download-paper

name	download_paper
description	Resolve paper identifiers, fetch the PDF and metadata, and prepare inputs for paper asset creation. Use when you need to download a research paper from partial identifiers.
model	claude-sonnet-4-6

Download Research Paper

Version: 1

Goal

Given partial paper identifiers (any combination of title, DOI, authors, year, arXiv ID, PMID), retrieve the full-text content of the paper in the best available format.

Inputs

• {{ title }} — paper title (optional if DOI or other ID provided)
• {{ doi }} — Digital Object Identifier (optional)
• {{ authors }} — author names, comma-separated (optional)
• {{ year }} — publication year (optional)
• {{ arxiv_id }} — arXiv identifier (optional)
• {{ pmid }} — PubMed identifier (optional)
• {{ output_dir }} — directory to save the downloaded file

At least one of title, doi, or arxiv_id must be provided. More identifiers improve resolution accuracy.

Context

Read before starting:

• This skill file (you are reading it now)
• arf/styleguide/python_styleguide.md — if writing helper scripts

If any temporary helper scripts are created during execution, delete them before completing the skill. Do not leave throwaway code in the repository.

Philosophy

This skill is not a simple downloader. It is a version-aware scholarly resolver. The agent identifies the work precisely, collects every known identifier, then searches for the best accessible version across all available channels. When the published version is unavailable, preprints, accepted manuscripts, working papers, and structured XML are all valid and valuable alternatives.

Prefer machine-readable formats over PDF when available. For an AI agent, structured XML/TEI/JATS or plain text is more useful than a PDF that requires extraction.

Format preference ranking:

1. Structured XML (JATS, TEI, BioC) or plain text
2. Born-digital PDF
3. Scanned PDF (last resort)

Version preference ranking:

1. Published version (Version of Record)
2. Open publisher copy (hybrid/bronze OA)
3. Repository copy (green OA)
4. Accepted manuscript (post-peer-review, pre-formatting)
5. Submitted manuscript / preprint
6. Working paper / technical report / dissertation chapter
7. Abstract + metadata only (if nothing else available)

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Steps

Phase 1: Canonical Identification

Build a complete metadata record before attempting any download. The more identifiers collected, the higher the success rate in later phases.

1. If DOI is provided, query CrossRef API (https://api.crossref.org/works/{doi}) to get full metadata: title, authors, year, ISSN, publisher, DOI prefix, and any relation fields linking to preprints.
2. If DOI is missing, resolve it:
   • Query CrossRef query.bibliographic endpoint with title + author + year filter: https://api.crossref.org/works?query.bibliographic={title}+{author}&filter=from-pub-date: {year}-01-01,until-pub-date:{year}-12-31&rows=3. Take the top match. Verify by fuzzy-matching the returned title against the input title (similarity > 0.85).
   • In parallel, query Semantic Scholar (/graph/v1/paper/search?query={title}) — returns paperId, DOI, arXiv ID, PMID.
   • In parallel, query OpenAlex (https://api.openalex.org/works?search={title}&filter= publication_year:{year}) for additional ID coverage.
3. From all responses, build a canonical record with normalized fields:
   • title (normalized: lowercase, stripped punctuation for matching)
   • doi and doi_prefix (e.g., 10.1371 for PLOS, 10.1016 for Elsevier)
   • pmid / pmcid
   • arxiv_id
   • openalex_id
   • semantic_scholar_id
   • authors (list of names)
   • year
   • venue (journal or conference name)
   • publisher (from CrossRef member field — more reliable than DOI prefix for routing)
   • preprint_doi (if CrossRef has-preprint relation exists)
4. If PMID is known but PMCID is not, use the NCBI ID Converter API (https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids={id}&format=json) to check for a PMC version. Batch up to 200 IDs per request.
5. Validate the DOI is globally resolvable. Some publishers issue internal pseudo-DOIs that do not resolve via doi.org. The most common case: ACM uses the 10.5555 prefix for cross-listed materials from other publishers (e.g., IEEE). If the DOI prefix is 10.5555, do not use it for downstream retrieval — instead, search by title to find the real publisher DOI (e.g., an IEEE DOI starting with 10.1109).

