@cyanheads/pubmed-mcp-server 2.10.2 → 2.10.3
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/AGENTS.md +8 -8
- package/CLAUDE.md +8 -8
- package/Dockerfile +9 -4
- package/LICENSE +1 -1
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +7 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.js +7 -4
- package/dist/services/europe-pmc/api-client.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +7 -7
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
- package/dist/services/europe-pmc/request-queue.js +9 -5
- package/dist/services/europe-pmc/request-queue.js.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +8 -2
- 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 +13 -11
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +9 -13
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +10 -6
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +29 -23
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/openalex/api-client.d.ts.map +1 -1
- package/dist/services/openalex/api-client.js +7 -5
- package/dist/services/openalex/api-client.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js +6 -6
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +16 -10
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +11 -11
- package/server.json +3 -3
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@@ -340,9 +340,7 @@ export class EuropePmcService {
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const retryDelay = Math.round(jitter);
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logger.warning(`Europe PMC ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
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operation: 'EuropePmcRetry',
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label,
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attempt: attempt + 1,
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retryDelay,
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additionalContext: { label, attempt: attempt + 1, retryDelay },
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}));
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await abortableSleep(retryDelay, signal);
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continue;
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@@ -385,10 +383,12 @@ export function initEuropePmcService() {
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_service = new EuropePmcService(client, queue, config.europepmcMaxRetries);
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logger.info('Europe PMC service initialized.', requestContextService.createRequestContext({
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operation: 'EuropePmcInit',
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-
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-
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-
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additionalContext: {
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requestDelayMs: config.europepmcRequestDelayMs,
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maxRetries: config.europepmcMaxRetries,
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timeoutMs: config.europepmcTimeoutMs,
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hasEmail: !!config.europepmcEmail,
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},
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}));
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}
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/** Returns the initialized service, or `undefined` when EPMC is disabled. */
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@@ -1 +1 @@
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1
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-
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAeH;;;;;;;;;;;;GAYG;AACH,qBAAa,qBAAqB;IAChC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAgB;IACxC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAK;IACrB,OAAO,CAAC,aAAa,CAAK;IAC1B,OAAO,CAAC,iBAAiB,CAA4C;IAErE,YAAY,aAAa,EAAE,MAAM,EAAE,aAAa,GAAE,MAA+B,EAGhF;IAED,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,CA6BlF;IAED,OAAO,CAAC,WAAW;
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1
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+
{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAeH;;;;;;;;;;;;GAYG;AACH,qBAAa,qBAAqB;IAChC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAgB;IACxC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAK;IACrB,OAAO,CAAC,aAAa,CAAK;IAC1B,OAAO,CAAC,iBAAiB,CAA4C;IAErE,YAAY,aAAa,EAAE,MAAM,EAAE,aAAa,GAAE,MAA+B,EAGhF;IAED,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,CA6BlF;IAED,OAAO,CAAC,WAAW;CAwDpB"}
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@@ -83,17 +83,21 @@ export class EuropePmcRequestQueue {
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83
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this.inFlight += 1;
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84
84
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logger.debug(`Executing Europe PMC request via queue: ${waiter.label}`, requestContextService.createRequestContext({
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operation: 'EuropePmcQueueDispatch',
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86
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-
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-
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-
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+
additionalContext: {
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+
label: waiter.label,
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88
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+
inFlight: this.inFlight,
