name: paper-fetch description: Use when the user wants to download a paper PDF from a DOI (or title, resolved to a DOI first). Tries Unpaywall, arXiv, bioRxiv/medRxiv, PubMed Central, Semantic Scholar, and Sci-Hub mirrors as a last-resort fallback. homepage: https://github.com/Agents365-ai/paper-fetch metadata: {"openclaw":{"requires":{"bins":["python3"]},"emoji":"📄"},"pimo":{"category":"research","tags":["paper","pdf","doi","open-access","download"]}}

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.

Agent-native. Structured JSON envelope on stdout, NDJSON progress on stderr (with a session header emitting schema_version / cli_version for drift detection), stable exit codes, machine-readable schema, TTY-aware format default, idempotent retries. retry_after_hours is emitted on every retryable error class.

Step 0. Update check (notify, don't pull) — first use per conversation

Throttle to one check per 24 hours per installation; never mutate the skill directory without explicit user consent.

1. If <this-skill-dir>/.last_update exists and is less than 24 hours old, skip this step entirely.

2. Otherwise, fetch the latest tag from upstream:

   git -C <this-skill-dir> ls-remote --tags origin 'v*' 2>/dev/null \
     | awk '{print $2}' | sed 's|refs/tags/||' \
     | sort -V | tail -1
   

3. Compare with this skill's metadata.version from the frontmatter. If the upstream tag is strictly newer (semver), tell the user one line and ask:

   "A newer version of this skill is available: vX.Y.Z → vA.B.C. Want me to git pull?"

   If they say yes, run git -C <this-skill-dir> pull --ff-only. Refresh .last_update either way so the prompt doesn't repeat for 24 hours.

4. If upstream is the same or older, refresh .last_update silently and continue.

5. On any failure (offline, not a git checkout — e.g. ClawHub-installed copy, read-only path, no permission), swallow the error silently and continue with the user's task. Do not mention the failure.

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

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 asta-skill is registered, the agent can alternatively resolve title → DOI through the Asta MCP first, then pass the DOI directly here. This skips paper-fetch's two-stage Crossref/S2 chain in favor of Asta's richer search surface (relevance ranking, snippet search, citation graph). Workflow: call asta__search_paper_by_title("<title>", fields="title,year,authors,externalIds"), read externalIds.DOI (or 10.48550/arXiv.<ArXiv> when only ArXiv is present), then paper-fetch <doi>. Use --title when Asta isn't available or when a single command is preferred.

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

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": "1.3.0",
    "cli_version": "0.7.0",
    "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": "0.6.1", "schema_version": "1.3.0"}
{"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. 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

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.
• No browser automation, no Playwright, no stealth.
• 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.
• Institutional mode is opt-in via PAPER_FETCH_INSTITUTIONAL=1 and uses the caller's own subscription (IP, cookies, or EZproxy).
• Default output directory: ./pdfs/.

Auto-update

See Step 0 at the top of this file. When installed via git clone, the agent runs a synchronous git pull --ff-only on the first invocation per conversation, throttled to once per 24h via <skill_dir>/.last_update. Updates apply to the current invocation.

Force an immediate check with rm <skill_dir>/.last_update.