@cyanheads/pubmed-mcp-server 2.6.10 → 2.6.12
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 +2 -2
- package/README.md +4 -3
- package/dist/config/server-config.d.ts +1 -0
- package/dist/config/server-config.d.ts.map +1 -1
- package/dist/config/server-config.js +7 -0
- package/dist/config/server-config.js.map +1 -1
- package/dist/index.js +1 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +0 -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 +21 -41
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +6 -7
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +11 -11
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts +26 -11
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +94 -52
- 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 +8 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +8 -8
- package/server.json +3 -3
package/CLAUDE.md
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@@ -1,8 +1,8 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.6.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.
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**Version:** 2.6.12
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.1`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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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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@@ -97,7 +97,7 @@ Find articles related to a source article via ELink.
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- Three relationship types: `similar` (content similarity), `cited_by`, `references`
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- Results enriched with title, authors, publication date, and source via ESummary
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- Results returned in NCBI's relevance order
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---
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@@ -285,7 +285,8 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
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| `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
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| `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
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| `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
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| `NCBI_REQUEST_DELAY_MS` |
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| `NCBI_REQUEST_DELAY_MS` | Minimum gap between NCBI request starts in ms | 334 (100 with key) |
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| `NCBI_MAX_CONCURRENT` | Max concurrent in-flight NCBI requests | `8` |
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| `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
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| `NCBI_TIMEOUT_MS` | Per-request HTTP timeout in ms | `30000` |
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| `NCBI_TOTAL_DEADLINE_MS` | Total deadline across all retry attempts for one NCBI call, in ms | `60000` |
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@@ -10,6 +10,7 @@ declare const ServerConfigSchema: z.ZodObject<{
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toolIdentifier: z.ZodDefault<z.ZodString>;
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adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
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requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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maxConcurrent: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
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{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAU3C,QAAA,MAAM,kBAAkB
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{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAU3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;iBAiCtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAyB9C"}
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@@ -17,6 +17,12 @@ const ServerConfigSchema = z.object({
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toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
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adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
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requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
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maxConcurrent: z.coerce
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.number()
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.min(1)
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.max(16)
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.default(8)
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.describe('Max concurrent in-flight NCBI requests'),
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maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
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timeoutMs: z.coerce
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.number()
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toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
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adminEmail: 'NCBI_ADMIN_EMAIL',
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requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
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maxConcurrent: 'NCBI_MAX_CONCURRENT',
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maxRetries: 'NCBI_MAX_RETRIES',
