Paper Fetch

paper-fetch

Fetch the PDF for a paper given a DOI (or title). Tries multiple sources in priority order and stops at the first hit.

Resolution order

1. Unpaywall — https://api.unpaywall.org/v2/{doi}?email=$UNPAYWALL_EMAIL, read best_oa_location.url_for_pdf (skipped if UNPAYWALL_EMAIL not set)
2. Semantic Scholar — https://api.semanticscholar.org/graph/v1/paper/DOI:{doi}?fields=openAccessPdf,externalIds
3. arXiv — if externalIds.ArXiv present, https://arxiv.org/pdf/{arxiv_id}.pdf
4. PubMed Central OA — if PMCID present, https://www.ncbi.nlm.nih.gov/pmc/articles/{pmcid}/pdf/
5. bioRxiv / medRxiv — if DOI prefix is 10.1101, query https://api.biorxiv.org/details/{server}/{doi} for the latest version PDF URL
6. Publisher direct (institutional mode only — PAPER_FETCH_INSTITUTIONAL=1) — DOI-prefix → publisher PDF template (Nature / Science / Wiley / Springer / ACS / PNAS / NEJM / Sage / T&F / Elsevier). The caller's own subscription IP / cookies / EZproxy are what authorize the fetch; unauthorized responses fail the %PDF check and fall through to step 7.
7. Sci-Hub mirrors (on by default; disable with PAPER_FETCH_NO_SCIHUB=1) — last-resort fallback. Tries the mirror list in PAPER_FETCH_SCIHUB_MIRRORS (or built-in defaults sci-hub.ru, sci-hub.st, sci-hub.su, sci-hub.box, sci-hub.red, sci-hub.al, sci-hub.mk, sci-hub.ee) in order; on full miss, scrapes https://www.sci-hub.pub/ once per process for fresh mirrors. CAPTCHA / missing-paper pages have no PDF iframe and fall through silently.
8. Otherwise → report failure with title/authors so the user can request via ILL

CloakBrowser fallback (download layer, opt-in — PAPER_FETCH_CLOAK=1). This is not a separate source: it sits at the download chokepoint, so it applies to any of the sources above. When a resolved PDF URL is blocked by Cloudflare — HTTP 403/429, or a "Just a moment…" HTML interstitial served in place of the file — and the operator opted in, the URL is retried through CloakBrowser (a stealth Chromium that passes the JS challenge) via the cloak_pdf.py companion. Bytes it returns are re-validated through the same %PDF magic-byte + 50 MB checks; on success the result carries via: "cloak". Off by default, fails closed (missing CloakBrowser → silent fall-through), and the agent cannot opt in — see CloakBrowser access below.

If only a title is given, pass it directly via --title "<title>". Resolution chain:

1. Crossref query.title — primary; covers all major journal/conference DOIs
2. Semantic Scholar /paper/search/match — fallback when Crossref's top match is low-confidence (match_score < 40) or the gap to the runner-up is < 3. Critically, S2 covers arXiv-only preprints (no Crossref DOI). When S2 surfaces a paper that has only an arXiv id, the canonical 10.48550/arXiv.<id> is synthesized so the download chain stays uniform.
3. Crossref's best guess (low-confidence) — used only when both resolvers struggled. The result envelope sets meta.title_resolution.low_confidence: true plus a low_confidence_reason (score_below_threshold / ambiguous_runner_up) so an agent can either bail or confirm via --dry-run.

Either way the resolved DOI, the winning resolver, the full resolvers_tried list, and the top candidate matches are all surfaced under meta.title_resolution.

If semanticscholar-skill is registered, it can serve as a richer pre-step for title → DOI resolution — useful when you also need relevance ranking, snippet search, or citation context, not just a DOI. The agent writes a Python script using the skill's match_title() to read externalIds.DOI, then runs paper-fetch <doi>. When the result has only an ArXiv id (no DOI), synthesize 10.48550/arXiv.<ArXiv> and pass that to paper-fetch.

When only the DOI is needed, --title is the single-command path — paper-fetch's built-in Crossref → S2 chain handles most cases.

