@cyanheads/pubmed-mcp-server 2.2.2 → 2.2.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/dist/services/ncbi/api-client.d.ts +4 -3
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +22 -34
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +8 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +41 -5
- 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 +7 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +1 -1
- 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:** 2.2.
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**Version:** 2.2.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/README.md
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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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@@ -1,19 +1,20 @@
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/**
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* @fileoverview Core HTTP client for NCBI E-utility requests. Handles URL construction,
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* API key injection, GET/POST selection based on payload size
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* API key injection, and GET/POST selection based on payload size. Single-attempt only;
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* retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
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* @module src/services/ncbi/api-client
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*/
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import { type NcbiRequestOptions, type NcbiRequestParams } from './types.js';
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export interface NcbiApiClientConfig {
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adminEmail?: string;
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apiKey?: string;
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maxRetries: number;
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timeoutMs: number;
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toolIdentifier: string;
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}
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/**
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* Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
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* chooses GET/POST
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* and chooses GET/POST based on payload size. Single-attempt — retry logic lives
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* in {@link NcbiService.performRequest} so it covers both HTTP and XML-level errors.
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*/
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export declare class NcbiApiClient {
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private readonly config;
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{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA
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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;IAiClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
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/**
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* @fileoverview Core HTTP client for NCBI E-utility requests. Handles URL construction,
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* API key injection, GET/POST selection based on payload size
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* API key injection, and GET/POST selection based on payload size. Single-attempt only;
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* retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
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* @module src/services/ncbi/api-client
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*/
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import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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@@ -10,7 +11,8 @@ import { NCBI_EUTILS_BASE_URL } from './types.js';
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const POST_THRESHOLD = 2000;
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/**
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* Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
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* chooses GET/POST
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* and chooses GET/POST based on payload size. Single-attempt — retry logic lives
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* in {@link NcbiService.performRequest} so it covers both HTTP and XML-level errors.
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*/
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export class NcbiApiClient {
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config;
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const finalParams = this.buildParams(params);
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const usePost = this.shouldPost(finalParams, options);
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const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}.fcgi`;
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return await response.text();
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}
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catch (error) {
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if (error instanceof McpError) {
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if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
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error.code !== JsonRpcErrorCode.Timeout) {
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throw error;
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}
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}
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if (attempt < this.config.maxRetries) {
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const retryDelay = 2 ** attempt * 200;
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logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.config.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
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await new Promise((r) => setTimeout(r, retryDelay));
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continue;
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}
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if (error instanceof McpError)
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throw error;
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const msg = error instanceof Error ? error.message : String(error);
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logger.error(`NCBI request to ${endpoint} failed after ${this.config.maxRetries} retries.`, { endpoint, errorMessage: msg });
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throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed after retries: ${msg}`, { endpoint });
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try {
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logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
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endpoint,
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});
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const response = usePost
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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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throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API returned HTTP ${response.status}.`, { endpoint, status: response.status });
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}
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return await response.text();
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}
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catch (error) {
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if (error instanceof McpError)
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throw error;
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const msg = error instanceof Error ? error.message : String(error);
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throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed: ${msg}`, {
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endpoint,
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});
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}
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throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
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endpoint,
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});
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}
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buildParams(params) {
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const raw = {
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{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA
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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,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,OAAO,CAAC;QAEvD,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,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,0BAA0B,QAAQ,CAAC,MAAM,GAAG,EAC5C,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CACtC,CAAC;YACJ,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;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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private readonly apiClient;
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private readonly queue;
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private readonly responseHandler;
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private readonly maxRetries;
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constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler, maxRetries: number);
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eSearch(params: NcbiRequestParams): Promise<ESearchResult>;
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eSummary(params: NcbiRequestParams): Promise<ESummaryResult>;
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eFetch<T = {
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eLink<T = Record<string, unknown>>(params: NcbiRequestParams): Promise<T>;
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eSpell(params: NcbiRequestParams): Promise<ESpellResult>;
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eInfo(params: NcbiRequestParams): Promise<unknown>;
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/**
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* Enqueues a request with retry logic that covers both HTTP-level failures
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* (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
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* with an error structure in the response body, e.g. connection resets
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* surfaced as C++ exception traces).
