npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.5.6 → 2.6.1 - Mend

@cyanheads/pubmed-mcp-server 2.5.6 → 2.6.1

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 (36) hide show

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED Viewed

@@ -28,5 +28,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         score: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     totalFound: z.ZodNumber;
+    notice: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>>;
 //# sourceMappingURL=find-related.tool.d.ts.map

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe~~;;;;;;;;;;;;;;;;;;;;;;;;kBAsK1B~~,CAAC"}
1	+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;kBAkM1B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -49,6 +49,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
             .describe('Related article with enriched summary'))
             .describe('Related articles'),
         totalFound: z.number().describe('Total related articles found before truncation'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when results are empty due to a known limitation — e.g. references for a non-PMC source. Absent on successful result pages.'),
     }),
     async handler(input, ctx) {
         const ncbi = getNcbiService();
@@ -102,11 +106,30 @@ export const findRelatedTool = tool('pubmed_find_related', {
         }
         const totalFound = foundPmids.length;
         if (foundPmids.length === 0) {
+            // NCBI's pubmed_pubmed_refs ELink only resolves reference lists for
+            // PMC-indexed sources, so a valid PMID without a PMCID looks identical
+            // to "this article cites nothing". Look up the source's PMCID so the
+            // caller gets a relationship-aware recovery hint.
+            let notice;
+            if (input.relationship === 'references') {
+                try {
+                    const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: input.pmid }, { signal: ctx.signal });
+                    const summaries = await extractBriefSummaries(summaryResult);
+                    const sourcePmcId = summaries[0]?.pmcId;
+                    notice = sourcePmcId
+                        ? `No reference list found in PMC for PMID ${input.pmid} (PMCID ${sourcePmcId}).`
+                        : `Reference lists require the source article to be indexed in PMC. PMID ${input.pmid} has no PMCID — references unavailable. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
+                }
+                catch (err) {
+                    ctx.log.debug('Failed to look up source PMCID for references hint', { err });
+                }
+            }
             return {
                 sourcePmid: input.pmid,
                 relationship: input.relationship,
                 articles: [],
                 totalFound: 0,
+                ...(notice && { notice }),
             };
         }
         if (foundPmids.every((p) => p.score !== undefined)) {
@@ -137,8 +160,11 @@ export const findRelatedTool = tool('pubmed_find_related', {
             `# Related Articles for PMID ${result.sourcePmid}`,
             `**Relationship:** ${result.relationship} | **Found:** ${result.totalFound}`,
         ];
+        if (result.notice)
+            lines.push(`\n> ${result.notice}`);
         if (result.articles.length === 0) {
-            lines.push('No related articles found.');
+            if (!result.notice)
+                lines.push('No related articles found.');
         }
         else {
             for (const a of result.articles) {

