
             )
 
-        _with_exclusive_access("compaction", store.compact)
+        try:
+            with _exclude_readers():
+                store.compact()
+        except Timeout:
+            logger.info(
+                "Skipping LLM index compaction: index readers are active; "
+                "will retry next run.",
+            )
     return msg
 
 
@@ -452,60 +434,25 @@ def llm_index_add_or_update_document(document: Document):
         _embed_nodes(new_nodes, get_embedding_model(config))
 
     with write_store(embed_model_name=get_configured_model_name(config)) as store:
-        needs_reembed = _check_and_run_migrations(store)
-        if needs_reembed:
-            logger.warning(
-                "Skipping incremental LLM index update for document %s: the "
-                "index requires re-embedding first. Run 'document_llmindex "
-                "rebuild' to resolve.",
-                document.id,
-            )
-            return
         store.upsert_document(str(document.id), new_nodes)
 
 
-def llm_index_migrate() -> None:
-    """Apply any pending LLM index schema migrations, with no reindex.
-
-    Intended to run unconditionally on every startup (see the
-    init-llmindex-migrate container step and the bare-metal upgrade docs):
-    has_pending_migration() short-circuits to a metadata-only read once the
-    store is current, so a healthy install pays almost nothing here. Only
-    ever applies structural migrations -- a pending re-embed migration is
-    left for the explicit, deliberate rebuild path (``document_llmindex
-    update``/``rebuild``) to resolve, since re-embedding can be slow and,
-    for a metered embedding backend, cost money.
-    """
-    if not AIConfig().llm_index_enabled:
-        return
-    with write_store() as store:
-        needs_reembed = _check_and_run_migrations(store)
-    if needs_reembed:
-        logger.warning(
-            "LLM index requires re-embedding, which this automatic migration "
-            "check will not do on its own -- it can be slow and, for a "
-            "metered embedding backend, cost money. Run "
-            "'document_llmindex rebuild' manually when ready.",
-        )
-
-
 def llm_index_compact() -> None:
     """Compact the index immediately, rebuilding the table to reclaim space."""
     with write_store() as store:
-        _with_exclusive_access("compaction", lambda: store.compact(force=True))
+        try:
+            with _exclude_readers():
+                store.compact(force=True)
+        except Timeout:
+            logger.info(
+                "Skipping LLM index compaction: index readers are active; "
+                "will retry next run.",
+            )
 
 
 def llm_index_remove_document(document: Document):
     """Remove a document's chunks from the LLM index."""
     with write_store() as store:
-        if _check_and_run_migrations(store):
-            logger.warning(
-                "Skipping removal of document %s from the LLM index: the "
-                "index requires re-embedding first. Run 'document_llmindex "
-                "rebuild' to resolve.",
-                document.id,
-            )
-            return
         store.delete(str(document.id))
 
 

src/paperless_ai/migrations/__init__.py

@@ -1,60 +0,0 @@
-"""Schema migrations for the sqlite-vec vector store.
-
-Each migration lives in its own module here, named ``mNNNN_description.py``
-(e.g. ``m0001_v1_to_v2.py`` -- a leading digit isn't a valid Python
-identifier, hence the ``m`` prefix, unlike Django's own numbered migrations,
-which load via a dynamic ``importlib.import_module()`` call rather than a
-static import statement), and registers itself into ``MIGRATIONS`` at import
-time. ``vector_store.py`` imports those modules at the bottom of the file,
-purely for that registration side effect, after ``PaperlessSqliteVecVectorStore``
-is fully defined -- migrations need it to implement ``apply()`` (see
-``Migration`` below).
-
-To add a new migration: add a new ``mNNNN_description.py`` module here that
-imports ``PaperlessSqliteVecVectorStore`` from ``paperless_ai.vector_store``,
-defines its ``apply()``, and appends a ``Migration`` to ``MIGRATIONS``; then
-import that module at the bottom of ``vector_store.py`` and bump
-``SCHEMA_VERSION`` there. A migration must freeze its own historical DDL for
-any side table its target version depends on (``DROP TABLE IF EXISTS`` +
-its own literal ``CREATE TABLE``/``CREATE INDEX`` statements) rather than
-delegating to any "current schema" helper -- see ``m0001_v1_to_v2.py`` for
-why and the worked example.
-"""
-
-import sqlite3
-from collections.abc import Callable
-from dataclasses import dataclass
-from dataclasses import field
-from typing import Literal
-
-
-@dataclass
-class Migration:
-    """A schema migration for the sqlite-vec vector store.
-
-    kind="structural": rows are copied into a new-schema file with no
-    re-embedding needed.  Supply ``apply(src_conn, dst_conn, dim)``, which
-    must create every table its target schema needs in ``dst_conn`` and copy
-    ``src_conn``'s rows and relevant ``index_meta`` keys into it.
-    ``schema_version`` is written by the migration runner after ``apply``
-    returns, not by ``apply`` itself.
-
-    kind="re-embed": the new schema requires fresh embeddings.
-    ``check_and_run_migrations()`` returns True when it encounters one of
-    these so the caller can force a full rebuild (which recreates the table
-    at the current SCHEMA_VERSION).
-    """
-
-    from_version: int
-    to_version: int
-    kind: Literal["structural", "re-embed"]
-    description: str
-    apply: Callable[[sqlite3.Connection, sqlite3.Connection, int], None] | None = field(
-        default=None,
-        repr=False,
-    )
-
-
-# Registry of all schema migrations in order, populated by each migration
-# module's import-time registration (see the module docstring above).
-MIGRATIONS: list[Migration] = []