Usage

python scripts/fetch.py <DOI> [options]
python scripts/fetch.py --title "<paper title>" [options]
python scripts/fetch.py --batch <FILE|-> [options]
python scripts/fetch.py schema           # machine-readable self-description

Flags

The flags below are the ones an agent composes in normal use. For the complete contract — including --dry-run, --pretty, --stream, --overwrite, --timeout, --version, plus parameter types and exit-code mappings — run python scripts/fetch.py schema (machine-readable, drift-checked via schema_version).

Agent discovery: schema subcommand

python scripts/fetch.py schema

Emits a complete machine-readable description of the CLI on stdout (no network). Includes cli_version, schema_version, parameter types, exit codes, error codes, envelope shapes, and environment variables. Agents should read this once, cache it against schema_version, and re-read when the cached version drifts.

Output contract

stdout emits a single JSON envelope. Every envelope carries a meta slot.

Success (all DOIs resolved):

{
  "ok": true,
  "data": {
    "results": [
      {
        "doi": "10.1038/s41586-021-03819-2",
        "success": true,
        "source": "unpaywall",
        "pdf_url": "https://www.nature.com/articles/s41586-021-03819-2.pdf",
        "file": "pdfs/Jumper_2021_Highly_accurate_protein_structure_predic.pdf",
        "meta": {"title": "Highly accurate protein structure prediction with AlphaFold", "year": 2021, "author": "Jumper"},
        "sources_tried": ["unpaywall"]
      }
    ],
    "summary": {"total": 1, "succeeded": 1, "failed": 0},
    "next": []
  },
  "meta": {
    "request_id": "req_a908f5156fc1",
    "latency_ms": 2036,
    "schema_version": "1.9.0",
    "cli_version": "0.13.1",
    "sources_tried": ["unpaywall"]
  }
}

Partial (batch mode — some DOIs failed, exit code reflects the failure class):

{
  "ok": "partial",
  "data": {
    "results": [
      { "doi": "10.1038/s41586-021-03819-2", "success": true, "source": "unpaywall", ... },
      {
        "doi": "10.1234/nonexistent",
        "success": false,
        "source": null,
        "pdf_url": null,
        "file": null,
        "meta": {},
        "sources_tried": ["unpaywall", "semantic_scholar"],
        "error": {
          "code": "not_found",
          "message": "No open-access PDF found",
          "retryable": true,
          "retry_after_hours": 168,
          "reason": "OA availability changes over time; retry after embargo lifts or preprint appears"
        }
      }
    ],
    "summary": {"total": 2, "succeeded": 1, "failed": 1},
    "next": ["paper-fetch 10.1234/nonexistent --out pdfs"]
  },
  "meta": { ... }
}

The next slot is an array of suggested follow-up commands: re-invoking them retries only the failed subset. Combine with --idempotency-key to make the whole batch safely retriable without re-downloading the already-succeeded items.

Failure (bad arguments, exit code 3):

{
  "ok": false,
  "error": {
    "code": "validation_error",
    "message": "Provide a DOI or --batch file",
    "retryable": false
  },
  "meta": { ... }
}

Per-item skipped (destination already exists, no --overwrite):

{
  "doi": "10.1038/s41586-021-03819-2",
  "success": true,
  "source": "unpaywall",
  "pdf_url": "https://...",
  "file": "pdfs/Jumper_2021_...pdf",
  "skipped": true,
  "skip_reason": "file_exists",
  "sources_tried": ["unpaywall"]
}

Idempotency replay (re-run with the same --idempotency-key):

The cached envelope is returned verbatim, but meta.request_id and meta.latency_ms are re-stamped for the current call, and meta.replayed_from_idempotency_key is set. No network I/O occurs.

