# Platform MCP Server

The **Quilt Platform MCP Server** lets AI assistants interact with your organization's data through natural language. Built on the open [Model Context Protocol](https://modelcontextprotocol.io/), it connects Claude, Cursor, and other MCP-compatible clients directly to your Quilt environment — so users can search, browse, read, create, and query data without leaving their AI workflow.

All actions respect your existing Quilt roles and permissions. Data never leaves your AWS environment.

## Capabilities

### Search

Ask your AI assistant to find packages or S3 objects by name, content, metadata, or any combination. Searches use Elasticsearch query syntax under the hood, so you can be as broad ("RNA-seq experiments") or specific (`ext:.parquet AND key:results/*`) as you like. Results are paginated automatically — just ask for more if the first page isn't enough.

### Packages

Your AI assistant can list packages in a bucket, browse a package's file tree, inspect revision metadata and history, create new packages from S3 objects or inline content, and patch existing packages by adding, updating, or removing entries — all without leaving the conversation. Workflows and user metadata are supported on create and update.

### S3 Objects

List, read, inspect, download, and upload S3 objects. The assistant can read text, images, and binary files directly from `s3://` or `quilt+s3://` URIs, retrieve object metadata (size, content type, last modified), generate presigned download URLs you can open in a browser, and upload new content to S3.

### Athena

Run SQL queries against your data lake through Amazon Athena and get results back in the conversation. This works with both standard Athena tables and Quilt Tabulator tables — the assistant automatically has access to available databases and catalogs.

### Tabulator

List, create, rename, and manage Tabulator table definitions that control how package data is projected into queryable Athena tables.

### Utilities

The assistant can list your accessible buckets, generate shareable Quilt catalog links for any resource, and read platform configuration such as search syntax help and Athena setup details.

***

## Resources

The Platform MCP Server also exposes read-only resources that give AI assistants additional context about your environment:

| Resource          | Description                                             |
| ----------------- | ------------------------------------------------------- |
| **Search Syntax** | Elasticsearch query string syntax reference for search  |
| **Athena**        | Available databases, catalogs, and query configuration  |
| **Buckets**       | Accessible buckets with names, titles, and descriptions |
| **Current User**  | Identity and role of the authenticated user             |

***

## Getting Started

### Supported Clients

The Platform MCP Server works with any MCP-compatible AI client, including:

* **Claude.ai** (web)
* **Cursor** (desktop)
* **Any client** supporting the [Model Context Protocol](https://modelcontextprotocol.io/)

### Connecting Claude.ai

An Organization administrator adds Quilt as a connector:

1. Go to [Organization Settings -> Connectors](https://claude.ai/admin-settings/connectors)
2. Click **Add Custom Connector**
3. Enter your Connect Server URL: `https://<connect-host>/mcp/platform/mcp`

### Connecting Cursor and other desktop clients

Add the following to your MCP client configuration (in Cursor: **Settings -> MCP -> Add new global MCP server**):

```json
{
  "mcpServers": {
    "quilt": {
      "url": "https://<connect-host>/mcp/platform/mcp"
    }
  }
}
```

> Your administrator must include the client's custom scheme (e.g. `cursor://`) in `ConnectAllowedHosts` for the OAuth flow to complete.

### User Authorization

Each user must authorize their MCP connection once:

**Web clients (e.g. Claude.ai):**

1. Log in to your Quilt stack as usual (e.g. via Okta SSO)
2. Go to [Settings -> Connectors](https://claude.ai/settings/connectors)
3. Click **Connect**

**Desktop clients (e.g. Cursor):** the OAuth flow starts automatically the first time the client connects to the MCP server.

In both cases, you will see the Quilt authorization page at `/connect/authorize`, showing the name of the AI client and what it is requesting access to. Click **Continue** to grant access or **Cancel** to deny it.

After authorizing, the AI assistant receives a session token scoped to your Quilt user — it cannot access data beyond what your assigned Quilt role permits. You do not need to re-authorize the same client unless your session expires or the Quilt stack is redeployed.

Once authenticated, you may also need to authorize individual tools when used. You can pre-authorize them by clicking **Configure** on the connector page.

![Quilt Connect Server](https://515699986-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LDNT6ZcFbSZLsyC6aK9-887967055%2Fuploads%2Fgit-blob-e5a633d9cb0ec7d14ef72a0bfdcbcaa7e069d3ea%2Fconnect-authorize.png?alt=media)

![Quilt MCP Configuration](https://515699986-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LDNT6ZcFbSZLsyC6aK9-887967055%2Fuploads%2Fgit-blob-fd571e0deeb1ee19eef2730887e1608933527535%2Fmcp-tools.png?alt=media)

***

## Administrator Reference

The Platform MCP Server runs behind [Quilt Connect Server](https://docs.quilt.bio/quilt-platform-administrator/connect), which handles OAuth authentication, session tokens, and request routing within your AWS environment. See the [Quilt Connect](https://docs.quilt.bio/quilt-platform-administrator/connect) page for CloudFormation parameters, DNS configuration, and IP allowlisting.