@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.2

package/LICENSE

@@ -0,0 +1,201 @@
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package/README.md

@@ -1,3 +1,290 @@
-# Temporary Holding Version
+<div align="center">
+  <h1>@cyanheads/interpro-mcp-server</h1>
+  <p><b>Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP.</b>
+  <div>6 Tools</div>
+  </p>
+</div>
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+<div align="center">
+
+[![Version](https://img.shields.io/badge/Version-0.1.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/interpro-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.3.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/interpro-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/interpro-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.4-blueviolet.svg?style=flat-square)](https://bun.sh/)
+
+</div>
+
+<div align="center">
+
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/interpro-mcp-server/releases/latest/download/interpro-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=interpro-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvaW50ZXJwcm8tbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22interpro-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Finterpro-mcp-server%22%5D%7D)
+
+[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+
+</div>
+
+<div align="center">
+
+**Public Hosted Server:** [https://interpro.caseyjhand.com/mcp](https://interpro.caseyjhand.com/mcp)
+
+</div>
+
+---
+
+## Overview
+
+Protein families, domains, repeats, and functional sites from [InterPro](https://www.ebi.ac.uk/interpro/) and the member databases it integrates (Pfam, PROSITE, SMART, CDD, PANTHER, and others), read through the keyless EMBL-EBI InterPro API. Search entries, read their full metadata, map a UniProt protein's annotations to residue coordinates, walk Pfam, CDD, and PIRSF clans, and find proteins that carry a signature. Runs over STDIO, Streamable HTTP, or the public hosted endpoint above, with no credentials to configure.
+
+### Tools
+
+| Tool | Description |
+|:---|:---|
+| `interpro_search_entries` | Find InterPro entries by GO annotation, or InterPro entries and member signatures by text, entry type, or integrating accession |
+| `interpro_get_entry` | Read one entry's description, hierarchy, member signatures, GO terms, literature, cross-references, clan membership, and coverage counters |
+| `interpro_get_protein_domains` | Map a UniProt protein's domains, families, repeats, and functional sites to sequence coordinates, optionally at one residue |
+| `interpro_get_clan` | Read a Pfam, CDD, or PIRSF set and page through its members, optionally with its relationship graph |
+| `interpro_find_proteins_by_domain` | Find UniProt proteins carrying an entry, defaulting to reviewed human proteins |
+| `interpro_list_reference` | Decode database slugs, entry types, accession patterns, common taxon IDs, and the current InterPro release |
+
+## Capability reference
+
+### `interpro_search_entries` <sub>tool</sub>
+
+- `sourceDatabase` (default `interpro`) plus optional `query` (1-300 characters), `entryType`, `goTerm` (`GO:0003677` form), `goCategory` (`P`, `F`, `C`), and `integratedInto` (an `IPR` accession, member databases only); no filter is required, so omitting all of them browses the database
+- `goTerm` and `goCategory` require `sourceDatabase: "interpro"`. For member signatures, search InterPro with the GO filter, then read `member_databases` with `interpro_get_entry` or search the member database with `integratedInto` set to the matching InterPro accession
+- Cursor-paged, positive integer `limit` capped at 100 (default 20); larger requests are clamped with a notice. Returns `entries`, `page` (`total`, `returned`, `limit`, `hasMore`, `nextCursor`), and the applied `query`; `page.limit` is the effective page size
+
+---
+
+### `interpro_get_entry` <sub>tool</sub>
+
+- `accession` required; `sourceDatabase` is inferred from standard accession prefixes when omitted. A set accession (`CL…`) fails as `entry_not_found` and points to `interpro_get_clan`
+- Wikipedia thumbnails are omitted unless `includeThumbnail: true`, and a notice reports what was left out
+- `entry.descriptionText` adds readable text with paragraph, list, and table boundaries alongside the unchanged source `entry.description`, including its HTML and annotation flags. It is omitted when no readable text is supplied