Batch optimization: When resolving multiple papers, use Semantic Scholar POST /paper/batch (up to 500 IDs per request) and OpenAlex pipe-separated DOI filter (GET /works?filter=doi:{doi1}|{doi2}|{doi3}&per_page=100, up to 50 DOIs).

Phase 2: Open Access Resolution (Primary Sources)

Query the major OA aggregators. Fire these in parallel — first success with a usable PDF/text URL wins.

1. Unpaywall (DOI required): GET https://api.unpaywall.org/v2/{doi}?email={your_email}. Check best_oa_location.url_for_pdf. If no direct PDF, check all entries in oa_locations[] — try each URL. Note the version field (publishedVersion / acceptedVersion / submittedVersion).
2. OpenAlex (DOI or OpenAlex ID): GET https://api.openalex.org/works/doi:{doi}. Check open_access.oa_url, best_oa_location, and iterate all locations[]. OpenAlex also exposes fulltext_origin and may provide TEI XML access for some papers.
3. Semantic Scholar (any supported ID): GET https://api.semanticscholar.org/graph/v1/paper/{id}?fields=openAccessPdf,isOpenAccess. Check openAccessPdf.url.
4. CrossRef TDM links (DOI required): From the CrossRef metadata already fetched in Phase 1, check message.link[] for entries with intended-application: "text-mining". These may provide direct full-text access (XML or PDF).
5. OpenCitations (DOI required): GET https://api.opencitations.net/index/v2/metadata/{doi}. Check the oa_link field for a direct OA URL. Free, no auth, 1B+ citation links indexed.

Phase 3: Publisher Direct Access

If Phase 2 returned no usable URL, try constructing the PDF URL directly from the DOI and publisher identity. Use the doi_prefix and publisher from the canonical record to route.

Fully open-access publishers (always free — try these URL patterns first):

• PLOS (10.1371): https://journals.plos.org/{journal}/article/file?id={doi}&type=printable
• MDPI (10.3390): append /pdf to article URL (e.g., https://www.mdpi.com/2073-8994/11/10/1189/pdf)
• Frontiers (10.3389): https://www.frontiersin.org/articles/{doi}/pdf
• BMC / SpringerOpen: https://link.springer.com/content/pdf/{doi}.pdf

Major subscription publishers (free for OA articles only):

• Elsevier (10.1016): https://www.sciencedirect.com/science/article/pii/{PII}/pdf for OA articles. TDM API: GET https://api.elsevier.com/content/article/doi/{doi}?httpAccept=text/xml (requires ELSEVIER_API_KEY).
• Springer Nature (10.1038, 10.1007): https://link.springer.com/content/pdf/{doi}.pdf for OA articles. Also check for SharedIt read-only links at https://rdcu.be/{hash} — these provide view access even for paywalled articles.
• Wiley (10.1002): https://onlinelibrary.wiley.com/doi/pdfdirect/{doi} for OA articles.
• IEEE (10.1109): https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber={article_number}. IEEE Access journal is fully OA.
• ACM (10.1145): https://dl.acm.org/doi/pdf/{doi}. ACM Author-izer service lets authors post free-access links.
• Taylor & Francis (10.1080): https://www.tandfonline.com/doi/pdf/{doi}
• SAGE (10.1177): https://journals.sagepub.com/doi/pdf/{doi}
• ACS (10.1021): https://pubs.acs.org/doi/pdf/{doi}. ACS AuthorChoice articles are CC-BY.

Note: DOI prefix alone is not always reliable for publisher identification — Elsevier alone has 26+ prefixes. The CrossRef member field from Phase 1 is the authoritative publisher identifier. Use prefix as a fast hint, fall back to CrossRef member for routing.

Phase 4: Domain-Specific Sources

If Phases 2-3 did not yield full text, try domain-specific repositories.

