Fix SAX parser state leakage for PubmedBookArticle#106
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paulalbert1 wants to merge 2 commits intomasterfrom
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Fix SAX parser state leakage for PubmedBookArticle#106paulalbert1 wants to merge 2 commits intomasterfrom
paulalbert1 wants to merge 2 commits intomasterfrom
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…icle The SAX parser uses a single instance-level `pubmedArticle` variable. When PubMed returns a batch containing both <PubmedArticle> and <PubmedBookArticle> elements, there was no handler for <PubmedBookArticle>. When a book article followed a regular article, `pubmedArticle` still referenced the previous article, causing the book article's AuthorList, Abstract, and other fields to overwrite the previous article's data. This corrupted data would then be saved to DynamoDB. For example, PMID 38461731 had its 8-author list replaced by 79 authors from book article PMID 41525446. Fix: null out `pubmedArticle` when <PubmedBookArticle> is encountered, so all subsequent element processing is skipped by the existing `if (pubmedArticle != null)` guard. Also remove a duplicate AuthorList handler block in startElement that re-initialized the author list unnecessarily. This is a short-term fix; long-term plan is to properly parse and support PubmedBookArticle types. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Fix SAX parser state leakage when PubmedBookArticle follows PubmedArticle
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Summary
Fixes a bug where
PubmedBookArticleelements in PubMed eFetch responses corrupt the previously-parsedPubmedArticlerecord's data (author list, abstract, etc.) via SAX parser state leakage.Changes
pubmedArticlewhen<PubmedBookArticle>is encountered — prevents book article fields from overwriting the previous article's dataAuthorListhandler block — identical code appeared twice instartElementRoot Cause
PubmedEFetchHandler.javauses a singlepubmedArticleinstance variable. When a<PubmedBookArticle>follows a<PubmedArticle>in the same batch, no new object is created — so the book article's AuthorList, Abstract, etc. overwrite the previous article via the still-live reference.Impact
Verified on dev
Merged to dev via PR #105 and deployed.
After merge to master
Re-retrieve articles for affected users with
refreshFlag=ALL_PUBLICATIONSto replace corrupted DynamoDB records.Long-term
Proper PubmedBookArticle parsing is planned as a separate effort (see MULTI_SOURCE_ARCHITECTURE.md in scoring research repo).