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timeoutMs: 'NCBI_TIMEOUT_MS',
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totalDeadlineMs: 'NCBI_TOTAL_DEADLINE_MS',
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{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,CAAC,CAAU,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAEpE,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC,CAAC,UAAU,CAAC,gBAAgB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,cAAc,CAAC;IACtF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IACxF,UAAU,EAAE,CAAC,CAAC,UAAU,CAAC,gBAAgB,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChG,cAAc,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChG,aAAa,EAAE,CAAC,CAAC,MAAM;SACpB,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,wCAAwC,CAAC;IACrD,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACtF,SAAS,EAAE,CAAC,CAAC,MAAM;SAChB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,gCAAgC,CAAC;IAC7C,eAAe,EAAE,CAAC,CAAC,MAAM;SACtB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,mEAAmE,CAAC;IAChF,cAAc,EAAE,CAAC;SACd,UAAU,CAAC,gBAAgB,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;SAClD,QAAQ,CAAC,uEAAuE,CAAC;IACpF,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,2EAA2E,CAAC;CACzF,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,MAAM,GAAG,cAAc,CAAC,kBAAkB,EAAE;YAChD,MAAM,EAAE,cAAc;YACtB,cAAc,EAAE,sBAAsB;YACtC,UAAU,EAAE,kBAAkB;YAC9B,cAAc,EAAE,uBAAuB;YACvC,aAAa,EAAE,qBAAqB;YACpC,UAAU,EAAE,kBAAkB;YAC9B,SAAS,EAAE,iBAAiB;YAC5B,eAAe,EAAE,wBAAwB;YACzC,cAAc,EAAE,iBAAiB;YACjC,kBAAkB,EAAE,sBAAsB;SAC3C,CAAC,CAAC;QACH;;;;WAIG;QACH,OAAO;YACL,MAAM,CAAC,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,qBAAqB,KAAK,SAAS;gBAC9D,CAAC,CAAC,EAAE,GAAG,MAAM,EAAE,cAAc,EAAE,GAAG,EAAE;gBACpC,CAAC,CAAC,MAAM,CAAC;IACf,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
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package/dist/index.js
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resources: [databaseInfoResource],
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prompts: [researchPlanPrompt],
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instructions: "PubMed/NCBI E-utilities wrapper. Typical research flow: `pubmed_search_articles` → `pubmed_fetch_articles` (metadata) → `pubmed_fetch_fulltext`. Prefer `pubmed_lookup_citation` over free-text search when you have a partial known reference — it's deterministic. Use `pubmed_lookup_mesh` and `pubmed_spell_check` to refine queries before searching, when needed.",
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landing: {
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tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
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repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AAEjF,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,mBAAmB;QACnB,eAAe;QACf,cAAc;QACd,cAAc;QACd,kBAAkB;QAClB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,YAAY,EACV,yWAAyW;IAC3W,OAAO,EAAE;QACP,OAAO,EACL,uGAAuG;QACzG,QAAQ,EAAE,gDAAgD;QAC1D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,kCAAkC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC7E;gBACE,KAAK,EAAE,kBAAkB;gBACzB,IAAI,EAAE,8CAA8C;gBACpD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,qBAAqB;gBAC5B,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD,EAAE,KAAK,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE,QAAQ,EAAE,IAAI,EAAE;SAC9E;QACD,UAAU,EAAE;YACV,YAAY,EAAE,mBAAmB;YACjC,gBAAgB,EAAE,iBAAiB;YACnC,eAAe,EAAE,iBAAiB;SACnC;KACF;IACD,KAAK;QACH,eAAe,EAAE,CAAC;QAClB,oBAAoB,EAAE,CAAC;IACzB,CAAC;CACF,CAAC,CAAC"}
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@@ -25,7 +25,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
|
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25
25
|
authors: z.ZodOptional<z.ZodString>;
|
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26
26
|
source: z.ZodOptional<z.ZodString>;
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27
27
|
pubDate: z.ZodOptional<z.ZodString>;
|
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28
|
-
score: z.ZodOptional<z.ZodNumber>;
|
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29
28
|
}, z.core.$strip>>;
|
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30
29
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totalFound: z.ZodNumber;
|
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31
30
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notice: z.ZodOptional<z.ZodString>;
|
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2L1B,CAAC"}
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@@ -44,10 +44,6 @@ export const findRelatedTool = tool('pubmed_find_related', {
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44
44
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authors: z.string().optional().describe('Author string'),
|
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45
45
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source: z.string().optional().describe('Journal source'),
|
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46
46
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pubDate: z.string().optional().describe('Publication date'),
|
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47
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-
score: z
|
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48
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-
.number()
|
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49
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-
.optional()
|
