npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.6 → 2.10.8 - Mend

@cyanheads/pubmed-mcp-server 2.10.6 → 2.10.8

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 (37) hide show

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

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

@@ -21,9 +21,9 @@ export declare function extractBodySections(body: JatsNode | undefined): ParsedP
 /**
  * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
  * `<element-citation>`, descending into `<citation-alternatives>` when a ref
- * carries both forms there rather than as direct children of `<ref>`. Mixed
- * citations are read verbatim; structured element citations are rendered
- * field-by-field with separators (see `renderElementCitation`).
+ * carries both forms there rather than as direct children of `<ref>`. Both
+ * forms are rendered child-by-child so adjacent elements stay separable (see
+ * `renderMixedCitation` and `renderElementCitation`).
  */
 export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
 /**

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

	@@ -1 +1 @@
1	- {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,~~EAKL~~,KAAK,QAAQ,~~EAGd~~,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;~~AAgFD~~;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,~~CAoClF~~;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
1	+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAML,KAAK,QAAQ,EAKd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AAsJD;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAiClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}

package/dist/services/ncbi/parsing/pmc-article-parser.js CHANGED Viewed

@@ -7,7 +7,7 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import { attrOf, childrenOf, findAll, findOne, tagNameOf, textContent, } from './pmc-xml-helpers.js';
+import { attrOf, childrenOf, findAll, findOne, isTextNode, rawTextContent, tagNameOf, textContent, textOf, } from './pmc-xml-helpers.js';
 // ─── Article IDs ────────────────────────────────────────────────────────────
 function extractArticleId(articleMeta, pubIdType) {
     if (!articleMeta)
@@ -263,12 +263,80 @@ function renderElementCitation(node) {
     }
     return parts.join(' ');
 }
+/**
+ * True when the citation text emitted so far already ends with a literal prefix
+ * naming this `pub-id-type` (`doi:`, `PMID `, `pmcid.`), so prepending the label
+ * would read `doi:DOI 10.1111/…`. (#115)
+ */
+function hasLiteralIdPrefix(rendered, pubIdType) {
+    const tail = rendered.trimEnd().replace(/[:.]$/, '').trimEnd();
+    return tail.toLowerCase().endsWith(pubIdType.toLowerCase());
+}
+/**
+ * Render a `<mixed-citation>` as a readable string.
+ *
+ * Mixed citations carry their punctuation in the text nodes between elements,
+ * so a flat `textContent()` reads correctly almost everywhere. Two adjacencies
+ * defeat it, both with zero characters between the elements: consecutive typed
+ * `<pub-id>`s fuse into one unreadable token (#115), and an inline title runs
+ * straight into the volume that follows it (#123). Walk the direct children so
+ * those two cases can be repaired without touching `textContent`, which
+ * abstracts, titles, and body paragraphs share and where zero-gap adjacency is
+ * often intentional.
+ *
+ * Typed `<pub-id>`s are labeled (unless literal prefix text already names the
+ * type), and a single space separates two adjacent elements that carry nothing
+ * between them. A label is text this renderer inserts rather than source
+ * content, so it is separated from whatever precedes it as well — publisher
+ * styles routinely close the prose on punctuation (`… (2020).`, `…021]`) and a
+ * label butted against that reads as one token. Source transitions that already
+ * carry punctuation or whitespace are emitted unchanged; the trailing whitespace
+ * collapse keeps a whitespace-only gap at one space.
+ */
+function renderMixedCitation(node) {
+    let rendered = '';
+    let prevWasElement = false;
+    for (const child of childrenOf(node)) {
+        if (isTextNode(child)) {
+            const raw = textOf(child);
+            if (raw) {
+                rendered += raw;
+                prevWasElement = false;
+            }
+            continue;
+        }
+        let part;
+        let labeled = false;
+        if (tagNameOf(child) === 'pub-id') {
+            const value = textContent(child);
+            if (!value)
+                continue;
+            const type = attrOf(child, 'pub-id-type') ?? '';
+            const label = PUB_ID_LABELS[type];
+            if (label && !hasLiteralIdPrefix(rendered, type)) {
+                labeled = true;
+                part = `${label} ${value}`;
+            }
+            else {
+                part = value;
+            }
+        }
+        else {
+            part = rawTextContent(child);
+        }
+        if (prevWasElement || labeled)
+            rendered += ' ';
+        rendered += part;
+        prevWasElement = true;
+    }
+    return rendered.replace(/\s+/g, ' ').trim();
+}
 /**
  * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
  * `<element-citation>`, descending into `<citation-alternatives>` when a ref
- * carries both forms there rather than as direct children of `<ref>`. Mixed
- * citations are read verbatim; structured element citations are rendered
- * field-by-field with separators (see `renderElementCitation`).
+ * carries both forms there rather than as direct children of `<ref>`. Both
+ * forms are rendered child-by-child so adjacent elements stay separable (see
+ * `renderMixedCitation` and `renderElementCitation`).
  */
 export function extractReferences(back) {
     if (!back)
@@ -285,12 +353,9 @@ export function extractReferences(back) {
         const container = findOne(ref, 'citation-alternatives') ?? ref;
         const mixedCitation = findOne(container, 'mixed-citation');
         const elementCitation = findOne(container, 'element-citation');
-        // <mixed-citation> carries punctuation in the text nodes between its
-        // elements, so textContent() reads correctly. <element-citation> children
-        // have no separators — render the structured fields explicitly. (#69)
         let citation = '';
         if (mixedCitation) {
-            citation = textContent(mixedCitation);
+            citation = renderMixedCitation(mixedCitation);
         }
         else if (elementCitation) {
             citation = renderElementCitation(elementCitation);

