--- name: paper-fetch description: Use whenever the user wants to obtain, download, or fetch a paper's PDF — given a DOI, an arXiv id, a paper title, a citation, or a list of DOIs. Trigger on phrases like "download this paper", "find the PDF for [DOI]", "grab me the [Nature/bioRxiv/arXiv] paper on X", "get the open-access version", "I need this article", or any bulk/batch paper download request, even when the user doesn't explicitly say "PDF" or "DOI". Resolves via Unpaywall → Semantic Scholar → arXiv → PubMed Central → bioRxiv/medRxiv → publisher direct (institutional opt-in) → Sci-Hub mirrors as 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"]},"author":"Agents365-ai","version":"0.14.0"} --- # 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](https://github.com/CloakHQ/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 ""`. 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 ```bash 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`). | Flag | Default | Description | |------|---------|-------------| | `doi` | — | DOI to fetch (positional). Use `-` to read a single DOI from stdin | | `--title TITLE` | — | Paper title; resolved to a DOI via Crossref before download. Mutually exclusive with positional DOI / `--batch` | | `--batch FILE` | — | File with one DOI per line for bulk download. Use `-` to read from stdin | | `--out DIR` | `pdfs` | Output directory | | `--format` | auto | `json` for agents, `text` for humans. Auto-detects: `json` when stdout is not a TTY, `text` when it is | | `--idempotency-key KEY` | — | Safe-retry key. Re-running with the same key replays the original envelope from `<out>/.paper-fetch-idem/` without network I/O | ### Agent discovery: `schema` subcommand ```bash 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): ```json { "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): ```json { "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): ```json { "ok": false, "error": { "code": "validation_error", "message": "Provide a DOI or --batch file", "retryable": false }, "meta": { ... } } ``` **Per-item skipped** (destination already exists, no `--overwrite`): ```json { "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`. 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 | Code | Meaning | Retryable class | |------|---------|-----------------| | `0` | All DOIs resolved / previewed | — | | `1` | Unresolved — one or more DOIs had no OA copy; no transport failure | Not now (retry after `retry_after_hours`) | | `2` | Reserved for auth errors (currently unused) | — | | `3` | Validation error (bad arguments, missing input) | No | | `4` | Transport error (network / download / IO failure) | Yes | 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. | Code | Meaning | Retryable | `retry_after_hours` | |------|---------|-----------|---------------------| | `validation_error` | Bad arguments or empty input | No | — | | `title_resolve_failed` | Crossref returned no items for the given `--title` query (try a longer / cleaner title, or pass the DOI directly) | No | — | | `not_found` | No open-access PDF found | Yes | `168` (one week — OA lands on embargo / preprint timescale) | | `download_network_error` | Network failure during download | Yes | `1` | | `download_not_a_pdf` | Response was not a PDF (HTML landing page) | No | — | | `download_host_not_allowed` | PDF URL failed SSRF safety check (private IP / non-http(s) / non-80,443 / blocked metadata host) | No | — | | `download_size_exceeded` | Response exceeded 50 MB limit | Yes | `24` | | `download_io_error` | Local filesystem write failed | Yes | `1` | | `internal_error` | Unexpected error | No | — | The canonical mapping lives in `RETRY_AFTER_HOURS` in `scripts/fetch.py` and is surfaced in `schema.error_codes`. ### Examples ```bash # 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 | Variable | Default | Purpose | |---|---|---| | `UNPAYWALL_EMAIL` | unset | Contact email for Unpaywall API. Optional but recommended. Without it, Unpaywall is skipped (remaining sources still work). | | `PAPER_FETCH_INSTITUTIONAL` | unset | Set to any value (e.g. `1`) to opt into **institutional mode** — activates a 1 req/s rate limiter and the publisher-direct fallback. See below. | | `PAPER_FETCH_NO_SCIHUB` | unset | Set to any value to disable the Sci-Hub fallback (step 7). | | `PAPER_FETCH_SCIHUB_MIRRORS` | unset | Comma-separated mirror hostnames to try in priority order (e.g. `sci-hub.ru,sci-hub.st,sci-hub.su`). Overrides built-in defaults. | | `PAPER_FETCH_CLOAK` | unset | Set to any value to enable the **CloakBrowser fallback** — Cloudflare-blocked PDFs (HTTP 403/429 or a non-PDF interstitial) are retried through a stealth Chromium. See *CloakBrowser access* below. | | `CLOAKBROWSER_PYTHON` | auto | Path to a Python that can `import cloakbrowser`, used by the cloak fallback. Auto-detect order: this var → `~/github/CloakBrowser/.venv/bin/python` → the current interpreter. | ## 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](https://github.com/CloakHQ/CloakBrowser) is a stealth Chromium that passes those challenges. This skill borrows the approach from [cloakFetch](https://github.com/Agents365-ai/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 solves the JS challenge, fetches the PDF through the browser context (carrying the `cf_clearance` cookie), and returns the bytes on stdout. `fetch.py` itself stays stdlib-only — it never imports `cloakbrowser`. **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:** | Aspect | Public (default) | Institutional | |---|---|---| | Host reachability | Any public HTTPS host passing SSRF defense | Same | | SSRF defense | Enforced (private IP / non-http(s) / non-80,443 / cloud metadata all blocked) | Enforced — same rules | | Publisher-direct fallback | Off | On — DOI-prefix → publisher PDF URL, last resort after all OA sources miss | | Rate limit | None | 1 req/s token bucket (all outbound) | | `meta.auth_mode` | `"public"` | `"institutional"` | **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/`.