/fulltext-retrieval

name: fulltext-retrieval
description: Use when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set. Batch-downloads open-access copies via Unpaywall, PMC, OpenAlex and Crossref, lists paywalled papers for manual access, and can convert PDFs to Markdown.
metadata:
  triggers: "PDF download, fulltext retrieval, open access PDF, batch download papers, meta-analysis PDF, PDF to markdown, convert PDF"

Fulltext Retrieval Skill

Batch download open-access full-text PDFs from a DOI list using legitimate OA APIs only. Paywalled articles fail by design and are listed in `manual_needed.txt` for institutional access or ILL; never work around a paywall or publisher access control.

Pipeline

DOI → arXiv (10.48550/arXiv.* DOIs) → Unpaywall → PMC (Europe PMC / OA FTP / web) → OpenAlex → Crossref → landing page

Each DOI goes through these sources in order until a valid PDF (≥10 KB, `%PDF-` header) is found. arXiv DOIs (`10.48550/arXiv.2401.01234`, version suffixes, old-style `hep-th/9901001`, or a bare `arXiv:` id) resolve directly to the arXiv PDF first.

Run

Requires Python 3.10+ (stdlib only) and a contact email, which Unpaywall's Terms of Service require. The script paces its requests (0.3–0.5 s delays) for the APIs' rate limits.

python "${CLAUDE_SKILL_DIR}/fetch_oa.py" dois.txt --output pdfs/ --email your@email.com

# Verbose mode for debugging (per-DOI source trace)
python "${CLAUDE_SKILL_DIR}/fetch_oa.py" dois.txt -o pdfs/ -e your@email.com --verbose

Input formats:

• **Plain text** — one DOI per line.
• **TSV / CSV with header**, or a **Markdown pipe table** — must contain a `DOI` column; optional

`PMID`, `Title`, and `FirstAuthor` (surname or full name) columns.

A PMID makes the PMC lookup more reliable (PMID → PMCID conversion). Supply `Title` where available: a DOI-only worklist can download a PDF but cannot establish title agreement. `FirstAuthor` is optional additional evidence.

Output

• PDFs saved as `{DOI_safe}.pdf` (slashes replaced with underscores).
• `pdfs/retrieval_report.json` — structured per-DOI report (below); override with `--report PATH`.
• `<output>/manual_needed.txt` — DOIs that could not be retrieved via OA; when a PMCID was

resolved, the line also carries it and the PubMed Central article URL to open in a browser.

• Summary with arXiv/OA/PMC/fail/skip counts.

Retrieval report (`--report`)

Every run writes the report (default `<output>/retrieval_report.json`), schema 2:

{
  "schema_version": 2,
  "generated_by": "fetch_oa.py",
  "counts": {"total": 4, "retrieved": 3, "not_retrieved": 1, "title_mismatch": 1,
             "source_identity": {"consistent": 1, "conflict": 1, "unresolved": 1, "unavailable": 1}},
  "items": [
    {"doi": "10.1000/synthetic.example", "pmid": "", "title": "Example title",
     "first_author": "", "status": "oa", "source": "unpaywall",
     "file": "10.1000_synthetic.example.pdf", "size_bytes": 482113, "page_count": 9,
     "file_sha256": "<SHA-256 of the downloaded file>", "title_match": "match",
     "source_identity": {"status": "consistent", "reason": "title_and_identifier_agree",
                         "text_scope": "first_page_front_matter", "title_match": "match",
                         "doi_match": "match", "observed_identifiers": ["10.1000/synthetic.example"],
                         "first_author_match": "unavailable"}}
  ]
}

`status` (`arxiv | oa | pmc | skip | fail`), `source`, and `counts.retrieved` describe the resolver result, including existing files (`skip`). **They do not count identity-verified papers.** No PDF is automatically deleted or rejected. `page_count` comes from Poppler's `pdfinfo` (null without it) and is recorded, not judged — a 3-page "article" or a 4-page "book" is worth opening.

| `source_identity.status` | Meaning / action | |---|---| | `consistent` | Complete normalized title and a compatible DOI/arXiv identifier occur in the bounded first-page front matter, with no supplement / preface / table-of-contents heading and no retraction / erratum / correction / corrigendum / expression-of-concern heading there; an optional supplied author must also match. Evidence agrees, but this is not independent source verification or claim validation. | | `conflict` | Both the title and observed identifier differ. Inspect the PDF and requested record. | | `unresolved` | Evidence is incomplete or ambiguous: title-only, DOI-only, missing author, multiple identifiers, a matching title with another DOI/version, or a supplement / preface / table-of-contents file that names the work without being it (`supplement_or_front_matter`). A retraction notice, erratum, correction, corrigendum or expression of concern whose heading line sits in that area is likewise `unresolved` (`correction_or_retraction_notice`). Inspect before using as evidence. | | `unavailable` | No usable extracted text, Poppler unavailable, no output PDF, or the PDF changed during assessment. No current identity assessment was possible. |

Evidence is limited to the first page before a recognized abstract/body/reference heading (at most 40 lines / 4,000 characters), so a title cited in the body or references does not count. A `title_match` of `match` needs the complete normalized title on up to six consecutive lines; partial overlap is `unavailable` and low overlap an advisory `mismatch`. Cover sheets, unusual reading order, short or changed titles and DOI footers outside that area can stay unresolved. PDF metadata and the filename alone are not identity evidence. Explicit arXiv versions must agree; a preprint/published-version DOI difference needs review, not automatic rejection.

Downstream reports must preserve `source_identity` and `file_sha256`, keep unresolved items visible, and check the hash still identifies the file being used. Older reports without identity evidence remain **unassessed**; do not infer identity from `retrieved` or `title_match=match`. Full-text