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89
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+
queueDepth: this.waiters.length,
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90
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+
},
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}));
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Promise.resolve()
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.then(() => waiter.task())
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.then(waiter.resolve, (err) => {
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logger.error('Error processing Europe PMC request from queue.', requestContextService.createRequestContext({
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operation: 'EuropePmcQueueProcess',
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95
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-
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96
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-
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97
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+
additionalContext: {
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98
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+
label: waiter.label,
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99
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errorMessage: err instanceof Error ? err.message : String(err),
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100
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+
},
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97
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}));
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waiter.reject(err);
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99
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})
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE7E,MAAM,sBAAsB,GAAG,CAAC,CAAC;AAWjC;;;;;;;;;;;;GAYG;AACH,MAAM,OAAO,qBAAqB;IACf,OAAO,GAAa,EAAE,CAAC;IACvB,aAAa,CAAS;IACtB,aAAa,CAAS;IAC/B,QAAQ,GAAG,CAAC,CAAC;IACb,aAAa,GAAG,CAAC,CAAC;IAClB,iBAAiB,CAA4C;IAErE,YAAY,aAAqB,EAAE,aAAa,GAAW,sBAAsB;QAC/E,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;IACrC,CAAC;IAED,OAAO,CAAI,IAAsB,EAAE,KAAa,EAAE,MAAoB;QACpE,OAAO,IAAI,OAAO,CAAI,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACxC,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;gBACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACtB,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAc;gBACxB,OAAO;gBACP,MAAM;gBACN,IAAI;gBACJ,KAAK;gBACL,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC;YAEF,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,GAAG,EAAE;oBACnB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAgB,CAAC,CAAC;oBACnD,IAAI,GAAG,KAAK,CAAC,CAAC;wBAAE,OAAO;oBACvB,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,CAAC,CAAC;gBACF,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;gBACzB,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;YAC5D,CAAC;YAED,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAgB,CAAC,CAAC;YACpC,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,WAAW;QACjB,IAAI,IAAI,CAAC,iBAAiB,KAAK,SAAS;YAAE,OAAO;QAEjD,OAAO,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrE,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACvB,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC;YAC5D,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,IAAI,CAAC,iBAAiB,GAAG,UAAU,CAAC,GAAG,EAAE;oBACvC,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAC;oBACnC,IAAI,CAAC,WAAW,EAAE,CAAC;gBACrB,CAAC,EAAE,GAAG,CAAC,CAAC;gBACR,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACpC,IAAI,CAAC,MAAM;gBAAE,OAAO;YAEpB,IAAI,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpC,MAAM,CAAC,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;YAC7D,CAAC;YAED,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnB,MAAM,CAAC,KAAK,CACV,2CAA2C,MAAM,CAAC,KAAK,EAAE,EACzD,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,wBAAwB;gBACnC,KAAK,EAAE,MAAM,CAAC,KAAK;
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1
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+
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE7E,MAAM,sBAAsB,GAAG,CAAC,CAAC;AAWjC;;;;;;;;;;;;GAYG;AACH,MAAM,OAAO,qBAAqB;IACf,OAAO,GAAa,EAAE,CAAC;IACvB,aAAa,CAAS;IACtB,aAAa,CAAS;IAC/B,QAAQ,GAAG,CAAC,CAAC;IACb,aAAa,GAAG,CAAC,CAAC;IAClB,iBAAiB,CAA4C;IAErE,YAAY,aAAqB,EAAE,aAAa,GAAW,sBAAsB;QAC/E,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;IACrC,CAAC;IAED,OAAO,CAAI,IAAsB,EAAE,KAAa,EAAE,MAAoB;QACpE,OAAO,IAAI,OAAO,CAAI,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACxC,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;gBACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACtB,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAc;gBACxB,OAAO;gBACP,MAAM;gBACN,IAAI;gBACJ,KAAK;gBACL,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC;YAEF,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,GAAG,EAAE;oBACnB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAgB,CAAC,CAAC;oBACnD,IAAI,GAAG,KAAK,CAAC,CAAC;wBAAE,OAAO;oBACvB,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,CAAC,CAAC;gBACF,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;gBACzB,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;YAC5D,CAAC;YAED,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAgB,CAAC,CAAC;YACpC,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,WAAW;QACjB,IAAI,IAAI,CAAC,iBAAiB,KAAK,SAAS;YAAE,OAAO;QAEjD,OAAO,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrE,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACvB,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC;YAC5D,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,IAAI,CAAC,iBAAiB,GAAG,UAAU,CAAC,GAAG,EAAE;oBACvC,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAC;oBACnC,IAAI,CAAC,WAAW,EAAE,CAAC;gBACrB,CAAC,EAAE,GAAG,CAAC,CAAC;gBACR,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACpC,IAAI,CAAC,MAAM;gBAAE,OAAO;YAEpB,IAAI,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpC,MAAM,CAAC,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;YAC7D,CAAC;YAED,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnB,MAAM,CAAC,KAAK,CACV,2CAA2C,MAAM,CAAC,KAAK,EAAE,EACzD,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,wBAAwB;gBACnC,iBAAiB,EAAE;oBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;oBACnB,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM;iBAChC;aACF,CAAC,CACH,CAAC;YAEF,OAAO,CAAC,OAAO,EAAE;iBACd,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;iBACzB,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE;gBAC5B,MAAM,CAAC,KAAK,CACV,iDAAiD,EACjD,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,uBAAuB;oBAClC,iBAAiB,EAAE;wBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;wBACnB,YAAY,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;qBAC/D;iBACF,CAAC,CACH,CAAC;gBACF,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACrB,CAAC,CAAC;iBACD,OAAO,CAAC,GAAG,EAAE;gBACZ,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;gBACnB,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,CAAC,CAAC,CAAC;QACP,CAAC;IACH,CAAC;CACF"}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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;IAAnC,YAA6B,MAAM,EAAE,mBAAmB,EAAI;IAEtD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC,
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1
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+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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;IAAnC,YAA6B,MAAM,EAAE,mBAAmB,EAAI;IAEtD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC,CA0CjB;IAED;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC,CA4CjB;IAED,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB;;;;;OAKG;IACH,OAAO,CAAC,UAAU;IAUlB,sFAAsF;IACtF,OAAO,CAAC,WAAW;IAcnB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;CAI3B"}
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@@ -26,7 +26,10 @@ export class NcbiApiClient {
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26
26
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const suffix = endpoint.includes('.') ? '' : '.fcgi';
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27
27
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const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
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28
28
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try {
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29
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-
logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({
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29
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+
logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({
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30
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+
operation: 'NcbiHttpRequest',
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31
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+
additionalContext: { endpoint },
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32
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+
}));
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30
33
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const response = usePost
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31
34
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? await this.postRequest(url, finalParams, options?.signal)
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32
35
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: await this.getRequest(url, finalParams, options?.signal);
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@@ -69,7 +72,10 @@ export class NcbiApiClient {
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69
72
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const fullUrl = qs ? `${url}?${qs}` : url;
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70
73
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const signal = this.buildTimeoutSignal(externalSignal);
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71
74
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try {
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72
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-
logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({
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75
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+
logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({
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76
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+
operation: 'NcbiExternalRequest',
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77
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+
additionalContext: { url },
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78
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+
}));
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73
79
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const response = await fetch(fullUrl, { signal });
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74
80
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const body = await response.text();
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75
81
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if (!response.ok) {
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@@ -1 +1 @@
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1
