@cyanheads/pubmed-mcp-server 2.5.3 → 2.5.5

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Files changed (31) hide show
  1. package/CLAUDE.md +6 -4
  2. package/README.md +1 -1
  3. package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
  4. package/dist/mcp-server/resources/definitions/database-info.resource.js +4 -2
  5. package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +4 -2
  8. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +84 -86
  11. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  13. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +58 -53
  14. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/find-related.tool.js +4 -2
  17. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/format-citations.tool.js +4 -2
  20. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +8 -4
  23. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +4 -2
  26. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/search-articles.tool.js +4 -2
  29. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  30. package/package.json +4 -3
  31. 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:** 2.5.3
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+ **Version:** 2.5.4
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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.
@@ -19,8 +19,9 @@ When the user asks what to do next, what's left, or needs direction, suggest rel
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  5. **Add tests** — scaffold tests for existing definitions using the `add-test` skill
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  6. **Field-test definitions** — exercise tools/resources/prompts with real inputs using the `field-test` skill, get a report of issues and pain points
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  7. **Run `devcheck`** — lint, format, typecheck, and security audit
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- 8. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
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- 9. **Run the `maintenance` skill** — sync skills and dependencies after framework updates
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+ 8. **Run the `security-pass` skill** — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
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+ 9. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
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+ 10. **Run the `maintenance` skill** — sync skills and dependencies after framework updates
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  Tailor suggestions to what's actually missing or stale — don't recite the full list every time.
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@@ -212,7 +213,7 @@ src/
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  Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
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- **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, re-copy to pick up changes.
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+ **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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  Available skills:
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@@ -227,6 +228,7 @@ Available skills:
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  | `add-service` | Scaffold a new service integration |
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  | `add-test` | Scaffold test file for a tool, resource, or service |
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  | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
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+ | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
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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` |
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-2.5.3-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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+ [![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-2.5.5-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/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"database-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkBrD,eAAO,MAAM,oBAAoB;;;;;;;;;;kBA+C/B,CAAC"}
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+ {"version":3,"file":"database-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoBrD,eAAO,MAAM,oBAAoB;;;;;;;;;;kBA+C/B,CAAC"}
package/dist/mcp-server/resources/definitions/database-info.resource.js CHANGED
@@ -6,11 +6,13 @@
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  import { resource, z } from '@cyanheads/mcp-ts-core';
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  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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  import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
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- const FieldSchema = z.object({
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+ const FieldSchema = z
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+ .object({
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  name: z.string().describe('Short field name used in queries'),
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  fullName: z.string().optional().describe('Full display name'),
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  description: z.string().optional().describe('Field description'),
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- });
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+ })
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+ .describe('Searchable field entry');
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  const OutputSchema = z.object({
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  dbName: z.string().describe('Database name'),
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  description: z.string().optional().describe('Database description'),
package/dist/mcp-server/resources/definitions/database-info.resource.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA+EzB,CAAC"}
1
+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBAiFzB,CAAC"}
package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED
@@ -23,13 +23,15 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
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  }),
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  output: z.object({
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  records: z
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- .array(z.object({
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+ .array(z
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+ .object({
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  requestedId: z.string().describe('The ID that was submitted'),
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  pmid: z.string().optional().describe('PubMed ID'),
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  pmcid: z.string().optional().describe('PubMed Central ID'),
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  doi: z.string().optional().describe('Digital Object Identifier'),
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  errmsg: z.string().optional().describe('Error message if conversion failed'),
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- }))
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+ })
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+ .describe('Per-ID conversion record'))
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  .describe('Conversion results, one per input ID'),
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  totalConverted: z.number().describe('Number of IDs successfully converted'),
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  totalSubmitted: z.number().describe('Number of IDs submitted'),
package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"convert-ids.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,gQAAgQ;IAC7Q,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,sIAAsI,CACvI;QACH,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;aAC9B,QAAQ,CACP,sFAAsF,CACvF;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACjD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAChE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;SAC7E,CAAC;aACD,QAAQ,CAAC,0BAA0B,CAAC,CACxC;aACA,QAAQ,CAAC,sCAAsC,CAAC;QACnD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KAC/D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAE9F,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9B,WAAW,EAAE,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC;YACtC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;YACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;SAC5D,CAAC,CAAC,CAAC;QAEJ,MAAM,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC/D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,cAAc;YACd,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;IACvE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;YAClE,EAAE;YACF,+CAA+C;YAC/C,4BAA4B;SAC7B,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,MAAM,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CACrG,CAAC;QACJ,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4P5B,CAAC"}
1
+ {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2J5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -9,6 +9,89 @@ import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.