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

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts CHANGED Viewed

@@ -30,6 +30,14 @@ export declare function attrOf(node: JatsNode, name: string): string | undefined
 export declare function isTextNode(node: JatsNode): boolean;
 /** Stringified text value of a text node. */
 export declare function textOf(node: JatsNode): string;
+/**
+ * Extract all text from a node or sibling list in document order with the
+ * source spacing intact — no whitespace collapsing, no trimming. Use it when
+ * the caller assembles several fragments itself and needs to collapse once over
+ * the joined result; {@link textContent} is the normalizing form for everything
+ * else.
+ */
+export declare function rawTextContent(input: JatsNode | JatsNodeList | undefined): string;
 /**
  * Extract all text from a node or sibling list in document order, collapsing
  * runs of whitespace to a single space and trimming the result. Use this for

package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"pmc-xml-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH;;;;GAIG;AACH,MAAM,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE/C;;;;GAIG;AACH,MAAM,MAAM,YAAY,GAAG,QAAQ,EAAE,CAAC;AAKtC,uFAAuF;AACvF,wBAAgB,SAAS,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,GAAG,SAAS,CAK5D;AAED,iFAAiF;AACjF,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,YAAY,CAKvD;AAED,sDAAsD;AACtD,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAIvE;AAED,yCAAyC;AACzC,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,OAAO,CAElD;AAED,6CAA6C;AAC7C,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,CAG7C;AAmBD;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAG9E;AAED,kDAAkD;AAClD,wBAAgB,OAAO,CACrB,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAC1C,OAAO,EAAE,MAAM,GACd,QAAQ,GAAG,SAAS,CAItB;AAED,mDAAmD;AACnD,wBAAgB,OAAO,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,QAAQ,EAAE,CAI/F"}
1	+ {"version":3,"file":"pmc-xml-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH;;;;GAIG;AACH,MAAM,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE/C;;;;GAIG;AACH,MAAM,MAAM,YAAY,GAAG,QAAQ,EAAE,CAAC;AAKtC,uFAAuF;AACvF,wBAAgB,SAAS,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,GAAG,SAAS,CAK5D;AAED,iFAAiF;AACjF,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,YAAY,CAKvD;AAED,sDAAsD;AACtD,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAIvE;AAED,yCAAyC;AACzC,wBAAgB,UAAU,CAAC,IAAI,EAAE,QAAQ,GAAG,OAAO,CAElD;AAED,6CAA6C;AAC7C,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,CAG7C;AAmBD;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAEjF;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,GAAG,MAAM,CAG9E;AAED,kDAAkD;AAClD,wBAAgB,OAAO,CACrB,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAC1C,OAAO,EAAE,MAAM,GACd,QAAQ,GAAG,SAAS,CAItB;AAED,mDAAmD;AACnD,wBAAgB,OAAO,CAAC,KAAK,EAAE,QAAQ,GAAG,YAAY,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,QAAQ,EAAE,CAI/F"}

package/dist/services/ncbi/parsing/pmc-xml-helpers.js CHANGED Viewed

@@ -58,6 +58,16 @@ function concatText(input) {
     }
     return parts.join('');
 }
+/**
+ * Extract all text from a node or sibling list in document order with the
+ * source spacing intact — no whitespace collapsing, no trimming. Use it when
+ * the caller assembles several fragments itself and needs to collapse once over
+ * the joined result; {@link textContent} is the normalizing form for everything
+ * else.
+ */
+export function rawTextContent(input) {
+    return input ? concatText(input) : '';
+}
 /**
  * Extract all text from a node or sibling list in document order, collapsing
  * runs of whitespace to a single space and trimming the result. Use this for

package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/types.d.ts CHANGED Viewed

@@ -533,7 +533,11 @@ export interface ECitMatchCitation {
     firstPage?: string | undefined;
     /** Journal title or ISO abbreviation */
     journal?: string | undefined;
-    /** Arbitrary key for tracking this citation in results */
+    /**
+     * 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.
+     */
     key: string;
     /** Volume number */
     volume?: string | undefined;
@@ -549,7 +553,7 @@ export interface ECitMatchResult {
     candidatePmids?: string[];
     /** Raw non-match detail returned by ECitMatch when present */
     detail?: string;
-    /** The tracking key from the input citation */
+    /** The label from the input citation this result describes, echoed verbatim */
     key: string;
     /** Whether a PMID was found */
     matched: boolean;

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.6",
+  "version": "2.10.8",
   "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",
@@ -81,7 +81,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.7",
+    "@cyanheads/mcp-ts-core": "^0.12.8",
     "defuddle": "^0.19.3",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.6",
+  "version": "2.10.8",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.6",
+      "version": "2.10.8",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.6",
+      "version": "2.10.8",
       "packageArguments": [
         {
           "type": "positional",