From 4bf880a272e2e2e6c84cba16d178fe04cd212824 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cle=CC=81ment=20Doumouro?= Date: Wed, 10 Jun 2026 16:07:39 +0200 Subject: [PATCH] refactor: split in extract-core and extract-python --- .dockerignore | 6 - .github/workflows/publish-extract-core.yml | 45 + ...publish.yml => publish-extract-python.yml} | 6 +- .github/workflows/tests-extract-core.yml | 49 + .../{tests.yml => tests-extract-python.yml} | 16 +- Dockerfile | 76 - Makefile | 6 + docker-compose.yml | 107 - extract | 42 - .gitignore => extract-core/.gitignore | 0 README.md => extract-core/README.md | 0 extract-core/extract_core/__init__.py | 63 + .../extract_core/configs.py | 17 +- extract-core/extract_core/docling_.py | 268 ++ extract-core/extract_core/marker_.py | 40 + extract-core/extract_core/miner_u.py | 76 + .../extract_core}/objects.py | 56 +- extract-core/extract_core/pipeline.py | 14 + extract-core/extract_core/utils.py | 9 + extract-core/pyproject.toml | 121 + extract-core/tests/test_docling.py | 46 + extract-core/tests/test_objects.py | 40 + extract-core/uv.lock | 3017 +++++++++++++++++ extract-python/.gitignore | 19 + .../.python-version | 0 extract-python/README.md | 0 .../benches}/__init__.py | 0 .../benches}/compare.ipynb | 4 +- .../benches}/compare.py | 12 +- .../benches}/constants.py | 0 {data => extract-python/data}/.gitignore | 0 extract-python/extract_python/__init__.py | 23 + extract-python/extract_python/constants.py | 2 + extract-python/extract_python/docling_.py | 130 + .../extract_python}/marker_.py | 14 +- .../extract_python}/miner_u.py | 84 +- .../extract_python}/utils.py | 14 +- .../pyproject.toml | 9 +- {tests => extract-python/tests}/__init__.py | 0 {tests => extract-python/tests}/conftest.py | 2 +- .../tests}/data/computer_generated.pdf | Bin .../tests}/data/scanned.pdf | Bin extract-python/tests/test_docling.py | 56 + .../tests}/test_marker.py | 6 +- .../tests}/test_miner_u.py | 6 +- uv.lock => extract-python/uv.lock | 480 +-- extract_python/__init__.py | 41 - extract_python/constants.py | 6 - extract_python/docling_.py | 278 -- scripts/lock.sh | 6 + tests/test_docling.py | 100 - tests/test_objects.py | 40 - 52 files changed, 4276 insertions(+), 1176 deletions(-) delete mode 100644 .dockerignore create mode 100644 .github/workflows/publish-extract-core.yml rename .github/workflows/{publish.yml => publish-extract-python.yml} (89%) create mode 100644 .github/workflows/tests-extract-core.yml rename .github/workflows/{tests.yml => tests-extract-python.yml} (76%) delete mode 100644 Dockerfile create mode 100644 Makefile delete mode 100644 docker-compose.yml delete mode 100755 extract rename .gitignore => extract-core/.gitignore (100%) rename README.md => extract-core/README.md (100%) create mode 100644 extract-core/extract_core/__init__.py rename extract_python/pipeline.py => extract-core/extract_core/configs.py (55%) create mode 100644 extract-core/extract_core/docling_.py create mode 100644 extract-core/extract_core/marker_.py create mode 100644 extract-core/extract_core/miner_u.py rename {extract_python => extract-core/extract_core}/objects.py (86%) create mode 100644 extract-core/extract_core/pipeline.py create mode 100644 extract-core/extract_core/utils.py create mode 100644 extract-core/pyproject.toml create mode 100644 extract-core/tests/test_docling.py create mode 100644 extract-core/tests/test_objects.py create mode 100644 extract-core/uv.lock create mode 100644 extract-python/.gitignore rename .python-version => extract-python/.python-version (100%) create mode 100644 extract-python/README.md rename {benches => extract-python/benches}/__init__.py (100%) rename {benches => extract-python/benches}/compare.ipynb (97%) rename {benches => extract-python/benches}/compare.py (95%) rename {benches => extract-python/benches}/constants.py (100%) rename {data => extract-python/data}/.gitignore (100%) create mode 100644 extract-python/extract_python/__init__.py create mode 100644 extract-python/extract_python/constants.py create mode 100644 extract-python/extract_python/docling_.py rename {extract_python => extract-python/extract_python}/marker_.py (95%) rename {extract_python => extract-python/extract_python}/miner_u.py (69%) rename {extract_python => extract-python/extract_python}/utils.py (82%) rename pyproject.toml => extract-python/pyproject.toml (90%) rename {tests => extract-python/tests}/__init__.py (100%) rename {tests => extract-python/tests}/conftest.py (95%) rename {tests => extract-python/tests}/data/computer_generated.pdf (100%) rename {tests => extract-python/tests}/data/scanned.pdf (100%) create mode 100644 extract-python/tests/test_docling.py rename {tests => extract-python/tests}/test_marker.py (95%) rename {tests => extract-python/tests}/test_miner_u.py (95%) rename uv.lock => extract-python/uv.lock (91%) delete mode 100644 extract_python/__init__.py delete mode 100644 extract_python/constants.py delete mode 100644 extract_python/docling_.py create mode 100755 scripts/lock.sh delete mode 100644 tests/test_docling.py delete mode 100644 tests/test_objects.py diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index 093e2fa..0000000 --- a/.dockerignore +++ /dev/null @@ -1,6 +0,0 @@ -* -!extract_python -!uv.lock -!pyproject.toml -!README.md - diff --git a/.github/workflows/publish-extract-core.yml b/.github/workflows/publish-extract-core.yml new file mode 100644 index 0000000..b00fc33 --- /dev/null +++ b/.github/workflows/publish-extract-core.yml @@ -0,0 +1,45 @@ +name: Publish extra-core + +on: + workflow_dispatch: + push: + tags: + - 'extract-python-*' + +jobs: + create-release: + runs-on: ubuntu-latest + env: + PYTHON_VERSION: 3.12 + ASTRAL_VERSION: 0.11.6 + steps: + - uses: actions/checkout@v6 + - name: Create GH release + run: gh release create "$tag" --generate-notes + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + tag: ${{ github.ref_name }} + + publish-extra-python-to-pypi: + runs-on: ubuntu-latest + permissions: + id-token: write + environment: + name: pypi + url: https://pypi.org/p/extract-python + steps: + - uses: actions/checkout@v6 + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + version: "0.10.8" + - name: Install Python 3.12 + run: uv python install 3.12 + - name: Build + run: cd extract-core && uv build + - name: Publish + run: cd extract-core && publish + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: false diff --git a/.github/workflows/publish.yml b/.github/workflows/publish-extract-python.yml similarity index 89% rename from .github/workflows/publish.yml rename to .github/workflows/publish-extract-python.yml index 1acd43e..ff5b065 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish-extract-python.yml @@ -4,7 +4,7 @@ on: workflow_dispatch: push: tags: - - '*' + - 'extract-python-*' jobs: create-release: @@ -36,9 +36,9 @@ jobs: - name: Install Python 3.12 run: uv python install 3.12 - name: Build - run: uv build + run: cd extract-python && uv build - name: Publish - run: uv publish + run: cd extract-python && publish concurrency: group: ${{ github.workflow }}-${{ github.ref }} diff --git a/.github/workflows/tests-extract-core.yml b/.github/workflows/tests-extract-core.yml new file mode 100644 index 0000000..bee8e04 --- /dev/null +++ b/.github/workflows/tests-extract-core.yml @@ -0,0 +1,49 @@ +name: Tests extract-core + +on: + push: + branches: [ 'main' ] + pull_request: + paths: + - 'extract-core/**' + +jobs: + lint-core: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - uses: astral-sh/ruff-action@v3 + with: + args: "--version" # skips test by displaying the version + - name: Check formatting + run: ruff format --config qa/ruff.toml --check extract-core + - name: Lint test + run: ruff check --config qa/ruff.toml extract-core + + tests-core: + runs-on: ubuntu-latest + env: + PYTHON_VERSION: 3.12 + ASTRAL_VERSION: 0.11.6 + steps: + - uses: actions/checkout@v6 + - name: Setup Python project + uses: actions/setup-python@v6 + with: + python-version: ${{ env.PYTHON_VERSION }} + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + version: ${{ env.ASTRAL_VERSION }} + python-version: ${{ env.PYTHON_VERSION }} + enable-cache: true + working-directory: extract-core + - name: Run tests + run: | + cd extract-core + uv sync --verbose --frozen --dev --all-extras + uv run --frozen python -m pytest -vvv --cache-clear --show-capture=all -r A tests + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true \ No newline at end of file diff --git a/.github/workflows/tests.yml b/.github/workflows/tests-extract-python.yml similarity index 76% rename from .github/workflows/tests.yml rename to .github/workflows/tests-extract-python.yml index b53a149..a7efdde 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests-extract-python.yml @@ -4,6 +4,9 @@ on: push: branches: [ 'main' ] pull_request: + paths: + - 'extract-core/**' + - 'extract-python/**' jobs: lint: @@ -14,9 +17,9 @@ jobs: with: args: "--version" # skips test by displaying the version - name: Check formatting - run: ruff format --config qa/ruff.toml --check extract_python tests + run: ruff format --config qa/ruff.toml --check extract-python - name: Lint test - run: ruff check --config qa/ruff.toml extract_python tests + run: ruff check --config qa/ruff.toml extract-python tests-no-miner-u: runs-on: ubuntu-latest @@ -51,7 +54,9 @@ jobs: echo "TESSDATA_PREFIX=$(sudo dpkg -L tesseract-ocr-eng | grep tessdata$)" >> $GITHUB_ENV - name: Run tests run: | - uv run --dev --extra docling --extra marker --frozen pytest -m "not miner_u" -vvv --cache-clear --show-capture=all -r A tests + cd extract-python + uv sync --dev --extra docling --extra marker --frozen + uv run --frozen pytest -m "not miner_u" -vvv --cache-clear --show-capture=all -r A tests tests-miner-u: runs-on: ubuntu-latest @@ -70,9 +75,12 @@ jobs: version: ${{ env.ASTRAL_VERSION }} python-version: ${{ env.PYTHON_VERSION }} enable-cache: true + working-directory: extract-python - name: Run tests run: | - uv run --dev --extra mineru --frozen pytest -m "miner_u" -vvv --cache-clear --show-capture=all -r A tests + cd extract-python + uv sync --verbose --dev --extra mineru --frozen + uv run --frozen python -m pytest -m "miner_u" -vvv --cache-clear --show-capture=all -r A tests concurrency: group: ${{ github.workflow }}-${{ github.ref }} diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 17209c8..0000000 --- a/Dockerfile +++ /dev/null @@ -1,76 +0,0 @@ -# syntax=docker/dockerfile:1.14.0 -FROM python:3.10-slim-bullseye AS python-base - -ENV HOME=/home/user -WORKDIR $HOME -RUN apt-get update && apt-get install -y curl - -RUN curl -LsSf https://astral.sh/uv/0.6.7/install.sh | sh -ENV PATH="$HOME/.local/bin:$PATH" -ENV UV_LINK_MODE=copy -ENV UV_COMPILE_BYTECODE=1 - -FROM python-base AS worker-base - -ARG dbmate_arch -WORKDIR $HOME/src/app -RUN curl -fsSL -o /usr/local/bin/dbmate https://github.com/amacneil/dbmate/releases/download/v2.19.0/dbmate-linux-${dbmate_arch} \ - && chmod +x /usr/local/bin/dbmate - -FROM worker-base AS worker-cpu -# TODO: add more languages here -RUN apt-get install -y tesseract-ocr \ - tesseract-ocr-eng \ - tesseract-ocr-fra \ - tesseract-ocr-deu \ - tesseract-ocr-spa \ - tesseract-ocr-lat \ - tesseract-ocr-jpn \ - libtesseract-dev \ - libleptonica-dev \ - pkg-config -ENV TESSDATA_PREFIX=/usr/share/tesseract-ocr/4.00/tessdata -# We skip opencv since we already depend on opencv-python-headless which is the lib we need to use -# Install deps first to optimize layer cache -RUN --mount=type=cache,target=~/.cache/uv \ - --mount=type=bind,source=uv.lock,target=uv.lock \ - --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ - uv sync -v --frozen --no-editable --no-sources --no-install-project --no-install-package opencv-python --extra cpu -RUN uv run --no-sync docling-tools models download -o ~/.cache/docling/models -# Then copy code -ADD uv.lock pyproject.toml README.md ./ -ADD extract_python ./extract_python/ -# Then install service -RUN uv sync -v --frozen --no-editable --no-sources --no-install-package opencv-python --extra cpu - -RUN rm -rf ~/.cache/pip $(uv cache dir) - -ENTRYPOINT ["uv", "run", "--no-sync", "icij-worker", "workers", "start", "-g", "cpu", "extract_python.app:app"] - - -FROM worker-base AS worker-miner-u -RUN apt-get update && apt-get install -y wget -# We skip opencv since we already depend on opencv-python-headless which is the lib we need to use -# Install deps first to optimize layer cache -RUN --mount=type=cache,target=~/.cache/uv \ - --mount=type=bind,source=uv.lock,target=uv.lock \ - --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ - uv sync -v --frozen --no-editable --no-sources --no-install-project --no-install-package opencv-python --extra miner-u -# TODO: elegantly handle the version here... -# Download models -RUN wget "https://raw.githubusercontent.com/opendatalab/MinerU/refs/tags/magic_pdf-1.3.1-released/scripts/download_models_hf.py" -O download_models_hf.py \ - && uv run python download_models_hf.py -# Then copy code -ADD uv.lock pyproject.toml README.md ./ -ADD extract_python ./extract_python/ -# Then install service -RUN uv sync -v --frozen --no-editable --no-sources --no-install-package opencv-python --extra miner-u - -RUN rm -rf ~/.cache/pip $(uv cache dir) - -ENTRYPOINT ["uv", "run", "--no-sync", "icij-worker", "workers", "start", "-g", "miner-u", "extract_python.app:app"] - -FROM icij/task-service:icij-worker-0.17.21 AS http-service -ADD uv.lock pyproject.toml README.md ./extract-python/ -ADD extract_python ./extract-python/extract_python/ -RUN uv pip install -e ./extract-python diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..6b00574 --- /dev/null +++ b/Makefile @@ -0,0 +1,6 @@ +lock-all: + ./scripts/lock.sh extract-core + ./scripts/lock.sh extract-python + +lock-dist: + ./scripts/lock.sh ${project} diff --git a/docker-compose.yml b/docker-compose.yml deleted file mode 100644 index 65a7700..0000000 --- a/docker-compose.yml +++ /dev/null @@ -1,107 +0,0 @@ -version: '3.7' - -x-tm-amqp-config-variables: &tm-amqp-config - TASK_MANAGER__RABBITMQ_HOST: rabbitmq - -x-postgres-storage-config: &tm-postgres-storage-config - TASK_MANAGER__BACKEND: amqp - # Change this to a FSKeyValueStorageConfig if you don't want to use postgres - TASK_MANAGER__STORAGE__HOST: postgres - TASK_MANAGER__STORAGE__PORT: 5432 - TASK_MANAGER__STORAGE__PASSWORD: changeme - -x-worker-config-variables: &worker-config - ICIJ_WORKER_TYPE: amqp - ICIJ_WORKER_RABBITMQ_HOST: rabbitmq - ICIJ_WORKER_RABBITMQ_PORT: 5672 - -x-async-app-variables: &async-app - EXTRACT_DATA_DIR: /usr/src/data - EXTRACT_WORK_DIR: /usr/src/data/workdir - EXTRACT_LOG_LEVEL: DEBUG - - -services: - rabbitmq: - image: rabbitmq:3.12.0-management - container_name: extract-rabbitmq - healthcheck: - test: rabbitmq-diagnostics -q status - interval: 5s - timeout: 2s - retries: 10 - start_period: 5s - ports: - - "5672:5672" - - "15672:15672" - - postgres: - image: postgres - container_name: extract-postgres - environment: - POSTGRES_PASSWORD: changeme - healthcheck: - test: pg_isready - interval: 2s - timeout: 2s - retries: 10 - start_period: 5s - ports: - - "5435:5432" - - http-service: - depends_on: - rabbitmq: - condition: service_healthy - postgres: - condition: service_healthy - build: - context: . - target: http-service - container_name: extract-http-service - environment: - <<: [ *tm-amqp-config, *tm-postgres-storage-config ] - PORT: "8000" - HOST: "0.0.0.0" - LOG_LEVEL: DEBUG - TASK_MANAGER__APP_PATH: extract_app - healthcheck: - test: curl -f http://localhost:8000/health - interval: 5s - timeout: 2s - retries: 10 - start_period: 5s - ports: - - "8000:8000" - - extract-worker-cpu: - depends_on: - http-service: - condition: service_healthy - build: - context: . - args: - dbmate_arch: $DBMATE_ARCH - target: worker-cpu - environment: - <<: [ *worker-config, *async-app ] - volumes: - - type: bind - source: ./data - target: /usr/src/data - - extract-worker-miner-u: - depends_on: - http-service: - condition: service_healthy - build: - context: . - args: - dbmate_arch: $DBMATE_ARCH - target: worker-miner-u - environment: - <<: [ *worker-config, *async-app ] - volumes: - - type: bind - source: ./data - target: /usr/src/data diff --git a/extract b/extract deleted file mode 100755 index b8dace0..0000000 --- a/extract +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env bash - -function _export_globals() { - DBMATE_ARCH=$(dbmate_arch) - export DBMATE_ARCH -} - -function _helpers() { - function dbmate_arch() { - local host_arch - if command -v arch >/dev/null 2>&1; then - host_arch=$(arch) - else - host_arch=$(uname -m) - fi - local dbmate_arch_ - if [ "$host_arch" == "x86_64" ] ||[ "$host_arch" == "amd64" ]; then - dbmate_arch_="amd64" - elif [ "$host_arch" == "aarch64" ] || [ "$host_arch" == "arm64" ]; then - dbmate_arch_="arm64" - elif [ "$host_arch" == "i386" ] ; then - dbmate_arch_="386" - else - _exit_with_message "Unsupported architecture $host_arch" - fi - echo "$dbmate_arch_" - } - -} - -function _main() { - set -e - function _exit_with_message() { - echo "$1" - exit "${2:-1}" - } - _helpers - _export_globals - docker compose "$@" -} - -_main "$@" diff --git a/.gitignore b/extract-core/.gitignore similarity index 100% rename from .gitignore rename to extract-core/.gitignore diff --git a/README.md b/extract-core/README.md similarity index 100% rename from README.md rename to extract-core/README.md diff --git a/extract-core/extract_core/__init__.py b/extract-core/extract_core/__init__.py new file mode 100644 index 0000000..3ce3065 --- /dev/null +++ b/extract-core/extract_core/__init__.py @@ -0,0 +1,63 @@ +from typing import Annotated + +from icij_common.pydantic_utils import make_enum_discriminator, tagged_union +from pydantic import Discriminator + +from .configs import BasePipelineConfig, PipelineType +from .objects import ( + BaseModel, + ConversionOutput, + Error, + InputDoc, + MarkdownDoc, + OutputFormat, + PageIndexes, + Result, + Status, +) +from .pipeline import Pipeline + +try: + from .docling_ import DoclingFormatOption, DoclingPipelineConfig +except ImportError: + DoclingPipelineConfig, DoclingFormatOption = None, None +try: + from .marker_ import MarkerPipelineConfig +except ImportError: + MarkerPipelineConfig = None + + +try: + from .miner_u import MinerUBackend, MinerUConfig, MinerUPipelineConfig +except ImportError: + MinerUBackend, MinerUPipelineConfig, MinerUConfig = None, None, None + + +pipeline_type_discriminator = make_enum_discriminator("pipeline", PipelineType) +PipelineConfig = Annotated[ + tagged_union( + BasePipelineConfig.__subclasses__(), lambda t: t.pipeline.default.value + ), + Discriminator(pipeline_type_discriminator), +] + + +__all__ = [ + "BaseModel", + "BasePipelineConfig", + "ConversionOutput", + "DoclingPipelineConfig", + "Error", + "InputDoc", + "MarkdownDoc", + "MarkerPipelineConfig", + "MinerUBackend", + "MinerUConfig", + "MinerUPipelineConfig", + "OutputFormat", + "PageIndexes", + "Pipeline", + "PipelineType", + "Result", + "Status", +] diff --git a/extract_python/pipeline.py b/extract-core/extract_core/configs.py similarity index 55% rename from extract_python/pipeline.py rename to extract-core/extract_core/configs.py index 5cd9fdb..b9242ea 100644 --- a/extract_python/pipeline.py +++ b/extract-core/extract_core/configs.py @@ -1,16 +1,12 @@ from abc import ABC, abstractmethod -from collections.abc import AsyncGenerator, Iterable from enum import StrEnum -from pathlib import Path from typing import ClassVar from icij_common.pydantic_utils import icij_config, merge_configs, no_enum_values_config -from icij_common.registrable import RegistrableConfig, RegistrableFromConfig +from icij_common.registrable import RegistrableConfig from pydantic import Field -from .objects import InputDoc, OutputFormat, Result, SupportedExt - -StructuredContent = str +from .objects import SupportedExt class PipelineType(StrEnum): @@ -19,7 +15,7 @@ class PipelineType(StrEnum): MINER_U = "miner_u" -class PipelineConfig(RegistrableConfig, ABC): +class BasePipelineConfig(RegistrableConfig, ABC): # TODO: move this icij_config() to RegistrableConfig model_config = merge_configs(icij_config(), no_enum_values_config()) @@ -29,10 +25,3 @@ class PipelineConfig(RegistrableConfig, ABC): @classmethod @abstractmethod def supported_exts(cls) -> set[SupportedExt]: ... - - -class Pipeline(RegistrableFromConfig, ABC): - @abstractmethod - async def extract_content( - self, docs: Iterable[InputDoc], output_format: OutputFormat, output_path: Path - ) -> AsyncGenerator[Result, None]: ... diff --git a/extract-core/extract_core/docling_.py b/extract-core/extract_core/docling_.py new file mode 100644 index 0000000..f518767 --- /dev/null +++ b/extract-core/extract_core/docling_.py @@ -0,0 +1,268 @@ +import importlib +from functools import cache +from typing import Annotated, Any, ClassVar, TypeVar, get_type_hints + +from docling.datamodel.backend_options import BackendOptions, BaseBackendOptions +from docling.datamodel.base_models import ( + BaseFormatOption, + FormatToExtensions, + InputFormat, +) +from docling.datamodel.pipeline_options import ( + BaseLayoutOptions, + BaseTableStructureOptions, + EasyOcrOptions, + LayoutOptions, + OcrOptions, + PictureDescriptionBaseOptions, + PictureDescriptionVlmEngineOptions, + PipelineOptions, + TableStructureOptions, + ThreadedPdfPipelineOptions, +) +from icij_common.pydantic_utils import ( + merge_configs, + tagged_union, + to_lower_snake_case, +) +from pydantic import ( + ConfigDict, + Discriminator, + Field, + TypeAdapter, + WrapSerializer, +) +from pydantic_core.core_schema import SerializerFunctionWrapHandler + +from .configs import BasePipelineConfig, PipelineType +from .objects import BaseModel, SupportedExt +from .utils import all_subclasses + + +@cache +def _ext_to_docling_input_format() -> dict: + + mapping = dict() + supported = DoclingPipelineConfig.supported_exts() + for input_f, exts in FormatToExtensions.items(): + for ext in exts: + try: + ext = SupportedExt(f".{ext.lower()}") # noqa: PLW2901 + except ValueError: + continue + if ext in supported: + mapping[ext] = input_f + return mapping + + +def _validate_pipeline_opts(v: PipelineOptions) -> PipelineOptions: + generate_picture_images = getattr(v, "generate_picture_images", None) + if generate_picture_images is False: + msg = "generate_picture_images should be set to True" + raise ValueError(msg) + return v + + +T = TypeVar("T") + + +def _find_subcls(cls: type[T], name: str) -> type[T]: + # Check if the class available + for c in all_subclasses(cls): + if c.