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feat(uploads): add pymupdf4llm PDF converter with auto-fallback and async offload (#1727)
* feat(uploads): add pymupdf4llm PDF converter with auto-fallback and async offload - Introduce pymupdf4llm as an optional PDF converter with better heading detection and table preservation than MarkItDown - Auto mode: prefer pymupdf4llm when installed; fall back to MarkItDown when output is suspiciously sparse (image-based / scanned PDFs) - Sparsity check uses chars-per-page (< 50 chars/page) rather than an absolute threshold, correctly handling both short and long documents - Large files (> 1 MB) are offloaded to asyncio.to_thread() to avoid blocking the event loop (related: #1569) - Add UploadsConfig with pdf_converter field (auto/pymupdf4llm/markitdown) - Add pymupdf4llm as optional dependency: pip install deerflow-harness[pymupdf] - Add 14 unit tests covering sparsity heuristic, routing logic, and async path * fix(uploads): address Copilot review comments on PDF converter - Fix docstring: MIN_CHARS_PYMUPDF -> _MIN_CHARS_PER_PAGE (typo) - Fix file handle leak: wrap pymupdf.open in try/finally to ensure doc.close() - Fix silent fallback gap: _convert_pdf_with_pymupdf4llm now catches all conversion exceptions (not just ImportError), so encrypted/corrupt PDFs fall back to MarkItDown instead of propagating - Tighten type: pdf_converter field changed from str to Literal[auto|pymupdf4llm|markitdown] - Normalize config value: _get_pdf_converter() strips and lowercases the raw config string, warns and falls back to 'auto' on unknown values
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@ -1,7 +1,7 @@
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import logging
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import os
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from pathlib import Path
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from typing import Any, Self
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from typing import Any, Literal, Self
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import yaml
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from dotenv import load_dotenv
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@ -28,11 +28,26 @@ load_dotenv()
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logger = logging.getLogger(__name__)
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class UploadsConfig(BaseModel):
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"""Configuration for file upload handling."""
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pdf_converter: Literal["auto", "pymupdf4llm", "markitdown"] = Field(
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default="auto",
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description=(
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"PDF-to-Markdown converter. "
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"'auto': prefer pymupdf4llm when installed, fall back to MarkItDown for image-based PDFs; "
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"'pymupdf4llm': always use pymupdf4llm (must be installed); "
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"'markitdown': always use MarkItDown (original behaviour)."
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),
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)
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class AppConfig(BaseModel):
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"""Config for the DeerFlow application"""
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log_level: str = Field(default="info", description="Logging level for deerflow modules (debug/info/warning/error)")
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token_usage: TokenUsageConfig = Field(default_factory=TokenUsageConfig, description="Token usage tracking configuration")
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uploads: UploadsConfig = Field(default_factory=UploadsConfig, description="File upload handling configuration")
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models: list[ModelConfig] = Field(default_factory=list, description="Available models")
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sandbox: SandboxConfig = Field(description="Sandbox configuration")
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tools: list[ToolConfig] = Field(default_factory=list, description="Available tools")
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@ -1,9 +1,20 @@
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"""File conversion utilities.
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Converts document files (PDF, PPT, Excel, Word) to Markdown using markitdown.
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Converts document files (PDF, PPT, Excel, Word) to Markdown.
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PDF conversion strategy (auto mode):
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1. Try pymupdf4llm if installed — better heading detection, faster on most files.
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2. If output is suspiciously short (< _MIN_CHARS_PER_PAGE chars/page, or < 200 chars
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total when page count is unavailable), treat as image-based and fall back to MarkItDown.
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3. If pymupdf4llm is not installed, use MarkItDown directly (existing behaviour).
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Large files (> ASYNC_THRESHOLD_BYTES) are converted in a thread pool via
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asyncio.to_thread() to avoid blocking the event loop (fixes #1569).
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No FastAPI or HTTP dependencies — pure utility functions.
