@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.19

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

@@ -1,27 +1,142 @@
 /**
  * @fileoverview PubMed search tool. Searches PubMed with full query syntax,
  * field-specific filters, date ranges, pagination, and optional brief summaries.
- * A query with no search term — blank, markup only, a bare field tag, or empty
- * parentheses — is rejected before NCBI is called. `limit` is accepted as an
- * alias for `maxResults`. The total match count rides in `output` so `format()`
- * can state it in the header beside the returned count, and a summary's
- * `docType` is rendered only when it marks something other than an ordinary
- * journal article (`citation`).
+ * A query with no search term — blank, invisible characters only, markup only, a
+ * bare field tag, or empty parentheses — is rejected before NCBI is called, as
+ * is a filter value with no term once sanitized (`"   "`, `"()"`), a
+ * `dateRange` bound that is no real calendar date, and a range whose `minDate`
+ * falls after its `maxDate`. `limit` is accepted as an alias for `maxResults`.
+ * The total match count rides in `output` so `format()` can state it in the
+ * header beside the returned count, and a summary's `docType` is rendered only
+ * when it marks something other than an ordinary journal article (`citation`).
  * @module src/mcp-server/tools/definitions/search-articles.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { sanitization } from '@cyanheads/mcp-ts-core/utils';
-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 { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
 import { escapeMarkdownInline } from './_text.js';
+import { hasVisibleText } from './_visible-text.js';
 /**
  * Accepts empty strings (treated as "no filter" by the handler) or dates in
  * YYYY, YYYY/MM, or YYYY/MM/DD form with `/`, `-`, or `.` separators.
  * Catches obvious typos at the edge so they don't degrade silently to 0 results.
+ * Calendar validity and bound order are checked in the handler
+ * ({@link dateRangeProblem}).
  */
 const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
+/**
+ * Days in `month` (1–12) of `year`, leap years included. `setUTCFullYear` reads
+ * the year literally, where `Date.UTC` would map 0–99 onto 1900–1999.
+ */
+function daysInMonth(year, month) {
+    const date = new Date(0);
+    date.setUTCFullYear(year, month, 0);
+    return date.getUTCDate();
+}
+/**
+ * The first and last day a `dateRange` bound covers, as zero-padded
+ * `YYYY/MM/DD` strings that sort in calendar order — PubMed reads a partial
+ * date as its whole year or month — or why the bound names no real date. The
+ * value has already matched {@link DATE_RE}, so it splits into one to three
+ * numbers with a four-digit year.
+ */
+function dateBoundSpan(value) {
+    const [yearText = '', monthText, dayText] = value.split(/[/\-.]/);
+    const year = Number(yearText);
+    const month = monthText === undefined ? undefined : Number(monthText);
+    const day = dayText === undefined ? undefined : Number(dayText);
+    const ymd = (m, d) => `${yearText}/${String(m).padStart(2, '0')}/${String(d).padStart(2, '0')}`;
+    if (month !== undefined && (month < 1 || month > 12)) {
+        return { problem: `month ${monthText} is outside 01–12` };
+    }
+    if (month !== undefined && day !== undefined) {
+        if (day < 1)
+            return { problem: `day ${dayText} is not a day; days start at 01` };
+        const monthDays = daysInMonth(year, month);
+        if (day > monthDays) {
+            return { problem: `${ymd(month, 1).slice(0, 7)} has ${monthDays} days` };
+        }
+    }
+    return {
+        first: ymd(month ?? 1, day ?? 1),
+        last: ymd(month ?? 12, day ?? daysInMonth(year, month ?? 12)),
+    };
+}
+/**
+ * Why a `dateRange` names no real span, or `undefined` when it does. Every
+ * non-empty bound must be a real calendar date, even beside an empty bound that
+ * drops the filter, and `minDate` must not fall after `maxDate` once each is
+ * expanded the way PubMed reads a partial date: `minDate` from the start of its
+ * year or month, `maxDate` to the end. `2024/06 : 2024` is a range;
+ * `2024/07 : 2024/06/30` is reversed. PubMed answers either mistake with zero
+ * hits and reports the valid date tag as unrecognized. (#177)
+ */
+function dateRangeProblem(minDate, maxDate) {
+    const min = minDate ? dateBoundSpan(minDate) : undefined;
+    const max = maxDate ? dateBoundSpan(maxDate) : undefined;
+    const fields = [];
+    const problems = [];
+    for (const [field, value, span] of [
+        ['dateRange.minDate', minDate, min],
+        ['dateRange.maxDate', maxDate, max],
+    ]) {
+        if (span && 'problem' in span) {
+            fields.push(field);
+            problems.push(`\`${field}\` "${value}" is not a real calendar date: ${span.problem}.`);
+        }
+    }
+    if (fields.length > 0)
+        return { fields, message: problems.join(' ') };
+    if (min && max && 'first' in min && 'last' in max && min.first > max.last) {
+        return {
+            fields: ['dateRange.minDate', 'dateRange.maxDate'],
+            message: `\`dateRange.minDate\` "${minDate}" (from ${min.first}) falls after \`dateRange.maxDate\` "${maxDate}" (through ${max.last}), so the range covers no dates.`,
+        };
+    }
+    return;
+}
+/**
+ * PubMed query syntax a filter value can hold without holding a term:
+ * grouping parentheses, field-tag brackets, and phrase quotes.
