@cyanheads/pubmed-mcp-server 2.6.11 → 2.6.12

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Files changed (20) hide show
  1. package/CLAUDE.md +2 -2
  2. package/README.md +4 -3
  3. package/dist/config/server-config.d.ts +1 -0
  4. package/dist/config/server-config.d.ts.map +1 -1
  5. package/dist/config/server-config.js +7 -0
  6. package/dist/config/server-config.js.map +1 -1
  7. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +0 -1
  8. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/find-related.tool.js +21 -41
  10. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  11. package/dist/services/ncbi/ncbi-service.d.ts +6 -7
  12. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  13. package/dist/services/ncbi/ncbi-service.js +11 -11
  14. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  15. package/dist/services/ncbi/request-queue.d.ts +26 -11
  16. package/dist/services/ncbi/request-queue.d.ts.map +1 -1
  17. package/dist/services/ncbi/request-queue.js +94 -52
  18. package/dist/services/ncbi/request-queue.js.map +1 -1
  19. package/package.json +4 -4
  20. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,8 +1,8 @@
1
1
  # Agent Protocol
2
2
 
3
3
  **Server:** @cyanheads/pubmed-mcp-server
4
- **Version:** 2.6.11
5
- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.0`
4
+ **Version:** 2.6.12
5
+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.1`
6
6
  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
7
7
 
8
8
  > **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.
package/README.md CHANGED
@@ -7,7 +7,7 @@
7
7
 
8
8
  <div align="center">
9
9
 
10
- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.6.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
10
+ [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.6.12-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
11
11
 
12
12
  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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13
 
@@ -97,7 +97,7 @@ Find articles related to a source article via ELink.
97
97
 
98
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  - Three relationship types: `similar` (content similarity), `cited_by`, `references`
99
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  - Results enriched with title, authors, publication date, and source via ESummary
100
- - Similarity scores included for `similar` relationship type
100
+ - Results returned in NCBI's relevance order
101
101
 