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yFAAyF,CAC1F;SACJ,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACjF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+IAA+I,CAChJ;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0BAA0B,EAAE;YACxC,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,YAAY,EAAE,KAAK,CAAC,YAAY;SACjC,CAAC,CAAC;QAEH,MAAM,WAAW,GAA2B;YAC1C,MAAM,EAAE,QAAQ;YAChB,EAAE,EAAE,QAAQ;YACZ,EAAE,EAAE,KAAK,CAAC,IAAI;YACd,OAAO,EAAE,KAAK;SACf,CAAC;QACF,QAAQ,KAAK,CAAC,YAAY,EAAE,CAAC;YAC3B,KAAK,SAAS;gBACZ,WAAW,CAAC,GAAG,GAAG,gBAAgB,CAAC;gBACnC,MAAM;YACR,KAAK,UAAU;gBACb,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,uBAAuB,CAAC;gBAC/C,MAAM;YACR,KAAK,YAAY;gBACf,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,oBAAoB,CAAC;gBAC5C,MAAM;QACV,CAAC;QAED,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAkB,CAAC;QAC7F,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QAChE,MAAM,WAAW,GAAG,iBAAiB,CAAC,CAAC,CAAgC,CAAC;QAExE,IAAI,WAAW,EAAE,KAAK,EAAE,CAAC;YACvB,MAAM,IAAI,KAAK,CACb,gBAAgB,OAAO,WAAW,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,CAChH,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,WAAW,EAAE,OAAO,CAAC;QACrC,IAAI,UAAU,GAAuC,EAAE,CAAC;QAExD,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;YACvB,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YACtD,MAAM,gBAAgB,GACpB,KAAK,CAAC,YAAY,KAAK,UAAU;gBAC/B,CAAC,CAAC,uBAAuB;gBACzB,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,YAAY;oBACnC,CAAC,CAAC,oBAAoB;oBACtB,CAAC,CAAC,eAAe,CAAC;YACxB,MAAM,QAAQ,GACZ,cAAc,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,gBAAgB,CAAC,IAAI,cAAc,CAAC,CAAC,CAAC,CAAC;YAErF,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;gBACnB,UAAU,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC;qBACpC,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE,CAAC,CAAC;oBAC5B,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;iBACjF,CAAC,CAAC;qBACF,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;QAED,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,oEAAoE;YACpE,uEAAuE;YACvE,qEAAqE;YACrE,kDAAkD;YAClD,IAAI,MAA0B,CAAC;YAC/B,IAAI,KAAK,CAAC,YAAY,KAAK,YAAY,EAAE,CAAC;gBACxC,IAAI,CAAC;oBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;oBACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;oBAC7D,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC;oBACxC,MAAM,GAAG,WAAW;wBAClB,CAAC,CAAC,2CAA2C,KAAK,CAAC,IAAI,WAAW,WAAW,IAAI;wBACjF,CAAC,CAAC,yEAAyE,KAAK,CAAC,IAAI,+IAA+I,CAAC;gBACzO,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,GAAG,CAAC,GAAG,CAA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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAgT7B~~,CAAC"}
1	+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAqT7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED Viewed

@@ -310,6 +310,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         if (result.pmids.length > 0)
             lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
         if (result.summaries?.length) {
+            if (result.summaries.length < result.pmids.length) {
+                lines.push(`\n> Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs. Increase \`summaryCount\` (max 50) to fetch more.`);
+            }
             lines.push('\n### Summaries');
             for (const s of result.summaries) {
                 lines.push(`\n#### ${s.title ?? s.pmid}`);

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED Viewed

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

@@ -5,6 +5,24 @@
  * @module src/services/ncbi/response-handler
  */
 import type { NcbiRequestOptions } from './types.js';
+/**
+ * Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
+ * `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
+ * runs. The non-ordered parser used for EFetch responses doesn't preserve
+ * mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
+ * 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
+ * digit is silently dropped from abstracts and titles.
+ *
+ * Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
+ * falls back to a `^X` / `_X` ASCII prefix so the content survives in a
+ * recognizable form. Italic / bold / underline / small-caps tags are
+ * stripped (content kept) since they don't carry meaning in our text
+ * rendering. Only invoked on the regular parser path; the PMC JATS path
+ * already preserves inline markup via `preserveOrder: true`.
+ *
+ * @internal exported for direct unit tests
+ */
+export declare function flattenInlineMarkup(xml: string): string;
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.

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;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;~~AAsHrD~~;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;OAGG;IACH,OAAO,CAAC,cAAc;IAatB,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;~~CAyHL~~"}
1	+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAsLrD;;;;;;;;;;;;;;;;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;;;OAGG;IACH,OAAO,CAAC,cAAc;IAatB,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;CA6HL"}