9
9
  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
10
10
  import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
11
11
  import { pmidStringSchema } from './_schemas.js';
12
+ const AuthorSchema = z
13
+ .object({
14
+ lastName: z.string().optional().describe('Last name'),
15
+ firstName: z.string().optional().describe('First/given name'),
16
+ initials: z.string().optional().describe('Author initials'),
17
+ collectiveName: z.string().optional().describe('Group/collective author name'),
18
+ affiliationIndices: z
19
+ .array(z.number())
20
+ .optional()
21
+ .describe('Indices into the top-level affiliations array'),
22
+ orcid: z.string().optional().describe('ORCID identifier'),
23
+ })
24
+ .describe('Author record');
25
+ const JournalPublicationDateSchema = z
26
+ .object({
27
+ year: z.string().optional().describe('Publication year'),
28
+ month: z.string().optional().describe('Publication month'),
29
+ day: z.string().optional().describe('Publication day'),
30
+ medlineDate: z.string().optional().describe('Non-standard date string (e.g. "2000 Spring")'),
31
+ })
32
+ .describe('Journal publication date');
33
+ const JournalInfoSchema = z
34
+ .object({
35
+ title: z.string().optional().describe('Full journal title'),
36
+ isoAbbreviation: z.string().optional().describe('ISO journal abbreviation'),
37
+ issn: z.string().optional().describe('Print ISSN'),
38
+ eIssn: z.string().optional().describe('Electronic ISSN'),
39
+ volume: z.string().optional().describe('Volume number'),
40
+ issue: z.string().optional().describe('Issue number'),
41
+ pages: z.string().optional().describe('Page range (e.g. "48-55")'),
42
+ publicationDate: JournalPublicationDateSchema.optional(),
43
+ })
44
+ .describe('Journal information');
45
+ const MeshQualifierSchema = z
46
+ .object({
47
+ qualifierName: z.string().describe('Qualifier/subheading name'),
48
+ qualifierUi: z.string().optional().describe('Qualifier unique ID'),
49
+ isMajorTopic: z.boolean().describe('Whether this qualifier is a major topic'),
50
+ })
51
+ .describe('MeSH qualifier/subheading');
52
+ const MeshTermSchema = z
53
+ .object({
54
+ descriptorName: z.string().optional().describe('MeSH descriptor name'),
55
+ descriptorUi: z.string().optional().describe('MeSH descriptor unique ID'),
56
+ isMajorTopic: z.boolean().describe('Whether this is a major topic of the article'),
57
+ qualifiers: z.array(MeshQualifierSchema).optional().describe('MeSH qualifiers/subheadings'),
58
+ })
59
+ .describe('MeSH descriptor term');
60
+ const GrantSchema = z
61
+ .object({
62
+ grantId: z.string().optional().describe('Grant identifier'),
63
+ acronym: z.string().optional().describe('Grant acronym'),
64
+ agency: z.string().optional().describe('Funding agency'),
65
+ country: z.string().optional().describe('Agency country'),
66
+ })
67
+ .describe('Grant record');
68
+ const ArticleDateSchema = z
69
+ .object({
70
+ dateType: z.string().optional().describe('Date type'),
71
+ year: z.string().optional().describe('Year'),
72
+ month: z.string().optional().describe('Month'),
73
+ day: z.string().optional().describe('Day'),
74
+ })
75
+ .describe('Dated article event');
76
+ const FetchedArticleSchema = z
77
+ .object({
78
+ pmid: z.string().optional().describe('PubMed ID'),
79
+ title: z.string().optional().describe('Article title'),
80
+ abstractText: z.string().optional().describe('Abstract text'),
81
+ affiliations: z.array(z.string()).optional().describe('Deduplicated author affiliations'),
82
+ authors: z.array(AuthorSchema).optional().describe('Author list'),
83
+ journalInfo: JournalInfoSchema.optional(),
84
+ doi: z.string().optional().describe('DOI'),
85
+ pmcId: z.string().optional().describe('PMC ID'),
86
+ pubmedUrl: z.string().optional().describe('PubMed article URL'),
87
+ pmcUrl: z.string().optional().describe('PMC full text URL'),
88
+ publicationTypes: z.array(z.string()).optional().describe('Publication types'),
89
+ keywords: z.array(z.string()).optional().describe('Keywords'),
90