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50
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-
.describe('NCBI relevance score (arbitrary scale, higher = more related; only present for similar)'),
|
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51
47
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})
|
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52
48
|
.describe('Related article with enriched summary'))
|
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53
49
|
.describe('Related articles'),
|
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@@ -63,45 +59,34 @@ export const findRelatedTool = tool('pubmed_find_related', {
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63
59
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pmid: input.pmid,
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64
60
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relationship: input.relationship,
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65
61
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});
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66
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-
|
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62
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+
// `cmd=neighbor_score` is unstable on NCBI's side — it intermittently fails
|
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63
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+
// with a TXCLIENT::readAll EOF for high-traffic PMIDs. `cmd=neighbor` returns
|
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64
|
+
// the `pubmed_pubmed` list in relevance order anyway, so we keep the ranking
|
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65
|
+
// without the (arbitrary-scale) numeric score.
|
|
66
|
+
const linkName = input.relationship === 'cited_by'
|
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67
|
+
? 'pubmed_pubmed_citedin'
|
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68
|
+
: input.relationship === 'references'
|
|
69
|
+
? 'pubmed_pubmed_refs'
|
|
70
|
+
: 'pubmed_pubmed';
|
|
71
|
+
const eLinkResult = (await ncbi.eLink({
|
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67
72
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dbfrom: 'pubmed',
|
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68
73
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db: 'pubmed',
|
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69
74
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id: input.pmid,
|
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75
|
+
cmd: 'neighbor',
|
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76
|
+
linkname: linkName,
|
|
70
77
|
retmode: 'xml',
|
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71
|
-
};
|
|
72
|
-
switch (input.relationship) {
|
|
73
|
-
case 'similar':
|
|
74
|
-
eLinkParams.cmd = 'neighbor_score';
|
|
75
|
-
break;
|
|
76
|
-
case 'cited_by':
|
|
77
|
-
eLinkParams.cmd = 'neighbor';
|
|
78
|
-
eLinkParams.linkname = 'pubmed_pubmed_citedin';
|
|
79
|
-
break;
|
|
80
|
-
case 'references':
|
|
81
|
-
eLinkParams.cmd = 'neighbor';
|
|
82
|
-
eLinkParams.linkname = 'pubmed_pubmed_refs';
|
|
83
|
-
break;
|
|
84
|
-
}
|
|
85
|
-
const eLinkResult = (await ncbi.eLink(eLinkParams, { signal: ctx.signal }));
|
|
78
|
+
}, { signal: ctx.signal }));
|
|
86
79
|
const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
|
|
87
80
|
const firstResult = eLinkResultsArray[0];
|
|
88
81
|
const linkSet = firstResult?.LinkSet;
|
|
89
82
|
let foundPmids = [];
|
|
90
83
|
if (linkSet?.LinkSetDb) {
|
|
91
84
|
const linkSetDbArray = ensureArray(linkSet.LinkSetDb);
|
|
92
|
-
const
|
|
93
|
-
? 'pubmed_pubmed_citedin'
|
|
94
|
-
: input.relationship === 'references'
|
|
95
|
-
? 'pubmed_pubmed_refs'
|
|
96
|
-
: 'pubmed_pubmed';
|
|
97
|
-
const targetDb = linkSetDbArray.find((db) => db.LinkName === expectedLinkName) ?? linkSetDbArray[0];
|
|
85
|
+
const targetDb = linkSetDbArray.find((db) => db.LinkName === linkName) ?? linkSetDbArray[0];
|
|
98
86
|
if (targetDb?.Link) {
|
|
99
87
|
foundPmids = ensureArray(targetDb.Link)
|
|
100
|
-
.map((link) => (
|
|
101
|
-
pmid
|
|
102
|
-
...(extractValue(link.Score) ? { score: Number(extractValue(link.Score)) } : {}),
|
|
103
|
-
}))
|
|
104
|
-
.filter((item) => item.pmid && item.pmid !== input.pmid && item.pmid !== '0');
|
|
88
|
+
.map((link) => extractValue(link.Id))
|
|
89
|
+
.filter((pmid) => pmid && pmid !== input.pmid && pmid !== '0');
|
|
105
90
|
}
|
|
106
91
|
}
|
|
107
92
|
const totalFound = foundPmids.length;
|
|
@@ -152,25 +137,21 @@ export const findRelatedTool = tool('pubmed_find_related', {
|
|
|
152
137
|
...(notice && { notice }),
|
|
153
138
|
};
|
|
154
139
|
}
|
|
155
|
-
if (foundPmids.every((p) => p.score !== undefined)) {
|
|
156
|
-
foundPmids.sort((a, b) => (b.score ?? 0) - (a.score ?? 0));
|
|
157
|
-
}
|
|
158
140
|
const pmidsToEnrich = foundPmids.slice(0, input.maxResults);
|
|
159
141
|
const summaryResult = await ncbi.eSummary({
|
|
160
142
|
db: 'pubmed',
|
|
161
|
-
id: pmidsToEnrich.
|
|
143
|
+
id: pmidsToEnrich.join(','),
|
|
162
144
|
}, { signal: ctx.signal });
|
|
163
145
|
const briefSummaries = await extractBriefSummaries(summaryResult);
|
|
164
146
|
const summaryMap = new Map(briefSummaries.map((bs) => [bs.pmid, bs]));
|
|
165
|
-
const articles = pmidsToEnrich.map((
|
|
166
|
-
const details = summaryMap.get(
|
|
147
|
+
const articles = pmidsToEnrich.map((pmid) => {
|
|
148
|
+
const details = summaryMap.get(pmid);
|
|
167
149
|
return {
|
|
168
|
-
pmid
|
|
150
|
+
pmid,
|
|
169
151
