@cyanheads/pubmed-mcp-server 2.10.21 → 2.10.22

package/dist/services/ncbi/types.d.ts

@@ -33,24 +33,17 @@ export interface NcbiRequestOptions {
      */
     signal?: AbortSignal;
     /**
-     * Parse XML in `preserveOrder: true` mode (returns `JatsNodeList`). Required
-     * for JATS mixed-content responses (PMC full-text) where inline element order
-     * must be preserved in the output. Leave false for all other E-utilities.
+     * Parse XML in `preserveOrder: true` mode (returns `JatsNodeList`), with tag
+     * values kept as text and whitespace untrimmed. Required for JATS
+     * mixed-content responses (PMC full-text), where inline element order must
+     * be preserved, and for ESpell, whose `<SpelledQuery>` segments are read in
+     * document order with their spacing and whose echoed `<Query>` must not be
+     * coerced to a number (`007`, `1e5`). Leave false for all other E-utilities.
+     * (#108, #241)
      */
     useOrderedParser?: boolean;
     /** Force HTTP POST (for large payloads). */
     usePost?: boolean;
-    /**
-     * Parse XML with `parseTagValue: false` while keeping the flat, named-key
-     * object shape (`response.eSpellResult.Query`). Required wherever a response
-     * echoes an arbitrary caller-supplied token that must survive verbatim: the
-     * coercing default turns `007` into `7` and `1e5` into `100000` before any
-     * application code runs, so a read-site `String()` cannot recover the text.
-     * Distinct from `useOrderedParser`, which also sets `preserveOrder` and hands
-     * back a document-ordered node array. Ignored when `useOrderedParser` is set.
-     * (#108)
-     */
-    useVerbatimParser?: boolean;
 }
 /**
  * Runtime options accepted by public NCBI service methods.
@@ -92,6 +85,8 @@ export interface XmlAuthor {
     Identifier?: XmlIdentifier[] | XmlIdentifier;
     Initials?: XmlTextElement;
     LastName?: XmlTextElement;
+    /** Generational suffix as NCBI writes it — `Jr`, `2nd`, `3rd`, `4th` — never normalized. */
+    Suffix?: XmlTextElement;
 }
 /**
  * One member of a collective author, from `InvestigatorList`. The DTD gives an
@@ -332,6 +327,8 @@ export interface ParsedArticleAuthor {
     initials?: string;
     lastName?: string;
     orcid?: string;
+    /** Generational suffix verbatim from NCBI `Suffix` (`Jr`, `2nd`). Absent when NCBI gives none. (#226) */
+    suffix?: string;
 }
 /**
  * A member of a collective author, from `InvestigatorList`. Not an author: kept
@@ -346,6 +343,7 @@ export interface ParsedInvestigator {
     initials?: string;
     lastName?: string;
     orcid?: string;
+    suffix?: string;
 }
 export interface ParsedArticleDate {
     dateType?: string;
@@ -421,6 +419,7 @@ export interface ParsedBookEditor {
     firstName?: string;
     initials?: string;
     lastName?: string;
+    suffix?: string;
 }
 /**
  * The containing book of a `book-chapter`, or the book itself for a `book`
@@ -685,25 +684,18 @@ export interface ESearchResult {
     warningList?: ESearchWarningList;
     webEnv?: string;
 }
-/** Normalized ESpell result. */
+/**
+ * Normalized ESpell result. The response is read with the ordered parser (a
+ * `JatsNodeList`), so no raw container type is declared for it.
+ */
 export interface ESpellResult {
+    /** The caller's query with ESpell's accepted replacements applied; `original` when none was. */
     corrected: string;
+    /** Whether at least one replacement was applied. */
     hasSuggestion: boolean;
+    /** The query as ESpell echoed it. */
     original: string;
 }
-/**
- * Raw parsed XML container for eSpellResult. `Query` and `CorrectedQuery` are
- * strings at runtime as well as in this declaration: the ESpell request opts
- * into `useVerbatimParser`, so the coercing default parser never sees the
- * echoed term. (#108)
- */
-export interface ESpellResponseContainer {
-    eSpellResult: {
-        Query?: string;
-        CorrectedQuery?: string;
-        SpelledQuery?: unknown;
-    };
-}
 export interface EFetchArticleSet {
     articles: ParsedArticle[];
 }
@@ -771,7 +763,10 @@ export interface ParsedPmcAsset {
     href?: string;
     /** The `id` attribute, when the deposit carries one. */
     id?: string;
-    /** Display label, e.g. `Fig. 1`. */
+    /**
+     * Display label, e.g. `Fig. 1`, without the one trailing ` |`, `.` or `:` some
+     * deposits print after it (`Figure 1.` reads `Figure 1`).
+     */
     label?: string;
     /**
      * Title of the innermost enclosing section wherever it sits — body, back
@@ -785,6 +780,8 @@ export interface ParsedPmcAuthor {
     collectiveName?: string;
     givenNames?: string;
     lastName?: string;
+    /** JATS `<name>/<suffix>` verbatim (`IV`, `Jr`). Absent when the deposit gives none. (#226) */
+    suffix?: string;
 }
 /** Parsed PMC journal info. */
 export interface ParsedPmcJournal {
@@ -838,7 +835,10 @@ export interface ParsedPmcTable {
     headerRowCount: number;
     /** The `id` attribute, when the deposit carries one. */
     id?: string;
-    /** Display label, e.g. `TABLE 1`. */
+    /**
+     * Display label, e.g. `TABLE 1`, without the one trailing ` |`, `.` or `:`
+     * some deposits print after it (`Table 1.` reads `Table 1`).
+     */
     label?: string;
     /** Cell text by grid column, spans expanded. Empty when unextractable. */
     rows: string[][];

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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.21",
+  "version": "2.10.22",
   "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",
@@ -86,7 +86,7 @@
     }
   ],
   "license": "Apache-2.0",
-  "packageManager": "bun@1.4.2",
+  "packageManager": "bun@1.4.3",
   "engines": {
     "bun": ">=1.4.0",
     "node": ">=24.0.0"
@@ -95,7 +95,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.14",
+    "@cyanheads/mcp-ts-core": "^0.13.15",
     "defuddle": "^0.19.4",
     "fast-xml-parser": "^5.11.2",
     "linkedom": "^0.18.13",
@@ -107,7 +107,7 @@
   "devDependencies": {
     "@biomejs/biome": "^2.5.15",
     "@socketsecurity/bun-security-scanner": "^1.1.3",
-    "@types/node": "^26.6.4",
+    "@types/node": "^26.6.5",
     "@types/sanitize-html": "^2.16.2",
     "@vitest/coverage-istanbul": "^5.0.3",
     "depcheck": "^1.4.7",
@@ -118,7 +118,7 @@
     "vitest": "^5.0.3"
   },
   "overrides": {
-    "@hono/node-server": "^2.0.11",
+    "@hono/node-server": "^2.1.4",
     "brace-expansion": "^2.1.2",
     "fast-uri": "^3.1.4",
     "postcss": "^8.5.22"

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.21",
+  "version": "2.10.22",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "npx",
-      "version": "2.10.21",
+      "version": "2.10.22",
       "environmentVariables": [
         {
           "name": "MCP_LOG_LEVEL",
@@ -56,7 +56,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "npx",
-      "version": "2.10.21",
+      "version": "2.10.22",
       "environmentVariables": [
         {
           "name": "MCP_TRANSPORT_TYPE",