doily

An MCP server that gives an AI agent unpaywalled access to research papers, biomedical sciences first. It runs on Cloudflare Workers, is locked to a single owner, and is MIT licensed.

An agent can search the literature, pull merged metadata, judge a journal or an author, and read the full text of a paper through a fallback chain that tries every open-access route before it reaches Sci-Hub and, as a last resort, posts a Sci-Net bounty request and waits for it to be fulfilled.

Tools

Nine tools, all returning JSON text. Arguments, return shapes and errors are in docs/tools.md.

Every tool except request_paper is read-only and says so in its annotations.

Related MCP server: omnisearch-mcp

Full-text fallback chain

get_full_text and get_pdf walk these sources in order and stop at the first that delivers. Every hop is short-circuited by an R2 cache, and anything fetched is cached indefinitely.

1. PMC / Europe PMC JATS XML (Europe PMC full-text XML, NCBI efetch from db=pmc, BioC JSON). Only NCBI and Europe PMC APIs are used; PMC HTML is never scraped.

2. Unpaywall: the best open-access location, then the others.

3. OpenAlex and Semantic Scholar open-access links.

4. bioRxiv / medRxiv.

5. CORE (skipped when no CORE_API_KEY is set).

6. Sci-Hub.

7. A Sci-Net request token. get_full_text never posts a request by itself; it returns a request_token and the agent decides whether to call request_paper.

Any PDF is checked for the %PDF magic bytes. PDF text comes from unpdf, with Workers AI toMarkdown() as the fallback for failures and scanned pages.

Legal note

Sci-Hub and Sci-Net are enabled by default. Whether retrieving a paper through them is lawful depends on where you are and what you do with it, and both are blocked in some countries. You are responsible for your own use. Everything above them in the chain (steps 1 to 5) is open access.

Journal signals

get_journal, and the journal block inside get_paper, report evidence and leave the judgement to the reader:

• Impact proxy. OpenAlex's 2yr_mean_citedness (the mean citations that the last two years of the journal's works have received) stands in for an impact factor, alongside h-index, DOAJ membership, is_core, listed_in and the APC.

• SJR. A committed snapshot of the SCImago Journal Rank (sjr, quartile, year), credited to SCImago. Refreshed by hand about once a year.

• Predatory lists. Matches against snapshots of Beall's list and predatoryjournals.org are returned as listed_on: [...] with the source named. This is evidence, never a verdict: the lists are opinions, include stale and disputed entries, and miss newer journals. Absence proves nothing.

• Retractions. get_paper reports Crossref update-to relations, which carry Retraction Watch data, as retracted, corrected or concern notices.

Quick start: Claude Code

Once doily is deployed (see Self-hosting):

claude mcp add --transport http -s user doily https://<your-host>/mcp

Then run /mcp inside a session and finish the OAuth consent in the browser tab it opens. The consent page sits behind Cloudflare Access, so sign in as the owner when asked.

To skip OAuth and use the static bearer instead:

claude mcp add --transport http -s user doily https://<your-host>/mcp \
  --header "Authorization: Bearer <your DOILY_BEARER value>"

Quick start: claude.ai

1. In claude.ai, open Settings > Connectors > Add custom connector.

2. Enter the server URL https://<your-host>/mcp (no trailing slash).

3. Leave the OAuth client ID and secret fields empty. claude.ai registers itself through dynamic client registration, then sends your browser to the consent page. Sign in through Cloudflare Access and approve.

Alternatively, paste Authorization: Bearer <your DOILY_BEARER value> under Request headers and skip OAuth entirely.

Other MCP clients that speak streamable HTTP and OAuth 2.1 with PKCE work the same way.

Self-hosting

doily is built to be deployed by its owner onto their own Cloudflare account: one Worker, one D1 database, one R2 bucket, two KV namespaces, one Durable Object class, and a Cloudflare Access application in front of the consent page. The full walk-through, including every secret and the optional Sci-Hub proxy, is in docs/setup.md.

Upstream API keys (NCBI, OpenAlex, Semantic Scholar, CORE) are all optional; every path works without them, only slower or with fewer sources.

Development

npm ci
npm run check        # lint, typecheck, format, ASCII, tests, dry-run build
npm test             # unit and integration suites
npm run test:unit
npm run test:integration
npm run test:live    # LIVE=1, hits real upstream APIs, never in CI
npm run dev          # wrangler dev on :8787 (needs .dev.vars)

Copy .dev.vars.example to .dev.vars for local runs. See CONTRIBUTING.md for conventions and SECURITY.md for the auth model and how to report a vulnerability. The locked design spec is .claude/doily-spec.md.

License

MIT. See LICENSE. SJR data is credited to SCImago Journal & Country Rank; see data/README.md for the terms of each snapshot.