@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts

@@ -40,15 +40,22 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
+    readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
+    readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
+    readonly retryable: true;
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'ncbi_rate_limited';
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
+    readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
+    readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
-    readonly when: 'Total request deadline expired before NCBI returned a response.';
-    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
+    readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
+    readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {

package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkI9B,CAAC"}
+{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkI9B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts

@@ -3,27 +3,25 @@
  * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
  * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
  * returns a PMID whose author roster doesn't contain the queried author.
- * `citations` takes an array or a single citation object, and `citation` is
- * accepted as an alias for it.
+ * `citations` is advertised as an array of 1–25 citations. A lone citation
+ * object is wrapped into a one-element array before validation, and `citation`
+ * is accepted as an alias for `citations`. Every citation-shape rule lives in
+ * the schema, so a citation that cannot match is rejected under its
+ * `citations.N.<field>` path before ECitMatch is called: `year` is four digits,
+ * the other bibliographic fields hold a visible character, and each citation
+ * carries a journal or a year.
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
-    citations: z.ZodUnion<readonly [z.ZodArray<z.ZodObject<{
-        journal: z.ZodOptional<z.ZodString>;
-        year: z.ZodOptional<z.ZodString>;
-        volume: z.ZodOptional<z.ZodString>;
-        firstPage: z.ZodOptional<z.ZodString>;
-        authorName: z.ZodOptional<z.ZodString>;
-        key: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>>, z.ZodObject<{
-        journal: z.ZodOptional<z.ZodString>;
-        year: z.ZodOptional<z.ZodString>;
-        volume: z.ZodOptional<z.ZodString>;
-        firstPage: z.ZodOptional<z.ZodString>;
-        authorName: z.ZodOptional<z.ZodString>;
-        key: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>]>;
+    citations: z.ZodPreprocess<z.ZodArray<z.ZodObject<{
+        journal: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        year: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        volume: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        firstPage: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        authorName: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        key: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    }, z.core.$strip>>, unknown>;
 }, z.core.$strip>, z.ZodObject<{
     results: z.ZodArray<z.ZodObject<{
         key: z.ZodString;
@@ -58,15 +56,22 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
+    readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
+    readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
+    readonly retryable: true;
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'ncbi_rate_limited';
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
+    readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
+    readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
-    readonly when: 'Total request deadline expired before NCBI returned a response.';
-    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
+    readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
+    readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyFjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAqR7B,CAAC"}
+{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAwS7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js

