Function `parse_medline_xml` only return the first affiliation if author has multiple affiliations.

[ZhangWoW123]

Hi team,

Describe the bug I encountered another issue when using the package to extract PubMed affiliation information from XML files. When author has multiple affiliations, the parse_medline_xml function will only extract the first affiliation.

To Reproduce An example of this issue is PMID 39029952. In the XML file, the section is structured as follows. Each author has multiple affinations

<AuthorList CompleteYN="Y">
  <Author ValidYN="Y">
    <LastName>Kim</LastName>
    <ForeName>Jennifer</ForeName>
    <Initials>J</Initials>
    <AffiliationInfo>
      <Affiliation>Graduate Program in Neuroscience, University of British Columbia, Vancouver, Canada.</Affiliation>
    </AffiliationInfo>
    <AffiliationInfo>
      <Affiliation>Djavad Mowafaghian Centre for Brain Health, Vancouver, Canada.</Affiliation>
    </AffiliationInfo>
  </Author>
  ...
</AuthorList>

The medline_parser.parse_author_affiliation use author.find("AffiliationInfo/Affiliation") to find the affilation infromation. However, the find will only return one object (i.e. first element). Thus, the first affiliation is returned.

Expected behavior I expect the parser to return all author's affiliations as a list. Might consider changing the author.find("AffiliationInfo/Affiliation").text with list(chain(*([c.text] for c in author.findall("AffiliationInfo/Affiliation"))))?

Screenshots

XML file example pmid_39029952.txt

Thank you all for the great support.

[Michael-E-Rose]

I expect the parser to return all author's affiliations as a list. Might consider changing the author.find("AffiliationInfo/Affiliation").text with list(chain(*([c.text] for c in author.findall("AffiliationInfo/Affiliation"))))?

This looks like the solution to me. Do you want to provide a PR? Ideally with an additional test case in https://github.com/titipata/pubmed_parser/blob/master/tests/test_medline_parser.py#L33.

[ZhangWoW123]

@Michael-E-Rose,

Sure, I created the PR https://github.com/titipata/pubmed_parser/pull/162

[Michael-E-Rose]

Thank you for your service!