1. PubMed Central / Europe PMC (biomedical papers):
   • If PMCID is known: GET https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/ BioC_json/{PMCID}/unicode for structured full text.
   • Europe PMC: GET https://www.ebi.ac.uk/europepmc/webservices/rest/{PMCID}/fullTextXML for JATS XML. Also try direct PDF: https://europepmc.org/articles/{pmcid}?pdf=render.
   • Also check PMC OA subset via efetch: Entrez.efetch(db="pmc", id=PMCID, rettype="full", retmode="xml").
   • PubMed LinkOut: Query https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id={pmid}&cmd=llinks to get third-party free full-text links registered with NCBI. Publishers and repositories register these links directly — a source most agents miss.
   • NIH mandate awareness: Papers from NIH-funded research accepted after 2025-07-01 must be in PMC with no embargo. If the paper acknowledges NIH funding and is recent, PMC is very likely to have it.
   • PMC migration note: PMC is transitioning from FTP to Cloud Service between Feb–Aug 2026. For bulk access, prefer the PMC Cloud Service (s3://pmc-oa-opendata/) over FTP.
2. arXiv (CS, math, physics, stats, quant-bio, quant-fin, EE):
   • If arxiv_id is known: download directly from https://arxiv.org/pdf/{arxiv_id}.pdf or https://export.arxiv.org/pdf/{arxiv_id}.
   • If arxiv_id is unknown: search by title via http://export.arxiv.org/api/query?search_query=ti:{title}&max_results=3. Verify match by title similarity + author overlap.
3. bioRxiv / medRxiv (biology, medicine preprints):
   • Query by DOI: GET https://api.biorxiv.org/details/biorxiv/{doi}/na/json.
   • Use the /pubs/ endpoint to find preprint-to-published mappings: GET https://api.biorxiv.org/pubs/biorxiv/{published_doi}.
   • PDF URL pattern: https://www.biorxiv.org/content/{doi}v{version}.full.pdf.
4. SSRN (social sciences, law, economics): Search by title on SSRN. PDF URL pattern: https://papers.ssrn.com/sol3/Delivery.cfm/SSRN_ID{id}.pdf?abstractid={id}.
5. RePEc / EconPapers (economics): Search for working paper versions that may be freely available.
6. OSF Preprints (multidisciplinary): Query OSF API for preprint matches by title. PDF download at https://osf.io/preprints/{provider}/{id}/download.
7. Conference proceedings — many top venues are 100% open access with predictable URLs:
   • ACL Anthology: https://aclanthology.org/{id}.pdf (all computational linguistics)
   • NeurIPS: https://proceedings.neurips.cc/paper_files/paper/{year}/file/{hash}-Paper.pdf
   • ICML / PMLR: https://proceedings.mlr.press/v{volume}/{author}{suffix}/{author}{suffix}.pdf
   • CVF (CVPR, ICCV, ECCV): https://openaccess.thecvf.com/ (CVPR 2013 onward)
   • AAAI: https://ojs.aaai.org/ (OJS-based, supports OAI-PMH)
   • IJCAI: https://www.ijcai.org/proceedings/{year}/{number}.pdf
   • USENIX: all proceedings freely available as PDFs
   • JMLR: https://jmlr.org/papers/ (all open access)
   • OpenReview.net (ICLR, NeurIPS workshops): API at https://api.openreview.net/
8. NASA ADS (astronomy, astrophysics): GET https://api.adsabs.harvard.edu/v1/search/query?q={query}. API key required. Full-text links via /resolver/{bibcode}/esource. Covers 15M+ records.
9. INSPIRE-HEP (high-energy physics): GET https://inspirehep.net/api/literature?q={query}. No auth required. PDF links in metadata.documents[].url. Covers 1.5M+ records.
10. Government repositories:
    • ERIC (education): GET https://api.ies.ed.gov/eric/?search={query}&format=json. PDFs at https://files.eric.ed.gov/fulltext/{ED_number}.pdf. ~1.5M records, ~25% full text.
    • OSTI.gov (DOE-funded research): GET https://www.osti.gov/api/v1/records?title={query}. Covers journal articles and technical reports. OAI-PMH also available.

Phase 5: Repository Aggregators

Search aggregators that index institutional repositories, author deposits, and funder-mandated copies.

