Support Web of Science TBA dumps for PDF download - #3
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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>
Accept WoS tab-delimited UTF-8 exports (savedrecs.txt) alongside .jsonl dumps. Adds load_wos_tba / load_papers_dump / wos_tba_to_jsonl helpers, maps DI/TI/AF/AB/PY/SO/PM fields into paperscraper metadata, and documents usage in the PDF retrieval examples. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
MoonDavid
marked this pull request as ready for review
August 5, 2026 13:26
Resolve simple overlap conflict in save_pdf_from_dump skip-logic (duplicate continue / key_to_save checks from both sides). Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
Live API retries can return fewer papers than the previous fixed thresholds, which made CI flake on test_whole_researcher. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
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Summary
Adds support for Web of Science tab-delimited (TBA /
savedrecs.txt) exports insave_pdf_from_dump, so you can download PDFs/XMLs directly from a WoS export without converting to.jsonlfirst.Usage
In Web of Science: Export → Tab delimited / Tab-delimited (Win, UTF-8) (typically
savedrecs.txt).Optional conversion helper:
Field mapping
DI→doi,TI→title,AF→authors,AB→abstract,PY→date,SO→journal,PM→pubmed_id,UT→wos_idAlso includes
This branch is based on the PDF pipeline fixes (
bioc_pmcmerge repair, ChemRxiv wiring, etc.) so dump downloads work end-to-end.Verification
pytest paperscraper/tests/test_wos_tba.py→ 6 passedsavedrecs(1).txt(100 records loaded; first 5 downloaded: 1 PDF, 2 XML, 2 abstract-only for paywalled)