|
title: details?.title,
|
|
170
152
|
authors: details?.authors,
|
|
171
153
|
source: details?.source,
|
|
172
154
|
pubDate: details?.pubDate,
|
|
173
|
-
score: p.score,
|
|
174
155
|
};
|
|
175
156
|
});
|
|
176
157
|
return { sourcePmid: input.pmid, relationship: input.relationship, articles, totalFound };
|
|
@@ -188,8 +169,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
|
|
|
188
169
|
}
|
|
189
170
|
else {
|
|
190
171
|
for (const a of result.articles) {
|
|
191
|
-
|
|
192
|
-
lines.push(`- **[PMID ${a.pmid}](https://pubmed.ncbi.nlm.nih.gov/${a.pmid}/)**${scorePart}`);
|
|
172
|
+
lines.push(`- **[PMID ${a.pmid}](https://pubmed.ncbi.nlm.nih.gov/${a.pmid}/)**`);
|
|
193
173
|
if (a.title)
|
|
194
174
|
lines.push(` ${a.title}`);
|
|
195
175
|
if (a.authors)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;
|
|
1
|
+
{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAqBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;SAC5D,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACjF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uJAAuJ,CACxJ;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0BAA0B,EAAE;YACxC,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,YAAY,EAAE,KAAK,CAAC,YAAY;SACjC,CAAC,CAAC;QAEH,4EAA4E;QAC5E,8EAA8E;QAC9E,6EAA6E;QAC7E,+CAA+C;QAC/C,MAAM,QAAQ,GACZ,KAAK,CAAC,YAAY,KAAK,UAAU;YAC/B,CAAC,CAAC,uBAAuB;YACzB,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,YAAY;gBACnC,CAAC,CAAC,oBAAoB;gBACtB,CAAC,CAAC,eAAe,CAAC;QAExB,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CACnC;YACE,MAAM,EAAE,QAAQ;YAChB,EAAE,EAAE,QAAQ;YACZ,EAAE,EAAE,KAAK,CAAC,IAAI;YACd,GAAG,EAAE,UAAU;YACf,QAAQ,EAAE,QAAQ;YAClB,OAAO,EAAE,KAAK;SACf,EACD,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAkB,CAAC;QACpB,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QAChE,MAAM,WAAW,GAAG,iBAAiB,CAAC,CAAC,CAAgC,CAAC;QACxE,MAAM,OAAO,GAAG,WAAW,EAAE,OAAO,CAAC;QACrC,IAAI,UAAU,GAAa,EAAE,CAAC;QAE9B,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;YACvB,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,QAAQ,CAAC,IAAI,cAAc,CAAC,CAAC,CAAC,CAAC;YAE5F,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;gBACnB,UAAU,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC;qBACpC,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;qBAClD,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,IAAI,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,IAAI,KAAK,GAAG,CAAC,CAAC;YACnE,CAAC;QACH,CAAC;QAED,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,yEAAyE;YACzE,0EAA0E;YAC1E,yEAAyE;YACzE,yEAAyE;YACzE,wEAAwE;YACxE,IAAI,aAA6C,CAAC;YAClD,IAAI,sBAAsB,GAAG,KAAK,CAAC;YACnC,IAAI,CAAC;gBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;gBACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;gBAC7D,aAAa,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;gBAC7B,uEAAuE;gBACvE,IAAI,CAAC,aAAa,EAAE,KAAK;oBAAE,sBAAsB,GAAG,IAAI,CAAC;YAC3D,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,6BAA6B,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC;gBACtD,yEAAyE;gBACzE,sEAAsE;gBACtE,wEAAwE;gBACxE,uBAAuB;gBACvB,MAAM,MAAM,GACV,GAAG,YAAY,QAAQ;oBACrB,CAAC,CAAE,GAAG,CAAC,IAAwC,EAAE,MAAM;oBACvD,CAAC,CAAC,SAAS,CAAC;gBAChB,IAAI,MAAM,KAAK,yBAAyB,EAAE,CAAC;oBACzC,sBAAsB,GAAG,IAAI,CAAC;gBAChC,CAAC;YACH,CAAC;YAED,IAAI,MAA0B,CAAC;YAC/B,IAAI,sBAAsB,EAAE,CAAC;gBAC3B,MAAM,GAAG,eAAe,KAAK,CAAC,IAAI,mGAAmG,CAAC;YACxI,CAAC;iBAAM,IAAI,aAAa,EAAE,KAAK,IAAI,KAAK,CAAC,YAAY,KAAK,YAAY,EAAE,CAAC;gBACvE,MAAM,WAAW,GAAG,aAAa,CAAC,KAAK,CAAC;gBACxC,MAAM,GAAG,WAAW;oBAClB,CAAC,CAAC,2CAA2C,KAAK,CAAC,IAAI,WAAW,WAAW,IAAI;oBACjF,CAAC,CAAC,yEAAyE,KAAK,CAAC,IAAI,+IAA+I,CAAC;YACzO,CAAC;YAED,OAAO;gBACL,UAAU,EAAE,KAAK,CAAC,IAAI;gBACtB,YAAY,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@@ -56,14 +56,13 @@ export declare class NcbiService {
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*/
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private withRetry;
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/**
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*
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-
*
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-
*
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62
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-
* connection resets surfaced as C++ exception traces).
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+
* Runs a request under a service-level deadline that bounds queue wait time
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60
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+
* + retry chain + HTTP execution. The deadline is constructed *outside* the
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+
* queue so a backlog can't burn a request's budget before it even dispatches.
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*
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-
* The combined deadline+caller signal is threaded into
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*
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66
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-
*
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63
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+
* The combined deadline+caller signal is threaded into the queue (cancels a
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64
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+
* still-waiting task), the retry chain (cancels pending backoff sleeps),
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65
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+
* and the HTTP fetch (cancels wedged requests).
