@cyanheads/pubmed-mcp-server 2.6.4 → 2.6.6
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 +41 -15
- package/README.md +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts.map +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts +41 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js +45 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +25 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +12 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +25 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +15 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +25 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +20 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +8 -3
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +15 -7
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +4 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +26 -15
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +14 -36
- 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 +24 -19
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +9 -9
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +2 -2
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +50 -29
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +22 -18
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +4 -5
- package/server.json +3 -3
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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 {
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import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
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import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
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import { NCBI_EUTILS_BASE_URL } from './types.js';
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/** Maximum encoded query-string length before automatically switching to POST. */
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const POST_THRESHOLD = 2000;
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@@ -25,26 +25,14 @@ export class NcbiApiClient {
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const suffix = endpoint.includes('.') ? '' : '.fcgi';
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const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
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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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logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({ operation: 'NcbiHttpRequest', endpoint }));
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const response = usePost
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? await this.postRequest(url, finalParams, options?.signal)
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: await this.getRequest(url, finalParams, options?.signal);
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if (!response.ok) {
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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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throw await httpErrorFromResponse(response, {
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service: 'NCBI',
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data: { endpoint },
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});
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}
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return await response.text();
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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
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endpoint,
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});
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throw serviceUnavailable(`NCBI request failed: ${msg}`, { endpoint }, { cause: error });
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}
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}
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/**
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? AbortSignal.any([timeoutSignal, externalSignal])
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: timeoutSignal;
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try {
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logger.debug(`NCBI external request: GET ${fullUrl}`, { url });
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logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({ operation: 'NcbiExternalRequest', url }));
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const response = await fetch(fullUrl, { signal });
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const body = await response.text();
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if (!response.ok) {
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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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throw await httpErrorFromResponse(response, {
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service: 'NCBI',
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captureBody: false,
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data: { url, body: body.substring(0, 500) },
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});
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}
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return body;
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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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throw
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url,
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});
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throw serviceUnavailable(`NCBI request failed: ${msg}`, { url }, { cause: error });
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}
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}
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buildParams(params) {
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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,
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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,QAAQ,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC7E,OAAO,EACL,gBAAgB,EAChB,qBAAqB,EACrB,MAAM,EACN,qBAAqB,GACtB,MAAM,8BAA8B,CAAC;AAEtC,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,CACV,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EACvD,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,iBAAiB,EAAE,QAAQ,EAAE,CAAC,CACvF,CAAC;YAEF,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,CAAC;gBAC3D,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,CAAC,CAAC;YAE7D,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,MAAM,qBAAqB,CAAC,QAAQ,EAAE;oBAC1C,OAAO,EAAE,MAAM;oBACf,IAAI,EAAE,EAAE,QAAQ,EAAE;iBACnB,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,kBAAkB,CAAC,wBAAwB,GAAG,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;QAC1F,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,mBAAmB,CACvB,GAAW,EACX,MAAyB,EACzB,cAA4B;QAE5B,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,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;QACjE,MAAM,MAAM,GAAG,cAAc;YAC3B,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC;YAClD,CAAC,CAAC,aAAa,CAAC;QAElB,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CACV,8BAA8B,OAAO,EAAE,EACvC,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,qBAAqB,EAAE,GAAG,EAAE,CAAC,CACtF,CAAC;YACF,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;YAElD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAEnC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,MAAM,qBAAqB,CAAC,QAAQ,EAAE;oBAC1C,OAAO,EAAE,MAAM;oBACf,WAAW,EAAE,KAAK;oBAClB,IAAI,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE;iBAC5C,CAAC,CAAC;YACL,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,kBAAkB,CAAC,wBAAwB,GAAG,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;QACrF,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,CAChB,GAAW,EACX,MAA8B,EAC9B,MAAoB;QAEpB,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,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChG,CAAC;IAEO,WAAW,CACjB,GAAW,EACX,MAA8B,EAC9B,MAAoB;QAEpB,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;YACJ,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC,CAAC;IACL,CAAC;CACF"}
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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;AAYH,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;AA8BpB;;;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;IAsD7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAoC7B,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;IA8B7B;;;;;OAKG;YACW,SAAS;IA0DvB;;;;;;;;;OASG;IACH,OAAO,CAAC,cAAc;CA0BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA2BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -4,8 +4,8 @@
|
|
|
4
4
|
* typed methods for each E-utility endpoint. Uses init/accessor pattern.