Stderr progress (NDJSON)

When --format json, stderr emits one JSON object per line for liveness:

{"event": "session",     "request_id": "req_...", "elapsed_ms": 0,    "cli_version": "0.13.1", "schema_version": "1.9.0"}
{"event": "start",       "request_id": "req_...", "elapsed_ms": 2,    "doi": "10.1038/..."}
{"event": "source_try",  "request_id": "req_...", "elapsed_ms": 2,    "doi": "...", "source": "unpaywall"}
{"event": "source_hit",  "request_id": "req_...", "elapsed_ms": 2036, "doi": "...", "source": "unpaywall", "pdf_url": "..."}
{"event": "download_ok", "request_id": "req_...", "elapsed_ms": 4120, "doi": "...", "file": "..."}

Event types: session, start, source_try, source_hit, source_miss, source_skip, source_enrich, source_enrich_failed, download_ok, download_error, download_skip, dry_run, not_found, resolve_error. All events share request_id and elapsed_ms, letting an orchestrator correlate progress across stderr and the final stdout envelope. The session event fires once per invocation, before any DOI work or network I/O, and carries cli_version / schema_version so agents can detect schema drift against a cached copy without waiting for the final envelope.

source_enrich fires when Semantic Scholar is called purely to backfill missing author / title after another source already provided the PDF URL; its fields array lists exactly which fields were filled in. source_enrich_failed fires when that enrichment call fails — the Unpaywall PDF URL is still used and the filename falls back to unknown_<year>_….

When --format text, stderr emits human-readable prose.

Exit codes

The taxonomy lets an orchestrator route failures deterministically: exit 4 is worth retrying immediately, exit 1 is not, exit 3 is a bug in the caller.

Error codes in JSON

Every retryable error carries a retry_after_hours hint in the error object, so an orchestrator can schedule retries without guessing.

The canonical mapping lives in RETRY_AFTER_HOURS in scripts/fetch.py and is surfaced in schema.error_codes.

Examples

# Single DOI (JSON output when piped; text when in a terminal)
python scripts/fetch.py 10.1038/s41586-020-2649-2

# Single title (resolved to DOI via Crossref, then downloaded)
python scripts/fetch.py --title "Highly accurate protein structure prediction with AlphaFold"

# Dry-run preview (resolve without downloading)
python scripts/fetch.py 10.1038/s41586-020-2649-2 --dry-run

# Title + dry-run — preview the resolved DOI and candidate matches
python scripts/fetch.py --title "Attention Is All You Need" --dry-run

# Force JSON (for agents even inside a terminal)
python scripts/fetch.py 10.1038/s41586-020-2649-2 --format json

# Human-readable with pretty colors in a pipeline
python scripts/fetch.py 10.1038/s41586-020-2649-2 --format text

# Batch download, safely retriable
python scripts/fetch.py --batch dois.txt --out ./papers \
    --idempotency-key monday-review-batch

# Pipe DOIs from another tool
zot -F ids.json query ... | jq -r '.[].doi' | python scripts/fetch.py --batch -

# Agent discovery
python scripts/fetch.py schema --pretty

# Streaming mode — one result per line as each DOI resolves
python scripts/fetch.py --batch dois.txt --stream

# Works without UNPAYWALL_EMAIL (skips Unpaywall, uses remaining 4 sources)
python scripts/fetch.py 10.1038/s41586-020-2649-2

Environment

CloakBrowser access (opt-in)

Some publishers (e.g. science.org) sit behind Cloudflare, which answers a plain HTTP client with a 403/429 or a "Just a moment…" JS-challenge page instead of the PDF — so the default urllib download can't get through even when the URL is legitimately accessible from a browser. CloakBrowser is a stealth Chromium that passes those challenges. This skill borrows the approach from cloakFetch.

Opt in: export PAPER_FETCH_CLOAK=1 (plus a cloakbrowser-importable Python — see CLOAKBROWSER_PYTHON).

How it works: the fallback lives at the download layer, not as a new source — so it applies to any resolved URL (Unpaywall, publisher-direct, Sci-Hub, …). On a Cloudflare block, fetch.py shells out to the cloak_pdf.py companion via the resolved Python; CloakBrowser loads the PDF host's origin to solve the JS challenge, then fetches the PDF with an in-page fetch() (so the request carries the browser's real fingerprint and cf_clearance cookie) and returns the bytes on stdout. fetch.py itself stays stdlib-only — it never imports cloakbrowser.

Headless vs. headed. The companion runs headless by default. Some challenges (e.g. science.org) defeat headless Chromium and stay stuck on "Just a moment…" — set PAPER_FETCH_CLOAK_HEADED=1 to use a visible window, which clears them. Verified: a www.science.org/doi/pdf/… PDF that returns 403 to the plain client downloads cleanly via the headed cloak fallback.

