@cyanheads/pubmed-mcp-server 2.9.8 → 2.9.9

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js

@@ -1,6 +1,7 @@
 /**
  * @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
- * Searches the NCBI MeSH database and optionally retrieves detailed records.
+ * Searches the NCBI MeSH database with offset pagination and optionally
+ * retrieves detailed records.
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -90,7 +91,7 @@ function parseSummaryRecords(data, ids, includeDetails) {
 }
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const lookupMeshTool = tool('pubmed_lookup_mesh', {
-    description: 'Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms.',
+    description: 'Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([
         SCHEMA_DEFINED_TERM,
@@ -103,6 +104,12 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
     input: z.object({
         query: z.string().min(1).describe('MeSH descriptor name or free-text term to look up'),
         maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Result offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only.'),
         includeDetails: z
             .boolean()
             .default(true)
@@ -110,6 +117,11 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
     }),
     output: z.object({
         query: z.string().describe('Original search query'),
+        offset: z.number().describe('Result offset this page was read from'),
+        nextOffset: z
+            .number()
+            .optional()
+            .describe('Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.'),
         results: z
             .array(z
             .object({
@@ -130,40 +142,70 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             .describe('Matching MeSH descriptor record'))
             .describe('Matching MeSH records'),
     }),
-    // Result-set context — total match count for disclosure against the maxResults cap,
-    // and recovery guidance when no descriptor matched. Surfaced via ctx.enrich(...)
-    // to structuredContent and content[]; absent on success.
+    // Result-set context — the upstream match count for disclosure against the maxResults
+    // cap, and recovery guidance when no descriptor matched or the offset overshot.
+    // Surfaced via ctx.enrich(...) to structuredContent and content[] alike.
     enrichment: {
-        totalCount: z.number().describe('Total matching MeSH descriptors'),
+        totalCount: z
+            .number()
+            .describe('Total MeSH descriptors matching the query upstream, before the maxResults cap'),
         notice: z
             .string()
             .optional()
-            .describe('Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results.'),
+            .describe('Optional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages.'),
     },
     async handler(input, ctx) {
-        const { query, maxResults, includeDetails } = input;
+        const { query, maxResults, offset, includeDetails } = input;
         const ncbi = getNcbiService();
-        ctx.log.debug('MeSH lookup started', { query, maxResults, includeDetails });
+        ctx.log.debug('MeSH lookup started', { query, maxResults, offset, includeDetails });
         const hasFieldTag = /\[.+\]/.test(query);
         const callOpts = { signal: ctx.signal };
-        const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults }, callOpts);
+        const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults, retstart: offset }, callOpts);
+        // The exact-descriptor match is resolved on every page, not just the first: it is
+        // normally a member of the ranked list too, so every page has to know which UID to
+        // hold back. The first page leads with it; later pages skip it where it ranks.
         const exactSearch = hasFieldTag
             ? undefined
             : ncbi.eSearch({ db: 'mesh', term: `${query}[MH]`, retmax: 1 }, callOpts);
         const [broadResult, exactResult] = await Promise.all([broadSearch, exactSearch]);
-        const seen = new Set();
+        const totalCount = broadResult.count;
+        const pinnedUid = exactResult?.idList[0];
         const ids = [];
-        for (const id of [...(exactResult?.idList ?? []), ...broadResult.idList]) {
-            if (!seen.has(id)) {
-                seen.add(id);
-                ids.push(id);
+        if (pinnedUid !== undefined && offset === 0)
+            ids.push(pinnedUid);
+        // Count the ranked records this page consumed rather than assuming maxResults:
+        // a pinned exact match outside the ranked window displaces one, and the next
+        // offset has to resume exactly where this page stopped or that record is lost.
+        let consumed = 0;
+        for (const id of broadResult.idList) {
+            // The pinned descriptor is served once, on the first page. Count its rank slot
+            // as consumed wherever it lands so no later page hands it back a second time.
+            if (id === pinnedUid) {
+                consumed++;
+                continue;
             }
+            if (ids.length >= maxResults)
+                break;
+            consumed++;
+            ids.push(id);
         }
-        ids.length = Math.min(ids.length, maxResults);
+        const nextOffset = offset + consumed;
+        const hasMore = consumed > 0 && nextOffset < totalCount;
         if (ids.length === 0) {
-            ctx.enrich.total(0);
-            ctx.enrich.notice(`No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`);
-            return { query, results: [] };
+            ctx.enrich.total(totalCount);
+            let notice;
+            if (totalCount === 0) {
+                notice = `No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`;
+            }
+            else if (consumed > 0) {
+                // The window held nothing but the pinned descriptor, already served at offset 0.
+                notice = `Offset ${offset} held only the exact-descriptor match for "${query}", which was returned on the first page.${hasMore ? ` Continue with offset ${nextOffset}.` : ''}`;
+            }
+            else {
+                notice = `Offset ${offset} returned no records — "${query}" matches ${totalCount} MeSH descriptor(s). Reset offset to 0 or lower it below ${totalCount}.`;
+            }
+            ctx.enrich.notice(notice);
+            return { query, offset, ...(hasMore && { nextOffset }), results: [] };
         }
         const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
         const results = parseSummaryRecords(summaryData, ids, includeDetails);
@@ -173,14 +215,23 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             const bExact = b.name.toLowerCase() === queryLower ? 0 : 1;
             return aExact - bExact;
         });
-        ctx.enrich.total(results.length);
-        return { query, results };
+        ctx.enrich.total(totalCount);
+        // A page filled entirely by the pinned exact match consumed no ranked record,
+        // so there is no offset that advances — say so instead of emitting one that
+        // would replay this page.
+        if (consumed === 0 && totalCount > 0) {
+            ctx.enrich.notice(`The exact-descriptor match filled this page of ${maxResults}. Raise maxResults to see the ${totalCount} ranked match(es) for "${query}".`);
+        }
+        return { query, offset, ...(hasMore && { nextOffset }), results };
     },
     format: (result) => {
         const lines = [
             `# MeSH Lookup: "${result.query}"`,
-            `Found **${result.results.length}** result(s).`,
+            `Found **${result.results.length}** result(s) at offset **${result.offset}**.`,
         ];
+        if (result.nextOffset !== undefined) {
+            lines.push(`More available — call again with \`offset: ${result.nextOffset}\`.`);
+        }
         for (const r of result.results) {
             lines.push(`\n## ${r.name}`);
             lines.push(`- **MeSH ID:** ${r.meshId}`);