__name__ == name: + return c + # Then apply ad-hoc search + if "pipeline" in cls.__name__.lower(): + module_name = f"docling.pipeline.{to_lower_snake_case(name)}" + try: + module = importlib.import_module(module_name) + return getattr(module, name) + except (ModuleNotFoundError, AttributeError): + pass + raise ValueError(f"unknown {cls.__name__} subclass {name}") + + +def _find_init_arg_type(cls: type[Any], arg: str) -> type[BaseModel]: + hints = get_type_hints(cls.__init__) + return hints[arg] + + +def _resolve_pipeline_cls(v: str) -> Any: + if isinstance(v, str): + from docling.pipeline.base_pipeline import BasePipeline # noqa: PLC0415 + + return _find_subcls(BasePipeline, v) + return v + + +def _ser_as_str(v: type) -> str: + return v.__name__ + + +def _ser_with_backend_option_kind( + v: Any, handler: SerializerFunctionWrapHandler +) -> Any: + serialized = handler(v) + if isinstance(v, BaseBackendOptions): + kind = getattr(v, "kind", None) + if kind is not None: + serialized["kind"] = kind + return serialized + + +def _resolve_backend(v: Any) -> Any: + from docling.backend.abstract_backend import ( # noqa: PLC0415 + AbstractDocumentBackend, + ) + + if isinstance(v, str): + return _find_subcls(AbstractDocumentBackend, v) + return v + + +@cache +def _picture_descr_opts_type_adapter() -> TypeAdapter: + _PictureDescriptionModel = Annotated[ # noqa: N806 + tagged_union( + PictureDescriptionBaseOptions.__subclasses__(), tag_getter=lambda x: x.kind + ), + Discriminator(lambda x: x["kind"]), + ] + return TypeAdapter(_PictureDescriptionModel) + + +@cache +def _ocr_opts_type_adapter() -> TypeAdapter: + _OcrOptions = Annotated[ # noqa: N806 + tagged_union(OcrOptions.__subclasses__(), tag_getter=lambda x: x.kind), + Discriminator(lambda x: x.pop("kind")), + ] + return TypeAdapter(_OcrOptions) + + +@cache +def _layout_opts_type_adapter() -> TypeAdapter: + _LayoutOptions = Annotated[ # noqa: N806 + tagged_union(BaseLayoutOptions.__subclasses__(), tag_getter=lambda x: x.kind), + Discriminator(lambda x: x["kind"]), + ] + return TypeAdapter(_LayoutOptions) + + +@cache +def _table_structure_opts_type_adapter() -> TypeAdapter: + _TableStructureOptions = Annotated[ # noqa: N806 + tagged_union( + BaseTableStructureOptions.__subclasses__(), tag_getter=lambda x: x.kind + ), + Discriminator(lambda x: x["kind"]), + ] + return TypeAdapter(_TableStructureOptions) + + +def _resolve_pipeline_options( + pipeline_options: dict[str, Any] | None | PipelineOptions, pipeline_cls: type +) -> PipelineOptions: + option_cls = _find_init_arg_type(pipeline_cls, "pipeline_options") + picture_descr_opts = pipeline_options.get("picture_description_options") + if picture_descr_opts is not None: + if "kind" not in picture_descr_opts: + msg = f"missing picture description options kind: {picture_descr_opts}" + raise ValueError(msg) + + picture_descr_opts = _picture_descr_opts_type_adapter().validate_python( + picture_descr_opts + ) + pipeline_options["picture_description_options"] = picture_descr_opts + ocr_opts = pipeline_options.get("ocr_options") + if ocr_opts is not None: + if "kind" not in ocr_opts: + msg = f"missing ocr options kind: {ocr_opts}" + raise ValueError(msg) + ocr_opts = _ocr_opts_type_adapter().validate_python(ocr_opts) + pipeline_options["ocr_options"] = ocr_opts + layout_opts = pipeline_options.get("layout_options") + if layout_opts is not None: + if "kind" not in layout_opts: + msg = f"missing layout options kind: {layout_opts}" + raise ValueError(msg) + layout_opts = _layout_opts_type_adapter().validate_python(layout_opts) + pipeline_options["layout_options"] = layout_opts + table_structure_opts = pipeline_options.get("table_structure_options") + if table_structure_opts is not None: + if "kind" not in table_structure_opts: + msg = f"missing table structure options kind: {table_structure_opts}" + raise ValueError(msg) + table_structure_opts = _table_structure_opts_type_adapter().validate_python( + table_structure_opts + ) + pipeline_options["table_structure_options"] = table_structure_opts + pipeline_options = option_cls.model_validate(pipeline_options) + return pipeline_options + + +# Mimics the docling FormatOption but only with lightweight types, +# the heavy convertion is done at runtime +class DoclingFormatOption(BaseFormatOption): + model_config = merge_configs( + BaseModel.model_config, ConfigDict(polymorphic_serialization=True) + ) + backend: str + backend_options: Annotated[ + BackendOptions | None, WrapSerializer(_ser_with_backend_option_kind) + ] = None + pipeline_cls: str + pipeline_options: dict[str, Any] | None = None + + def to_docling(self) -> BaseFormatOption: # noqa: ANN201 + from docling.document_converter import FormatOption # noqa: PLC0415 + + pipeline_cls = _resolve_pipeline_cls(self.pipeline_cls) + pipeline_opts = _resolve_pipeline_options(self.pipeline_options, pipeline_cls) + pipeline_opts = _validate_pipeline_opts(pipeline_opts) + return FormatOption( + pipeline_cls=pipeline_cls, + pipeline_options=pipeline_opts, + backend=_resolve_backend(self.backend), + backend_options=self.backend_options, + ) + + +@cache +def _default_format_opts() -> dict[InputFormat, DoclingFormatOption]: + pipeline_opts = ThreadedPdfPipelineOptions( + ocr_options=EasyOcrOptions(), generate_picture_images=True + ).model_dump(polymorphic_serialization=True) + pipeline_opts["picture_description_options"]["kind"] = ( + PictureDescriptionVlmEngineOptions.kind + ) + pipeline_opts["ocr_options"]["kind"] = EasyOcrOptions.kind + pipeline_opts["layout_options"]["kind"] = LayoutOptions.kind + pipeline_opts["table_structure_options"]["kind"] = TableStructureOptions.kind + return { + InputFormat.PDF: DoclingFormatOption( + pipeline_cls="StandardPdfPipeline", + backend="DoclingParseDocumentBackend", + pipeline_options=pipeline_opts, + ), + } + + +class DoclingPipelineConfig(BasePipelineConfig): + pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.DOCLING) + + format_options: dict[InputFormat, DoclingFormatOption] = Field( + default_factory=_default_format_opts + ) + + @classmethod + @cache + def supported_exts(cls) -> set[SupportedExt]: + unsupported = {InputFormat.AUDIO, InputFormat.METS_GBS, InputFormat.VTT} + supported = set() + for f in InputFormat: + if f in unsupported: + continue + for ext in FormatToExtensions[f]: + supported.add(SupportedExt(f".{ext.lower()}")) + return supported diff --git a/extract-core/extract_core/marker_.py b/extract-core/extract_core/marker_.py new file mode 100644 index 0000000..8ebba04 --- /dev/null +++ b/extract-core/extract_core/marker_.py @@ -0,0 +1,40 @@ +from functools import cache +from typing import Any, ClassVar + +from pydantic import Field + +from .configs import BasePipelineConfig, PipelineType +from .objects import SupportedExt + + +class MarkerPipelineConfig(BasePipelineConfig): + pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.MARKER) + + config: dict[str, Any] = dict() + + @classmethod + @cache + def supported_exts(cls) -> set[SupportedExt]: + # Subset of https://documentation.datalab.to/docs/common/supportedfiletypes + return { + SupportedExt.PDF, + SupportedExt.XLS, + SupportedExt.XLSX, + SupportedExt.XLSM, + SupportedExt.CSV, + SupportedExt.ODS, + SupportedExt.DOC, + SupportedExt.DOCX, + SupportedExt.ODT, + SupportedExt.PPT, + SupportedExt.PPTX, + SupportedExt.ODP, + SupportedExt.HTLM, + SupportedExt.EPUB, + SupportedExt.PNG, + SupportedExt.JPG, + SupportedExt.JPEG, + SupportedExt.WEBP, + SupportedExt.GIF, + SupportedExt.TIFF, + } diff --git a/extract-core/extract_core/miner_u.py b/extract-core/extract_core/miner_u.py new file mode 100644 index 0000000..3ebeb5d --- /dev/null +++ b/extract-core/extract_core/miner_u.py @@ -0,0 +1,76 @@ +from collections.abc import Callable +from copy import copy +from enum import StrEnum +from functools import cache +from typing import Any, ClassVar + +from pydantic import Field +from pydantic_extra_types.language_code import LanguageAlpha2 + +from .configs import BasePipelineConfig, PipelineType +from .objects import BaseModel, SupportedExt + +_MINER_U_CONVERSION_ERRORS = tuple() +MDMakeFunction = Callable[[list, str, str], str | None] + + +class MinerUBackend(StrEnum): + PIPELINE = "pipeline" + VLM = "vlm" + + +class MinerUConfig(BaseModel): + backend: MinerUBackend = MinerUBackend.PIPELINE + enable_formula_extraction: bool = True + enable_table_extraction: bool = True + # TODO: use enum or literal here + parse_method: str = "auto" + + def as_parse_kwargs(self) -> dict[str, Any]: + kwargs = copy(self._get_default_kwargs()) + kwargs["backend"] = self.backend + kwargs["parse_method"] = self.parse_method + kwargs["formula_enable"] = self.enable_formula_extraction + kwargs["table_enable"] = self.enable_table_extraction + return kwargs + + @classmethod + @cache + def _get_default_kwargs(cls) -> dict[str, Any]: + from mineru.utils.enum_class import MakeMode # noqa: PLC0415 + + return { + "server_url": None, + # We don't dump md directly we process, we dump the middle json in order + # to be able to get page indexes + "parse_method": "auto", + "dump_md": False, + "dump_middle_json": True, + "f_draw_layout_bbox": False, + "f_draw_span_bbox": False, + "f_dump_model_output": False, # might be useful for debug though + "f_dump_orig_pdf": False, + "f_dump_content_list": False, # might be useful for debug though + "start_page_id": 0, + "f_make_md_mode": MakeMode.MM_MD, + "image_analysis": True, + "end_page_id": None, + "client_side_output_generation": False, + } + + +class MinerUPipelineConfig(BasePipelineConfig): # noqa: F821 + pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.MINER_U) + + config: MinerUConfig = Field(frozen=True, default=MinerUConfig()) + language: LanguageAlpha2 = Field(frozen=True, default="en") + + @classmethod + @cache + def supported_exts(cls) -> set[SupportedExt]: + return { + SupportedExt.PDF, + SupportedExt.DOCX, + SupportedExt.PPTX, + SupportedExt.XLSX, + } diff --git a/extract_python/objects.py b/extract-core/extract_core/objects.py similarity index 86% rename from extract_python/objects.py rename to extract-core/extract_core/objects.py index 55e5c46..1c6a66e 100644 --- a/extract_python/objects.py +++ b/extract-core/extract_core/objects.py @@ -1,5 +1,3 @@ -from __future__ import annotations - import logging import os import traceback @@ -20,41 +18,10 @@ from pydantic import AfterValidator, RootModel, TypeAdapter from pydantic import BaseModel as _BaseModel -try: - from docling.datamodel.base_models import ( - ConversionStatus, - ErrorItem, - FormatToExtensions, - InputFormat, - ) - from docling.datamodel.document import InputDocument - from docling_core.types.io import DocumentStream -except ImportError: - ConversionStatus, ErrorItem, InputFormat = None, None, None - InputDocument = None - DocumentStream = None - logger = logging.getLogger(__name__) base_config = merge_configs(icij_config(), no_enum_values_config()) -@cache -def _ext_to_docling_input_format() -> dict: - from .docling_ import DoclingPipelineConfig # noqa: PLC0415 - - mapping = dict() - supported = DoclingPipelineConfig.supported_exts() - for input_f, exts in FormatToExtensions.items(): - for ext in exts: - try: - ext = SupportedExt(f".