From 89089afb4a8d0bb43e20969bd1d3fb26d7cb5c70 Mon Sep 17 00:00:00 2001 From: emrgnt-cmplxty <68796651+emrgnt-cmplxty@users.noreply.github.com> Date: Mon, 14 Oct 2024 11:34:25 -0700 Subject: [PATCH] Feature/add zerox parser (#1394) * Add KG tests (#1351) * cli tests * add sdk tests * typo fix * change workflow ordering * add collection integration tests (#1352) * bump pkg * remove workflows * fix sdk test port * fix delete collection return check * Fix document info serialization (#1353) * Update integration-test-workflow-debian.yml * pre-commit * slightly modify * up * up * smaller file * up * typo, change order * up * up * change order --------- Co-authored-by: emrgnt-cmplxty <68796651+emrgnt-cmplxty@users.noreply.github.com> Co-authored-by: emrgnt-cmplxty Co-authored-by: Nolan Tremelling <34580718+NolanTrem@users.noreply.github.com> * add graphrag docs (#1362) * add documentation * up * Update js/sdk/src/models.tsx Co-authored-by: ellipsis-dev[bot] <65095814+ellipsis-dev[bot]@users.noreply.github.com> * pre-commit --------- Co-authored-by: ellipsis-dev[bot] <65095814+ellipsis-dev[bot]@users.noreply.github.com> * Concurrent index creation, allow -1 for paginated entries (#1363) * update webdev-template for current next.js and r2r-js sdk (#1218) Co-authored-by: Simeon * Feature/extend integration tests rebased (#1361) * cleanups * add back overzealous edits * extend workflows * fix full setup * simplify cli * add ymls * rename to light * try again * start light * add cli tests * fix * fix * testing.. * trying complete matrix testflow * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * up * up * up * All actions * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * try offic pgvec formula * sudo make * sudo make * push and pray * push and pray * add new actions * add new actions * docker push & pray * inspect manifests during launch * inspect manifests during launch * inspect manifests during launch * inspect manifests during launch * setup docker * setup docker * fix default * fix default * Feature/rebase to r2r vars (#1364) * cleanups * add back overzealous edits * extend workflows * fix full setup * simplify cli * add ymls * rename to light * try again * start light * add cli tests * fix * fix * testing.. * trying complete matrix testflow * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * cleanup matrix logic * up * up * up * All actions * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * rename to runner * try offic pgvec formula * sudo make * sudo make * push and pray * push and pray * add new actions * add new actions * docker push & pray * inspect manifests during launch * inspect manifests during launch * inspect manifests during launch * inspect manifests during launch * setup docker * setup docker * fix default * fix default * make changes * update the windows workflow * update the windows workflow * remove extra workflows for now * bump pkg * push and pray * revive full workflow * revive full workflow * revive full workflow * revive full workflow * revive full workflow * revive full workflow * revive full workflow * revive full workflow * revive tests * revive tests * revive tests * revive tests * update tests * fix typos (#1366) * update tests * up * up * up * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * bump max connections * Add ingestion concurrency limit (#1367) * up * up * up --------- Co-authored-by: --global=Shreyas Pimpalgaonkar <--global=shreyas.gp.7@gmail.com> * tweaks and fixes * Fix Ollama Tool Calling (#1372) * Update graphrag.mdx * Fix Ollama tool calling --------- Co-authored-by: Shreyas Pimpalgaonkar * Clean up Docker Compose (#1368) * Fix hatchet, dockerfile * Update compose * point to correct docker image * Fix bug in deletion, better validation error handling (#1374) * Update graphrag.mdx * Fix bug in deletion, better validation error handling --------- Co-authored-by: Shreyas Pimpalgaonkar * vec index creation endpoint (#1373) * Update graphrag.mdx * upload files * create vector index endpoint * add to fastapi background task * pre-commit * move logging * add api spec, support for all vecs * pre-commit * add workflow * Modify