@@ -3,8 +3,13 @@
  * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
  * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
  * returns a PMID whose author roster doesn't contain the queried author.
- * `citations` takes an array or a single citation object, and `citation` is
- * accepted as an alias for it.
+ * `citations` is advertised as an array of 1–25 citations. A lone citation
+ * object is wrapped into a one-element array before validation, and `citation`
+ * is accepted as an alias for `citations`. Every citation-shape rule lives in
+ * the schema, so a citation that cannot match is rejected under its
+ * `citations.N.<field>` path before ECitMatch is called: `year` is four digits,
+ * the other bibliographic fields hold a visible character, and each citation
+ * carries a journal or a year.
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -12,6 +17,7 @@ import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
+import { hasVisibleText } from './_visible-text.js';
 /** Extract the surname token (first whitespace-separated part) from an author string. */
 function surname(name) {
     return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
@@ -29,73 +35,118 @@ function surname(name) {
  * wire (the service submits positional tokens instead), so it stays free-form.
  */
 const BDATA_FIELD_RE = /^[^|\r\n]*$/;
-const BDATA_FIELD_HINT = 'Cannot contain a pipe ("|") or a line break.';
-const BDATA_FIELD_ERROR = `${BDATA_FIELD_HINT} Those characters shift ECitMatch's field layout — remove them or replace them with a space.`;
+const BDATA_FIELD_ERROR = 'Cannot contain a pipe ("|") or a line break. Those characters shift ECitMatch\'s field layout — remove them or replace them with a space.';
+const TEXT_FIELD_HINT = 'Must contain a visible character, and cannot contain a pipe ("|") or a line break.';
+const VISIBLE_TEXT_ERROR = 'Must contain a visible character. Omit the field rather than sending only spaces or invisible characters.';
+/**
+ * The only year ECitMatch matches on: four ASCII digits, padding with spaces or
+ * tabs tolerated. Every other form — `1991a`, `91`, `1991-1992`, `1991 May` —
+ * misses, and a journal-less citation carrying one makes ECitMatch drop that
+ * line and every line after it. No CR or LF, so the bdata layout rule above
+ * holds for this field too. (#187)
+ */
+const YEAR_RE = /^[ \t]*\d{4}[ \t]*$/;
+/**
+ * A safe integer sent for a string field, read as its decimal string — the
+ * framework's own repair rule (a safe integer other than `-0`), applied here
+ * because that repair cannot reach a lone citation object: it re-reads the
+ * failing path `citations.0.year` against the raw arguments, where `citations`
+ * is still the object this schema wraps. Converting before validation gives the
+ * object and array forms the same citation. Anything else passes through to be
+ * rejected as before. (#198)
+ */
+const integerAsString = (value) => typeof value === 'number' && Number.isSafeInteger(value) && !Object.is(value, -0)
+    ? String(value)
+    : value;
+/**
+ * An exactly-empty string from a form client means "unset", never a value to
+ * validate: it parses to `undefined` before the field's checks run, so the
+ * advertised schema keeps its plain `pattern`. Whitespace and invisible-only
+ * values still reach the checks and are rejected. An integer is read as its
+ * decimal string first. (#187, #198)
+ */
+const blankAsUnset = (schema) => z.preprocess((value) => {
+    const read = integerAsString(value);
+    return read === '' ? undefined : read;
+}, schema);
+/**
+ * A bibliographic text field: rejected when it would shift the bdata layout or
+ * holds no visible character — whitespace or a zero-width space sent as a
+ * journal reads as present here but constrains nothing upstream. (#125, #187)
+ */
+const textField = () => blankAsUnset(z
+    .string()
+    .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
+    .refine(hasVisibleText, VISIBLE_TEXT_ERROR)
+    .optional());
 const CitationSchema = z
     .object({
-    journal: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${BDATA_FIELD_HINT}`),
-    year: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Publication year (e.g., "1991"). ${BDATA_FIELD_HINT}`),
-    volume: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Volume number. ${BDATA_FIELD_HINT}`),
-    firstPage: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`First page number. ${BDATA_FIELD_HINT}`),
-    authorName: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${BDATA_FIELD_HINT}`),
+    journal: textField().describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${TEXT_FIELD_HINT}`),
+    year: blankAsUnset(z.string().regex(YEAR_RE, 'Must be a four-digit year, e.g. "1991".').optional()).describe('Publication year as four digits (e.g., "1991").'),
+    volume: textField().describe(`Volume number. ${TEXT_FIELD_HINT}`),
+    firstPage: textField().describe(`First page number. ${TEXT_FIELD_HINT}`),
+    authorName: textField().describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${TEXT_FIELD_HINT}`),
     key: z
-        .string()
-        .optional()
+        .preprocess(integerAsString, z.string().optional())
         .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.'),
 })
-    .describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
-    .refine((c) => !!(c.journal || c.year), {
+    .describe('Citation to match against PubMed. Must include at least journal or a four-digit year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
+    /**
+     * Zod still runs this beside a field that failed its own check, handing it the
