@cyanheads/pubmed-mcp-server 2.7.8 → 2.7.10
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.
- package/AGENTS.md +7 -2
- package/CLAUDE.md +7 -2
- package/README.md +5 -5
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +4 -4
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +6 -1
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +11 -1
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/package.json +5 -4
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,8 +1,8 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.7.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.
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**Version:** 2.7.10
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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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.
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@@ -269,8 +269,10 @@ Available skills:
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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| `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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| `api-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `api-context` | Context interface, logger, state, progress |
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| `api-errors` | McpError, JsonRpcErrorCode, error patterns |
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@@ -283,6 +285,8 @@ Available skills:
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| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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---
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| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
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| `bun run list-skills` | List skills in `skills/` with name + description |
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| `bun run bundle` | Build and pack as `dist/pubmed-mcp-server.mcpb` for one-click Claude Desktop install |
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| `bun run release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |
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| `bun run start:stdio` | Production mode (stdio) |
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| `bun run start:http` | Production mode (HTTP) |
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package/CLAUDE.md
CHANGED
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.7.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.
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**Version:** 2.7.10
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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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.
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@@ -269,8 +269,10 @@ Available skills:
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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| `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
|
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275
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+
| `api-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `api-context` | Context interface, logger, state, progress |
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| `api-errors` | McpError, JsonRpcErrorCode, error patterns |
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@@ -283,6 +285,8 @@ Available skills:
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| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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+
**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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+
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When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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291
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---
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@@ -303,6 +307,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
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| `bun run list-skills` | List skills in `skills/` with name + description |
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| `bun run bundle` | Build and pack as `dist/pubmed-mcp-server.mcpb` for one-click Claude Desktop install |
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| `bun run release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |
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| `bun run start:stdio` | Production mode (stdio) |
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| `bun run start:http` | Production mode (HTTP) |
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package/README.md
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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```json
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{
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"mcpServers": {
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"pubmed": {
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"pubmed-mcp-server": {
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"type": "streamable-http",
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"url": "https://pubmed.caseyjhand.com/mcp"
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}
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```json
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{
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"mcpServers": {
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"pubmed": {
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"pubmed-mcp-server": {
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"type": "stdio",
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"command": "bunx",
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"args": ["@cyanheads/pubmed-mcp-server@latest"],
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```json
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{
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"mcpServers": {
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"pubmed": {
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"pubmed-mcp-server": {
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"type": "stdio",
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"args": ["-y", "@cyanheads/pubmed-mcp-server@latest"],
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```json
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"mcpServers": {
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"pubmed": {
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"pubmed-mcp-server": {
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"command": "docker",
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"args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubmed-mcp-server:latest"]
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.filter((s) => s.length > 0 && s !== 'et');
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}
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export const lookupCitationTool = tool('pubmed_lookup_citation', {
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description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least
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description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
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.optional()
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.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
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})
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.describe('Citation to match against PubMed. Must include at least
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.refine((c) => !!(c.journal || c.year
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message: 'Each citation must include at least
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.describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
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.refine((c) => !!(c.journal || c.year), {
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message: 'Each citation must include at least a journal or year field — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.',
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}))
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.min(1)
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.max(25)
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+
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,2FAA2F;AAC3F,SAAS,cAAc,CAAC,OAAe;IACrC,OAAO,OAAO;SACX,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;SACtB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC;AAC/C,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,qbAAqb;IAClc,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,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,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,CACP,mLAAmL,CACpL;aACA,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,EAAE;YACtC,OAAO,EACL,uKAAuK;SAC1K,CAAC,CACL;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;YAC5E,cAAc,EAAE,CAAC;iBACd,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;iBAClC,QAAQ,EAAE;iBACV,QAAQ,CACP,sMAAsM,CACvM;YACH,kBAAkB,EAAE,CAAC;iBAClB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,sGAAsG,CACvG;YACH,QAAQ,EAAE,CAAC;iBACR,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,IAAI,CAAC,CAAC,iBAAiB,EAAE,eAAe,CAAC,CAAC;qBAC1C,QAAQ,CAAC,+BAA+B,CAAC;gBAC5C,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;aAC1E,CAAC;iBACD,QAAQ,CAAC,mCAAmC,CAAC,CACjD;iBACA,QAAQ,EAAE;iBACV,QAAQ,CACP,yLAAyL,CAC1L;SACJ,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;QACpE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CAAC,6DAA6D,CAAC;KAC3E,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,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,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAExE,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACrD,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACnD,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;YAC1B,IAAI,CAAC,CAAC,UAAU;gBAAE,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC;YAC9D,IAAI,CAAC,CAAC,IAAI;gBAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC;QAClD,CAAC;QAED,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAC7B,IAAI,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAc,CAAC,CAAC,CACjF,CAAC;QAEF,MAAM,aAAa,GAAG,IAAI,GAAG,EAAkD,CAAC;QAChF,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAC5C,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;YACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;YAC7D,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE;oBACxB,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;oBACxC,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;iBACzC,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAkBD,MAAM,MAAM,GAAmB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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;
|
|
1
|
+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAyClB;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC;IA8ClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}
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@@ -4,7 +4,7 @@
|
|
|
4
4
|
* retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
|
|
5
5
|
* @module src/services/ncbi/api-client
|
|
6
6
|
*/
|
|
7
|
-
import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
7
|
+
import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
8
|
import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
|
|
9
9
|
import { recoveryFor } from '../../services/error-contracts.js';
|
|
10
10
|
import { NCBI_EUTILS_BASE_URL } from './types.js';
|
|
@@ -33,6 +33,11 @@ export class NcbiApiClient {
|
|
|
33
33
|
if (!response.ok) {
|
|
34
34
|
throw await httpErrorFromResponse(response, {
|
|
35
35
|
service: 'NCBI',
|
|
36
|
+
// NCBI's eutils proxy returns HTTP 500 for transient mesh-layer failures
|
|
37
|
+
// that are safe to retry. Reclassify as ServiceUnavailable so the retry
|
|
38
|
+
// loop in NcbiService.withRetry picks it up — 501 (Not Implemented) is
|
|
39
|
+
// left as InternalError since those are not transient.