+ meshTerms: z.array(MeshTermSchema).optional().describe('MeSH terms'),
91
+ grantList: z.array(GrantSchema).optional().describe('Grant information'),
92
+ articleDates: z.array(ArticleDateSchema).optional().describe('Article dates'),
93
+ })
94
+ .describe('Parsed PubMed article');
12
95
  export const fetchArticlesTool = tool('pubmed_fetch_articles', {
13
96
  description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.',
14
97
  annotations: { readOnlyHint: true, openWorldHint: true },
@@ -20,92 +103,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
20
103
  includeGrants: z.boolean().default(false).describe('Include grant information'),
21
104
  }),
22
105
  output: z.object({
23
- articles: z
24
- .array(z.object({
25
- pmid: z.string().optional().describe('PubMed ID'),
26
- title: z.string().optional().describe('Article title'),
27
- abstractText: z.string().optional().describe('Abstract text'),
28
- affiliations: z.array(z.string()).optional().describe('Deduplicated author affiliations'),
29
- authors: z
30
- .array(z.object({
31
- lastName: z.string().optional().describe('Last name'),
32
- firstName: z.string().optional().describe('First/given name'),
33
- initials: z.string().optional().describe('Author initials'),
34
- collectiveName: z.string().optional().describe('Group/collective author name'),
35
- affiliationIndices: z
36
- .array(z.number())
37
- .optional()
38
- .describe('Indices into the top-level affiliations array'),
39
- orcid: z.string().optional().describe('ORCID identifier'),
40
- }))
41
- .optional()
42
- .describe('Author list'),
43
- journalInfo: z
44
- .object({
45
- title: z.string().optional().describe('Full journal title'),
46
- isoAbbreviation: z.string().optional().describe('ISO journal abbreviation'),
47
- issn: z.string().optional().describe('Print ISSN'),
48
- eIssn: z.string().optional().describe('Electronic ISSN'),
49
- volume: z.string().optional().describe('Volume number'),
50
- issue: z.string().optional().describe('Issue number'),
51
- pages: z.string().optional().describe('Page range (e.g. "48-55")'),
52
- publicationDate: z
53
- .object({
54
- year: z.string().optional().describe('Publication year'),
55
- month: z.string().optional().describe('Publication month'),
56
- day: z.string().optional().describe('Publication day'),
57
- medlineDate: z
58
- .string()
59
- .optional()
60
- .describe('Non-standard date string (e.g. "2000 Spring")'),
61
- })
62
- .optional()
63
- .describe('Journal publication date'),
64
- })
65
- .optional()
66
- .describe('Journal information'),
67
- doi: z.string().optional().describe('DOI'),
68
- pmcId: z.string().optional().describe('PMC ID'),
69
- pubmedUrl: z.string().optional().describe('PubMed article URL'),
70
- pmcUrl: z.string().optional().describe('PMC full text URL'),
71
- publicationTypes: z.array(z.string()).optional().describe('Publication types'),
72
- keywords: z.array(z.string()).optional().describe('Keywords'),
73
- meshTerms: z
74
- .array(z.object({
75
- descriptorName: z.string().optional().describe('MeSH descriptor name'),
76
- descriptorUi: z.string().optional().describe('MeSH descriptor unique ID'),
77
- isMajorTopic: z.boolean().describe('Whether this is a major topic of the article'),
78
- qualifiers: z
79
- .array(z.object({
80
- qualifierName: z.string().describe('Qualifier/subheading name'),
81
- qualifierUi: z.string().optional().describe('Qualifier unique ID'),
82
- isMajorTopic: z.boolean().describe('Whether this qualifier is a major topic'),
83
- }))
84
- .optional()
85
- .describe('MeSH qualifiers/subheadings'),
86
- }))
87
- .optional()
88
- .describe('MeSH terms'),
89
- grantList: z
90
- .array(z.object({
91
- grantId: z.string().optional().describe('Grant identifier'),
92
- acronym: z.string().optional().describe('Grant acronym'),
93
- agency: z.string().optional().describe('Funding agency'),
94
- country: z.string().optional().describe('Agency country'),
95
- }))
96
- .optional()
97
- .describe('Grant information'),
98
- articleDates: z
99