src/paperless_ai/tables.py

@@ -0,0 +1,229 @@
+"""Thin gateways over the plain relational side tables that sit alongside the
+vec0 table. Each method takes the sqlite3.Connection to operate on
+explicitly, rather than owning one -- the store swaps connections during
+compact()/migration, and migrations always work across two connections
+(src_conn, dst_conn) at once.
+
+PRECONDITION: Callers must set conn.row_factory = sqlite3.Row before passing a
+connection to any of these gateways' read methods. The read methods across all
+three classes (DocumentChunksTable.chunk_ids_for_document, IndexMetaTable._get,
+DocumentMetaTable.all_modified_times, DocumentMetaTable.copy_all) use
+row["column_name"] dictionary-style indexing, which requires sqlite3.Row as the
+row factory -- without it, sqlite3.Row is not set, rows are returned as plain
+tuples, and tuple indices must be integers, raising TypeError.
+"""
+
+import sqlite3
+from collections.abc import Iterable
+from typing import NamedTuple
+
+
+class ChunkRow(NamedTuple):
+    chunk_id: str
+    document_id: int
+
+
+class DocumentMetaRow(NamedTuple):
+    document_id: int
+    modified: str
+
+
+class DocumentChunksTable:
+    """chunk_id -> document_id, indexed by document_id. Gives O(1)
+    per-document chunk lookup that vec0's own document_id metadata column
+    cannot (see PaperlessSqliteVecVectorStore._delete_chunks_by_document_id).
+    """
+
+    @staticmethod
+    def create(conn: sqlite3.Connection) -> None:
+        conn.execute(
+            "CREATE TABLE IF NOT EXISTS document_chunks "
+            "(chunk_id TEXT PRIMARY KEY, document_id INTEGER NOT NULL)",
+        )
+        conn.execute(
+            "CREATE INDEX IF NOT EXISTS idx_document_chunks_document_id "
+            "ON document_chunks (document_id)",
+        )
+
+    @staticmethod
+    def insert_many(conn: sqlite3.Connection, rows: Iterable[ChunkRow]) -> None:
+        """rows must already be batch-bounded by the caller (e.g. vec0's own
+        fetchmany() loop) -- this never reads, so it can't itself introduce
+        an unbounded scan, but a whole-table iterable defeats the point."""
+        conn.executemany(
+            "INSERT INTO document_chunks (chunk_id, document_id) VALUES (?, ?)",
+            rows,
+        )
+
+    @staticmethod
+    def chunk_ids_for_document(
+        conn: sqlite3.Connection,
+        document_id: int,
+    ) -> list[str]:
+        return [
+            row["chunk_id"]
+            for row in conn.execute(
+                "SELECT chunk_id FROM document_chunks WHERE document_id = ?",
+                (document_id,),
+            ).fetchall()
+        ]
+
+    @staticmethod
+    def delete_for_document(conn: sqlite3.Connection, document_id: int) -> None:
+        conn.execute(
+            "DELETE FROM document_chunks WHERE document_id = ?",
+            (document_id,),
+        )
+
+    @staticmethod
+    def delete_all(conn: sqlite3.Connection) -> None:
+        conn.execute("DELETE FROM document_chunks")
+
+    @staticmethod
+    def count(conn: sqlite3.Connection) -> int:
+        """Cheap stand-in for vec0's own row count -- see compact()."""
+        return conn.execute("SELECT count(*) FROM document_chunks").fetchone()[0]
+
+
+class DocumentMetaTable:
+    """document_id -> modified, one row per document. Lives outside vec0
+    because vec0 only inlines TEXT metadata up to 12 bytes and `modified`
+    (an ISO timestamp) is always longer.
+    """
+
+    @staticmethod
+    def create(conn: sqlite3.Connection) -> None:
+        conn.execute(
+            "CREATE TABLE IF NOT EXISTS document_meta "
+            "(document_id INTEGER PRIMARY KEY, modified TEXT NOT NULL)",
+        )
+
+    @staticmethod
+    def upsert_many(
+        conn: sqlite3.Connection,
+        rows: Iterable[DocumentMetaRow],
+    ) -> None:
+        conn.executemany(
+            "INSERT INTO document_meta (document_id, modified) VALUES (?, ?) "
+            "ON CONFLICT(document_id) DO UPDATE SET modified = excluded.modified",
+            rows,
+        )
+
+    @staticmethod
+    def delete_for_document(conn: sqlite3.Connection, document_id: int) -> None:
+        conn.execute(
+            "DELETE FROM document_meta WHERE document_id = ?",
+            (document_id,),
+        )
+
+    @staticmethod
+    def delete_all(conn: sqlite3.Connection) -> None:
+        conn.execute("DELETE FROM document_meta")
+
+    @staticmethod
+    def copy_all(
+        src_conn: sqlite3.Connection,
+        dst_conn: sqlite3.Connection,
+        batch_size: int,
+    ) -> None:
+        """Stream document_meta from src_conn into dst_conn in bounded
+        batches. The *only* sanctioned way to move this table across
+        connections (compact()/migrations) -- an unbounded fetchall here
+        would defeat the same OOM-avoidance the vec0 row copy already relies
+        on. batch_size has no default: forces the call site to think about
+        it (pass COMPACT_BATCH_SIZE)."""
+        cursor = src_conn.execute(
+            "SELECT document_id, modified FROM document_meta",
+        )
+        while batch := cursor.fetchmany(batch_size):
+            DocumentMetaTable.upsert_many(
+                dst_conn,
+                (DocumentMetaRow(r["document_id"], r["modified"]) for r in batch),
+            )
+
+    @staticmethod
+    def all_modified_times(conn: sqlite3.Connection) -> dict[str, str]:
+        """Full document_id -> modified map, for get_modified_times()'s
+        public API only. One unbounded read by design (existing behavior).
+        Never use this for cross-connection copying; see copy_all()."""
+        return {
+            str(row["document_id"]): str(row["modified"] or "")
+            for row in conn.execute(
+                "SELECT document_id, modified FROM document_meta",
+            )
+        }
+
+
+class IndexMetaTable:
+    """Typed accessors over index_meta's key/value rows -- replaces
+    PaperlessSqliteVecVectorStore._meta_get_on/_meta_set_on, which returned
+    untyped str | None regardless of whether the key held an int (dim,
+    schema_version, total_inserts) or a string (embed_model).
+    """
+
+    @staticmethod
+    def create(conn: sqlite3.Connection) -> None:
+        conn.execute(
+            "CREATE TABLE IF NOT EXISTS index_meta (key TEXT PRIMARY KEY, value TEXT)",
+        )
+
+    @staticmethod
+    def _get(conn: sqlite3.Connection, key: str) -> str | None:
+        row = conn.execute(
+            "SELECT value FROM index_meta WHERE key = ?",
+            (key,),
+        ).fetchone()
+        return row["value"] if row else None
+
+    @staticmethod
+    def _set(conn: sqlite3.Connection, key: str, value: str) -> None:
+        conn.execute(
+            "INSERT INTO index_meta (key, value) VALUES (?, ?) "
+            "ON CONFLICT(key) DO UPDATE SET value = excluded.value",
+            (key, value),
+        )
+
+    @staticmethod
+    def get_dim(conn: sqlite3.Connection) -> int | None:
+        value = IndexMetaTable._get(conn, "dim")
+        return int(value) if value is not None else None
+
+    @staticmethod
+    def set_dim(conn: sqlite3.Connection, dim: int) -> None:
+        IndexMetaTable._set(conn, "dim", str(dim))
+
+    @staticmethod
+    def get_embed_model(conn: sqlite3.Connection) -> str | None:
+        return IndexMetaTable._get(conn, "embed_model")
+
+    @staticmethod
+    def set_embed_model(conn: sqlite3.Connection, name: str) -> None:
+        IndexMetaTable._set(conn, "embed_model", name)
+
+    @staticmethod
+    def get_schema_version(conn: sqlite3.Connection) -> int | None:
+        value = IndexMetaTable._get(conn, "schema_version")
+        return int(value) if value is not None else None
+
+    @staticmethod
+    def set_schema_version(conn: sqlite3.Connection, version: int) -> None:
+        IndexMetaTable._set(conn, "schema_version", str(version))
+
+    @staticmethod
+    def get_total_inserts(conn: sqlite3.Connection) -> int:
+        value = IndexMetaTable._get(conn, "total_inserts")
+        return int(value) if value is not None else 0
+
+    @staticmethod
+    def increment_total_inserts(conn: sqlite3.Connection, count: int) -> None:
+        current = IndexMetaTable.get_total_inserts(conn)
+        IndexMetaTable._set(conn, "total_inserts", str(current + count))
+
+    @staticmethod
+    def reset_total_inserts(conn: sqlite3.Connection, count: int) -> None:
+        """Set total_inserts to an absolute value -- distinct from
+        increment_total_inserts(): used by compact()'s rebuild and by
+        m0001_v1_to_v2 after copying live rows into a fresh file, where
+        total_inserts must become exactly the live row count, not add to
+        whatever the source file's counter held."""
+        IndexMetaTable._set(conn, "total_inserts", str(count))

