npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.18 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

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 (121) hide show

package/dist/services/ncbi/types.d.ts CHANGED Viewed

@@ -197,11 +197,28 @@ export interface XmlGrantList {
     '@_CompleteYN'?: 'Y' | 'N';
     Grant: XmlGrant[] | XmlGrant;
 }
+/**
+ * One `CommentsCorrections` entry — a link from the article to a separately
+ * published record: a retraction, erratum, expression of concern, comment, or
+ * update. `RefType` is the DTD's link type, e.g. `RetractionIn`. `RefSource` and
+ * `Note` arrive as the text NCBI wrote, even when it is purely numeric: the
+ * response handler exempts both from the flat parser's numeric coercion. (#178)
+ */
+export interface XmlCommentsCorrections {
+    '@_RefType'?: string;
+    Note?: XmlTextElement | string;
+    PMID?: XmlPMID;
+    RefSource?: XmlTextElement | string;
+}
+export interface XmlCommentsCorrectionsList {
+    CommentsCorrections?: XmlCommentsCorrections[] | XmlCommentsCorrections;
+}
 export interface XmlMedlineCitation {
     '@_Owner'?: string;
     '@_Status'?: string;
     Article?: XmlArticle;
     CitationSubset?: XmlTextElement[] | XmlTextElement;
+    CommentsCorrectionsList?: XmlCommentsCorrectionsList;
     DateCompleted?: XmlArticleDate;
     DateCreated?: XmlArticleDate;
     DateRevised?: XmlArticleDate;
@@ -406,6 +423,17 @@ export interface ParsedBookInfo {
     publisherLocation?: string;
     title?: string;
 }
+/**
+ * A linked notice from `MedlineCitation/CommentsCorrectionsList`. `refType` is
+ * the verbatim DTD value, kept a plain string so a type NCBI adds later still
+ * parses. `pmid` and `note` are absent unless NCBI supplies them. (#178)
+ */
+export interface ParsedCommentsCorrection {
+    note?: string;
+    pmid?: string;
+    refSource: string;
+    refType: string;
+}
 export interface ParsedArticle {
     abstractText?: string;
     affiliations?: string[];
@@ -413,6 +441,11 @@ export interface ParsedArticle {
     authors?: ParsedArticleAuthor[];
     /** Set on `book-chapter` and `book` records only. */
     book?: ParsedBookInfo;
+    /**
+     * Linked notices, `Cites` entries excluded, in upstream order. Journal
+     * articles only: the DTD gives a Bookshelf record no such list.
+     */
+    commentsCorrections?: ParsedCommentsCorrection[];
     doi?: string;
     grantList?: ParsedGrant[];
     /**
@@ -787,8 +820,8 @@ export interface ECitMatchCitation {
     journal?: string | undefined;
     /**
      * Arbitrary label echoed onto this citation's result. Not a correlation key:
-     * it may repeat across citations, so `eCitMatch` submits a separate
-     * per-request token and matches upstream rows on that instead.
+     * it may repeat across citations, so `eCitMatch` submits the citation's
+     * position in the call as its token and matches upstream rows on that instead.
      */
     key: string;
     /** Volume number */

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

	@@ -1 +1 @@
1	- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;~~AAMH~~,OAAO,EAGL,KAAK,YAAY,EAElB,MAAM,YAAY,CAAC;AAIpB,MAAM,WAAW,uBAAuB;IACtC,sEAAsE;IACtE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,qBAAa,iBAAiB;IAChB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,uBAAuB,EAAI;IAEhE;;;;;;;;;OASG;IACG,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CA0CpF;IAED;;;;;;;;;OASG;IACH,mBAAmB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAiBlF;IAED;;;;;;;OAOG;IACG,UAAU,CACd,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC;QAAE,KAAK,EAAE,YAAY,EAAE,CAAC;QAAC,UAAU,EAAE,MAAM,CAAA;KAAE,CAAC,CAiExD;IAED,gEAAgE;YAClD,cAAc;CAqC7B"}
1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAGL,KAAK,YAAY,EAElB,MAAM,YAAY,CAAC;AAIpB,MAAM,WAAW,uBAAuB;IACtC,sEAAsE;IACtE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,qBAAa,iBAAiB;IAChB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,uBAAuB,EAAI;IAEhE;;;;;;;;;OASG;IACG,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CA0CpF;IAED;;;;;;;;;OASG;IACH,mBAAmB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAiBlF;IAED;;;;;;;OAOG;IACG,UAAU,CACd,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC;QAAE,KAAK,EAAE,YAAY,EAAE,CAAC;QAAC,UAAU,EAAE,MAAM,CAAA;KAAE,CAAC,CAiExD;IAED,gEAAgE;YAClD,cAAc;CAqC7B"}

