npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.19 → 2.10.21 - Mend

@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.21

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 (110) hide show

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

@@ -1,7 +1,8 @@
 /**
  * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
  * every misspelled token of a PubMed search query in one call — the recovery
- * step after a zero-hit or thin `pubmed_search_articles` result.
+ * step after a zero-hit or thin `pubmed_search_articles` result. `term` is
+ * accepted as an alias for `query`.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';

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

	@@ -1 +1 @@
1	- {"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA~~;;;;;GAKG~~;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cA8DzB~~,CAAC"}
1	+ {"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkEzB,CAAC"}

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

@@ -1,7 +1,8 @@
 /**
  * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
  * every misspelled token of a PubMed search query in one call — the recovery
- * step after a zero-hit or thin `pubmed_search_articles` result.
+ * step after a zero-hit or thin `pubmed_search_articles` result. `term` is
+ * accepted as an alias for `query`.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -15,6 +16,9 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
     errors: [...NCBI_SERVICE_ERRORS, ...QUERY_INPUT_ERRORS],
+    // Never advertised; rewritten to the canonical key before the schema parses.
+    // ESpell's own name for the query. (#190)
+    inputAliases: { term: 'query' },
     input: z.object({
         query: z
             .string()

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

	@@ -1 +1 @@
1	- {"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA~~;;;;;GAKG~~;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACxF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEpD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8bAA8b;IAChc,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,EAAE,GAAG,kBAAkB,CAAU;IAEhE,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,gLAAgL,CACjL;KACJ,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,4EAA4E;QAC5E,4EAA4E;QAC5E,wEAAwE;QACxE,yEAAyE;QACzE,0CAA0C;QAC1C,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;YACjC,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,yDAAyD,CAAC,CAAC;QAC3F,CAAC;QACD,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"}
1	+ {"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACxF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEpD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8bAA8b;IAChc,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,EAAE,GAAG,kBAAkB,CAAU;IAEhE,6EAA6E;IAC7E,0CAA0C;IAC1C,YAAY,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE;IAE/B,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,gLAAgL,CACjL;KACJ,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,4EAA4E;QAC5E,4EAA4E;QAC5E,wEAAwE;QACxE,yEAAyE;QACzE,0CAA0C;QAC1C,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;YACjC,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,yDAAyD,CAAC,CAAC;QAC3F,CAAC;QACD,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 CHANGED Viewed

@@ -122,7 +122,7 @@ export declare const OPENALEX_SERVICE_ERRORS: readonly [{
 }, {
     readonly reason: 'openalex_invalid_response';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'OpenAlex returned a body that could not be parsed (invalid JSON).';
+    readonly when: 'The last of the retry attempts against OpenAlex returned a body that could not be parsed as JSON.';
     readonly recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.';
     readonly retryable: true;
     readonly thrownBy: 'service';

