diff --git a/.mailmap b/.mailmap index bc4072974..8470c3c31 100644 --- a/.mailmap +++ b/.mailmap @@ -12,3 +12,4 @@ Michael Skarlinski mskarlin <12701035+mskarlin@use Odhran O'Donoghue odhran-o-d Odhran O'Donoghue <39832722+odhran-o-d@users.noreply.github.com> Samantha Cox +takeru fukushima <100330935+takeruhukushima@users.noreply.github.com> diff --git a/README.md b/README.md index 7c83252a1..9063d48fc 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg) ![PyPI Python Versions](https://img.shields.io/pypi/pyversions/paper-qa) -PaperQA2 is a package for doing high-accuracy retrieval augmented generation (RAG) on PDFs or text files, +PaperQA2 is a package for doing high-accuracy retrieval augmented generation (RAG) on PDFs, text files, Microsoft Office documents, and source code files, with a focus on the scientific literature. See our [recent 2024 paper](https://paper.wikicrow.ai) to see examples of PaperQA2's superhuman performance in scientific tasks like @@ -395,7 +395,7 @@ It just removes the automation associated with an agent picking the documents to ```python from paperqa import Docs, Settings -# valid extensions include .pdf, .txt, .md, and .html +# valid extensions include .pdf, .txt, .md, .html, .docx, .xlsx, .pptx, and code files (e.g., .py, .ts, .yaml) doc_paths = ("myfile.pdf", "myotherfile.pdf") # Prepare the Docs object by adding a bunch of documents @@ -438,7 +438,7 @@ from paperqa import Docs async def main() -> None: docs = Docs() - # valid extensions include .pdf, .txt, .md, and .html + # valid extensions include .pdf, .txt, .md, .html, .docx, .xlsx, .pptx, and code files (e.g., .py, .ts, .yaml) for doc in ("myfile.pdf", "myotherfile.pdf"): await docs.aadd(doc) diff --git a/pyproject.toml b/pyproject.toml index ea4dfc3b7..5950ae3ae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ dev = [ "ipython>=8", # Pin to keep recent "litellm>=1.71", # Lower pin for aiohttp transport adoption "mypy>=1.8", # Pin for mutable-override - "paper-qa[docling,image,ldp,memory,pypdf-media,pymupdf,typing,zotero,local,qdrant]", + "paper-qa[docling,image,ldp,memory,pypdf-media,pymupdf,typing,zotero,local,qdrant,office]", "prek", "pydantic~=2.11", # Pin for start of model_fields deprecation "pylint-pydantic", @@ -92,6 +92,9 @@ memory = [ "paper-qa[ldp]", "usearch>=2.16.4", # Pin for Python 3.13 support ] +office = [ + "unstructured[docx,xlsx,pptx]", +] openreview = [ "openreview-py", ] diff --git a/src/paperqa/readers.py b/src/paperqa/readers.py index 2e3c45d2e..dd3e51c10 100644 --- a/src/paperqa/readers.py +++ b/src/paperqa/readers.py @@ -3,6 +3,7 @@ import asyncio import os from collections.abc import Awaitable, Callable +from importlib.metadata import version from math import ceil from pathlib import Path from typing import Literal, Protocol, cast, overload, runtime_checkable @@ -171,6 +172,61 @@ def parse_text( ) +def parse_office_doc( + path: str | os.PathLike, + **kwargs, +) -> ParsedText: + """Parse office documents (.docx, .xlsx, .pptx) using unstructured, extracting text and images.""" + try: + import unstructured + from unstructured.documents.elements import Image, Table + from unstructured.partition.auto import partition + except ImportError as exc: + raise ImportError( + "Could not import `unstructured` dependencies. " + "Please install with `pip install paper-qa[office]`." + ) from exc + UNSTRUCTURED_VERSION = version(unstructured.