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package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts

@@ -18,11 +18,11 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
     pageSize: z.ZodDefault<z.ZodNumber>;
     cursorMark: z.ZodDefault<z.ZodString>;
     sources: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        AGR: "AGR";
         MED: "MED";
+        PAT: "PAT";
         PMC: "PMC";
         PPR: "PPR";
-        PAT: "PAT";
-        AGR: "AGR";
     }>>>;
     resultType: z.ZodDefault<z.ZodEnum<{
         core: "core";
@@ -32,11 +32,11 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
 }, z.core.$strip>, z.ZodObject<{
     hits: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
+            AGR: "AGR";
             MED: "MED";
+            PAT: "PAT";
             PMC: "PMC";
             PPR: "PPR";
-            PAT: "PAT";
-            AGR: "AGR";
         }>;
         epmcId: z.ZodString;
         title: z.ZodOptional<z.ZodString>;
@@ -57,37 +57,37 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
     nextCursorMark: z.ZodOptional<z.ZodString>;
     searchUrl: z.ZodString;
 }, z.core.$strip>, readonly [{
-    readonly reason: "europepmc_unreachable";
+    readonly reason: 'europepmc_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Europe PMC was unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly when: 'Europe PMC was unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_response";
+    readonly reason: 'europepmc_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
-    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
+    readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_input";
+    readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
-    readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
+    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
+    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
     readonly retryable: false;
 }, {
-    readonly reason: "europepmc_disabled";
+    readonly reason: 'europepmc_disabled';
     readonly code: JsonRpcErrorCode.ConfigurationError;
-    readonly when: "Europe PMC service is disabled via EUROPEPMC_ENABLED=false.";
-    readonly recovery: "Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.";
+    readonly when: 'Europe PMC service is disabled via EUROPEPMC_ENABLED=false.';
+    readonly recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.';
 }], {
     readonly query: z.ZodString;
     readonly totalCount: z.ZodNumber;
     readonly appliedSources: z.ZodArray<z.ZodEnum<{
+        AGR: "AGR";
         MED: "MED";
+        PAT: "PAT";
         PMC: "PMC";
         PPR: "PPR";
-        PAT: "PAT";
-        AGR: "AGR";
     }>>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+PpC,CAAC"}
+{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAiPjG,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts

