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Parse the DeleteCitation tag in parse_medline_xml() #168

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Parse the DeleteCitation tag in parse_medline_xml() #168

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547ca3f
fix: Restore handling of DeleteCitation and ensure memory safety
iacopy Jun 3, 2025
337560b
Modified fix for deleted articles regression
nils-herrmann Jun 4, 2025
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13 changes: 11 additions & 2 deletions pubmed_parser/medline_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -740,13 +740,17 @@ def parse_medline_xml(
------
An iterator of dictionary containing information about articles in NLM format.
see `parse_article_info`). Articles that have been deleted will be
added with no information other than the field `delete` being `True`
added with no information other than the fields `delete` being `True`,
and `pmid`.

Examples
--------
>>> article_iterator = pubmed_parser.parse_medline_xml('data/pubmed20n0014.xml.gz')
>>> for article in article_iterator:
... print(article['title'])
... if article.get('delete'):
... print(f"Deleted PMID: {article['pmid']}")
... else:
... print(article['title'])
"""
with gzip.open(path, "rb") as f:
for event, element in etree.iterparse(f, events=("end",)):
Expand All @@ -762,3 +766,8 @@ def parse_medline_xml(
res['grant_ids'] = parse_grant_id(element)
element.clear()
yield res

elif element.tag == "DeleteCitation":
for pmid_elem in element.iterchildren(tag="PMID"):
yield {"pmid": pmid_elem.text, "delete": True}
element.clear()
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