- .array(z.object({
100
- dateType: z.string().optional().describe('Date type'),
101
- year: z.string().optional().describe('Year'),
102
- month: z.string().optional().describe('Month'),
103
- day: z.string().optional().describe('Day'),
104
- }))
105
- .optional()
106
- .describe('Article dates'),
107
- }))
108
- .describe('Parsed articles'),
106
+ articles: z.array(FetchedArticleSchema).describe('Parsed articles'),
109
107
  totalReturned: z.number().describe('Number of articles returned'),
110
108
  unavailablePmids: z
111
109
  .array(z.string())
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2O5B,CAAC"}
1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAqL5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -27,17 +27,70 @@ function filterSections(sections, sectionFilter) {
27
27
  return sections.filter((s) => s.title && lowerFilter.some((f) => s.title?.toLowerCase().includes(f)));
28
28
  }
29
29
  // ─── Tool Definition ─────────────────────────────────────────────────────────
30
- const SubsectionSchema = z.object({
30
+ const SubsectionSchema = z
31
+ .object({
31
32
  title: z.string().optional().describe('Subsection heading'),
32
33
  label: z.string().optional().describe('Subsection label'),
33
34
  text: z.string().describe('Subsection body text'),
34
- });
35
- const SectionSchema = z.object({
35
+ })
36
+ .describe('Article subsection');
37
+ const SectionSchema = z
38
+ .object({
36
39
  title: z.string().optional().describe('Section heading'),
37
40
  label: z.string().optional().describe('Section label'),
38
41
  text: z.string().describe('Section body text'),
39
42
  subsections: z.array(SubsectionSchema).optional().describe('Nested subsections'),
40
- });
43
+ })
44
+ .describe('Article body section');
45
+ const AuthorSchema = z
46
+ .object({
47
+ collectiveName: z.string().optional().describe('Group name'),
48
+ givenNames: z.string().optional().describe('Given names'),
49
+ lastName: z.string().optional().describe('Last name'),
50
+ })
51
+ .describe('Author entry');
52
+ const JournalSchema = z
53
+ .object({
54
+ title: z.string().optional().describe('Journal title'),
55
+ issn: z.string().optional().describe('ISSN'),
56
+ volume: z.string().optional().describe('Volume number'),
57
+ issue: z.string().optional().describe('Issue number'),
58
+ pages: z.string().optional().describe('Page range'),
59
+ })
60
+ .describe('Journal information');
61
+ const ReferenceSchema = z
62
+ .object({
63
+ citation: z.string().describe('Citation text'),
64
+ id: z.string().optional().describe('Reference ID'),
65
+ label: z.string().optional().describe('Reference label'),
66
+ })
67
+ .describe('Reference entry');
68
+ const PublicationDateSchema = z
69
+ .object({
70
+ year: z.string().optional().describe('Publication year'),
71
+ month: z.string().optional().describe('Publication month'),
72
+ day: z.string().optional().describe('Publication day'),
73
+ })
74
+ .describe('Publication date');
75
+ const FulltextArticleSchema = z
76
+ .object({
77
+ pmcId: z.string().describe('PMC ID'),
78
+ pmcUrl: z.string().describe('PMC URL'),
79
+ pmid: z.string().optional().describe('PubMed ID'),
80
+ pubmedUrl: z.string().optional().describe('PubMed URL'),
81
+ title: z.string().optional().describe('Article title'),
82
+ abstract: z.string().optional().describe('Abstract'),
83
+ authors: z.array(AuthorSchema).optional().describe('Authors'),
84
+ doi: z.string().optional().describe('DOI'),
85
+ journal: JournalSchema.optional(),
86
+ keywords: z.array(z.string()).optional().describe('Keywords'),
87
+ sections: z.array(SectionSchema).describe('Article body sections'),
88
+ references: z.array(ReferenceSchema).optional().describe('Reference list'),
89
+ articleType: z.string().optional().describe('Article type'),
90
+ affiliations: z.array(z.string()).optional().describe('Author affiliations'),
91
+ publicationDate: PublicationDateSchema.optional(),
92
+ })
93
+ .describe('Full-text PMC article');
41
94
  export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
