From 12aa536923c1bc3fea4266e5a993ffd46f694cf4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=81=93=E8=BE=95?= Date: Sat, 14 Feb 2026 15:37:10 +0800 Subject: [PATCH] WIP Co-authored-by: Cursor --- README.md | 6 + data_juicer/ops/mapper/__init__.py | 4 + .../ops/mapper/arxiv_to_markdown_mapper.py | 321 +++++ .../ops/mapper/pdf_to_markdown_mapper.py | 165 +++ .../mapper/arxiv_to_markdown_mapper.md | 44 + .../mapper/pdf_to_markdown_mapper.md | 40 + pyproject.toml | 7 + .../mapper/test_arxiv_to_markdown_mapper.py | 71 ++ .../ops/mapper/test_pdf_to_markdown_mapper.py | 73 ++ tools/run_op.py | 122 ++ uv.lock | 1059 ++++++++++++++--- 11 files changed, 1741 insertions(+), 171 deletions(-) create mode 100644 data_juicer/ops/mapper/arxiv_to_markdown_mapper.py create mode 100644 data_juicer/ops/mapper/pdf_to_markdown_mapper.py create mode 100644 docs/operators/mapper/arxiv_to_markdown_mapper.md create mode 100644 docs/operators/mapper/pdf_to_markdown_mapper.md create mode 100644 tests/ops/mapper/test_arxiv_to_markdown_mapper.py create mode 100644 tests/ops/mapper/test_pdf_to_markdown_mapper.py create mode 100644 tools/run_op.py diff --git a/README.md b/README.md index 0c47f191f8..154d8e733d 100644 --- a/README.md +++ b/README.md @@ -57,6 +57,12 @@ for s in res_ds: print(s) ``` +**Quick one-shot op test** (run a single operator on one sample): +```bash +dj-op --list # list operator names +dj-op whitespace_normalization_mapper '{"text":" hello "}' +echo '{"arxiv_id":"2501.14755"}' | dj-op arxiv_to_markdown_mapper +``` --- diff --git a/data_juicer/ops/mapper/__init__.py b/data_juicer/ops/mapper/__init__.py index 59d110c9a4..db6155100b 100644 --- a/data_juicer/ops/mapper/__init__.py +++ b/data_juicer/ops/mapper/__init__.py @@ -1,6 +1,7 @@ from .annotation.human_preference_annotation_mapper import ( HumanPreferenceAnnotationMapper, ) +from .arxiv_to_markdown_mapper import ArxivToMarkdownMapper from .audio_add_gaussian_noise_mapper import AudioAddGaussianNoiseMapper from .audio_ffmpeg_wrapped_mapper import AudioFFmpegWrappedMapper from .calibrate_qa_mapper import CalibrateQAMapper @@ -55,6 +56,7 @@ from .optimize_query_mapper import OptimizeQueryMapper from .optimize_response_mapper import OptimizeResponseMapper from .pair_preference_mapper import PairPreferenceMapper +from .pdf_to_markdown_mapper import PdfToMarkdownMapper from .punctuation_normalization_mapper import PunctuationNormalizationMapper from .python_file_mapper import PythonFileMapper from .python_lambda_mapper import PythonLambdaMapper @@ -114,6 +116,7 @@ from .whitespace_normalization_mapper import WhitespaceNormalizationMapper __all__ = [ + "ArxivToMarkdownMapper", "AudioAddGaussianNoiseMapper", "AudioFFmpegWrappedMapper", "CalibrateQAMapper", @@ -167,6 +170,7 @@ "OptimizeQueryMapper", "OptimizeResponseMapper", "PairPreferenceMapper", + "PdfToMarkdownMapper", "PunctuationNormalizationMapper", "PythonFileMapper", "PythonLambdaMapper", diff --git a/data_juicer/ops/mapper/arxiv_to_markdown_mapper.py b/data_juicer/ops/mapper/arxiv_to_markdown_mapper.py new file mode 100644 index 0000000000..2afd1c9bcc --- /dev/null +++ b/data_juicer/ops/mapper/arxiv_to_markdown_mapper.py @@ -0,0 +1,321 @@ +# Copyright 2025 The DataJuicer Authors. All rights reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Mapper to convert arXiv paper ID to high-precision structured Markdown. + +Given an arXiv paper ID (e.g. 2501.14755 or hep-th/9901001), downloads the PDF +or crawls the HTML/abstract page, converts to a single structured Markdown string +(images can be discarded), suitable for chunking or feeding to LLM / knowledge base. +""" + +import io +import re +import tempfile +import time +import xml.etree.ElementTree as ET +from typing import Optional + +import pdfplumber +import requests +from loguru import logger + +from data_juicer.utils.lazy_loader import LazyLoader + +from ..base_op import OPERATORS, Mapper + +# Optional backends for high-precision conversion +magic_pdf = LazyLoader("magic_pdf", "magic-pdf") +crawl4ai = LazyLoader("crawl4ai", "crawl4ai") + +OP_NAME = "arxiv_to_markdown_mapper" + +# arXiv API, PDF, and HTML URLs +ARXIV_PDF_URL_TEMPLATE = "https://arxiv.org/pdf/{arxiv_id}.pdf" +ARXIV_ABS_URL_TEMPLATE = "https://arxiv.org/abs/{arxiv_id}" +ARXIV_HTML_URL_TEMPLATE = "https://arxiv.org/html/{arxiv_id}" +ARXIV_API_QUERY = "http://export.arxiv.org/api/query?id_list={arxiv_id}" + +# Default request settings +DEFAULT_TIMEOUT = 60 +DEFAULT_DOWNLOAD_DELAY = 1.0 # be nice to arXiv + + +def _normalize_arxiv_id(raw: str) -> Optional[str]: + """Normalize input to arXiv ID without version (e.g. 2501.14755 or hep-th/9901001).""" + s = _normalize_arxiv_id_keep_version(raw) + if not s: + return None + if re.search(r"v\d+$", s): + s = re.sub(r"v\d+$", "", s) + return s if s else None + + +def _normalize_arxiv_id_keep_version(raw: str) -> Optional[str]: + """Normalize to arXiv ID but keep version suffix for HTML URL (e.g. 2501.14755v1).""" + if not raw or not isinstance(raw, str): + return None + s = raw.strip() + if "arxiv.org/abs/" in s: + s = s.split("arxiv.org/abs/")[-1].split("?")[0].split("#")[0].strip("/") + if "arxiv.org/pdf/" in s: + s = s.split("arxiv.org/pdf/")[-1].replace(".pdf", "").split("?")[0].strip("/") + if "arxiv.org/html/" in s: + s = s.split("arxiv.org/html/")[-1].split("?")[0].split("#")[0].strip("/") + return s if s else None + + +def _fetch_arxiv_metadata(arxiv_id: str, timeout: int = 15) -> dict: + """Fetch title and authors from arXiv API (XML).""" + out = {"title": "", "authors": [], "abstract": ""} + try: + url = ARXIV_API_QUERY.format(arxiv_id=arxiv_id) + r = requests.get(url, timeout=timeout) + r.raise_for_status() + root = ET.fromstring(r.content) + ns = {"atom": "http://www.w3.org/2005/Atom"} + entry = root.find("atom:entry", ns) + if entry is None: + return out + title_el = entry.find("atom:title", ns) + if title_el is not None and title_el.text: + out["title"] = title_el.text.strip().replace("\n", " ") + summary_el = entry.find("atom:summary", ns) + if summary_el is not None and summary_el.text: + out["abstract"] = summary_el.text.strip().replace("\n", " ") + for author in entry.findall("atom:author", ns): + name_el = author.find("atom:name", ns) + if name_el is not None and name_el.text: + out["authors"].append(name_el.text.strip()) + except Exception as e: + logger.debug(f"arXiv metadata fetch failed for {arxiv_id}: {e}") + return out + + +def _download_arxiv_pdf(arxiv_id: str, timeout: int, delay: float) -> Optional[bytes]: + """Download PDF bytes from arXiv.""" + url = ARXIV_PDF_URL_TEMPLATE.format(arxiv_id=arxiv_id) + if delay > 0: + time.sleep(delay) + try: + r = requests.get(url, timeout=timeout, stream=True) + r.raise_for_status() + return r.content + except Exception as e: + logger.error(f"Failed to download arXiv PDF {arxiv_id}: {e}") + return None + + +def _pdf_to_markdown_pdfplumber(pdf_bytes: bytes) -> str: + """Convert PDF bytes to plain text with minimal structure using pdfplumber.""" + try: + with io.BytesIO(pdf_bytes) as f: + with pdfplumber.open(f) as pdf: + parts = [] + for i, page in enumerate(pdf.pages): + tables = page.find_tables() + for table in tables: + page = page.outside_bbox(table.bbox) + text = page.extract_text() + if not text: + continue + page_num = str(page.page_number) + if text.rstrip().endswith(page_num): + text = text.rstrip()[: -len(page_num)] + if text.strip(): + parts.append(f"## Page {i + 1}\n\n{text.strip()}") + return "\n\n".join(parts) if parts else "" + except Exception as e: + logger.warning(f"pdfplumber failed to parse PDF: {e}") + return "" + + +def _pdf_to_markdown_mineru(pdf_bytes: bytes, keep_images: bool = False) -> str: + """Convert PDF bytes to structured Markdown using MinerU (magic-pdf).""" + try: + from magic_pdf.data.data_reader_writer import FileBasedDataWriter + from magic_pdf.data.dataset import PymuDocDataset + from magic_pdf.model.doc_analyze_by_custom_model import doc_analyze + from magic_pdf.config.enums import SupportedPdfParseMethod + except ImportError as e: + logger.warning(f"magic-pdf not available, fallback to pdfplumber: {e}") + return _pdf_to_markdown_pdfplumber(pdf_bytes) + + with tempfile.TemporaryDirectory() as tmpdir: + import os + + image_dir = os.path.join(tmpdir, "images") + os.makedirs(image_dir, exist_ok=True) + image_writer = FileBasedDataWriter(image_dir) + + try: + ds = PymuDocDataset(pdf_bytes) + if ds.classify() == SupportedPdfParseMethod.OCR: + infer_result = ds.apply(doc_analyze, ocr=True) + pipe_result = infer_result.pipe_ocr_mode(image_writer) + else: + infer_result = ds.apply(doc_analyze, ocr=False) + pipe_result = infer_result.pipe_txt_mode(image_writer) + + image_dir_basename = "images" + md_content = pipe_result.get_markdown(image_dir_basename) + if not keep_images and md_content: + # Remove image markdown refs: ![](images/...) or ![alt](images/...) + md_content = re.sub(r"!