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

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merged 4 commits into from
Feb 17, 2025
Merged

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

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21a99fc
chore(xml-jats): separate authors and affiliations
ceberam Feb 5, 2025
c9ae5f6
fix(xml-jats): replace new line character by a space
ceberam Feb 5, 2025
011dd6c
feat(xml-jats): improve existing parser and extend features
ceberam Feb 14, 2025
93eb9de
chore(xml-jats): rename PubMed objects to JATS
ceberam Feb 14, 2025
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772 changes: 772 additions & 0 deletions docling/backend/xml/jats_backend.py
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592 changes: 0 additions & 592 deletions docling/backend/xml/pubmed_backend.py
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6 changes: 3 additions & 3 deletions docling/datamodel/base_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,14 @@ class InputFormat(str, Enum):
DOCX = "docx"
PPTX = "pptx"
HTML = "html"
XML_PUBMED = "xml_pubmed"
IMAGE = "image"
PDF = "pdf"
ASCIIDOC = "asciidoc"
MD = "md"
CSV = "csv"
XLSX = "xlsx"
XML_USPTO = "xml_uspto"
XML_JATS = "xml_jats"
JSON_DOCLING = "json_docling"


Expand All @@ -59,7 +59,7 @@ class OutputFormat(str, Enum):
InputFormat.PDF: ["pdf"],
InputFormat.MD: ["md"],
InputFormat.HTML: ["html", "htm", "xhtml"],
InputFormat.XML_PUBMED: ["xml", "nxml"],
InputFormat.XML_JATS: ["xml", "nxml"],
InputFormat.IMAGE: ["jpg", "jpeg", "png", "tif", "tiff", "bmp"],
InputFormat.ASCIIDOC: ["adoc", "asciidoc", "asc"],
InputFormat.CSV: ["csv"],
Expand All @@ -79,7 +79,7 @@ class OutputFormat(str, Enum):
"application/vnd.openxmlformats-officedocument.presentationml.presentation",
],
InputFormat.HTML: ["text/html", "application/xhtml+xml"],
InputFormat.XML_PUBMED: ["application/xml"],
InputFormat.XML_JATS: ["application/xml"],
InputFormat.IMAGE: [
"image/png",
"image/jpeg",
Expand Down
8 changes: 4 additions & 4 deletions docling/datamodel/document.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,11 +333,11 @@ def _guess_from_content(
):
input_format = InputFormat.XML_USPTO

if (
InputFormat.XML_PUBMED in formats
and "/NLM//DTD JATS" in xml_doctype
if InputFormat.XML_JATS in formats and (
"JATS-journalpublishing" in xml_doctype
or "JATS-archive" in xml_doctype
):
input_format = InputFormat.XML_PUBMED
input_format = InputFormat.XML_JATS

elif mime == "text/plain":
if InputFormat.XML_USPTO in formats and content_str.startswith("PATN\r\n"):
Expand Down
10 changes: 5 additions & 5 deletions docling/document_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
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,
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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
Expand Down
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