Fix: skip incremental index writes when a re-embed migration is pending

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

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

@@ -0,0 +1,12 @@
+#!/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

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

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

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

docs/administration.md

@@ -212,6 +212,16 @@ 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
@@ -532,7 +542,7 @@ index is updated automatically on the schedule set by
 can manage it manually:
 
 ```
-document_llmindex {rebuild,update,compact}
+document_llmindex {rebuild,update,compact,migrate}
 ```
 
 Specify `rebuild` to build the index from scratch from all documents in the database. Use

src/documents/consumer.py

@@ -57,7 +57,9 @@ from paperless.models import ArchiveFileGenerationChoices
 from paperless.parsers import ParserContext
 from paperless.parsers import ParserProtocol
 from paperless.parsers.registry import get_parser_registry
-from paperless.parsers.utils import pdf_born_digital_text
+from paperless.parsers.utils import PDF_TEXT_MIN_LENGTH
+from paperless.parsers.utils import extract_pdf_text
+from paperless.parsers.utils import is_tagged_pdf
 
 LOGGING_NAME: Final[str] = "paperless.consumer"
 
@@ -136,45 +138,53 @@ def should_produce_archive(
 
     # Must produce a PDF so the frontend can display the original format at all.
     if parser.requires_pdf_rendition:
-        _log.debug("Archive: yes - parser requires PDF rendition for frontend display")
+        _log.debug("Archive: yes — parser requires PDF rendition for frontend display")
         return True
 
     # Parser cannot produce an archive (e.g. TextDocumentParser).
     if not parser.can_produce_archive:
-        _log.debug("Archive: no - parser cannot produce archives")
+        _log.debug("Archive: no — parser cannot produce archives")
         return False
 
     generation = OcrConfig().archive_file_generation
 
     if generation == ArchiveFileGenerationChoices.ALWAYS:
-        _log.debug("Archive: yes - ARCHIVE_FILE_GENERATION=always")
+        _log.debug("Archive: yes — ARCHIVE_FILE_GENERATION=always")
         return True
     if generation == ArchiveFileGenerationChoices.NEVER:
-        _log.debug("Archive: no - ARCHIVE_FILE_GENERATION=never")
+        _log.debug("Archive: no — ARCHIVE_FILE_GENERATION=never")
         return False
 
     # auto: produce archives for scanned/image documents; skip for born-digital PDFs.
     if mime_type.startswith("image/"):
-        _log.debug("Archive: yes - image document, ARCHIVE_FILE_GENERATION=auto")
+        _log.debug("Archive: yes — image document, ARCHIVE_FILE_GENERATION=auto")
         return True
     if mime_type == "application/pdf":
-        text, born_digital = pdf_born_digital_text(document_path, log=_log)
-        text_length = len(text) if text else 0
-        if born_digital:
+        text = extract_pdf_text(document_path)
+        has_text = text is not None and len(text) > 0
+        if has_text and is_tagged_pdf(document_path):
             _log.debug(
-                "Archive: no - born-digital PDF (text_length=%d),"
+                "Archive: no — born-digital PDF (structure tags detected),"
                 " ARCHIVE_FILE_GENERATION=auto",
-                text_length,
             )
             return False
+        if text is None or len(text) <= PDF_TEXT_MIN_LENGTH:
+            _log.debug(
+                "Archive: yes — scanned PDF (text_length=%d ≤ %d),"
+                " ARCHIVE_FILE_GENERATION=auto",
+                len(text) if text else 0,
+                PDF_TEXT_MIN_LENGTH,
+            )
+            return True
         _log.debug(
-            "Archive: yes - scanned/textless PDF (text_length=%d),"
+            "Archive: no — born-digital PDF (text_length=%d > %d),"
             " ARCHIVE_FILE_GENERATION=auto",
-            text_length,
+            len(text),
+            PDF_TEXT_MIN_LENGTH,
         )
-        return True
+        return False
     _log.debug(
-        "Archive: no - MIME type %r not eligible for auto archive generation",
+        "Archive: no — MIME type %r not eligible for auto archive generation",
         mime_type,
     )
     return False

src/documents/management/commands/document_llmindex.py

@@ -3,6 +3,7 @@ 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):
@@ -13,12 +14,18 @@ class Command(PaperlessCommand):
 
     def add_arguments(self, parser: Any) -> None:
         super().add_arguments(parser)
-        parser.add_argument("command", choices=["rebuild", "update", "compact"])
+        parser.add_argument(
+            "command",
+            choices=["rebuild", "update", "compact", "migrate"],
+        )
 