1. CORE (requires free API key): GET https://api.core.ac.uk/v3/search/works?q={title}. CORE aggregates 40M+ full-text papers from 10,000+ institutional repositories. Check results for downloadUrl or direct PDF links.
2. OpenAIRE Graph: Query the Graph API for publications matching the DOI or title. Especially strong for EU-funded research (Horizon 2020/Europe mandates OA within 6-12 months).
3. HAL (strong for French/European research): GET https://api.archives-ouvertes.fr/search/?q={title}&fq=submitType_s:file&fl=uri_s,files_s. Filter for records that actually have deposited files using submitType_s:file. PDF in fileMain_s field or at https://hal.science/{halId}/document.
4. Zenodo (conference papers, reports, datasets with papers): GET https://zenodo.org/api/records?q={title}. Check file attachments in record metadata. Direct file download at https://zenodo.org/records/{id}/files/{filename}?download=1.
5. BASE (Bielefeld Academic Search Engine): 400M+ documents from 12,000+ providers. API at https://api.base-search.net/ uses Solr query syntax. Requires IP whitelisting — request access via their contact form. Key fields: dctitle: (title), dcauthor: (author), dclink: (document URL), dcoa:1 (OA filter).
6. DOAJ OAI-PMH (gold OA journals): Harvest article records from https://doaj.org/oai.article. The Dublin Core relation field contains direct full-text URLs. If a paper is in a DOAJ-indexed journal, this is a reliable path to a legal PDF.

Phase 6: Preprint Linkage (Creative Fallback)

If the published version is paywalled, actively hunt for preprint or accepted manuscript versions.

1. Check CrossRef relation fields for has-preprint / is-preprint-of links discovered in Phase 1.
2. Query bioRxiv /pubs/ endpoint with the published DOI to find a linked preprint.
3. Search arXiv by exact title — many published papers have arXiv preprints even when the metadata does not link them.
4. Search OpenAlex locations[] — it often lists preprint server copies that other services miss.
5. Search Semantic Scholar — its corpus links preprints to published versions.
6. Use Dissemin API (https://dissem.in/api/) — query by DOI or title+authors+date. Returns OA classification and pdf_url when available. Also indicates self-archiving policy.

Phase 7: Web Discovery (Broad Search)

If structured APIs have not yielded the paper, search the open web.

1. Google Scholar via the scholarly Python library: scholarly.search_pubs(title). Check eprint_url for free PDF links. Scholar often finds PDFs on author homepages, lab websites, and university course pages that no API indexes.
   • Be aware: Google may rate-limit or CAPTCHA. Use sparingly and only after API sources are exhausted.
2. Web search with file-type targeting: Search for "{exact paper title}" filetype:pdf using a web search API. This surfaces PDFs on university servers, personal pages, and course materials. Also try "{author name}" "{paper title}" filetype:pdf site:edu for faculty-hosted copies.
3. Internet Archive Scholar (https://scholar.archive.org/): Full-text search over 25M+ open papers. Built on the Fatcat open catalog (api.fatcat.wiki/v0/). Also check the Wayback Machine for cached versions of known publisher URLs: GET https://archive.org/wayback/available?url={publisher_url}. For raw PDFs from the archive, use the id_ suffix: https://web.archive.org/web/{timestamp}id_/{original_url}.
4. Author homepage / lab page discovery: From metadata, identify the first/corresponding author's affiliation. Search for their university profile page or lab publications page — researchers often self-host PDFs of their papers. Also query the ORCID API (https://pub.orcid.org/v3.0/{orcid}/works, requires OAuth2 /read-public token, 24 req/sec) to find author work listings with URLs to self-archived copies.

Phase 8: HTML Full-Text Extraction

Some publisher sites display full text in HTML but restrict PDF download. HTML pages also often contain machine-readable pointers to the PDF that are invisible to casual browsing.

1. If a publisher landing page URL is known (from DOI resolution), fetch the HTML.
2. Quick paywall check via Schema.org JSON-LD — before any heavy parsing, look for a <script type="application/ld+json"> block in the HTML. If it contains "isAccessibleForFree": false, the article is paywalled on this site — skip directly to the next phase instead of wasting time parsing the page. Many publishers embed this structured data for Google indexing.
3. Check citation_pdf_url meta tag — parse the HTML <head> for <meta name="citation_pdf_url" content="...">. This is the standard mechanism used by Google Scholar, Unpaywall, and Zotero to discover PDFs. If present, download directly from that URL. Also check related tags: citation_title, citation_doi, citation_authors to verify you are on the correct article page.
4. If no citation_pdf_url is found but the full article text is present in the page body, extract the article text using content-extraction techniques (main content detection, stripping navigation/ads). Note: some "soft paywalls" load full text in the DOM but hide it behind CSS overlays or JavaScript modals — check the raw HTML, not just the rendered view.
5. Save as plain text — this is often sufficient for AI processing and avoids PDF extraction issues entirely.