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

@@ -6,7 +6,6 @@
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
-import { recoveryFor } from '../error-contracts.js';
 import { OPENALEX_API_BASE, OPENALEX_MAX_PAGE_SIZE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -59,14 +58,14 @@ export class OpenAlexApiClient {
                 throw error;
             }
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
         }
         const text = await response.text();
         try {
             return JSON.parse(text);
         }
         catch (error) {
-            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response' }, { cause: error });
         }
     }
     /**
@@ -131,7 +130,7 @@ export class OpenAlexApiClient {
             if (error instanceof McpError)
                 throw error;
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
         }
         const text = await response.text();
         let parsed;
@@ -139,7 +138,7 @@ export class OpenAlexApiClient {
             parsed = JSON.parse(text);
         }
         catch (error) {
-            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response' }, { cause: error });
         }
         logger.debug('OpenAlex cited_by response', requestContextService.createRequestContext({
             operation: 'OpenAlexGetCitedByDone',
@@ -169,7 +168,7 @@ export class OpenAlexApiClient {
             if (error instanceof McpError)
                 throw error;
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable' }, { cause: error });
         }
         const text = await response.text();
         let parsed;
@@ -177,7 +176,7 @@ export class OpenAlexApiClient {
             parsed = JSON.parse(text);
         }
         catch (error) {
-            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response' }, { cause: error });
         }
         return parsed.results ?? [];
     }

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

	@@ -1 +1 @@
1	- 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package/dist/services/openalex/openalex-service.d.ts CHANGED Viewed

@@ -13,8 +13,10 @@
  * serving an unexplained empty window.
  *
  * Transient failures retry with capped exponential backoff. Once retries run
- * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
- * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ * out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
+ * a body that is not JSON), and only a `ServiceUnavailable` with no reason is
+ * reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
+ * code and any upstream `retryAfter`.
  *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
@@ -70,10 +72,12 @@ export declare class OpenAlexService {
     private finish;
     /**
      * Retry wrapper for transient errors. On exhaustion the last error keeps its
-     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
-     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` and its hint — the
-     * one code that reason is declared for; a `Timeout` or `RateLimited` keeps its
-     * code with no reason, as the NCBI and Europe PMC services report them.
+     * code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
+     * caller how long to wait and an unparseable body stays
+     * `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
+     * gains `openalex_unreachable` — the one code that reason is declared for; a
+     * `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
+     * service reports them.
      */
     private withRetry;
 }

package/dist/services/openalex/openalex-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA~~;;;;;;;;;;;;;;;;;;;;;;GAsBG~~;~~AAOH~~,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd~~;;;;;;OAMG~~;YACW,SAAS;CAkDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
1	+ {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAMH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd;;;;;;;;OAQG;YACW,SAAS;CAkDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}

package/dist/services/openalex/openalex-service.js CHANGED Viewed

@@ -13,8 +13,10 @@
  * serving an unexplained empty window.
  *
  * Transient failures retry with capped exponential backoff. Once retries run
- * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
- * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ * out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
+ * a body that is not JSON), and only a `ServiceUnavailable` with no reason is
+ * reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
+ * code and any upstream `retryAfter`.
  *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
@@ -24,7 +26,6 @@
 import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
-import { recoveryFor } from '../error-contracts.js';
 import { OpenAlexApiClient } from './api-client.js';
 import { OPENALEX_MAX_FILTER_VALUES, OPENALEX_MAX_PAGE_SIZE, OPENALEX_MAX_UPSTREAM_REQUESTS, } from './types.js';
 const MAX_BACKOFF_MS = 30_000;
@@ -204,10 +205,12 @@ export class OpenAlexService {
     }
     /**
      * Retry wrapper for transient errors. On exhaustion the last error keeps its
-     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
-     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` and its hint — the
-     * one code that reason is declared for; a `Timeout` or `RateLimited` keeps its
-     * code with no reason, as the NCBI and Europe PMC services report them.
+     * code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
+     * caller how long to wait and an unparseable body stays
+     * `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
+     * gains `openalex_unreachable` — the one code that reason is declared for; a
+     * `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
+     * service reports them.
      */
     async withRetry(execute, label, signal) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
@@ -235,11 +238,10 @@ export class OpenAlexService {
                     continue;
                 }
                 const attempts = this.maxRetries + 1;
-                throw new McpError(error.code, `${error.message} (failed after ${attempts} attempts)`, {
-                    ...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
-                        reason: 'openalex_unreachable',
-                        ...recoveryFor('openalex_unreachable'),
-                    }),
+                const reason = error.data?.reason ??
+                    (error.code === JsonRpcErrorCode.ServiceUnavailable ? 'openalex_unreachable' : undefined);
+                throw new McpError(error.code, `${error.message} (failed after ${attempts} attempt${attempts === 1 ? '' : 's'})`, {
+                    ...(reason !== undefined && { reason }),
                     label,
                     attempts,
                     ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),

package/dist/services/openalex/openalex-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/unpaywall/unpaywall-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;~~AAYH~~,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAF5B,YACmB,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EAChC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC,~~CAqE7E~~;IAED;;;;;;;;;;;;OAYG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA6C/F;IAED;;;;;;;;;OASG;YACW,OAAO;CA+CtB;AAgCD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
1	+ {"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAWH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAF5B,YACmB,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EAChC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC,CAoE7E;IAED;;;;;;;;;;;;OAYG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA6C/F;IAED;;;;;;;;;OASG;YACW,OAAO;CA+CtB;AAgCD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/unpaywall/unpaywall-service.js CHANGED Viewed