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

@@ -117,6 +117,88 @@ function sanitizeNcbiError(message) {
  * to the caller which reports it via `unavailablePmcIds`.
  */
 const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
+/**
+ * Unicode superscript map. Covers digits, common operators, and the few
+ * letters that have superscript codepoints (n, i). `−` (U+2212, the proper
+ * minus) is normalized to U+207B alongside ASCII `-`.
+ */
+const SUPERSCRIPT_MAP = {
+    '0': '⁰',
+    '1': '¹',
+    '2': '²',
+    '3': '³',
+    '4': '⁴',
+    '5': '⁵',
+    '6': '⁶',
+    '7': '⁷',
+    '8': '⁸',
+    '9': '⁹',
+    '+': '⁺',
+    '-': '⁻',
+    '−': '⁻',
+    '=': '⁼',
+    '(': '⁽',
+    ')': '⁾',
+    n: 'ⁿ',
+    i: 'ⁱ',
+};
+/**
+ * Unicode subscript map. Covers digits and operators; alphabetic subscripts
+ * are limited in Unicode and rarely appear in MEDLINE so they fall through
+ * to the `_X` ASCII fallback.
+ */
+const SUBSCRIPT_MAP = {
+    '0': '₀',
+    '1': '₁',
+    '2': '₂',
+    '3': '₃',
+    '4': '₄',
+    '5': '₅',
+    '6': '₆',
+    '7': '₇',
+    '8': '₈',
+    '9': '₉',
+    '+': '₊',
+    '-': '₋',
+    '−': '₋',
+    '=': '₌',
+    '(': '₍',
+    ')': '₎',
+};
+function mapInlineContent(content, table, asciiPrefix) {
+    let out = '';
+    for (const ch of content) {
+        const mapped = table[ch];
+        if (mapped === undefined)
+            return `${asciiPrefix}${content}`;
+        out += mapped;
+    }
+    return out;
+}
+/**
+ * Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
+ * `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
+ * runs. The non-ordered parser used for EFetch responses doesn't preserve
+ * mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
+ * 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
+ * digit is silently dropped from abstracts and titles.
+ *
+ * Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
+ * falls back to a `^X` / `_X` ASCII prefix so the content survives in a
+ * recognizable form. Italic / bold / underline / small-caps tags are
+ * stripped (content kept) since they don't carry meaning in our text
+ * rendering. Only invoked on the regular parser path; the PMC JATS path
+ * already preserves inline markup via `preserveOrder: true`.
+ *
+ * @internal exported for direct unit tests
+ */
+export function flattenInlineMarkup(xml) {
+    return xml
+        .replace(/<sup>([^<]*)<\/sup>/g, (_, c) => mapInlineContent(c, SUPERSCRIPT_MAP, '^'))
+        .replace(/<sub>([^<]*)<\/sub>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
+        .replace(/<inf>([^<]*)<\/inf>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
+        .replace(/<\/?(?:i|b|u|sc)>/g, '');
+}
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.
@@ -215,9 +297,13 @@ export class NcbiResponseHandler {
                 this.throwNcbiError(errorParsed, endpoint);
             }
             const parser = useOrdered ? this.orderedXmlParser : this.xmlParser;
+            // Pre-flatten <sup>/<sub>/<inf>/<i>/<b>/<u>/<sc> on the regular parser
+            // path. The ordered parser walks mixed content correctly via
+            // preserveOrder; the regular parser does not.
+            const xmlForParse = useOrdered ? responseText : flattenInlineMarkup(responseText);
             let parsedXml;
             try {
-                parsedXml = parser.parse(responseText);
+                parsedXml = parser.parse(xmlForParse);
             }
             catch (error) {
                 const parserError = error instanceof Error ? error.message : String(error);

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

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1	+ 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package/dist/services/unpaywall/types.d.ts ADDED Viewed