\[[^\]]*\]\([^)]+\)", "", md_content) + md_content = re.sub(r"\n{3,}", "\n\n", md_content).strip() + return md_content or _pdf_to_markdown_pdfplumber(pdf_bytes) + except Exception as e: + logger.warning(f"MinerU conversion failed, fallback to pdfplumber: {e}") + return _pdf_to_markdown_pdfplumber(pdf_bytes) + + +def _crawl_url_to_markdown(url: str, timeout: int, delay: float) -> Optional[str]: + """Crawl a URL with crawl4ai and return raw markdown.""" + if delay > 0: + time.sleep(delay) + try: + import asyncio + + async def _crawl(): + from crawl4ai import AsyncWebCrawler + from crawl4ai.markdown_generation_strategy import DefaultMarkdownGenerator + + config = {"markdown_generator": DefaultMarkdownGenerator()} + async with AsyncWebCrawler() as crawler: + result = await crawler.arun(url, config=config) + md = getattr(result, "markdown", None) + if md is None: + return None + if hasattr(md, "raw_markdown"): + return md.raw_markdown + return str(md) if md else None + + return asyncio.run(_crawl()) + except Exception as e: + logger.debug(f"crawl4ai failed for {url}: {e}") + return None + + +def _arxiv_html_to_markdown_crawl4ai(arxiv_id_html: str, timeout: int, delay: float) -> Optional[str]: + """Crawl arXiv full HTML version (e.g. https://arxiv.org/html/2501.14755v1) to Markdown.""" + url = ARXIV_HTML_URL_TEMPLATE.format(arxiv_id=arxiv_id_html) + body = _crawl_url_to_markdown(url, timeout, delay) + if body and len(body.strip()) > 500: + return body + return None + + +def _arxiv_abs_to_markdown_crawl4ai(arxiv_id: str, timeout: int, delay: float) -> Optional[str]: + """Crawl arXiv abstract page and return as Markdown (abstract + metadata only).""" + url = ARXIV_ABS_URL_TEMPLATE.format(arxiv_id=arxiv_id) + return _crawl_url_to_markdown(url, timeout, delay) + + +@OPERATORS.register_module(OP_NAME) +class ArxivToMarkdownMapper(Mapper): + """Convert arXiv paper ID to a single high-precision structured Markdown document. + + Downloads the paper PDF (or crawls the abstract page when backend is crawl4ai), + converts to Markdown with optional metadata header. Images are dropped by default + for smaller output and easier chunking/LLM consumption. + """ + + _batched_op = False + + _requirements = ["magic-pdf", "crawl4ai"] + + def __init__( + self, + arxiv_id_key: str = "arxiv_id", + backend: str = "mineru", + add_metadata_header: bool = True, + keep_images: bool = False, + timeout: int = DEFAULT_TIMEOUT, + download_delay: float = DEFAULT_DOWNLOAD_DELAY, + output_key: Optional[str] = None, + *args, + **kwargs, + ): + """ + :param arxiv_id_key: Field name containing arXiv ID (or URL). + :param backend: Conversion backend: "mineru" (recommended; MinerU/magic-pdf, best quality), + "pdfplumber" (built-in fallback, text-only), "crawl4ai" (HTML full page if available, + else abstract page; fallback to PDF if both fail). + :param add_metadata_header: Prepend title, authors, abstract from arXiv API. + :param keep_images: If True, keep image references in Markdown (mineru only). + :param timeout: Request timeout in seconds. + :param download_delay: Delay in seconds before each download (rate limiting). + :param output_key: Field to write Markdown to; default is text_key. + """ + super().