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FIX: PMCID extraction #55

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Merged
adelavega merged 2 commits into from
Aug 25, 2025
Merged

FIX: PMCID extraction #55

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1991108
Extract PMCID in both ways
adelavega Aug 19, 2025
e0d3656
Extract pmcid correctly in article
adelavega Aug 19, 2025
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2 changes: 1 addition & 1 deletion src/pubget/_text.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,5 +39,5 @@ def extract(
for part_name in self.fields:
elem = transformed.find(part_name)
result[part_name] = elem.text
result["pmcid"] = int(result["pmcid"])
result["pmcid"] = _utils.get_pmcid(article)
return result
13 changes: 11 additions & 2 deletions src/pubget/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,9 +132,18 @@ def load_stylesheet(stylesheet_name: str) -> etree.XSLT:

def get_pmcid(article: Union[etree.ElementTree, etree.Element]) -> int:
"""Extract the PubMedCentral ID from an XML article."""
return int(
article.find("front/article-meta/article-id[@pub-id-type='pmc']").text
pmc = article.find("front/article-meta/article-id[@pub-id-type='pmc']")
pmcid = article.find(
"front/article-meta/article-id[@pub-id-type='pmcid']"
)
if pmc is None and pmcid is None:
raise ValueError("No PMC ID found in the article XML.")
if pmc:
val = pmc.text
else:
val = pmcid.text.replace("PMC", "")

return int(val)


def get_pmcid_from_article_dir(article_dir: Path) -> int:
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