102
102
  ---
103
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@@ -285,7 +285,8 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
285
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  | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
286
286
  | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
287
287
  | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
288
- | `NCBI_REQUEST_DELAY_MS` | Delay between NCBI requests in ms | 334 (100 with key) |
288
+ | `NCBI_REQUEST_DELAY_MS` | Minimum gap between NCBI request starts in ms | 334 (100 with key) |
289
+ | `NCBI_MAX_CONCURRENT` | Max concurrent in-flight NCBI requests | `8` |
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290
  | `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
290
291
  | `NCBI_TIMEOUT_MS` | Per-request HTTP timeout in ms | `30000` |
291
292
  | `NCBI_TOTAL_DEADLINE_MS` | Total deadline across all retry attempts for one NCBI call, in ms | `60000` |
package/dist/config/server-config.d.ts CHANGED
@@ -10,6 +10,7 @@ declare const ServerConfigSchema: z.ZodObject<{
10
10
  toolIdentifier: z.ZodDefault<z.ZodString>;
11
11
  adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
12
12
  requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
13
+ maxConcurrent: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
13
14
  maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
14
15
  timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
15
16
  totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
package/dist/config/server-config.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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;;;;;;;;;;iBA2BtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAwB9C"}
1
+ {"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"}
package/dist/config/server-config.js CHANGED
@@ -17,6 +17,12 @@ const ServerConfigSchema = z.object({
17
17
  toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
18
18
  adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
19
19
  requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
20
+ maxConcurrent: z.coerce
21
+ .number()
22
+ .min(1)
23
+ .max(16)
24
+ .default(8)
25
+ .describe('Max concurrent in-flight NCBI requests'),
20
26
  maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
21
27
  timeoutMs: z.coerce
22
28
  .number()
@@ -48,6 +54,7 @@ export function getServerConfig() {
48
54
  toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
49
55
  adminEmail: 'NCBI_ADMIN_EMAIL',
50
56
  requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
57
+ maxConcurrent: 'NCBI_MAX_CONCURRENT',
51
58
  maxRetries: 'NCBI_MAX_RETRIES',
52
59
  timeoutMs: 'NCBI_TIMEOUT_MS',
53
60
  totalDeadlineMs: 'NCBI_TOTAL_DEADLINE_MS',
package/dist/config/server-config.js.map CHANGED
@@ -1 +1 @@
1
- {"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,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,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"}
1
+ {"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"}
package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED
@@ -25,7 +25,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
25
25
  authors: z.ZodOptional<z.ZodString>;
26
26
  source: z.ZodOptional<z.ZodString>;
27
27
  pubDate: z.ZodOptional<z.ZodString>;
28
- score: z.ZodOptional<z.ZodNumber>;
29
28
  }, z.core.$strip>>;
30
29
  totalFound: z.ZodNumber;
31
30
  notice: z.ZodOptional<z.ZodString>;
package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED
@@ -1 +1 @@
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;AAsCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkN1B,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"}
package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED
@@ -44,10 +44,6 @@ export const findRelatedTool = tool('pubmed_find_related', {
44
44
  authors: z.string().optional().describe('Author string'),
45
45
  source: z.string().optional().describe('Journal source'),
46
46
  pubDate: z.string().optional().describe('Publication date'),
47
- score: z
48
- .number()
49
- .optional()
50
- .describe('NCBI relevance score (arbitrary scale, higher = more related; only present for similar)'),
51
47
  })
52
48
  .describe('Related article with enriched summary'))
53
49
  .describe('Related articles'),
@@ -63,45 +59,34 @@ export const findRelatedTool = tool('pubmed_find_related', {
63
59
  pmid: input.pmid,
64
60
  relationship: input.relationship,
65
61
  });
66
- const eLinkParams = {
62
+ // `cmd=neighbor_score` is unstable on NCBI's side — it intermittently fails
63
+ // with a TXCLIENT::readAll EOF for high-traffic PMIDs. `cmd=neighbor` returns
64
+ // the `pubmed_pubmed` list in relevance order anyway, so we keep the ranking
65
+ // without the (arbitrary-scale) numeric score.
66
+ const linkName = input.relationship === 'cited_by'
67
+ ? 'pubmed_pubmed_citedin'
68
+ : input.relationship === 'references'
69
+ ? 'pubmed_pubmed_refs'
70
+ : 'pubmed_pubmed';
71
+ const eLinkResult = (await ncbi.eLink({
67
72
  dbfrom: 'pubmed',
68
73
  db: 'pubmed',
69
74
  id: input.pmid,
75
+ cmd: 'neighbor',
76
+ linkname: linkName,
70
77
  retmode: 'xml',
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 expectedLinkName = input.relationship === 'cited_by'
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: extractValue(link.Id),
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.map((p) => p.pmid).join(','),
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((p) => {
166
- const details = summaryMap.get(p.pmid);
147
+ const articles = pmidsToEnrich.map((pmid) => {
148
+ const details = summaryMap.get(pmid);
167
149
  return {
168
- pmid: p.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
- const scorePart = a.score !== undefined ? ` (score: ${a.score})` : '';