|
|
40
|
+
codeOverride: (s) => (s === 500 ? JsonRpcErrorCode.ServiceUnavailable : undefined),
|
|
36
41
|
data: { endpoint },
|
|
37
42
|
});
|
|
38
43
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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AAG,EAAE;YACvD,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;YACJ,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC,CAAC;IACL,CAAC;CACF"}
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;
|
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1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAoE7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAwD7B,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
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@@ -139,7 +139,7 @@ export class NcbiService {
|
|
|
139
139
|
.map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
|
|
140
140
|
.join('\r');
|
|
141
141
|
const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
|
|
142
|
-
|
|
142
|
+
const parsed = text
|
|
143
143
|
.split(/[\r\n]+/)
|
|
144
144
|
.filter((line) => line.trim().length > 0)
|
|
145
145
|
.map((line) => {
|
|
@@ -174,6 +174,16 @@ export class NcbiService {
|
|
|
174
174
|
...(rawOutcome && { detail: rawOutcome }),
|
|
175
175
|
};
|
|
176
176
|
});
|
|
177
|
+
// ECitMatch omits lines for citations it cannot classify. Reconcile against
|
|
178
|
+
// the submitted citations so every input gets a result row — callers can rely
|
|
179
|
+
// on results.length === citations.length and correlate by key.
|
|
180
|
+
const parsedByKey = new Map(parsed.map((r) => [r.key, r]));
|
|
181
|
+
return citations.map((c) => parsedByKey.get(c.key) ?? {
|
|
182
|
+
key: c.key,
|
|
183
|
+
matched: false,
|
|
184
|
+
pmid: null,
|
|
185
|
+
status: 'not_found',
|
|
186
|
+
});
|
|
177
187
|
}
|
|
178
188
|
/**
|
|
179
189
|
* Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
|
|
@@ -1 +1 @@
|
|
|
1
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-
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1
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ACtC,MAAM,CAAC,OAAO,CACZ,mBAAmB,KAAK,sBAAsB,OAAO,GAAG,CAAC,IAAI,IAAI,CAAC,UAAU,QAAQ,UAAU,KAAK,EACnG,qBAAqB,CAAC,oBAAoB,CAAC;wBACzC,SAAS,EAAE,WAAW;wBACtB,QAAQ,EAAE,KAAK;wBACf,OAAO,EAAE,OAAO,GAAG,CAAC;wBACpB,UAAU;qBACX,CAAC,CACH,CAAC;oBACF,MAAM,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;oBACzC,SAAS;gBACX,CAAC;gBAED,MAAM,QAAQ,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC;gBACrC,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;gBACnE,gFAAgF;gBAChF,8EAA8E;gBAC9E,kFAAkF;gBAClF,yDAAyD;gBACzD,MAAM,MAAM,GACV,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,SAAS,CAAC;gBACtF,MAAM,IAAI,QAAQ,CAChB,KAAK,CAAC,IAAI,EACV,GAAG,GAAG,kBAAkB,QAAQ,YAAY,EAC5C;oBACE,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;oBACjD,QAAQ,EAAE,KAAK;oBACf,QAAQ;iBACT,EACD,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,aAAa,CAAC,mCAAmC,EAAE;YACvD,MAAM,EAAE,kBAAkB;YAC1B,QAAQ,EAAE,KAAK;YACf,GAAG,WAAW,CAAC,kBAAkB,CAAC;SACnC,CAAC,CAAC;IACL,CAAC;IAED;;;;;;;;OAQG;IACK,cAAc,CACpB,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,OAAO,IAAI,CAAC,eAAe,CACzB,CAAC,MAAM,EAAE,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,OAAO,CAChB,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