@cyanheads/pubmed-mcp-server 2.3.3 → 2.3.5
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/CLAUDE.md +1 -1
- package/README.md +2 -2
- package/dist/config/server-config.js +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +20 -6
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +7 -2
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +23 -9
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +28 -2
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +5 -5
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
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@@ -1,7 +1,7 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.3.
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**Version:** 2.3.5
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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.
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package/README.md
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@@ -7,7 +7,7 @@
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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@@ -284,7 +284,7 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
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| `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
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| `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
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| `NCBI_REQUEST_DELAY_MS` | Delay between NCBI requests in ms | 334 (100 with key) |
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| `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests |
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| `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
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| `NCBI_TIMEOUT_MS` | NCBI request timeout in ms | `30000` |
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| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
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@@ -15,7 +15,7 @@ const ServerConfigSchema = z.object({
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/** Minimum delay between NCBI requests in ms. NCBI requires ~334ms without API key. */
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requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
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/** Maximum retry attempts for failed NCBI requests. */
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maxRetries: z.coerce.number().min(0).max(10).default(
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maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
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/** Request timeout in ms. */
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timeoutMs: z.coerce
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.number()
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{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,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;
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{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,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,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;IA8ClF,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
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@@ -32,9 +32,16 @@ export class NcbiApiClient {
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? await this.postRequest(url, finalParams)
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: await this.getRequest(url, finalParams);
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if (!response.ok) {
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let code;
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if (response.status === 429) {
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code = JsonRpcErrorCode.RateLimited;
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}
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else if (response.status >= 500) {
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code = JsonRpcErrorCode.ServiceUnavailable;
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}
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else {
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code = JsonRpcErrorCode.InvalidRequest;
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}
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throw new McpError(code, `NCBI API returned HTTP ${response.status}.`, {
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endpoint,
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status: response.status,
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});
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const body = await response.text();
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let code;
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if (response.status === 429) {
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code = JsonRpcErrorCode.RateLimited;
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}
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else if (response.status >= 500) {
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code = JsonRpcErrorCode.ServiceUnavailable;
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}
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else {
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code = JsonRpcErrorCode.InvalidRequest;
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}
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throw new McpError(code, `NCBI API returned HTTP ${response.status}: ${body.substring(0, 300)}`, { url, status: response.status, body: body.substring(0, 500) });
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}
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return body;
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@@ -1 +1 @@
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-
