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428b656793
* 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>
74 lines
2.3 KiB
Python
74 lines
2.3 KiB
Python
import json
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import os
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from io import BytesIO
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from pathlib import Path
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from docling_core.types.doc import DoclingDocument
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from docling.datamodel.base_models import DocumentStream, InputFormat
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from docling.datamodel.document import ConversionResult
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from docling.document_converter import DocumentConverter
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GENERATE = False
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def get_pubmed_paths():
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directory = Path(os.path.dirname(__file__) + f"/data/pubmed/")
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xml_files = sorted(directory.rglob("*.xml"))
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return xml_files
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def get_converter():
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converter = DocumentConverter(allowed_formats=[InputFormat.XML_JATS])
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return converter
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def verify_export(pred_text: str, gtfile: str):
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if not os.path.exists(gtfile) or GENERATE:
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with open(gtfile, "w") as fw:
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fw.write(pred_text)
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return True
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else:
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with open(gtfile, "r") as fr:
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true_text = fr.read()
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assert pred_text == true_text, f"pred_text!=true_text for {gtfile}"
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return pred_text == true_text
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def test_e2e_pubmed_conversions(use_stream=False):
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pubmed_paths = get_pubmed_paths()
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converter = get_converter()
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for pubmed_path in pubmed_paths:
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gt_path = (
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pubmed_path.parent.parent / "groundtruth" / "docling_v2" / pubmed_path.name
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)
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if use_stream:
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buf = BytesIO(pubmed_path.open("rb").read())
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stream = DocumentStream(name=pubmed_path.name, stream=buf)
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conv_result: ConversionResult = converter.convert(stream)
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else:
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conv_result: ConversionResult = converter.convert(pubmed_path)
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doc: DoclingDocument = conv_result.document
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pred_md: str = doc.export_to_markdown()
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assert verify_export(pred_md, str(gt_path) + ".md"), "export to md"
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pred_itxt: str = doc._export_to_indented_text(
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max_text_len=70, explicit_tables=False
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)
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assert verify_export(
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pred_itxt, str(gt_path) + ".itxt"
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), "export to indented-text"
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pred_json: str = json.dumps(doc.export_to_dict(), indent=2)
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assert verify_export(pred_json, str(gt_path) + ".json"), "export to json"
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def test_e2e_pubmed_conversions_stream():
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test_e2e_pubmed_conversions(use_stream=True)
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def test_e2e_pubmed_conversions_no_stream():
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test_e2e_pubmed_conversions(use_stream=False)
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