@cyanheads/pubmed-mcp-server 2.5.2 → 2.5.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/CLAUDE.md +11 -5
  2. package/README.md +1 -1
  3. package/package.json +2 -2
  4. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.5.2
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+ **Version:** 2.5.3
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -230,6 +230,7 @@ Available skills:
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  | `devcheck` | Lint, format, typecheck, audit |
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  | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills after `bun update --latest` |
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+ | `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR |
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  | `api-auth` | Auth modes, scopes, JWT/OAuth |
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  | `api-config` | AppConfig, parseConfig, env vars |
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  | `api-context` | Context interface, logger, state, progress |
@@ -267,7 +268,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  ## Publishing
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- After a version bump and final commit, publish to both npm and GHCR:
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+ Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, and GHCR, halting on the first failure. For reference, the underlying commands are:
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  ```bash
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  bun publish --access public
@@ -276,9 +277,9 @@ docker buildx build --platform linux/amd64,linux/arm64 \
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  -t ghcr.io/cyanheads/pubmed-mcp-server:<version> \
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  -t ghcr.io/cyanheads/pubmed-mcp-server:latest \
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  --push .
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- ```
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- Remind the user to run these after completing a release flow.
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+ mcp-publisher publish
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+ ```
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  ---
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@@ -297,10 +298,15 @@ import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
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  ## Checklist
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- - [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, etc.)
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+ - [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, `z.bigint()`, `z.symbol()`, `z.void()`, `z.map()`, `z.set()`, `z.function()`, `z.nan()`)
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+ - [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`)
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  - [ ] JSDoc `@fileoverview` + `@module` on every file
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  - [ ] `ctx.log` for logging, `ctx.state` for storage
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  - [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
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+ - [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Claude Code → `structuredContent`, Claude Desktop → `content[]`); both must carry the same data
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+ - [ ] NCBI wrapping: raw/domain/output schemas reviewed against real upstream sparsity/nullability before finalizing required vs optional fields
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+ - [ ] NCBI wrapping: normalization and `format()` preserve uncertainty; do not fabricate facts from missing upstream data
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+ - [ ] NCBI wrapping: tests include at least one sparse payload case with omitted upstream fields
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  - [ ] Registered in `createApp()` arrays (directly or via barrel exports)
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  - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
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  - [ ] `bun run devcheck` passes
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.5.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.5.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@cyanheads/pubmed-mcp-server",
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- "version": "2.5.2",
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+ "version": "2.5.3",
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  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
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  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
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  "type": "module",
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  "access": "public"
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  },
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  "dependencies": {
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- "@cyanheads/mcp-ts-core": "^0.6.8",
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+ "@cyanheads/mcp-ts-core": "^0.6.10",
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  "fast-xml-parser": "^5.7.1",
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  "pino-pretty": "^13.1.3",
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  "sanitize-html": "^2.17.3"
package/server.json CHANGED
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  "url": "https://github.com/cyanheads/pubmed-mcp-server",
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  "source": "github"
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  },
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- "version": "2.5.2",
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+ "version": "2.5.3",
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  "remotes": [
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  {
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  "type": "streamable-http",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.5.2",
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+ "version": "2.5.3",
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  "packageArguments": [
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  {
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  "type": "positional",
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.5.2",
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+ "version": "2.5.3",
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  "packageArguments": [
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  {
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  "type": "positional",