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)
package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/ncbi-service.d.ts CHANGED
@@ -56,14 +56,13 @@ export declare class NcbiService {
56
56
  */
57
57
  private withRetry;
58
58
  /**
59
- * Enqueues a request with a service-level deadline and retry logic that covers
60
- * both HTTP-level failures (network errors, timeouts) and XML-level errors
61
- * (NCBI returning 200 OK with an error structure in the response body, e.g.
62
- * connection resets surfaced as C++ exception traces).
59
+ * Runs a request under a service-level deadline that bounds queue wait time
60
+ * + retry chain + HTTP execution. The deadline is constructed *outside* the
61
+ * queue so a backlog can't burn a request's budget before it even dispatches.
63
62
  *
64
- * The combined deadline+caller signal is threaded into both the HTTP fetch
65
- * (cancels wedged requests) and the backoff sleep (cancels pending retries),
66
- * bounding the total time to `totalDeadlineMs` regardless of retry count.
63
+ * The combined deadline+caller signal is threaded into the queue (cancels a
64
+ * still-waiting task), the retry chain (cancels pending backoff sleeps),
65
+ * and the HTTP fetch (cancels wedged requests).
67
66
  */
68
67
  private performRequest;
69
68
  }
package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED
@@ -1 +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;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"}
package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -187,7 +187,7 @@ export class NcbiService {
187
187
  };
188
188
  let text;
189
189
  try {
190
- text = await this.queue.enqueue(() => this.runWithDeadline((signal) => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params, signal), 'idconv', signal), options?.signal), 'idconv', params);
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);
191
191
  }
192
192
  catch (error) {
193
193
  // PMC ID Converter returns 400 (InvalidParams) for malformed inputs and
@@ -308,23 +308,22 @@ export class NcbiService {
308
308
  });
309
309
  }
310
310
  /**
311
- * Enqueues a request with a service-level deadline and retry logic that covers
312
- * both HTTP-level failures (network errors, timeouts) and XML-level errors
313
- * (NCBI returning 200 OK with an error structure in the response body, e.g.
314
- * connection resets surfaced as C++ exception traces).
311
+ * Runs a request under a service-level deadline that bounds queue wait time
312
+ * + retry chain + HTTP execution. The deadline is constructed *outside* the
313
+ * queue so a backlog can't burn a request's budget before it even dispatches.
315
314
  *
316
- * The combined deadline+caller signal is threaded into both the HTTP fetch
317
- * (cancels wedged requests) and the backoff sleep (cancels pending retries),
318
- * bounding the total time to `totalDeadlineMs` regardless of retry count.
315
+ * The combined deadline+caller signal is threaded into the queue (cancels a
316
+ * still-waiting task), the retry chain (cancels pending backoff sleeps),
317
+ * and the HTTP fetch (cancels wedged requests).
319
318
  */
320
319
  performRequest(endpoint, params, options) {
321
- return this.queue.enqueue(() => this.runWithDeadline((signal) => this.withRetry(async () => {
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
323
  signal,
325
324
  });
326
325
  return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
327
- }, endpoint, signal), options?.signal), endpoint, params);
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 }),
340
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
  }
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/request-queue.d.ts CHANGED
@@ -1,21 +1,36 @@
1
1
  /**
2
- * @fileoverview FIFO request queue for NCBI E-utility calls that enforces a minimum
3
- * delay between requests to comply with NCBI rate limits.
2
+ * @fileoverview Rate-limited request scheduler for NCBI E-utility calls. Caps
3
+ * concurrent in-flight requests and enforces a minimum start-gap between
4
+ * dispatches to stay within NCBI's documented per-second ceiling. Supports
5
+ * abort-during-wait so callers' deadlines can bound queue time end-to-end.
4
6
  * @module src/services/ncbi/request-queue
5
7
  */
6
8
  import type { NcbiRequestParams } from './types.js';
7
9
  /**
8
- * Processes NCBI API requests through a FIFO queue, inserting a configurable
9
- * delay between consecutive calls to stay within NCBI's rate-limit window.
10
+ * Schedules NCBI API requests against two independent ceilings:
11
+ *
12
+ * - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
13
+ * dispatch times. Matches NCBI's per-second start-rate cap (≈3/s without
14
+ * an API key, ≈10/s with one).
15
+ * - **Concurrency** (`maxConcurrent`): maximum number of requests in flight
16
+ * simultaneously. Decouples concurrency from rate, so slow upstream
17
+ * responses don't block new dispatches.
18
+ *
19
+ * Enqueue accepts an optional `AbortSignal` so callers can bound their total
20
+ * time inside the scheduler — when the signal fires, a still-waiting task
21
+ * rejects immediately instead of sitting behind a saturated worker for
22
+ * minutes.
10
23
  */
11
24
  export declare class NcbiRequestQueue {
12
- private readonly queue;
13
- private readonly delayMs;
25
+ private readonly waiters;
26
+ private readonly minStartGapMs;
27
+ private readonly maxConcurrent;
14
28
  private readonly maxQueueSize;
15
- private processing;
16
- private lastRequestTime;
17
- constructor(delayMs: number, maxQueueSize?: number);
18
- enqueue<T>(task: () => Promise<T>, endpoint: string, params: NcbiRequestParams): Promise<T>;
19
- private processQueue;
29
+ private inFlight;
30
+ private lastStartTime;
31