42
95
  description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via the PMC ID Converter).',
43
96
  annotations: { readOnlyHint: true, openWorldHint: true },
@@ -70,55 +123,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
70
123
  .describe('Filter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"])'),
71
124
  }),
72
125
  output: z.object({
73
- articles: z
74
- .array(z.object({
75
- pmcId: z.string().describe('PMC ID'),
76
- pmcUrl: z.string().describe('PMC URL'),
77
- pmid: z.string().optional().describe('PubMed ID'),
78
- pubmedUrl: z.string().optional().describe('PubMed URL'),
79
- title: z.string().optional().describe('Article title'),
80
- abstract: z.string().optional().describe('Abstract'),
81
- authors: z
82
- .array(z.object({
83
- collectiveName: z.string().optional().describe('Group name'),
84
- givenNames: z.string().optional().describe('Given names'),
85
- lastName: z.string().optional().describe('Last name'),
86
- }))
87
- .optional()
88
- .describe('Authors'),
89
- doi: z.string().optional().describe('DOI'),
90
- journal: z
91
- .object({
92
- title: z.string().optional().describe('Journal title'),
93
- issn: z.string().optional().describe('ISSN'),
94
- volume: z.string().optional().describe('Volume number'),
95
- issue: z.string().optional().describe('Issue number'),
96
- pages: z.string().optional().describe('Page range'),
97
- })
98
- .optional()
99
- .describe('Journal information'),
100
- keywords: z.array(z.string()).optional().describe('Keywords'),
101
- sections: z.array(SectionSchema).describe('Article body sections'),
102
- references: z
103
- .array(z.object({
104
- citation: z.string().describe('Citation text'),
105
- id: z.string().optional().describe('Reference ID'),
106
- label: z.string().optional().describe('Reference label'),
107
- }))
108
- .optional()
109
- .describe('Reference list'),
110
- articleType: z.string().optional().describe('Article type'),
111
- affiliations: z.array(z.string()).optional().describe('Author affiliations'),
112
- publicationDate: z
113
- .object({
114
- year: z.string().optional().describe('Publication year'),
115
- month: z.string().optional().describe('Publication month'),
116
- day: z.string().optional().describe('Publication day'),
117
- })
118
- .optional()
119
- .describe('Publication date'),
120
- }))
121
- .describe('Full-text articles'),
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+ articles: z.array(FulltextArticleSchema).describe('Full-text articles'),
122
127
  totalReturned: z.number().describe('Number of articles returned'),
123
128
  unavailablePmids: z.array(z.string()).optional().describe('PMIDs not available in PMC'),
124
129
  unavailablePmcIds: z.array(z.string()).optional().describe('PMC IDs that returned no data'),
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBAoK1B,CAAC"}
1
+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBAsK1B,CAAC"}
package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED
@@ -34,7 +34,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
34
34
  sourcePmid: z.string().describe('Source PubMed ID'),
35
35
  relationship: z.enum(['similar', 'cited_by', 'references']).describe('Relationship type used'),
36
36
  articles: z
37
- .array(z.object({
37
+ .array(z
38
+ .object({
38
39
  pmid: z.string().describe('PubMed ID'),
39
40
  title: z.string().optional().describe('Article title'),
40
41
  authors: z.string().optional().describe('Author string'),
@@ -44,7 +45,8 @@ export const findRelatedTool = tool('pubmed_find_related', {
44
45
  .number()
45
46
  .optional()
46
47
  .describe('NCBI relevance score (arbitrary scale, higher = more related; only present for similar)'),
47
- }))
48
+ })
49
+ .describe('Related article with enriched summary'))
48
50
  .describe('Related articles'),
49
51
  totalFound: z.number().describe('Total related articles found before truncation'),
50
52
  }),
package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBA0F9B,CAAC"}
1
+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBA4F9B,CAAC"}