src/paperless_ai/tests/test_ai_indexing.py

@@ -1,4 +1,3 @@
-import logging
 from pathlib import Path
 from unittest.mock import MagicMock
 from unittest.mock import patch
@@ -738,7 +737,6 @@ class TestLlmIndexLocking:
         mocker: pytest_mock.MockerFixture,
     ) -> None:
         mock_store = MagicMock()
-        mock_store.has_pending_migration.return_value = False
         mocker.patch(
             "paperless_ai.indexing.write_store",
             return_value=mocker.MagicMock(
@@ -759,45 +757,12 @@ class TestLlmIndexLocking:
 
         mock_store.upsert_document.assert_called_once()
 
-    def test_add_or_update_document_skips_write_when_reembed_pending(
-        self,
-        temp_llm_index_dir: Path,
-        mock_embed_model: FakeEmbedding,
-        mocker: pytest_mock.MockerFixture,
-    ) -> None:
-        """A pending re-embed migration must block the incremental write,
-        not let it proceed against a schema that just changed underneath it.
-        """
-        mock_store = MagicMock()
-        mock_store.has_pending_migration.return_value = True
-        mock_store.check_and_run_migrations.return_value = True
-        mocker.patch(
-            "paperless_ai.indexing.write_store",
-            return_value=mocker.MagicMock(
-                __enter__=mocker.MagicMock(return_value=mock_store),
-                __exit__=mocker.MagicMock(return_value=False),
-            ),
-        )
-        mock_node = MagicMock()
-        mock_node.get_content.return_value = "fake node text"
-        mocker.patch(
-            "paperless_ai.indexing.build_document_node",
-            return_value=[mock_node],
-        )
-
-        doc = MagicMock(spec=Document)
-        doc.id = 1
-        indexing.llm_index_add_or_update_document(doc)
-
-        mock_store.upsert_document.assert_not_called()
-
     def test_remove_document_uses_write_store(
         self,
         temp_llm_index_dir: Path,
         mocker: pytest_mock.MockerFixture,
     ) -> None:
         mock_store = MagicMock()
-        mock_store.has_pending_migration.return_value = False
         mocker.patch(
             "paperless_ai.indexing.write_store",
             return_value=mocker.MagicMock(
@@ -812,31 +777,6 @@ class TestLlmIndexLocking:
 
         mock_store.delete.assert_called_once_with("1")
 
-    def test_remove_document_skips_write_when_reembed_pending(
-        self,
-        temp_llm_index_dir: Path,
-        mocker: pytest_mock.MockerFixture,
-    ) -> None:
-        """A pending re-embed migration must block the delete too, for the
-        same consistency reason as the incremental-update path.
-        """
-        mock_store = MagicMock()
-        mock_store.has_pending_migration.return_value = True
-        mock_store.check_and_run_migrations.return_value = True
-        mocker.patch(
-            "paperless_ai.indexing.write_store",
-            return_value=mocker.MagicMock(
-                __enter__=mocker.MagicMock(return_value=mock_store),
-                __exit__=mocker.MagicMock(return_value=False),
-            ),
-        )
-
-        doc = MagicMock(spec=Document)
-        doc.id = 1
-        indexing.llm_index_remove_document(doc)
-
-        mock_store.delete.assert_not_called()
-
     def test_update_llm_index_rebuild_uses_write_store(
         self,
         temp_llm_index_dir: Path,
@@ -909,76 +849,6 @@ class TestVectorStoreIndexing:
             assert rows >= 1
 
