npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.18 → 2.10.19 - Mend

@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.19

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 (96) hide show

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

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package/dist/services/ncbi/parsing/article-parser.d.ts CHANGED Viewed

@@ -3,7 +3,7 @@
  * typically from EFetch results.
  * @module src/services/ncbi/parsing/article-parser
  */
-import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedBookInfo, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlBookDocument, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle, XmlPubmedArticleSet, XmlPubmedBookArticle } from '../types.js';
+import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedBookInfo, ParsedCommentsCorrection, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlBookDocument, XmlCommentsCorrectionsList, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle, XmlPubmedArticleSet, XmlPubmedBookArticle } from '../types.js';
 /**
  * Result of extracting authors with deduplicated affiliations.
  */
@@ -61,6 +61,20 @@ export declare function extractPmcId(articleXml?: XmlArticle, pubmedDataArticleI
  * @returns An array of publication type strings.
  */
 export declare function extractPublicationTypes(publicationTypeListXml?: XmlPublicationTypeList): string[];
+/**
+ * Extracts the linked notices from `MedlineCitation/CommentsCorrectionsList` —
+ * retractions, errata, expressions of concern, comments, updates — in upstream
+ * order. `Cites` entries are dropped: they list a bibliography rather than a
+ * linked record, which NLM now carries in `PubmedData/ReferenceList`. (#178)
+ *
+ * `RefSource` and `Note` reach this function as the text NCBI wrote: the response
+ * handler exempts both from numeric coercion, which would otherwise reduce `007` to
+ * `7`. A `PMID` is still coerced, and `getText` turns it back into a string — PMIDs
+ * carry no leading zeros, so none is lost.
+ * @param commentsCorrectionsListXml - The XML CommentsCorrectionsList element.
+ * @returns The linked notices; empty when the record carries none.
+ */
+export declare function extractCommentsCorrections(commentsCorrectionsListXml?: XmlCommentsCorrectionsList): ParsedCommentsCorrection[];
 /**
  * Extracts keywords from XML. Handles single or multiple KeywordList elements.
  * @param keywordListsXml - The XML KeywordList element or an array of them.

package/dist/services/ncbi/parsing/article-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/article-parser.js CHANGED Viewed

@@ -276,6 +276,33 @@ export function extractPublicationTypes(publicationTypeListXml) {
     const pubTypes = ensureArray(publicationTypeListXml.PublicationType);
     return pubTypes.map((pt) => getText(pt)).filter(Boolean);
 }
+/**
+ * Extracts the linked notices from `MedlineCitation/CommentsCorrectionsList` —
+ * retractions, errata, expressions of concern, comments, updates — in upstream
+ * order. `Cites` entries are dropped: they list a bibliography rather than a
+ * linked record, which NLM now carries in `PubmedData/ReferenceList`. (#178)
+ *
+ * `RefSource` and `Note` reach this function as the text NCBI wrote: the response
+ * handler exempts both from numeric coercion, which would otherwise reduce `007` to
+ * `7`. A `PMID` is still coerced, and `getText` turns it back into a string — PMIDs
+ * carry no leading zeros, so none is lost.
+ * @param commentsCorrectionsListXml - The XML CommentsCorrectionsList element.
+ * @returns The linked notices; empty when the record carries none.
+ */
+export function extractCommentsCorrections(commentsCorrectionsListXml) {
+    return ensureArray(commentsCorrectionsListXml?.CommentsCorrections)
+        .filter((entry) => getAttribute(entry, 'RefType') !== 'Cites')
+        .map((entry) => {
+        const pmid = getOptionalText(entry.PMID);
+        const note = getOptionalText(entry.Note);
+        return {
+            refType: getAttribute(entry, 'RefType'),
+            refSource: getText(entry.RefSource),
+            ...(pmid && { pmid }),
+            ...(note && { note }),
+        };
+    });
+}
 /**
  * Extracts keywords from XML. Handles single or multiple KeywordList elements.
  * @param keywordListsXml - The XML KeywordList element or an array of them.
@@ -372,6 +399,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
     const pmcId = extractPmcId(article, pubmedDataArticleIdList);
     const { authors, affiliations } = extractAuthors(article?.AuthorList);
     const publicationTypes = extractPublicationTypes(article?.PublicationTypeList);
+    const commentsCorrections = extractCommentsCorrections(medlineCitation?.CommentsCorrectionsList);
     const keywords = extractKeywords(medlineCitation?.KeywordList ?? article?.KeywordList);
     const articleDates = extractArticleDates(article);
     const meshTerms = includeMesh ? extractMeshTerms(medlineCitation?.MeshHeadingList) : undefined;
@@ -385,6 +413,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
         authors,
         ...(journalInfo !== undefined && { journalInfo }),
         ...(publicationTypes.length > 0 && { publicationTypes }),
+        ...(commentsCorrections.length > 0 && { commentsCorrections }),
         ...(keywords.length > 0 && { keywords }),
         ...(meshTerms !== undefined && meshTerms.length > 0 && { meshTerms }),
         ...(grantList !== undefined && grantList.length > 0 && { grantList }),