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{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,GAAG,MAAM,EAAE,CAAC;QAE3D,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EAAE;gBACpE,QAAQ;aACA,CAAC,CAAC;YAEZ,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,CAAC;gBAC1C,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,WAAW,CAAC,CAAC;YAE5C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,IAAI,IAAY,CAAC;gBACjB,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;oBAC5B,IAAI,GAAG,gBAAgB,CAAC,WAAW,CAAC;gBACtC,CAAC;qBAAM,IAAI,QAAQ,CAAC,MAAM,IAAI,GAAG,EAAE,CAAC;oBAClC,IAAI,GAAG,gBAAgB,CAAC,kBAAkB,CAAC;gBAC7C,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,gBAAgB,CAAC,cAAc,CAAC;gBACzC,CAAC;gBACD,MAAM,IAAI,QAAQ,CAAC,IAAI,EAAE,0BAA0B,QAAQ,CAAC,MAAM,GAAG,EAAE;oBACrE,QAAQ;oBACR,MAAM,EAAE,QAAQ,CAAC,MAAM;iBACxB,CAAC,CAAC;YACL,CAAC;YAED,OAAO,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAE3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,QAAQ;aACT,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,mBAAmB,CAAC,GAAW,EAAE,MAAyB;QAC9D,MAAM,WAAW,GAA2B;YAC1C,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,CAAC;SACjE,CAAC;QACF,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;YAClD,IAAI,KAAK,IAAI,IAAI;gBAAE,WAAW,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;QACtD,CAAC;QAED,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC;QACvD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAE1C,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,8BAA8B,OAAO,EAAE,EAAE,EAAE,GAAG,EAAW,CAAC,CAAC;YACxE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,EAAE;gBACpC,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC;aACnD,CAAC,CAAC;YAEH,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAEnC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,IAAI,IAAY,CAAC;gBACjB,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;oBAC5B,IAAI,GAAG,gBAAgB,CAAC,WAAW,CAAC;gBACtC,CAAC;qBAAM,IAAI,QAAQ,CAAC,MAAM,IAAI,GAAG,EAAE,CAAC;oBAClC,IAAI,GAAG,gBAAgB,CAAC,kBAAkB,CAAC;gBAC7C,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,gBAAgB,CAAC,cAAc,CAAC;gBACzC,CAAC;gBACD,MAAM,IAAI,QAAQ,CAChB,IAAI,EACJ,0BAA0B,QAAQ,CAAC,MAAM,KAAK,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EACtE,EAAE,GAAG,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC/D,CAAC;YACJ,CAAC;YAED,OAAO,IAAI,CAAC;QACd,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAC3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,GAAG;aACJ,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAEO,WAAW,CAAC,MAAyB;QAC3C,MAAM,GAAG,GAAgD;YACvD,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU;YAC7B,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM;YAC3B,GAAG,MAAM;SACV,CAAC;QAEF,MAAM,MAAM,GAA2B,EAAE,CAAC;QAC1C,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;gBAClB,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEO,UAAU,CAAC,MAA8B,EAAE,OAA4B;QAC7E,IAAI,OAAO,EAAE,OAAO;YAAE,OAAO,IAAI,CAAC;QAClC,MAAM,WAAW,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAC3D,OAAO,WAAW,CAAC,MAAM,GAAG,cAAc,CAAC;IAC7C,CAAC;IAEO,UAAU,CAAC,GAAW,EAAE,MAA8B;QAC5D,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAClD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAC1C,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC;QAC/F,OAAO,gBAAgB,CAAC,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IAC/D,CAAC;IAEO,WAAW,CAAC,GAAW,EAAE,MAA8B;QAC7D,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QACpD,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,CAAC;QACvF,OAAO,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;YACvD,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;SACL,CAAC,CAAC;IACL,CAAC;CACF"}
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* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
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*/
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idConvert(ids: string[], idtype?: string): Promise<IdConvertRecord[]>;
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/** Error codes that are transient and worth retrying with backoff. */
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private static readonly RETRYABLE_CODES;
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/** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
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private static readonly MAX_BACKOFF_MS;
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/**
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* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
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* Non-transient
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* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
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* Non-transient McpErrors and unexpected plain Errors fail immediately.
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* Uses capped exponential backoff with jitter.
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*/
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-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAEpB;;;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;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,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,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA8C3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAEpB;;;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;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,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,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA8C3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;OAIG;YACW,SAAS;IAuCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -135,9 +135,18 @@ export class NcbiService {
|
|
|
135
135
|
}
|
|
136
136
|
return parsed.records ?? [];
|
|
137
137
|
}
|
|
138
|
+
/** Error codes that are transient and worth retrying with backoff. */
|
|
139
|
+
static RETRYABLE_CODES = new Set([
|
|
140
|
+
JsonRpcErrorCode.ServiceUnavailable,
|
|
141
|
+
JsonRpcErrorCode.Timeout,
|
|
142
|
+
JsonRpcErrorCode.RateLimited,
|
|
143
|
+
]);
|
|
144
|
+
/** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
|
|
145
|
+
static MAX_BACKOFF_MS = 30_000;
|
|
138
146
|
/**
|
|
139
|
-
* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
|
|
140
|
-
* Non-transient
|
|
147
|
+
* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
|
|
148
|
+
* Non-transient McpErrors and unexpected plain Errors fail immediately.
|
|
149
|
+
* Uses capped exponential backoff with jitter.
