fix: preserve all PubMed structured abstract sections - #123
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njzjz merged 3 commits intoAug 16, 2026
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Collect every AbstractText node in document order instead of silently keeping only the first section. Agent: ChatGPT Model: GPT-5.6 Sol
Add regression tests for multiple sections, nested inline XML, single-section abstracts, and missing abstracts. Agent: ChatGPT Model: GPT-5.6 Sol
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #123 +/- ##
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+ Coverage 94.41% 94.43% +0.01%
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Files 15 15
Lines 949 952 +3
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+ Hits 896 899 +3
Misses 53 53 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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njzjz
marked this pull request as ready for review
August 16, 2026 12:30
njzjz
approved these changes
Aug 16, 2026
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Summary
AbstractTextnode in document order_text()helperRoot cause
The PubMed parser used
tree.find()forAbstract/AbstractText, which returns only the first sibling node and silently truncated structured abstracts.Validation
The production diff is limited to the abstract extraction branch in
wenxian/feeder/pubmed.py, plus focused tests intests/test_pubmed_structured_abstract.py. Full repository CI should run on this PR.Fixes #117
Agent: ChatGPT
Model: GPT-5.6 Sol