     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

@@ -9,6 +9,7 @@ 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:
@@ -17,6 +18,11 @@ 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/documents/tests/test_consumer.py

@@ -1329,7 +1329,7 @@ class PreConsumeTestCase(DirectoriesMixin, GetConsumerMixin, TestCase):
         with self.get_consumer(self.test_file) as c:
             c.run()
             # Verify no pre-consume script subprocess was invoked
-            # (run_subprocess may still be called by pdf_born_digital_text via pdftotext)
+            # (run_subprocess may still be called by _extract_text_for_archive_check)
             script_calls = [
                 call
                 for call in m.call_args_list
@@ -1354,7 +1354,7 @@ class PreConsumeTestCase(DirectoriesMixin, GetConsumerMixin, TestCase):
                     self.assertTrue(m.called)
 
                     # Find the call that invoked the pre-consume script
-                    # (run_subprocess may also be called by pdf_born_digital_text via pdftotext)
+                    # (run_subprocess may also be called by _extract_text_for_archive_check)
                     script_call = next(
                         call
                         for call in m.call_args_list

src/documents/tests/test_consumer_archive.py

@@ -134,32 +134,60 @@ class TestShouldProduceArchive:
         assert should_produce_archive(parser, mime, Path("/tmp/doc")) is expected
 
     @pytest.mark.parametrize(
-        ("born_digital", "expected"),
+        ("extracted_text", "expected"),
         [
-            pytest.param(True, False, id="born-digital-skips-archive"),
-            pytest.param(False, True, id="not-born-digital-produces-archive"),
+            pytest.param(
+                "This is a born-digital PDF with lots of text content. " * 10,
+                False,
+                id="born-digital-long-text-skips-archive",
+            ),
+            pytest.param(None, True, id="no-text-scanned-produces-archive"),
+            pytest.param("tiny", True, id="short-text-treated-as-scanned"),
         ],
     )
     def test_auto_pdf_archive_decision(
         self,
         mocker: MockerFixture,
         settings,
-        born_digital: bool,  # noqa: FBT001
+        extracted_text: str | None,
         expected: bool,  # noqa: FBT001
     ) -> None:
-        """Archive decision tracks pdf_born_digital_text()'s verdict exactly.
-
-        should_produce_archive() defers entirely to pdf_born_digital_text()
-        for the has-real-text decision, so both callers of that predicate
-        (this function and RasterisedDocumentParser.parse()) always agree.
-        """
         settings.ARCHIVE_FILE_GENERATION = "auto"
-        mocker.patch(
-            "documents.consumer.pdf_born_digital_text",
-            return_value=("some text", born_digital),
-        )
+        mocker.patch("documents.consumer.is_tagged_pdf", return_value=False)
+        mocker.patch("documents.consumer.extract_pdf_text", return_value=extracted_text)
         parser = _parser_instance(can_produce=True, requires_rendition=False)
         assert (
             should_produce_archive(parser, "application/pdf", Path("/tmp/doc.pdf"))
             is expected
         )
+
+    def test_tagged_pdf_skips_archive_in_auto_mode(
+        self,
+        mocker: MockerFixture,
+        settings,
+    ) -> None:
+        """Tagged PDFs (e.g. Word exports) with real text are treated as born-digital, even below PDF_TEXT_MIN_LENGTH."""
+        settings.ARCHIVE_FILE_GENERATION = "auto"
+        mocker.patch("documents.consumer.is_tagged_pdf", return_value=True)
+        mocker.patch("documents.consumer.extract_pdf_text", return_value="tiny")
+        parser = _parser_instance(can_produce=True, requires_rendition=False)
+        assert (
+            should_produce_archive(parser, "application/pdf", Path("/tmp/doc.pdf"))
+            is False
+        )
+
+    def test_tagged_pdf_without_text_produces_archive(
+        self,
+        mocker: MockerFixture,
+        settings,
+    ) -> None:
+        """A tagged PDF with no actual extractable text (e.g. some scanner firmware) is not
+        trusted as born-digital — the tag alone must not bypass OCR."""
+        settings.ARCHIVE_FILE_GENERATION = "auto"
+        mocker.patch("documents.consumer.is_tagged_pdf", return_value=True)
+        mocker.patch("documents.consumer.extract_pdf_text", return_value=None)
+        parser = _parser_instance(can_produce=True, requires_rendition=False)
+        assert (
+            should_produce_archive(parser, "application/pdf", Path("/tmp/doc.pdf"))
+            is True
+        )