|
|
141
150
|
*/
|
|
142
151
|
async withRetry(execute, label) {
|
|
143
152
|
for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
|
|
@@ -145,21 +154,26 @@ export class NcbiService {
|
|
|
145
154
|
return await execute();
|
|
146
155
|
}
|
|
147
156
|
catch (error) {
|
|
148
|
-
if (error instanceof McpError) {
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
152
|
-
|
|
157
|
+
if (!(error instanceof McpError)) {
|
|
158
|
+
throw error;
|
|
159
|
+
}
|
|
160
|
+
if (!NcbiService.RETRYABLE_CODES.has(error.code)) {
|
|
161
|
+
throw error;
|
|
153
162
|
}
|
|
154
163
|
if (attempt < this.maxRetries) {
|
|
155
|
-
const
|
|
164
|
+
const baseDelay = Math.min(1000 * 2 ** attempt, NcbiService.MAX_BACKOFF_MS);
|
|
165
|
+
const jitter = baseDelay * (0.75 + 0.5 * Math.random()); // ±25%
|
|
166
|
+
const retryDelay = Math.round(jitter);
|
|
156
167
|
logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint: label, attempt: attempt + 1, retryDelay });
|
|
157
168
|
await new Promise((r) => setTimeout(r, retryDelay));
|
|
158
169
|
continue;
|
|
159
170
|
}
|
|
160
171
|
const attempts = this.maxRetries + 1;
|
|
161
172
|
const msg = error instanceof Error ? error.message : String(error);
|
|
162
|
-
throw new McpError(error
|
|
173
|
+
throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
|
|
174
|
+
endpoint: label,
|
|
175
|
+
attempts,
|
|
176
|
+
});
|
|
163
177
|
}
|
|
164
178
|
}
|
|
165
179
|
throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.js","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,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,EAWL,mBAAmB,GAIpB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,MAAM,OAAO,WAAW;IAEH;IACA;IACA;IACA;IAJnB,YACmB,SAAwB,EACxB,KAAuB,EACvB,eAAoC,EACpC,UAAkB;QAHlB,cAAS,GAAT,SAAS,CAAe;QACxB,UAAK,GAAL,KAAK,CAAkB;QACvB,oBAAe,GAAf,eAAe,CAAqB;QACpC,eAAU,GAAV,UAAU,CAAQ;IAClC,CAAC;IAEJ,KAAK,CAAC,OAAO,CAAC,MAAyB;QACrC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA2B,SAAS,EAAE,MAAM,EAAE;YACtF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC;QACxC,OAAO;YACL,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC,IAAI,CAAC;YACxC,MAAM,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC;YAC1C,QAAQ,EAAE,QAAQ,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,CAAC,IAAI,CAAC;YAC9C,GAAG,CAAC,QAAQ,CAAC,QAAQ,KAAK,SAAS,IAAI,EAAE,QAAQ,EAAE,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACvE,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC;YACjE,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YAC/C,gBAAgB,EAAE,QAAQ,CAAC,gBAAgB;YAC3C,GAAG,CAAC,QAAQ,CAAC,SAAS,KAAK,SAAS,IAAI,EAAE,SAAS,EAAE,QAAQ,CAAC,SAAS,EAAE,CAAC;YAC1E,GAAG,CAAC,QAAQ,CAAC,WAAW,KAAK,SAAS,IAAI,EAAE,WAAW,EAAE,QAAQ,CAAC,WAAW,EAAE,CAAC;SACjF,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAyB;QACtC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,KAAK,KAAK,IAAI,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC;QACvF,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA4B,UAAU,EAAE,MAAM,EAAE;YACxF,OAAO;SACR,CAAC,CAAC;QACH,OAAO,QAAQ,CAAC,cAAc,CAAC;IACjC,CAAC;IAED,MAAM,CACJ,MAAyB,EACzB,UAA8B,EAAE,OAAO,EAAE,KAAK,EAAE;QAEhD,MAAM,OAAO,GACX,OAAO,CAAC,OAAO,IAAI,CAAC,OAAO,MAAM,CAAC,EAAE,KAAK,QAAQ,IAAI,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC;QAC1F,OAAO,IAAI,CAAC,cAAc,CAAI,QAAQ,EAAE,MAAM,EAAE,EAAE,GAAG,OAAO,EAAE,OAAO,EAAE,CAAC,CAAC;IAC3E,CAAC;IAED,KAAK,CAA8B,MAAyB;QAC1D,OAAO,IAAI,CAAC,cAAc,CAAI,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,MAAyB;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA0B,QAAQ,