+     * raw value, so the rule tests the journal and year itself: a whitespace
+     * journal or a malformed year never satisfies it. (#187)
+     */
+    .refine((c) => (c.journal !== undefined && hasVisibleText(c.journal)) ||
+    (c.year !== undefined && YEAR_RE.test(c.year)), {
     message: 'Each citation must include at least a journal or year field — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.',
 });
 /**
- * The union issue's own message, in place of Zod's bare `Invalid input`. A value
- * that fails only a check inside one branch — a pipe in a field, a missing
- * journal and year — keeps that branch's issue and path. A value that fails both
- * branches outright (a string, or an array element of the wrong type) is one
- * union issue carrying this message, with each branch's issues nested under it.
+ * Message for a `citations` value the array check refuses (a string, a number, a
+ * missing field, or an array outside 1–25) in place of Zod's bare `expected
+ * array`, so the caller learns both shapes that parse. A lone object never
+ * reaches this check: it is wrapped first, and its own field issues report under
+ * `citations.0`.
  */
 const CITATIONS_SHAPE_ERROR = 'Invalid input: expected a citation object or an array of 1–25 citation objects';
+/** A citation sent on its own rather than in an array. JSON input has no other object kind. */
+const isCitationObject = (value) => typeof value === 'object' && value !== null && !Array.isArray(value);
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
-    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
+    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or a four-digit year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
     errors: [...NCBI_SERVICE_ERRORS],
-    // Never advertised; rewritten to the canonical key before the schema parses.
-    // A single object usually arrives under this name, which the union below
-    // accepts. (#156)
+    /**
+     * Never advertised; rewritten to the canonical key before the schema parses.
+     * A single object usually arrives under this name, and `citations` wraps it
+     * into a one-element array. (#156)
+     */
     inputAliases: { citation: 'citations' },
     input: z.object({
+        /**
+         * The wrap runs before validation and stays off the advertised schema, which
+         * remains a plain `type: "array"`. A top-level union would advertise
+         * `citations` with no `type` for a client to build the parameter from. (#173)
+         *
+         * A string is refused here, as one `invalid_type` issue: left to the array,
+         * its `length` runs the size checks after the type check fails and the shape
+         * message reports twice. The pipe stops on this issue, and its code keeps
+         * the framework's "Send citations as an array, not a string." recovery.
+         */
         citations: z
-            .union([
-            z
-                .array(CitationSchema)
-                .min(1)
-                .max(25)
-                .describe('Up to 25 citations, each matched independently.'),
-            CitationSchema,
-        ], { error: CITATIONS_SHAPE_ERROR })
-            .describe('Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy.'),
+            .preprocess((value, ctx) => {
+            if (typeof value === 'string') {
+                ctx.issues.push({
+                    code: 'invalid_type',
+                    expected: 'array',
+                    input: value,
+                    message: CITATIONS_SHAPE_ERROR,
+                });
+                return value;
+            }
+            return isCitationObject(value) ? [value] : value;
+        }, z.array(CitationSchema, { error: CITATIONS_SHAPE_ERROR }).min(1).max(25))
+            .describe('Citations to look up, 1–25, each matched independently. More fields = better match accuracy.'),
     }),
     output: z.object({
         results: z
@@ -140,9 +191,8 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
             .describe('Number of matched citations that carry at least one warning'),
     }),
     async handler(input, ctx) {
-        const submitted = Array.isArray(input.citations) ? input.citations : [input.citations];
-        ctx.log.info('Executing pubmed_lookup_citation', { count: submitted.length });
-        const citations = submitted.map((c, i) => ({
+        ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
+        const citations = input.citations.map((c, i) => ({
             journal: c.journal,
             year: c.year,
             volume: c.volume,
@@ -159,7 +209,11 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
         const matchedPmids = Array.from(new Set(results.filter((r) => r.matched && r.pmid).map((r) => r.pmid)));
         const summaryByPmid = new Map();
         if (matchedPmids.length > 0) {
-            const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: matchedPmids.join(',') }, { signal: ctx.signal });
+            // Version 2.0, because the version 1 DocSum drops what verification
+            // needs: it lists a consortium as a `CollectiveName` item the roster
+            // never reads, and it has no `DocDate`, so a Bookshelf chapter would be
+            // dated by its book's start year. (#199, #201)
+            const summaryResult = await ncbi.eSummary({ db: 'pubmed', version: '2.0', retmode: 'xml', id: matchedPmids.join(',') }, { signal: ctx.signal });
             const summaries = await extractBriefSummaries(summaryResult);
             for (const s of summaries) {
                 summaryByPmid.set(s.pmid, {