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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,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC/F,OAAO,EAAE,qBAAqB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAEpG,OAAO,EAAE,WAAW,EAAE,MAAM,+BAA+B,CAAC;AAC5D,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK,MAAM;IAAnC,YAA6B,MAA2B;sBAA3B,MAAM;IAAwB,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,
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1
|
+
{"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,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC/F,OAAO,EAAE,qBAAqB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAEpG,OAAO,EAAE,WAAW,EAAE,MAAM,+BAA+B,CAAC;AAC5D,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK,MAAM;IAAnC,YAA6B,MAA2B;sBAA3B,MAAM;IAAwB,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;gBACzC,SAAS,EAAE,iBAAiB;gBAC5B,iBAAiB,EAAE,EAAE,QAAQ,EAAE;aAChC,CAAC,CACH,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,yEAAyE;oBACzE,wEAAwE;oBACxE,uEAAuE;oBACvE,uDAAuD;oBACvD,YAAY,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,gBAAgB,CAAC,kBAAkB,CAAC,CAAC,CAAC,SAAS,CAAC;oBAClF,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,CACtB,wBAAwB,GAAG,EAAE,EAC7B,EAAE,MAAM,EAAE,kBAAkB,EAAE,QAAQ,EAAE,GAAG,WAAW,CAAC,kBAAkB,CAAC,EAAE,EAC5E,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,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,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAC;QAEvD,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CACV,8BAA8B,OAAO,EAAE,EACvC,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,qBAAqB;gBAChC,iBAAiB,EAAE,EAAE,GAAG,EAAE;aAC3B,CAAC,CACH,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,CACtB,wBAAwB,GAAG,EAAE,EAC7B,EAAE,MAAM,EAAE,kBAAkB,EAAE,GAAG,EAAE,GAAG,WAAW,CAAC,kBAAkB,CAAC,EAAE,EACvE,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,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;IAED;;;;;OAKG;IACK,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,OAAO,KAAK,CAAC,OAAO,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,sFAAsF;IAC9E,WAAW,CACjB,GAAW,EACX,MAA8B,EAC9B,MAAoB;QAEpB,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QACpD,OAAO,KAAK,CAAC,GAAG,EAAE;YAChB,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;YACJ,MAAM,EAAE,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC;SACxC,CAAC,CAAC;IACL,CAAC;IAED;;;OAGG;IACK,kBAAkB,CAAC,cAA4B;QACrD,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;QACjE,OAAO,cAAc,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;IAC3F,CAAC;CACF"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgEpB;;;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;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,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,CAIZ;IAED,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,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgEpB;;;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;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,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,CAIZ;IAED,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,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CA2BxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAkE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAiE5B;IAED,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAgEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA8BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -131,9 +131,11 @@ export class NcbiService {
|
|
|
131
131
|
const corrected = spellResult.CorrectedQuery ?? '';
|
|
132
132
|
logger.debug('ESpell result parsed.', requestContextService.createRequestContext({
|
|
133
133
|
operation: 'NcbiESpell',
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
134
|
+
additionalContext: {
|
|
135
|
+
original,
|
|
136
|
+
corrected,
|
|
137
|
+
hasSuggestion: corrected.length > 0 && corrected !== original,
|
|
138
|
+
},
|
|
137
139
|
}));
|
|
138
140
|
return {
|
|
139
141
|
original,
|
|
@@ -317,9 +319,7 @@ export class NcbiService {
|
|
|
317
319
|
const retryDelay = Math.round(jitter);
|
|
318
320
|
logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
|
|
319
321
|
operation: 'NcbiRetry',
|
|
320
|
-
endpoint: label,
|
|
321
|
-
attempt: attempt + 1,
|
|
322
|
-
retryDelay,
|
|
322
|
+
additionalContext: { endpoint: label, attempt: attempt + 1, retryDelay },
|
|
323
323
|
}));
|
|
324
324
|
await abortableSleep(retryDelay, signal);
|
|
325
325
|
continue;
|
|
@@ -379,11 +379,13 @@ export function initNcbiService() {
|
|
|
379
379
|
_service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
|
|
380
380
|
logger.info('NCBI service initialized.', requestContextService.createRequestContext({
|
|
381
381
|
operation: 'NcbiInit',
|
|
382
|
-
|
|
383
|
-
|
|
384
|
-
|
|
385
|
-
|
|
386
|
-
|
|
382
|
+
additionalContext: {
|
|
383
|
+
toolIdentifier: config.toolIdentifier,
|
|
384
|
+
hasApiKey: !!config.apiKey,
|
|
385
|
+
requestDelayMs: config.requestDelayMs,
|
|
386
|
+
maxConcurrent: config.maxConcurrent,
|
|
387
|
+
totalDeadlineMs: config.totalDeadlineMs,
|
|
388
|
+
},
|
|
387
389
|
}));
|
|
388
390
|
}
|
|
389
391
|
/** Get the initialized NCBI service. Throws if not initialized. */
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,
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1
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+
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAsQD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAkD/B"}
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@@ -4,7 +4,7 @@
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4
4
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* consistent ParsedBriefSummary objects.