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"""
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import asyncio
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import logging
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import re
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from pathlib import Path
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@ -21,30 +32,136 @@ CONVERTIBLE_EXTENSIONS = {
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".docx",
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}
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# Files larger than this threshold are converted in a background thread.
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# Small files complete in < 1s synchronously; spawning a thread adds unnecessary
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# scheduling overhead for them.
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_ASYNC_THRESHOLD_BYTES = 1 * 1024 * 1024 # 1 MB
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# If pymupdf4llm produces fewer characters *per page* than this threshold,
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# the PDF is likely image-based or encrypted — fall back to MarkItDown.
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# Rationale: normal text PDFs yield 200-2000 chars/page; image-based PDFs
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# yield close to 0. 50 chars/page gives a wide safety margin.
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# Falls back to absolute 200-char check when page count is unavailable.
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_MIN_CHARS_PER_PAGE = 50
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def _pymupdf_output_too_sparse(text: str, file_path: Path) -> bool:
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"""Return True if pymupdf4llm output is suspiciously short (image-based PDF).
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Uses chars-per-page rather than an absolute threshold so that both short
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documents (few pages, few chars) and long documents (many pages, many chars)
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are handled correctly.
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"""
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chars = len(text.strip())
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doc = None
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pages: int | None = None
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try:
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import pymupdf
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doc = pymupdf.open(str(file_path))
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pages = len(doc)
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except Exception:
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pass
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finally:
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if doc is not None:
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try:
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doc.close()
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except Exception:
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pass
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if pages is not None and pages > 0:
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return (chars / pages) < _MIN_CHARS_PER_PAGE
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# Fallback: absolute threshold when page count is unavailable
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return chars < 200
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def _convert_pdf_with_pymupdf4llm(file_path: Path) -> str | None:
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"""Attempt PDF conversion with pymupdf4llm.
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Returns the markdown text, or None if pymupdf4llm is not installed or
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if conversion fails (e.g. encrypted/corrupt PDF).
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"""
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try:
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import pymupdf4llm
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except ImportError:
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return None
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try:
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return pymupdf4llm.to_markdown(str(file_path))
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except Exception:
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logger.exception("pymupdf4llm failed to convert %s; falling back to MarkItDown", file_path.name)
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return None
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def _convert_with_markitdown(file_path: Path) -> str:
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"""Convert any supported file to markdown text using MarkItDown."""
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from markitdown import MarkItDown
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md = MarkItDown()
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return md.convert(str(file_path)).text_content
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def _do_convert(file_path: Path, pdf_converter: str) -> str:
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"""Synchronous conversion — called directly or via asyncio.to_thread.
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Args:
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file_path: Path to the file.
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pdf_converter: "auto" | "pymupdf4llm" | "markitdown"
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"""
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is_pdf = file_path.suffix.lower() == ".pdf"
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if is_pdf and pdf_converter != "markitdown":
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# Try pymupdf4llm first (auto or explicit)
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pymupdf_text = _convert_pdf_with_pymupdf4llm(file_path)
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if pymupdf_text is not None:
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# pymupdf4llm is installed
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if pdf_converter == "pymupdf4llm":
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# Explicit — use as-is regardless of output length
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return pymupdf_text
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# auto mode: fall back if output looks like a failed parse.
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# Use chars-per-page to distinguish image-based PDFs (near 0) from
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# legitimately short documents.
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if not _pymupdf_output_too_sparse(pymupdf_text, file_path):
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return pymupdf_text
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logger.warning(
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"pymupdf4llm produced only %d chars for %s (likely image-based PDF); falling back to MarkItDown",
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len(pymupdf_text.strip()),
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file_path.name,
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)
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# pymupdf4llm not installed or fallback triggered → use MarkItDown
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return _convert_with_markitdown(file_path)
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async def convert_file_to_markdown(file_path: Path) -> Path | None:
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"""Convert a file to markdown using markitdown.
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"""Convert a supported document file to Markdown.
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PDF files are handled with a two-converter strategy (see module docstring).
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Large files (> 1 MB) are offloaded to a thread pool to avoid blocking the
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event loop.
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Args:
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file_path: Path to the file to convert.