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

	@@ -1 +1 @@
1	- {"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,gLAAgL;aACtL,QAAQ,EACN,iIAAiI;aACnI,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,4IAA4I;aAClJ,QAAQ,EAAE,yEAAyE;aACnF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,mBAAmB;aAC3B,IAAI;aACJ,IAAI,EAAE,gOAAgO;aACtO,QAAQ,EACN,0ZAA0Z;aAC5Z,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,mIAAmI;aACzI,QAAQ,EACN,8GAA8G;aAChH,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;;;;;;GASG;AACH,eAAO,MAAM,kBAAkB;aAE3B,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,qYAAqY;aAC3Y,QAAQ,EAAE,6EAA6E;aACvF,SAAS;EAEH,CAAC;AAEX;;;;;;;;GAQG;AACH,eAAO,MAAM,oBAAoB;aAE7B,MAAM,EAAE,cAAc;aACtB,IAAI;aACJ,IAAI,EAAE,0LAA0L;aAChM,QAAQ,EACN,uHAAuH;aACzH,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;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,~~mEAAmE~~;~~aACzE~~,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qKAAqK;aAC3K,QAAQ,EACN,iGAAiG;aACnG,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,6UAA6U;aACnV,QAAQ,EACN,iNAAiN;aACnN,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC"}
1	+ {"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,gLAAgL;aACtL,QAAQ,EACN,iIAAiI;aACnI,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,4IAA4I;aAClJ,QAAQ,EAAE,yEAAyE;aACnF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,mBAAmB;aAC3B,IAAI;aACJ,IAAI,EAAE,gOAAgO;aACtO,QAAQ,EACN,0ZAA0Z;aAC5Z,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,mIAAmI;aACzI,QAAQ,EACN,8GAA8G;aAChH,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;;;;;;GASG;AACH,eAAO,MAAM,kBAAkB;aAE3B,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,qYAAqY;aAC3Y,QAAQ,EAAE,6EAA6E;aACvF,SAAS;EAEH,CAAC;AAEX;;;;;;;;GAQG;AACH,eAAO,MAAM,oBAAoB;aAE7B,MAAM,EAAE,cAAc;aACtB,IAAI;aACJ,IAAI,EAAE,0LAA0L;aAChM,QAAQ,EACN,uHAAuH;aACzH,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;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mGAAmG;aACzG,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qKAAqK;aAC3K,QAAQ,EACN,iGAAiG;aACnG,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;aACT,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,6UAA6U;aACnV,QAAQ,EACN,iNAAiN;aACnN,SAAS;aACT,QAAQ,EAAE,SAAS;EAEb,CAAC"}

package/dist/services/error-contracts.js CHANGED Viewed

@@ -135,7 +135,7 @@ export const OPENALEX_SERVICE_ERRORS = [
     {
         reason: 'openalex_invalid_response',
         code: JsonRpcErrorCode.ServiceUnavailable,
-        when: 'OpenAlex returned a body that could not be parsed (invalid JSON).',
+        when: 'The last of the retry attempts against OpenAlex returned a body that could not be parsed as JSON.',
         recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.',
         retryable: true,
         thrownBy: 'service',

package/dist/services/error-contracts.js.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

@@ -10,6 +10,7 @@
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { readBody } from '../fetch-redaction.js';
 import { EUROPEPMC_API_BASE } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -73,7 +74,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
-        return response.text();
+        return readBody(response.text());
     }
     /**
      * Fetch the JATS full-text XML for an EPMC record by its internal id.
@@ -112,7 +113,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId }, { cause: error });
         }
-        const xml = await response.text();
+        const xml = await readBody(response.text());
         if (!xml.trim()) {
             logger.debug('Europe PMC returned an empty fullTextXML body.', requestContextService.createRequestContext({
                 operation: 'EuropePmcFullTextXmlEmpty',
@@ -159,7 +160,7 @@ export class EuropePmcApiClient {
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
-        return response.text();
+        return readBody(response.text());
     }
     buildSearchUrl(params) {
         const finalParams = {

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

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/services/fetch-redaction.d.ts ADDED Viewed

@@ -0,0 +1,23 @@
+/**
+ * @fileoverview Keeps request URLs out of the text of fetch rejections. Runtimes can
+ * quote the whole request URL in a rejection message (Bun 1.4 does, for some malformed
+ * responses, in both the header and the body phase), and these services' query strings
+ * carry an API key, the operator's contact email, and the caller's query. The message
+ * becomes caller-facing error text, and the rejection rides `cause` into the log
+ * record's cause chain, so every URL in it is cut to its origin first.
+ * @module src/services/fetch-redaction
+ */
+/**
+ * A fetch rejection with every URL its text quotes reduced to the URL's origin. An
+ * `Error` is rewritten in place, keeping its identity and transport `code`; one whose
+ * `message` refuses the write is replaced by a stand-in carrying its `name` and `code`.
+ * A non-`Error` rejection comes back as its redacted text.
+ */
+export declare function redactRejection(error: unknown): unknown;
+/**
+ * Awaits a response-body read (`response.text()`, `.json()`, `.arrayBuffer()`),
+ * rethrowing its rejection with {@link redactRejection} applied. A failure while the
+ * body streams is otherwise unchanged: same error, same classification.
+ */
+export declare function readBody<T>(read: Promise<T>): Promise<T>;
+//# sourceMappingURL=fetch-redaction.d.ts.map