KG Endpoints and update API spec (#1369) * Update graphrag.mdx * modify API endpoints and update documentation * Update ingestion_router.py * try different docker setup (#1371) * try different docker setup * action * add login * add full * update action * cleanup upload script * cleanup upload script * tweak action * tweak action * tweak action * tweak action * tweak action * tweak action * Nolan/ingest chunks js (#1375) * Update graphrag.mdx * Clean up ingest chunks, add to JS SDK * Update JS docs --------- Co-authored-by: Shreyas Pimpalgaonkar * up (#1376) * Bump JS package (#1378) * add conversation * checkin progress * checkin progress * Fix Create Graph (#1379) * up * up * modify assertion * up * up * increase entity limit * changing aristotle back to v2 * pre-commit * typos * add test_ingest_sample_file_2_sdk * Update server.py * checkin progress * up * update * Graphrag docs (#1382) * add docs and refine code * add python SDK documentation * up * update * checkin * up * cleanup * working sync logging * test conversation history * fix runner tests, rename `CHUNKS` to `chunks` * adding zerox parser --------- Co-authored-by: Shreyas Pimpalgaonkar Co-authored-by: Nolan Tremelling <34580718+NolanTrem@users.noreply.github.com> Co-authored-by: ellipsis-dev[bot] <65095814+ellipsis-dev[bot]@users.noreply.github.com> Co-authored-by: FutureProofTechOps Co-authored-by: Simeon Co-authored-by: --global=Shreyas Pimpalgaonkar <--global=shreyas.gp.7@gmail.com> --- py/Dockerfile | 2 + py/core/base/parsers/base_parser.py | 4 +- py/core/base/providers/ingestion.py | 1 + py/core/parsers/media/__init__.py | 2 + py/core/parsers/media/audio_parser.py | 2 +- py/core/parsers/media/docx_parser.py | 2 +- py/core/parsers/media/img_parser.py | 2 +- py/core/parsers/media/pdf_parser.py | 59 +- py/core/parsers/media/ppt_parser.py | 2 +- py/core/parsers/media/zerox | 1 + py/core/providers/ingestion/r2r/base.py | 91 +- py/poetry.lock | 1377 ++++++++++++----------- py/pyproject.toml | 25 +- py/r2r.toml | 4 + 14 files changed, 900 insertions(+), 674 deletions(-) create mode 160000 py/core/parsers/media/zerox diff --git a/py/Dockerfile b/py/Dockerfile index e04be3e7c..0db577a1e 100644 --- a/py/Dockerfile +++ b/py/Dockerfile @@ -3,11 +3,13 @@ FROM python:3.10-slim AS builder # Install system dependencies RUN apt-get update && apt-get install -y --no-install-recommends \ gcc g++ musl-dev curl libffi-dev gfortran libopenblas-dev \ + poppler-utils \ && apt-get clean && rm -rf /var/lib/apt/lists/* \ && curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y RUN pip install --no-cache-dir poetry + # Add Rust to PATH ENV PATH="/root/.cargo/bin:${PATH}" diff --git a/py/core/base/parsers/base_parser.py b/py/core/base/parsers/base_parser.py index f2d7cd02c..d0bc8633c 100644 --- a/py/core/base/parsers/base_parser.py +++ b/py/core/base/parsers/base_parser.py @@ -10,5 +10,7 @@ class AsyncParser(ABC, Generic[T]): @abstractmethod - async def ingest(self, data: T) -> AsyncGenerator[DataType, None]: + async def ingest( + self, data: T, **kwargs + ) -> AsyncGenerator[DataType, None]: pass diff --git a/py/core/base/providers/ingestion.py b/py/core/base/providers/ingestion.py index b11ec5c84..706d7e264 100644 --- a/py/core/base/providers/ingestion.py +++ b/py/core/base/providers/ingestion.py @@ -10,6 +10,7 @@ class IngestionConfig(ProviderConfig): provider: str = "r2r" excluded_parsers: list[str] = ["mp4"] + extra_parsers: dict[str, str] = {} @property def supported_providers(self) -> list[str]: diff --git a/py/core/parsers/media/__init__.py b/py/core/parsers/media/__init__.py index 075276e33..71c9bf0df 100644 --- a/py/core/parsers/media/__init__.py +++ b/py/core/parsers/media/__init__.py @@ -5,6 +5,7 @@ PDFParser, PDFParserMarker, PDFParserUnstructured, + ZeroxPDFParser, ) from .ppt_parser import PPTParser @@ -14,6 +15,7 @@ "ImageParser", "PDFParser", "PDFParserUnstructured", + "ZeroxPDFParser", "PDFParserMarker", "PPTParser", ] diff --git a/py/core/parsers/media/audio_parser.py b/py/core/parsers/media/audio_parser.py index 149b6352c..d6a3b2913 100644 --- a/py/core/parsers/media/audio_parser.py +++ b/py/core/parsers/media/audio_parser.py @@ -15,7 +15,7 @@ def __init__( self.openai_api_key = os.environ.get("OPENAI_API_KEY") async def ingest( # type: ignore - self, data: bytes, chunk_size: int = 1024 + self, data: bytes, chunk_size: int = 1024, **kwargs ) -> AsyncGenerator[str, None]: """Ingest audio data and yield a transcription.""" temp_audio_path = "temp_audio.wav" diff --git a/py/core/parsers/media/docx_parser.py b/py/core/parsers/media/docx_parser.py index acf471d9a..8fbb9fd69 100644 --- a/py/core/parsers/media/docx_parser.py +++ b/py/core/parsers/media/docx_parser.py @@ -18,7 +18,7 @@ def __init__(self): "Error, `python-docx` is required to run `DOCXParser`. Please install it using `pip install python-docx`." ) - async def ingest(self, data: DataType) -> AsyncGenerator[str, None]: # type: ignore + async def ingest(self, data: DataType, **kwargs) -> AsyncGenerator[str, None]: # type: ignore """Ingest DOCX data and yield text from each paragraph.""" if isinstance(data, str): raise ValueError("DOCX data must be in bytes format.") diff --git a/py/core/parsers/media/img_parser.py b/py/core/parsers/media/img_parser.py index 29aeda54b..a844ec78e 100644 --- a/py/core/parsers/media/img_parser.py +++ b/py/core/parsers/media/img_parser.py @@ -27,7 +27,7 @@ def __init__( self.max_image_size = max_image_size async def ingest( # type: ignore - self, data: DataType, chunk_size: int = 1024 + self, data: DataType, chunk_size: int = 1024, **kwargs ) -> AsyncGenerator[str, None]: """Ingest image data and yield a description.""" diff --git a/py/core/parsers/media/pdf_parser.py b/py/core/parsers/media/pdf_parser.py index 9f3e7ad27..237efaf8d 100644 --- a/py/core/parsers/media/pdf_parser.py +++ b/py/core/parsers/media/pdf_parser.py @@ -10,6 +10,7 @@ from core.base.parsers.base_parser import AsyncParser logger = logging.getLogger(__name__) +ZEROX_DEFAULT_MODEL = "openai/gpt-4o-mini" class PDFParser(AsyncParser[DataType]): @@ -25,7 +26,9 @@ def __init__(self): "Error, `pypdf` is required to run `PyPDFParser`. Please install it using `pip install pypdf`." ) - async def ingest(self, data: DataType) -> AsyncGenerator[str, None]: + async def ingest( + self, data: DataType, **kwargs + ) -> AsyncGenerator[str, None]: """Ingest PDF data and yield text from each page.""" if isinstance(data, str): raise ValueError("PDF data must be in bytes format.") @@ -76,7 +79,7 @@ def __init__(self): "Error, `pdfminer.six` is required to run `PDFParser`. Please install it using `pip install pdfminer.six`." ) - async def ingest(self, data: bytes) -> AsyncGenerator[str, None]: + async def ingest(self, data: bytes, **kwargs) -> AsyncGenerator[str, None]: """Ingest PDF data and yield text from each page.""" if not isinstance(data, bytes): raise ValueError("PDF data must be in bytes format.") @@ -156,7 +159,9 @@ def __init__(self): f"Error, marker is not installed {e}, please install using `pip install marker-pdf` " ) - async def ingest(self, data: DataType) -> AsyncGenerator[str, None]: + async def ingest( + self, data: DataType, **kwargs + ) -> AsyncGenerator[str, None]: if isinstance(data, str): raise ValueError("PDF data must be in bytes format.") @@ -164,3 +169,51 @@ async def ingest(self, data: DataType) -> AsyncGenerator[str, None]: BytesIO(data), PDFParserMarker.model_refs ) yield text + + +class ZeroxPDFParser(AsyncParser[DataType]): + """An advanced PDF parser using zerox.""" + + def __init__(self): + """ + Use the zerox library to parse PDF data. + + Args: + cleanup (bool, optional): Whether to clean up temporary files after processing. Defaults to True. + concurrency (int, optional): The number of concurrent processes to run. Defaults to 10. + file_data (Optional[str], optional): The file data to process. Defaults to an empty string. + maintain_format (bool, optional): Whether to maintain the format from the previous page. Defaults to False. + model (str, optional): The model to use for generating completions. Defaults to "gpt-4o-mini". Refer to LiteLLM Providers for the correct model name, as it may differ depending on the provider. + temp_dir (str, optional): The directory to store temporary files, defaults to some named