|
|
5
5
|
* @module src/services/ncbi/ncbi-service
|
|
6
6
|
*/
|
|
7
|
-
import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
|
|
8
|
-
import { logger } from '@cyanheads/mcp-ts-core/utils';
|
|
7
|
+
import { internalError, JsonRpcErrorCode, McpError, serializationError, timeout, } from '@cyanheads/mcp-ts-core/errors';
|
|
8
|
+
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
9
9
|
import { getServerConfig } from '../../config/server-config.js';
|
|
10
10
|
import { NcbiApiClient } from './api-client.js';
|
|
11
11
|
import { NcbiRequestQueue } from './request-queue.js';
|
|
@@ -100,11 +100,12 @@ export class NcbiService {
|
|
|
100
100
|
const spellResult = response.eSpellResult;
|
|
101
101
|
const original = spellResult.Query ?? params.term ?? '';
|
|
102
102
|
const corrected = spellResult.CorrectedQuery ?? '';
|
|
103
|
-
logger.debug('ESpell result parsed.', {
|
|
103
|
+
logger.debug('ESpell result parsed.', requestContextService.createRequestContext({
|
|
104
|
+
operation: 'NcbiESpell',
|
|
104
105
|
original,
|
|
105
106
|
corrected,
|
|
106
107
|
hasSuggestion: corrected.length > 0 && corrected !== original,
|
|
107
|
-
});
|
|
108
|
+
}));
|
|
108
109
|
return {
|
|
109
110
|
original,
|
|
110
111
|
corrected: corrected || original,
|
|
@@ -177,8 +178,8 @@ export class NcbiService {
|
|
|
177
178
|
try {
|
|
178
179
|
parsed = JSON.parse(text);
|
|
179
180
|
}
|
|
180
|
-
catch {
|
|
181
|
-
throw
|
|
181
|
+
catch (error) {
|
|
182
|
+
throw serializationError('Failed to parse ID Converter JSON response.', { responseSnippet: text.substring(0, 200) }, { cause: error });
|
|
182
183
|
}
|
|
183
184
|
return parsed.records ?? [];
|
|
184
185
|
}
|
|
@@ -207,9 +208,7 @@ export class NcbiService {
|
|
|
207
208
|
}
|
|
208
209
|
catch (error) {
|
|
209
210
|
if (error instanceof NcbiDeadlineExceeded) {
|
|
210
|
-
throw
|
|
211
|
-
deadlineMs: this.totalDeadlineMs,
|
|
212
|
-
});
|
|
211
|
+
throw timeout(error.message, { reason: 'ncbi_deadline_exceeded', deadlineMs: this.totalDeadlineMs }, { cause: error });
|
|
213
212
|
}
|
|
214
213
|
throw error;
|
|
215
214
|
}
|
|
@@ -243,21 +242,26 @@ export class NcbiService {
|
|
|
243
242
|
const baseDelay = Math.min(1000 * 2 ** attempt, NcbiService.MAX_BACKOFF_MS);
|
|
244
243
|
const jitter = baseDelay * (0.75 + 0.5 * Math.random()); // ±25%
|
|
245
244
|
const retryDelay = Math.round(jitter);
|
|
246
|
-
logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, {
|
|
245
|
+
logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
|
|
246
|
+
operation: 'NcbiRetry',
|
|
247
|
+
endpoint: label,
|
|
248
|
+
attempt: attempt + 1,
|
|
249
|
+
retryDelay,
|
|
250
|
+
}));
|
|
247
251
|
await abortableSleep(retryDelay, signal);
|
|
248
252
|
continue;
|
|
249
253
|
}
|
|
250
254
|
const attempts = this.maxRetries + 1;
|
|
251
255
|
const msg = error instanceof Error ? error.message : String(error);
|
|
252
|
-
|
|
253
|
-
|
|
254
|
-
|
|
255
|
-
|
|
256
|
+
// Tag transient ServiceUnavailable retries-exhausted with `ncbi_unreachable` so
|
|
257
|
+
// tool callers can switch on a stable reason. Other retryable codes (Timeout,
|
|
258
|
+
// RateLimited) keep their original code with no reason — `ncbi_deadline_exceeded`
|
|
259
|
+
// and `queue_full` are stamped at their own throw sites.