+ */
+const FILTER_SYNTAX = /[()[\]"]/g;
+/**
+ * Sanitizes one filter value, recording `path` in `blank` when it holds no term
+ * once {@link FILTER_SYNTAX} is disregarded (`"   "`, `"<b></b>"`, `"&#8203;"`,
+ * `"()"`): sent as written, it would put a field clause with no term in the
+ * query PubMed runs, and PubMed answers `asthma AND ()[Author]` with every
+ * `asthma` match. A value that passes is returned sanitized, syntax characters
+ * included. An exactly-empty string sets no filter — form clients send one for a
+ * field left untouched (#14) — so it returns `undefined`, like an omitted field.
+ * (#176)
+ */
+async function sanitizeFilter(value, path, blank) {
+    if (!value)
+        return;
+    const sanitized = await sanitization.sanitizeString(value, { context: 'text' });
+    if (hasVisibleText(sanitized.replace(FILTER_SYNTAX, '')))
+        return sanitized;
+    blank.push(path);
+    return;
+}
+/**
+ * {@link sanitizeFilter} for each list element, naming a blank one by its
+ * index in the framework's dotted path style (`meshTerms.1`) and dropping an
+ * empty one. `undefined` when no element is left to filter on.
+ */
+async function sanitizeFilterList(values, path, blank) {
+    const kept = [];
+    for (const [index, value] of (values ?? []).entries()) {
+        const sanitized = await sanitizeFilter(value, `${path}.${index}`, blank);
+        if (sanitized !== undefined)
+            kept.push(sanitized);
+    }
+    return kept.length > 0 ? kept : undefined;
+}
 /**
  * NCBI's eSearch serves `retstart` up to 9998 for PubMed and fails the whole
  * request above it, so the ceiling is enforced at the edge where the caller can
@@ -60,13 +175,16 @@ const PUBMED_FIELD_TAGS = new Set([
 /**
  * The query with every parenthesis and every bracketed field tag removed — what
  * the blank-term check tests. A tag's search modifier (`[mh:noexp]`,
- * `[tiab:~3]`) does not change what it is; an empty bracket carries no term.
+ * `[tiab:~3]`) does not change what it is; a bracket with no visible text
+ * carries no term.