__init__(*args, **kwargs) + self._init_parameters = self.remove_extra_parameters(locals()) + self.arxiv_id_key = arxiv_id_key + self.backend = backend.lower() + self.add_metadata_header = add_metadata_header + self.keep_images = keep_images + self.timeout = timeout + self.download_delay = download_delay + self.output_key = output_key or self.text_key + if self.backend not in ("mineru", "pdfplumber", "crawl4ai"): + raise ValueError(f"backend must be one of mineru, pdfplumber, crawl4ai, got {backend}") + + def process_single(self, sample): + raw_id = sample.get(self.arxiv_id_key) + arxiv_id = _normalize_arxiv_id(raw_id) + if not arxiv_id: + logger.warning(f"Missing or invalid {self.arxiv_id_key}: {raw_id}") + sample[self.output_key] = sample.get(self.text_key, "") + return sample + arxiv_id_for_html = _normalize_arxiv_id_keep_version(raw_id) or arxiv_id + + md_parts = [] + + if self.add_metadata_header: + meta = _fetch_arxiv_metadata(arxiv_id, timeout=min(15, self.timeout)) + if meta["title"]: + md_parts.append(f"# {meta['title']}\n") + if meta["authors"]: + md_parts.append("**Authors:** " + ", ".join(meta["authors"]) + "\n") + md_parts.append(f"**arXiv:** {arxiv_id} \n") + if meta["abstract"]: + md_parts.append("## Abstract\n\n" + meta["abstract"] + "\n") + md_parts.append("---\n\n") + + if self.backend == "crawl4ai": + body = _arxiv_html_to_markdown_crawl4ai( + arxiv_id_for_html, self.timeout, self.download_delay + ) + if not body: + body = _arxiv_abs_to_markdown_crawl4ai( + arxiv_id, self.timeout, self.download_delay + ) + if not body: + # Use pdfplumber for fallback so crawl4ai users need not install magic-pdf + body = _pdf_to_markdown_pdfplumber( + _download_arxiv_pdf(arxiv_id, self.timeout, self.download_delay) or b"" + ) + md_parts.append(body or "") + else: + pdf_bytes = _download_arxiv_pdf(arxiv_id, self.timeout, self.download_delay) + if not pdf_bytes: + sample[self.output_key] = "\n".join(md_parts).strip() if md_parts else "" + return sample + if self.backend == "mineru": + body = _pdf_to_markdown_mineru(pdf_bytes, keep_images=self.keep_images) + else: + body = _pdf_to_markdown_pdfplumber(pdf_bytes) + md_parts.append(body) + + sample[self.output_key] = "\n".join(md_parts).strip() + return sample diff --git a/data_juicer/ops/mapper/pdf_to_markdown_mapper.py b/data_juicer/ops/mapper/pdf_to_markdown_mapper.py new file mode 100644 index 0000000000..a15f251d55 --- /dev/null +++ b/data_juicer/ops/mapper/pdf_to_markdown_mapper.py @@ -0,0 +1,165 @@ +# Copyright 2025 The DataJuicer Authors. All rights reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +""" +Mapper to convert PDF content to high-precision structured Markdown. + +Reads PDF from a field (file path or bytes), converts to a single structured +Markdown string. Supports mineru (MinerU/magic-pdf) for high precision or +pdfplumber as built-in fallback. Images can be discarded for chunking/LLM use. +""" + +import io +import os +import re +import tempfile +from typing import Optional, Union + +import pdfplumber +from loguru import logger + +from data_juicer.utils.lazy_loader import LazyLoader + +from ..base_op import OPERATORS, Mapper + +magic_pdf = LazyLoader("magic_pdf", "magic-pdf") + +OP_NAME = "pdf_to_markdown_mapper" + + +def _ensure_pdf_bytes(pdf_field_value: Union[str, bytes]) -> Optional[bytes]: + """Return PDF bytes from path or bytes.""" + if isinstance(pdf_field_value, bytes): + return pdf_field_value if pdf_field_value else None + if isinstance(pdf_field_value, str) and os.path.isfile(pdf_field_value): + try: + with open(pdf_field_value, "rb") as f: + return f.read() + except Exception as e: + logger.warning(f"Failed to read PDF file {pdf_field_value}: {e}") + return None + return None + + +def _pdf_to_markdown_pdfplumber(pdf_bytes: bytes) -> str: + """Convert PDF bytes to plain text with minimal structure using pdfplumber.""" + try: + with io.BytesIO(pdf_bytes) as f: + with pdfplumber.open(f) as pdf: + parts = [] + for i, page in enumerate(pdf.pages): + tables = page.find_tables() + for table in tables: + page = page.outside_bbox(table.bbox) + text = page.extract_text() + if not text: + continue + page_num = str(page.page_number) + if text.rstrip().endswith(page_num): + text = text.rstrip()[: -len(page_num)] + if text.strip(): + parts.append(f"## Page {i + 1}\n\n{text.strip()}") + return "\n\n".join(parts) if parts else "" + except Exception as e: + logger.warning(f"pdfplumber failed to parse PDF: {e}") + return "" + + +def _pdf_to_markdown_mineru(pdf_bytes: bytes, keep_images: bool = False) -> str: + """Convert PDF bytes to structured Markdown using MinerU (magic-pdf).""" + try: + from magic_pdf.data.data_reader_writer import FileBasedDataWriter + from magic_pdf.data.dataset import PymuDocDataset + from magic_pdf.model.doc_analyze_by_custom_model import doc_analyze + from magic_pdf.config.enums import SupportedPdfParseMethod + except ImportError as e: + logger.warning(f"magic-pdf not available, fallback to pdfplumber: {e}") + return _pdf_to_markdown_pdfplumber(pdf_bytes) + + with tempfile.TemporaryDirectory() as tmpdir: + image_dir = os.path.join(tmpdir, "images") + os.makedirs(image_dir, exist_ok=True) + image_writer = FileBasedDataWriter(image_dir) + + try: + ds = PymuDocDataset(pdf_bytes) + if ds.classify() == SupportedPdfParseMethod.OCR: + infer_result = ds.apply(doc_analyze, ocr=True) + pipe_result = infer_result.pipe_ocr_mode(image_writer) + else: + infer_result = ds.apply(doc_analyze, ocr=False) + pipe_result = infer_result.pipe_txt_mode(image_writer) + + image_dir_basename = "images" + md_content = pipe_result.get_markdown(image_dir_basename) + if not keep_images and md_content: + md_content = re.sub(r"!\[[^\]]*\]\([^)]+\)", "", md_content) + md_content = re.sub(r"\n{3,}", "\n\n", md_content).strip() + return md_content or _pdf_to_markdown_pdfplumber(pdf_bytes) + except Exception as e: + logger.warning(f"MinerU conversion failed, fallback to pdfplumber: {e}") + return _pdf_to_markdown_pdfplumber(pdf_bytes) + + +@OPERATORS.register_module(OP_NAME) +class PdfToMarkdownMapper(Mapper): + """Convert PDF (path or bytes) to a single structured Markdown document. + + Use with download_file_mapper (save_field as bytes or path) for URLs, or + with datasets that already contain PDF paths/bytes. Images are dropped by + default for easier chunking and LLM consumption. + """ + + _batched_op = False + + _requirements = ["magic-pdf"] + + def __init__( + self, + pdf_key: str = "pdf", + backend: str = "mineru", + keep_images: bool = False, + output_key: Optional[str] = None, + *args, + **kwargs, + ): + """ + :param pdf_key: Field name containing PDF file path (str) or PDF bytes (bytes). + :param backend: "mineru" (MinerU/magic-pdf, high precision) or "pdfplumber" (built-in). + :param keep_images: If True, keep image references in Markdown (mineru only). + :param output_key: Field to write Markdown to; default is text_key. + """ + super().__init__(*args, **kwargs) + self._init_parameters = self.remove_extra_parameters(locals()) + self.pdf_key = pdf_key + self.backend = backend.lower() + self.keep_images = keep_images + self.output_key = output_key or self.text_key + if self.backend not in ("mineru", "pdfplumber"): + raise ValueError("backend must be one of mineru, pdfplumber") + + def process_single(self, sample): + raw = sample.get(self.pdf_key) + pdf_bytes = _ensure_pdf_bytes(raw) + if not pdf_bytes: + logger.warning(f"Missing or invalid PDF at key {self.pdf_key}") + sample[self.output_key] = sample.get(self.text_key, "") + return sample + + if self.backend == "mineru": + md = _pdf_to_markdown_mineru(pdf_bytes, keep_images=self.keep_images) + else: + md = _pdf_to_markdown_pdfplumber(pdf_bytes) + sample[self.output_key] = md + return sample diff --git a/docs/operators/mapper/arxiv_to_markdown_mapper.md b/docs/operators/mapper/arxiv_to_markdown_mapper.md new file mode 100644 index 0000000000..518bde1f7b --- /dev/null +++ b/docs/operators/mapper/arxiv_to_markdown_mapper.md @@ -0,0 +1,44 @@ +# arxiv_to_markdown_mapper + +Mapper to convert arXiv paper ID to high-precision structured Markdown in a single document. + +Given an arXiv paper ID (e.g. `2501.14755` or `hep-th/9901001`), this operator downloads the PDF or crawls the page and converts it to a single structured Markdown string. **MinerU** (default) gives the best conversion quality; **crawl4ai** first tries the **HTML full-text page** (e.g. `https://arxiv.org/html/2501.14755v1`) when available, then the abstract page, then falls back to PDF. Images are dropped by default for smaller output and easier chunking or LLM consumption. + +根据 arXiv 论文 ID 将论文转换为高精度结构化的 Markdown 单文件。默认 **MinerU** 转换质量最佳；**crawl4ai** 会优先抓取 **HTML 全文页**（如 `https://arxiv.org/html/2501.14755v1`），若无则抓摘要页，再失败则回退到 PDF。图片默认丢弃。 + +Type 算子类型: **mapper** + +Tags 标签: cpu, text + +## 🔧 Parameter Configuration 参数配置 + +| name 参数名 | type 类型 | default 默认值 | desc 说明 | +|--------|------|--------|------| +| `arxiv_id_key` | str | `"arxiv_id"` | Field name for arXiv ID or URL. 存 arXiv ID 或 URL 的字段名。 | +| `backend` | str | `"mineru"` | `mineru` (推荐，MinerU 高精度), `pdfplumber` (内置回退，仅文本), `crawl4ai` (优先 HTML 全文页，再摘要页，最后 PDF). 转换后端。 | +| `add_metadata_header` | bool | `True` | Prepend title, authors, abstract from arXiv API. 是否从 API 拉取并写入元数据头部。 | +| `keep_images` | bool | `False` | Keep image refs in Markdown (mineru only). 是否保留图片引用。 | +| `timeout` | int | `60` | Request timeout (seconds). 请求超时（秒）。 | +| `download_delay` | float | `1.0` | Delay before each download (rate limiting). 每次下载前延迟（秒）。 | +| `output_key` | str | `text_key` | Field to write Markdown to. 写入 Markdown 的字段名。 | + +## 📦 Dependencies 依赖 + +- Built-in: `pdfplumber`, `requests` +- Optional: `magic-pdf` (MinerU), `crawl4ai`. Install: `pip install py-data-juicer[document]` + +## 📋 YAML Example 配置示例 + +```yaml +- arxiv_to_markdown_mapper: + arxiv_id_key: arxiv_id + backend: mineru # recommended; use pdfplumber if magic-pdf not installed + add_metadata_header: true + output_key: text +``` + +## 🔗 Related links 相关链接 + +- [source code 源代码](../../../data_juicer/ops/mapper/arxiv_to_markdown_mapper.py) +- [unit test 单元测试](../../../tests/ops/mapper/test_arxiv_to_markdown_mapper.py) +- [Return operator list 返回算子列表](../../Operators.md) diff --git a/docs/operators/mapper/pdf_to_markdown_mapper.md b/docs/operators/mapper/pdf_to_markdown_mapper.md new file mode 100644 index 0000000000..a00e3fe2df --- /dev/null +++ b/docs/operators/mapper/pdf_to_markdown_mapper.md @@ -0,0 +1,40 @@ +# pdf_to_markdown_mapper + +Mapper to convert PDF (path or bytes) to high-precision structured Markdown. + +Reads PDF from a field (file path or bytes), converts to a single structured Markdown string. Use with `download_file_mapper` to download PDFs first. Images are dropped by default for chunking or LLM use. + +将 PDF（路径或字节）转换为高精度结构化的 Markdown 单文件。可与 download_file_mapper 配合使用。图片默认丢弃。 + +Type 算子类型: **mapper** + +Tags 标签: cpu, text + +## 🔧 Parameter Configuration 参数配置 + +| name 参数名 | type 类型 | default 默认值 | desc 说明 | +|--------|------|--------|------| +| `pdf_key` | str | `"pdf"` | Field containing PDF path (str) or bytes. 存 PDF 路径或字节的字段名。 | +| `backend` | str | `"mineru"` | `mineru` (推荐，MinerU 高精度) 或 `pdfplumber` (内置回退). 转换后端。 | +| `keep_images` | bool | `False` | Keep image refs in Markdown (mineru only). 是否保留图片引用。 | +| `output_key` | str | `text_key` | Field to write Markdown to. 写入 Markdown 的字段名。 | + +## 📦 Dependencies 依赖 + +- Built-in: `pdfplumber` +- Optional: `magic-pdf`. Install: `pip install py-data-juicer[document]` + +## 📋 YAML Example 配置示例 + +```yaml +- pdf_to_markdown_mapper: + pdf_key: pdf + backend: mineru # recommended; use pdfplumber if magic-pdf not installed + output_key: text +``` + +## 🔗 Related links 相关链接 + +- [source code 源代码](../../../data_juicer/ops/mapper/pdf_to_markdown_mapper.py) +- [unit test 单元测试](../../../tests/ops/mapper/test_pdf_to_markdown_mapper.py) +- [Return operator list 返回算子列表](../../Operators.md) diff --git a/pyproject.toml b/pyproject.toml index 195d29ec2a..aadf86a698 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -118,6 +118,12 @@ audio = [ "audiomentations", ] +# Document / arXiv to Markdown (arxiv_to_markdown_mapper, pdf_to_markdown_mapper) +document = [ + "mineru", # MinerU: high-precision PDF to Markdown + "crawl4ai", # arXiv abstract page to Markdown (optional backend) +] + # Distributed Computing distributed = [ "ray[default]>=2.51.0", # distributed computing @@ -175,6 +181,7 @@ dj-process = "data_juicer.tools.process_data:main" dj-analyze = "data_juicer.tools.analyze_data:main" dj-install = "data_juicer.tools.dj_install:main" dj-mcp = "data_juicer.tools.mcp_server:main" +dj-op = "data_juicer.tools.run_op:main" [build-system] requires = [ diff --git a/tests/ops/mapper/test_arxiv_to_markdown_mapper.py b/tests/ops/mapper/test_arxiv_to_markdown_mapper.py new file mode 100644 index 0000000000..d0d9c90e8c --- /dev/null +++ b/tests/ops/mapper/test_arxiv_to_markdown_mapper.py @@ -0,0 +1,71 @@ +import unittest + +from data_juicer.ops.mapper.arxiv_to_markdown_mapper import ( + ARXIV_HTML_URL_TEMPLATE, + _normalize_arxiv_id, + _normalize_arxiv_id_keep_version, + ArxivToMarkdownMapper, +) +from data_juicer.utils.unittest_utils import DataJuicerTestCaseBase + + +class ArxivToMarkdownMapperTest(DataJuicerTestCaseBase): + def setUp(self): + super().setUp() + self.op = ArxivToMarkdownMapper(arxiv_id_key="arxiv_id", backend="pdfplumber") + + def test_normalize_arxiv_id(self): + self.assertEqual(_normalize_arxiv_id("2501.14755"), "2501.14755") + self.assertEqual(_normalize_arxiv_id(" 2501.14755 "), "2501.14755") + self.assertEqual( + _normalize_arxiv_id("https://arxiv.org/abs/2501.14755"), + "2501.14755", + ) + self.assertEqual( + _normalize_arxiv_id("https://arxiv.org/pdf/2501.14755.pdf"), + "2501.14755", + ) + self.assertEqual(_normalize_arxiv_id("hep-th/9901001"), "hep-th/9901001") + self.assertEqual(_normalize_arxiv_id("2501.14755v1"), "2501.14755") + self.assertEqual(_normalize_arxiv_id("hep-th/9901001v2"), "hep-th/9901001") + self.assertIsNone(_normalize_arxiv_id("")) + self.assertIsNone(_normalize_arxiv_id(None)) + + def test_normalize_arxiv_id_keep_version(self): + self.assertEqual(_normalize_arxiv_id_keep_version("2501.14755v1"), "2501.14755v1") + self.assertEqual(_normalize_arxiv_id_keep_version("2501.14755"), "2501.14755") + self.assertEqual( + _normalize_arxiv_id_keep_version("https://arxiv.org/html/2501.14755v1"), + "2501.14755v1", + ) + self.assertEqual( + _normalize_arxiv_id_keep_version("https://arxiv.org/abs/2501.14755v1"), + "2501.14755v1", + ) + self.assertIsNone(_normalize_arxiv_id_keep_version("")) + + def test_html_url_template(self): + self.assertEqual( + ARXIV_HTML_URL_TEMPLATE.format(arxiv_id="2501.14755v1"), + "https://arxiv.org/html/2501.14755v1", + ) + + def test_missing_arxiv_id(self): + sample = {"text": "original"} + out = self.op.process_single(sample) + self.assertIn("text", out) + self.assertEqual(out["text"], "original") + + def test_output_key(self): + op = ArxivToMarkdownMapper( + arxiv_id_key="id", + backend="pdfplumber", + output_key="markdown", + ) + sample = {"id": "invalid_blank", "text": "x"} + out = op.process_single(sample) + self.assertIn("markdown", out) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/ops/mapper/test_pdf_to_markdown_mapper.py b/tests/ops/mapper/test_pdf_to_markdown_mapper.py new file mode 100644 index 0000000000..2aa65d93a1 --- /dev/null +++ b/tests/ops/mapper/test_pdf_to_markdown_mapper.py @@ -0,0 +1,73 @@ +import unittest + +from data_juicer.ops.mapper.pdf_to_markdown_mapper import ( + PdfToMarkdownMapper, + _ensure_pdf_bytes, + _pdf_to_markdown_pdfplumber, +) +from data_juicer.utils.unittest_utils import DataJuicerTestCaseBase + + +def _make_minimal_pdf_bytes() -> bytes: + """Create minimal valid PDF bytes for testing.""" + # Minimal PDF with one empty page (pdfplumber can open it) + return b"""%PDF-1.4 +1 0 obj << /Type /Catalog /Pages 2 0 R >> endobj +2 0 obj << /Type /Pages /Kids [3 0 R] /Count 1 >> endobj +3 0 obj << /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >> endobj +xref +0 4 +0000000000 65535 f +0000000009 00000 n +0000000058 00000 n +0000000115 00000 n +trailer << /Size 4 /Root 1 0 R >> +startxref +190 +%%EOF""" + + +class PdfToMarkdownMapperTest(DataJuicerTestCaseBase): + def setUp(self): + super().setUp() + self.op = PdfToMarkdownMapper(pdf_key="pdf", backend="pdfplumber") + + def test_ensure_pdf_bytes_from_bytes(self): + raw = b"%PDF-1.4 dummy" + self.assertEqual(_ensure_pdf_bytes(raw), raw) + self.assertIsNone(_ensure_pdf_bytes(b"")) + + def test_ensure_pdf_bytes_from_path(self): + import tempfile + with tempfile.NamedTemporaryFile(suffix=".pdf", delete=False) as f: + f.write(b"%PDF-1.4 x") + path = f.name + try: + out = _ensure_pdf_bytes(path) + self.assertIsInstance(out, bytes) + self.assertEqual(out, b"%PDF-1.4 x") + finally: + import os + os.unlink(path) + + def test_missing_pdf(self): + sample = {"text": "original"} + out = self.op.process_single(sample) + self.assertEqual(out["text"], "original") + + def test_pdfplumber_empty_page(self): + pdf_bytes = _make_minimal_pdf_bytes() + md = _pdf_to_markdown_pdfplumber(pdf_bytes) + # May be empty or have "Page 1" depending on pdfplumber + self.assertIsInstance(md, str) + + def test_output_key(self): + op = PdfToMarkdownMapper(pdf_key="content", backend="pdfplumber", output_key="md") + sample = {"content": _make_minimal_pdf_bytes(), "text": "x"} + out = op.process_single(sample) + self.assertIn("md", out) + self.assertIsInstance(out["md"], str) + + +if __name__ == "__main__": + unittest.main() diff --git a/tools/run_op.py b/tools/run_op.py new file mode 100644 index 0000000000..cde60e9c6a --- /dev/null +++ b/tools/run_op.