src/paperless/parsers/tesseract.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 import importlib.resources
 import logging
 import os
+import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -24,9 +25,9 @@ from paperless.config import OcrConfig
 from paperless.models import CleanChoices
 from paperless.models import ModeChoices
 from paperless.models import OutputTypeChoices
+from paperless.parsers.utils import PDF_TEXT_MIN_LENGTH
 from paperless.parsers.utils import extract_pdf_text
-from paperless.parsers.utils import is_born_digital_text
-from paperless.parsers.utils import post_process_text
+from paperless.parsers.utils import is_tagged_pdf
 from paperless.parsers.utils import read_file_handle_unicode_errors
 from paperless.version import __full_version_str__
 
@@ -509,10 +510,10 @@ class RasterisedDocumentParser:
 
         if mime_type == "application/pdf":
             text_original = self.extract_text(None, document_path)
-            original_has_text = is_born_digital_text(
-                text_original,
-                document_path,
-                log=self.log,
+            has_text = text_original is not None and len(text_original) > 0
+            original_has_text = has_text and (
+                is_tagged_pdf(document_path, log=self.log)
+                or len(text_original) > PDF_TEXT_MIN_LENGTH
             )
         else:
             text_original = None
@@ -657,3 +658,17 @@ class RasterisedDocumentParser:
                     f"No text was found in {document_path}, the content will be empty.",
                 )
                 self.text = ""
+
+
+def post_process_text(text: str | None) -> str | None:
+    if not text:
+        return None
+
+    collapsed_spaces = re.sub(r"([^\S\r\n]+)", " ", text)
+    no_leading_whitespace = re.sub(r"([\n\r]+)([^\S\n\r]+)", "\\1", collapsed_spaces)
+    no_trailing_whitespace = re.sub(r"([^\S\n\r]+)$", "", no_leading_whitespace)
+
+    # TODO: this needs a rework
+    # replace \0 prevents issues with saving to postgres.
+    # text may contain \0 when this character is present in PDF files.
+    return no_trailing_whitespace.strip().replace("\0", " ")