{ext.lower()}") # noqa: PLW2901 - except ValueError: - continue - if ext in supported: - mapping[ext] = input_f - return mapping - - class BaseModel(_BaseModel): model_config = base_config @@ -109,7 +76,9 @@ class SupportedExt(StrEnum): XLTX = ".xltx" XML = ".xml" - def to_docling(self) -> InputFormat: + def to_docling(self): # noqa: ANN201 + from .docling_ import _ext_to_docling_input_format # noqa: PLC0415 + return _ext_to_docling_input_format()[self] @@ -167,7 +136,7 @@ def from_exception(cls, exception: BaseException) -> Self: return error @classmethod - def from_docling(cls, docling_error: ErrorItem) -> Self: + def from_docling(cls, docling_error) -> Self: # noqa: ANN001 title = "DoclingConversionError" error_id = f"{_id_title(title)}-{uuid.uuid4().hex}" detail = ( @@ -198,9 +167,12 @@ def from_path(cls, path: str | Path) -> Self: ext = SupportedExt(path.suffix) return cls(path=path, ext=ext) - def to_docling(self) -> Path | DocumentStream: + def to_docling(self): # noqa: ANN201 + from docling_core.types.io import DocumentStream # noqa: PLC0415 + if self.content is not None: return DocumentStream(name=str(self.path), stream=BytesIO(self.content)) + if not self.path.suffix: return DocumentStream( name=str(self.path), stream=BytesIO(self.path.read_bytes()) @@ -229,7 +201,7 @@ class MarkdownDoc(ConversionOutput): @classmethod @property @cache - def _valid_conversion_statuses(cls) -> set[ConversionStatus]: + def _valid_conversion_statuses(cls) -> set: from docling.datamodel.base_models import ConversionStatus # noqa: PLC0415 return {ConversionStatus.SUCCESS, ConversionStatus.PARTIAL_SUCCESS} @@ -247,6 +219,11 @@ class _BaseResult(BaseModel, ABC): errors: list[Error] = [] +class ResponseResult(_BaseResult): + input: Annotated[InputDoc, AfterValidator(func=_input_should_not_have_content)] + output_path: Path + + class Result(_BaseResult): # TODO: we could also use generics here when we add more output formats output: ConversionOutput | None @@ -260,11 +237,6 @@ def to_response(self) -> ResponseResult: ) -class ResponseResult(_BaseResult): - input: Annotated[InputDoc, AfterValidator(func=_input_should_not_have_content)] - output_path: Path - - class ExtractionResponse(BaseModel): results: list[ResponseResult] diff --git a/extract-core/extract_core/pipeline.py b/extract-core/extract_core/pipeline.py new file mode 100644 index 0000000..41cb0ba --- /dev/null +++ b/extract-core/extract_core/pipeline.py @@ -0,0 +1,14 @@ +from abc import ABC, abstractmethod +from collections.abc import AsyncGenerator, Iterable +from pathlib import Path + +from icij_common.registrable import RegistrableFromConfig + +from .objects import InputDoc, OutputFormat, Result + + +class Pipeline(RegistrableFromConfig, ABC): + @abstractmethod + async def extract_content( + self, docs: Iterable[InputDoc], output_format: OutputFormat, output_path: Path + ) -> AsyncGenerator[Result, None]: ... diff --git a/extract-core/extract_core/utils.py b/extract-core/extract_core/utils.py new file mode 100644 index 0000000..3710f8f --- /dev/null +++ b/extract-core/extract_core/utils.py @@ -0,0 +1,9 @@ +from typing import TypeVar + +T = TypeVar("T") + + +def all_subclasses(cls: type[T]) -> set[type[T]]: + return set(cls.__subclasses__()).union( + [s for c in cls.__subclasses__() for s in all_subclasses(c)] + ) diff --git a/extract-core/pyproject.toml b/extract-core/pyproject.toml new file mode 100644 index 0000000..d0494cf --- /dev/null +++ b/extract-core/pyproject.toml @@ -0,0 +1,121 @@ +[project] +name = "extract-core" +dynamic = ["version"] +description = "Core of extract-python" +authors = [ + { name = "Clément Doumouro", email = "cdoumouro@icij.org" }, +] +readme = "README.md" +requires-python = ">=3.11,<3.14" +dependencies = [ + "docling-slim~=2.96", + "icij-common~=0.8.2", + "pydantic~=2.13", + "marker-pdf~=1.10", + "mineru~=3.2", + "pydantic-extra-types[pycountry]>=2.11.1", +] + +[tool.uv] +package = true +override-dependencies = [ + "certifi~=2024.12", + "pillow~=11.3", + "transformers~=5.1" +] + +exclude-dependencies = [ + "anthropic", + "fast-langdetect", + "fastapi", + "google-genai", + "magika", + "pdftext", + "pypdf", + "pypptx-with-oxml", + "opencv-python", + "surya-ocr", + "uvicorn", + "cuda-bindings", + "cuda-pathfinder", + "cuda-toolkit", + "fsspec", + "jinja2", + "markupsafe", + "networkx", + "nvidia-cublas", + "nvidia-cuda-cupti", + "nvidia-cuda-nvrtc", + "nvidia-cuda-runtime", + "nvidia-cudnn-cu13", + "nvidia-cufft", + "nvidia-cufile", + "nvidia-curand", + "nvidia-cusolver", + "nvidia-cusparse", + "nvidia-cusparselt-cu13", + "nvidia-nccl-cu13", + "nvidia-nvjitlink", + "nvidia-nvshmem-cu13", + "nvidia-nvtx", + "triton", +] + +[[tool.uv.index]] +name = "pytorch-cpu" +url = "https://download.pytorch.org/whl/cpu" +explicit = true + +[tool.uv.sources] +torch = [ + { index = "pytorch-cpu"}, +] +torchvision = [ + { index = "pytorch-cpu"}, +] + +[dependency-groups] +dev = [ + "docling~=2.96", + "docling-slim[models-vlm-inline]~=2.96", + "mpmath~=1.3.0", + "pytest~=8.3.5", + "pytest-asyncio~=0.25.3", + "sympy~=1.14.0", + "ruff==0.15.2", + "torch==2.12.0", + "torchvision==0.27.0", +] + +[project.urls] +Homepage = "https://github.com/ICIJ/extract-python" +Repository = "https://github.com/ICIJ/extract-python" +Issues = "https://github.com/ICIJ/extract-python/issues" + + +[tool.pytest.ini_options] +asyncio_mode = "auto" +asyncio_default_fixture_loop_scope = "session" +log_cli = true +log_cli_level = "INFO" +log_cli_format = "[%(levelname)s][%(asctime)s.%(msecs)03d][%(name)s]: %(message)s" +markers = [] + +[build-system] +requires = ["hatchling", "uv-dynamic-versioning"] +build-backend = "hatchling.build" + +[tool.hatch.version] +source = "uv-dynamic-versioning" + +[tool.hatch.build.targets.wheel] +packages = ["extract_core"] + +[tool.hatch.build.targets.sdist] +exclude = [ + "tests", +] +[tool.uv-dynamic-versioning] +fallback-version = "0.0.0" +pattern-prefix = "extract-core-" +pattern = "default-unprefixed" diff --git a/extract-core/tests/test_docling.py b/extract-core/tests/test_docling.py new file mode 100644 index 0000000..efaab2f --- /dev/null +++ b/extract-core/tests/test_docling.py @@ -0,0 +1,46 @@ +from docling.datamodel.backend_options import PdfBackendOptions +from docling.datamodel.base_models import InputFormat +from extract_core import DoclingFormatOption, DoclingPipelineConfig + + +def test_format_option_derser() -> None: + # Given + config = { + "format_options": { + "pdf": { + "pipeline_cls": "LegacyStandardPdfPipeline", + "backend": "PyPdfiumDocumentBackend", + "backend_options": {"kind": "pdf"}, + } + } + } + # When + deserialized = DoclingPipelineConfig.model_validate(config) + # Then + expected = DoclingPipelineConfig( + format_options={ + InputFormat.PDF: DoclingFormatOption( + pipeline_cls="LegacyStandardPdfPipeline", + backend_options=PdfBackendOptions(), + backend="PyPdfiumDocumentBackend", + ) + }, + ) + assert deserialized == expected + + +def test_format_option_ser() -> None: + # Given + config = DoclingPipelineConfig( + format_options={ + InputFormat.PDF: DoclingFormatOption( + pipeline_cls="LegacyStandardPdfPipeline", + backend_options=PdfBackendOptions(), + backend="PyPdfiumDocumentBackend", + ) + }, + ) + # When + serialized = config.model_dump_json(indent=2) + deserialized = DoclingPipelineConfig.model_validate_json(serialized) + assert deserialized == config diff --git a/extract-core/tests/test_objects.py b/extract-core/tests/test_objects.py new file mode 100644 index 0000000..c332e48 --- /dev/null +++ b/extract-core/tests/test_objects.py @@ -0,0 +1,40 @@ +from docling.datamodel.base_models import InputFormat +from docling.datamodel.pipeline_options import ( + TesseractOcrOptions, + ThreadedPdfPipelineOptions, +) +from docling.document_converter import PdfFormatOption +from extract_core import DoclingPipelineConfig, PipelineConfig +from pydantic import TypeAdapter + + +def test_docling_pipeline_config() -> None: + # Given + ta = TypeAdapter(PipelineConfig) + config = { + "pipeline": "docling", + "format_options": { + "pdf": { + "pipeline_cls": "StandardPdfPipeline", + "backend": "DoclingParseDocumentBackend", + "pipeline_options": { + "ocr_options": {"kind": "tesserocr", "lang": ["auto"]}, + "generate_picture_images": True, + }, + } + }, + } + # When + pipeline_config = ta.validate_python(config) + # Then + assert isinstance(pipeline_config, DoclingPipelineConfig) + format_options = pipeline_config.format_options + pdf_options = format_options[InputFormat.PDF] + pdf_pipeline_options = pdf_options.to_docling() + expected_options = PdfFormatOption( + pipeline_options=ThreadedPdfPipelineOptions( + ocr_options=TesseractOcrOptions(lang=["auto"]), + generate_picture_images=True, + ) + ) + assert pdf_pipeline_options.model_dump() == expected_options.model_dump() diff --git a/extract-core/uv.lock b/extract-core/uv.lock new file mode 100644 index 0000000..76b8d45 --- /dev/null +++ b/extract-core/uv.lock @@ -0,0 +1,3017 @@ +version = 1 +revision = 3 +requires-python = ">=3.11, <3.14" +resolution-markers = [ + "sys_platform == 'win32'", + "sys_platform == 'emscripten'", + "sys_platform != 'darwin' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "sys_platform == 'darwin'", +] + +[manifest] +overrides = [ + { name = "certifi", specifier = "~=2024.12" }, + { name = "pillow", specifier = "~=11.3" }, + { name = "transformers", specifier = "~=5.1" }, +] +excludes = [ + "anthropic", + "cuda-bindings", + "cuda-pathfinder", + "cuda-toolkit", + "fast-langdetect", + "fastapi", + "fsspec", + "google-genai", + "jinja2", + "magika", + "markupsafe", + "networkx", + "nvidia-cublas", + "nvidia-cuda-cupti", + "nvidia-cuda-nvrtc", + 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100644 index 0000000..b14303e --- /dev/null +++ b/extract-python/.gitignore @@ -0,0 +1,19 @@ +.idea + +# Python +*.log +venv +*.egg-info +.eggs +__pycache__ +*.pytest_cache +*.pyc +build +dist +test/.env +.cache +tmp +./*.csv + +# VS code +.vscode diff --git a/.python-version b/extract-python/.python-version similarity index 100% rename from .python-version rename to extract-python/.python-version diff --git a/extract-python/README.md b/extract-python/README.md new file mode 100644 index 0000000..e69de29 diff --git a/benches/__init__.py b/extract-python/benches/__init__.py similarity index 100% rename from benches/__init__.py rename to extract-python/benches/__init__.py diff --git a/benches/compare.ipynb b/extract-python/benches/compare.ipynb similarity index 97% rename from benches/compare.ipynb rename to extract-python/benches/compare.ipynb index 2c6dc1c..eb767ae 100644 --- a/benches/compare.ipynb +++ b/extract-python/benches/compare.ipynb @@ -13,8 +13,8 @@ "from extract_python.benches.compare import (\n", " compare,\n", ")\n", - "from extract_python.pipelines import DoclingPipeline, MarkerPipeline\n", - "from extract_python.objects import InputDoc, OutputFormat" + "from extract_python.objects import InputDoc, OutputFormat\n", + "from extract_python.pipelines import