papers-mcp

# Papers by Ouroboros Apps

Papers by Ouroboros Apps is a remote MCP server for students, researchers, writers, and clinicians who want an assistant to search and cite real papers. It is a lighter, independent alternative to Consensus, SciSpace, and Elicit.

The assistant can search OpenAlex, Semantic Scholar, PubMed, Crossref, and arXiv, open a paper by DOI, PMID, or arXiv id, see what cites a paper or what that paper cites, and format APA, MLA, Chicago, or BibTeX. Every result includes a source link and an identifier that came back from one of those APIs. If an API returns nothing, Papers returns nothing. It does not fill gaps with invented citations.

- MCP endpoint: `https://<your-host>/mcp`
- Works with ChatGPT, Claude, Gemini, Grok, Cursor, and any client that speaks Streamable HTTP plus OAuth 2.1 (dynamic client registration and PKCE)

`server.json` is the MCP Registry manifest (`io.github.LAHutchins91/papers`). Its `remotes[0].url` is a placeholder (`https://papers-mcp.vercel.app/mcp`). Change it to the origin you actually deploy, and set `APP_BASE_URL` to that same origin.

## Hosted server

- MCP server URL: `https://papers-mcp.vercel.app/mcp` (Streamable HTTP, OAuth sign-in)
- Docs: https://ouroborosapps.com/docs/papers
- Status: early access. Paste the URL into Claude, Cursor, Grok, or ChatGPT developer mode.
- Registry name: `io.github.LAHutchins91/papers`

## Connect

Leave the client id and secret empty so the client can register itself.

Cursor, in `~/.cursor/mcp.json` or a project `.cursor/mcp.json`:

```json
{
  "mcpServers": {
    "papers": {
      "url": "https://<your-host>/mcp"
    }
  }
}
```

Claude Code:

```bash
claude mcp add --transport http papers https://<your-host>/mcp
```

Other clients: add the same URL and choose OAuth. The consent screen names the assistant and the `papers` scope. Tool discovery (`initialize`, `tools/list`, `ping`) does not require a token. Calling a tool does.

## Tools

- `search_papers` — question or keywords, with optional year range, field, open-access flag, and source (`openalex`, `semantic_scholar`, `pubmed`, `crossref`, `arxiv`, or `all`)
- `get_paper` — one record and its abstract, by DOI, PMID, arXiv id, or OpenAlex work id
- `find_related_papers` — `cited_by` or `references` for that identifier
- `format_citation` — `apa`, `mla`, `chicago`, or `bibtex` from the fetched metadata

Titles are kept as the source wrote them. Author names are split from display names, so particles such as “van” can land in the wrong part and deserve a look before you publish the citation.

## Trial and billing

Start a 14-day trial from the account page after you connect an assistant. Stripe Checkout is the only place an amount is shown. Monthly and yearly plans use the price ids you configure. Papers does not create Stripe products.

When `STRIPE_SECRET_KEY`, `STRIPE_PRICE_MONTHLY`, and `STRIPE_PRICE_YEARLY` are all set, tool calls require a Stripe subscription in `trialing` or `active` status. When they are not set, `GET /health` reports `billingConfigured: false` and an OAuth-signed caller can use the tools. Set the Stripe variables before you expose a deployment publicly.

## Storage

Paper search is stateless. Subscription snapshots and used authorization-code ids share one store:

| `STORAGE_BACKEND` | Behavior |
| --- | --- |
| `memory` (default) | Process-local. Fine for tests and a single Node process. A second process can still accept a code this process already used. |
| `file` | One JSON document at `STORAGE_PATH` (default `data/accounts.json`). For a single Docker host. |
| `blob` | One private Vercel Blob at `STORAGE_BLOB_PATH` (default `papers/accounts.json`). Use this on Vercel so a code cannot be replayed across instances. Requires `BLOB_READ_WRITE_TOKEN`. |

The document is `{ accounts, usedCodes }`. Each account is `{ userId, stripeCustomerId, subscriptionId, subscriptionStatus, currentPeriodEnd, plan, updatedAt }`. `usedCodes` maps an authorization-code id to its expiry, in unix seconds. Expired ids are dropped on every write. An older file that is only a map of accounts is still read. There is no separate database schema. When billing is configured, Stripe is the source of truth: a cold process looks the customer up by `metadata.papers_user_id` if the snapshot is missing.

OAuth access tokens and client registrations are signed tokens, not rows. Set `AUTH_SIGNING_SECRET` in production so tokens survive a restart. On Vercel, set `STORAGE_BACKEND=blob` before the deployment is public.

