npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.6.5 → 2.6.7 - Mend

@cyanheads/pubmed-mcp-server 2.6.5 → 2.6.7

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.

Files changed (27) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,9 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.6.5
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+**Version:** 2.6.7
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.8.19`
+**Engines:** Bun ≥1.3.2, Node ≥24.0.0
 > **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.
@@ -145,9 +146,10 @@ Handlers receive a unified `ctx` object. Key properties:
 |:---------|:------------|
 | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
 | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
+| `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
 | `ctx.signal` | `AbortSignal` for cancellation. |
 | `ctx.requestId` | Unique request ID. |
-| `ctx.tenantId` | Tenant ID from JWT or `'default'` for stdio. |
+| `ctx.tenantId` | Tenant ID from JWT, `'default'` for stdio or HTTP+`MCP_AUTH_MODE=none`. |
 ---
@@ -155,15 +157,22 @@ Handlers receive a unified `ctx` object. Key properties:
 Handlers throw — the framework catches, classifies, and formats.
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, retryable? }]` on `tool()` / `resource()` to advertise the failure surface in `tools/list` (under `_meta['mcp-ts-core/errors']`) and receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
 ```ts
 errors: [
-  { reason: 'no_match', code: JsonRpcErrorCode.NotFound, when: 'No requested PMID returned data' },
+  { reason: 'no_match', code: JsonRpcErrorCode.NotFound,
+    when: 'No requested PMID returned data',
+    recovery: 'Try pubmed_search_articles to discover valid PMIDs first.' },
 ],
 async handler(input, ctx) {
   const articles = await ncbi.fetch(input.pmids);
-  if (articles.length === 0) throw ctx.fail('no_match', `None of ${input.pmids.length} PMIDs returned data`);
+  if (articles.length === 0) {
+    // Static contract recovery
+    throw ctx.fail('no_match', `None of ${input.pmids.length} PMIDs returned data`, {
+      ...ctx.recoveryFor('no_match'),
+    });
+  }
   return { articles };
 }
 ```
@@ -248,19 +257,22 @@ Available skills:
 | `add-service` | Scaffold a new service integration |
 | `add-test` | Scaffold test file for a tool, resource, or service |
 | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
+| `tool-defs-analysis` | Read-only audit of definition language: voice, leaks, defaults, recovery hints, examples |
 | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
 | `maintenance` | Investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest` |
 | `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
+| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
 | `api-config` | AppConfig, parseConfig, env vars |
 | `api-context` | Context interface, logger, state, progress |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
 | `api-linter` | Definition lint rules reference (`format-parity`, `schema-*`, `server-json-*`, …) |
 | `api-services` | LLM, Speech, Graph services |
+| `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
 | `api-testing` | createMockContext, test patterns |
-| `api-utils` | Formatting, parsing, security, pagination, scheduling |
+| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
 | `api-workers` | Cloudflare Workers runtime |
 | `report-issue-framework` | File bug/feature request against @cyanheads/mcp-ts-core |
 | `report-issue-local` | File bug/feature request against this server's repo |
@@ -281,8 +293,6 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run format` | Auto-fix formatting |
 | `bun run test` | Run tests |
 | `bun run lint:mcp` | Validate MCP definitions against spec |
-| `bun run dev:stdio` | Dev mode (stdio) |
-| `bun run dev:http` | Dev mode (HTTP) |
 | `bun run start:stdio` | Production mode (stdio) |
 | `bun run start:http` | Production mode (HTTP) |

package/Dockerfile CHANGED Viewed

@@ -4,7 +4,7 @@
 # This stage installs all dependencies (including dev), builds the TypeScript
 # source code into JavaScript, and prepares the production assets.
 # ==============================================================================
-FROM oven/bun:1 AS build
+FROM oven/bun:1.3 AS build
 WORKDIR /usr/src/app
@@ -28,7 +28,7 @@ RUN bun run build
 # application. It uses a slim base image and only includes production
 # dependencies and build artifacts.
 # ==============================================================================
-FROM oven/bun:1-slim AS production
+FROM oven/bun:1.3-slim AS production
 WORKDIR /usr/src/app

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![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-2.6.5-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/)
+[![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-2.6.7-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/)
 [![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/)

package/dist/config/server-config.d.ts CHANGED Viewed

@@ -6,14 +6,14 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 declare const ServerConfigSchema: z.ZodObject<{
-    apiKey: z.ZodPipe<z.ZodTransform<unknown, unknown>, z.ZodOptional<z.ZodString>>;
+    apiKey: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
     toolIdentifier: z.ZodDefault<z.ZodString>;
-    adminEmail: z.ZodPipe<z.ZodTransform<unknown, unknown>, z.ZodOptional<z.ZodEmail>>;
+    adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    unpaywallEmail: z.ZodPipe<z.ZodTransform<unknown, unknown>, z.ZodOptional<z.ZodEmail>>;
+    unpaywallEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     unpaywallTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;