Phase 9: Non-Standard Sources

If the major APIs and aggregators failed, try less conventional but still structured sources:

• Search for the paper title in PhD theses and dissertations — a thesis chapter may reproduce the paper's content. Check OATD (https://oatd.org/, 7M+ theses from 1,100+ institutions) and NDLTD.
• Check if the venue uses OpenReview (https://openreview.net/) — all submissions are openly hosted.
• Search for conference workshop versions, extended abstracts, or supplementary materials hosted separately from the main paper.
• Look for slide decks, posters, or technical reports by the same authors covering the same results.
• Search GitHub — authors sometimes include paper PDFs alongside their code implementations.
• Check if the paper appears in a government or NGO report under open-access terms.
• Try alternate URL patterns on the publisher site — some expose PDFs at predictable paths that differ from the landing page.

Phase 10: Creative Last-Resort Discovery

If every method above has failed, do not give up. Stop following the playbook. Use the canonical record from Phase 1 — title, authors, year, venue, topic — and think creatively about where this specific paper's text might exist. Consider the field, the authors, the institution, the funding source, the publication venue, the time period, and any other clue. There are no prescribed steps here. Improvise. Try anything that might work.

Phase 11: Download, Validate, and Save

Throughout Phases 2-10, collect all discovered URLs into a ranked candidate list using the scoring system below. Do not stop at the first URL found — gather candidates from multiple sources, then work through the list from highest to lowest score. This resilience matters because the top-ranked URL may be temporarily down, geo-blocked, or rate-limited.

1. Download the best candidate found (highest version quality, best format).
2. Validate the download:
   • If PDF: check HTTP Content-Type header is application/pdf. Verify the file starts with %PDF- magic bytes and contains an %%EOF marker (truncated PDFs lack it). Check file size > 10 KB (a typical paper is 100KB-5MB). Extract text from the first page using pymupdf or pdfplumber and fuzzy-match the extracted title against the canonical title (similarity > 0.80). For stronger verification, run pdf2doi against the downloaded file to extract the embedded DOI from text/metadata and compare it against the canonical DOI.
   • If XML/text: verify the content contains the expected title and is not an error page or login redirect.
   • If any validation fails, discard the candidate and try the next best from the scored list.
3. Save to {{ output_dir }} with filename format: {first_author_last_name}_{year}_{short_title_slug}.{ext} (e.g., vaswani_2017_attention_is_all_you_need.pdf).
4. Return a result record containing:
   • status: "success" | "partial" | "not_found"
   • file_path: path to the saved file (if downloaded)
   • format: "pdf" | "xml" | "text" | "html"
   • version: "published" | "accepted" | "submitted" | "preprint" | "working_paper" | "unknown"
   • source: URL or API name where the file was obtained
   • confidence: float 0.0-1.0 (based on title match, author overlap, year match)
   • canonical_record: the full metadata record built in Phase 1
   • all_attempted_sources: list of sources tried and their status

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API Keys and Credentials

All API keys are stored as environment variables in .env (loaded automatically via direnv). Read keys from environment variables at runtime using os.environ. NEVER hardcode keys in source files.

Before starting, check which keys are available. Skip services whose required keys are missing — do not fail, just move to the next source in the cascade.

Environment Variable	Service	Required?
SCHOLAR_EMAIL	CrossRef, Unpaywall	Yes — mailto: for CrossRef polite pool and email param for Unpaywall
OPENALEX_API_KEY	OpenAlex	Yes — required since Feb 2025, free at openalex.org
SEMANTIC_SCHOLAR_API_KEY	Semantic Scholar	Recommended — free at semanticscholar.org
CORE_API_KEY	CORE	Required for CORE — free at core.ac.uk
NCBI_API_KEY	PMC / PubMed	Optional — raises rate limit 3→10 req/sec
ELSEVIER_API_KEY	Elsevier / ScienceDirect	Optional — free at dev.elsevier.com
SPRINGER_API_KEY	Springer Nature	Optional — free at dev.springernature.com

Services that need no key at all: arXiv, bioRxiv, medRxiv, Europe PMC, Zenodo, HAL, Dissemin, OSF, DOAJ, Internet Archive, OpenCitations, INSPIRE-HEP, ORCID (public data).