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*/
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private performRequest;
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}
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;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;
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;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;IAwD7B,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
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@@ -187,7 +187,7 @@ export class NcbiService {
|
|
|
187
187
|
};
|
|
188
188
|
let text;
|
|
189
189
|
try {
|
|
190
|
-
text = await this.
|
|
190
|
+
text = await this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params, signal), 'idconv', signal), 'idconv', params, signal), options?.signal);
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catch (error) {
|
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|
// PMC ID Converter returns 400 (InvalidParams) for malformed inputs and
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|
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/**
|
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*
|
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*
|
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*
|
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* connection resets surfaced as C++ exception traces).
|
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* Runs a request under a service-level deadline that bounds queue wait time
|
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* + retry chain + HTTP execution. The deadline is constructed *outside* the
|
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* queue so a backlog can't burn a request's budget before it even dispatches.
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|
|
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* The combined deadline+caller signal is threaded into
|
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|
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*
|
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|
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*
|
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|
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* The combined deadline+caller signal is threaded into the queue (cancels a
|
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|
+
* still-waiting task), the retry chain (cancels pending backoff sleeps),
|
|
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|
+
* and the HTTP fetch (cancels wedged requests).
|
|
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|
*/
|
|
320
319
|
performRequest(endpoint, params, options) {
|
|
321
|
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return this.
|
|
320
|
+
return this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(async () => {
|
|
322
321
|
const text = await this.apiClient.makeRequest(endpoint, params, {
|
|
323
322
|
...options,
|
|
324
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|
signal,
|
|
325
324
|
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|
|
326
325
|
return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
|
|
327
|
-
}, endpoint, signal),
|
|
326
|
+
}, endpoint, signal), endpoint, params, signal), options?.signal);
|
|
328
327
|
}
|
|
329
328
|
}
|
|
330
329
|
// ─── Init / Accessor ────────────────────────────────────────────────────────
|
|
@@ -338,7 +337,7 @@ export function initNcbiService() {
|
|
|
338
337
|
...(config.apiKey && { apiKey: config.apiKey }),
|
|
339
338
|
...(config.adminEmail && { adminEmail: config.adminEmail }),
|
|
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339
|
});
|
|
341
|
-
const queue = new NcbiRequestQueue(config.requestDelayMs);
|
|
340
|
+
const queue = new NcbiRequestQueue(config.requestDelayMs, config.maxConcurrent);
|
|
342
341
|
const responseHandler = new NcbiResponseHandler();
|
|
343
342
|
_service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
|
|
344
343
|
logger.info('NCBI service initialized.', requestContextService.createRequestContext({
|
|
@@ -346,6 +345,7 @@ export function initNcbiService() {
|
|
|
346
345
|
toolIdentifier: config.toolIdentifier,
|
|
347
346
|
hasApiKey: !!config.apiKey,
|
|
348
347
|
requestDelayMs: config.requestDelayMs,
|
|
348
|
+
maxConcurrent: config.maxConcurrent,
|
|
349
349
|
totalDeadlineMs: config.totalDeadlineMs,
|
|
350
350
|
}));
|
|
351
351
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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* @fileoverview Rate-limited request scheduler for NCBI E-utility calls. Caps
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* concurrent in-flight requests and enforces a minimum start-gap between
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* dispatches to stay within NCBI's documented per-second ceiling. Supports
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* abort-during-wait so callers' deadlines can bound queue time end-to-end.
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import type { NcbiRequestParams } from './types.js';
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* Schedules NCBI API requests against two independent ceilings:
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*
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* - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
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* dispatch times. Matches NCBI's per-second start-rate cap (≈3/s without
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* an API key, ≈10/s with one).
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* - **Concurrency** (`maxConcurrent`): maximum number of requests in flight
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* simultaneously. Decouples concurrency from rate, so slow upstream
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* responses don't block new dispatches.
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*
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* Enqueue accepts an optional `AbortSignal` so callers can bound their total
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* rejects immediately instead of sitting behind a saturated worker for
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export declare class NcbiRequestQueue {
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private readonly
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private readonly waiters;
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private readonly minStartGapMs;
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private readonly maxConcurrent;
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constructor(minStartGapMs: number, maxConcurrent?: number, maxQueueSize?: number);
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enqueue<T>(task: () => Promise<T>, endpoint: string, params: NcbiRequestParams, signal?: AbortSignal): Promise<T>;
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private tryDispatch;
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}
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//# sourceMappingURL=request-queue.d.ts.map
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{"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA
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{"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;gBAGnE,aAAa,EAAE,MAAM,EACrB,aAAa,GAAE,MAA+B,EAC9C,YAAY,GAAE,MAA+B;IAO/C,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;IA+Cb,OAAO,CAAC,WAAW;CAgEpB"}
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/**
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* @fileoverview
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*
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* @fileoverview Rate-limited request scheduler for NCBI E-utility calls. Caps
|
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3
|
+
* concurrent in-flight requests and enforces a minimum start-gap between
|
|
4
|
+
* dispatches to stay within NCBI's documented per-second ceiling. Supports
|
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5
|
+
* abort-during-wait so callers' deadlines can bound queue time end-to-end.