CACZ,KAAK,IAAI,EAAE;YACT,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE;gBAC9D,GAAG,OAAO;gBACV,MAAM;aACP,CAAC,CAAC;YACH,OAAO,IAAI,CAAC,eAAe,CAAC,sBAAsB,CAAI,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;QACjF,CAAC,EACD,QAAQ,EACR,MAAM,CACP,EACH,QAAQ,EACR,MAAM,EACN,MAAM,CACP,EACH,OAAO,EAAE,MAAM,CAChB,CAAC;IACJ,CAAC;;AAGH,+EAA+E;AAE/E,IAAI,QAAiC,CAAC;AAEtC,qEAAqE;AACrE,MAAM,UAAU,eAAe;IAC7B,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;IACjC,MAAM,SAAS,GAAG,IAAI,aAAa,CAAC;QAClC,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,SAAS,EAAE,MAAM,CAAC,SAAS;QAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QAC/C,GAAG,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,UAAU,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC;KAC5D,CAAC,CAAC;IACH,MAAM,KAAK,GAAG,IAAI,gBAAgB,CAAC,MAAM,CAAC,cAAc,EAAE,MAAM,CAAC,aAAa,CAAC,CAAC;IAChF,MAAM,eAAe,GAAG,IAAI,mBAAmB,EAAE,CAAC;IAClD,QAAQ,GAAG,IAAI,WAAW,CACxB,SAAS,EACT,KAAK,EACL,eAAe,EACf,MAAM,CAAC,UAAU,EACjB,MAAM,CAAC,eAAe,CACvB,CAAC;IACF,MAAM,CAAC,IAAI,CACT,2BAA2B,EAC3B,qBAAqB,CAAC,oBAAoB,CAAC;QACzC,SAAS,EAAE,UAAU;QACrB,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM;QAC1B,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,aAAa,EAAE,MAAM,CAAC,aAAa;QACnC,eAAe,EAAE,MAAM,CAAC,eAAe;KACxC,CAAC,CACH,CAAC;AACJ,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU,cAAc;IAC5B,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,6DAA6D,CAAC,CAAC;IAC9F,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.7.
|
|
3
|
+
"version": "2.7.10",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -26,6 +26,7 @@
|
|
|
26
26
|
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubmed-mcp-server.mcpb",
|
|
27
27
|
"changelog:build": "bun run scripts/build-changelog.ts",
|
|
28
28
|
"changelog:check": "bun run scripts/build-changelog.ts --check",
|
|
29
|
+
"release:github": "bun run scripts/release-github.ts",
|
|
29
30
|
"publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
|
|
30
31
|
"start:stdio": "MCP_TRANSPORT_TYPE=stdio bun ./dist/index.js",
|
|
31
32
|
"start:http": "MCP_TRANSPORT_TYPE=http bun ./dist/index.js"
|
|
@@ -80,7 +81,7 @@
|
|
|
80
81
|
"access": "public"
|
|
81
82
|
},
|
|
82
83
|
"dependencies": {
|
|
83
|
-
"@cyanheads/mcp-ts-core": "^0.9.
|
|
84
|
+
"@cyanheads/mcp-ts-core": "^0.9.21",
|
|
84
85
|
"defuddle": "^0.18.1",
|
|
85
86
|
"fast-xml-parser": "^5.8.0",
|
|
86
87
|
"linkedom": "^0.18.12",
|
|
@@ -93,12 +94,12 @@
|
|
|
93
94
|
"@biomejs/biome": "^2.4.16",
|
|
94
95
|
"@types/node": "^25.9.1",
|
|
95
96
|
"@types/sanitize-html": "^2.16.1",
|
|
96
|
-
"@vitest/coverage-istanbul": "^4.1.
|
|
97
|
+
"@vitest/coverage-istanbul": "^4.1.8",
|
|
97
98
|
"depcheck": "^1.4.7",
|
|
98
99
|
"fast-check": "^4.8.0",
|
|
99
100
|
"ignore": "^7.0.5",
|
|
100
101
|
"tsc-alias": "^1.8.17",
|
|
101
102
|
"typescript": "^6.0.3",
|
|
102
|
-
"vitest": "^4.1.
|
|
103
|
+
"vitest": "^4.1.8"
|
|
103
104
|
}
|
|
104
105
|
}
|
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": "2.7.
|
|
9
|
+
"version": "2.7.10",
|
|
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": "2.7.
|
|
22
|
+
"version": "2.7.10",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.7.
|
|
69
|
+
"version": "2.7.10",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|