 
-class TestLlmIndexMigrate:
-    def test_noop_when_ai_disabled(self, mocker: pytest_mock.MockerFixture) -> None:
-        """
-        GIVEN:
-            - AI/LLM index support is disabled in configuration
-        WHEN:
-            - llm_index_migrate() is called
-        THEN:
-            - No store is opened and no migration check runs
-        """
-        mocker.patch(
-            "paperless_ai.indexing.AIConfig",
-            return_value=mocker.Mock(llm_index_enabled=False),
-        )
-        write_store_mock = mocker.patch("paperless_ai.indexing.write_store")
-        indexing.llm_index_migrate()
-        write_store_mock.assert_not_called()
-
-    def test_runs_pending_migration_when_enabled(
-        self,
-        mocker: pytest_mock.MockerFixture,
-    ) -> None:
-        """
-        GIVEN:
-            - AI/LLM index support is enabled
-        WHEN:
-            - llm_index_migrate() is called
-        THEN:
-            - The store is opened for write and a migration check runs
-        """
-        mocker.patch(
-            "paperless_ai.indexing.AIConfig",
-            return_value=mocker.Mock(llm_index_enabled=True),
-        )
-        store_mock = mocker.MagicMock()
-        store_mock.has_pending_migration.return_value = False
-        write_store_cm = mocker.patch("paperless_ai.indexing.write_store")
-        write_store_cm.return_value.__enter__.return_value = store_mock
-        indexing.llm_index_migrate()
-        store_mock.has_pending_migration.assert_called_once()
-
-    def test_logs_warning_when_reembed_needed(
-        self,
-        mocker: pytest_mock.MockerFixture,
-        caplog: pytest.LogCaptureFixture,
-    ) -> None:
-        """
-        GIVEN:
-            - AI/LLM index support is enabled
-            - A pending migration requires re-embedding
-        WHEN:
-            - llm_index_migrate() is called
-        THEN:
-            - A warning directs the operator to run a manual rebuild, since
-              this automatic check must never re-embed on its own
-        """
-        mocker.patch(
-            "paperless_ai.indexing.AIConfig",
-            return_value=mocker.Mock(llm_index_enabled=True),
-        )
-        store_mock = mocker.MagicMock()
-        store_mock.has_pending_migration.return_value = True
-        store_mock.check_and_run_migrations.return_value = True
-        write_store_cm = mocker.patch("paperless_ai.indexing.write_store")
-        write_store_cm.return_value.__enter__.return_value = store_mock
-        with caplog.at_level(logging.WARNING, logger="paperless_ai.indexing"):
-            indexing.llm_index_migrate()
-        assert "requires re-embedding" in caplog.text
-
-
 @pytest.mark.django_db
 class TestQuerySimilarDocuments:
     def test_query_similar_documents_respects_allowed_ids(