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Returns:
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Path to the markdown file if conversion was successful, None otherwise.
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Path to the generated .md file, or None if conversion failed.
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"""
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try:
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from markitdown import MarkItDown
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pdf_converter = _get_pdf_converter()
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file_size = file_path.stat().st_size
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md = MarkItDown()
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result = md.convert(str(file_path))
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if file_size > _ASYNC_THRESHOLD_BYTES:
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text = await asyncio.to_thread(_do_convert, file_path, pdf_converter)
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else:
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text = _do_convert(file_path, pdf_converter)
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# Save as .md file with same name
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md_path = file_path.with_suffix(".md")
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md_path.write_text(result.text_content, encoding="utf-8")
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md_path.write_text(text, encoding="utf-8")
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logger.info(f"Converted {file_path.name} to markdown: {md_path.name}")
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logger.info("Converted %s to markdown: %s (%d chars)", file_path.name, md_path.name, len(text))
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return md_path
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except Exception as e:
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logger.error(f"Failed to convert {file_path.name} to markdown: {e}")
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logger.error("Failed to convert %s to markdown: %s", file_path.name, e)
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return None
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@ -69,6 +186,8 @@ _BOLD_HEADING_RE = re.compile(r"^\*\*((ITEM|PART|SECTION|SCHEDULE|EXHIBIT|APPEND
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# Keeps prompt size bounded even for very long documents.
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MAX_OUTLINE_ENTRIES = 50
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_ALLOWED_PDF_CONVERTERS = {"auto", "pymupdf4llm", "markitdown"}
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def extract_outline(md_path: Path) -> list[dict]:
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"""Extract document outline (headings) from a Markdown file.
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@ -122,14 +241,23 @@ def extract_outline(md_path: Path) -> list[dict]:
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def _get_pdf_converter() -> str:
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"""Read pdf_converter setting from app config, defaulting to 'auto'."""
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"""Read pdf_converter setting from app config, defaulting to 'auto'.
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Normalizes the value to lowercase and validates it against the allowed set
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so that values like 'AUTO' or 'MarkItDown' from config.yaml don't silently
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fall through to unexpected behaviour.
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"""
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try:
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from deerflow.config.app_config import get_app_config
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cfg = get_app_config()
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uploads_cfg = getattr(cfg, "uploads", None)
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if uploads_cfg is not None:
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return str(getattr(uploads_cfg, "pdf_converter", "auto"))
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raw = str(getattr(uploads_cfg, "pdf_converter", "auto")).strip().lower()
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if raw not in _ALLOWED_PDF_CONVERTERS:
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logger.warning("Invalid pdf_converter value %r; falling back to 'auto'", raw)
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return "auto"
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return raw
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except Exception:
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pass
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return "auto"
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@ -34,6 +34,9 @@ dependencies = [
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"langgraph-sdk>=0.1.51",
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]
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[project.optional-dependencies]
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pymupdf = ["pymupdf4llm>=0.0.17"]
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[build-system]
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requires = ["hatchling"]
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build-backend = "hatchling.build"
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"""Tests for extract_outline() in file_conversion utilities (PR2: document outline injection)."""
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"""Tests for file_conversion utilities (PR1: pymupdf4llm + asyncio.to_thread; PR2: extract_outline)."""
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from __future__ import annotations
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import asyncio
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import sys
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from types import ModuleType
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from unittest.mock import MagicMock, patch
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from deerflow.utils.file_conversion import (
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_ASYNC_THRESHOLD_BYTES,
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_MIN_CHARS_PER_PAGE,
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MAX_OUTLINE_ENTRIES,
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_do_convert,
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_pymupdf_output_too_sparse,
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convert_file_to_markdown,
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extract_outline,
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)
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def _make_pymupdf_mock(page_count: int) -> ModuleType:
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"""Return a fake *pymupdf* module whose ``open()`` reports *page_count* pages."""