EAAE,MAAM,EAAE;YACpF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,WAAW,GAAG,QAAQ,CAAC,YAAY,CAAC;QAC1C,MAAM,QAAQ,GAAG,WAAW,CAAC,KAAK,IAAK,MAAM,CAAC,IAAe,IAAI,EAAE,CAAC;QACpE,MAAM,SAAS,GAAG,WAAW,CAAC,cAAc,IAAI,EAAE,CAAC;QAEnD,MAAM,CAAC,KAAK,CAAC,uBAAuB,EAAE;YACpC,QAAQ;YACR,SAAS;YACT,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SACrD,CAAC,CAAC;QAEZ,OAAO;YACL,QAAQ;YACR,SAAS,EAAE,SAAS,IAAI,QAAQ;YAChC,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SAC9D,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,MAAyB;QAC7B,OAAO,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IAClE,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,SAA8B;QAC5C,MAAM,KAAK,GAAG,SAAS;aACpB,GAAG,CACF,CAAC,CAAC,EAAE,EAAE,CACJ,GAAG,CAAC,CAAC,OAAO,IAAI,EAAE,IAAI,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,IAAI,EAAE,IAAI,CAAC,CAAC,SAAS,IAAI,EAAE,IAAI,CAAC,CAAC,UAAU,IAAI,EAAE,IAAI,CAAC,CAAC,GAAG,GAAG,CAC9G;aACA,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,cAAc,CACpC,eAAe,EACf,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,EACvC,EAAE,OAAO,EAAE,MAAM,EAAE,CACpB,CAAC;QAEF,OAAO,IAAI;aACR,KAAK,CAAC,SAAS,CAAC;aAChB,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC;aACxC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE;YACZ,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YACnC,MAAM,UAAU,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YAE1C,IAAI,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC7B,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,EAAE,SAAkB,EAAE,CAAC;YAC9E,CAAC;YAED,IAAI,UAAU,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;gBACvC,OAAO;oBACL,GAAG;oBACH,OAAO,EAAE,KAAK;oBACd,IAAI,EAAE,IAAI;oBACV,MAAM,EAAE,WAAoB;oBAC5B,MAAM,EAAE,UAAU;iBACnB,CAAC;YACJ,CAAC;YAED,OAAO;gBACL,GAAG;gBACH,OAAO,EAAE,KAAK;gBACd,IAAI,EAAE,IAAI;gBACV,MAAM,EAAE,WAAoB;gBAC5B,GAAG,CAAC,UAAU,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;aAC1C,CAAC;QACJ,CAAC,CAAC,CAAC;IACP,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,GAAa,EAAE,MAAe;QAC5C,MAAM,MAAM,GAAsB;YAChC,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC;YAClB,MAAM,EAAE,MAAM;YACd,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC;QAEF,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CACnC,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CACZ,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,mBAAmB,CAAC,mBAAmB,EAAE,MAAM,CAAC,EACrE,QAAQ,CACT,EACH,QAAQ,EACR,MAAM,CACP,CAAC;QAEF,IAAI,MAAe,CAAC;QACpB,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5B,CAAC;QAAC,MAAM,CAAC;YACP,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,6CAA6C,EAC7C,EAAE,eAAe,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC5C,CAAC;QACJ,CAAC;QAED,OAAQ,MAA4B,CAAC,OAAO,IAAI,EAAE,CAAC;IACrD,CAAC;IAED
|
|
1
|
+
{"version":3,"file":"ncbi-service.js","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,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,EAWL,mBAAmB,GAIpB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,MAAM,OAAO,WAAW;IAEH;IACA;IACA;IACA;IAJnB,YACmB,SAAwB,EACxB,KAAuB,EACvB,eAAoC,EACpC,UAAkB;QAHlB,cAAS,GAAT,SAAS,CAAe;QACxB,UAAK,GAAL,KAAK,CAAkB;QACvB,oBAAe,GAAf,eAAe,CAAqB;QACpC,eAAU,GAAV,UAAU,CAAQ;IAClC,CAAC;IAEJ,KAAK,CAAC,OAAO,CAAC,MAAyB;QACrC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA2B,SAAS,EAAE,MAAM,EAAE;YACtF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC;QACxC,OAAO;YACL,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC,IAAI,CAAC;YACxC,MAAM,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC;YAC1C,QAAQ,EAAE,QAAQ,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