package/dist/mcp-server/tools/definitions/_error-contracts.d.ts CHANGED Viewed

@@ -23,16 +23,19 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
     readonly reason: "queue_full";
     readonly code: JsonRpcErrorCode.RateLimited;
     readonly when: "Local NCBI request queue is at capacity.";
+    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_unreachable";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: "Total request deadline expired before NCBI returned a response.";
+    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
     readonly retryable: true;
 }];
 //# sourceMappingURL=_error-contracts.d.ts.map

package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"_error-contracts.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;EAsBtB,CAAC"}

package/dist/mcp-server/tools/definitions/_error-contracts.js CHANGED Viewed

@@ -24,18 +24,21 @@ export const NCBI_SERVICE_ERRORS = [
         reason: 'queue_full',
         code: JsonRpcErrorCode.RateLimited,
         when: 'Local NCBI request queue is at capacity.',
+        recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.',
         retryable: true,
     },
     {
         reason: 'ncbi_unreachable',
         code: JsonRpcErrorCode.ServiceUnavailable,
         when: 'NCBI E-utilities is unreachable after all retry attempts.',
+        recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.',
         retryable: true,
     },
     {
         reason: 'ncbi_deadline_exceeded',
         code: JsonRpcErrorCode.Timeout,
         when: 'Total request deadline expired before NCBI returned a response.',
+        recovery: 'Reduce batch size or retry; NCBI may be under temporary load.',
         retryable: true,
     },
 ];

package/dist/mcp-server/tools/definitions/_error-contracts.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"_error-contracts.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,SAAS,EAAE,IAAI;KAChB;CACO,CAAC"}
1	+ {"version":3,"file":"_error-contracts.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;CACO,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     ids: z.ZodArray<z.ZodString>;
-    idtype: z.ZodEnum<{
+    idType: z.ZodEnum<{
         pmcid: "pmcid";
         pmid: "pmid";
         doi: "doi";

package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED Viewed

@@ -24,7 +24,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             .min(1)
             .max(50)
             .describe('Article identifiers to convert. All IDs must be the same type. DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190".'),
-        idtype: z
+        idType: z
             .enum(['pmcid', 'pmid', 'doi'])
             .describe('The type of IDs being submitted. Required so the API can unambiguously resolve them.'),
     }),
@@ -55,9 +55,9 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_convert_ids', {
             count: input.ids.length,
-            idtype: input.idtype,
+            idType: input.idType,
         });
-        const raw = await getNcbiService().idConvert(input.ids, input.idtype, { signal: ctx.signal });
+        const raw = await getNcbiService().idConvert(input.ids, input.idType, { signal: ctx.signal });
         // NCBI returns pmid as a number in JSON — coerce all ID fields to strings
         const records = raw.map((r) => {
             const requestedId = String(r['requested-id']);

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts CHANGED Viewed

@@ -73,20 +73,24 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly reason: "queue_full";
     readonly code: JsonRpcErrorCode.RateLimited;
     readonly when: "Local NCBI request queue is at capacity.";
+    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_unreachable";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: "Total request deadline expired before NCBI returned a response.";
+    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
     readonly retryable: true;
 }, {
     readonly reason: "invalid_efetch_response";
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
+    readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
 }]>;
 //# sourceMappingURL=fetch-articles.tool.d.ts.map

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED Viewed

@@ -105,6 +105,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             reason: 'invalid_efetch_response',
             code: JsonRpcErrorCode.SerializationError,
             when: 'NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.',
+            recovery: 'Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.',
         },
     ],
     input: z.object({
@@ -124,7 +125,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
         ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
         const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
         if (!xmlData || !('PubmedArticleSet' in xmlData)) {
-            throw ctx.fail('invalid_efetch_response', 'Invalid EFetch response from NCBI: missing PubmedArticleSet', { requestedPmids: input.pmids.length });
+            throw ctx.fail('invalid_efetch_response', 'Invalid EFetch response from NCBI: missing PubmedArticleSet', { requestedPmids: input.pmids.length, ...ctx.recoveryFor('invalid_efetch_response') });
         }
         const rawArticles = xmlData.PubmedArticleSet?.PubmedArticle;
         const xmlArticles = rawArticles ? ensureArray(rawArticles) : [];

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED Viewed

@@ -95,20 +95,24 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly reason: "queue_full";
     readonly code: JsonRpcErrorCode.RateLimited;
     readonly when: "Local NCBI request queue is at capacity.";
+    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_unreachable";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: "Total request deadline expired before NCBI returned a response.";
+    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
     readonly retryable: true;
 }, {
     readonly reason: "invalid_pmc_efetch_response";
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: "PMC EFetch returned a payload missing the pmc-articleset wrapper.";
+    readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMC IDs at once.";
 }]>;
 //# sourceMappingURL=fetch-fulltext.tool.d.ts.map