__name__) + elements = partition(str(path), **kwargs) + + content_dict = {} + media_list: list[ParsedMedia] = [] + current_text = "" + media_index = 0 + + for el in elements: + if isinstance(el, Image): + image_data = el.metadata.image_data + # Create a ParsedMedia object + parsed_media = ParsedMedia( + index=media_index, + data=image_data, + info={"suffix": el.metadata.image_mime_type}, + ) + media_list.append(parsed_media) + media_index += 1 + elif isinstance(el, Table): + # For tables, we could get the HTML representation for better structure + if el.metadata.text_as_html: + current_text += el.metadata.text_as_html + "\n\n" + else: + current_text += str(el) + "\n\n" + + # For office docs, we can treat the whole document as a single "page" + content_dict["1"] = (current_text, media_list) + + return ParsedText( + content=content_dict, + metadata=ParsedMetadata( + parsing_libraries=[f"{unstructured.__name__} ({UNSTRUCTURED_VERSION})"], + paperqa_version=pqa_version, + total_parsed_text_length=len(current_text), + count_parsed_media=len(media_list), + name=f"office_doc|path={path}", + ), + ) + + def chunk_text( parsed_text: ParsedText, doc: Doc, @@ -276,7 +332,7 @@ def chunk_code_text( IMAGE_EXTENSIONS = tuple({".png", ".jpg", ".jpeg"}) # When HTML reader supports images, add here -ENRICHMENT_EXTENSIONS = tuple({".pdf", *IMAGE_EXTENSIONS}) +ENRICHMENT_EXTENSIONS = tuple({".pdf", ".docx", ".xlsx", ".pptx", *IMAGE_EXTENSIONS}) @overload @@ -383,6 +439,9 @@ async def read_doc( # noqa: PLR0912 ) elif str_path.endswith(IMAGE_EXTENSIONS): parsed_text = await parse_image(path, **parser_kwargs) + elif str_path.endswith((".docx", ".xlsx", ".pptx")): + # TODO: Make parse_office_doc async + parsed_text = await asyncio.to_thread(parse_office_doc, path, **parser_kwargs) else: parsed_text = await asyncio.to_thread( parse_text, path, split_lines=True, **parser_kwargs @@ -412,7 +471,7 @@ async def read_doc( # noqa: PLR0912 f"|reduction=cl100k_base{enrichment_summary}" ), ) - elif str_path.endswith(".pdf"): + elif str_path.endswith((".pdf", ".docx", ".xlsx", ".pptx")): chunked_text = chunk_pdf( parsed_text, doc, chunk_chars=chunk_chars, overlap=overlap ) @@ -420,7 +479,7 @@ async def read_doc( # noqa: PLR0912 size=chunk_chars, overlap=overlap, name=( - f"paper-qa={pqa_version}|algorithm=overlap-pdf" + f"paper-qa={pqa_version}|algorithm=overlap-document" f"|size={chunk_chars}|overlap={overlap}{enrichment_summary}" ), ) @@ -445,6 +504,7 @@ async def read_doc( # noqa: PLR0912 f"|size={chunk_chars}|overlap={overlap}{enrichment_summary}" ), ) + else: chunked_text = chunk_code_text( parsed_text, doc, chunk_chars=chunk_chars, overlap=overlap diff --git a/src/paperqa/settings.py b/src/paperqa/settings.py index 2ade04db7..d90d35621 100644 --- a/src/paperqa/settings.py +++ b/src/paperqa/settings.py @@ -598,7 +598,7 @@ class IndexSettings(BaseModel): default=lambda f: ( f.suffix # TODO: add images after embeddings are supported - in {".txt", ".pdf", ".html", ".md"} + in {".txt", ".pdf", ".html", ".md", ".xlsx", ".docx", ".pptx"} ), exclude=True, description=( diff --git a/tests/stub_data/dummy.docx b/tests/stub_data/dummy.docx new file mode 100644 index 000000000..66ea45f30 Binary files /dev/null and b/tests/stub_data/dummy.docx differ diff --git a/tests/stub_data/dummy.pptx b/tests/stub_data/dummy.pptx new file mode 100644 index 000000000..f08325fb5 Binary files /dev/null and b/tests/stub_data/dummy.pptx differ diff --git