|
|
260
|
+
const reason = error.code === JsonRpcErrorCode.ServiceUnavailable ? 'ncbi_unreachable' : undefined;
|
|
261
|
+
throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, { ...(reason && { reason }), endpoint: label, attempts }, { cause: error });
|
|
256
262
|
}
|
|
257
263
|
}
|
|
258
|
-
throw
|
|
259
|
-
endpoint: label,
|
|
260
|
-
});
|
|
264
|
+
throw internalError('Request failed after all retries.', { endpoint: label });
|
|
261
265
|
}
|
|
262
266
|
/**
|
|
263
267
|
* Enqueues a request with a service-level deadline and retry logic that covers
|
|
@@ -293,12 +297,13 @@ export function initNcbiService() {
|
|
|
293
297
|
const queue = new NcbiRequestQueue(config.requestDelayMs);
|
|
294
298
|
const responseHandler = new NcbiResponseHandler();
|
|
295
299
|
_service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
|
|
296
|
-
logger.info('NCBI service initialized.', {
|
|
300
|
+
logger.info('NCBI service initialized.', requestContextService.createRequestContext({
|
|
301
|
+
operation: 'NcbiInit',
|
|
297
302
|
toolIdentifier: config.toolIdentifier,
|
|
298
303
|
hasApiKey: !!config.apiKey,
|
|
299
304
|
requestDelayMs: config.requestDelayMs,
|
|
300
305
|
totalDeadlineMs: config.totalDeadlineMs,
|
|
301
|
-
});
|
|
306
|
+
}));
|
|
302
307
|
}
|
|
303
308
|
/** Get the initialized NCBI service. Throws if not initialized. */
|
|
304
309
|
export function getNcbiService() {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAYpD;;;GAGG;AACH,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAuB;IAC7C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,eAAe,CAAK;gBAEhB,OAAO,EAAE,MAAM,EAAE,YAAY,SAAyB;IAKlE,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;YA0B7E,YAAY;
|
|
1
|
+
{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAYpD;;;GAGG;AACH,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAuB;IAC7C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,eAAe,CAAK;gBAEhB,OAAO,EAAE,MAAM,EAAE,YAAY,SAAyB;IAKlE,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;YA0B7E,YAAY;CAqD3B"}
|
|
@@ -4,7 +4,7 @@
|
|
|
4
4
|
* @module src/services/ncbi/request-queue
|
|
5
5
|
*/
|
|
6
6
|
import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
|
|
7
|
-
import { logger } from '@cyanheads/mcp-ts-core/utils';
|
|
7
|
+
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
8
8
|
const DEFAULT_MAX_QUEUE_SIZE = 100;
|
|
9
9
|
/**
|
|
10
10
|
* Processes NCBI API requests through a FIFO queue, inserting a configurable
|
|
@@ -22,7 +22,7 @@ export class NcbiRequestQueue {
|
|
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22
22
|
}
|
|
23
23
|
enqueue(task, endpoint, params) {
|
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24
24
|
if (this.queue.length >= this.maxQueueSize) {
|
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25
|
-
return Promise.reject(new McpError(JsonRpcErrorCode.RateLimited, `NCBI request queue is full (max ${this.maxQueueSize}).`, { endpoint, queueSize: this.queue.length }));
|
|
25
|
+
return Promise.reject(new McpError(JsonRpcErrorCode.RateLimited, `NCBI request queue is full (max ${this.maxQueueSize}).`, { reason: 'queue_full', endpoint, queueSize: this.queue.length }));
|
|
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26
|
}
|
|
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27
|
return new Promise((resolve, reject) => {
|
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28
28
|
this.queue.push({
|
|
@@ -52,24 +52,24 @@ export class NcbiRequestQueue {
|
|
|
52
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|
const elapsed = now - this.lastRequestTime;
|
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|
const wait = this.delayMs - elapsed;
|
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|
if (wait > 0) {
|
|
55
|
-
logger.debug(`Delaying NCBI request by ${wait}ms to respect rate limit.`, {
|
|
55
|
+
logger.debug(`Delaying NCBI request by ${wait}ms to respect rate limit.`, requestContextService.createRequestContext({
|
|
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|
+
operation: 'NcbiQueueWait',
|
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|
endpoint,
|
|
57
58
|
delayMs: wait,
|
|
58
|
-
});
|
|
59
|
+
}));
|
|
59
60
|
await new Promise((r) => setTimeout(r, wait));
|
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|
}
|
|
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this.lastRequestTime = Date.now();
|