src/paperless/parsers/utils.py

@@ -111,88 +111,6 @@ def extract_pdf_text(
         return None
 
 
-def post_process_text(text: str | None) -> str | None:
-    """Normalize extracted PDF/OCR text: collapse whitespace, strip padding.
-
-    Returns ``None`` for ``None`` or whitespace-only input, so callers can
-    treat "no text" and "only layout padding" the same way.
-    """
-    if not text:
-        return None
-
-    collapsed_spaces = re.sub(r"([^\S\r\n]+)", " ", text)
-    no_leading_whitespace = re.sub(r"([\n\r]+)([^\S\n\r]+)", "\\1", collapsed_spaces)
-    no_trailing_whitespace = re.sub(r"([^\S\n\r]+)$", "", no_leading_whitespace)
-
-    # replace \0 prevents issues with saving to postgres.
-    # text may contain \0 when this character is present in PDF files.
-    result = no_trailing_whitespace.strip().replace("\0", " ")
-    return result or None
-
-
-def is_born_digital_text(
-    text: str | None,
-    path: Path,
-    log: logging.Logger | None = None,
-) -> bool:
-    """Decide whether already-extracted, normalized PDF text counts as born-digital.
-
-    This is the single source of truth for "does this PDF already have real
-    text", used both to decide whether to produce an archive file and to
-    decide whether OCR can be skipped. Both decisions must agree, or a
-    tagged-but-textless PDF can end up with no archive AND a forced OCR pass
-    (see GH #13387): raw ``pdftotext -layout`` output can be non-empty
-    (whitespace/form-feed padding) even when there is no real content, so
-    *text* must already be normalized via :func:`post_process_text`, not the
-    raw extraction.
-
-    Parameters
-    ----------
-    text:
-        The normalized extracted text (or ``None``) to evaluate.
-    path:
-        Absolute path to the PDF file, used for the tagged-PDF check.
-    log:
-        Logger for warnings.  Falls back to the module-level logger when omitted.
-
-    Returns
-    -------
-    bool
-        Whether the PDF counts as born-digital (has real text, and is either
-        tagged or exceeds ``PDF_TEXT_MIN_LENGTH``).
-    """
-    if not text:
-        return False
-    return is_tagged_pdf(path, log=log) or len(text) > PDF_TEXT_MIN_LENGTH
-
-
-def pdf_born_digital_text(
-    path: Path,
-    log: logging.Logger | None = None,
-) -> tuple[str | None, bool]:
-    """Extract a PDF's text and decide whether it should be treated as born-digital.
-
-    Convenience wrapper around :func:`is_born_digital_text` for callers that
-    don't already have the PDF's text extracted (e.g. the archive-generation
-    decision, which runs before any parser has touched the file).
-
-    Parameters
-    ----------
-    path:
-        Absolute path to the PDF file.
-    log:
-        Logger for warnings.  Falls back to the module-level logger when omitted.
-
-    Returns
-    -------
-    tuple[str | None, bool]
-        The normalized extracted text (or ``None``), and whether the PDF
-        counts as born-digital.
-    """
-    text = post_process_text(extract_pdf_text(path, log=log))
-    return text, is_born_digital_text(text, path, log=log)
-
-
 def read_file_handle_unicode_errors(
     filepath: Path,
     log: logging.Logger | None = None,

src/paperless/tests/conftest.py

@@ -36,23 +36,6 @@ def samples_dir() -> Path:
     return (Path(__file__).parent / "samples").resolve()
 
 
-@pytest.fixture(scope="session")
-def tagged_no_text_pdf_file(samples_dir: Path) -> Path:
-    """Path to a tagged PDF whose only "text" is pdftotext layout padding.
-
-    Reproduces GH #13387: ``/MarkInfo /Marked true`` is set, but the only
-    extractable content is a form-feed byte, not real text. Lives here
-    rather than in parsers/conftest.py so both parser tests and
-    paperless/tests/test_parser_utils.py can use it.
-
-    Returns
-    -------
-    Path
-        Absolute path to ``tesseract/tagged-but-no-text.pdf``.
-    """
-    return samples_dir / "tesseract" / "tagged-but-no-text.pdf"
-
-
 @pytest.fixture(autouse=True)
 def clean_registry() -> Generator[None, None, None]:
     """Reset the parser registry before and after every test.

src/paperless/tests/parsers/test_tesseract_parser.py

@@ -21,7 +21,7 @@ from documents.parsers import run_convert
 from paperless.models import ModeChoices
 from paperless.parsers import ParserProtocol
 from paperless.parsers.tesseract import RasterisedDocumentParser
-from paperless.parsers.utils import is_tagged_pdf
+from paperless.parsers.tesseract import post_process_text
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -151,6 +151,36 @@ class TestRasterisedDocumentParserLifecycle:
         assert tempdir is not None and not tempdir.exists()
 
