@cyanheads/pubmed-mcp-server 2.9.8 → 2.9.10

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 @@
-{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqCtB,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;EAS3B,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;EAgB1B,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;EAyB3B,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
+{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,0CAA0C;aAChD,QAAQ,EAAE,qEAAqE;aAC/E,SAAS;;aAGT,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;;aAGT,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;;aAGT,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qEAAqE;aAC3E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,oDAAoD;aAC1D,QAAQ,EACN,4FAA4F;aAC9F,SAAS;;aAGT,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;EAEH,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,sDAAsD;aAC5D,QAAQ,EACN,iGAAiG;aACnG,SAAS;;aAGT,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,+FAA+F;aACrG,QAAQ,EACN,8GAA8G;aAChH,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}

package/dist/services/europe-pmc/api-client.d.ts

@@ -20,7 +20,15 @@ export type EuropePmcFullTextFetchResult = {
     kind: 'not-available';
     reason: string;
 };
-/** Low-level HTTP client for Europe PMC. Single-attempt — retries upstream. */
+/**
+ * Low-level HTTP client for Europe PMC. Single-attempt — retries upstream.
+ *
+ * Every method here resolves only on HTTP 2xx: `fetchWithTimeout` throws a
+ * status-mapped `McpError` for any non-2xx rather than returning the failing
+ * `Response`, so a `!response.ok` check after the call can never run. A status
+ * that needs graceful handling is converted in the catch block by inspecting
+ * `error.code` — see `fullTextXml`'s 404 → `not-available`. (#90)
+ */
 export declare class EuropePmcApiClient {
     private readonly config;
     constructor(config: EuropePmcApiClientConfig);
@@ -34,6 +42,11 @@ export declare class EuropePmcApiClient {
      * Fetch the JATS full-text XML for an EPMC record by its internal id.
      * Returns `{ kind: 'not-available' }` for 404 — EPMC has the record but
      * doesn't publish a full-text XML for it (very common for preprints).
+     *
+     * `fetchWithTimeout` throws a status-mapped `McpError` on any non-2xx rather
+     * than resolving with the `Response` (`expectedStatuses` only lowers the log
+     * severity), so the 404 arrives here as `McpError(NotFound)` and must be
+     * converted in the catch block. Every other failure keeps throwing. (#90)
      */
     fullTextXml(epmcId: string, signal?: AbortSignal): Promise<EuropePmcFullTextFetchResult>;
     /**

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

@@ -1 +1 @@
-{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAsB,KAAK,qBAAqB,EAAE,MAAM,YAAY,CAAC;AAI5E,MAAM,WAAW,wBAAwB;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,MAAM,MAAM,4BAA4B,GACpC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAC9B;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAE9C,+EAA+E;AAC/E,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,wBAAwB;IAE7D;;;;OAIG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC;IAiC5D;;;;OAIG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC;IAmD9F;;;;OAIG;IACH,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAK9F;;;;OAIG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAK/F,iFAAiF;YACnE,cAAc;IAkC5B,OAAO,CAAC,cAAc;IActB;;;;OAIG;IACH,OAAO,CAAC,gBAAgB;CAMzB"}
+{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAsB,KAAK,qBAAqB,EAAE,MAAM,YAAY,CAAC;AAI5E,MAAM,WAAW,wBAAwB;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,MAAM,MAAM,4BAA4B,GACpC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAC9B;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAE9C;;;;;;;;GAQG;AACH,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,wBAAwB,EAAI;IAEjE;;;;OAIG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC,CAwB3D;IAED;;;;;;;;;OASG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC,CA4C7F;IAED;;;;OAIG;IACH,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAG7F;IAED;;;;OAIG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAG9F;IAED,iFAAiF;YACnE,cAAc;IA2B5B,OAAO,CAAC,cAAc;IActB;;;;OAIG;IACH,OAAO,CAAC,gBAAgB;CAMzB"}

package/dist/services/europe-pmc/api-client.js

@@ -4,12 +4,20 @@
  * fullTextXML calls. Retry logic lives in `EuropePmcService`.
  * @module src/services/europe-pmc/api-client
  */
-import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
-import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
+import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { recoveryFor } from '../../services/error-contracts.js';
 import { EUROPEPMC_API_BASE } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
-/** Low-level HTTP client for Europe PMC. Single-attempt — retries upstream. */
+/**
+ * Low-level HTTP client for Europe PMC. Single-attempt — retries upstream.
+ *
+ * Every method here resolves only on HTTP 2xx: `fetchWithTimeout` throws a
+ * status-mapped `McpError` for any non-2xx rather than returning the failing
+ * `Response`, so a `!response.ok` check after the call can never run. A status
+ * that needs graceful handling is converted in the catch block by inspecting
+ * `error.code` — see `fullTextXml`'s 404 → `not-available`. (#90)
+ */
 export class EuropePmcApiClient {
     config;
     constructor(config) {
@@ -39,18 +47,17 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
         }
-        if (!response.ok) {
-            throw await httpErrorFromResponse(response, {
-                service: 'Europe PMC',
-                data: { url, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
-            });
-        }
         return response.text();
     }
     /**
      * Fetch the JATS full-text XML for an EPMC record by its internal id.
      * Returns `{ kind: 'not-available' }` for 404 — EPMC has the record but
      * doesn't publish a full-text XML for it (very common for preprints).
+     *
+     * `fetchWithTimeout` throws a status-mapped `McpError` on any non-2xx rather
+     * than resolving with the `Response` (`expectedStatuses` only lowers the log
+     * severity), so the 404 arrives here as `McpError(NotFound)` and must be
+     * converted in the catch block. Every other failure keeps throwing. (#90)
      */
     async fullTextXml(epmcId, signal) {
         const url = `${EUROPEPMC_API_BASE}/${encodeURIComponent(epmcId)}/fullTextXML`;
@@ -65,24 +72,20 @@ export class EuropePmcApiClient {
                     Accept: 'application/xml, text/xml, */*;q=0.5',
                     'User-Agent': USER_AGENT,
                 },
+                expectedStatuses: [404],
                 ...(signal && { signal }),
             });
         }
         catch (error) {
-            if (error instanceof McpError)
+            if (error instanceof McpError) {
+                if (error.code === JsonRpcErrorCode.NotFound) {
+                    return { kind: 'not-available', reason: 'EPMC has no fullTextXML for this record' };
+                }
                 throw error;
+            }
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId, ...recoveryFor('europepmc_unreachable') }, { cause: error });
         }
-        if (response.status === 404) {
-            return { kind: 'not-available', reason: 'EPMC has no fullTextXML for this record' };
-        }
-        if (!response.ok) {
-            throw await httpErrorFromResponse(response, {
-                service: 'Europe PMC fullTextXML',
-                data: { epmcId, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
-            });
-        }
         const xml = await response.text();
         if (!xml.trim()) {
             logger.debug('Europe PMC returned an empty fullTextXML body.', requestContextService.createRequestContext({
@@ -127,12 +130,6 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
         }
-        if (!response.ok) {
-            throw await httpErrorFromResponse(response, {
-                service: 'Europe PMC',
-                data: { url, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
-            });
-        }
         return response.text();
     }
     buildSearchUrl(params) {

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

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

@@ -1 +1 @@
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package/dist/services/europe-pmc/request-queue.d.ts.map

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package/dist/services/europe-pmc/request-queue.js.map

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

@@ -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

package/dist/services/europe-pmc/types.d.ts.map

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package/dist/services/ncbi/api-client.js.map

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package/dist/services/ncbi/ncbi-service.d.ts.map

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