package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED
@@ -24,11 +24,13 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
24
24
  }),
25
25
  output: z.object({
26
26
  citations: z
27
- .array(z.object({
27
+ .array(z
28
+ .object({
28
29
  pmid: z.string().describe('PubMed ID'),
29
30
  title: z.string().optional().describe('Article title'),
30
31
  citations: z.record(z.string(), z.string()).describe('Citations keyed by style'),
31
- }))
32
+ })
33
+ .describe('Citations for a single article'))
32
34
  .describe('Citations per article'),
33
35
  totalSubmitted: z.number().describe('Number of PMIDs submitted for citation formatting'),
34
36
  totalFormatted: z.number().describe('Number of PMIDs successfully formatted'),
package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBA2H7B,CAAC"}
1
+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBA+H7B,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED
@@ -13,7 +13,8 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
13
13
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
14
14
  input: z.object({
15
15
  citations: z
16
- .array(z.object({
16
+ .array(z
17
+ .object({
17
18
  journal: z
18
19
  .string()
19
20
  .optional()
@@ -29,14 +30,16 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
29
30
  .string()
30
31
  .optional()
31
32
  .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
32
- }))
33
+ })
34
+ .describe('Citation to match against PubMed'))
33
35
  .min(1)
34
36
  .max(25)
35
37
  .describe('Citations to look up. More fields = better match accuracy.'),
36
38
  }),
37
39
  output: z.object({
38
40
  results: z
39
- .array(z.object({
41
+ .array(z
42
+ .object({
40
43
  key: z.string().describe('Citation tracking key'),
41
44
  pmid: z.string().optional().describe('Matched PubMed ID'),
42
45
  matched: z.boolean().describe('Whether a PMID was found'),
@@ -47,7 +50,8 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
47
50
  .string()
48
51
  .optional()
49
52
  .describe('Additional detail returned by ECitMatch for non-exact matches'),
50
- }))
53
+ })
54
+ .describe('Per-citation match result'))
51
55
  .describe('Match results, one per input citation'),
52
56
  totalMatched: z.number().describe('Number of citations with PMID matches'),
53
57
  totalSubmitted: z.number().describe('Number of citations submitted'),
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,sPAAsP;IACnQ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,EAAE,cAAc,CAAC,CAAC;IACnF,SAAS,EACP,mHAAmH;IAErH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;YACvE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACvD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8EAA8E,CAC/E;SACJ,CAAC;aACD,QAAQ,CAAC,kCAAkC,CAAC,CAChD;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YACzD,MAAM,EAAE,CAAC;iBACN,IAAI,CAAC,CAAC,SAAS,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC;iBAC3C,QAAQ,CAAC,iDAAiD,CAAC;YAC9D,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,+DAA+D,CAAC;SAC7E,CAAC;aACD,QAAQ,CAAC,2BAA2B,CAAC,CACzC;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YAChC,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;gBACxE,MAAM,IAAI,KAAK,CACb,gHAAgH,CACjH,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,OAAO,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjC,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,GAAG,CAAC,CAAC,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;SACtC,CAAC,CAAC,CAAC;QAEJ,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAC5D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE;YAC/C,YAAY;YACZ,cAAc,EAAE,SAAS,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,cAAc,EAAE,SAAS,CAAC,MAAM,EAAE,CAAC;IAC7E,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,4BAA4B;YAC5B,gBAAgB,MAAM,CAAC,YAAY,IAAI,MAAM,CAAC,cAAc,EAAE;SAC/D,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YAC7B,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC9C,IAAI,CAAC,CAAC,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACpD,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,6EAA6E,CAAC,CAAC;gBAC1F,SAAS;YACX,CAAC;YAED,IAAI,CAAC,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBAC7B,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;gBACpC,KAAK,CAAC,IAAI,CACR,8GAA8G,CAC/G,CAAC;gBACF,SAAS;YACX,CAAC;YAED,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,2EAA2E,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;kBAyFzB,CAAC"}