+- A withdrawn record fails as `entry_withdrawn` with its deletion date and short name
+
+---
+
+### `interpro_get_protein_domains` <sub>tool</sub>
+
+- Canonical six- or ten-character UniProt `accession` (no isoform suffix); optional `residuePosition` (1-based, inclusive) keeps every match with a fragment covering it, with all of that match's fragments intact; `includeExtraFeatures` adds predicted features such as disorder and transmembrane regions
+- Large maps arrive in segments of whole matches within a 100,000-byte response budget, following `coverage.nextCursor` until `hasMore` is `false`. The first segment carries the protein metadata, and an empty segment cannot establish that nothing is annotated
+- Discontinuous fragments, models, and upstream scores are kept as returned; `residue_out_of_range` and `protein_not_found` are typed failures
+
+---
+
+### `interpro_get_clan` <sub>tool</sub>
+
+- `accession` for a Pfam (`CL0016`), CDD (`cl21453`), or PIRSF (`PIRSF000047`) set, with `sourceDatabase` (`pfam`, `cdd`, `pirsf`) inferred from the prefix; members page by `cursor`, with positive integer `limit` capped at 100 (default 20). Larger requests are clamped with a notice; `page.limit` reports the effective size
+- `includeRelationships: true` adds the relationship graph in slices that fit the response budget; `relationshipsPage.nextOffset` goes back in as `relationshipOffset`, which needs `includeRelationships` set
+- `includeThumbnail` works as on `interpro_get_entry`; a missing set is `clan_not_found`
+
+---
+
+### `interpro_find_proteins_by_domain` <sub>tool</sub>
+
+- `accession` plus optional `sourceDatabase`; `taxonId` (NCBI, default `9606`) and `reviewedOnly` (default `true`; `false` covers reviewed and unreviewed proteins) are echoed in `query`
+- Optional `isFragment` selects proteins annotated as fragments (`true`) or not annotated as fragments (`false`); omit it to include both. False does not establish sequence completeness. Explicit selections appear in `query` and must stay unchanged when following cursors
+- Cursor-paged, positive integer `limit` capped at 50 (default 20); larger requests are clamped with a notice, and `page.limit` is the effective size. Each result keeps the protein summary, matched entry locations, taxon lineage, and native `extra_fields.is_fragment` annotation; missing or null status remains unknown
+- No hits is a success with a notice, since the API answers an unknown entry, an unknown taxon, and an empty intersection the same way
+
+---
+
+### `interpro_list_reference` <sub>tool</sub>
+
+- `topic` required: `databases`, `entry_types`, `accession_patterns`, `taxa`, or `release`. The first four are local and make no network call; `taxa` lists common examples, not every taxon
+- `release` reads the current InterPro version, date, and per-database entry counts, and fails as `release_changed` if the two upstream responses disagree on the version
+
+## Features
+
+Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.
+
+InterPro-specific:
+
+- 15 database slugs (`interpro`, `pfam`, `prosite`, `profile`, `smart`, `cdd`, `panther`, `cathgene3d`, `ssf`, `ncbifam`, `hamap`, `prints`, `pirsf`, `sfld`, `antifam`) and 11 entry types, with the entry database inferred from standard accession prefixes and conflicting routes rejected locally
+- One process-wide request pacer at one upstream request per second, a 50-second budget per tool call covering pacing, retries, and every request, and a 4 MiB cap on upstream responses
+- Upstream HTTP/1.1 client that handles the API's bodyless 204 responses, which native `fetch` rejects on Node
+- Sparse upstream metadata passes through as `null` or omitted rather than filled in
+
+Agent-friendly output:
+
+- `content[]` carries the complete output as compact JSON plus an index of every URL as a link and every image as an image, so clients that read only one surface get the same data
+- Opaque cursors bound to their query, with a notice naming the exact next call whenever a result is partial
+- Typed failure reasons (`entry_not_found`, `invalid_cursor`, `upstream_rate_limited`, and others) each paired with a recovery hint
+- Coordinates describe sequence annotation, not pathogenicity or clinical significance
+
+## Getting started
+
+### Public Hosted Instance
+
+A public instance is available at `https://interpro.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:
+
+```json
+{
+  "mcpServers": {
