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feat(xml-jats): parse XML JATS documents (#967)

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* chore(xml-jats): separate authors and affiliations

In XML PubMed (JATS) backend, convert authors and affiliations as they
are typically rendered on PDFs.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* fix(xml-jats): replace new line character by a space

Instead of removing new line character from text, replace it by a space character.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* feat(xml-jats): improve existing parser and extend features

Partially support lists, respect reading order, parse more sections, support equations, better text formatting.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* chore(xml-jats): rename PubMed objects to JATS

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

---------

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Cesar Berrospi Ramis
2025-02-17 10:43:31 +01:00
committed by GitHub
parent e1436a8b05
commit 428b656793
35 changed files with 13688 additions and 30671 deletions
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10
docling/document_converter.py
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@@ -18,7 +18,7 @@ from docling.backend.md_backend import MarkdownDocumentBackend
from docling.backend.msexcel_backend import MsExcelDocumentBackend
from docling.backend.mspowerpoint_backend import MsPowerpointDocumentBackend
from docling.backend.msword_backend import MsWordDocumentBackend
from docling.backend.xml.pubmed_backend import PubMedDocumentBackend
from docling.backend.xml.jats_backend import JatsDocumentBackend
from docling.backend.xml.uspto_backend import PatentUsptoDocumentBackend
from docling.datamodel.base_models import (
ConversionStatus,
@@ -102,9 +102,9 @@ class PatentUsptoFormatOption(FormatOption):
backend: Type[PatentUsptoDocumentBackend] = PatentUsptoDocumentBackend
class XMLPubMedFormatOption(FormatOption):
class XMLJatsFormatOption(FormatOption):
pipeline_cls: Type = SimplePipeline
backend: Type[AbstractDocumentBackend] = PubMedDocumentBackend
backend: Type[AbstractDocumentBackend] = JatsDocumentBackend
class ImageFormatOption(FormatOption):
@@ -143,8 +143,8 @@ def _get_default_option(format: InputFormat) -> FormatOption:
InputFormat.XML_USPTO: FormatOption(
pipeline_cls=SimplePipeline, backend=PatentUsptoDocumentBackend
),
InputFormat.XML_PUBMED: FormatOption(
pipeline_cls=SimplePipeline, backend=PubMedDocumentBackend
InputFormat.XML_JATS: FormatOption(
pipeline_cls=SimplePipeline, backend=JatsDocumentBackend
),
InputFormat.IMAGE: FormatOption(
pipeline_cls=StandardPdfPipeline, backend=DoclingParseV2DocumentBackend