DoclingPipeline, MarkerPipeline" ] }, { diff --git a/benches/compare.py b/extract-python/benches/compare.py similarity index 95% rename from benches/compare.py rename to extract-python/benches/compare.py index 41d90c6..16cbd19 100644 --- a/benches/compare.py +++ b/extract-python/benches/compare.py @@ -3,12 +3,11 @@ import markdown2 import pypdfium2 -from extract_python.pipelines.utils import chdir +from extract_core import BaseModel, OutputFormat, PageIndexes +from extract_python.utils import chdir from html2image import Html2Image from PIL import Image, ImageDraw -from extract_python.objects import BaseModel, OutputFormat, PageIndexes - _WHITE_BACKGROUND_CSS = "body {background: white;}" @@ -146,7 +145,10 @@ def _scan_pages( ).root for compared in comparison.compared ] - all_pages = zip(*all_pages) + all_pages = zip(*all_pages, strict=True) compared_names = (p.parent.name for p in comparison.compared) - pages = [dict(zip(compared_names, page_comp_ixs)) for page_comp_ixs in all_pages] + pages = [ + dict(zip(compared_names, page_comp_ixs, strict=True)) + for page_comp_ixs in all_pages + ] return pages diff --git a/benches/constants.py b/extract-python/benches/constants.py similarity index 100% rename from benches/constants.py rename to extract-python/benches/constants.py diff --git a/data/.gitignore b/extract-python/data/.gitignore similarity index 100% rename from data/.gitignore rename to extract-python/data/.gitignore diff --git a/extract-python/extract_python/__init__.py b/extract-python/extract_python/__init__.py new file mode 100644 index 0000000..3f06a07 --- /dev/null +++ b/extract-python/extract_python/__init__.py @@ -0,0 +1,23 @@ +try: + from .docling_ import DOCLING_DEFAULT_ARTIFACTS_PATH, DoclingPipeline +except ImportError: + DOCKING_DEFAULT_ARTIFACTS_PATH, DoclingPipeline = None, None + +try: + from .marker_ import MarkerPipeline +except ImportError: + MarkerPipeline = None + + +try: + from .miner_u import MinerUPipeline +except ImportError: + MinerUPipeline = None + + +__all__ = [ + "DoclingPipeline", + "DOCLING_DEFAULT_ARTIFACTS_PATH", + "MarkerPipeline", + "MinerUPipeline", +] diff --git a/extract-python/extract_python/constants.py b/extract-python/extract_python/constants.py new file mode 100644 index 0000000..9a5cc9c --- /dev/null +++ b/extract-python/extract_python/constants.py @@ -0,0 +1,2 @@ +ARTIFACTS = "artifacts" +DEFAULT_MD_PAGE_SEP = '
' diff --git a/extract-python/extract_python/docling_.py b/extract-python/extract_python/docling_.py new file mode 100644 index 0000000..e25550e --- /dev/null +++ b/extract-python/extract_python/docling_.py @@ -0,0 +1,130 @@ +import shutil +import tempfile +from collections.abc import AsyncGenerator, Iterable, Iterator +from pathlib import Path + +from docling.datamodel.base_models import InputFormat +from docling.datamodel.document import ConversionResult +from docling.document_converter import DocumentConverter + +# TODO: this is long to load improve it +from docling_core.types.doc import ImageRefMode +from docling_core.types.io import DocumentStream +from extract_core import ( + DoclingFormatOption, + DoclingPipelineConfig, + Error, + InputDoc, + MarkdownDoc, + OutputFormat, + PageIndexes, + Pipeline, + PipelineType, + Result, + Status, +) +from icij_common.registrable import FromConfig + +from .constants import ARTIFACTS, DEFAULT_MD_PAGE_SEP +from .utils import chdir, map_and_preserve, path_to_artifacts_dirname + +DOCLING_DEFAULT_ARTIFACTS_PATH = Path.home().joinpath(".cache", "docling", "models") + + +@Pipeline.register(PipelineType.DOCLING) +class DoclingPipeline(Pipeline): + def __init__( + self, format_options: dict["InputFormat", DoclingFormatOption] | None = None + ): + format_options = {k: v.to_docling() for k, v in format_options.items()} + allowed_format = [ + f.to_docling() for f in DoclingPipelineConfig.supported_exts() + ] + self._converter = DocumentConverter( + allowed_formats=allowed_format, format_options=format_options + ) + + async def extract_content( + self, docs: Iterable[InputDoc], output_format: OutputFormat, output_path: Path + ) -> AsyncGenerator[Result, None]: + docs, path_or_streams = map_and_preserve(_to_docling, docs) + outputs = self._converter.convert_all(path_or_streams, raises_on_error=False) + for doc, res in zip(docs, outputs, strict=True): + yield _to_result(res, doc, output_format, output_path=output_path) + + @classmethod + def _from_config(cls, config: DoclingPipelineConfig) -> FromConfig: + return cls(config.format_options) + + +def _to_docling(docs: Iterable[InputDoc]) -> Iterator["Path | DocumentStream"]: + for d in docs: + yield d.to_docling() + + +def _to_result( + res: ConversionResult, + input_document: InputDoc, + output_format: OutputFormat, + output_path: Path, + **kwargs, +) -> Result: + output_path.mkdir(parents=True, exist_ok=True) + output = None + status = Status.from_docling(res.status) + if status.allows_conversion: + match output_format: + case OutputFormat.MARKDOWN: + output = _to_markdown_doc(res, output_path, **kwargs) + case _: + raise NotImplementedError(f"unsupported output format {output_format}") + errors = [Error.from_docling(e) for e in res.errors] + input_doc = input_document.without_content() + return Result(input=input_doc, status=status, errors=errors, output=output) + + +def _to_markdown_doc( + res: ConversionResult, + output_path: Path, + page_sep: str = DEFAULT_MD_PAGE_SEP, + **kwargs, +) -> MarkdownDoc: + # TODO: Should we add a hash to avoid collision between files with same names + # nested in the tree structured + md_dir_name = path_to_artifacts_dirname(res.input.file) + md_dir = output_path / md_dir_name + if md_dir.exists(): + raise FileExistsError(f"directory {md_dir} already exists") + # Let's avoid issue of duplicated input file names flattened top level + md_filename = md_dir_name + OutputFormat.MARKDOWN + total_length = 0 + n_pages = len(res.pages) + + with tempfile.TemporaryDirectory(ignore_cleanup_errors=True) as td: + tmp_dir = Path(td) + page_path = Path("page.md") + # We do a chdir to bypass a Docling bug which only allows to maintain relative + # image ref when saving the markdown to a relative path + with (tmp_dir / md_filename).open("w") as f, chdir(tmp_dir): + end_indices = [] + for page_i in range(n_pages): + res.document.save_as_markdown( + page_path, + page_no=page_i + 1, + image_mode=ImageRefMode.REFERENCED, + artifacts_dir=Path(ARTIFACTS), + **kwargs, + ) + content = page_path.read_text() + if page_i > 0: + content += "\n" + if page_i < n_pages - 1: + content += page_sep + total_length += len(content) + end_indices.append(total_length) + f.write(content) + f.flush() + page_path.unlink() + shutil.move(tmp_dir, md_dir) + pages = PageIndexes.from_page_end_indices(end_indices) + return MarkdownDoc(path=Path(md_dir_name), pages=pages) diff --git a/extract_python/marker_.py b/extract-python/extract_python/marker_.py similarity index 95% rename from extract_python/marker_.py rename to extract-python/extract_python/marker_.py index e2520fc..602f489 100644 --- a/extract_python/marker_.py +++ b/extract-python/extract_python/marker_.py @@ -5,10 +5,8 @@ from pathlib import Path from typing import TYPE_CHECKING, Any, ClassVar, Self -from pydantic import Field - -from .constants import ARTIFACTS -from .objects import ( +from extract_core import BasePipelineConfig, Pipeline, PipelineType +from extract_core.objects import ( InputDoc, MarkdownDoc, OutputFormat, @@ -17,7 +15,9 @@ Status, SupportedExt, ) -from .pipeline import Pipeline, PipelineConfig, PipelineType +from pydantic import Field + +from .constants import ARTIFACTS from .utils import path_to_artifacts_dirname, report_recoverable_errors if TYPE_CHECKING: @@ -25,10 +25,10 @@ from PIL import Image -class MarkerPipelineConfig(PipelineConfig): +class MarkerPipelineConfig(BasePipelineConfig): pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.MARKER) - config: dict[str, Any] = dict() + config: dict[str, Any] = Field(default_factory=dict) @classmethod @cache diff --git a/extract_python/miner_u.py b/extract-python/extract_python/miner_u.py similarity index 69% rename from extract_python/miner_u.py rename to extract-python/extract_python/miner_u.py index e58db67..86a8117 100644 --- a/extract_python/miner_u.py +++ b/extract-python/extract_python/miner_u.py @@ -1,96 +1,32 @@ import json import shutil from collections.abc import AsyncGenerator, Callable, Iterable -from copy import copy -from enum import StrEnum -from functools import cache, partial +from functools import partial from pathlib import Path from tempfile import TemporaryDirectory -from typing import Any, ClassVar, Self +from typing import Self -from pydantic import Field -from pydantic_extra_types.language_code import LanguageAlpha2 - -from .constants import ARTIFACTS, DEFAULT_MD_PAGE_SEP -from .objects import ( - BaseModel, +from extract_core import ( ConversionOutput, InputDoc, + MinerUBackend, + MinerUConfig, + MinerUPipelineConfig, OutputFormat, PageIndexes, + Pipeline, + PipelineType, Result, Status, - SupportedExt, ) -from .pipeline import Pipeline, PipelineConfig, PipelineType + +from .constants import ARTIFACTS, DEFAULT_MD_PAGE_SEP from .utils import path_to_artifacts_dirname _MINER_U_CONVERSION_ERRORS = tuple() MDMakeFunction = Callable[[list, str, str], str | None] -class MinerUBackend(StrEnum): - PIPELINE = "pipeline" - VLM = "vlm" - - -class MinerUConfig(BaseModel): - backend: MinerUBackend = MinerUBackend.PIPELINE - enable_formula_extraction: bool = True - enable_table_extraction: bool = True - # TODO: use enum or literal here - parse_method: str = "auto" - - def as_parse_kwargs(self) -> dict[str, Any]: - kwargs = copy(self._get_default_kwargs()) - kwargs["backend"] = self.backend - kwargs["parse_method"] = self.parse_method - kwargs["formula_enable"] = self.enable_formula_extraction - kwargs["table_enable"] = self.enable_table_extraction - return kwargs - - @classmethod - @cache - def _get_default_kwargs(cls) -> dict[str, Any]: - from mineru.utils.enum_class import MakeMode # noqa: PLC0415 - - return { - "server_url": None, - # We don't dump md directly we process, we dump the middle json in order - # to be able to get page indexes - "parse_method": "auto", - "dump_md": False, - "dump_middle_json": True, - "f_draw_layout_bbox": False, - "f_draw_span_bbox": False, - "f_dump_model_output": False, # might be useful for debug though - "f_dump_orig_pdf": False, - "f_dump_content_list": False, # might be useful for debug though - "start_page_id": 0, - "f_make_md_mode": MakeMode.MM_MD, - "image_analysis": True, - "end_page_id": None, - "client_side_output_generation": False, - } - - -class MinerUPipelineConfig(PipelineConfig): # noqa: F821 - pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.MINER_U) - - config: MinerUConfig = Field(frozen=True, default=MinerUConfig()) - language: LanguageAlpha2 = Field(frozen=True, default="en") - - @classmethod - @cache - def supported_exts(cls) -> set[SupportedExt]: - return { - SupportedExt.PDF, - SupportedExt.DOCX, - SupportedExt.PPTX, - SupportedExt.XLSX, - } - - @Pipeline.register(PipelineType.MINER_U) class MinerUPipeline(Pipeline): def __init__(self, config: MinerUConfig, language: str): diff --git a/extract_python/utils.py b/extract-python/extract_python/utils.py similarity index 82% rename from extract_python/utils.py rename to extract-python/extract_python/utils.py index 5e728eb..e1f73be 100644 --- a/extract_python/utils.py +++ b/extract-python/extract_python/utils.py @@ -6,26 +6,20 @@ from pathlib import Path, PurePath from typing import Protocol, TypeVar -from .objects import Error, InputDoc, Result, Status +from extract_core import Error, InputDoc, Result, Status R = TypeVar("R") -T = TypeVar("T") +In = TypeVar("In") def map_and_preserve( - fn: Callable[[Iterable[T]], Iterator[R]], inputs: Iterable[T] -) -> tuple[Iterable[T], Iterator[R]]: + fn: Callable[[Iterable[In]], Iterator[R]], inputs: Iterable[In] +) -> tuple[Iterable[In], Iterator[R]]: save_inputs, function_inputs = tee(inputs) outputs = iter(fn(function_inputs)) return save_inputs, outputs -def all_subclasses(cls: type[T]) -> set[type[T]]: - return set(cls.