,CAAC,IAAI,CAAC;YAC9C,GAAG,CAAC,QAAQ,CAAC,QAAQ,KAAK,SAAS,IAAI,EAAE,QAAQ,EAAE,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACvE,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC;YACjE,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YAC/C,gBAAgB,EAAE,QAAQ,CAAC,gBAAgB;YAC3C,GAAG,CAAC,QAAQ,CAAC,SAAS,KAAK,SAAS,IAAI,EAAE,SAAS,EAAE,QAAQ,CAAC,SAAS,EAAE,CAAC;YAC1E,GAAG,CAAC,QAAQ,CAAC,WAAW,KAAK,SAAS,IAAI,EAAE,WAAW,EAAE,QAAQ,CAAC,WAAW,EAAE,CAAC;SACjF,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAyB;QACtC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,KAAK,KAAK,IAAI,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC;QACvF,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA4B,UAAU,EAAE,MAAM,EAAE;YACxF,OAAO;SACR,CAAC,CAAC;QACH,OAAO,QAAQ,CAAC,cAAc,CAAC;IACjC,CAAC;IAED,MAAM,CACJ,MAAyB,EACzB,UAA8B,EAAE,OAAO,EAAE,KAAK,EAAE;QAEhD,MAAM,OAAO,GACX,OAAO,CAAC,OAAO,IAAI,CAAC,OAAO,MAAM,CAAC,EAAE,KAAK,QAAQ,IAAI,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC;QAC1F,OAAO,IAAI,CAAC,cAAc,CAAI,QAAQ,EAAE,MAAM,EAAE,EAAE,GAAG,OAAO,EAAE,OAAO,EAAE,CAAC,CAAC;IAC3E,CAAC;IAED,KAAK,CAA8B,MAAyB;QAC1D,OAAO,IAAI,CAAC,cAAc,CAAI,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,MAAyB;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA0B,QAAQ,EAAE,MAAM,EAAE;YACpF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,WAAW,GAAG,QAAQ,CAAC,YAAY,CAAC;QAC1C,MAAM,QAAQ,GAAG,WAAW,CAAC,KAAK,IAAK,MAAM,CAAC,IAAe,IAAI,EAAE,CAAC;QACpE,MAAM,SAAS,GAAG,WAAW,CAAC,cAAc,IAAI,EAAE,CAAC;QAEnD,MAAM,CAAC,KAAK,CAAC,uBAAuB,EAAE;YACpC,QAAQ;YACR,SAAS;YACT,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SACrD,CAAC,CAAC;QAEZ,OAAO;YACL,QAAQ;YACR,SAAS,EAAE,SAAS,IAAI,QAAQ;YAChC,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SAC9D,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,MAAyB;QAC7B,OAAO,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IAClE,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,SAA8B;QAC5C,MAAM,KAAK,GAAG,SAAS;aACpB,GAAG,CACF,CAAC,CAAC,EAAE,EAAE,CACJ,GAAG,CAAC,CAAC,OAAO,IAAI,EAAE,IAAI,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,IAAI,EAAE,IAAI,CAAC,CAAC,SAAS,IAAI,EAAE,IAAI,CAAC,CAAC,UAAU,IAAI,EAAE,IAAI,CAAC,CAAC,GAAG,GAAG,CAC9G;aACA,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,cAAc,CACpC,eAAe,EACf,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,EACvC,EAAE,OAAO,EAAE,MAAM,EAAE,CACpB,CAAC;QAEF,OAAO,IAAI;aACR,KAAK,CAAC,SAAS,CAAC;aAChB,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC;aACxC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE;YACZ,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YACnC,MAAM,UAAU,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YAE1C,IAAI,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC7B,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,EAAE,SAAkB,EAAE,CAAC;YAC9E,CAAC;YAED,IAAI,UAAU,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;gBACvC,OAAO;oBACL,GAAG;oBACH,OAAO,EAAE,KAAK;oBACd,IAAI,EAAE,IAAI;oBACV,MAAM,EAAE,WAAoB;oBAC5B,MAAM,EAAE,UAAU;iBACnB,CAAC;YACJ,CAAC;YAED,OAAO;gBACL,GAAG;gBACH,OAAO,EAAE,KAAK;gBACd,IAAI,EAAE,IAAI;gBACV,MAAM,EAAE,WAAoB;gBAC5B,GAAG,CAAC,UAAU,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;aAC1C,CAAC;QACJ,CAAC,CAAC,CAAC;IACP,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,GAAa,EAAE,MAAe;QAC5C,MAAM,MAAM,GAAsB;YAChC,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC;YAClB,MAAM,EAAE,MAAM;YACd,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC;QAEF,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CACnC,