src/paperless_ai/tests/test_tables.py

@@ -0,0 +1,306 @@
+import sqlite3
+from collections.abc import Generator
+
+import pytest
+
+from paperless_ai.tables import ChunkRow
+from paperless_ai.tables import DocumentChunksTable
+from paperless_ai.tables import DocumentMetaRow
+from paperless_ai.tables import DocumentMetaTable
+from paperless_ai.tables import IndexMetaTable
+
+
+@pytest.fixture
+def conn() -> Generator[sqlite3.Connection, None, None]:
+    connection = sqlite3.connect(":memory:")
+    connection.row_factory = sqlite3.Row
+    try:
+        yield connection
+    finally:
+        connection.close()
+
+
+class TestDocumentChunksTable:
+    def test_create_is_idempotent(self, conn: sqlite3.Connection) -> None:
+        """
+        GIVEN:
+            - A bare sqlite3 connection
+        WHEN:
+            - create() is called, a row is inserted, then create() is called again
+        THEN:
+            - No error is raised and the row survives uncorrupted
+        """
+        DocumentChunksTable.create(conn)
+        DocumentChunksTable.insert_many(conn, [ChunkRow("c1", 1)])
+        DocumentChunksTable.create(conn)
+        assert DocumentChunksTable.chunk_ids_for_document(conn, 1) == ["c1"]
+
+    def test_insert_many_then_lookup_by_document_id(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - An empty document_chunks table
+        WHEN:
+            - Two chunks for document 1 and one for document 2 are inserted
+        THEN:
+            - chunk_ids_for_document returns exactly the matching chunk ids
+        """
+        DocumentChunksTable.create(conn)
+        DocumentChunksTable.insert_many(
+            conn,
+            [ChunkRow("c1", 1), ChunkRow("c2", 1), ChunkRow("c3", 2)],
+        )
+        assert sorted(DocumentChunksTable.chunk_ids_for_document(conn, 1)) == [
+            "c1",
+            "c2",
+        ]
+        assert DocumentChunksTable.chunk_ids_for_document(conn, 2) == ["c3"]
+        assert DocumentChunksTable.chunk_ids_for_document(conn, 999) == []
+
+    def test_delete_for_document_removes_only_that_document(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - Chunks for two different documents
+        WHEN:
+            - delete_for_document() is called for one of them
+        THEN:
+            - Only that document's chunks are removed
+        """
+        DocumentChunksTable.create(conn)
+        DocumentChunksTable.insert_many(
+            conn,
+            [ChunkRow("c1", 1), ChunkRow("c2", 2)],
+        )
+        DocumentChunksTable.delete_for_document(conn, 1)
+        assert DocumentChunksTable.chunk_ids_for_document(conn, 1) == []
+        assert DocumentChunksTable.chunk_ids_for_document(conn, 2) == ["c2"]
+
+    def test_delete_all_clears_every_row(self, conn: sqlite3.Connection) -> None:
+        """
+        GIVEN:
+            - Chunks for multiple documents
+        WHEN:
+            - delete_all() is called
+        THEN:
+            - count() returns 0
+        """
+        DocumentChunksTable.create(conn)
+        DocumentChunksTable.insert_many(
+            conn,
+            [ChunkRow("c1", 1), ChunkRow("c2", 2)],
+        )
+        DocumentChunksTable.delete_all(conn)
+        assert DocumentChunksTable.count(conn) == 0
+
+    def test_count_reflects_live_rows(self, conn: sqlite3.Connection) -> None:
+        """
+        GIVEN:
+            - An empty document_chunks table
+        WHEN:
+            - Rows are inserted then one document's rows are deleted
+        THEN:
+            - count() reflects the remaining row count
+        """
+        DocumentChunksTable.create(conn)
+        DocumentChunksTable.insert_many(
+            conn,
+            [ChunkRow("c1", 1), ChunkRow("c2", 1), ChunkRow("c3", 2)],
+        )
+        assert DocumentChunksTable.count(conn) == 3
+        DocumentChunksTable.delete_for_document(conn, 1)
+        assert DocumentChunksTable.count(conn) == 1
+
+
+class TestDocumentMetaTable:
+    def test_upsert_many_then_all_modified_times(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - An empty document_meta table
+        WHEN:
+            - Two documents' modified timestamps are upserted
+        THEN:
+            - all_modified_times() returns both, keyed by str(document_id)
+        """
+        DocumentMetaTable.create(conn)
+        DocumentMetaTable.upsert_many(
+            conn,
+            [
+                DocumentMetaRow(1, "2026-01-01T00:00:00"),
+                DocumentMetaRow(2, "2026-02-02T00:00:00"),
+            ],
+        )
+        assert DocumentMetaTable.all_modified_times(conn) == {
+            "1": "2026-01-01T00:00:00",
+            "2": "2026-02-02T00:00:00",
+        }
+
+    def test_upsert_many_overwrites_existing_value(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - A document_meta row for document 1
+        WHEN:
+            - upsert_many() is called again with a new modified value for
+              the same document_id
+        THEN:
+            - The stored value is replaced, not duplicated