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mock_doc = MagicMock()
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mock_doc.__len__ = MagicMock(return_value=page_count)
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fake_pymupdf = ModuleType("pymupdf")
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fake_pymupdf.open = MagicMock(return_value=mock_doc) # type: ignore[attr-defined]
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return fake_pymupdf
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def _run(coro):
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loop = asyncio.new_event_loop()
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try:
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return loop.run_until_complete(coro)
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finally:
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loop.close()
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# ---------------------------------------------------------------------------
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# _pymupdf_output_too_sparse
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# ---------------------------------------------------------------------------
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class TestPymupdfOutputTooSparse:
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"""Check the chars-per-page sparsity heuristic."""
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def test_dense_text_pdf_not_sparse(self, tmp_path):
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"""Normal text PDF: many chars per page → not sparse."""
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pdf = tmp_path / "dense.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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# 10 pages × 10 000 chars → 1000/page ≫ threshold
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with patch.dict(sys.modules, {"pymupdf": _make_pymupdf_mock(page_count=10)}):
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result = _pymupdf_output_too_sparse("x" * 10_000, pdf)
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assert result is False
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def test_image_based_pdf_is_sparse(self, tmp_path):
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"""Image-based PDF: near-zero chars per page → sparse."""
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pdf = tmp_path / "image.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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# 612 chars / 31 pages ≈ 19.7/page < _MIN_CHARS_PER_PAGE (50)
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with patch.dict(sys.modules, {"pymupdf": _make_pymupdf_mock(page_count=31)}):
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result = _pymupdf_output_too_sparse("x" * 612, pdf)
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assert result is True
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def test_fallback_when_pymupdf_unavailable(self, tmp_path):
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"""When pymupdf is not installed, fall back to absolute 200-char threshold."""
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pdf = tmp_path / "broken.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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# Remove pymupdf from sys.modules so the `import pymupdf` inside the
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# function raises ImportError, triggering the absolute-threshold fallback.
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with patch.dict(sys.modules, {"pymupdf": None}):
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sparse = _pymupdf_output_too_sparse("x" * 100, pdf)
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not_sparse = _pymupdf_output_too_sparse("x" * 300, pdf)
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assert sparse is True
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assert not_sparse is False
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def test_exactly_at_threshold_is_not_sparse(self, tmp_path):
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"""Chars-per-page == threshold is treated as NOT sparse (boundary inclusive)."""
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pdf = tmp_path / "boundary.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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# 2 pages × _MIN_CHARS_PER_PAGE chars = exactly at threshold
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with patch.dict(sys.modules, {"pymupdf": _make_pymupdf_mock(page_count=2)}):
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result = _pymupdf_output_too_sparse("x" * (_MIN_CHARS_PER_PAGE * 2), pdf)
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assert result is False
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# ---------------------------------------------------------------------------
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# _do_convert — routing logic
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# ---------------------------------------------------------------------------
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class TestDoConvert:
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"""Verify that _do_convert routes to the right sub-converter."""
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def test_non_pdf_always_uses_markitdown(self, tmp_path):
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"""DOCX / XLSX / PPTX always go through MarkItDown regardless of setting."""
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docx = tmp_path / "report.docx"
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docx.write_bytes(b"PK fake docx")
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with patch(
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"deerflow.utils.file_conversion._convert_with_markitdown",
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return_value="# Markdown from MarkItDown",
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) as mock_md:
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result = _do_convert(docx, "auto")
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mock_md.assert_called_once_with(docx)
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assert result == "# Markdown from MarkItDown"
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def test_pdf_auto_uses_pymupdf4llm_when_dense(self, tmp_path):
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"""auto mode: use pymupdf4llm output when it's dense enough."""
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pdf = tmp_path / "report.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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dense_text = "# Heading\n" + "word " * 2000 # clearly dense
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with (
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patch(
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"deerflow.utils.file_conversion._convert_pdf_with_pymupdf4llm",
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return_value=dense_text,
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),
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patch(
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"deerflow.utils.file_conversion._pymupdf_output_too_sparse",
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return_value=False,
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),
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patch("deerflow.utils.file_conversion._convert_with_markitdown") as mock_md,
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):
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result = _do_convert(pdf, "auto")
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mock_md.assert_not_called()
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assert result == dense_text
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def test_pdf_auto_falls_back_when_sparse(self, tmp_path):
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"""auto mode: fall back to MarkItDown when pymupdf4llm output is sparse."""