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5
5
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* @module src/services/ncbi/parsing/esummary-parser
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6
6
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*/
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7
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-
import { dateParser, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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7
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+
import { dateParser, logger, requestContextService, withExtra } from '@cyanheads/mcp-ts-core/utils';
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8
8
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import { ensureArray, getAttribute, getText } from './xml-helpers.js';
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9
9
|
/**
|
|
10
10
|
* Formats an array of ESummary authors into a string.
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@@ -85,7 +85,7 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
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85
85
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const currentContext = parentContext ||
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86
86
|
requestContextService.createRequestContext({
|
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87
87
|
operation: 'standardizeESummaryDateInternal',
|
|
88
|
-
inputDate: dateInputString,
|
|
88
|
+
additionalContext: { inputDate: dateInputString },
|
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89
89
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});
|
|
90
90
|
try {
|
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91
91
|
const parsedDate = await dateParser.parseDate(dateInputString, currentContext);
|
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@@ -95,10 +95,7 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
|
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|
95
95
|
logger.debug(`standardizeESummaryDate: could not parse "${dateInputString}", returning undefined.`, currentContext);
|
|
96
96
|
}
|
|
97
97
|
catch (e) {
|
|
98
|
-
logger.warning(`standardizeESummaryDate: dateParser.parseDate error for "${dateInputString}", returning undefined.`, {
|
|
99
|
-
...currentContext,
|
|
100
|
-
error: e instanceof Error ? e.message : String(e),
|
|
101
|
-
});
|
|
98
|
+
logger.warning(`standardizeESummaryDate: dateParser.parseDate error for "${dateInputString}", returning undefined.`, withExtra(currentContext, { error: e instanceof Error ? e.message : String(e) }));
|
|
102
99
|
}
|
|
103
100
|
return;
|
|
104
101
|
}
|
|
@@ -141,7 +138,7 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
|
|
|
141
138
|
const authInputString = JSON.stringify(authorObj);
|
|
142
139
|
logger.warning(`Unhandled author structure in parseESummaryAuthorsFromDocumentSummary. authInput: ${authInputString.substring(0, 100)}`, requestContextService.createRequestContext({
|
|
143
140
|
operation: 'parseESummaryAuthorsFromDocumentSummary',
|
|
144
|
-
detail: 'Unhandled author structure',
|
|
141
|
+
additionalContext: { detail: 'Unhandled author structure' },
|
|
145
142
|
}));
|
|
146
143
|
const keys = Object.keys(authorObj);
|
|
147
144
|
if (keys.length === 1 &&
|
|
@@ -196,8 +193,10 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
|
|
|
196
193
|
catch (e) {
|
|
197
194
|
logger.debug(`Failed to parse Authors string as JSON: ${authorsProp.substring(0, 100)}`, requestContextService.createRequestContext({
|
|
198
195
|
operation: 'parseESummaryAuthorsFromString',
|
|
199
|
-
|
|
200
|
-
|
|
196
|
+
additionalContext: {
|
|
197
|
+
input: authorsProp.substring(0, 100),
|
|
198
|
+
error: e instanceof Error ? e.message : String(e),
|
|
199
|
+
},
|
|
201
200
|
}));
|
|
202
201