1
+ {"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;kBA2FzB,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js CHANGED
@@ -89,13 +89,15 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
89
89
  output: z.object({
90
90
  term: z.string().describe('Original search term'),
91
91
  results: z
92
- .array(z.object({
92
+ .array(z
93
+ .object({
93
94
  meshId: z.string().describe('MeSH descriptor unique identifier'),
94
95
  name: z.string().describe('Descriptor name'),
95
96
  treeNumbers: z.array(z.string()).optional().describe('MeSH tree numbers'),
96
97
  scopeNote: z.string().optional().describe('Scope note'),
97
98
  entryTerms: z.array(z.string()).optional().describe('Synonyms / entry terms'),
98
- }))
99
+ })
100
+ .describe('Matching MeSH descriptor record'))
99
101
  .describe('Matching MeSH records'),
100
102
  }),
101
103
  async handler(input, ctx) {
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8S7B,CAAC"}
1
+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAgT7B,CAAC"}
package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED
@@ -127,7 +127,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
127
127
  offset: z.number().describe('Result offset used'),
128
128
  pmids: z.array(z.string()).describe('PubMed IDs'),
129
129
  summaries: z
130
- .array(z.object({
130
+ .array(z
131
+ .object({
131
132
  pmid: z.string().describe('PubMed ID'),
132
133
  title: z.string().optional().describe('Article title'),
133
134
  authors: z.string().optional().describe('Formatted author string'),
@@ -137,7 +138,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
137
138
  pmcId: z.string().optional().describe('PMC ID'),
138
139
  pmcUrl: z.string().optional().describe('PMC URL'),
139
140
  pubmedUrl: z.string().optional().describe('PubMed URL'),
140
- }))
141
+ })
142
+ .describe('Brief article summary'))
141
143
  .describe('Brief summaries (empty array when summaryCount is 0)'),
142
144
  searchUrl: z.string().describe('PubMed search URL'),
143
145
  notice: z
package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.5.3",
3
+ "version": "2.5.5",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
6
6
  "type": "module",
@@ -19,6 +19,7 @@
19
19
  "format": "biome check --write --unsafe",
20
20
  "test": "bunx vitest run",
21
21
  "lint:mcp": "bun run scripts/lint-mcp.ts",
22
+ "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
22
23
  "dev:stdio": "MCP_TRANSPORT_TYPE=stdio bun --watch src/index.ts",
23
24
  "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",
24
25
  "start:stdio": "MCP_TRANSPORT_TYPE=stdio bun ./dist/index.js",
@@ -67,13 +68,13 @@
67
68
  "access": "public"
68
69
  },
69
70
  "dependencies": {
70
- "@cyanheads/mcp-ts-core": "^0.6.10",
71
+ "@cyanheads/mcp-ts-core": "^0.7.0",
71
72
  "fast-xml-parser": "^5.7.1",
72
73
  "pino-pretty": "^13.1.3",
73
74
  "sanitize-html": "^2.17.3"
74
75
  },
75
76
  "devDependencies": {
76
- "@biomejs/biome": "^2.4.12",
77
+ "@biomejs/biome": "^2.4.13",
77
78
  "@types/node": "^25.6.0",
78
79
  "@types/sanitize-html": "^2.16.1",
79
80
  "@vitest/coverage-istanbul": "^4.1.5",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.5.3",
9
+ "version": "2.5.5",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.5.3",
22
+ "version": "2.5.5",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -60,7 +60,7 @@
60
60
  "registryBaseUrl": "https://registry.npmjs.org",
61
61
  "identifier": "@cyanheads/pubmed-mcp-server",
62
62
  "runtimeHint": "bun",
63
- "version": "2.5.3",
63
+ "version": "2.5.5",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",