package/dist/services/fetch-redaction.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"fetch-redaction.d.ts","sourceRoot":"","sources":["../../src/services/fetch-redaction.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAiBH;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,CAcvD;AAED;;;;GAIG;AACH,wBAAsB,QAAQ,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAM9D"}

package/dist/services/fetch-redaction.js ADDED Viewed

@@ -0,0 +1,62 @@
+/**
+ * @fileoverview Keeps request URLs out of the text of fetch rejections. Runtimes can
+ * quote the whole request URL in a rejection message (Bun 1.4 does, for some malformed
+ * responses, in both the header and the body phase), and these services' query strings
+ * carry an API key, the operator's contact email, and the caller's query. The message
+ * becomes caller-facing error text, and the rejection rides `cause` into the log
+ * record's cause chain, so every URL in it is cut to its origin first.
+ * @module src/services/fetch-redaction
+ */
+/** An absolute `http:`/`https:` URL inside free text, up to the first quote, bracket, or space. */
+const EMBEDDED_URL = /https?:\/\/[^\s"'`<>]+/gi;
+/**
+ * Names a URL by its origin, path and query elided behind markers
+ * (`https://host/…?…`); an unparseable one becomes a fixed placeholder.
+ */
+function redactUrl(url) {
+    const parsed = URL.parse(url);
+    if (!parsed)
+        return '[unparseable URL]';
+    const path = parsed.pathname === '/' ? '' : '/…';
+    const query = parsed.search ? '?…' : '';
+    return `${parsed.origin}${path}${query}`;
+}
+/**
+ * A fetch rejection with every URL its text quotes reduced to the URL's origin. An
+ * `Error` is rewritten in place, keeping its identity and transport `code`; one whose
+ * `message` refuses the write is replaced by a stand-in carrying its `name` and `code`.
+ * A non-`Error` rejection comes back as its redacted text.
+ */
+export function redactRejection(error) {
+    if (!(error instanceof Error))
+        return String(error).replace(EMBEDDED_URL, redactUrl);
+    const message = error.message.replace(EMBEDDED_URL, redactUrl);
+    if (message === error.message)
+        return error;
+    try {
+        error.message = message;
+    }
+    catch {
+        // A frozen or read-only `message`; the stand-in below takes over.
+    }
+    if (error.message === message)
+        return error;
+    const standIn = new Error(message);
+    standIn.name = error.name;
+    const { code } = error;
+    return typeof code === 'string' ? Object.assign(standIn, { code }) : standIn;
+}
+/**
+ * Awaits a response-body read (`response.text()`, `.json()`, `.arrayBuffer()`),
+ * rethrowing its rejection with {@link redactRejection} applied. A failure while the
+ * body streams is otherwise unchanged: same error, same classification.
+ */
+export async function readBody(read) {
+    try {
+        return await read;
+    }
+    catch (error) {
+        throw redactRejection(error);
+    }
+}
+//# sourceMappingURL=fetch-redaction.js.map

package/dist/services/fetch-redaction.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"fetch-redaction.js","sourceRoot":"","sources":["../../src/services/fetch-redaction.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,mGAAmG;AACnG,MAAM,YAAY,GAAG,0BAA0B,CAAC;AAEhD;;;GAGG;AACH,SAAS,SAAS,CAAC,GAAW;IAC5B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC9B,IAAI,CAAC,MAAM;QAAE,OAAO,mBAAmB,CAAC;IACxC,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;IACjD,MAAM,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IACxC,OAAO,GAAG,MAAM,CAAC,MAAM,GAAG,IAAI,GAAG,KAAK,EAAE,CAAC;AAC3C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAAC,KAAc;IAC5C,IAAI,CAAC,CAAC,KAAK,YAAY,KAAK,CAAC;QAAE,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;IACrF,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;IAC/D,IAAI,OAAO,KAAK,KAAK,CAAC,OAAO;QAAE,OAAO,KAAK,CAAC;IAC5C,IAAI,CAAC;QACH,KAAK,CAAC,OAAO,GAAG,OAAO,CAAC;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,kEAAkE;IACpE,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,KAAK,OAAO;QAAE,OAAO,KAAK,CAAC;IAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC;IACnC,OAAO,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC;IAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,KAA2B,CAAC;IAC7C,OAAO,OAAO,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;AAC/E,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAI,IAAgB;IAChD,IAAI,CAAC;QACH,OAAO,MAAM,IAAI,CAAC;IACpB,CAAC;IAAC,OAAO,KAAc,EAAE,CAAC;QACxB,MAAM,eAAe,CAAC,KAAK,CAAC,CAAC;IAC/B,CAAC;AACH,CAAC"}