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python3 +""" +Quick one-shot run of a Data-Juicer operator on a single sample. + +Usage: + dj-op [sample_json] + echo '{"arxiv_id":"2501.14755"}' | dj-op arxiv_to_markdown_mapper + dj-op whitespace_normalization_mapper '{"text":" hello "}' + dj-op arxiv_to_markdown_mapper '{"arxiv_id":"2501.14755"}' --backend mineru + +Sample can be a JSON object from positional arg, stdin, or minimal default. +Output: JSON object of the processed sample to stdout. +""" +import argparse +import base64 +import json +import sys + +from loguru import logger + +from data_juicer.ops import OPERATORS + + +def main(): + parser = argparse.ArgumentParser( + description="Run a Data-Juicer operator on one sample (minimal/quick test).", + epilog="Example: dj-op arxiv_to_markdown_mapper '{\"arxiv_id\":\"2501.14755\"}' (default: mineru)", + ) + parser.add_argument( + "--list", + action="store_true", + help="List available operator names and exit", + ) + parser.add_argument( + "op_name", + type=str, + nargs="?", + default=None, + help="Operator name (e.g. arxiv_to_markdown_mapper, whitespace_normalization_mapper)", + ) + parser.add_argument( + "sample_json", + type=str, + nargs="?", + default=None, + help="JSON object for one sample; if omitted, read from stdin or use minimal default", + ) + # Forward unknown args as op kwargs (e.g. --backend mineru) + args, unknown = parser.parse_known_args() + + if args.list: + names = sorted(OPERATORS.modules.keys()) + for n in names: + print(n) + return 0 + + if not args.op_name or args.op_name not in OPERATORS.modules: + logger.error(f"Unknown operator: {args.op_name!r}. Use --list to list names.") + return 1 + + # Parse op kwargs from --key val + op_kwargs = {} + i = 0 + while i < len(unknown): + key = unknown[i] + if key.startswith("--"): + key = key[2:].replace("-", "_") + if i + 1 < len(unknown) and not unknown[i + 1].startswith("--"): + val = unknown[i + 1] + try: + val = json.loads(val) + except json.JSONDecodeError: + pass + op_kwargs[key] = val + i += 2 + else: + op_kwargs[key] = True + i += 1 + else: + i += 1 + + # Sample: from arg, stdin, or minimal default + if args.sample_json: + try: + sample = json.loads(args.sample_json) + except json.JSONDecodeError as e: + logger.error(f"Invalid sample JSON: {e}") + return 1 + elif not sys.stdin.isatty(): + try: + sample = json.load(sys.stdin) + except json.JSONDecodeError as e: + logger.error(f"Invalid JSON from stdin: {e}") + return 1 + else: + sample = {} + if "text" not in sample and "arxiv_id" not in sample: + sample["text"] = "" + + op_class = OPERATORS.modules[args.op_name] + op = op_class(**op_kwargs) + out = op.process(sample) + if isinstance(out, dict) and not any(isinstance(v, list) for v in out.values()): + result = out + else: + # Batched return: dict of lists -> take first + result = {k: (v[0] if isinstance(v, list) else v) for k, v in out.items()} + + def _json_serial(obj): + if isinstance(obj, bytes): + return "" + raise TypeError(f"Object of type {type(obj).__name__} is not JSON serializable") + + try: + print(json.dumps(result, ensure_ascii=False, indent=2, default=_json_serial)) + except TypeError: + print(json.dumps(result, ensure_ascii=False, indent=2)) + return 0 + + +if __name__ == "__main__": + sys.exit(main() or 0) diff --git a/uv.lock b/uv.lock index 30ec79b554..3c38adfc99 100644 --- a/uv.lock +++ b/uv.lock @@ -191,6 +191,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/95/2a/d275ec4ce5cd0096665043995a7d76f5d0524853c76a3d04656de49f8808/aiobotocore-2.25.1-py3-none-any.whl", hash = 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