+    "interpro-mcp-server": {
+      "type": "streamable-http",
+      "url": "https://interpro.caseyjhand.com/mcp"
+    }
+  }
+}
+```
+
+### Self-Hosted / Local
+
+Add the following to your MCP client configuration file. No API key is needed.
+
+```json
+{
+  "mcpServers": {
+    "interpro-mcp-server": {
+      "type": "stdio",
+      "command": "bunx",
+      "args": ["@cyanheads/interpro-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with npx (no Bun required):
+
+```json
+{
+  "mcpServers": {
+    "interpro-mcp-server": {
+      "type": "stdio",
+      "command": "npx",
+      "args": ["-y", "@cyanheads/interpro-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with Docker:
+
+```json
+{
+  "mcpServers": {
+    "interpro-mcp-server": {
+      "type": "stdio",
+      "command": "docker",
+      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/interpro-mcp-server:latest"]
+    }
+  }
+}
+```
+
+For Streamable HTTP, set the transport and start the server:
+
+```sh
+MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
+# Server listens at http://localhost:3010/mcp
+```
+
+### Prerequisites
+
+- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).
+
+### Installation
+
+1. **Clone the repository:**
+
+```sh
+git clone https://github.com/cyanheads/interpro-mcp-server.git
+```
+
+2. **Navigate into the directory:**
+
+```sh
+cd interpro-mcp-server
+```
+
+3. **Install dependencies:**
+
+```sh
+bun install
+```
+
+4. **Configure environment (optional):**
+
+```sh
+cp .env.example .env
+```
+
+## Configuration
+
+The server defines no variables of its own; the InterPro API is keyless. These framework variables are the ones most often set:
+
+| Variable | Description | Default |
+|:---|:---|:---|
+| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
+| `MCP_HTTP_PORT` | HTTP server port. | `3010` |
+| `MCP_HTTP_HOST` | HTTP server host. | `127.0.0.1` |
+| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path. | `/mcp` |
+| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto`. | `stateless` |
+| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth`. With auth on, each tool requires its `tool:<tool_name>:read` scope. | `none` |
+| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `notice`, `warning`, `error`). | `info` |
+| `LOGS_DIR` | Directory for log files (Node.js only). | `<app-root>/logs` |
+| `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1`. | `in-memory` |
+| `OTEL_ENABLED` | Enable [OpenTelemetry](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |
+
+See [`.env.example`](./.env.example) for the common framework overrides.
+
+## Running the server
+
+### Local development
+
+- **Build and run the production version**:
+
+  ```sh
+  # One-time build
+  bun run rebuild
+
+  # Run the built server
+  bun run start:http
+  # or
+  bun run start:stdio
+  ```
+
+- **Run checks and tests**:
+  ```sh
+  bun run devcheck  # Lints, formats, type-checks, and more
+  bun run test      # Runs the test suite
+  ```
+
+## Project structure
+
+| Directory | Purpose |
+|:---|:---|
+| `src/index.ts` | `createApp()` entry point: registers the tools and starts the InterPro service. |
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Six tools. |
+| `src/services/interpro` | InterPro service: HTTP/1.1 adapter, pacer and deadlines, accession routing, cursors, schemas, and the shared result formatter. |
+| `tests/` | Unit and integration tests, mirroring the `src/` structure. |
+
+## Development guide
+
+See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
+
+- Handlers throw, framework catches, with no `try/catch` in tool logic
+- Use `ctx.log` for request-scoped logging
+- Register new tools in the `createApp()` array in `src/index.ts`
+- Wrap external API calls: validate raw, normalize to the domain type, return the output schema; never fabricate missing fields
+
+## Contributing
+
+Issues are welcome. Run checks and tests before submitting:
+
+```sh
+bun run devcheck
+bun run test
+```
+
+## License
+
+This project is licensed under the Apache 2.0 License. See the [LICENSE](./LICENSE) file for details.
+
+Data comes from InterPro and its member databases through the EMBL-EBI API. Licensing varies by member database, so attribute InterPro and the originating database; see [InterPro's license page](https://interpro-documentation.readthedocs.io/en/latest/license.html) and the [EMBL-EBI terms of use](https://www.ebi.ac.uk/about/terms-of-use/).