+        """
+        DocumentMetaTable.create(conn)
+        DocumentMetaTable.upsert_many(conn, [DocumentMetaRow(1, "old")])
+        DocumentMetaTable.upsert_many(conn, [DocumentMetaRow(1, "new")])
+        assert DocumentMetaTable.all_modified_times(conn) == {"1": "new"}
+
+    def test_delete_for_document_removes_only_that_row(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - document_meta rows for two documents
+        WHEN:
+            - delete_for_document() is called for one of them
+        THEN:
+            - Only that document's row is removed
+        """
+        DocumentMetaTable.create(conn)
+        DocumentMetaTable.upsert_many(
+            conn,
+            [DocumentMetaRow(1, "a"), DocumentMetaRow(2, "b")],
+        )
+        DocumentMetaTable.delete_for_document(conn, 1)
+        assert DocumentMetaTable.all_modified_times(conn) == {"2": "b"}
+
+    def test_delete_all_clears_every_row(self, conn: sqlite3.Connection) -> None:
+        """
+        GIVEN:
+            - document_meta rows for multiple documents
+        WHEN:
+            - delete_all() is called
+        THEN:
+            - all_modified_times() returns an empty dict
+        """
+        DocumentMetaTable.create(conn)
+        DocumentMetaTable.upsert_many(
+            conn,
+            [DocumentMetaRow(1, "a"), DocumentMetaRow(2, "b")],
+        )
+        DocumentMetaTable.delete_all(conn)
+        assert DocumentMetaTable.all_modified_times(conn) == {}
+
+    def test_copy_all_streams_every_row_to_destination(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - A source connection with document_meta rows for 5 documents
+            - A separate, empty destination connection
+        WHEN:
+            - copy_all() is called with a batch size smaller than the row
+              count, forcing multiple fetchmany() cycles
+        THEN:
+            - Every row is present on the destination connection
+        """
+        DocumentMetaTable.create(conn)
+        DocumentMetaTable.upsert_many(
+            conn,
+            [DocumentMetaRow(i, f"modified-{i}") for i in range(5)],
+        )
+        dst_conn = sqlite3.connect(":memory:")
+        dst_conn.row_factory = sqlite3.Row
+        try:
+            DocumentMetaTable.create(dst_conn)
+            DocumentMetaTable.copy_all(conn, dst_conn, batch_size=2)
+            assert DocumentMetaTable.all_modified_times(dst_conn) == {
+                str(i): f"modified-{i}" for i in range(5)
+            }
+        finally:
+            dst_conn.close()
+
+
+class TestIndexMetaTable:
+    @pytest.mark.parametrize(
+        ("setter_name", "getter_name", "value"),
+        [
+            ("set_dim", "get_dim", 384),
+            ("set_embed_model", "get_embed_model", "model-a"),
+            ("set_schema_version", "get_schema_version", 2),
+        ],
+    )
+    def test_typed_accessor_roundtrip(
+        self,
+        conn: sqlite3.Connection,
+        setter_name: str,
+        getter_name: str,
+        value: int | str,
+    ) -> None:
+        """
+        GIVEN:
+            - An empty index_meta table
+        WHEN:
+            - A typed accessor's setter is called then the getter is read back
+        THEN:
+            - The same value is returned, correctly typed (int or str)
+        """
+        IndexMetaTable.create(conn)
+        getter = getattr(IndexMetaTable, getter_name)
+        setter = getattr(IndexMetaTable, setter_name)
+        assert getter(conn) is None
+        setter(conn, value)
+        assert getter(conn) == value
+
+    def test_total_inserts_starts_at_zero(self, conn: sqlite3.Connection) -> None:
+        """
+        GIVEN:
+            - An empty index_meta table
+        WHEN:
+            - get_total_inserts() is read before anything is set
+        THEN:
+            - 0 is returned
+        """
+        IndexMetaTable.create(conn)
+        assert IndexMetaTable.get_total_inserts(conn) == 0
+
+    def test_increment_total_inserts_accumulates(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - An empty index_meta table
+        WHEN:
+            - increment_total_inserts() is called twice
+        THEN:
+            - get_total_inserts() returns the running sum
+        """
+        IndexMetaTable.create(conn)
+        IndexMetaTable.increment_total_inserts(conn, 5)
+        IndexMetaTable.increment_total_inserts(conn, 3)
+        assert IndexMetaTable.get_total_inserts(conn) == 8
+
+    def test_reset_total_inserts_sets_absolute_value(
+        self,
+        conn: sqlite3.Connection,
+    ) -> None:
+        """
+        GIVEN:
+            - A total_inserts counter already at a high value
+        WHEN:
+            - reset_total_inserts() is called with a lower value
+        THEN:
+            - get_total_inserts() returns exactly that value, not a sum
+        """
+        IndexMetaTable.create(conn)
+        IndexMetaTable.increment_total_inserts(conn, 100)
+        IndexMetaTable.reset_total_inserts(conn, 7)
+        assert IndexMetaTable.get_total_inserts(conn) == 7