@@ -0,0 +1,55 @@
+/**
+ * @fileoverview Types for the Unpaywall API and the content extracted from
+ * open-access copies it indexes.
+ * @module src/services/unpaywall/types
+ */
+export declare const UNPAYWALL_API_BASE = "https://api.unpaywall.org/v2";
+/**
+ * Shape of a single OA location record returned by Unpaywall. Fields mirror
+ * the public API — see https://unpaywall.org/data-format for the full contract.
+ * All fields beyond `url` are best-effort.
+ */
+export interface UnpaywallLocation {
+    /** `open`, `closed`, `embargoed`, `gold`, `hybrid`, `bronze`, `green`, etc. */
+    host_type?: 'publisher' | 'repository' | string | null;
+    /** SPDX-ish license identifier (`cc-by`, `cc0`, `public-domain`, …). */
+    license?: string | null;
+    /** Direct link to the OA copy (HTML landing page or PDF). */
+    url: string;
+    /** Direct link to a PDF when one is known; separate from `url`. */
+    url_for_pdf?: string | null;
+    /** `submittedVersion`, `acceptedVersion`, `publishedVersion`. */
+    version?: 'submittedVersion' | 'acceptedVersion' | 'publishedVersion' | string | null;
+}
+/**
+ * Subset of the Unpaywall `/v2/{doi}` response this server consumes.
+ * Upstream response has many more fields — we narrow to what's actually used.
+ */
+export interface UnpaywallResponse {
+    best_oa_location?: UnpaywallLocation | null;
+    doi?: string;
+    is_oa?: boolean;
+    oa_locations?: UnpaywallLocation[];
+    oa_status?: 'gold' | 'green' | 'hybrid' | 'bronze' | 'closed' | string;
+}
+/** Outcome of resolving a DOI to an OA copy. */
+export type UnpaywallResolution = {
+    kind: 'found';
+    location: UnpaywallLocation;
+} | {
+    kind: 'no-oa';
+    reason: string;
+};
+/** Raw content + type tag, pre-extraction. Discriminated on `kind` so the body type narrows. */
+export type UnpaywallContent = {
+    kind: 'html';
+    fetchedUrl: string;
+    body: string;
+} | {
+    kind: 'pdf';
+    fetchedUrl: string;
+    body: Uint8Array;
+};
+/** Kind of content body returned by a successful Unpaywall fetch. */
+export type UnpaywallContentKind = UnpaywallContent['kind'];
+//# sourceMappingURL=types.d.ts.map

package/dist/services/unpaywall/types.d.ts.map ADDED Viewed

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package/dist/services/unpaywall/types.js ADDED Viewed

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Types for the Unpaywall API and the content extracted from
+ * open-access copies it indexes.
+ * @module src/services/unpaywall/types
+ */
+export const UNPAYWALL_API_BASE = 'https://api.unpaywall.org/v2';
+//# sourceMappingURL=types.js.map

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package/dist/services/unpaywall/unpaywall-service.d.ts ADDED Viewed

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+/**
+ * @fileoverview Unpaywall service. Resolves a DOI to an open-access location
+ * and fetches the raw content (HTML or PDF) for downstream extraction. Enabled
+ * only when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
+ *
+ * Philosophy: best-effort. Upstream 404s and non-OA DOIs return a `no-oa`
+ * resolution; only genuine service failures (5xx, network, timeout) throw.
+ * @module src/services/unpaywall/unpaywall-service
+ */
+import { type UnpaywallContent, type UnpaywallLocation, type UnpaywallResolution } from './types.js';
+/**
+ * Resolves a DOI to an open-access copy via Unpaywall and fetches its bytes.
+ * Constructed only when `UNPAYWALL_EMAIL` is present; absent config → no service.
+ */
+export declare class UnpaywallService {
+    private readonly email;
+    private readonly timeoutMs;
+    constructor(email: string, timeoutMs: number);
+    /**
+     * Look up a DOI in Unpaywall. Returns a structured outcome — never throws
+     * for a DOI that simply has no OA copy or that Unpaywall doesn't know.
+     * Throws `McpError(ServiceUnavailable)` only for network/server failures.
+     */
+    resolve(doi: string, signal?: AbortSignal): Promise<UnpaywallResolution>;
+    /**
+     * Fetch the content at an Unpaywall location. Prefers `url_for_pdf` when
+     * present (direct PDF bytes) and falls back to `url` (HTML landing page).
+     * Throws `McpError(ServiceUnavailable)` on network/server failures or
+     * unreadable responses — caller handles partial failures.
+     */
+    fetchContent(location: UnpaywallLocation, signal?: AbortSignal): Promise<UnpaywallContent>;
+    private fetchAs;
+}
+/**
+ * Initialize the Unpaywall service if `UNPAYWALL_EMAIL` is configured.
+ * Safe to call regardless — absence of the env var leaves the service unset,
+ * and `getUnpaywallService()` returns `undefined`.
+ */
+export declare function initUnpaywallService(): void;
+/** Returns the initialized service, or `undefined` when the fallback is disabled. */
+export declare function getUnpaywallService(): UnpaywallService | undefined;
+//# sourceMappingURL=unpaywall-service.d.ts.map

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