package/changelog/0.1.x/0.1.1.md

@@ -0,0 +1,20 @@
+---
+summary: "First public release: six read-only tools for InterPro entries, protein domain maps, and clans over the keyless EMBL-EBI InterPro API, with 100 KB response budgets that continue by whole record, on STDIO or Streamable HTTP."
+breaking: false
+security: false
+---
+
+# 0.1.1 — 2026-10-21
+
+## Added
+
+- **`interpro_search_entries`** and **`interpro_get_entry`** search InterPro and 14 member databases (Pfam, PROSITE, SMART, CDD, PANTHER, and others) by text, entry type, GO annotation, or integrating InterPro accession, and read one entry's full metadata. The entry database is inferred from standard accession prefixes.
+- **`interpro_get_protein_domains`** maps a UniProt protein's domains, families, repeats, and functional sites to residue coordinates, optionally at one residue or with predicted features. Discontinuous fragments, models, and upstream scores are kept as returned.
+- **`interpro_get_clan`** reads a Pfam, CDD, or PIRSF set, pages its members, and optionally returns its relationship graph.
+- **`interpro_find_proteins_by_domain`** finds UniProt proteins carrying an entry, defaulting to reviewed human proteins (`taxonId` and `reviewedOnly` change the scope).
+- **`interpro_list_reference`** decodes database slugs, entry types, accession patterns, common taxon IDs, and the current InterPro release.
+- **Response budgets**: results over 100,000 bytes are cut between whole records (protein-map matches and clan relationship slices) and continue through opaque cursors bound to their query, with a notice naming the next call.
+- **Request limits**: one upstream request per second process-wide, a 50-second budget per tool call, and a 4 MiB cap on upstream responses. The HTTP/1.1 client handles the API's bodyless 204 responses, which native `fetch` rejects on Node.
+- **Rendering**: `content[]` carries the full output as compact JSON plus an index of every URL and image, matching `structuredContent`. Upstream text never shapes server-written Markdown or error lines.
+- **Typed failures** (`entry_not_found`, `entry_withdrawn`, `invalid_cursor`, `upstream_rate_limited`, and others), each with a recovery hint.
+- **Transports**: STDIO or Streamable HTTP, stateless sessions, no API key or server-specific environment variables.

package/changelog/0.1.x/0.1.2.md

@@ -0,0 +1,27 @@
+---
+summary: "GO-aware entry search, readable descriptions, and fragment-aware protein discovery."
+breaking: false
+security: false
+---
+
+# 0.1.2 — 2026-10-24
+
+## Added
+
+- **`interpro_get_entry`** adds readable `entry.descriptionText` with paragraph, list, and table boundaries alongside raw descriptions and annotation flags. ([#15](https://github.com/cyanheads/interpro-mcp-server/issues/15))
+- **`interpro_find_proteins_by_domain`** accepts optional `isFragment`, returns native fragment annotations on every page, and binds explicit selections to cursors; missing/null status remains unknown, and false does not establish sequence completeness. ([#16](https://github.com/cyanheads/interpro-mcp-server/issues/16))
+
+## Changed
+
+- **Paged reads** clamp oversized positive integer limits to 100 entries/members or 50 proteins, with requested/effective disclosure composed with continuation and omission notices. ([#14](https://github.com/cyanheads/interpro-mcp-server/issues/14))
+- **Hosted access** is documented in the README and advertised through MCP Registry remote metadata.
+
+## Fixed
+
+- **`interpro_search_entries`** rejects member-database GO filters before requesting data, with recovery through InterPro `member_databases` or member searches using `integratedInto`. ([#13](https://github.com/cyanheads/interpro-mcp-server/issues/13))
+
+## Dependencies
+
+- Add **`htmlparser2` ^12.0.0** for HTML fragment tokenization and entity decoding.
+- **`ignore`** ^7.0.12 → ^7.0.13.
+- **Bun** 1.4.3 → 1.4.4 in package-manager metadata and Docker images.