@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.11

package/dist/services/ncbi/parsing/article-parser.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/esummary-parser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAsQD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAkD/B"}
+{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAqSD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAwD/B"}

package/dist/services/ncbi/parsing/esummary-parser.js

@@ -207,9 +207,25 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
     }
     return parsedAuthors.filter((author) => author.name);
 }
+/**
+ * Split an ESummary contributor list into the record's own authors and the
+ * containing book's editors.
+ *
+ * ESummary lists a book's editors ahead of the chapter's authors, so a display
+ * string built from the first few names credits the series editors instead of
+ * the people who wrote the chapter — PMID 20301425 reads "Adam MP, Bick S,
+ * Mirzaa GM, et al." where the authors are Petrucelli, Daly and Pal. A record
+ * whose only contributors are editors keeps them: they are the best attribution
+ * it has. (#114)
+ */
+function splitContributors(contributors) {
+    const editors = contributors.filter((c) => c.authtype?.toLowerCase() === 'editor');
+    const authors = contributors.filter((c) => c.authtype?.toLowerCase() !== 'editor');
+    return { authors: authors.length > 0 ? authors : contributors, editors };
+}
 function parseSingleDocumentSummary(docSummary) {
     const pmid = docSummary['@_uid'];
-    const authorsArray = parseESummaryAuthorsFromDocumentSummary(docSummary);
+    const { authors: authorsArray, editors } = splitContributors(parseESummaryAuthorsFromDocumentSummary(docSummary));
     let idsArray = [];
     const articleIdsProp = docSummary.ArticleIds;
     if (articleIdsProp) {
@@ -230,12 +246,21 @@ function parseSingleDocumentSummary(docSummary) {
     const source = getText(docSummary.Source) || getText(docSummary.FullJournalName) || getText(docSummary.SO);
     const rawPubDate = getText(docSummary.PubDate);
     const rawEPubDate = getText(docSummary.EPubDate);
+    // A Bookshelf record leaves Source and FullJournalName empty and carries its
+    // venue here instead, so without these a book summary renders with none. (#114)
+    const bookTitle = getText(docSummary.BookTitle);
+    const publisherName = getText(docSummary.PublisherName);
+    const docType = getText(docSummary.DocType);
     return {
         pmid: String(pmid),
         ...(title && { title }),
         authors: formatESummaryAuthors(authorsArray),
         authorNames: authorsArray.map((a) => a.name),
+        ...(editors.length > 0 && { editors: editors.map((e) => e.name) }),
         ...(source && { source }),
+        ...(bookTitle && { bookTitle }),
+        ...(publisherName && { publisherName }),
+        ...(docType && { docType }),
         ...(doiValue && { doi: doiValue }),
         ...(pmcIdValue && { pmcId: pmcIdValue }),
         ...(rawPubDate && { rawPubDate }),
@@ -333,7 +358,13 @@ export async function extractBriefSummaries(eSummaryResult, context) {
             ...(rawSummary.title !== undefined && { title: rawSummary.title }),
             ...(rawSummary.authors !== undefined && { authors: rawSummary.authors }),
             ...(rawSummary.authorNames !== undefined && { authorNames: rawSummary.authorNames }),
+            ...(rawSummary.editors !== undefined && { editors: rawSummary.editors }),
             ...(rawSummary.source !== undefined && { source: rawSummary.source }),
+            ...(rawSummary.bookTitle !== undefined && { bookTitle: rawSummary.bookTitle }),
+            ...(rawSummary.publisherName !== undefined && {
+                publisherName: rawSummary.publisherName,
+            }),
+            ...(rawSummary.docType !== undefined && { docType: rawSummary.docType }),
             ...(rawSummary.doi !== undefined && { doi: rawSummary.doi }),
             ...(rawSummary.pmcId !== undefined && { pmcId: rawSummary.pmcId }),
             ...(pubDate !== undefined && { pubDate }),

package/dist/services/ncbi/parsing/esummary-parser.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts

@@ -7,15 +7,22 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
+import type { ParsedPmcArticle, ParsedPmcAsset, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
 import { type JatsNode } from './pmc-xml-helpers.js';
 /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
 export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
 /**
  * Extract body sections from a `<body>` node, walking children in document order.
- * Consecutive bare `<p>` siblings are collected into an untitled section so
- * articles with mixed structure (direct paragraphs + trailing `<sec>`, common
- * in manuscript-submitted PMC deposits) preserve their main text.
+ * Consecutive bare `<p>` siblings — and any block element sitting directly under
+ * `<body>` — are collected into an untitled section so articles with mixed
+ * structure (direct paragraphs + trailing `<sec>`, common in
+ * manuscript-submitted PMC deposits) preserve their main text.
+ *
+ * A `<body>` whose whole content is one block and no `<sec>` therefore yields a
+ * section carrying that block's text, rather than the empty list the tool layer
+ * reads as an article with no body at all. Legacy
+ * `<preformat preformat-type="pmc-ocr-text">` deposits, which put the entire
+ * article in one such element, are the case that matters. (#130)
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
@@ -48,6 +55,19 @@ export declare function extractPmcTables(root: JatsNode | undefined): ParsedPmcT
  * source `<tr>` elements and needs no cap of its own. (#111)
  */
 export declare const MAX_TABLE_COLUMNS = 512;
+/**
+ * Extract every `<fig>` and `<supplementary-material>` under `root` in document
+ * order — pass the `<article>` node.
+ *
+ * Whole-article, for the reason the table walk is: 17% of figures and 23% of
+ * supplementary material sit outside `<body>` entirely — `<floats-group>`
+ * deposits, `<back>/<sec>` and `<app-group>/<app>` placements, and figures
+ * hanging off the abstract in `<front>`. Each asset names the innermost
+ * enclosing `<sec>` wherever that sits, an untitled one inheriting its parent's
+ * title, so the reader keeps a positional cue; an asset inside no `<sec>` at all
+ * carries no section name. (#130)
+ */
+export declare function extractPmcAssets(root: JatsNode | undefined): ParsedPmcAsset[];
 /**
  * Extract references from anywhere under `root` — pass the `<article>` node to
  * cover a whole document, or a `<back>` node to scope the search to it.

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

@@ -1 +1 @@
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