folder in system's temp directory. If already exists, the contents will be deleted before zerox uses it. + custom_system_prompt (str, optional): The system prompt to use for the model, this overrides the default system prompt of zerox.Generally it is not required unless you want some specific behaviour. When set, it will raise a friendly warning. Defaults to None. + kwargs (dict, optional): Additional keyword arguments to pass to the litellm.completion method. Refer to the LiteLLM Documentation and Completion Input for details. + + """ + try: + # from pyzerox import zerox + from .zerox.py_zerox.pyzerox import zerox + + self.zerox = zerox + + except ImportError as e: + raise ValueError( + f"Error, zerox is not installed {e}, please install using `pip install py-zerox` " + ) + + async def ingest( + self, data: DataType, **kwargs + ) -> AsyncGenerator[str, None]: + if isinstance(data, str): + raise ValueError("PDF data must be in bytes format.") + + model = kwargs.get("zerox_parsing_model", ZEROX_DEFAULT_MODEL) + model = model.split("/")[-1] # remove the provider prefix + + result = await self.zerox( + file_data=data, + model=model, + verbose=True, + ) + + for page in result.pages: + yield page.content diff --git a/py/core/parsers/media/ppt_parser.py b/py/core/parsers/media/ppt_parser.py index b623752ce..5f19a0171 100644 --- a/py/core/parsers/media/ppt_parser.py +++ b/py/core/parsers/media/ppt_parser.py @@ -18,7 +18,7 @@ def __init__(self): "Error, `python-pptx` is required to run `PPTParser`. Please install it using `pip install python-pptx`." ) - async def ingest(self, data: DataType) -> AsyncGenerator[str, None]: # type: ignore + async def ingest(self, data: DataType, **kwargs) -> AsyncGenerator[str, None]: # type: ignore """Ingest PPT data and yield text from each slide.""" if isinstance(data, str): raise ValueError("PPT data must be in bytes format.") diff --git a/py/core/parsers/media/zerox b/py/core/parsers/media/zerox new file mode 160000 index 000000000..bdc5f3d25 --- /dev/null +++ b/py/core/parsers/media/zerox @@ -0,0 +1 @@ +Subproject commit bdc5f3d258c3409ecb26c411870a1ff48f1f4cfd diff --git a/py/core/providers/ingestion/r2r/base.py b/py/core/providers/ingestion/r2r/base.py index 889c7b463..98f308f46 100644 --- a/py/core/providers/ingestion/r2r/base.py +++ b/py/core/providers/ingestion/r2r/base.py @@ -31,23 +31,33 @@ class R2RIngestionConfig(IngestionConfig): class R2RIngestionProvider(IngestionProvider): - AVAILABLE_PARSERS = { - DocumentType.CSV: [parsers.CSVParser, parsers.CSVParserAdvanced], - DocumentType.DOCX: [parsers.DOCXParser], - DocumentType.HTML: [parsers.HTMLParser], - DocumentType.HTM: [parsers.HTMLParser], - DocumentType.JSON: [parsers.JSONParser], - DocumentType.MD: [parsers.MDParser], - DocumentType.PDF: [parsers.PDFParser, parsers.PDFParserUnstructured], - DocumentType.PPTX: [parsers.PPTParser], - DocumentType.TXT: [parsers.TextParser], - DocumentType.XLSX: [parsers.XLSXParser, parsers.XLSXParserAdvanced], - DocumentType.GIF: [parsers.ImageParser], - DocumentType.JPEG: [parsers.ImageParser], - DocumentType.JPG: [parsers.ImageParser], - DocumentType.PNG: [parsers.ImageParser], - DocumentType.SVG: [parsers.ImageParser], - DocumentType.MP3: [parsers.AudioParser], + DEFAULT_PARSERS = { + DocumentType.CSV: parsers.CSVParser, + DocumentType.DOCX: parsers.DOCXParser, + DocumentType.HTML: parsers.HTMLParser, + DocumentType.HTM: parsers.HTMLParser, + DocumentType.JSON: parsers.JSONParser, + DocumentType.MD: parsers.MDParser, + DocumentType.PDF: parsers.PDFParser, + DocumentType.PPTX: parsers.PPTParser, + DocumentType.TXT: parsers.TextParser, + DocumentType.XLSX: parsers.XLSXParser, + DocumentType.GIF: parsers.ImageParser, + DocumentType.JPEG: parsers.ImageParser, + DocumentType.JPG: parsers.ImageParser, + DocumentType.PNG: parsers.ImageParser, + DocumentType.SVG: parsers.ImageParser, + DocumentType.MP3: parsers.AudioParser, + } + + EXTRA_PARSERS = { + DocumentType.CSV: {"advanced": parsers.CSVParserAdvanced}, + DocumentType.PDF: { + "unstructured": parsers.PDFParserUnstructured, + "zerox": parsers.ZeroxPDFParser, + "marker": parsers.PDFParserMarker, + }, + DocumentType.XLSX: {"advanced": parsers.XLSXParserAdvanced}, } IMAGE_TYPES = { @@ -70,14 +80,14 @@ def __init__(self, config: R2RIngestionConfig): ) def _initialize_parsers(self): - for doc_type, parser_infos in self.AVAILABLE_PARSERS.items(): - for parser_info in parser_infos: - if ( - doc_type not in self.config.excluded_parsers - and doc_type not in self.parsers - ): - # will choose the first parser in the list - self.parsers[doc_type] = parser_info() + for doc_type, parser in self.DEFAULT_PARSERS.items(): + # will choose the first parser in the list + if doc_type not in self.config.excluded_parsers: + self.parsers[doc_type] = parser() + for doc_type, doc_parser_name in self.config.extra_parsers.items(): + self.parsers[f"{doc_parser_name}_{str(doc_type)}"] = ( + R2RIngestionProvider.EXTRA_PARSERS[doc_type][doc_parser_name]() + ) def _build_text_splitter( self, ingestion_config_override: Optional[dict] = None @@ -178,8 +188,35 @@ async def parse( # type: ignore t0 = time.time() contents = "" - async for text in self.parsers[document.type].ingest(file_content): - contents += text + "\n" + parser_overrides = ingestion_config_override.get( + "parser_overrides", {} + ) + print("parser_overrides = ", parser_overrides) + print("document.type.value = ", document.type.value) + print( + "document.type.value in parser_overrides = ", + document.type.value in parser_overrides, + ) + if document.type.value in parser_overrides: + print("In zerox parser ...") + # TODO - Cleanup this approach to be less hardcoded + if ( + document.type != DocumentType.PDF + or parser_overrides[DocumentType.PDF.value] != "zerox" + ): + raise ValueError( + "Only Zerox PDF parser override is available." + ) + print("keys = ", self.parsers.keys()) + async for text in self.parsers[ + f"zerox_{DocumentType.PDF.value}" + ].ingest(file_content, **ingestion_config_override): + contents += text + "\n" + else: + async for text in self.parsers[document.type].ingest( + file_content, **ingestion_config_override + ): + contents += text + "\n" iteration = 0 chunks = self.chunk(contents, ingestion_config_override) diff --git a/py/poetry.lock b/py/poetry.lock index 07906bb8e..60b792c19 100644 --- a/py/poetry.lock +++ b/py/poetry.lock @@ -1,4 +1,15 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "24.1.0" +description = "File support for asyncio." +optional = false +python-versions = ">=3.8" +files = [ + {file = "aiofiles-24.1.0-py3-none-any.whl", hash = "sha256:b4ec55f4195e3eb5d7abd1bf7e061763e864dd4954231fb8539a0ef8bb8260e5"}, + {file = "aiofiles-24.1.0.tar.gz", hash = "sha256:22a075c9e5a3810f0c2e48f3008c94d68c65d763b9b03857924c99e57355166c"}, +] [[package]] name = "aiohappyeyeballs" @@ -13,108 +24,107 @@ files = [ [[package]] name = "aiohttp" -version = "3.10.8" +version = "3.10.10" description = "Async http client/server framework (asyncio)" optional = true python-versions = ">=3.8" files = [ - {file = "aiohttp-3.10.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a1ba7bc139592339ddeb62c06486d0fa0f4ca61216e14137a40d626c81faf10c"}, - {file = "aiohttp-3.10.8-cp310-cp310-macosx_10_9_x86_64.whl", hash = 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optional = true } python-pptx = { version = "^1.0.1", optional = true } python-docx = { version = "^1.1.0", optional = true } -beautifulsoup4 = { version = "^4.12.3", optional = true } -bs4 = "^0.0.2" [tool.poetry.extras] @@ -86,9 +87,11 @@ core = [ "boto3", "deepdiff", "fire", + "fsspec", "future", "graspologic", "gunicorn", + "hatchet-sdk", "litellm", "networkx", "ollama", @@ -104,17 +107,19 @@ core = [ "uvicorn", "vecs", "python-multipart", - "hatchet-sdk", ] -hatchet = ["hatchet-sdk"] ingestion-bundle = [ + "aiofiles", + "aioshutil", + "beautifulsoup4", + "bs4", "numpy", "markdown", "openpyxl", + "pdf2image", "pypdf", "python-pptx", "python-docx", - "beautifulsoup4", ] [tool.poetry.group.dev.dependencies] @@ -156,7 +161,7 @@ profile = "black" [tool.mypy] ignore_missing_imports = true -exclude = 'playground/.*|deprecated/.*|dump/.*|docs/source|vecs/*|core/examples/*|sdk/examples/*|cli/examples/*|tests/*' +exclude = 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