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkP5B~~,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuP5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -156,6 +156,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             reason: 'invalid_pmc_efetch_response',
             code: JsonRpcErrorCode.SerializationError,
             when: 'PMC EFetch returned a payload missing the pmc-articleset wrapper.',
+            recovery: 'Retry once; if it persists, NCBI returned malformed data — try fewer PMC IDs at once.',
         },
     ],
     input: z
@@ -248,7 +249,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             });
             const articleSet = findOne(xmlData, 'pmc-articleset');
             if (!articleSet)
-                throw ctx.fail('invalid_pmc_efetch_response', 'Invalid PMC EFetch response: missing pmc-articleset', { requestedPmcIdCount: pmcIds.length });
+                throw ctx.fail('invalid_pmc_efetch_response', 'Invalid PMC EFetch response: missing pmc-articleset', {
+                    requestedPmcIdCount: pmcIds.length,
+                    ...ctx.recoveryFor('invalid_pmc_efetch_response'),
+                });
             let parsed = findAll(articleSet, 'article').map(parsePmcArticle);
             if (input.sections?.length) {
                 const sectionFilter = input.sections;

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED Viewed

@@ -34,20 +34,24 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly reason: "queue_full";
     readonly code: JsonRpcErrorCode.RateLimited;
     readonly when: "Local NCBI request queue is at capacity.";
+    readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_unreachable";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: "Total request deadline expired before NCBI returned a response.";
+    readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
     readonly retryable: true;
 }, {
     readonly reason: "elink_error";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.";
+    readonly recovery: "Verify the source PMID exists or try a different relationship type.";
 }]>;
 //# sourceMappingURL=find-related.tool.d.ts.map

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED Viewed

	@@ -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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,eAAe~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiN1B~~,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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmN1B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -30,6 +30,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
             reason: 'elink_error',
             code: JsonRpcErrorCode.ServiceUnavailable,
             when: 'NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.',
+            recovery: 'Verify the source PMID exists or try a different relationship type.',
         },
     ],
     input: z.object({
@@ -100,6 +101,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 pmid: input.pmid,
                 relationship: input.relationship,
                 ncbiError: firstResult.ERROR,
+                ...ctx.recoveryFor('elink_error'),
             });
         }
         const linkSet = firstResult?.LinkSet;

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAcjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;~~6BAiG9B~~,CAAC"}
1	+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAcjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;6BAuG9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -19,7 +19,13 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
     input: z.object({
         pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
         format: z
-            .union([CitationStyleEnum, z.array(CitationStyleEnum).min(1)])
+            .union([
+            CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris.'),
+            z
+                .array(CitationStyleEnum)
+                .min(1)
+                .describe('Multiple citation styles to generate. Each entry: apa, mla, bibtex, or ris.'),
+        ])
             .default('apa')
             .describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris.'),
     }),

package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,iBAAiB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;AAElE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,qJAAqJ;IACvJ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC;YACL,iBAAiB,CAAC,QAAQ,CAAC,uDAAuD,CAAC;YACnF,CAAC;iBACE,KAAK,CAAC,iBAAiB,CAAC;iBACxB,GAAG,CAAC,CAAC,CAAC;iBACN,QAAQ,CAAC,6EAA6E,CAAC;SAC3F,CAAC;aACD,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2HAA2H,CAC5H;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,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,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,OAAO,GAAoB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO;SACR,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,OAAO,CAAC;aAC5C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,IAAI,MAAM,CAAC,cAAc,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CACR,6NAA6N,CAC9N,CAAC;QACJ,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.5",
+  "version": "2.6.7",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "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.",
   "type": "module",
@@ -22,8 +22,6 @@
     "changelog:build": "bun run scripts/build-changelog.ts",
     "changelog:check": "bun run scripts/build-changelog.ts --check",
     "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
-    "dev:stdio": "MCP_TRANSPORT_TYPE=stdio bun --watch src/index.ts",
-    "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",
     "start:stdio": "MCP_TRANSPORT_TYPE=stdio bun ./dist/index.js",
     "start:http": "MCP_TRANSPORT_TYPE=http bun ./dist/index.js"
   },
@@ -67,29 +65,29 @@
   "packageManager": "bun@1.3.2",
   "engines": {
     "bun": ">=1.3.2",
-    "node": ">=22.0.0"
+    "node": ">=24.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.8.2",
+    "@cyanheads/mcp-ts-core": "^0.8.19",
     "defuddle": "^0.18.1",
-    "fast-xml-parser": "^5.7.2",
+    "fast-xml-parser": "^5.7.3",
     "linkedom": "^0.18.12",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.3",
-    "unpdf": "^1.6.1"
+    "unpdf": "^1.6.2"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.13",
-    "@types/node": "^25.6.0",
+    "@biomejs/biome": "^2.4.14",
+    "@types/node": "^25.6.2",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.5",
     "depcheck": "^1.4.7",
     "fast-check": "^4.7.0",
     "ignore": "^7.0.5",
-    "tsc-alias": "^1.8.16",
+    "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
     "vitest": "^4.1.5"
   }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.5",
+  "version": "2.6.6",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.5",
+      "version": "2.6.7",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.5",
+      "version": "2.6.7",
       "packageArguments": [
         {
           "type": "positional",