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* @module src/services/ncbi/request-queue
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*/
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import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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import { recoveryFor } from '../../services/error-contracts.js';
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const DEFAULT_MAX_CONCURRENT = 8;
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const DEFAULT_MAX_QUEUE_SIZE = 100;
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/**
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*
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*
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* Schedules NCBI API requests against two independent ceilings:
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*
|
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16
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* - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
|
|
17
|
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* dispatch times. Matches NCBI's per-second start-rate cap (≈3/s without
|
|
18
|
+
* an API key, ≈10/s with one).
|
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19
|
+
* - **Concurrency** (`maxConcurrent`): maximum number of requests in flight
|
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* simultaneously. Decouples concurrency from rate, so slow upstream
|
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* responses don't block new dispatches.
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*
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* Enqueue accepts an optional `AbortSignal` so callers can bound their total
|
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* time inside the scheduler — when the signal fires, a still-waiting task
|
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* rejects immediately instead of sitting behind a saturated worker for
|
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* minutes.
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*/
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export class NcbiRequestQueue {
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waiters = [];
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minStartGapMs;
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maxConcurrent;
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maxQueueSize;
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inFlight = 0;
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lastStartTime = 0;
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nextDispatchTimer;
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constructor(minStartGapMs, maxConcurrent = DEFAULT_MAX_CONCURRENT, maxQueueSize = DEFAULT_MAX_QUEUE_SIZE) {
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this.minStartGapMs = minStartGapMs;
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this.maxConcurrent = maxConcurrent;
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this.maxQueueSize = maxQueueSize;
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}
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enqueue(task, endpoint, params) {
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25
|
-
if (this.
|
|
41
|
+
enqueue(task, endpoint, params, signal) {
|
|
42
|
+
if (this.waiters.length >= this.maxQueueSize) {
|
|
26
43
|
return Promise.reject(new McpError(JsonRpcErrorCode.RateLimited, `NCBI request queue is full (max ${this.maxQueueSize}).`, {
|
|
27
44
|
reason: 'queue_full',
|
|
28
45
|
endpoint,
|
|
29
|
-
queueSize: this.
|
|
46
|
+
queueSize: this.waiters.length,
|
|
30
47
|
...recoveryFor('queue_full'),
|
|
31
48
|
}));
|
|
32
49
|
}
|
|
33
50
|
return new Promise((resolve, reject) => {
|
|
34
|
-
|
|
35
|
-
|
|
51
|
+
if (signal?.aborted) {
|
|
52
|
+
reject(signal.reason);
|
|
53
|
+
return;
|
|
54
|
+
}
|
|
55
|
+
const waiter = {
|
|
56
|
+
resolve,
|
|
36
57
|
reject,
|
|
37
58
|
task,
|
|
38
59
|
endpoint,
|
|
39
60
|
params,
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
61
|
+
...(signal && { signal }),
|
|
62
|
+
};
|
|
63
|
+
if (signal) {
|
|
64
|
+
const onAbort = () => {
|
|
65
|
+
const idx = this.waiters.indexOf(waiter);
|
|
66
|
+
if (idx === -1)
|
|
67
|
+
return; // already dispatched — the task forwards its own signal
|
|
68
|
+
this.waiters.splice(idx, 1);
|
|
69
|
+
reject(signal.reason);
|
|
70
|
+
};
|
|
71
|
+
waiter.onAbort = onAbort;
|
|
72
|
+
signal.addEventListener('abort', onAbort, { once: true });
|
|
43
73
|
}
|
|
74
|
+
this.waiters.push(waiter);
|
|
75
|
+
this.tryDispatch();
|
|
44
76
|
});
|
|
45
77
|
}
|
|
46
|
-
|
|
47
|
-
if (this.