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62
|
-
logger.info(`Executing NCBI request via queue: ${endpoint}`, {
|
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|
-
endpoint,
|
|
64
|
-
});
|
|
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|
+
logger.info(`Executing NCBI request via queue: ${endpoint}`, requestContextService.createRequestContext({ operation: 'NcbiQueueDispatch', endpoint }));
|
|
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|
const result = await task();
|
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resolve(result);
|
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}
|
|
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|
catch (error) {
|
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-
logger.error('Error processing NCBI request from queue.', {
|
|
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|
+
logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
|
|
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|
+
operation: 'NcbiQueueProcess',
|
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endpoint,
|
|
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errorMessage: error instanceof Error ? error.message : String(error),
|
|
72
|
-
});
|
|
72
|
+
}));
|
|
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|
reject(error);
|
|
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|
}
|
|
75
75
|
finally {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAC;
|
|
1
|
+
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAI7E,MAAM,sBAAsB,GAAG,GAAG,CAAC;AAUnC;;;GAGG;AACH,MAAM,OAAO,gBAAgB;IACV,KAAK,GAAoB,EAAE,CAAC;IAC5B,OAAO,CAAS;IAChB,YAAY,CAAS;IAC9B,UAAU,GAAG,KAAK,CAAC;IACnB,eAAe,GAAG,CAAC,CAAC;IAE5B,YAAY,OAAe,EAAE,YAAY,GAAG,sBAAsB;QAChE,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;QACvB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAC;IACnC,CAAC;IAED,OAAO,CAAI,IAAsB,EAAE,QAAgB,EAAE,MAAyB;QAC5E,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC;YAC3C,OAAO,OAAO,CAAC,MAAM,CACnB,IAAI,QAAQ,CACV,gBAAgB,CAAC,WAAW,EAC5B,mCAAmC,IAAI,CAAC,YAAY,IAAI,EACxD,EAAE,MAAM,EAAE,YAAY,EAAE,QAAQ,EAAE,SAAS,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CACjE,CACF,CAAC;QACJ,CAAC;QAED,OAAO,IAAI,OAAO,CAAI,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC;gBACd,OAAO,EAAE,OAAmC;gBAC5C,MAAM;gBACN,IAAI;gBACJ,QAAQ;gBACR,MAAM;aACP,CAAC,CAAC;YAEH,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC;gBACrB,cAAc,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,KAAK,CAAC,YAAY;QACxB,IAAI,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO;QACvD,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC;QAEvB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC;QAChC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,IAAI,CAAC,UAAU,GAAG,KAAK,CAAC;YACxB,OAAO;QACT,CAAC;QACD,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;QAEjD,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACvB,MAAM,OAAO,GAAG,GAAG,GAAG,IAAI,CAAC,eAAe,CAAC;YAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;YAEpC,IAAI,IAAI,GAAG,CAAC,EAAE,CAAC;gBACb,MAAM,CAAC,KAAK,CACV,4BAA4B,IAAI,2BAA2B,EAC3D,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,eAAe;oBAC1B,QAAQ;oBACR,OAAO,EAAE,IAAI;iBACd,CAAC,CACH,CAAC;gBACF,MAAM,IAAI,OAAO,CAAO,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC;YACtD,CAAC;YAED,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAClC,MAAM,CAAC,IAAI,CACT,qCAAqC,QAAQ,EAAE,EAC/C,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,mBAAmB,EAAE,QAAQ,EAAE,CAAC,CACzF,CAAC;YAEF,MAAM,MAAM,GAAG,MAAM,IAAI,EAAE,CAAC;YAC5B,OAAO,CAAC,MAAM,CAAC,CAAC;QAClB,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,CAAC,KAAK,CACV,2CAA2C,EAC3C,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,kBAAkB;gBAC7B,QAAQ;gBACR,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC;aACrE,CAAC,CACH,CAAC;YACF,MAAM,CAAC,KAAK,CAAC,CAAC;QAChB,CAAC;gBAAS,CAAC;YACT,IAAI,CAAC,UAAU,GAAG,KAAK,CAAC;YACxB,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC1B,cAAc,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC;IACH,CAAC;CACF"}
|
|
@@ -38,8 +38,8 @@ export declare class NcbiResponseHandler {
|
|
|
38
38
|
private readonly orderedXmlParser;
|
|
39
39
|
constructor();
|
|
40
40
|
/**
|
|
41
|
-
* Extract a structured error from a parsed NCBI XML body and throw it
|
|
42
|
-
* `
|
|
41
|
+
* Extract a structured error from a parsed NCBI XML body and throw it via
|
|
42
|
+
* `serviceUnavailable()`. Never returns.