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CACZ,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,mBAAmB,CAAC,mBAAmB,EAAE,MAAM,CAAC,EACrE,QAAQ,CACT,EACH,QAAQ,EACR,MAAM,CACP,CAAC;QAEF,IAAI,MAAe,CAAC;QACpB,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5B,CAAC;QAAC,MAAM,CAAC;YACP,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,6CAA6C,EAC7C,EAAE,eAAe,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC5C,CAAC;QACJ,CAAC;QAED,OAAQ,MAA4B,CAAC,OAAO,IAAI,EAAE,CAAC;IACrD,CAAC;IAED,sEAAsE;IAC9D,MAAM,CAAU,eAAe,GAAG,IAAI,GAAG,CAAC;QAChD,gBAAgB,CAAC,kBAAkB;QACnC,gBAAgB,CAAC,OAAO;QACxB,gBAAgB,CAAC,WAAW;KAC7B,CAAC,CAAC;IAEH,6FAA6F;IACrF,MAAM,CAAU,cAAc,GAAG,MAAM,CAAC;IAEhD;;;;OAIG;IACK,KAAK,CAAC,SAAS,CAAI,OAAyB,EAAE,KAAa;QACjE,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,IAAI,CAAC,UAAU,EAAE,OAAO,EAAE,EAAE,CAAC;YAC5D,IAAI,CAAC;gBACH,OAAO,MAAM,OAAO,EAAE,CAAC;YACzB,CAAC;YAAC,OAAO,KAAc,EAAE,CAAC;gBACxB,IAAI,CAAC,CAAC,KAAK,YAAY,QAAQ,CAAC,EAAE,CAAC;oBACjC,MAAM,KAAK,CAAC;gBACd,CAAC;gBAED,IAAI,CAAC,WAAW,CAAC,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;oBACjD,MAAM,KAAK,CAAC;gBACd,CAAC;gBAED,IAAI,OAAO,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;oBAC9B,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,IAAI,OAAO,EAAE,WAAW,CAAC,cAAc,CAAC,CAAC;oBAC5E,MAAM,MAAM,GAAG,SAAS,GAAG,CAAC,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,OAAO;oBAChE,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;oBACtC,MAAM,CAAC,OAAO,CACZ,mBAAmB,KAAK,sBAAsB,OAAO,GAAG,CAAC,IAAI,IAAI,CAAC,UAAU,QAAQ,UAAU,KAAK,EACnG,EAAE,QAAQ,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,UAAU,EAAW,CAC/D,CAAC;oBACF,MAAM,IAAI,OAAO,CAAO,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC;oBAC1D,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,MAAM,IAAI,QAAQ,CAAC,KAAK,CAAC,IAAI,EAAE,GAAG,GAAG,kBAAkB,QAAQ,YAAY,EAAE;oBAC3E,QAAQ,EAAE,KAAK;oBACf,QAAQ;iBACT,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAED,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,aAAa,EAAE,mCAAmC,EAAE;YACtF,QAAQ,EAAE,KAAK;SAChB,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACK,cAAc,CACpB,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CACvB,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CAAC,KAAK,IAAI,EAAE;YACxB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC;YACzE,OAAO,IAAI,CAAC,eAAe,CAAC,sBAAsB,CAAI,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;QACjF,CAAC,EAAE,QAAQ,CAAC,EACd,QAAQ,EACR,MAAM,CACP,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,CAAC,CAAC;IAC1D,MAAM,eAAe,GAAG,IAAI,mBAAmB,EAAE,CAAC;IAClD,QAAQ,GAAG,IAAI,WAAW,CAAC,SAAS,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,CAAC,UAAU,CAAC,CAAC;IACjF,MAAM,CAAC,IAAI,CAAC,2BAA2B,EAAE;QACvC,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM;QAC1B,cAAc,EAAE,MAAM,CAAC,cAAc;KAC7B,CAAC,CAAC;AACd,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;
|
|
1
|
+
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA4GrD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;;IAa1C,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CAoHL"}
|
|
@@ -60,6 +60,16 @@ const WARNING_PATHS = [
|
|
|
60
60
|
'eSearchResult.WarningList.QuotedPhraseNotFound',
|
|
61
61
|
'eSearchResult.WarningList.OutputMessage',
|
|
62
62
|
];
|
|
63
|
+
/**
|
|
64
|
+
* NCBI responses routinely contain numeric character references for punctuation
|
|
65
|
+
* and diacritics, especially in page ranges and author names. Keep entity
|
|
66
|
+
* processing enabled, but raise the aggregate expansion ceiling high enough for
|
|
67
|
+
* trusted PubMed payloads.
