@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.1

package/LICENSE

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

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-# 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-0.1.1-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-v1.4.3-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>
+
+---
+
+## 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 or Streamable HTTP, with no credentials to configure.
+
+### Tools
+
+| Tool | Description |
+|:---|:---|
+| `interpro_search_entries` | Find InterPro entries or member signatures by text, entry type, GO annotation, or integrating InterPro 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
+- Cursor-paged, `limit` 1-100 (default 20); returns `entries`, `page` (`total`, `returned`, `hasMore`, `nextCursor`), and the applied `query`
+
+---
+
+### `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
+- 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`, `limit` 1-100 (default 20)
+- `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`
+- Cursor-paged, `limit` 1-50 (default 20); each result keeps the protein summary, matched entry locations, and taxon lineage
+- 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
+
+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/template.md

@@ -0,0 +1,151 @@
+---
+# FORMAT REFERENCE — do not edit. Copy this file to
+# `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.8.x/0.8.6.md`)
+# to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
+# with a concrete date.
+
+# Required. One-line GitHub Release-style headline. 350 character cap — a
+# ceiling, not a target. Default short and scannable. Don't pad, don't stitch
+# unrelated changes with commas/semicolons into an inventory — pick the one
+# headline the release is about. Quotes required: unquoted YAML treats
+# `: ` inside the value as a key separator and fails GitHub's strict parser.
+summary: ""
+
+# Set `true` when consumers must change code to upgrade: API removals,
+# signature changes, config renames, behavior changes that break existing
+# usage. Flagged as `Breaking` in the rollup.
+breaking: false
+
+# Set `true` ONLY for a security fix in THIS project's own source code — a
+# vulnerability or hardening in code you ship. A dependency or transitive CVE
+# bump is routine maintenance, NOT a security release: record it under
+# `## Dependencies` (with the advisory ID) and leave this `false`. When true,
+# pairs with the `## Security` section below and flags `Security` in the rollup.
+security: false
+
+# Optional free-form notes for maintenance agents processing this release.
+# Not rendered in CHANGELOG — consumed by agents running `maintenance` on
+# downstream servers. ADOPTION STEPS ONLY — new files to create, fields to
+# populate, one-time migration steps. Never a second rendering of the body:
+# if a body bullet already says it, name the bullet's symbol instead of
+# re-explaining. Omit the field entirely when there's nothing to say.
+# agent-notes: |
+#   <instructions for downstream maintenance agents>
+---
+
+# <version> — YYYY-MM-DD
+
+<!--
+  AUTHORING GUIDE — applies to the new per-version file you create from this
+  template.
+
+  Audience: someone scanning release notes to decide what affects them. Lead
+  each bullet with the symbol or concept name in **bold** so they can skip
+  what's irrelevant and zoom in on what's not.
+
+  Tone: terse, fact-dense, not verbose. Bullet shape: **symbol** + what
+  changed + at most one consumer-facing caveat. One sentence by default, two
+  when the second carries weight — a bullet past ~40 words or three sentences
+  is wrong. The depth lives one hop away: the linked issue carries the why,
+  the commit diff carries the how. The changelog names what changed and what
+  a consumer does about it; a reader who wants mechanism opens the link.
+
+  Model length on THIS guide, never on the previous entry — entries modeled
+  on entries compound.
+
+  Cut (each has shipped as a wall of text; these are the cruft):
+  - History/justification narration — how the bug worked, why the old
+    behavior was wrong. One short clause at most; the issue carries the story.
+  - Design-rationale defense — "chosen over Y because…", "guarding the
+    getter is not enough…". That is the author arguing with a reviewer;
+    reviewers read the PR, not the changelog.
+  - Defensive unchanged-clauses — "X is unchanged", "byte-identical to
+    <prev>". Keep one only where its absence would cause a real misread,
+    as a short parenthetical.
+  - Edge-case inventories — marker lists, not-flagged lists, escape tables.
+    Tests and the issue carry those.
+  - Mechanism walkthroughs (JSDoc, CLAUDE.md/AGENTS.md, or the relevant
+    skill own those), ceremonial framings ("This release introduces…"),
+    backwards-compat paragraphs, file-by-file test enumerations. Prefer
+    code/symbol names over English re-explanations.
+
+  Verified ≠ included: the every-claim-verified-from-the-diff rule bounds
+  the TRUTH of what you write, never the AMOUNT.
+
+  Example — same fact, right size:
+
+    TOO LONG: **`fetchWithTimeout`'s `timeoutMs` bounds the whole exchange**
+    (#341). `fetch` resolves once headers arrive and the deadline was
+    cleared as the helper returned, so a peer that answered promptly and
+    then stalled the stream held the request open indefinitely. A 2xx
+    carrying a body now comes back as a passthrough wrapper that disarms
+    the deadline when the body closes, errors, or is cancelled; …
+    [+90 more words of mechanism and edge cases]
+
+    RIGHT: **`fetchWithTimeout`'s `timeoutMs` now bounds the whole
+    exchange, not just the headers** (#341). A stalled body aborts with
+    the same `Timeout` error; the returned `Response` is a wrapper, so
+    identity assertions (`toBe(response)`) no longer hold.
+
+  Narrative intro: skip by default. Add one short sentence only when the
+  release theme genuinely needs framing the bullets can't carry. When many
+  bullets share one upgrade consequence, state it ONCE — intro line or
+  agent-notes — never per bullet.
+
+  Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
+  Fixed, Security. Include only sections with entries; delete the rest
+  (including the commented-out scaffolding below). Don't ship empty headers.
+
+  Include: every distinct fact a reader needs to adopt or audit the release —
+  new exports, signatures, lint rule IDs, env vars, breaking changes, version
+  bumps on shipped skills. Nothing more.
+
+  Links: link issues, PRs, docs, or skills where they help a reader jump to
+  context. Once per item per entry — don't re-link the same issue in summary,
+  narrative, and bullet. Skip links for inline symbol names; code spans speak
+  for themselves.
+
+  Issue/PR URLs: use full URLs. GitHub's bare `#NN` auto-link only resolves
+  inside its own UI, not in npm reads or local editors.
+
+      [#38](https://github.com/cyanheads/mcp-ts-core/issues/38)   ← issue
+      [#42](https://github.com/cyanheads/mcp-ts-core/pull/42)     ← PR
+
+  Verify numbers exist before linking (`gh issue view NN`, `gh pr view NN`).
+  Never speculate on a future number — `#42` for an upcoming PR silently
+  resolves to whatever real item already owns 42, and timeline previews pull
+  in that unrelated item's metadata.
+
+  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
+  via `gh release create --notes-from-tag`. It is a condensed digest of this
+  entry, never a copy, and its format is owned by the `release-and-publish`
+  skill (step 4, "Create the annotated tag"): a short subject line without the
+  version, flat headline bullets — no Keep-a-Changelog section headers, no
+  gates line — at most one deps line, issue backlinks, and the changelog link
+  last. In release-PR mode the `git-wrapup` skill authors those bullets as the
+  PR body's `## Changes` and the tag copies them.
+-->
+
+## Added
+
+-
+
+## Changed
+
+-
+
+<!-- ## Deprecated
+
+- -->
+
+<!-- ## Removed
+
+- -->
+
+## Fixed
+
+-
+
+<!-- ## Security
+
+- -->

package/dist/index.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * @fileoverview interpro-mcp-server MCP server entry point.
+ * @module index
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG"}