|
|
48
|
-
return;
|
|
49
|
-
this.processing = true;
|
|
50
|
-
const item = this.queue.shift();
|
|
51
|
-
if (!item) {
|
|
52
|
-
this.processing = false;
|
|
78
|
+
tryDispatch() {
|
|
79
|
+
if (this.nextDispatchTimer !== undefined)
|
|
53
80
|
return;
|
|
54
|
-
|
|
55
|
-
const { resolve, reject, task, endpoint } = item;
|
|
56
|
-
try {
|
|
81
|
+
while (this.inFlight < this.maxConcurrent && this.waiters.length > 0) {
|
|
57
82
|
const now = Date.now();
|
|
58
|
-
const
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
logger.debug(`Delaying NCBI request by ${wait}ms to respect rate limit.`, requestContextService.createRequestContext({
|
|
83
|
+
const gap = this.minStartGapMs - (now - this.lastStartTime);
|
|
84
|
+
if (gap > 0) {
|
|
85
|
+
logger.debug(`Delaying next NCBI dispatch by ${gap}ms to respect rate limit.`, requestContextService.createRequestContext({
|
|
62
86
|
operation: 'NcbiQueueWait',
|
|
63
|
-
|
|
64
|
-
delayMs: wait,
|
|
87
|
+
delayMs: gap,
|
|
65
88
|
}));
|
|
66
|
-
|
|
89
|
+
this.nextDispatchTimer = setTimeout(() => {
|
|
90
|
+
this.nextDispatchTimer = undefined;
|
|
91
|
+
this.tryDispatch();
|
|
92
|
+
}, gap);
|
|
93
|
+
return;
|
|
67
94
|
}
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
operation: 'NcbiQueueProcess',
|
|
76
|
-
endpoint,
|
|
77
|
-
errorMessage: error instanceof Error ? error.message : String(error),
|
|
78
|
-
}));
|
|
79
|
-
reject(error);
|
|
80
|
-
}
|
|
81
|
-
finally {
|
|
82
|
-
this.processing = false;
|
|
83
|
-
if (this.queue.length > 0) {
|
|
84
|
-
queueMicrotask(() => this.processQueue());
|
|
95
|
+
const waiter = this.waiters.shift();
|
|
96
|
+
if (!waiter)
|
|
97
|
+
return;
|
|
98
|
+
// Detach the cancel listener now that we're about to start; the task is
|
|
99
|
+
// responsible for forwarding its own signal to downstream I/O.
|
|
100
|
+
if (waiter.signal && waiter.onAbort) {
|
|
101
|
+
waiter.signal.removeEventListener('abort', waiter.onAbort);
|
|
85
102
|
}
|
|
103
|
+
this.lastStartTime = Date.now();
|
|
104
|
+
this.inFlight += 1;
|
|
105
|
+
logger.info(`Executing NCBI request via queue: ${waiter.endpoint}`, requestContextService.createRequestContext({
|
|
106
|
+
operation: 'NcbiQueueDispatch',
|
|
107
|
+
endpoint: waiter.endpoint,
|
|
108
|
+
inFlight: this.inFlight,
|
|
109
|
+
queueDepth: this.waiters.length,
|
|
110
|
+
}));
|
|
111
|
+
// `Promise.resolve().then(() => task())` converts any sync throw from
|
|
112
|
+
// `task()` into a rejected promise so the finally() bookkeeping always
|
|
113
|
+
// runs.
|
|
114
|
+
Promise.resolve()
|
|
115
|
+
.then(() => waiter.task())
|
|
116
|
+
.then(waiter.resolve, (err) => {
|
|
117
|
+
logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
|
|
118
|
+
operation: 'NcbiQueueProcess',
|
|
119
|
+
endpoint: waiter.endpoint,
|
|
120
|
+
errorMessage: err instanceof Error ? err.message : String(err),
|
|
121
|
+
}));
|
|
122
|
+
waiter.reject(err);
|
|
123
|
+
})
|
|
124
|
+
.finally(() => {
|
|
125
|
+
this.inFlight -= 1;
|
|
126
|
+
this.tryDispatch();
|
|
127
|
+
});
|
|
86
128
|
}
|
|
87
129
|
}
|
|
88
130
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE7E,OAAO,EAAE,WAAW,EAAE,MAAM,+BAA+B,CAAC;AAG5D,MAAM,sBAAsB,GAAG,CAAC,CAAC;AACjC,MAAM,sBAAsB,GAAG,GAAG,CAAC;AAYnC;;;;;;;;;;;;;;GAcG;AACH,MAAM,OAAO,gBAAgB;IACV,OAAO,GAAa,EAAE,CAAC;IACvB,aAAa,CAAS;IACtB,aAAa,CAAS;IACtB,YAAY,CAAS;IAC9B,QAAQ,GAAG,CAAC,CAAC;IACb,aAAa,GAAG,CAAC,CAAC;IAClB,iBAAiB,CAA4C;IAErE,YACE,aAAqB,EACrB,gBAAwB,sBAAsB,EAC9C,eAAuB,sBAAsB;QAE7C,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAC;IACnC,CAAC;IAED,OAAO,CACL,IAAsB,EACtB,QAAgB,EAChB,MAAyB,EACzB,MAAoB;QAEpB,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC;YAC7C,OAAO,OAAO,CAAC,MAAM,CACnB,IAAI,QAAQ,CACV,gBAAgB,CAAC,WAAW,EAC5B,mCAAmC,IAAI,CAAC,YAAY,IAAI,EACxD;gBACE,MAAM,EAAE,YAAY;gBACpB,QAAQ;gBACR,SAAS,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM;gBAC9B,GAAG,WAAW,CAAC,YAAY,CAAC;aAC7B,CACF,CACF,CAAC;QACJ,CAAC;QAED,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,QAAQ;gBACR,MAAM;gBACN,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