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*/
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private performRequest;
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}
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/** Initialize the NCBI service. Call from `setup()` in createApp. */
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{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
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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,KAAK,EAEV,aAAa,EAEb,YAAY,EAEZ,cAAc,EACd,kBAAkB,EAClB,iBAAiB,EACjB,mBAAmB,EACpB,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;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAqDvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
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* typed methods for each E-utility endpoint. Uses init/accessor pattern.
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* @module src/services/ncbi/ncbi-service
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*/
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import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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import { logger } from '@cyanheads/mcp-ts-core/utils';
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import { getServerConfig } from '../../config/server-config.js';
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import { NcbiApiClient } from './api-client.js';
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apiClient;
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queue;
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responseHandler;
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maxRetries;
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|
22
|
+
constructor(apiClient, queue, responseHandler, maxRetries) {
|
|
21
23
|
this.apiClient = apiClient;
|
|
22
24
|
this.queue = queue;
|
|
23
25
|
this.responseHandler = responseHandler;
|
|
26
|
+
this.maxRetries = maxRetries;
|
|
24
27
|
}
|
|
25
28
|
async eSearch(params) {
|
|
26
29
|
const response = await this.performRequest('esearch', params, {
|
|
@@ -74,10 +77,44 @@ export class NcbiService {
|
|
|
74
77
|
eInfo(params) {
|
|
75
78
|
return this.performRequest('einfo', params, { retmode: 'xml' });
|
|
76
79
|
}
|
|
80
|
+
/**
|
|
81
|
+
* Enqueues a request with retry logic that covers both HTTP-level failures
|
|
82
|
+
* (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
|
|
83
|
+
* with an error structure in the response body, e.g. connection resets
|
|
84
|
+
* surfaced as C++ exception traces).
|
|
85
|
+
*/
|
|
77
86
|
performRequest(endpoint, params, options) {
|
|
78
87
|
return this.queue.enqueue(async () => {
|
|
79
|
-
|
|
80
|
-
|
|
88
|
+
for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
|
|
89
|
+
try {
|
|
90
|
+
const text = await this.apiClient.makeRequest(endpoint, params, options);
|
|
91
|
+
return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
|
|
92
|
+
}
|
|
93
|
+
catch (error) {
|
|
94
|
+
// Only retry transient errors (ServiceUnavailable, Timeout).
|
|
95
|
+
// Validation, serialization, and other errors fail immediately.
|
|
96
|
+
if (error instanceof McpError) {
|
|
97
|
+
if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
|
|
98
|
+
error.code !== JsonRpcErrorCode.Timeout) {
|
|
99
|
+
throw error;
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
if (attempt < this.maxRetries) {
|
|
103
|
+
const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
|
|
104
|
+
logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
|
|
105
|
+
await new Promise((r) => setTimeout(r, retryDelay));
|
|
106
|
+
continue;
|
|
107
|
+
}
|
|
108
|
+
// Final attempt exhausted — surface retry context so the caller
|
|
109
|
+
// knows this wasn't a single failed request.