|
|
43
43
|
*/
|
|
44
44
|
private throwNcbiError;
|
|
45
45
|
extractNcbiErrorMessages(parsedXml: Record<string, unknown>): string[];
|
|
@@ -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;AAsLrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;OAGG;IACH,OAAO,CAAC,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;AAsLrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;OAGG;IACH,OAAO,CAAC,cAAc;IAgBtB,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;CA8KL"}
|
|
@@ -4,8 +4,8 @@
|
|
|
4
4
|
* NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
|
|
5
5
|
* @module src/services/ncbi/response-handler
|
|
6
6
|
*/
|
|
7
|
-
import {
|
|
8
|
-
import { logger } from '@cyanheads/mcp-ts-core/utils';
|
|
7
|
+
import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
|
+
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
9
9
|
import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
|
|
10
10
|
/**
|
|
11
11
|
* jpaths that NCBI may return as either a single value or an array.
|
|
@@ -232,16 +232,20 @@ export class NcbiResponseHandler {
|
|
|
232
232
|
});
|
|
233
233
|
}
|
|
234
234
|
/**
|
|
235
|
-
* Extract a structured error from a parsed NCBI XML body and throw it
|
|
236
|
-
* `
|
|
235
|
+
* Extract a structured error from a parsed NCBI XML body and throw it via
|
|
236
|
+
* `serviceUnavailable()`. Never returns.
|
|
237
237
|
*/
|
|
238
238
|
throwNcbiError(parsedXml, endpoint) {
|
|
239
239
|
const errorMessages = this.extractNcbiErrorMessages(parsedXml);
|
|
240
|
-
logger.error('NCBI API returned an error in XML response.', {
|
|
240
|
+
logger.error('NCBI API returned an error in XML response.', requestContextService.createRequestContext({
|
|
241
|
+
operation: 'NcbiXmlError',
|
|
241
242
|
endpoint,
|
|
242
243
|
errors: errorMessages,
|
|
244
|
+
}));
|
|
245
|
+
throw serviceUnavailable(`NCBI API Error: ${errorMessages.join('; ')}`, {
|
|
246
|
+
endpoint,
|
|
247
|
+
ncbiErrors: errorMessages,
|
|
243
248
|
});
|
|
244
|
-
throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API Error: ${errorMessages.join('; ')}`, { endpoint, ncbiErrors: errorMessages });
|
|
245
249
|
}
|
|
246
250
|
extractNcbiErrorMessages(parsedXml) {
|
|
247
251
|
const messages = [];
|
|
@@ -264,26 +268,36 @@ export class NcbiResponseHandler {
|
|
|
264
268
|
parseAndHandleResponse(responseText, endpoint, options) {
|
|
265
269
|
const retmode = options?.retmode ?? 'xml';
|
|
266
270
|
if (retmode === 'text') {
|
|
267
|
-
logger.debug('Received text response from NCBI.', {
|
|
271
|
+
logger.debug('Received text response from NCBI.', requestContextService.createRequestContext({
|
|
272
|
+
operation: 'NcbiParseText',
|
|
273
|
+
endpoint,
|
|
274
|
+
retmode,
|
|
275
|
+
}));
|
|
268
276
|
return responseText;
|
|
269
277
|
}
|
|
270
278
|
if (retmode === 'xml') {
|
|
271
|
-
logger.debug('Parsing XML response from NCBI.', {
|
|
279
|
+
logger.debug('Parsing XML response from NCBI.', requestContextService.createRequestContext({
|
|
280
|
+
operation: 'NcbiParseXml',
|
|
281
|
+
endpoint,
|
|
282
|
+
retmode,
|
|
283
|
+
}));
|
|
272
284
|
const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