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}
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for (const namePart of authorsProp.split(/[,;]/)) {
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@@ -312,10 +311,7 @@ export async function extractBriefSummaries(eSummaryResult, context) {
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operation: 'extractBriefSummariesInternal',
|
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|
});
|
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314
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|
if (eSummaryResult.ERROR) {
|
|
315
|
-
logger.warning('ESummary result contains an error', {
|
|
316
|
-
...opContext,
|
|
317
|
-
errorDetails: eSummaryResult.ERROR,
|
|
318
|
-
});
|
|
314
|
+
logger.warning('ESummary result contains an error', withExtra(opContext, { errorDetails: eSummaryResult.ERROR }));
|
|
319
315
|
return [];
|
|
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316
|
}
|
|
321
317
|
let rawSummaries = [];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAepD;;;;;;;;;;;;;;GAcG;AACH,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAgB;IACxC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAK;IACrB,OAAO,CAAC,aAAa,CAAK;IAC1B,OAAO,CAAC,iBAAiB,CAA4C;IAErE,YACE,aAAa,EAAE,MAAM,EACrB,aAAa,GAAE,MAA+B,EAC9C,YAAY,GAAE,MAA+B,EAK9C;IAED,OAAO,CAAC,CAAC,EACP,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EACtB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,CAAC,CAAC,CAyCZ;IAED,OAAO,CAAC,WAAW;
|
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1
|
+
{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAepD;;;;;;;;;;;;;;GAcG;AACH,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAgB;IACxC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAK;IACrB,OAAO,CAAC,aAAa,CAAK;IAC1B,OAAO,CAAC,iBAAiB,CAA4C;IAErE,YACE,aAAa,EAAE,MAAM,EACrB,aAAa,GAAE,MAA+B,EAC9C,YAAY,GAAE,MAA+B,EAK9C;IAED,OAAO,CAAC,CAAC,EACP,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EACtB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,CAAC,CAAC,CAyCZ;IAED,OAAO,CAAC,WAAW;CAoEpB"}
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@@ -84,7 +84,7 @@ export class NcbiRequestQueue {
|
|
|
84
84
|
if (gap > 0) {
|
|
85
85
|
logger.debug(`Delaying next NCBI dispatch by ${gap}ms to respect rate limit.`, requestContextService.createRequestContext({
|
|
86
86
|
operation: 'NcbiQueueWait',
|
|
87
|
-
delayMs: gap,
|
|
87
|
+
additionalContext: { delayMs: gap },
|
|
88
88
|
}));
|
|
89
89
|
this.nextDispatchTimer = setTimeout(() => {
|
|
90
90
|
this.nextDispatchTimer = undefined;
|
|
@@ -104,9 +104,11 @@ export class NcbiRequestQueue {
|
|
|
104
104
|
this.inFlight += 1;
|
|
105
105
|
logger.info(`Executing NCBI request via queue: ${waiter.endpoint}`, requestContextService.createRequestContext({
|
|
106
106
|
operation: 'NcbiQueueDispatch',
|
|
107
|
-
|
|
108
|
-
|
|
109
|
-
|
|
107
|
+
additionalContext: {
|
|
108
|
+
endpoint: waiter.endpoint,
|
|
109
|
+
inFlight: this.inFlight,
|
|
110
|
+
queueDepth: this.waiters.length,
|
|
111
|
+
},
|
|
110
112
|
}));
|
|
111
113
|
// `Promise.resolve().then(() => task())` converts any sync throw from
|
|
112
114
|
// `task()` into a rejected promise so the finally() bookkeeping always
|
|
@@ -116,8 +118,10 @@ export class NcbiRequestQueue {
|
|
|
116
118
|
.then(waiter.resolve, (err) => {
|
|
117
119
|
logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
|
|
118
120
|
operation: 'NcbiQueueProcess',
|
|
119
|
-
|
|
120
|
-
|
|
121
|
+
additionalContext: {
|
|
122
|
+
endpoint: waiter.endpoint,
|
|
123
|
+
errorMessage: err instanceof Error ? err.message : String(err),
|
|
124
|
+
},
|
|
121
125
|
}));
|
|
122
126
|
waiter.reject(err);
|
|
123
127
|
})
|
|
@@ -1 +1 @@
|
|
|
1
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-
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