@@ -11,7 +11,6 @@
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
-import { recoveryFor } from '../error-contracts.js';
 import { UNPAYWALL_API_BASE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -65,7 +64,6 @@ export class UnpaywallService {
             throw serviceUnavailable(`Unpaywall request failed: ${msg}`, {
                 reason: 'unpaywall_unreachable',
                 doi: normalized,
-                ...recoveryFor('unpaywall_unreachable'),
             }, { cause: error });
         }
         const data = (await response.json());
@@ -172,7 +170,7 @@ export class UnpaywallService {
         }
         catch (error) {
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { reason: 'unpaywall_unreachable', url, ...recoveryFor('unpaywall_unreachable') }, { cause: error });
+            throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { reason: 'unpaywall_unreachable', url }, { cause: error });
         }
         if (!response.ok) {
             throw await httpErrorFromResponse(response, {

package/dist/services/unpaywall/unpaywall-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.18",
+  "version": "2.10.20",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -12,6 +12,7 @@
   "files": [
     "changelog/",
     "dist/",
+    "!dist/*.mcpb",
     "README.md",
     "LICENSE",
     "CLAUDE.md",
@@ -29,6 +30,8 @@
     "format:unsafe": "biome check --write --unsafe .",
     "test": "bunx vitest run",
     "test:coverage": "bunx vitest run --coverage",
+    "test:corpus": "bunx vitest run tests/corpus",
+    "corpus:snapshot": "PUBMED_CORPUS_UPDATE=1 bunx vitest run tests/corpus",
     "audit:fix": "bun audit fix",
     "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "list-skills": "bun run scripts/list-skills.ts",
@@ -83,7 +86,7 @@
     }
   ],
   "license": "Apache-2.0",
-  "packageManager": "bun@1.4.0",
+  "packageManager": "bun@1.4.2",
   "engines": {
     "bun": ">=1.4.0",
     "node": ">=24.0.0"
@@ -92,27 +95,27 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.6",
+    "@cyanheads/mcp-ts-core": "^0.13.11",
     "defuddle": "^0.19.4",
-    "fast-xml-parser": "^5.11.1",
+    "fast-xml-parser": "^5.11.2",
     "linkedom": "^0.18.13",
     "pino-pretty": "^13.1.3",
-    "sanitize-html": "^2.17.7",
+    "sanitize-html": "^2.18.0",
     "unpdf": "^1.8.1",
     "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.14",
-    "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.6.2",
-    "@types/sanitize-html": "^2.16.1",
-    "@vitest/coverage-istanbul": "^5.0.1",
+    "@biomejs/biome": "^2.5.15",
+    "@socketsecurity/bun-security-scanner": "^1.1.3",
+    "@types/node": "^26.6.3",
+    "@types/sanitize-html": "^2.16.2",
+    "@vitest/coverage-istanbul": "^5.0.3",
     "depcheck": "^1.4.7",
     "fast-check": "^4.10.2",
-    "ignore": "^7.0.9",
-    "tsc-alias": "^1.9.5",
+    "ignore": "^7.0.11",
+    "tsc-alias": "^1.9.7",
     "typescript": "^7.0.2",
-    "vitest": "^5.0.1"
+    "vitest": "^5.0.3"
   },
   "overrides": {
     "@hono/node-server": "^2.0.11",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.18",
+  "version": "2.10.20",
   "remotes": [
     {
       "type": "streamable-http",
@@ -18,18 +18,8 @@
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
-      "runtimeHint": "bun",
-      "version": "2.10.18",
-      "packageArguments": [
-        {
-          "type": "positional",
-          "value": "run"
-        },
-        {
-          "type": "positional",
-          "value": "start:stdio"
-        }
-      ],
+      "runtimeHint": "npx",
+      "version": "2.10.20",
       "environmentVariables": [
         {
           "name": "MCP_LOG_LEVEL",
@@ -65,19 +55,15 @@
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
-      "runtimeHint": "bun",
-      "version": "2.10.18",
-      "packageArguments": [
+      "runtimeHint": "npx",
+      "version": "2.10.20",
+      "environmentVariables": [
         {
-          "type": "positional",
-          "value": "run"
+          "name": "MCP_TRANSPORT_TYPE",
+          "description": "Selects the HTTP transport.",
+          "format": "string",
+          "value": "http"
         },
-        {
-          "type": "positional",
-          "value": "start:http"
-        }
-      ],
-      "environmentVariables": [
         {
           "name": "MCP_HTTP_HOST",
           "description": "The hostname for the HTTP server.",