fix: Restore handling of DeleteCitation #167
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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)
Michael-E-Rose
approved these changes
Jun 5, 2025
Collaborator
|
Hi & thanks for this PR! Much appreciated. Can you confirm if works in your end? The automatic tests failed but that might not be your fault. |
Contributor
Author
|
@Michael-E-Rose Hi, thanks, you're welcome. Yes, all the tests pass locally, including |
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This commit fixes a regression introduced in v0.4.0 where the parsing of 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:
{'pmid': <pmid_value>, 'delete': True}is yielded, consistent with the updated function docstring.element.clear()is called for both and 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 #166 (addresses the core bug of not handling deleted articles)
Related to #165 (clarifies behavior for the 'delete' flag)
Addresses regression from v0.4.0 (restores DeleteCitation parsing)
Given the nature of this fix, it's recommended that this be part of version 0.5.2.