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package/dist/services/ncbi/response-handler.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;~~AA2BH~~,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;~~AA4IrD~~;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,MAAM,EAChB,EAAE,EAAE,OAAO,GACV,MAAM,GAAG,SAAS,CAKpB;AAED;;;;;;;GAOG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,~~CAoBjF~~;AAsJD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;~~AAeD~~;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;~~IA2BtB~~,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,~~CAsOH~~;CACF"}
1	+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AA0BH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA6IrD;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,MAAM,EAChB,EAAE,EAAE,OAAO,GACV,MAAM,GAAG,SAAS,CAKpB;AAED;;;;;;;GAOG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAmBjF;AAsJD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AA+BD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IAyBtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAiOH;CACF"}

package/dist/services/ncbi/response-handler.js CHANGED Viewed

@@ -20,7 +20,6 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
  */
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
 import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
-import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS, XML_PROCESS_ENTITIES_OPTIONS, } from './parsing/ordered-xml-parser-options.js';
 import { decodeHtmlEntities } from './parsing/text-helpers.js';
 /**
@@ -52,6 +51,7 @@ const NCBI_ARRAY_JPATHS = new Set([
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.AuthorList.Author.AffiliationInfo',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.GrantList.Grant',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.PublicationTypeList.PublicationType',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.KeywordList.Keyword',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading.QualifierName',
@@ -187,7 +187,6 @@ export function reclassifyNcbiHttpError(error, endpoint) {
         endpoint,
         status: error.data?.status,
         ncbiErrors,
-        ...recoveryFor('ncbi_unreachable'),
     }, { cause: error });
 }
 /**
@@ -353,16 +352,27 @@ export function flattenInlineMarkup(xml) {
         .replace(/<\/?(?:i|b|u|sc)>/g, '');
 }
 /**
- * Keeps `Book/Isbn` out of fast-xml-parser's numeric coercion.
+ * Free-text elements of a linked notice, matched by path: an element named `Note`
+ * elsewhere keeps the default coercion. (#178)
+ */
+const VERBATIM_TEXT_JPATHS = new Set([
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections.RefSource',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections.Note',
+]);
+/**
+ * Keeps text that must survive exactly as NCBI wrote it out of fast-xml-parser's
+ * numeric coercion: `Book/Isbn`, and a linked notice's `RefSource` and `Note`.
  *
  * An ISBN-10 can start with a zero (`0309605393`); coerced, it becomes the
  * number 309605393 and the leading digit is gone before any read site sees it,
- * so the record ships a wrong ISBN with no error anywhere. The processor's
- * contract does the work: returning `undefined` leaves the raw text alone,
- * while returning the value unchanged for every other tag keeps the existing
- * coercion exactly as it was. (#114)
+ * so the record ships a wrong ISBN with no error anywhere (#114). A purely
+ * numeric `RefSource` or `Note` loses its spelling the same way — `1.50` → `1.5`,
+ * `007` → `7`, `0x1A` → `26` (#178). The processor's contract does the work:
+ * returning `undefined` leaves the raw text alone, while returning the value
+ * unchanged for every other tag keeps the existing coercion exactly as it was.
+ * The flat parsers keep the default `jPath: true`, so the path arrives as a string.
  */
-const preserveIsbnText = (tagName, tagValue) => tagName === 'Isbn' ? undefined : tagValue;
+const preserveVerbatimText = (tagName, tagValue, jPath) => tagName === 'Isbn' || VERBATIM_TEXT_JPATHS.has(jPath) ? undefined : tagValue;
