Fix PDF-from-dump pipeline and fallbacks - #2
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Restore a working fallback_bioc_pmc after a bad merge (syntax error that blocked importing paperscraper.pdf), re-add NCBIRateLimitError, fix missing as_completed/tqdm imports for medRxiv S3, load SPRINGER_API_KEY, and wire ChemRxiv Open Engage helpers into save_pdf. Also validate key_to_save and align the Elsevier mock test with header-based auth. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
- Guard bioRxiv/medRxiv S3 when AWS keys are missing - Recognize 10.1101 DOIs for preprint S3 fallbacks - Validate PDF bytes before opening files (fixes empty leftovers under mocks) - Skip S3 sections in tests without AWS credentials - Update paywalled-chapter expectation now that arXiv fallback can succeed Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
MoonDavid
marked this pull request as ready for review
August 5, 2026 13:26
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Summary
Repairs the broken PDF download path so
save_pdf/save_pdf_from_dumpwork again, and closes related gaps in the existing fallback stack.Fixes
fallback_bioc_pmc: restore after a bad merge that left aSyntaxError(blocked importingpaperscraper.pdfentirely). Re-addsNCBIRateLimitError, PMCID assignment, retries, andncbi_emailsupport.medrxiv_s3: add missingas_completed/tqdmimports.load_api_keys: loadSPRINGER_API_KEY.save_pdf(HTML scraping is Cloudflare-blocked).save_pdf_from_dump: validatekey_to_save(doi/title/date), create output dir, skip papers missing the filename key.X-ELS-APIKeyauth.Verification