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pdf = tmp_path / "scanned.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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with (
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patch(
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"deerflow.utils.file_conversion._convert_pdf_with_pymupdf4llm",
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return_value="x" * 612, # 19.7 chars/page for 31-page doc
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),
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patch(
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"deerflow.utils.file_conversion._pymupdf_output_too_sparse",
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return_value=True,
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),
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patch(
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"deerflow.utils.file_conversion._convert_with_markitdown",
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return_value="OCR result via MarkItDown",
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) as mock_md,
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):
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result = _do_convert(pdf, "auto")
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mock_md.assert_called_once_with(pdf)
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assert result == "OCR result via MarkItDown"
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def test_pdf_explicit_pymupdf4llm_skips_sparsity_check(self, tmp_path):
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"""'pymupdf4llm' mode: use output as-is even if sparse."""
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pdf = tmp_path / "explicit.pdf"
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pdf.write_bytes(b"%PDF-1.4 fake")
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sparse_text = "x" * 10 # very short
|
||||
|
||||
with (
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._convert_pdf_with_pymupdf4llm",
|
||||
return_value=sparse_text,
|
||||
),
|
||||
patch("deerflow.utils.file_conversion._convert_with_markitdown") as mock_md,
|
||||
):
|
||||
result = _do_convert(pdf, "pymupdf4llm")
|
||||
|
||||
mock_md.assert_not_called()
|
||||
assert result == sparse_text
|
||||
|
||||
def test_pdf_explicit_markitdown_skips_pymupdf4llm(self, tmp_path):
|
||||
"""'markitdown' mode: never attempt pymupdf4llm."""
|
||||
pdf = tmp_path / "force_md.pdf"
|
||||
pdf.write_bytes(b"%PDF-1.4 fake")
|
||||
|
||||
with (
|
||||
patch("deerflow.utils.file_conversion._convert_pdf_with_pymupdf4llm") as mock_pymu,
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._convert_with_markitdown",
|
||||
return_value="MarkItDown result",
|
||||
),
|
||||
):
|
||||
result = _do_convert(pdf, "markitdown")
|
||||
|
||||
mock_pymu.assert_not_called()
|
||||
assert result == "MarkItDown result"
|
||||
|
||||
def test_pdf_auto_falls_back_when_pymupdf4llm_not_installed(self, tmp_path):
|
||||
"""auto mode: if pymupdf4llm is not installed, use MarkItDown directly."""
|
||||
pdf = tmp_path / "no_pymupdf.pdf"
|
||||
pdf.write_bytes(b"%PDF-1.4 fake")
|
||||
|
||||
with (
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._convert_pdf_with_pymupdf4llm",
|
||||
return_value=None, # None signals not installed
|
||||
),
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._convert_with_markitdown",
|
||||
return_value="MarkItDown fallback",
|
||||
) as mock_md,
|
||||
):
|
||||
result = _do_convert(pdf, "auto")
|
||||
|
||||
mock_md.assert_called_once_with(pdf)
|
||||
assert result == "MarkItDown fallback"
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# convert_file_to_markdown — async + file writing
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
|
||||
class TestConvertFileToMarkdown:
|
||||
def test_small_file_runs_synchronously(self, tmp_path):
|
||||
"""Small files (< 1 MB) are converted in the event loop thread."""