a/tests/stub_data/dummy.xlsx b/tests/stub_data/dummy.xlsx new file mode 100644 index 000000000..2abcb4925 Binary files /dev/null and b/tests/stub_data/dummy.xlsx differ diff --git a/tests/test_agents.py b/tests/test_agents.py index d1f9719b9..a4b0b852a 100644 --- a/tests/test_agents.py +++ b/tests/test_agents.py @@ -91,11 +91,12 @@ async def test_get_directory_index( ], "Incorrect fields in index" assert not index.changed, "Expected index to not have changes at this point" # bates.txt + empty.txt + flag_day.html + gravity_hill.md + influence.pdf - # + obama.txt + paper.pdf + pasa.pdf + duplicate_media.pdf, + # + obama.txt + paper.pdf + pasa.pdf + duplicate_media.pdf + # + dummy.docx + dummy.pptx + dummy.xlsx, # but empty.txt fails to be added path_to_id = await index.index_files assert ( - sum(id_ != FAILED_DOCUMENT_ADD_ID for id_ in path_to_id.values()) == 8 + sum(id_ != FAILED_DOCUMENT_ADD_ID for id_ in path_to_id.values()) == 11 ), "Incorrect number of parsed index files" with subtests.test(msg="check-txt-query"): @@ -159,9 +160,9 @@ async def test_get_directory_index( ), ): index = await get_directory_index(settings=agent_test_settings) - # Subtract 1 for the removed obama.txt file, + # Subtract 4 for the removed obama.txt, dummy.docx, dummy.pptx, and dummy.xlsx files, # and another 1 for the filtered out flag_day.html - assert len(await index.index_files) == len(path_to_id) - 2 + assert len(await index.index_files) == len(path_to_id) - 4 - 1 mock_aadd.assert_not_awaited(), "Expected we didn't re-add files" # Note let's delete files.zip, and confirm we can't load the index @@ -261,6 +262,9 @@ async def test_getting_manifest( "obama.txt", "paper.pdf", "pasa.pdf", + "dummy.docx", + "dummy.pptx", + "dummy.xlsx", } diff --git a/tests/test_paperqa.py b/tests/test_paperqa.py index b31049dae..53dfeab2d 100644 --- a/tests/test_paperqa.py +++ b/tests/test_paperqa.py @@ -1385,7 +1385,7 @@ async def test_chunk_metadata_reader( assert "pdf" in metadata.name assert isinstance(metadata.chunk_metadata, ChunkMetadata) assert metadata.chunk_metadata.name - assert "overlap-pdf" in metadata.chunk_metadata.name + assert "overlap-document" in metadata.chunk_metadata.name assert metadata.chunk_metadata.overlap == 100 assert metadata.chunk_metadata.size == 3000 assert len(chunk_text) > 2, "Expected multiple chunks, for meaningful assertions" @@ -3108,3 +3108,36 @@ async def test_reader_config_propagation(stub_data_dir: Path) -> None: assert mock_read_doc.call_args.kwargs["chunk_chars"] == 2000 assert mock_read_doc.call_args.kwargs["overlap"] == 50 assert mock_read_doc.call_args.kwargs["dpi"] == 144 + + +@pytest.mark.asyncio +@pytest.mark.parametrize( + ("filename", "query"), + [ + ("dummy.docx", "What is the RAG system?"), + ("dummy.pptx", "What is the RAG system?"), + ("dummy.xlsx", "What is the price of a laptop?"), + ], +) +async def test_parse_office_doc(stub_data_dir: Path, filename: str, query: str) -> None: + docs = Docs() + + settings = Settings( + llm="gemini/gemini-2.5-flash", + embedding="gemini/text-embedding-004", + summary_llm="gemini/gemini-2.5-flash", + agent={"agent_llm": "gemini/gemini-2.5-flash"}, + parsing=ParsingSettings(use_doc_details=False), + ) + docname = await docs.aadd( + stub_data_dir / filename, + citation="dummy citation", + docname=filename, + settings=settings, + ) + assert docname is not None + assert 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