,CAAC,wDAAwD;oBAChF,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,MAAM,CAAC,KAAK,CACV,kCAAkC,GAAG,2BAA2B,EAChE,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,eAAe;oBAC1B,OAAO,EAAE,GAAG;iBACb,CAAC,CACH,CAAC;gBACF,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,wEAAwE;YACxE,+DAA+D;YAC/D,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,IAAI,CACT,qCAAqC,MAAM,CAAC,QAAQ,EAAE,EACtD,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,mBAAmB;gBAC9B,QAAQ,EAAE,MAAM,CAAC,QAAQ;gBACzB,QAAQ,EAAE,IAAI,CAAC,QAAQ;gBACvB,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM;aAChC,CAAC,CACH,CAAC;YAEF,sEAAsE;YACtE,uEAAuE;YACvE,QAAQ;YACR,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,2CAA2C,EAC3C,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,kBAAkB;oBAC7B,QAAQ,EAAE,MAAM,CAAC,QAAQ;oBACzB,YAAY,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;iBAC/D,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
|
|
1
|
+
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;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;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,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;CA0NL"}
|
|
@@ -6,6 +6,14 @@
|
|
|
6
6
|
*/
|
|
7
7
|
import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
8
|
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
9
|
+
/**
|
|
10
|
+
* fast-xml-parser is pinned to `~5.7.3` in package.json. 5.8.0 deprecates
|
|
11
|
+
* `XMLValidator` in favor of a new sibling package `fast-xml-validator`
|
|
12
|
+
* (published days before the deprecation, 0 dependents, by the same author).
|
|
13
|
+
* 5.8.0 carries no security fix or feature we need, so we stay on 5.7.x until
|
|
14
|
+
* `fast-xml-validator` has time in the wild. Re-evaluate during a future
|
|
15
|
+
* `maintenance` pass — if `bun update --latest` bumps this, restore the pin.
|
|
16
|
+
*/
|
|
9
17
|
import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
|
|
10
18
|
import { recoveryFor } from '../../services/error-contracts.js';
|
|
11
19
|
/**
|
|
@@ -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
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{
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|
2
2
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"name": "@cyanheads/pubmed-mcp-server",
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|
3
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-
"version": "2.6.
|
|
3
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+
"version": "2.6.12",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
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|
6
6
|
"type": "module",
|
|
@@ -71,24 +71,24 @@
|
|
|
71
71
|
"access": "public"
|
|
72
72
|
},
|
|
73
73
|
"dependencies": {
|
|
74
|
-
"@cyanheads/mcp-ts-core": "^0.
|
|
74
|
+
"@cyanheads/mcp-ts-core": "^0.9.1",
|
|
75
75
|
"defuddle": "^0.18.1",
|
|
76
|
-
"fast-xml-parser": "
|
|
76
|
+
"fast-xml-parser": "~5.7.3",
|
|
77
77
|
"linkedom": "^0.18.12",
|
|
78
78
|
"pino-pretty": "^13.1.3",
|
|
79
|
-
"sanitize-html": "^2.17.
|
|
79
|
+
"sanitize-html": "^2.17.4",
|
|
80
80
|
"unpdf": "^1.6.2"
|
|
81
81
|
},
|
|
82
82
|
"devDependencies": {
|
|
83
83
|
"@biomejs/biome": "^2.4.15",
|
|
84
|
-
"@types/node": "^25.
|
|
84
|
+
"@types/node": "^25.8.0",
|
|
85
85
|
"@types/sanitize-html": "^2.16.1",
|
|
86
|
-
"@vitest/coverage-istanbul": "^4.1.
|
|
86
|
+
"@vitest/coverage-istanbul": "^4.1.6",
|
|
87
87
|
"depcheck": "^1.4.7",
|
|
88
|
-
"fast-check": "^4.
|
|
88
|
+
"fast-check": "^4.8.0",
|
|
89
89
|
"ignore": "^7.0.5",
|
|
90
90
|
"tsc-alias": "^1.8.17",
|
|
91
91
|
"typescript": "^6.0.3",
|
|
92
|
-
"vitest": "^4.1.
|
|
92
|
+
"vitest": "^4.1.6"
|
|
93
93
|
}
|
|
94
94
|
}
|
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": "2.6.
|
|
9
|
+
"version": "2.6.12",
|
|
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": "2.6.
|
|
22
|
+
"version": "2.6.12",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.6.
|
|
69
|
+
"version": "2.6.12",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|