__subclasses__()).union( - [s for c in cls.__subclasses__() for s in all_subclasses(c)] - ) - - def path_to_artifacts_dirname(path: PurePath, sep: str = "_") -> str: dirname = f"{path.name[: -len(path.suffix)]}" ext = path.suffix diff --git a/pyproject.toml b/extract-python/pyproject.toml similarity index 90% rename from pyproject.toml rename to extract-python/pyproject.toml index fc5d6e9..5232014 100644 --- a/pyproject.toml +++ b/extract-python/pyproject.toml @@ -9,6 +9,7 @@ readme = "README.md" requires-python = ">=3.11,<3.14" dependencies = [ "icij-common~=0.8.2", + "extract-core~=0.1", ] [project.optional-dependencies] @@ -31,6 +32,7 @@ mineru = [ "mineru[pipeline,vlm]~=3.2", "mineru[mlx]~=3.2; sys_platform == 'darwin'", "pydantic-extra-types[pycountry]~=2.11", + "python-pptx~=1.0", "six~=1.17", ] @@ -45,7 +47,12 @@ required-environments = [ "sys_platform == 'darwin' and platform_machine == 'arm64'", "sys_platform == 'linux'", ] +override-dependencies = [ + "pillow==11.3.0", +] +[tool.uv.sources] +extract-core = { path = "../extract-core", editable = true } [dependency-groups] dev = [ @@ -87,4 +94,4 @@ exclude = [ ] [tool.uv-dynamic-versioning] fallback-version = "0.0.0" -pattern = "default-unprefixed" \ No newline at end of file +pattern = "default-unprefixed" diff --git a/tests/__init__.py b/extract-python/tests/__init__.py similarity index 100% rename from tests/__init__.py rename to extract-python/tests/__init__.py diff --git a/tests/conftest.py b/extract-python/tests/conftest.py similarity index 95% rename from tests/conftest.py rename to extract-python/tests/conftest.py index 14ab15b..6ba9a97 100644 --- a/tests/conftest.py +++ b/extract-python/tests/conftest.py @@ -3,8 +3,8 @@ from pathlib import Path import pytest +from extract_core import InputDoc -from extract_python.objects import InputDoc from tests import TEST_DATA_DIR diff --git a/tests/data/computer_generated.pdf b/extract-python/tests/data/computer_generated.pdf similarity index 100% rename from tests/data/computer_generated.pdf rename to extract-python/tests/data/computer_generated.pdf diff --git a/tests/data/scanned.pdf b/extract-python/tests/data/scanned.pdf similarity index 100% rename from tests/data/scanned.pdf rename to extract-python/tests/data/scanned.pdf diff --git a/extract-python/tests/test_docling.py b/extract-python/tests/test_docling.py new file mode 100644 index 0000000..95010ee --- /dev/null +++ b/extract-python/tests/test_docling.py @@ -0,0 +1,56 @@ +from pathlib import Path +from typing import cast + +import pytest +from extract_core import ( + DoclingPipelineConfig, + InputDoc, + OutputFormat, + Pipeline, + Status, +) +from extract_python import DoclingPipeline + +from . import TEST_DATA_DIR + + +@pytest.fixture(scope="session") +def config() -> DoclingPipelineConfig: + # TODO: for testing add a lightweight configuration + config = DoclingPipelineConfig() + return config + + +@pytest.fixture(scope="session") +def pipeline(config: DoclingPipelineConfig) -> DoclingPipeline: + return cast(DoclingPipeline, Pipeline.from_config(config=config)) + + +@pytest.mark.integration +async def test_docling_pdf_to_markdown( + pipeline: DoclingPipeline, docs: list[InputDoc], tmpdir: Path +) -> None: + # Given + output_path = Path(tmpdir) + # When + output_format = OutputFormat.MARKDOWN + res = [r async for r in pipeline.extract_content(docs, output_format, output_path)] + # Then + assert all(r.status == Status.SUCCESS for r in res) + expected_output_paths = ["scanned_pdf", "computer_generated_pdf"] + expected_output_paths = [Path(p) for p in expected_output_paths] + output_paths = [r.output.path for r in res] + assert output_paths == expected_output_paths + for p in expected_output_paths: + assert (output_path / p).exists() + assert (output_path / p).is_dir() + assert (output_path / p / p.name).with_suffix(".md").exists() + assert any((output_path / p).glob("artifacts/*.png")) + assert all(r.output.pages for r in res) + assert not any(r.errors for r in res) + input_path = [r.input.path for r in res] + expected_input_path = [ + TEST_DATA_DIR / "scanned.pdf", + TEST_DATA_DIR / "computer_generated.pdf", + ] + assert input_path == expected_input_path diff --git a/tests/test_marker.py b/extract-python/tests/test_marker.py similarity index 95% rename from tests/test_marker.py rename to extract-python/tests/test_marker.py index eb21a77..1f648ee 100644 --- a/tests/test_marker.py +++ b/extract-python/tests/test_marker.py @@ -2,15 +2,15 @@ from typing import cast import pytest - -from extract_python import ( +from extract_core import ( InputDoc, - MarkerPipeline, MarkerPipelineConfig, OutputFormat, Pipeline, Status, ) +from extract_python import MarkerPipeline + from tests import TEST_DATA_DIR diff --git a/tests/test_miner_u.py b/extract-python/tests/test_miner_u.py similarity index 95% rename from tests/test_miner_u.py rename to extract-python/tests/test_miner_u.py index 2f6ee22..b2897e3 100644 --- a/tests/test_miner_u.py +++ b/extract-python/tests/test_miner_u.py @@ -2,15 +2,15 @@ from typing import cast import pytest - -from extract_python import ( +from extract_core import ( InputDoc, - MinerUPipeline, MinerUPipelineConfig, OutputFormat, Pipeline, Status, ) +from extract_python import MinerUPipeline + from tests import TEST_DATA_DIR diff --git a/uv.lock b/extract-python/uv.lock similarity index 91% rename from uv.lock rename to extract-python/uv.lock index c26d2e6..a7af516 100644 --- a/uv.lock +++ b/extract-python/uv.lock @@ -2,27 +2,15 @@ version = 1 revision = 3 requires-python = ">=3.11, <3.14" resolution-markers = [ - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "python_full_version == '3.12.*' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "python_full_version < '3.12' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version >= '3.12' and sys_platform == 'darwin' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version < '3.12' and sys_platform == 'darwin' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", - "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", - "python_full_version >= '3.12' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version < '3.12' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", - "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", + "python_full_version >= '3.13' and sys_platform == 'darwin'", + "python_full_version == '3.12.*' and sys_platform == 'darwin'", + "python_full_version < '3.12' and sys_platform == 'darwin'", + "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')", ] required-markers = [ "platform_machine == 'arm64' and sys_platform == 'darwin'", @@ -33,6 +21,9 @@ conflicts = [[ { package = "extract-python", extra = "mineru" }, ]] +[manifest] +overrides = [{ name = "pillow", specifier = "==11.3.0" }] + [[package]] name = "accelerate" version = "1.10.1" @@ -549,18 +540,12 @@ name = "cysignals" version = "1.12.6" source = { registry = "https://pypi.org/simple" } resolution-markers = [ - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "python_full_version == '3.12.*' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version >= '3.12' and sys_platform == 'darwin' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra == 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", - "python_full_version >= '3.12' and sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", + "python_full_version >= '3.13' and sys_platform == 'darwin'", + "python_full_version == '3.12.*' and sys_platform == 'darwin'", + "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux')", ] sdist = { url = "https://files.pythonhosted.org/packages/b9/5a/d258fd8d6ee1538b8472f39051a87d3d6aa2ab26ffa2da4ac809fb851b88/cysignals-1.12.6.tar.gz", hash = "sha256:3ef3a37bdb244821b85475a08e2762ca1019570b369e321504995fa9a54675ce", size = 79583, upload-time = "2025-10-30T04:28:44.463Z" } wheels = [ @@ -677,8 +662,7 @@ dependencies = [ { name = "jsonschema" }, { name = "latex2mathml" }, { name = "pandas" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, { name = "pydantic" }, { name = "pydantic-settings" }, { name = "pyyaml" }, @@ -712,8 +696,7 @@ dependencies = [ { name = "huggingface-hub" }, { name = "jsonlines" }, { name = "numpy" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, { name = "pydantic" }, { name = "rtree" }, { name = "safetensors", extra = ["torch"] }, @@ -733,8 +716,7 @@ version = "6.2.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "docling-core" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, { name = "pydantic" }, { name = "pywin32", marker = "sys_platform == 'win32' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, { name = "tabulate" }, @@ -799,8 +781,7 @@ standard = [ { name = "marko" }, { name = "numpy" }, { name = "openpyxl" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, { name = "polyfactory" }, { name = "pylatexenc" }, { name = "pypdfium2" }, @@ -824,8 +805,7 @@ dependencies = [ { name = "ninja" }, { name = "numpy" }, { name = "opencv-python-headless" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, { name = "pyclipper" }, { name = "python-bidi" }, { name = "pyyaml" }, @@ -866,10 +846,44 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl", hash = "sha256:760643d3452b4d777d295bb167ccc74c64a81df23fb5e08eff250c425a4b2017", size = 28317, upload-time = "2025-09-01T09:48:08.5Z" }, ] +[[package]] +name = "extract-core" +source = { editable = "../extract-core" } +dependencies = [ + { name = "docling-slim" }, + { name = "icij-common" }, + { name = "marker-pdf" }, + { name = "mineru" }, + { name = "pydantic" }, + { name = "pydantic-extra-types", extra = ["pycountry"] }, +] + +[package.metadata] +requires-dist = [ + { name = "docling-slim", specifier = "~=2.96" }, + { name = "icij-common", specifier = "~=0.8.2" }, + { name = "marker-pdf", specifier = "~=1.10" }, + { name = "mineru", specifier = "~=3.2" }, + { name = "pydantic", specifier = "~=2.13" }, + { name = "pydantic-extra-types", extras = ["pycountry"], specifier = ">=2.11.1" }, +] + +[package.metadata.requires-dev] +dev = [ + { name = "docling", specifier = "~=2.96" }, + { name = "huggingface-hub", specifier = "~=0.36.2" }, + { name = "mpmath", specifier = "~=1.3.0" }, + { name = "pytest", specifier = "~=8.3.5" }, + { name = "pytest-asyncio", specifier = "~=0.25.3" }, + { name = "ruff", specifier = "==0.15.2" }, + { name = "sympy", specifier = "~=1.14.0" }, +] + [[package]] name = "extract-python" source = { editable = "." } dependencies = [ + { name = "extract-core" }, { name = "icij-common" }, ] @@ -890,6 +904,7 @@ mineru = [ { name = "mineru", extra = ["mlx"], marker = "(sys_platform == 'darwin' and extra == 'extra-14-extract-python-mineru') or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, { name = "mineru", extra = ["pipeline", "vlm"], marker = "extra == 'extra-14-extract-python-mineru'" }, { name = "pydantic-extra-types", extra = ["pycountry"], marker = "extra == 'extra-14-extract-python-mineru'" }, + { name = "python-pptx" }, { name = "six" }, ] @@ -903,6 +918,7 @@ dev = [ [package.metadata] requires-dist = [ { name = "docling-slim", extras = ["feat-ocr-easyocr", "feat-ocr-mac", "feat-ocr-tesserocr", "standard"], marker = "extra == 'docling'", specifier = "~=2.96" }, + { name = "extract-core", editable = "../extract-core" }, { name = "html2image", marker = "extra == 'benches'", specifier = "~=2.0.7" }, { name = "icij-common", specifier = "~=0.8.2" }, { name = "markdown2", marker = "extra == 'benches'", specifier = ">=2.5.4" }, @@ -912,6 +928,7 @@ requires-dist = [ { name = "notebook", marker = "extra == 'benches'", specifier = ">=7.4.5" }, { name = "pydantic-extra-types", extras = ["pycountry"], marker = "extra == 'mineru'", specifier = "~=2.11" }, { name = "pypdfium2", marker = "extra == 'benches'", specifier = ">=4.30.0" }, + { name = "python-pptx", marker = "extra == 'mineru'", specifier = "~=1.0" }, { name = "six", marker = "extra == 'mineru'", specifier = "~=1.17" }, ] provides-extras = ["benches", "docling", "marker", "mineru"] @@ -1301,7 +1318,7 @@ name = "humanfriendly" version = "10.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "pyreadline3", marker = "sys_platform == 'win32'" }, + { name = "pyreadline3", marker = "sys_platform == 'win32' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/cc/3f/2c29224acb2e2df4d2046e4c73ee2662023c58ff5b113c4c1adac0886c43/humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc", size = 360702, upload-time = "2021-09-17T21:40:43.31Z" } wheels = [ @@ -1346,8 +1363,7 @@ version = "2.37.3" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "numpy" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-marker'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-14-extract-python-mineru' or extra != 'extra-14-extract-python-marker'" }, + { name = "pillow" }, ] sdist = { url = "https://files.pythonhosted.org/packages/b1/84/93bcd1300216ea50811cee96873b84a1bebf8d0489ffaf7f2a3756bab866/imageio-2.37.3.tar.gz", hash = "sha256:bbb37efbfc4c400fcd534b367b91fcd66d5da639aaa138034431a1c5e0a41451", size = 389673, upload-time = "2026-03-09T11:31:12.573Z" } wheels = [ @@ -1791,8 +1807,8 @@ name = "loguru" version = "0.7.3" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "colorama", marker = "sys_platform == 'win32'" }, - { name = "win32-setctime", marker = "sys_platform == 'win32'" }, + { name = "colorama", marker = "sys_platform == 'win32' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, + { name = "win32-setctime", marker = "sys_platform == 'win32' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/3a/05/a1dae3dffd1116099471c643b8924f5aa6524411dc6c63fdae648c4f1aca/loguru-0.7.3.tar.gz", hash = "sha256:19480589e77d47b8d85b2c827ad95d49bf31b0dcde16593892eb51dd18706eb6", size = 63559, upload-time = "2024-12-06T11:20:56.608Z" } wheels = [ @@ -1934,13 +1950,13 @@ dependencies = [ { name = "markdownify" }, { name = "openai" }, { name = "pdftext" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" } }, + { name = "pillow" }, { name = "pre-commit" }, { name = "pydantic" }, { name = "pydantic-settings" }, { name = "python-dotenv" }, { name = "rapidfuzz" }, - { name = "regex", version = "2024.11.6", source = { registry = "https://pypi.org/simple" } }, + { name = "regex" }, { name = "scikit-learn" }, { name = "surya-ocr" }, { name = "torch" }, @@ -2050,11 +2066,11 @@ dependencies = [ { name = "modelscope" }, { name = "numpy" }, { name = "openai" }, - { name = "opencv-python", version = "4.11.0.86", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform != 'darwin' and extra == 'extra-14-extract-python-mineru') or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, - { name = "opencv-python", version = "4.13.0.92", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'darwin' and extra == 'extra-14-extract-python-mineru') or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, + { name = "opencv-python", version = "4.11.0.86", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, + { name = "opencv-python", version = "4.13.0.92", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, { name = "openpyxl" }, { name = "pdftext" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" } }, + { name = "pillow" }, { name = "pylatexenc" }, { name = "pypdf" }, { name = "pypdfium2" }, @@ -2100,7 +2116,7 @@ dependencies = [ { name = "httpx" }, { name = "httpx-retries" }, { name = "loguru" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" } }, + { name = "pillow" }, { name = "pydantic" }, ] wheels = [ @@ -2180,7 +2196,7 @@ dependencies = [ { name = "mlx-lm", marker = "sys_platform == 'darwin'" }, { name = "numpy", marker = "sys_platform == 'darwin'" }, { name = "opencv-python", version = "4.13.0.92", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin'" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin'" }, + { name = "pillow", marker = "sys_platform == 'darwin'" }, { name = "requests", marker = "sys_platform == 'darwin'" }, { name = "soundfile", marker = "sys_platform == 'darwin'" }, { name = "tqdm", marker = "sys_platform == 'darwin'" }, @@ -2686,8 +2702,7 @@ version = "1.0.1" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "click", marker = "sys_platform == 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, - { name = "pillow", version = "10.4.0", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'darwin' and extra == 'extra-14-extract-python-marker') or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, - { name = "pillow", version = "11.3.0", source = { registry = "https://pypi.org/simple" }, marker = "(sys_platform == 'darwin' and extra != 'extra-14-extract-python-marker') or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, + { name = "pillow", marker = "sys_platform == 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, { name = "pyobjc-framework-vision", marker = "sys_platform == 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/5e/07/3e15ab404f75875c5e48c47163300eb90b7409044d8711fc3aaf52503f2e/ocrmac-1.0.1.tar.gz", hash = "sha256:507fe5e4cbd67b2d03f6729a52bbc11f9d0b58241134eb958a5daafd4b9d93d9", size = 1454317, upload-time = "2026-01-08T16:44:26.412Z" } @@ -2761,20 +2776,12 @@ name = "opencv-python" version = "4.11.0.86" source = { registry = "https://pypi.org/simple" } resolution-markers = [ - "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru'", - "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')", - "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 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>= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", - "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru'", - "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and extra != 'extra-14-extract-python-marker' and extra != 'extra-14-extract-python-mineru')", + "python_full_version >= '3.13' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version >= '3.13' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.13' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version == '3.12.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version == '3.12.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')", ] dependencies = [ { name = "numpy", marker = "sys_platform != 'darwin' or (extra == 'extra-14-extract-python-marker' and extra == 'extra-14-extract-python-mineru')" }, @@ -2794,13 +2801,9 @@ name = "opencv-python" version = "4.13.0.92" source = { registry = "https://pypi.org/simple" } resolution-markers = [ - "python_full_version >= '3.13' and sys_platform == 'darwin' and extra != 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.miner_u import MinerUPipeline, MinerUPipelineConfig -except ImportError: - MinerUPipeline, MinerUPipelineConfig = None, None - - -__all__ = [ - "DoclingPipeline", - "DoclingPipelineConfig", - "InputDoc", - "DOCLING_DEFAULT_ARTIFACTS_PATH", - "MarkerPipeline", - "MarkerPipelineConfig", - "OutputFormat", - "Pipeline", - "PipelineType", - "PipelineConfig", - "Status", -] diff --git a/extract_python/constants.py b/extract_python/constants.py deleted file mode 100644 index c3d5e08..0000000 --- a/extract_python/constants.py +++ /dev/null @@ -1,6 +0,0 @@ -ARTIFACTS = "artifacts" -CPU_GROUP = "cpu" -MINER_U_GROUP = "miner-u" -EXTRACT_CONTENT_TASK = "extract-content" -EXTRACT_CONTENT_MINER_U_TASK = "extract-content-miner-u" -DEFAULT_MD_PAGE_SEP = '
' diff --git a/extract_python/docling_.py b/extract_python/docling_.py deleted file mode 100644 index 8070989..0000000 --- a/extract_python/docling_.py +++ /dev/null @@ -1,278 +0,0 @@ -import importlib -import shutil -import tempfile -from collections.abc import AsyncGenerator, Iterable, Iterator -from functools import cache -from pathlib import Path -from typing import Annotated, Any, ClassVar, Self, TypeVar, get_type_hints - -from docling.backend.abstract_backend import AbstractDocumentBackend -from docling.datamodel.backend_options import BackendOptions, BaseBackendOptions - -# Data model import are quick it's ok to leave it there -from docling.datamodel.base_models import FormatToExtensions, InputFormat -from docling.datamodel.document import ConversionResult -from docling.datamodel.pipeline_options import ( - EasyOcrOptions, - PdfPipelineOptions, - PipelineOptions, - ThreadedPdfPipelineOptions, -) -from docling.document_converter import DocumentConverter, FormatOption -from docling.pipeline.base_pipeline import BasePipeline - -# TODO: this is long to load improve it -from docling_core.types.doc import ImageRefMode -from docling_core.types.io import DocumentStream -from icij_common.pydantic_utils import to_lower_snake_case -from icij_common.registrable import FromConfig -from pydantic import ( - AfterValidator, - BeforeValidator, - Field, - PlainSerializer, - WrapSerializer, - model_validator, -) -from pydantic_core.core_schema import SerializerFunctionWrapHandler - -from .constants import ARTIFACTS, DEFAULT_MD_PAGE_SEP -from .objects import ( - Error, - InputDoc, - MarkdownDoc, - OutputFormat, - PageIndexes, - Result, - Status, - SupportedExt, -) -from .pipeline import Pipeline, PipelineConfig, PipelineType -from .utils import all_subclasses, chdir, map_and_preserve, path_to_artifacts_dirname - -DOCLING_DEFAULT_ARTIFACTS_PATH = Path.home().joinpath(".cache", "docling", "models") - - -def _validate_pipeline_opts(v: "PipelineOptions") -> None: - if isinstance(v, PdfPipelineOptions) and not v.generate_picture_images: - msg = "generate_picture_images should be set to true" - raise ValueError(msg) - return v - - -T = TypeVar("T") - - -def _find_subcls(cls: type[T], name: str) -> type[T]: - # Check if the class available - for c in all_subclasses(cls): - if c.