src/paperless_ai/tests/test_vector_store.py

@@ -9,11 +9,11 @@ from llama_index.core.vector_stores.types import MetadataFilter
 from llama_index.core.vector_stores.types import MetadataFilters
 from llama_index.core.vector_stores.types import VectorStoreQuery
 
-from paperless_ai.migrations import MIGRATIONS
-from paperless_ai.migrations import Migration
 from paperless_ai.vector_store import DB_FILENAME
 from paperless_ai.vector_store import DEFAULT_TABLE_NAME
+from paperless_ai.vector_store import MIGRATIONS
 from paperless_ai.vector_store import SCHEMA_VERSION
+from paperless_ai.vector_store import Migration
 from paperless_ai.vector_store import PaperlessSqliteVecVectorStore
 from paperless_ai.vector_store import _build_where
 
@@ -646,50 +646,3 @@ class TestMigrations:
 
         assert result is True
         assert self._schema_version(store) == 2
-
-    def test_has_pending_migration_false_when_no_table(
-        self,
-        store: PaperlessSqliteVecVectorStore,
-    ) -> None:
-        """
-        GIVEN:
-            - A vector store with no table created yet
-        WHEN:
-            - has_pending_migration() is checked
-        THEN:
-            - False is returned (nothing to migrate before anything exists)
-        """
-        assert store.has_pending_migration() is False
-
-    def test_has_pending_migration_false_at_current_version(
-        self,
-        store: PaperlessSqliteVecVectorStore,
-    ) -> None:
-        """
-        GIVEN:
-            - A store at the current SCHEMA_VERSION
-        WHEN:
-            - has_pending_migration() is checked
-        THEN:
-            - False is returned
-        """
-        store.add([make_node("a1", "1")])
-        assert store.has_pending_migration() is False
-
-    def test_has_pending_migration_true_when_behind(
-        self,
-        store: PaperlessSqliteVecVectorStore,
-    ) -> None:
-        """
-        GIVEN:
-            - A store whose schema_version has been forced behind SCHEMA_VERSION
-        WHEN:
-            - has_pending_migration() is checked
-        THEN:
-            - True is returned
-        """
-        store.add([make_node("a1", "1")])
-        store.client.execute(
-            "UPDATE index_meta SET value = '0' WHERE key = 'schema_version'",
-        )
-        assert store.has_pending_migration() is True

src/paperless_ai/vector_store.py

@@ -2,12 +2,16 @@ import json
 import logging
 import sqlite3
 import struct
+from collections.abc import Callable
 from collections.abc import Iterator
 from collections.abc import Sequence
 from contextlib import contextmanager
+from dataclasses import dataclass
+from dataclasses import field
 from pathlib import Path
 from types import TracebackType
 from typing import Any
+from typing import Literal
 
 import sqlite_vec
 from llama_index.core.bridge.pydantic import PrivateAttr
@@ -22,9 +26,6 @@ from llama_index.core.vector_stores.types import VectorStoreQueryResult
 from llama_index.core.vector_stores.utils import metadata_dict_to_node
 from llama_index.core.vector_stores.utils import node_to_metadata_dict
 