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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts

@@ -1,7 +1,8 @@
 /**
  * @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
  * Searches the NCBI MeSH database with offset pagination and optionally
- * retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
+ * retrieves detailed records. `limit`, `retmax`, and `pageSize` are accepted as
+ * aliases for `maxResults`, `retstart` for `offset`, and `term` for `query`.
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -32,15 +33,22 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
+    readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
+    readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
+    readonly retryable: true;
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'ncbi_rate_limited';
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
+    readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
+    readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
-    readonly when: 'Total request deadline expired before NCBI returned a response.';
-    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
+    readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
+    readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
     readonly retryable: true;
     readonly thrownBy: 'service';
 }, {
@@ -60,8 +68,8 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
 }, {
     readonly reason: 'blank_query';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
-    readonly when: 'The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there.';
-    readonly recovery: 'Supply a nonblank search term — a bare field tag or empty parentheses carry none; NCBI cannot search a blank term and retrying the same input will not help.';
+    readonly when: 'The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and `&nbsp;` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`.';
+    readonly recovery: 'Supply a nonblank search term; retrying the same blank input will not help.';
     readonly retryable: false;
 }], {
     readonly totalCount: z.ZodNumber;

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyMzB,CAAC"}
+{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+MzB,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js

@@ -1,14 +1,16 @@
 /**
  * @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
  * Searches the NCBI MeSH database with offset pagination and optionally
- * retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
+ * retrieves detailed records. `limit`, `retmax`, and `pageSize` are accepted as
+ * aliases for `maxResults`, `retstart` for `offset`, and `term` for `query`.
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
-import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { NCBI_SERVICE_ERRORS, QUERY_INPUT_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
+import { hasVisibleText } from './_visible-text.js';
 /**
  * NCBI Entrez mesh UIDs encode the canonical MeSH DescriptorUI as the ASCII code of the
  * UI's letter prefix followed by its 6-digit number: D=68, C=67 (supplementary concept),
@@ -100,14 +102,21 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         EDAM_DATA_RETRIEVAL,
     ]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
-    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
-    // Never advertised; rewritten to the canonical key before the schema parses. (#156)
-    inputAliases: { limit: 'maxResults' },
+    errors: [...NCBI_SERVICE_ERRORS, ...QUERY_INPUT_ERRORS],
+    // Never advertised; rewritten to the canonical key before the schema parses.
+    // ESearch's own names (`retmax`, `retstart`, `term`) and sibling tools' names. (#156, #190)
+    inputAliases: {
+        limit: 'maxResults',
+        retmax: 'maxResults',
+        pageSize: 'maxResults',
+        retstart: 'offset',
+        term: 'query',
+    },
     input: z.object({
         query: z
             .string()
             .min(1)
-            .describe('MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched.'),
+            .describe('MeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than searched.'),
         maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
         offset: z
             .number()
@@ -165,11 +174,10 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         ctx.log.debug('MeSH lookup started', { query, maxResults, offset, includeDetails });
         // ESearch on db=mesh answers a blank term with Count=0 and a WarningList
         // rather than an error, so the empty-result branch would report "no MeSH
-        // descriptors matched" for a term that was never really searched. (#133)
-        if (query.trim().length === 0) {
-            throw ctx.fail('blank_query', 'The `query` is blank — there is no term to look up.', {
-                ...ctx.recoveryFor('blank_query'),
-            });
+        // descriptors matched" for a term that was never really searched. Invisible
+        // characters such as a zero-width space count as blank. (#133, #176)
+        if (!hasVisibleText(query)) {
+            throw ctx.fail('blank_query', 'The `query` is blank — there is no term to look up.');
         }
         const hasFieldTag = /\[.+\]/.test(query);
         const callOpts = { signal: ctx.signal };