## Environment

| Variable | Required | Purpose |
| --- | --- | --- |
| `APP_BASE_URL` | Production | Public origin, no trailing slash. OAuth issuer and MCP audience. |
| `AUTH_SIGNING_SECRET` | Production | HMAC secret for OAuth tokens and the account cookie. |
| `SCHOLARLY_CONTACT_EMAIL` | Production | Mailto address in User-Agent and polite-pool parameters for OpenAlex, Crossref, and PubMed. Not shown on the public pages. |
| `REVIEWER_LOGIN_EMAIL` | For store review | Email typed on Reviewer sign-in. See below. |
| `REVIEWER_LOGIN_PASSWORD_HASH` | For store review | scrypt hash of the reviewer password. See below. |
| `COMP_ACCOUNT_EMAILS` | For store review | Comma-separated emails with permanent complimentary access. |
| `COMP_ACCOUNT_IDS` | No | Comma-separated account ids with permanent complimentary access. |
| `NCBI_API_KEY` | No | Higher PubMed rate limit. |
| `SEMANTIC_SCHOLAR_API_KEY` | No | Higher Semantic Scholar rate limit. Sent as `x-api-key`. |
| `STRIPE_SECRET_KEY` | To charge | Stripe secret key. |
| `STRIPE_PRICE_MONTHLY` | To charge | Existing monthly price id. |
| `STRIPE_PRICE_YEARLY` | To charge | Existing yearly price id. |
| `STRIPE_WEBHOOK_SECRET` | To charge | Webhook signature secret. Point Stripe at `POST /billing/webhook`. |
| `STORAGE_BACKEND` | No | `memory`, `file`, or `blob`. |
| `STORAGE_PATH` | No | JSON file used when the backend is `file`. |
| `STORAGE_BLOB_PATH` | No | Blob pathname when the backend is `blob`. Defaults to `papers/accounts.json`. |
| `BLOB_READ_WRITE_TOKEN` | With `blob` | Read-write token for the Vercel Blob store. The SDK reads this itself. |
| `PORT` | No | Defaults to `43127`. |

Do not commit secrets. Copy what you need into the host’s environment, not into the repo.

## Run locally

```bash
npm install
npm run dev
```

Open [http://127.0.0.1:43127](http://127.0.0.1:43127). Health is `GET /health`.

```bash
npm test
npm run typecheck
```

Tests call the public APIs that do not need keys. Stripe is not called. Semantic Scholar often answers `429` from shared IP space; the tool reports that rate limit and does not substitute a made-up paper.

## Deploy

Vercel: `vercel.json` builds `api/index.ts` and routes every path to that function, including `logo.jpg` in the function bundle. Repository files such as `/package.json` and `/src/*` are not served as static files. Set the environment variables above, set `APP_BASE_URL` to the deployment origin, set `STORAGE_BACKEND=blob`, and update `server.json` `remotes[0].url` to `https://<that-host>/mcp`. Create the Blob store in the Vercel project and leave its read-write token in `BLOB_READ_WRITE_TOKEN`. Stripe’s webhook endpoint is `POST /billing/webhook`.

Docker:

```bash
docker build -t papers-mcp .
docker run --rm -p 43127:43127 -e APP_BASE_URL=http://127.0.0.1:43127 -e AUTH_SIGNING_SECRET=replace-me -e SCHOLARLY_CONTACT_EMAIL=you@example.com papers-mcp
```

The container listens on `43127`.

## Rate limits

Requests are spaced per host: OpenAlex about 10/s, Crossref about 4/s, PubMed about 3/s without an NCBI key, Semantic Scholar about 1/s without a key, and arXiv at least 3 seconds between calls. A descriptive User-Agent is always sent. The contact email is included only when `SCHOLARLY_CONTACT_EMAIL` is set.

## License

MIT. Copyright Lawrence Hutchins. See [LICENSE](LICENSE).

---

## Contact

Public support, privacy, export, and deletion: [ouroborosplugins@gmail.com](mailto:ouroborosplugins@gmail.com)

- Privacy: `/privacy`
- Terms: `/terms`
- Support: `/support`
- Site: https://ouroborosapps.com

The public pages always show that mailbox. `SCHOLARLY_CONTACT_EMAIL` is sent only in scholarly API polite-use headers. It is not printed on the site. `SUPPORT_EMAIL` is not read.

`server.json`, `glama.json`, and `.cursor-plugin/plugin.json` have no contact-email field. The registry schema used by `server.json` does not define one.

## Store-reviewer sign-in

Reviewers sign in on the OAuth consent screen with **Reviewer sign-in**. There is no separate sign-up, no second factor, and no card. Set these on the host (Vercel project → Settings → Environment Variables), for Production and for any Preview URL a reviewer will open. Do not commit the values.

| Variable | Format |
| --- | --- |
| `REVIEWER_LOGIN_EMAIL` | One email address, the value the reviewer types. Lowercased when compared. |
| `REVIEWER_LOGIN_PASSWORD_HASH` | One line: `scrypt$16384$8$1$<salt-base64url>$<hash-base64url>`. Salt is 16 bytes. Hash is 32 bytes. scrypt parameters are N=16384, r=8, p=1. |
| `COMP_ACCOUNT_EMAILS` | Comma-separated emails. Include `REVIEWER_LOGIN_EMAIL`. Each email grants a permanent entitlement to the stable account id derived from it. |
| `COMP_ACCOUNT_IDS` | Optional comma-separated account ids. Use the derived reviewer id, or an anonymous account id you want to comp. |

Login checks the email and password hash. The allowlist is what skips the trial and Stripe. Set `COMP_ACCOUNT_EMAILS` to the same address as `REVIEWER_LOGIN_EMAIL`, or put the derived id in `COMP_ACCOUNT_IDS`. A normal anonymous account is unchanged and still needs a trial when billing is configured.

Generate the hash (the password is an argument, not a file in the repo):

```bash
node --input-type=module -e '
import crypto from "node:crypto";
const password = process.argv[1];
if (!password) { console.error("Pass the password as an argument."); process.exit(1); }
const salt = crypto.randomBytes(16);
const ha