package/dist/services/ncbi/api-client.d.ts CHANGED Viewed

@@ -25,6 +25,9 @@ export declare class NcbiApiClient {
      * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
      * error status codes — fetchWithTimeout throws before the body can be read.
      * Injects tool and email params but not api_key (eutils-specific).
+     *
+     * Records and error data name the URL's host and the caller's own params,
+     * never the request URL, whose query carries the operator's email.
      */
     makeExternalRequest(url: string, params: NcbiRequestParams, externalSignal?: AbortSignal): Promise<string>;
     private buildParams;

package/dist/services/ncbi/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAoBnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,mBAAmB,EAAI;IAEtD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC,CAqCjB;IAED;;;;;;;;OAQG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC,CAwCjB;IAED,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB;;;;OAIG;IACH,OAAO,CAAC,UAAU;IAUlB,sFAAsF;IACtF,OAAO,CAAC,WAAW;IAcnB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;CAI3B"}

package/dist/services/ncbi/api-client.js CHANGED Viewed

@@ -6,9 +6,20 @@
  */
 import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { httpErrorFromResponse, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { redactRejection } from '../fetch-redaction.js';
 import { NCBI_EUTILS_BASE_URL } from './types.js';
 /** Maximum encoded query-string length before automatically switching to POST. */
 const POST_THRESHOLD = 2000;
+/**
+ * Wraps a non-`McpError` fetch rejection — header or body phase — as `ncbi_unreachable`.
+ * The request URL carries `api_key` and the operator's `email`, and a runtime can quote
+ * it in the rejection text, so that text is redacted before it becomes the message.
+ */
+function unreachable(error, data) {
+    const cause = redactRejection(error);
+    const msg = cause instanceof Error ? cause.message : String(cause);
+    return serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', ...data }, { cause });
+}
 /**
  * Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
  * and chooses GET/POST based on payload size. Single-attempt — retry logic lives
@@ -25,7 +36,7 @@ export class NcbiApiClient {
         const suffix = endpoint.includes('.') ? '' : '.fcgi';
         const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
         try {
-            logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({
+            logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${endpoint}`, requestContextService.createRequestContext({
                 operation: 'NcbiHttpRequest',
                 additionalContext: { endpoint },
             }));
@@ -49,8 +60,7 @@ export class NcbiApiClient {
         catch (error) {
             if (error instanceof McpError)
                 throw error;
-            const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', endpoint }, { cause: error });
+            throw unreachable(error, { endpoint });
         }
     }
     /**
@@ -58,6 +68,9 @@ export class NcbiApiClient {
      * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
      * error status codes — fetchWithTimeout throws before the body can be read.
      * Injects tool and email params but not api_key (eutils-specific).
+     *
+     * Records and error data name the URL's host and the caller's own params,
+     * never the request URL, whose query carries the operator's email.
      */
     async makeExternalRequest(url, params, externalSignal) {
         const finalParams = {
@@ -70,11 +83,12 @@ export class NcbiApiClient {
         }
         const qs = new URLSearchParams(finalParams).toString();
         const fullUrl = qs ? `${url}?${qs}` : url;
+        const host = URL.parse(url)?.host;
         const signal = this.buildTimeoutSignal(externalSignal);
         try {
-            logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({
+            logger.debug('NCBI external request: GET', requestContextService.createRequestContext({
                 operation: 'NcbiExternalRequest',
-                additionalContext: { url },
+                additionalContext: { host, params },
             }));
             const response = await fetch(fullUrl, { signal });
             const body = await response.text();
@@ -82,7 +96,7 @@ export class NcbiApiClient {
                 throw await httpErrorFromResponse(response, {
                     service: 'NCBI',
                     captureBody: false,
-                    data: { url, body: body.substring(0, 500) },
+                    data: { host, body: body.substring(0, 500) },
                 });
             }
             return body;
@@ -90,8 +104,7 @@ export class NcbiApiClient {
         catch (error) {
             if (error instanceof McpError)
                 throw error;
-            const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', url }, { cause: error });
+            throw unreachable(error, { host });
         }
     }
     buildParams(params) {