 
+# ---------------------------------------------------------------------------
+# post_process_text
+# ---------------------------------------------------------------------------
+
+
+class TestPostProcessText:
+    @pytest.mark.parametrize(
+        ("source", "expected"),
+        [
+            pytest.param(
+                "simple     string",
+                "simple string",
+                id="collapse-spaces",
+            ),
+            pytest.param(
+                "simple    newline\n   testing string",
+                "simple newline\ntesting string",
+                id="preserve-newline",
+            ),
+            pytest.param(
+                "utf-8   строка с пробелами в конце  ",  # noqa: RUF001
+                "utf-8 строка с пробелами в конце",  # noqa: RUF001
+                id="utf8-trailing-spaces",
+            ),
+        ],
+    )
+    def test_post_process_text(self, source: str, expected: str) -> None:
+        assert post_process_text(source) == expected
+
+
 # ---------------------------------------------------------------------------
 # Page count
 # ---------------------------------------------------------------------------
@@ -880,25 +910,25 @@ class TestSkipArchive:
         self,
         mocker: MockerFixture,
         tesseract_parser: RasterisedDocumentParser,
-        tagged_no_text_pdf_file: Path,
+        tesseract_samples_dir: Path,
     ) -> None:
         """
         GIVEN:
-            - A real PDF that reports itself as tagged (/MarkInfo /Marked
-              true) but whose only pdftotext output is layout padding (a
-              lone form-feed byte), not real text (see GitHub issue #13387,
-              originally reported against #13349's tagged-PDF handling)
+            - A PDF that reports itself as tagged (/MarkInfo /Marked true) but
+              has no actual extractable text (some scanner firmware produces
+              this — see GitHub issue #13349)
             - Mode: auto, produce_archive=False
         WHEN:
             - Document is parsed
         THEN:
             - The tag alone is not trusted as "has text"; OCRmyPDF still runs
         """
-        assert is_tagged_pdf(tagged_no_text_pdf_file) is True
         tesseract_parser.settings.mode = ModeChoices.AUTO
+        mocker.patch("paperless.parsers.tesseract.is_tagged_pdf", return_value=True)
+        mocker.patch.object(tesseract_parser, "extract_text", return_value=None)
         mock_ocr = mocker.patch("ocrmypdf.ocr")
         tesseract_parser.parse(
-            tagged_no_text_pdf_file,
+            tesseract_samples_dir / "multi-page-images.pdf",
             "application/pdf",
             produce_archive=False,
         )

src/paperless/tests/test_parser_utils.py

@@ -4,18 +4,10 @@ from __future__ import annotations
 
 import codecs
 from pathlib import Path
-from typing import TYPE_CHECKING
-
-import pytest
 
 from paperless.parsers.utils import is_tagged_pdf
-from paperless.parsers.utils import pdf_born_digital_text
-from paperless.parsers.utils import post_process_text
 from paperless.parsers.utils import read_file_handle_unicode_errors
 
-if TYPE_CHECKING:
-    from pytest_mock import MockerFixture
-
 SAMPLES = Path(__file__).parent / "samples" / "tesseract"
 
 
@@ -68,105 +60,3 @@ class TestIsTaggedPdf:
         bad = tmp_path / "bad.pdf"
         bad.write_bytes(b"not a pdf")
         assert is_tagged_pdf(bad) is False
-
-
-class TestPostProcessText:
-    @pytest.mark.parametrize(
-        ("source", "expected"),
-        [
-            pytest.param(
-                "simple     string",
-                "simple string",
-                id="collapse-spaces",
-            ),
-            pytest.param(
-                "simple    newline\n   testing string",
-                "simple newline\ntesting string",
-                id="preserve-newline",
-            ),
-            pytest.param(
-                "utf-8   строка с пробелами в конце  ",  # noqa: RUF001
-                "utf-8 строка с пробелами в конце",  # noqa: RUF001
-                id="utf8-trailing-spaces",
-            ),
-            pytest.param(None, None, id="none-input"),
-            pytest.param("", None, id="empty-string"),
-            pytest.param("   \n\x0c  \n ", None, id="whitespace-and-formfeed-only"),
-        ],
-    )
-    def test_post_process_text(
-        self,
-        source: str | None,
-        expected: str | None,
-    ) -> None:
-        assert post_process_text(source) == expected
-
-
-class TestPdfBornDigitalText:
-    """Regression coverage for GH #13387.
-
-    should_produce_archive() and RasterisedDocumentParser.parse() must agree
-    on whether a PDF has real text, so both go through this one function.
-    """
-
-    @pytest.mark.parametrize(
-        ("extracted", "tagged", "expected_text", "expected_born_digital"),
-        [
-            pytest.param("tiny", True, "tiny", True, id="tagged-with-real-text"),
-            pytest.param("tiny", False, "tiny", False, id="untagged-below-min-length"),
-            pytest.param(
-                "x" * 51,
-                False,
-                "x" * 51,
-                True,
-                id="untagged-above-min-length",
-            ),
-            pytest.param(None, True, None, False, id="tagged-but-no-text"),
-        ],
-    )
-    def test_born_digital_decision(
-        self,
-        mocker: MockerFixture,
-        tmp_path: Path,
-        extracted: str | None,
-        tagged: bool,  # noqa: FBT001
-        expected_text: str | None,
-        expected_born_digital: bool,  # noqa: FBT001
-    ) -> None:
-        """
-        GIVEN:
-            - A PDF whose pdftotext output and /MarkInfo tag status vary
-        WHEN:
-            - pdf_born_digital_text() is called
-        THEN:
-            - The normalized text and born-digital verdict match; the tag
-              alone never counts as "has text"
-        """
-        mocker.patch(
-            "paperless.parsers.utils.extract_pdf_text",
-            return_value=extracted,
-        )
-        mocker.patch("paperless.parsers.utils.is_tagged_pdf", return_value=tagged)
-        text, born_digital = pdf_born_digital_text(tmp_path / "doc.pdf")
-        assert text == expected_text
-        assert born_digital is expected_born_digital
-
-    def test_tagged_but_textless_pdf_is_not_born_digital(
-        self,
-        tagged_no_text_pdf_file: Path,
-    ) -> None:
-        """
-        GIVEN:
-            - A real PDF that is tagged (/MarkInfo /Marked true) but whose
-              only "text" is layout padding (a stray form-feed byte)
-        WHEN:
-            - pdf_born_digital_text() is called with no mocking
-        THEN:
-            - The normalized text is None and the PDF is not treated as
-              born-digital. The raw, unnormalized pdftotext output is
-              non-empty for this file, which is exactly what caused the
-              archive decision to disagree with the OCR decision in #13387.
-        """
-        text, born_digital = pdf_born_digital_text(tagged_no_text_pdf_file)
-        assert text is None
-        assert born_digital is False