+ private nextDispatchTimer;
32
+ constructor(minStartGapMs: number, maxConcurrent?: number, maxQueueSize?: number);
33
+ enqueue<T>(task: () => Promise<T>, endpoint: string, params: NcbiRequestParams, signal?: AbortSignal): Promise<T>;
34
+ private tryDispatch;
20
35
  }
21
36
  //# sourceMappingURL=request-queue.d.ts.map
package/dist/services/ncbi/request-queue.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/request-queue.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAMH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAYpD;;;GAGG;AACH,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAuB;IAC7C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,eAAe,CAAK;gBAEhB,OAAO,EAAE,MAAM,EAAE,YAAY,SAAyB;IAKlE,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;YA+B7E,YAAY;CAqD3B"}
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;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"}
package/dist/services/ncbi/request-queue.js CHANGED
@@ -1,88 +1,130 @@
1
1
  /**
2
- * @fileoverview FIFO request queue for NCBI E-utility calls that enforces a minimum
3
- * delay between requests to comply with NCBI rate limits.
2
+ * @fileoverview Rate-limited request scheduler for NCBI E-utility calls. Caps
3
+ * concurrent in-flight requests and enforces a minimum start-gap between
4
+ * dispatches to stay within NCBI's documented per-second ceiling. Supports
5
+ * abort-during-wait so callers' deadlines can bound queue time end-to-end.
4
6
  * @module src/services/ncbi/request-queue
5
7
  */
6
8
  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
9
  import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
8
10
  import { recoveryFor } from '../../services/error-contracts.js';
11
+ const DEFAULT_MAX_CONCURRENT = 8;
9
12
  const DEFAULT_MAX_QUEUE_SIZE = 100;
10
13
  /**
11
- * Processes NCBI API requests through a FIFO queue, inserting a configurable
12
- * delay between consecutive calls to stay within NCBI's rate-limit window.
14
+ * Schedules NCBI API requests against two independent ceilings:
15
+ *
16
+ * - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
17
+ * dispatch times. Matches NCBI's per-second start-rate cap (≈3/s without
18
+ * an API key, ≈10/s with one).
19
+ * - **Concurrency** (`maxConcurrent`): maximum number of requests in flight
20
+ * simultaneously. Decouples concurrency from rate, so slow upstream
21
+ * responses don't block new dispatches.
22
+ *
23
+ * Enqueue accepts an optional `AbortSignal` so callers can bound their total
24
+ * time inside the scheduler — when the signal fires, a still-waiting task
25
+ * rejects immediately instead of sitting behind a saturated worker for
26
+ * minutes.
13
27
  */
14
28
  export class NcbiRequestQueue {
15
- queue = [];
16
- delayMs;
29
+ waiters = [];
30
+ minStartGapMs;
31
+ maxConcurrent;
17
32
  maxQueueSize;
18
- processing = false;
19
- lastRequestTime = 0;
20
- constructor(delayMs, maxQueueSize = DEFAULT_MAX_QUEUE_SIZE) {
21
- this.delayMs = delayMs;
33
+ inFlight = 0;
34
+ lastStartTime = 0;
35
+ nextDispatchTimer;
36
+ constructor(minStartGapMs, maxConcurrent = DEFAULT_MAX_CONCURRENT, maxQueueSize = DEFAULT_MAX_QUEUE_SIZE) {
37
+ this.minStartGapMs = minStartGapMs;
38
+ this.maxConcurrent = maxConcurrent;
22
39
  this.maxQueueSize = maxQueueSize;
23
40
  }
24
- enqueue(task, endpoint, params) {
25
- if (this.queue.length >= this.maxQueueSize) {
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.queue.length,
46
+ queueSize: this.waiters.length,
30
47
  ...recoveryFor('queue_full'),
31
48
  }));
32
49
  }
33
50
  return new Promise((resolve, reject) => {
34
- this.queue.push({
35
- resolve: resolve,
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
- if (!this.processing) {
42
- queueMicrotask(() => this.processQueue());
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
- async processQueue() {
47
- if (this.processing || this.queue.length === 0)
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 elapsed = now - this.lastRequestTime;
59
- const wait = this.delayMs - elapsed;
60
- if (wait > 0) {
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
- endpoint,
64
- delayMs: wait,
87
+ delayMs: gap,
65
88
  }));
66
- await new Promise((r) => setTimeout(r, wait));
89
+ this.nextDispatchTimer = setTimeout(() => {
90
+ this.nextDispatchTimer = undefined;
91
+ this.tryDispatch();
92
+ }, gap);
93
+ return;
67
94
  }
68
- this.lastRequestTime = Date.now();
69
- logger.info(`Executing NCBI request via queue: ${endpoint}`, requestContextService.createRequestContext({ operation: 'NcbiQueueDispatch', endpoint }));
70
- const result = await task();
71
- resolve(result);
72
- }
73
- catch (error) {
74
- logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
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
  }
package/dist/services/ncbi/request-queue.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.6.11",
3
+ "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.",
6
6
  "type": "module",
@@ -71,17 +71,17 @@
71
71
  "access": "public"
72
72
  },
73
73
  "dependencies": {
74
- "@cyanheads/mcp-ts-core": "^0.9.0",
74
+ "@cyanheads/mcp-ts-core": "^0.9.1",
75
75
  "defuddle": "^0.18.1",
76
76
  "fast-xml-parser": "~5.7.3",
77
77
  "linkedom": "^0.18.12",
78
78
  "pino-pretty": "^13.1.3",
79
- "sanitize-html": "^2.17.3",
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": "^25.7.0",
84
+ "@types/node": "^25.8.0",
85
85
  "@types/sanitize-html": "^2.16.1",
86
86
  "@vitest/coverage-istanbul": "^4.1.6",
87
87
  "depcheck": "^1.4.7",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.6.11",
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": "2.6.11",
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": "2.6.11",
69
+ "version": "2.6.12",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",