|
|
68
|
+
*/
|
|
69
|
+
const NCBI_PROCESS_ENTITIES_OPTIONS = {
|
|
70
|
+
enabled: true,
|
|
71
|
+
maxTotalExpansions: 100_000,
|
|
72
|
+
};
|
|
63
73
|
function resolvePath(obj, path) {
|
|
64
74
|
let current = obj;
|
|
65
75
|
for (const part of path.split('.')) {
|
|
@@ -109,7 +119,7 @@ export class NcbiResponseHandler {
|
|
|
109
119
|
ignoreAttributes: false,
|
|
110
120
|
attributeNamePrefix: '@_',
|
|
111
121
|
parseTagValue: true,
|
|
112
|
-
processEntities:
|
|
122
|
+
processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
|
|
113
123
|
htmlEntities: true,
|
|
114
124
|
isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
|
|
115
125
|
});
|
|
@@ -159,7 +169,23 @@ export class NcbiResponseHandler {
|
|
|
159
169
|
responseSnippet: responseText.substring(0, 200),
|
|
160
170
|
});
|
|
161
171
|
}
|
|
162
|
-
|
|
172
|
+
let parsedXml;
|
|
173
|
+
try {
|
|
174
|
+
parsedXml = this.xmlParser.parse(responseText);
|
|
175
|
+
}
|
|
176
|
+
catch (error) {
|
|
177
|
+
const parserError = error instanceof Error ? error.message : String(error);
|
|
178
|
+
logger.error('Failed to parse validated XML response from NCBI.', {
|
|
179
|
+
endpoint,
|
|
180
|
+
parserError,
|
|
181
|
+
responseSnippet: responseText.substring(0, 500),
|
|
182
|
+
});
|
|
183
|
+
throw new McpError(JsonRpcErrorCode.SerializationError, `Failed to parse XML response from NCBI: ${parserError}`, {
|
|
184
|
+
endpoint,
|
|
185
|
+
parserError,
|
|
186
|
+
responseSnippet: responseText.substring(0, 200),
|
|
187
|
+
});
|
|
188
|
+
}
|
|
163
189
|
const hasError = ERROR_PATHS.some((path) => resolvePath(parsedXml, path) !== undefined);
|
|
164
190
|
if (hasError) {
|
|
165
191
|
const errorMessages = this.extractNcbiErrorMessages(parsedXml);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.3.
|
|
3
|
+
"version": "2.3.5",
|
|
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",
|
|
@@ -78,14 +78,14 @@
|
|
|
78
78
|
"lodash": ">=4.17.24"
|
|
79
79
|
},
|
|
80
80
|
"dependencies": {
|
|
81
|
-
"@cyanheads/mcp-ts-core": "^0.3.
|
|
82
|
-
"fast-xml-parser": "^5.5.
|
|
81
|
+
"@cyanheads/mcp-ts-core": "^0.3.5",
|
|
82
|
+
"fast-xml-parser": "^5.5.12",
|
|
83
83
|
"pino-pretty": "^13.1.3",
|
|
84
84
|
"sanitize-html": "^2.17.2"
|
|
85
85
|
},
|
|
86
86
|
"devDependencies": {
|
|
87
|
-
"@biomejs/biome": "^2.4.
|
|
88
|
-
"@types/node": "^25.
|
|
87
|
+
"@biomejs/biome": "^2.4.11",
|
|
88
|
+
"@types/node": "^25.6.0",
|
|
89
89
|
"@types/sanitize-html": "^2.16.1",
|
|
90
90
|
"@vitest/coverage-istanbul": "^4.1.4",
|
|
91
91
|
"depcheck": "^1.4.7",
|
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": "2.3.
|
|
9
|
+
"version": "2.3.5",
|
|
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": "2.3.
|
|
22
|
+
"version": "2.3.5",
|
|
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": "2.3.
|
|
63
|
+
"version": "2.3.5",
|
|
64
64
|
"packageArguments": [
|
|
65
65
|
{
|
|
66
66
|
"type": "positional",
|