|
||||
pdf = tmp_path / "small.pdf"
|
||||
pdf.write_bytes(b"%PDF-1.4 " + b"x" * 100) # well under 1 MB
|
||||
|
||||
with (
|
||||
patch("deerflow.utils.file_conversion._get_pdf_converter", return_value="auto"),
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._do_convert",
|
||||
return_value="# Small PDF",
|
||||
) as mock_convert,
|
||||
patch("asyncio.to_thread") as mock_thread,
|
||||
):
|
||||
md_path = _run(convert_file_to_markdown(pdf))
|
||||
|
||||
# asyncio.to_thread must NOT have been called
|
||||
mock_thread.assert_not_called()
|
||||
mock_convert.assert_called_once()
|
||||
assert md_path == pdf.with_suffix(".md")
|
||||
assert md_path.read_text() == "# Small PDF"
|
||||
|
||||
def test_large_file_offloaded_to_thread(self, tmp_path):
|
||||
"""Large files (> 1 MB) are offloaded via asyncio.to_thread."""
|
||||
pdf = tmp_path / "large.pdf"
|
||||
# Write slightly more than the threshold
|
||||
pdf.write_bytes(b"%PDF-1.4 " + b"x" * (_ASYNC_THRESHOLD_BYTES + 1))
|
||||
|
||||
async def fake_to_thread(fn, *args, **kwargs):
|
||||
return fn(*args, **kwargs)
|
||||
|
||||
with (
|
||||
patch("deerflow.utils.file_conversion._get_pdf_converter", return_value="auto"),
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._do_convert",
|
||||
return_value="# Large PDF",
|
||||
),
|
||||
patch("asyncio.to_thread", side_effect=fake_to_thread) as mock_thread,
|
||||
):
|
||||
md_path = _run(convert_file_to_markdown(pdf))
|
||||
|
||||
mock_thread.assert_called_once()
|
||||
assert md_path == pdf.with_suffix(".md")
|
||||
assert md_path.read_text() == "# Large PDF"
|
||||
|
||||
def test_returns_none_on_conversion_error(self, tmp_path):
|
||||
"""If conversion raises, return None without propagating the exception."""
|
||||
pdf = tmp_path / "broken.pdf"
|
||||
pdf.write_bytes(b"%PDF-1.4 fake")
|
||||
|
||||
with (
|
||||
patch("deerflow.utils.file_conversion._get_pdf_converter", return_value="auto"),
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._do_convert",
|
||||
side_effect=RuntimeError("conversion failed"),
|
||||
),
|
||||
):
|
||||
result = _run(convert_file_to_markdown(pdf))
|
||||
|
||||
assert result is None
|
||||
|
||||
def test_writes_utf8_markdown_file(self, tmp_path):
|
||||
"""Generated .md file is written with UTF-8 encoding."""
|
||||
pdf = tmp_path / "report.pdf"
|
||||
pdf.write_bytes(b"%PDF-1.4 fake")
|
||||
chinese_content = "# 中文报告\n\n这是测试内容。"
|
||||
|
||||
with (
|
||||
patch("deerflow.utils.file_conversion._get_pdf_converter", return_value="auto"),
|
||||
patch(
|
||||
"deerflow.utils.file_conversion._do_convert",
|
||||
return_value=chinese_content,
|
||||
),
|
||||
):
|
||||
md_path = _run(convert_file_to_markdown(pdf))
|
||||
|
||||
assert md_path is not None
|
||||
assert md_path.read_text(encoding="utf-8") == chinese_content
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# extract_outline
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
@ -369,6 +369,15 @@ tool_search:
|
||||
|
||||
# Option 1: Local Sandbox (Default)
|
||||
# Executes commands directly on the host machine
|
||||
uploads:
|
||||
# PDF-to-Markdown converter used when a PDF is uploaded.
|
||||
# auto — prefer pymupdf4llm when installed; fall back to MarkItDown for
|
||||
# image-based or encrypted PDFs (recommended default).
|
||||
# pymupdf4llm — always use pymupdf4llm (must be installed: uv add pymupdf4llm).
|
||||
# Better heading/table extraction; faster on most files.
|
||||
# markitdown — always use MarkItDown (original behaviour, no extra dependency).
|
||||
pdf_converter: auto
|
||||
|
||||
sandbox:
|
||||
use: deerflow.sandbox.local:LocalSandboxProvider
|
||||
# Host bash execution is disabled by default because LocalSandboxProvider is
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user