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.
@@ -398,7 +408,7 @@ export class NcbiResponseHandler {
                 const path = jpath;
                 return NCBI_ARRAY_JPATHS.has(path) || ESUMMARY_ITEM_JPATH.test(path);
             },
-            tagValueProcessor: preserveIsbnText,
+            tagValueProcessor: preserveVerbatimText,
         };
         this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
         this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
@@ -424,14 +434,12 @@ export class NcbiResponseHandler {
                 reason: 'ncbi_resource_not_found',
                 endpoint,
                 ncbiErrors: errorMessages,
-                ...recoveryFor('ncbi_resource_not_found'),
             });
         }
         throw serviceUnavailable(`NCBI API Error: ${errorMessages.join('; ')}`, {
             reason: 'ncbi_unreachable',
             endpoint,
             ncbiErrors: errorMessages,
-            ...recoveryFor('ncbi_unreachable'),
         });
     }
     extractNcbiErrorMessages(parsedXml) {
@@ -472,7 +480,7 @@ export class NcbiResponseHandler {
                     operation: 'NcbiHtmlResponse',
                     additionalContext: { endpoint },
                 }));
-                throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+                throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint });
             }
             // NCBI's eLink (and occasionally other endpoints) drops the root element
             // when the upstream backend connection fails mid-response, yielding just
@@ -489,7 +497,7 @@ export class NcbiResponseHandler {
                     operation: 'NcbiEmptyResponse',
                     additionalContext: { endpoint, responseLength: responseText.length },
                 }));
-                throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+                throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint });
             }
             const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
             const validationResult = XMLValidator.validate(xmlForValidation);
@@ -505,7 +513,6 @@ export class NcbiResponseHandler {
                     reason: 'ncbi_invalid_response',
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 });
             }
             const useOrdered = options?.useOrderedParser ?? false;
@@ -546,7 +553,6 @@ export class NcbiResponseHandler {
                     endpoint,
                     parserError,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 }, { cause: error });
             }
             if (!useOrdered) {
@@ -583,7 +589,6 @@ export class NcbiResponseHandler {
                     reason: 'ncbi_invalid_response',
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 }, { cause: error });
             }
             if (parsed && typeof parsed === 'object' && 'error' in parsed) {
@@ -597,14 +602,12 @@ export class NcbiResponseHandler {
                         reason: 'ncbi_resource_not_found',
                         endpoint,
                         ncbiErrors: [errorMessage],
-                        ...recoveryFor('ncbi_resource_not_found'),
                     });
                 }
                 throw serviceUnavailable(`NCBI API Error: ${errorMessage}`, {
                     reason: 'ncbi_unreachable',
                     endpoint,
-                    ncbiError: errorMessage,
-                    ...recoveryFor('ncbi_unreachable'),
+                    ncbiErrors: [errorMessage],
                 });
             }
             logger.debug('Successfully parsed JSON response.', requestContextService.createRequestContext({

package/dist/services/ncbi/response-handler.js.map CHANGED Viewed

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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[];
     /**

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

	@@ -1 +1 @@
1	- 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