Parse the DeleteCitation tag in parse_medline_xml()#168
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nils-herrmann wants to merge 2 commits intotitipata:masterfrom
Open
Parse the DeleteCitation tag in parse_medline_xml()#168nils-herrmann wants to merge 2 commits intotitipata:masterfrom
DeleteCitation tag in parse_medline_xml()#168nils-herrmann wants to merge 2 commits intotitipata:masterfrom
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This commit fixes a regression introduced in v0.4.0 where the
parsing of <DeleteCitation> elements was inadvertently removed during
the refactor to an iterator-based model for `parse_medline_xml`.
The original functionality present in v0.3.1 for identifying deleted
articles is now restored, adapted for the memory-efficient iterator design.
Changes include:
- Added logic to process <DeleteCitation> elements within the iterparse loop.
For each deleted citation, a dictionary `{'pmid': <pmid_value>, 'delete': True}`
is yielded, consistent with the updated function docstring.
- Ensured `element.clear()` is called for both <DeleteCitation> and
<PubmedArticle> elements to prevent memory leaks, upholding the
memory-saving goals of the iterator pattern.
This change brings the parser's behavior in line with its documentation
regarding deleted articles and rectifies the omission from the previous
refactor.
Fixes titipata#166 (addresses the core bug of not handling deleted articles)
Related to titipata#165 (clarifies behavior for the 'delete' flag)
Addresses regression from v0.4.0 (restores DeleteCitation parsing)
Co-authored-by: @iacopy
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This PR follows the fix for #166 proposed in #167 with two minor changes:
"PMID"