|
|
273
285
|
const validationResult = XMLValidator.validate(xmlForValidation);
|
|
274
286
|
if (validationResult !== true) {
|
|
275
287
|
const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
|
|
276
288
|
if (isHtml) {
|
|
277
|
-
logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', {
|
|
289
|
+
logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', requestContextService.createRequestContext({
|
|
290
|
+
operation: 'NcbiHtmlResponse',
|
|
278
291
|
endpoint,
|
|
279
|
-
});
|
|
280
|
-
throw
|
|
292
|
+
}));
|
|
293
|
+
throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
|
|
281
294
|
}
|
|
282
|
-
logger.error('Invalid XML response from NCBI.', {
|
|
295
|
+
logger.error('Invalid XML response from NCBI.', requestContextService.createRequestContext({
|
|
296
|
+
operation: 'NcbiInvalidXml',
|
|
283
297
|
endpoint,
|
|
284
298
|
responseSnippet: responseText.substring(0, 500),
|
|
285
|
-
});
|
|
286
|
-
throw
|
|
299
|
+
}));
|
|
300
|
+
throw serializationError('Received invalid XML from NCBI.', {
|
|
287
301
|
endpoint,
|
|
288
302
|
responseSnippet: responseText.substring(0, 200),
|
|
289
303
|
});
|
|
@@ -307,16 +321,17 @@ export class NcbiResponseHandler {
|
|
|
307
321
|
}
|
|
308
322
|
catch (error) {
|
|
309
323
|
const parserError = error instanceof Error ? error.message : String(error);
|
|
310
|
-
logger.error('Failed to parse validated XML response from NCBI.', {
|
|
324
|
+
logger.error('Failed to parse validated XML response from NCBI.', requestContextService.createRequestContext({
|
|
325
|
+
operation: 'NcbiXmlParseError',
|
|
311
326
|
endpoint,
|
|
312
327
|
parserError,
|
|
313
328
|
responseSnippet: responseText.substring(0, 500),
|
|
314
|
-
});
|
|
315
|
-
throw
|
|
329
|
+
}));
|
|
330
|
+
throw serializationError(`Failed to parse XML response from NCBI: ${parserError}`, {
|
|
316
331
|
endpoint,
|
|
317
332
|
parserError,
|
|
318
333
|
responseSnippet: responseText.substring(0, 200),
|
|
319
|
-
});
|
|
334
|
+
}, { cause: error });
|
|
320
335
|
}
|
|
321
336
|
if (!useOrdered) {
|
|
322
337
|
const parsedObj = parsedXml;
|
|
@@ -326,39 +341,45 @@ export class NcbiResponseHandler {
|
|
|
326
341
|
}
|
|
327
342
|
}
|
|
328
343
|
if (options?.returnRawXml) {
|
|
329
|
-
logger.debug('Returning raw XML string after validation.', { endpoint });
|
|
344
|
+
logger.debug('Returning raw XML string after validation.', requestContextService.createRequestContext({ operation: 'NcbiRawXml', endpoint }));
|
|
330
345
|
return responseText;
|
|
331
346
|
}
|
|
332
|
-
logger.debug('Successfully parsed XML response.', { endpoint });
|
|
347
|
+
logger.debug('Successfully parsed XML response.', requestContextService.createRequestContext({ operation: 'NcbiParseXmlOk', endpoint }));
|
|
333
348
|
return parsedXml;
|
|
334
349
|
}
|
|
335
350
|
if (retmode === 'json') {
|
|
336
|
-
logger.debug('Parsing JSON response from NCBI.', {
|
|
351
|
+
logger.debug('Parsing JSON response from NCBI.', requestContextService.createRequestContext({
|
|
352
|
+
operation: 'NcbiParseJson',
|
|
353
|
+
endpoint,
|
|
354
|
+
retmode,
|
|
355
|
+
}));
|
|
337
356
|
let parsed;
|
