npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.9.7 → 2.9.9 - Mend

@cyanheads/pubmed-mcp-server 2.9.7 → 2.9.9

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 (66) hide show

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAiDzB,CAAC"}

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/error-contracts.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

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

	@@ -1 +1 @@
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package/dist/services/europe-pmc/api-client.js CHANGED Viewed

@@ -65,6 +65,7 @@ export class EuropePmcApiClient {
                     Accept: 'application/xml, text/xml, */*;q=0.5',
                     'User-Agent': USER_AGENT,
                 },
+                expectedStatuses: [404],
                 ...(signal && { signal }),
             });
         }

package/dist/services/europe-pmc/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/types.d.ts CHANGED Viewed

@@ -18,8 +18,8 @@ export declare const EUROPEPMC_API_BASE = "https://www.ebi.ac.uk/europepmc/webse
  */
 export type EuropePmcSource = 'MED' | 'PMC' | 'PPR' | 'PAT' | 'AGR' | 'CTX' | 'CBA' | 'ETH' | 'HIR';
 /** Allowed sources for `pubmed_europepmc_search` input. */
-export declare const EUROPEPMC_DEFAULT_SOURCES: readonly ["MED", "PMC", "PPR"];
-export declare const EUROPEPMC_ALL_SOURCES: readonly ["MED", "PMC", "PPR", "PAT", "AGR"];
+export declare const EUROPEPMC_DEFAULT_SOURCES: readonly ['MED', 'PMC', 'PPR'];
+export declare const EUROPEPMC_ALL_SOURCES: readonly ['MED', 'PMC', 'PPR', 'PAT', 'AGR'];
 /**
  * Single record from a Europe PMC search response. Only fields the server
  * actually consumes are typed; the upstream payload carries many more under

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