@cyanheads/pubmed-mcp-server 2.9.0 → 2.9.1

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Files changed (13) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +1 -1
  4. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +5 -3
  5. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  6. package/dist/services/ncbi/parsing/pmc-article-parser.js +74 -7
  7. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  8. package/dist/services/ncbi/response-handler.d.ts +6 -1
  9. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  10. package/dist/services/ncbi/response-handler.js +7 -2
  11. package/dist/services/ncbi/response-handler.js.map +1 -1
  12. package/package.json +1 -1
  13. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.9.0
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+ **Version:** 2.9.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.9.0
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+ **Version:** 2.9.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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package/README.md CHANGED
@@ -9,7 +9,7 @@
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- [![Version](https://img.shields.io/badge/Version-2.9.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-2.9.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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  </div>
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED
@@ -19,9 +19,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
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  */
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  export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
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  /**
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- * Extract references from a `<back>` node. Prefers mixed-citation over
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- * element-citation, descending into `<citation-alternatives>` when a ref carries
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- * both forms there rather than as direct children of `<ref>`.
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+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
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+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
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+ * carries both forms there rather than as direct children of `<ref>`. Mixed
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+ * citations are read verbatim; structured element citations are rendered
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+ * field-by-field with separators (see `renderElementCitation`).
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  */
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  export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
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  /**
package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"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"}
package/dist/services/ncbi/parsing/pmc-article-parser.js CHANGED
@@ -207,9 +207,68 @@ function extractSection(sec) {
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  }
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  // ─── References ─────────────────────────────────────────────────────────────
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  /**
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- * Extract references from a `<back>` node. Prefers mixed-citation over
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- * element-citation, descending into `<citation-alternatives>` when a ref carries
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- * both forms there rather than as direct children of `<ref>`.
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+ * `pub-id-type` → human label, so the trailing identifiers in a rendered
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+ * `<element-citation>` read as `PMID 37657419` rather than a bare number run.
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+ */
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+ const PUB_ID_LABELS = {
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+ pmid: 'PMID',
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+ doi: 'DOI',
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+ pmcid: 'PMCID',
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+ };
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+ /** Render one `<person-group>` child — a `<name>`, `<collab>`, or `<etal>`. */
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+ function renderCitationName(node) {
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+ const tag = tagNameOf(node);
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+ if (tag === 'name' || tag === 'string-name') {
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+ const surname = textContent(findOne(node, 'surname'));
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+ const given = textContent(findOne(node, 'given-names'));
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+ return [surname, given].filter(Boolean).join(' ') || textContent(node);
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+ }
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+ if (tag === 'collab')
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+ return textContent(node);
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+ if (tag === 'etal')
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+ return 'et al.';
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+ return '';
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+ }
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+ /**
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+ * Render a structured `<element-citation>` as a readable, delimited string.
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+ * Its child elements carry no punctuation between them, so a flat
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+ * `textContent()` runs every field together (`DomanJ.L.…Cell18618…`). Walk the
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+ * direct children in document order, joining author names with `, ` and
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+ * labeling typed `<pub-id>`s, so the output reads as a citation rather than a
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+ * token run. (#69)
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+ */
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+ function renderElementCitation(node) {
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+ const parts = [];
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+ for (const child of childrenOf(node)) {
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+ const tag = tagNameOf(child);
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+ if (tag === 'person-group') {
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+ const names = childrenOf(child).map(renderCitationName).filter(Boolean);
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+ if (names.length > 0)
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+ parts.push(names.join(', '));
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+ }
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+ else if (tag === 'pub-id') {
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+ const value = textContent(child);
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+ if (value) {
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+ const label = PUB_ID_LABELS[attrOf(child, 'pub-id-type') ?? ''];
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+ parts.push(label ? `${label} ${value}` : value);
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+ }
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+ }
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+ else {
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+ // Element field (source, volume, year, fpage, …) or a bare text node;
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+ // textContent renders both, and empty results drop out of the join.
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+ const text = textContent(child);
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+ if (text)
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+ parts.push(text);
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+ }
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+ }
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+ return parts.join(' ');
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+ }
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+ /**
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+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
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+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
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+ * carries both forms there rather than as direct children of `<ref>`. Mixed
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+ * citations are read verbatim; structured element citations are rendered
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+ * field-by-field with separators (see `renderElementCitation`).
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  */
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  export function extractReferences(back) {
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  if (!back)
@@ -224,10 +283,18 @@ export function extractReferences(back) {
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  // <mixed-citation>). findOne matches direct children only, so resolve that
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  // container first; refs with a direct citation node fall through to `ref`.
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  const container = findOne(ref, 'citation-alternatives') ?? ref;
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- const citationNode = findOne(container, 'mixed-citation') ?? findOne(container, 'element-citation');
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- if (!citationNode)
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- continue;
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- const citation = textContent(citationNode);
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+ const mixedCitation = findOne(container, 'mixed-citation');
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+ const elementCitation = findOne(container, 'element-citation');
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+ // <mixed-citation> carries punctuation in the text nodes between its
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+ // elements, so textContent() reads correctly. <element-citation> children
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+ // have no separators — render the structured fields explicitly. (#69)
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+ let citation = '';
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+ if (mixedCitation) {
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+ citation = textContent(mixedCitation);
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+ }
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+ else if (elementCitation) {
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+ citation = renderElementCitation(elementCitation);
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+ }
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  if (!citation)
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  continue;
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  const id = attrOf(ref, 'id');
package/dist/services/ncbi/parsing/pmc-article-parser.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts CHANGED
@@ -33,7 +33,12 @@ export declare class NcbiResponseHandler {
33
33
  * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
34
34
  * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
35
35
  * doesn't collapse into reordered text. `trimValues: false` retains spacing
36
- * between text nodes and adjacent inline children.
36
+ * between text nodes and adjacent inline children. `parseTagValue: false`
37
+ * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
38
+ * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
39
+ * every value on this path is `String()`-ed downstream, so coercion is pure
40
+ * downside. Entity decoding is unaffected (it's governed by `processEntities`/
41
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69)
37
42
  */
38
43
  private readonly orderedXmlParser;
39
44
  constructor();
package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
1
+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -230,7 +230,12 @@ export class NcbiResponseHandler {
230
230
  * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
231
231
  * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
232
232
  * doesn't collapse into reordered text. `trimValues: false` retains spacing
233
- * between text nodes and adjacent inline children.
233
+ * between text nodes and adjacent inline children. `parseTagValue: false`
234
+ * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
235
+ * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
236
+ * every value on this path is `String()`-ed downstream, so coercion is pure
237
+ * downside. Entity decoding is unaffected (it's governed by `processEntities`/
238
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69)
234
239
  */
235
240
  orderedXmlParser;
236
241
  constructor() {
@@ -246,7 +251,7 @@ export class NcbiResponseHandler {
246
251
  preserveOrder: true,
247
252
  ignoreAttributes: false,
248
253
  attributeNamePrefix: '@_',
249
- parseTagValue: true,
254
+ parseTagValue: false,
250
255
  trimValues: false,
251
256
  processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
252
257
  htmlEntities: true,
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.9.0",
3
+ "version": "2.9.1",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.9.0",
9
+ "version": "2.9.1",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.9.0",
22
+ "version": "2.9.1",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -66,7 +66,7 @@
66
66
  "registryBaseUrl": "https://registry.npmjs.org",
67
67
  "identifier": "@cyanheads/pubmed-mcp-server",
68
68
  "runtimeHint": "bun",
69
- "version": "2.9.0",
69
+ "version": "2.9.1",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",