|
338
357
|
try {
|
|
339
358
|
parsed = JSON.parse(responseText);
|
|
340
359
|
}
|
|
341
|
-
catch {
|
|
342
|
-
throw
|
|
360
|
+
catch (error) {
|
|
361
|
+
throw serializationError('Failed to parse NCBI JSON response.', { endpoint, responseSnippet: responseText.substring(0, 200) }, { cause: error });
|
|
343
362
|
}
|
|
344
363
|
if (parsed && typeof parsed === 'object' && 'error' in parsed) {
|
|
345
364
|
const errorMessage = String(parsed.error);
|
|
346
|
-
logger.error('NCBI API returned an error in JSON response.', {
|
|
365
|
+
logger.error('NCBI API returned an error in JSON response.', requestContextService.createRequestContext({
|
|
366
|
+
operation: 'NcbiJsonError',
|
|
347
367
|
endpoint,
|
|
348
368
|
error: errorMessage,
|
|
349
|
-
});
|
|
350
|
-
throw
|
|
369
|
+
}));
|
|
370
|
+
throw serviceUnavailable(`NCBI API Error: ${errorMessage}`, {
|
|
351
371
|
endpoint,
|
|
352
372
|
ncbiError: errorMessage,
|
|
353
373
|
});
|
|
354
374
|
}
|
|
355
|
-
logger.debug('Successfully parsed JSON response.', { endpoint });
|
|
375
|
+
logger.debug('Successfully parsed JSON response.', requestContextService.createRequestContext({ operation: 'NcbiParseJsonOk', endpoint }));
|
|
356
376
|
return parsed;
|
|
357
377
|
}
|
|
358
|
-
logger.warning(`Unhandled retmode "${retmode}". Returning raw response text.`, {
|
|
378
|
+
logger.warning(`Unhandled retmode "${retmode}". Returning raw response text.`, requestContextService.createRequestContext({
|
|
379
|
+
operation: 'NcbiUnknownRetmode',
|
|
359
380
|
endpoint,
|
|
360
381
|
retmode,
|
|
361
|
-
});
|
|
382
|
+
}));
|
|
362
383
|
return responseText;
|
|
363
384
|
}
|
|
364
385
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"response-handler.js","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"response-handler.js","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,kBAAkB,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACvF,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAC7E,OAAO,EAAE,SAAS,IAAI,aAAa,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAC;AAI3E;;;GAGG;AACH,MAAM,iBAAiB,GAAG,IAAI,GAAG,CAAC;IAChC,WAAW;IACX,yBAAyB;IACzB,gCAAgC;IAChC,sCAAsC;IACtC,mBAAmB;IACnB,iBAAiB;IACjB,6BAA6B;IAC7B,2BAA2B;IAC3B,iBAAiB;IACjB,qBAAqB;IACrB,qCAAqC;IACrC,uBAAuB;IACvB,wBAAwB;IACxB,SAAS;IACT,wBAAwB;IACxB,sBAAsB;IACtB,uBAAuB;IACvB,aAAa;IACb,sCAAsC;IACtC,qBAAqB;IACrB,eAAe;IACf,2BAA2B;IAC3B,wBAAwB;IACxB,yBAAyB;IACzB,uBAAuB;IACvB,uBAAuB;IACvB,eAAe;IACf,UAAU;IACV,SAAS;IACT,OAAO;IACP,cAAc;CACf,CAAC,CAAC;AAEH;;;GAGG;AACH,MAAM,WAAW,GAAG;IAClB,mBAAmB;IACnB,sBAAsB;IACtB,+CAA+C;IAC/C,OAAO;CACR,CAAC;AAEF,MAAM,aAAa,GAAG;IACpB,wCAAwC;IACxC,uCAAuC;IACvC,gDAAgD;IAChD,yCAAyC;CAC1C,CAAC;AAEF;;;;;GAKG;AACH,MAAM,6BAA6B,GAAG;IACpC,OAAO,EAAE,IAAI;IACb,kBAAkB,EAAE,OAAO;CACnB,CAAC;AAEX,SAAS,WAAW,CAAC,GAAY,EAAE,IAAY;IAC7C,IAAI,OAAO,GAAY,GAAG,CAAC;IAC3B,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QACnC,IAAI,OAAO,IAAI,OAAO,OAAO,KAAK,QAAQ,IAAI,IAAI,IAAK,OAAmC,EAAE,CAAC;YAC3F,OAAO,GAAI,OAAmC,CAAC,IAAI,CAAC,CAAC;QACvD,CAAC;aAAM,CAAC;YACN,OAAO;QACT,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,MAAe,EAAE,MAAM,GAAG,EAAE;IACrD,