@@ -11,16 +11,16 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     sort: z.ZodDefault<z.ZodEnum<{
         author: "author";
         journal: "journal";
-        relevance: "relevance";
         pub_date: "pub_date";
+        relevance: "relevance";
     }>>;
     dateRange: z.ZodOptional<z.ZodObject<{
         minDate: z.ZodString;
         maxDate: z.ZodString;
         dateType: z.ZodDefault<z.ZodEnum<{
-            pdat: "pdat";
-            mdat: "mdat";
             edat: "edat";
+            mdat: "mdat";
+            pdat: "pdat";
         }>>;
     }, z.core.$strip>>;
     publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -31,8 +31,8 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     hasAbstract: z.ZodOptional<z.ZodBoolean>;
     freeFullText: z.ZodOptional<z.ZodBoolean>;
     species: z.ZodOptional<z.ZodEnum<{
-        humans: "humans";
         animals: "animals";
+        humans: "humans";
     }>>;
     summaryCount: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
@@ -52,34 +52,34 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     }, z.core.$strip>>;
     searchUrl: z.ZodString;
 }, z.core.$strip>, readonly [{
-    readonly reason: "queue_full";
+    readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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 reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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 reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }], {
     readonly effectiveQuery: z.ZodString;
@@ -89,9 +89,9 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
             minDate: z.ZodString;
             maxDate: z.ZodString;
             dateType: z.ZodEnum<{
-                pdat: "pdat";
-                mdat: "mdat";
                 edat: "edat";
+                mdat: "mdat";
+                pdat: "pdat";
             }>;
         }, z.core.$strip>>;
         publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -102,8 +102,8 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
         hasAbstract: z.ZodOptional<z.ZodBoolean>;
         freeFullText: z.ZodOptional<z.ZodBoolean>;
         species: z.ZodOptional<z.ZodEnum<{
-            humans: "humans";
             animals: "animals";
+            humans: "humans";
         }>>;
     }, z.core.$strip>;
     readonly notice: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts

@@ -11,34 +11,34 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
     corrected: z.ZodString;
     hasSuggestion: z.ZodBoolean;
 }, z.core.$strip>, readonly [{
-    readonly reason: "queue_full";
+    readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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 reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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 reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }], undefined>;
 //# sourceMappingURL=spell-check.tool.d.ts.map

package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8CzB,CAAC"}
+{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAiDzB,CAAC"}

package/dist/mcp-server/tools/definitions/spell-check.tool.js

@@ -22,8 +22,8 @@ export const spellCheckTool = tool('pubmed_spell_check', {
         hasSuggestion: z.boolean().describe('Whether NCBI suggested a correction'),
     }),
     async handler(input, ctx) {
-        ctx.log.info('Executing pubmed_spell tool', { query: input.query });
-        const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query });
+        ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
+        const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query }, { signal: ctx.signal });
         return {
             original: result.original,
             corrected: result.corrected,

package/dist/mcp-server/tools/definitions/spell-check.tool.js.map

@@ -1 +1 @@
-{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;KACxE,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,6BAA6B,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QACpE,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAClF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;KACxE,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAC1C,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,EACnC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;QACF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/services/error-contracts.d.ts

@@ -20,34 +20,34 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
  * declared contract matches what actually reaches the wire.
  */
 export declare const NCBI_SERVICE_ERRORS: readonly [{
-    readonly reason: "queue_full";
+    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 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 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 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 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 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: "ncbi_invalid_response";
+    readonly reason: 'ncbi_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
-    readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
+    readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
+    readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "ncbi_resource_not_found";
+    readonly reason: 'ncbi_resource_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
-    readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
+    readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
+    readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }];
 /**
@@ -56,10 +56,10 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
  * these into their `errors[]`.
  */
 export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
-    readonly reason: "unpaywall_unreachable";
+    readonly reason: 'unpaywall_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Unpaywall was unreachable when resolving a DOI or fetching content.";
-    readonly recovery: "Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.";
+    readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
+    readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
     readonly retryable: true;
 }];
 /**
@@ -68,16 +68,16 @@ export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
  * these into their `errors[]`.
  */
 export declare const OPENALEX_SERVICE_ERRORS: readonly [{
-    readonly reason: "openalex_unreachable";
+    readonly reason: 'openalex_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "OpenAlex was unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.";
+    readonly when: 'OpenAlex was unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.';
     readonly retryable: true;
 }, {
-    readonly reason: "openalex_invalid_response";
+    readonly reason: 'openalex_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "OpenAlex returned a body that could not be parsed (invalid JSON).";
-    readonly recovery: "Retry the request; OpenAlex returned a malformed response that could not be parsed.";
+    readonly when: 'OpenAlex returned a body that could not be parsed (invalid JSON).';
+    readonly recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }];
 /**
@@ -85,22 +85,22 @@ export declare const OPENALEX_SERVICE_ERRORS: readonly [{
  * `getEuropePmcService()` should spread these into their `errors[]`.
  */
 export declare const EUROPEPMC_SERVICE_ERRORS: readonly [{
-    readonly reason: "europepmc_unreachable";
+    readonly reason: 'europepmc_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Europe PMC was unreachable after all retry attempts.";
-    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly when: 'Europe PMC was unreachable after all retry attempts.';
+    readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_response";
+    readonly reason: 'europepmc_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
-    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
+    readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
     readonly retryable: true;
 }, {
-    readonly reason: "europepmc_invalid_input";
+    readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
-    readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
+    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
+    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
     readonly retryable: false;
 }];
 /**

package/dist/services/error-contracts.d.ts.map

@@ -1 +1 @@
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package/dist/services/europe-pmc/api-client.d.ts.map

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