src/paperless_ai/indexing.py

@@ -144,6 +144,24 @@ 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.
@@ -168,6 +186,21 @@ 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,
@@ -339,15 +372,7 @@ def update_llm_index(
     happens, since a rebuild always covers the whole library regardless.
     """
     with write_store() as 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
+        needs_reembed = _check_and_run_migrations(store)
         if needs_reembed:
             logger.warning(
                 "LLM index migration requires re-embedding; forcing rebuild.",
@@ -412,14 +437,7 @@ def update_llm_index(
                 else "No changes detected in LLM index."
             )
 
-        try:
-            with _exclude_readers():
-                store.compact()
-        except Timeout:
-            logger.info(
-                "Skipping LLM index compaction: index readers are active; "
-                "will retry next run.",
-            )
+        _with_exclusive_access("compaction", store.compact)
     return msg
 
 
@@ -434,25 +452,60 @@ 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:
-        try:
-            with _exclude_readers():
-                store.compact(force=True)
-        except Timeout:
-            logger.info(
-                "Skipping LLM index compaction: index readers are active; "
-                "will retry next run.",
-            )
+        _with_exclusive_access("compaction", lambda: store.compact(force=True))
 
 
 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

@@ -0,0 +1,60 @@
+"""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/tests/test_ai_indexing.py

@@ -1,3 +1,4 @@
+import logging
 from pathlib import Path
 from unittest.mock import MagicMock
 from unittest.mock import patch
@@ -737,6 +738,7 @@ 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(
@@ -757,12 +759,45 @@ 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(
@@ -777,6 +812,31 @@ 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,
@@ -849,6 +909,76 @@ 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_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
 
@@ -646,3 +646,50 @@ 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

@@ -2,16 +2,12 @@ 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
@@ -26,6 +22,9 @@ 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"
@@ -53,38 +52,6 @@ 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)
 
@@ -551,6 +518,31 @@ 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.
 
@@ -559,15 +551,13 @@ 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.  No-op when the table does
-        not exist or is already 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.
         """
-        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:
+        current = self._stored_schema_version()
+        if current is None or current >= SCHEMA_VERSION:
             return False
 
         pending = sorted(
@@ -579,7 +569,7 @@ class PaperlessSqliteVecVectorStore(BasePydanticVectorStore):
             if migration.kind == "re-embed":
                 logger.warning(
                     "LLM index schema v%d -> v%d requires re-embedding (%s); "
-                    "forcing full rebuild.",
+                    "the caller must force a rebuild.",
                     migration.from_version,
                     migration.to_version,
                     migration.description,