paper-fetch

Fetch the legal open-access PDF for a paper given a DOI (or title). Tries multiple OA 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.

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) — last-resort 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. Otherwise → report failure with title/authors so the user can request via ILL

If only a title is given, resolve to a DOI first via Semantic Scholar search_paper_by_title (asta MCP) or Crossref.

Usage

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

Flags

Flag	Default	Description
doi	—	DOI to fetch (positional). Use - to read a single DOI from stdin
--batch FILE	—	File with one DOI per line for bulk download. Use - to read from stdin
--out DIR	pdfs	Output directory
--dry-run	off	Resolve sources without downloading; preview PDF URL and destination
--format	auto	json for agents, text for humans. Auto-detects: json when stdout is not a TTY, text when it is
--pretty	off	Pretty-print JSON with 2-space indent
--stream	off	Emit one NDJSON per line on stdout as each DOI resolves, then a summary line (batch mode)
--overwrite	off	Re-download even when destination file already exists
--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
--timeout SECONDS	30	HTTP timeout per request
--version	—	Print CLI + schema version and exit

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, update_check_spawned. 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	—
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

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

# Dry-run preview (resolve without downloading)
python scripts/fetch.py 10.1038/s41586-020-2649-2 --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 4 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 to protect the operator's IP from publisher-side throttling. See below.
PAPER_FETCH_NO_AUTO_UPDATE	unset	Set to any value to disable silent background self-update
PAPER_FETCH_UPDATE_INTERVAL	86400	Cooldown in seconds between update checks

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 honestly — it does not bypass paywalls, it just lets 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.
• 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}_{short_title}.pdf). Pair with --idempotency-key to also replay the exact envelope without any network I/O.
• Never bypasses paywalls. Optionally uses the caller's own institutional subscription (via IP, cookies, or EZproxy) when explicitly enabled via PAPER_FETCH_INSTITUTIONAL=1. If no OA copy exists and no institutional access is available, the skill reports failure honestly.
• Default output directory: ./pdfs/.

Auto-update

When installed via git clone, the skill keeps itself in sync with upstream automatically. On each invocation, fetch.py spawns a detached background git pull --ff-only in the skill directory:

• Non-blocking — the current invocation is not delayed; the pull runs in a new session and is fully detached
• Silent — all git output goes to /dev/null, the stdout envelope is never polluted
• Throttled — at most once every 24 hours (stamped via .git/.paper-fetch-last-update)
• Safe — --ff-only refuses to merge if you have local edits; conflicts never happen
• Observable — when a pull is spawned, stderr emits {"event": "update_check_spawned", ...} (JSON mode) or a prose notice (text mode)
• Convergence — updates apply on the next invocation, not the current one (because the pull is backgrounded)

Force an immediate check with rm <skill_dir>/.git/.paper-fetch-last-update.