If SCHOLAR_EMAIL is not set, abort with a clear error — it is the minimum required credential for this skill.

API Reference Summary

Service	Auth	Rate Limit
CrossRef	SCHOLAR_EMAIL	50 req/sec (polite)
Unpaywall	SCHOLAR_EMAIL	100K req/day
OpenAlex	OPENALEX_API_KEY	100K credits/day
Semantic Scholar	SEMANTIC_SCHOLAR_API_KEY	1 req/sec
CORE	CORE_API_KEY	5 req/10 sec
OpenCitations	None	Be polite
arXiv	None	Use export subdomain
bioRxiv/medRxiv	None	Be polite
PMC / NCBI	NCBI_API_KEY	3-10 req/sec
Europe PMC	None	Generous
NASA ADS	API key required	Per plan
INSPIRE-HEP	None	Be polite
ORCID	OAuth2 /read-public	24 req/sec
Zenodo	None	60-100 req/hour
HAL	None	Be polite
Dissemin	None	Be polite
OSF	None	100 req/hour
DOAJ	None	Be polite
Google Scholar	None (no official API)	Rate-limited by IP

All services expect a descriptive User-Agent header with SCHOLAR_EMAIL. Implement exponential backoff with jitter (base 1s, max 30s, factor 2x) on HTTP 429/5xx responses. Use a circuit breaker: if a source fails >5 times in 5 minutes, skip it for 30 minutes. Cache all API responses keyed by DOI (lowercase, URL-decoded) — never re-fetch the same identifier.

Python Libraries

Library	Purpose
habanero	CrossRef API client (DOI lookup, title-to-DOI)
unpywall	Unpaywall API (OA PDF discovery by DOI)
pyalex	OpenAlex API (works, authors, OA locations)
semanticscholar	Semantic Scholar API (paper search, OA PDF)
arxiv	arXiv search + PDF/source download
biopython	Bio.Entrez for PubMed/PMC efetch/esearch
pyeuropepmc	Europe PMC search + full-text XML retrieval
scholarly	Google Scholar search (use as last resort)
paperscraper	Multi-preprint server search (arXiv/bioRxiv)
sickle	OAI-PMH harvesting from institutional repositories
pymupdf	PDF text extraction and validation
pdf2doi	Reverse-extract DOI from a downloaded PDF for verification
findpapers	Multi-database parallel search (arXiv, IEEE, OpenAlex, PubMed, Scopus)
httpx	Async HTTP client for parallel API calls

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Candidate Scoring

When multiple versions are found, score candidates to pick the best:

• +5 exact DOI match
• +4 title similarity > 0.95
• +3 title similarity 0.85-0.95
• +2 author overlap > 50%
• +2 exact year match
• +1 year within +/- 1
• +3 published version
• +2 accepted manuscript
• +1 preprint / submitted
• +2 structured XML/text format
• +1 born-digital PDF
• -2 scanned PDF (no selectable text)

Pick the candidate with the highest total score. On ties, prefer the source with higher trust ranking: publisher > PMC > major repository > preprint server > personal page > other.

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Done When

• A result record is returned with status, source, version, confidence, and all_attempted_sources fields populated.
• If status is "success": a validated file exists at file_path with confirmed title match (confidence > 0.80).
• If status is "not_found": at least 10 distinct sources were attempted (documented in all_attempted_sources), including Unpaywall, OpenAlex, Semantic Scholar, CrossRef, at least one preprint server, and at least one repository aggregator.
• The canonical metadata record is complete with all discoverable IDs.

Forbidden

• NEVER fabricate a download URL. Every URL must come from an API response or a verified web page.
• NEVER return a file without validating that its content matches the requested paper (title fuzzy-match > 0.80).
• NEVER save login pages, error pages, or CAPTCHA pages as if they were paper content.
• NEVER skip Phase 1 (identification). Downloading without a canonical record leads to wrong-paper errors.
• Do not hammer a single API. Respect rate limits and implement backoff.
• Do not re-download a paper already present in {{ output_dir }} with matching DOI — check for existing files first.