|
|
110
|
+
const attempts = this.maxRetries + 1;
|
|
111
|
+
const msg = error instanceof Error ? error.message : String(error);
|
|
112
|
+
throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint, attempts });
|
|
113
|
+
}
|
|
114
|
+
}
|
|
115
|
+
throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
|
|
116
|
+
endpoint,
|
|
117
|
+
});
|
|
81
118
|
}, endpoint, params);
|
|
82
119
|
}
|
|
83
120
|
}
|
|
@@ -88,14 +125,13 @@ export function initNcbiService() {
|
|
|
88
125
|
const config = getServerConfig();
|
|
89
126
|
const apiClient = new NcbiApiClient({
|
|
90
127
|
toolIdentifier: config.toolIdentifier,
|
|
91
|
-
maxRetries: config.maxRetries,
|
|
92
128
|
timeoutMs: config.timeoutMs,
|
|
93
129
|
...(config.apiKey && { apiKey: config.apiKey }),
|
|
94
130
|
...(config.adminEmail && { adminEmail: config.adminEmail }),
|
|
95
131
|
});
|
|
96
132
|
const queue = new NcbiRequestQueue(config.requestDelayMs);
|
|
97
133
|
const responseHandler = new NcbiResponseHandler();
|
|
98
|
-
_service = new NcbiService(apiClient, queue, responseHandler);
|
|
134
|
+
_service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries);
|
|
99
135
|
logger.info('NCBI service initialized.', {
|
|
100
136
|
toolIdentifier: config.toolIdentifier,
|
|
101
137
|
hasApiKey: !!config.apiKey,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.js","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,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;AAa5D;;;GAGG;AACH,MAAM,OAAO,WAAW;IAEH;IACA;IACA;
|
|
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;AAa5D;;;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;;;;;OAKG;IACK,cAAc,CACpB,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CACvB,KAAK,IAAI,EAAE;YACT,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,IAAI,CAAC,UAAU,EAAE,OAAO,EAAE,EAAE,CAAC;gBAC5D,IAAI,CAAC;oBACH,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC;oBACzE,OAAO,IAAI,CAAC,eAAe,CAAC,sBAAsB,CAAI,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;gBACjF,CAAC;gBAAC,OAAO,KAAc,EAAE,CAAC;oBACxB,6DAA6D;oBAC7D,gEAAgE;oBAChE,IAAI,KAAK,YAAY,QAAQ,EAAE,CAAC;wBAC9B,IACE,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,kBAAkB;4BAClD,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,OAAO,EACvC,CAAC;4BACD,MAAM,KAAK,CAAC;wBACd,CAAC;oBACH,CAAC;oBAED,IAAI,OAAO,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;wBAC9B,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,IAAI,OAAO,CAAC,CAAC,aAAa;wBACrD,MAAM,CAAC,OAAO,CACZ,mBAAmB,QAAQ,sBAAsB,OAAO,GAAG,CAAC,IAAI,IAAI,CAAC,UAAU,QAAQ,UAAU,KAAK,EACtG,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,UAAU,EAAW,CACxD,CAAC;wBACF,MAAM,IAAI,OAAO,CAAO,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC;wBAC1D,SAAS;oBACX,CAAC;oBAED,gEAAgE;oBAChE,6CAA6C;oBAC7C,MAAM,QAAQ,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC;oBACrC,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;oBACnE,MAAM,IAAI,QAAQ,CAChB,KAAK,YAAY,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,gBAAgB,CAAC,kBAAkB,EAC5E,GAAG,GAAG,kBAAkB,QAAQ,YAAY,EAC5C,EAAE,QAAQ,EAAE,QAAQ,EAAE,CACvB,CAAC;gBACJ,CAAC;YACH,CAAC;YAED,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,aAAa,EAAE,mCAAmC,EAAE;gBACtF,QAAQ;aACT,CAAC,CAAC;QACL,CAAC,EACD,QAAQ,EACR,MAAM,CACP,CAAC;IACJ,CAAC;CACF;AAED,+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;AAiGrD;;;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;
|
|
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;AAiGrD;;;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;CAiGL"}
|
|
@@ -143,6 +143,13 @@ export class NcbiResponseHandler {
|
|
|
143
143
|
const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
|
|
144
144
|
const validationResult = XMLValidator.validate(xmlForValidation);
|
|
145
145
|
if (validationResult !== true) {
|
|
146
|
+
const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
|
|
147
|
+
if (isHtml) {
|
|
148
|
+
logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', {
|
|
149
|
+
endpoint,
|
|
150
|
+
});
|
|
151
|
+
throw new McpError(JsonRpcErrorCode.ServiceUnavailable, 'NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
|
|
152
|
+
}
|
|
146
153
|
logger.error('Invalid XML response from NCBI.', {
|
|
147
154
|
endpoint,
|
|
148
155
|
responseSnippet: responseText.substring(0, 500),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.2.
|
|
3
|
+
"version": "2.2.3",
|
|
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",
|
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": "2.2.
|
|
9
|
+
"version": "2.2.3",
|
|
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": "2.2.
|
|
22
|
+
"version": "2.2.3",
|
|
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": "2.2.
|
|
63
|
+
"version": "2.2.3",
|
|
64
64
|
"packageArguments": [
|
|
65
65
|
{
|
|
66
66
|
"type": "positional",
|