__name__ == name: - return c - # Then apply ad-hoc search - if "pipeline" in cls.__name__.lower(): - module_name = f"docling.pipeline.{to_lower_snake_case(name)}" - try: - module = importlib.import_module(module_name) - return getattr(module, name) - except (ModuleNotFoundError, AttributeError): - pass - raise ValueError(f"unknown {cls.__name__} subclass {name}") - - -def _find_init_arg_type(cls: type[Any], arg: str) -> type: - hints = get_type_hints(cls.__init__) - return hints[arg] - - -def _resolve_pipeline_cls(v: Any) -> Any: - if isinstance(v, str): - return _find_subcls(BasePipeline, v) - return v - - -def _ser_class_as_str(v: Any) -> Any: - if isinstance(v, type): - return v.__name__ - return v - - -def _ser_with_backend_option_kind( - v: Any, handler: SerializerFunctionWrapHandler -) -> Any: - serialized = handler(v) - if isinstance(v, BaseBackendOptions): - kind = getattr(v, "kind", None) - if kind is not None: - serialized["kind"] = kind - return serialized - - -def _resolve_backend(v: Any) -> Any: - if isinstance(v, str): - return _find_subcls(AbstractDocumentBackend, v) - return v - - -class DoclingFormatOption(FormatOption): - pipeline_cls: Annotated[ - str | type[BasePipeline], - BeforeValidator(_resolve_pipeline_cls), - PlainSerializer(_ser_class_as_str), - ] - pipeline_options: Annotated[ - dict | PipelineOptions | None, AfterValidator(_validate_pipeline_opts) - ] = None - backend: Annotated[ - str | type[AbstractDocumentBackend], - BeforeValidator(_resolve_backend), - PlainSerializer(_ser_class_as_str), - ] - backend_options: Annotated[ - BackendOptions | None, WrapSerializer(_ser_with_backend_option_kind) - ] = None - - @model_validator(mode="after") - def _resolve_pipeline_options(self) -> Self: - if isinstance(self.pipeline_options, dict): - option_cls = _find_init_arg_type(self.pipeline_cls, "pipeline_options") - self.pipeline_options = option_cls.model_validate(self.pipeline_options) - return self - - -@cache -def _default_format_opts() -> dict[InputFormat, DoclingFormatOption]: - from docling.backend.docling_parse_backend import ( # noqa: PLC0415 - DoclingParseDocumentBackend, - ) - from docling.pipeline.standard_pdf_pipeline import ( # noqa: PLC0415 - StandardPdfPipeline, - ) - - return { - InputFormat.PDF: DoclingFormatOption( - pipeline_cls=StandardPdfPipeline, - backend=DoclingParseDocumentBackend, - pipeline_options=ThreadedPdfPipelineOptions( - ocr_options=EasyOcrOptions(), generate_picture_images=True - ), - ), - } - - -class DoclingPipelineConfig(PipelineConfig): - pipeline: ClassVar[PipelineType] = Field(frozen=True, default=PipelineType.DOCLING) - - format_options: dict[InputFormat, DoclingFormatOption | FormatOption] = Field( - default_factory=_default_format_opts - ) - - @classmethod - @cache - def supported_exts(cls) -> set[SupportedExt]: - unsupported = {InputFormat.AUDIO, InputFormat.METS_GBS, InputFormat.VTT} - supported = set() - for f in InputFormat: - if f in unsupported: - continue - for ext in FormatToExtensions[f]: - supported.add(SupportedExt(f".{ext.lower()}")) - return supported - - -@Pipeline.register(PipelineType.DOCLING) -class DoclingPipeline(Pipeline): - def __init__( - self, format_options: dict["InputFormat", "FormatOption"] | None = None - ): - - allowed_format = [ - f.to_docling() for f in DoclingPipelineConfig.supported_exts() - ] - self._converter = DocumentConverter( - allowed_formats=allowed_format, format_options=format_options - ) - - async def extract_content( - self, docs: Iterable[InputDoc], output_format: OutputFormat, output_path: Path - ) -> AsyncGenerator[Result, None]: - docs, path_or_streams = map_and_preserve(_to_docling, docs) - outputs = self._converter.convert_all(path_or_streams, raises_on_error=False) - for doc, res in zip(docs, outputs, strict=True): - yield _to_result(res, doc, output_format, output_path=output_path) - - @classmethod - def _from_config(cls, config: DoclingPipelineConfig) -> FromConfig: - return cls(config.format_options) - - -def _to_docling(docs: Iterable[InputDoc]) -> Iterator["Path | DocumentStream"]: - for d in docs: - yield d.to_docling() - - -def _to_result( - res: ConversionResult, - input_document: InputDoc, - output_format: OutputFormat, - output_path: Path, - **kwargs, -) -> Result: - output_path.mkdir(parents=True, exist_ok=True) - output = None - status = Status.from_docling(res.status) - if status.allows_conversion: - match output_format: - case OutputFormat.MARKDOWN: - output = _to_markdown_doc(res, output_path, **kwargs) - case _: - raise NotImplementedError(f"unsupported output format {output_format}") - errors = [Error.from_docling(e) for e in res.errors] - input_doc = input_document.without_content() - return Result(input=input_doc, status=status, errors=errors, output=output) - - -def _to_markdown_doc( - res: ConversionResult, - output_path: Path, - page_sep: str = DEFAULT_MD_PAGE_SEP, - **kwargs, -) -> MarkdownDoc: - # TODO: Should we add a hash to avoid collision between files with same names - # nested in the tree structured - md_dir_name = path_to_artifacts_dirname(res.input.file) - md_dir = output_path / md_dir_name - if md_dir.exists(): - raise FileExistsError(f"directory {md_dir} already exists") - # Let's avoid issue of duplicated input file names flattened top level - md_filename = md_dir_name + OutputFormat.MARKDOWN - total_length = 0 - n_pages = len(res.pages) - - with tempfile.TemporaryDirectory(ignore_cleanup_errors=True) as td: - tmp_dir = Path(td) - page_path = Path("page.md") - # We do a chdir to bypass a Docling bug which only allows to maintain relative - # image ref when saving the markdown to a relative path - with (tmp_dir / md_filename).open("w") as f, chdir(tmp_dir): - end_indices = [] - for page_i in range(n_pages): - res.document.save_as_markdown( - page_path, - page_no=page_i + 1, - image_mode=ImageRefMode.REFERENCED, - artifacts_dir=Path(ARTIFACTS), - **kwargs, - ) - content = page_path.read_text() - if page_i > 0: - content += "\n" - if page_i < n_pages - 1: - content += page_sep - total_length += len(content) - end_indices.append(total_length) - f.write(content) - f.flush() - page_path.unlink() - shutil.move(tmp_dir, md_dir) - pages = PageIndexes.from_page_end_indices(end_indices) - return MarkdownDoc(path=Path(md_dir_name), pages=pages) diff --git a/scripts/lock.sh b/scripts/lock.sh new file mode 100755 index 0000000..20ade97 --- /dev/null +++ b/scripts/lock.sh @@ -0,0 +1,6 @@ +#!/bin/bash +set -e + +cd "$1" + +uv lock \ No newline at end of file diff --git a/tests/test_docling.py b/tests/test_docling.py deleted file mode 100644 index ffba8a0..0000000 --- a/tests/test_docling.py +++ /dev/null @@ -1,100 +0,0 @@ -from pathlib import Path -from typing import cast - -import pytest -from docling.backend.pypdfium2_backend import PyPdfiumDocumentBackend -from docling.datamodel.backend_options import PdfBackendOptions -from docling.datamodel.base_models import InputFormat -from docling.pipeline.legacy_standard_pdf_pipeline import LegacyStandardPdfPipeline - -from extract_python import DoclingPipeline, DoclingPipelineConfig, Pipeline -from extract_python.docling_ import DoclingFormatOption -from extract_python.objects import InputDoc, OutputFormat, Status - -from . import TEST_DATA_DIR - - -@pytest.fixture(scope="session") -def config() -> DoclingPipelineConfig: - # TODO: for testing add a lightweight configuration - config = DoclingPipelineConfig() - return config - - -@pytest.fixture(scope="session") -def pipeline(config: DoclingPipelineConfig) -> DoclingPipeline: - return cast(DoclingPipeline, Pipeline.from_config(config=config)) - - -def test_format_option_derser() -> None: - # Given - config = { - "format_options": { - "pdf": { - "pipeline_cls": "LegacyStandardPdfPipeline", - "backend": "PyPdfiumDocumentBackend", - "backend_options": {"kind": "pdf"}, - } - } - } - # When - deserialized = DoclingPipelineConfig.model_validate(config) - # Then - expected = DoclingPipelineConfig( - format_options={ - InputFormat.PDF: DoclingFormatOption( - pipeline_cls=LegacyStandardPdfPipeline, - backend_options=PdfBackendOptions(), - backend=PyPdfiumDocumentBackend, - ) - }, - ) - assert deserialized == expected - - -def test_format_option_ser() -> None: - # Given - - config = DoclingPipelineConfig( - format_options={ - InputFormat.PDF: DoclingFormatOption( - pipeline_cls=LegacyStandardPdfPipeline, - backend_options=PdfBackendOptions(), - backend=PyPdfiumDocumentBackend, - ) - }, - ) - # When - serialized = config.model_dump_json(indent=2) - deserialized = DoclingPipelineConfig.model_validate_json(serialized) - assert deserialized == config - - -@pytest.mark.integration -async def test_docling_pdf_to_markdown( - pipeline: DoclingPipeline, docs: list[InputDoc], tmpdir: Path -) -> None: - # Given - output_path = Path(tmpdir) - # When - output_format = OutputFormat.MARKDOWN - res = [r async for r in pipeline.extract_content(docs, output_format, output_path)] - # Then - assert all(r.status == Status.SUCCESS for r in res) - expected_output_paths = ["scanned_pdf", "computer_generated_pdf"] - expected_output_paths = [Path(p) for p in expected_output_paths] - output_paths = [r.output.path for r in res] - assert output_paths == expected_output_paths - for p in expected_output_paths: - assert (output_path / p).exists() - assert (output_path / p).is_dir() - assert (output_path / p / p.name).with_suffix(".md").exists() - assert any((output_path / p).glob("artifacts/*.png")) - assert all(r.output.pages for r in res) - assert not any(r.errors for r in res) - input_path = [r.input.path for r in res] - expected_input_path = [ - TEST_DATA_DIR / "scanned.pdf", - TEST_DATA_DIR / "computer_generated.pdf", - ] - assert input_path == expected_input_path diff --git a/tests/test_objects.py b/tests/test_objects.py deleted file mode 100644 index ddc49fc..0000000 --- a/tests/test_objects.py +++ /dev/null @@ -1,40 +0,0 @@ -try: - from docling.datamodel.base_models import InputFormat - from docling.datamodel.pipeline_options import ( - PdfPipelineOptions, - TesseractOcrOptions, - ) -except ImportError: - InputFormat = None - PdfPipelineOptions, TesseractOcrOptions = None, None - - -def test_docling_pipeline_config() -> None: - from extract_python import DoclingPipelineConfig, PipelineConfig # noqa: PLC0415 - - # Given - config = { - "pipeline": "docling", - "pipeline_options": [ - ["pdf", {"ocr_options": {"kind": "tesserocr", "lang": ["auto"]}}] - ], - "format_options": { - "pdf": { - "pipeline_cls": "StandardPdfPipeline", - "backend_cls": "DoclingParseDocumentBackend", - }, - }, - } - # When - - pipeline_config = PipelineConfig.model_validate(config) - # Then - assert isinstance(pipeline_config, DoclingPipelineConfig) - format_options = pipeline_config.to_format_options() - pdf_options = format_options[InputFormat.PDF] - pdf_pipeline_options = pdf_options.pipeline_options - expected_options = PdfPipelineOptions( - ocr_options=TesseractOcrOptions(lang=["auto"]), - generate_picture_images=True, - ) - assert pdf_pipeline_options.model_dump() == expected_options.model_dump()