-from paperless_ai.migrations import MIGRATIONS
-from paperless_ai.migrations import Migration
-
 logger = logging.getLogger("paperless_ai.vector_store")
 
 DB_FILENAME = "llmindex.db"
@@ -52,6 +53,38 @@ COMPACT_BATCH_SIZE = 500
 _FILTER_COLUMNS = frozenset({"document_id", "modified"})
 
 
+@dataclass
+class Migration:
+    """A schema migration for the sqlite-vec vector store.
+
+    kind="structural": rows are copied into a new-schema file with no
+    re-embedding needed.  Supply ``apply(src_conn, dst_conn, dim)`` which
+    must create the vec0 table in ``dst_conn``, copy all rows from
+    ``src_conn``, and write ``dim`` / ``embed_model`` / ``total_inserts`` to
+    ``dst_conn``'s ``index_meta``.  ``schema_version`` is written by the
+    migration runner after ``apply`` returns.
+
+    kind="re-embed": the new schema requires fresh embeddings.
+    ``check_and_run_migrations()`` returns True when it encounters one of
+    these so the caller can force a full rebuild (which recreates the table
+    at the current SCHEMA_VERSION).
+    """
+
+    from_version: int
+    to_version: int
+    kind: Literal["structural", "re-embed"]
+    description: str
+    apply: Callable[[sqlite3.Connection, sqlite3.Connection, int], None] | None = field(
+        default=None,
+        repr=False,
+    )
+
+
+# Registry of all schema migrations in order. Empty at v1 -- this is the
+# baseline. Add entries here (and bump SCHEMA_VERSION) when the schema changes.
+MIGRATIONS: list[Migration] = []
+
+
 def _pack(embedding: Sequence[float]) -> bytes:
     return struct.pack(f"{len(embedding)}f", *embedding)
 
@@ -518,31 +551,6 @@ class PaperlessSqliteVecVectorStore(BasePydanticVectorStore):
         Path(compact_path).replace(db_path)
         self._conn = self._open_connection(db_path)
 
-    def _stored_schema_version(self) -> int | None:
-        """The schema_version recorded in index_meta, or None if no table
-        exists. A missing key (a store predating version tracking) is
-        treated as SCHEMA_VERSION -- i.e. already current -- since no
-        migration in MIGRATIONS targets a version before tracking began.
-        """
-        if not self.table_exists():
-            return None
-        raw = self._meta_get("schema_version")
-        return int(raw) if raw is not None else SCHEMA_VERSION
-
-    def has_pending_migration(self) -> bool:
-        """Cheaply check whether a migration is pending, with no exclusive
-        access needed -- just a metadata read under the connection callers
-        already hold via the write FileLock.
-
-        Callers should only pay for check_and_run_migrations()'s exclusive
-        access (a structural migration's file swap must not run while
-        readers are active) when this returns True, so that the common
-        case -- already at SCHEMA_VERSION -- never contends with readers
-        or a concurrent compaction.
-        """
-        current = self._stored_schema_version()
-        return current is not None and current < SCHEMA_VERSION
-
     def check_and_run_migrations(self) -> bool:
         """Apply any pending schema migrations to the store.
 
@@ -551,13 +559,15 @@ class PaperlessSqliteVecVectorStore(BasePydanticVectorStore):
         this method returns True when one is encountered so the caller can
         force a full rebuild (which recreates the table at SCHEMA_VERSION).
 
-        Must be called under the write FileLock, with readers excluded (see
-        has_pending_migration() for a cheap pre-check that avoids paying for
-        that exclusion in the common case).  No-op when the table does not
-        exist or is already at SCHEMA_VERSION.
+        Must be called under the write FileLock.  No-op when the table does
+        not exist or is already at SCHEMA_VERSION.
         """
-        current = self._stored_schema_version()
-        if current is None or current >= SCHEMA_VERSION:
+        if not self.table_exists():
+            return False
+
+        raw = self._meta_get("schema_version")
+        current = int(raw) if raw is not None else SCHEMA_VERSION
+        if current >= SCHEMA_VERSION:
             return False
 
         pending = sorted(
@@ -569,7 +579,7 @@ class PaperlessSqliteVecVectorStore(BasePydanticVectorStore):
             if migration.kind == "re-embed":
                 logger.warning(
                     "LLM index schema v%d -> v%d requires re-embedding (%s); "
-                    "the caller must force a rebuild.",
+                    "forcing full rebuild.",
                     migration.from_version,
                     migration.to_version,
                     migration.description,