Same-origin only. The in-page fetch is same-origin, so the fallback works when the resolved URL is a direct PDF link on the blocked host (e.g. www.science.org/doi/pdf/…). A URL that cross-origin-redirects (e.g. a bare doi.org/… link) or a legacy host whose challenge never clears will fail closed and fall through to the next source.

What stays the same:

• Returned bytes are re-validated through the same %PDF magic-byte check and 50 MB size cap. SSRF defense still gates the URL before the browser is ever launched.
• No CAPTCHA solving. CloakBrowser passes automated JS challenges, not interactive ones; an interactive Turnstile still fails closed and falls through.
• Fails closed. No cloakbrowser-importable Python, helper missing, or any error → silent fall-through to the next source. The agent is never told a blocked fetch succeeded.
• Agent cannot opt in on its own — PAPER_FETCH_CLOAK must be set by the human operator. Same trust boundary as institutional mode.
• On success the per-result object carries via: "cloak" so an orchestrator can see the fallback was used.

Cost: a triggered fallback launches a real browser (~20–40 s, ~200 MB Chromium on first download). It only fires after a normal download was blocked, so the happy path is unaffected.

Institutional access (opt-in)

Many researchers have legitimate subscription access through their institution's IP range (on-campus or VPN). Paper-fetch can use that access by letting the publisher's own auth (your IP, your session cookies) decide whether to serve the PDF.

Host reachability does not differ between modes — public mode already trusts URLs returned by the OA APIs (Unpaywall, Semantic Scholar, bioRxiv, PMC) and fetches any HTTPS host that passes SSRF defense. Institutional mode adds two things: (1) a publisher-direct fallback (step 6 above) that constructs a publisher-side PDF URL by DOI prefix when every OA source missed, so your institutional IP/cookies can authorize the fetch, and (2) a 1 req/s rate limiter to keep batch jobs from getting your IP throttled or banned for "systematic downloading."

Opt in: export PAPER_FETCH_INSTITUTIONAL=1

What changes in institutional mode:

What stays the same:

• %PDF magic-byte check and 50 MB size cap (prevents HTML landing pages and oversized responses slipping through)
• No CAPTCHA solving, ever. If a publisher shows a challenge, the response won't start with %PDF and paper-fetch falls through to the next source.
• Institutional mode itself uses no browser automation, no Playwright, no stealth — it is a plain HTTP fetch against publisher-direct URLs. (Browser automation is a separate opt-in: the CloakBrowser fallback above, gated by PAPER_FETCH_CLOAK.)
• Agent cannot opt in on its own — PAPER_FETCH_INSTITUTIONAL must be set by the human operator in the shell environment. This is the trust boundary.

When paper-fetch can't find an OA copy and you're in public mode, the error envelope includes suggest_institutional: true and a hint telling the user to set the env var. Agents can surface this verbatim rather than failing silently.

ToS notice: almost every publisher subscription prohibits "systematic downloading." The 1 req/s rate limit plus the existing per-file idempotency are designed to keep individual research use within acceptable bounds. Running many parallel paper-fetch processes, or lifting the rate limit, can trigger a publisher-wide IP ban affecting your entire institution. Don't.

Notes

• Auth is delegated. The agent never runs a login subcommand. The human or the orchestrator sets UNPAYWALL_EMAIL in the environment; the agent inherits it. Missing email degrades gracefully to the remaining 4 sources.
• Trust is directional. CLI arguments are validated once at the entry point. SSRF defense, the %PDF magic-byte check, and the 50 MB size cap are enforced in the environment layer, not at the agent's request. An agent cannot loosen safety by passing a flag — opting into institutional mode (and its rate-limit risk profile) is an operator action via environment variable.
• Downloads are naturally idempotent. Re-running against the same --out skips files that already exist (deterministic filename: {first_author}_{year}_{journal_abbrev}_{short_title}.pdf; the journal segment is omitted if metadata lacks a journal/venue). Pair with --idempotency-key to also replay the exact envelope without any network I/O.
• Default output directory: ./pdfs/.