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;IACxD,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,OAAO,IAAI,KAAK,SAAS,EAAE,CAAC;YACtF,QAAQ,CAAC,IAAI,CAAC,GAAG,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5C,CAAC;aAAM,IAAI,IAAI,IAAI,OAAQ,IAAgC,CAAC,OAAO,CAAC,KAAK,QAAQ,EAAE,CAAC;YAClF,QAAQ,CAAC,IAAI,CAAC,GAAG,MAAM,GAAI,IAAgC,CAAC,OAAO,CAAW,EAAE,CAAC,CAAC;QACpF,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CAAC,OAAe;IACxC,IAAI,+CAA+C,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC;QAClE,IAAI,oCAAoC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC;YACvD,OAAO,mFAAmF,CAAC;QAC7F,CAAC;QACD,OAAO,mEAAmE,CAAC;IAC7E,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,eAAe,GAAG,qBAAqB,CAAC;AAE9C;;;;GAIG;AACH,MAAM,eAAe,GAAqC;IACxD,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;CACP,CAAC;AAEF;;;;GAIG;AACH,MAAM,aAAa,GAAqC;IACtD,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;CACT,CAAC;AAEF,SAAS,gBAAgB,CACvB,OAAe,EACf,KAAuC,EACvC,WAAmB;IAEnB,IAAI,GAAG,GAAG,EAAE,CAAC;IACb,KAAK,MAAM,EAAE,IAAI,OAAO,EAAE,CAAC;QACzB,MAAM,MAAM,GAAG,KAAK,CAAC,EAAE,CAAC,CAAC;QACzB,IAAI,MAAM,KAAK,SAAS;YAAE,OAAO,GAAG,WAAW,GAAG,OAAO,EAAE,CAAC;QAC5D,GAAG,IAAI,MAAM,CAAC;IAChB,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,MAAM,UAAU,mBAAmB,CAAC,GAAW;IAC7C,OAAO,GAAG;SACP,OAAO,CAAC,sBAAsB,EAAE,CAAC,CAAC,EAAE,CAAS,EAAE,EAAE,CAAC,gBAAgB,CAAC,CAAC,EAAE,eAAe,EAAE,GAAG,CAAC,CAAC;SAC5F,OAAO,CAAC,sBAAsB,EAAE,CAAC,CAAC,EAAE,CAAS,EAAE,EAAE,CAAC,gBAAgB,CAAC,CAAC,EAAE,aAAa,EAAE,GAAG,CAAC,CAAC;SAC1F,OAAO,CAAC,sBAAsB,EAAE,CAAC,CAAC,EAAE,CAAS,EAAE,EAAE,CAAC,gBAAgB,CAAC,CAAC,EAAE,aAAa,EAAE,GAAG,CAAC,CAAC;SAC1F,OAAO,CAAC,oBAAoB,EAAE,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;GAGG;AACH,MAAM,OAAO,mBAAmB;IACb,SAAS,CAAgB;IAC1C;;;;;OAKG;IACc,gBAAgB,CAAgB;IAEjD;QACE,IAAI,CAAC,SAAS,GAAG,IAAI,aAAa,CAAC;YACjC,gBAAgB,EAAE,KAAK;YACvB,mBAAmB,EAAE,IAAI;YACzB,aAAa,EAAE,IAAI;YACnB,eAAe,EAAE,6BAA6B;YAC9C,YAAY,EAAE,IAAI;YAClB,OAAO,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,iBAAiB,CAAC,GAAG,CAAC,KAAe,CAAC;SAClE,CAAC,CAAC;QACH,IAAI,CAAC,gBAAgB,GAAG,IAAI,aAAa,CAAC;YACxC,aAAa,EAAE,IAAI;YACnB,gBAAgB,EAAE,KAAK;YACvB,mBAAmB,EAAE,IAAI;YACzB,aAAa,EAAE,IAAI;YACnB,UAAU,EAAE,KAAK;YACjB,eAAe,EAAE,6BAA6B;YAC9C,YAAY,EAAE,IAAI;SACnB,CAAC,CAAC;IACL,CAAC;IAED;;;OAGG;IACK,cAAc,CAAC,SAAkC,EAAE,QAAgB;QACzE,MAAM,aAAa,GAAG,IAAI,CAAC,wBAAwB,CAAC,SAAS,CAAC,CAAC;QAC/D,MAAM,CAAC,KAAK,CACV,6CAA6C,EAC7C,qBAAqB,CAAC,oBAAoB,CAAC;YACzC,SAAS,EAAE,cAAc;YACzB,QAAQ;YACR,MAAM,EAAE,aAAa;SACtB,CAAC,CACH,CAAC;QACF,MAAM,kBAAkB,CAAC,mBAAmB,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE;YACtE,QAAQ;YACR,UAAU,EAAE,aAAa;SAC1B,CAAC,CAAC;IACL,CAAC;IAED,wBAAwB,CAAC,SAAkC;QACzD,MAAM,QAAQ,GAAa,EAAE,CAAC;QAE9B,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;YAC/B,MAAM,KAAK,GAAG,WAAW,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;YAC3C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,QAAQ,CAAC,IAAI,CAAC,GAAG,iBAAiB,CAAC,KAAK,CAAC,CAAC,CAAC;YAC7C,CAAC;QACH,CAAC;QAED,IAAI,QAAQ,CAAC,M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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;
|
|
1
|
+
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