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

	@@ -1 +1 @@
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package/dist/services/ncbi/formatting/citation-formatter.d.ts CHANGED Viewed

@@ -4,9 +4,23 @@
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
-import type { ParsedArticle } from '../types.js';
+import type { ParsedArticle, ParsedCommentsCorrection } from '../types.js';
 /** Supported citation output formats. */
 export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
+/**
+ * NCBI `RefType`s that qualify the cited article itself — it was retracted,
+ * corrected, or questioned. A link from a record that is itself a notice
+ * (`RetractionOf`, `ErratumFor`) and comment or update links are not among them:
+ * citing a retraction notice is not citing a retracted work. (#215)
+ */
+export declare const CITATION_NOTICE_TYPES: readonly ['RetractionIn', 'RetractedandRepublishedIn', 'ExpressionOfConcernIn', 'ErratumIn', 'CorrectedandRepublishedIn'];
+export type CitationNoticeType = (typeof CITATION_NOTICE_TYPES)[number];
+/** A linked notice that qualifies the cited article. */
+export type CitationNotice = ParsedCommentsCorrection & {
+    refType: CitationNoticeType;
+};
+/** The record's linked notices that qualify the cited article, in NCBI's order. */
+export declare function citationNotices(article: ParsedArticle): CitationNotice[];
 /**
  * Format a PubMed article as an APA 7th edition citation.
  *
@@ -18,9 +32,19 @@ export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
  * ```
  * Title. (Year). *Journal*, *Volume*(Issue), Pages. https://doi.org/DOI
  * ```
- * A Bookshelf record routes to {@link formatApaBook}.
+ * A retracted article ends on `(Retraction published <RefSource>)`. A Bookshelf
+ * record routes to {@link formatApaBook}.
  */
 export declare function formatApa(article: ParsedArticle): string;
+/**
+ * Format a PubMed article as an MLA 9th edition citation.
+ *
+ * Pattern:
+ * ```
+ * Last, First, et al. "Title." *Journal*, vol. 12, no. 3, 2024, pp. 45-67. DOI.
+ * ```
+ * A Bookshelf record routes to {@link formatMlaBook}.
+ */
 export declare function formatMla(article: ParsedArticle): string;
 /**
  * Format a PubMed article as a BibTeX entry.
@@ -43,6 +67,22 @@ export declare function formatBibtex(article: ParsedArticle): string;
  * Record ends with `ER  - ` (trailing spaces per spec).
  */
 export declare function formatRis(article: ParsedArticle): string;
+/**
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
+ *
+ * Pattern (the leading list number is the consumer's responsibility — entries
+ * are formatted independently, so this returns the unnumbered reference body):
+ * ```
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
+ * ```
+ * Journal name uses the NLM/ISO abbreviation when available; pages are used as
+ * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
+ * period so it stays copy-pasteable, unless a note follows it. An article number replaces nothing — with
+ * no pagination it trails the source as an NLM note (`. pii: 2400512.`). A
+ * retraction or erratum follows as a note (`Retraction in: <RefSource>`). A
+ * Bookshelf record routes to {@link formatVancouverBook}.
+ */
 export declare function formatVancouver(article: ParsedArticle): string;
 /**
  * Format a single article in the requested citation style.

package/dist/services/ncbi/formatting/citation-formatter.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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