  */
 function withoutTermlessMarkup(query) {
     return query
         .replace(/\[([^\]]*)\]/g, (bracket, content) => {
         const tag = content.trim().toLowerCase();
-        return tag === '' || PUBMED_FIELD_TAGS.has(tag.replace(/\s*:.*$/, '')) ? '' : bracket;
+        return !hasVisibleText(content) || PUBMED_FIELD_TAGS.has(tag.replace(/\s*:.*$/, ''))
+            ? ''
+            : bracket;
     })
         .replace(/[()]/g, '');
 }
@@ -164,7 +282,24 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
-    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
+    errors: [
+        ...NCBI_SERVICE_ERRORS,
+        ...QUERY_INPUT_ERRORS,
+        {
+            reason: 'invalid_date_range',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'A `dateRange` bound is not a real calendar date — a month outside 01–12, day 00, or a day past the end of its month such as `2023/02/29` — or `minDate` falls after `maxDate` once PubMed expands each partial date: `minDate` from the start of its year or month, `maxDate` to the end.',
+            recovery: 'Correct the named bound to a real calendar date, or swap the bounds so minDate does not fall after maxDate; the same range will be rejected again.',
+            retryable: false,
+        },
+        {
+            reason: 'blank_filter',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'An `author`, `journal`, or `language` value, or a `publicationTypes` or `meshTerms` element, holds no term once markup is removed and HTML entities are decoded — only whitespace, invisible characters such as a zero-width space, parentheses, brackets, or double quotes are left, as in `()` or `""` — so its field clause would carry no term. An exactly-empty string is not blank here; it sets no filter.',
+            recovery: 'Give each named filter a value, or pass an empty string or omit it for no filter; the same blank value will be rejected again.',
+            retryable: false,
+        },
+    ],
     // Never advertised; rewritten to the canonical key before the schema parses.
     // `max_results` needs no entry — the framework's case-style repair maps it. (#156)
     inputAliases: { limit: 'maxResults' },
@@ -172,7 +307,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         query: z
             .string()
             .min(1)
-            .describe('PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), and parentheses are removed is rejected rather than sent to PubMed as an empty term.'),
+            .describe('PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), parentheses, and invisible characters such as a zero-width space are disregarded is rejected rather than sent to PubMed.'),
         maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
         offset: z
             .number()
@@ -190,29 +325,38 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             minDate: z
                 .string()
                 .regex(DATE_RE, 'Date must be YYYY, YYYY/MM, or YYYY/MM/DD (/, -, or . separators)')
-                .describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound'),
+                .describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected.'),
             maxDate: z
                 .string()
                 .regex(DATE_RE, 'Date must be YYYY, YYYY/MM, or YYYY/MM/DD (/, -, or . separators)')
-                .describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound'),
+                .describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected.'),
             dateType: z
                 .enum(['pdat', 'mdat', 'edat'])
                 .default('pdat')
                 .describe('Date type: pdat (publication), mdat (modification), edat (entrez)'),
         })
             .optional()
-            .describe('Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range.'),
+            .describe('Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range. A partial date covers its whole year or month, and a range whose `minDate` falls after its `maxDate` is rejected: `2024/06` to `2024` is valid, `2024/07` to `2024/06/30` is not.'),
         publicationTypes: z
             .array(z.string())
             .optional()
-            .describe('Filter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis"). Multiple values are OR\'d — any match qualifies.'),
-        author: z.string().optional().describe('Filter by author name (e.g. "Smith J")'),
-        journal: z.string().optional().describe('Filter by journal name'),
+            .describe('Filter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis"). Multiple values are OR\'d — any match qualifies. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected.'),
+        author: z
+            .string()
+            .optional()
+            .describe('Filter by author name (e.g. "Smith J"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected.'),
+        journal: z
+            .string()
+            .optional()
+            .describe('Filter by journal name. An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected.'),
         meshTerms: z
             .array(z.string())
             .optional()
-            .describe("Filter by MeSH terms. Multiple terms are AND'd — all must match."),
-        language: z.string().optional().describe('Filter by language (e.g. "english")'),
+            .describe("Filter by MeSH terms. Multiple terms are AND'd — all must match. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."),
+        language: z
+            .string()
+            .optional()
+            .describe('Filter by language (e.g. "english"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected.'),
         hasAbstract: z.boolean().optional().describe('Only include articles with abstracts'),
         freeFullText: z.boolean().optional().describe('Only include free full text articles'),
         species: z.enum(['humans', 'animals']).optional().describe('Filter by species'),
@@ -337,14 +481,33 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         // sent as written. A bracket that is not a field tag (`[18F]`) is a term, and
         // boolean operators are kept: NCBI reads an operand-less `NOT[ti]` as
         // literal text and returns real matches. (#145)
-        if (withoutTermlessMarkup(effectiveQuery).trim().length === 0) {
-            throw ctx.fail('blank_query', 'The `query` carries no search term — it is blank once markup, bracketed field tags, and parentheses are removed.', { ...ctx.recoveryFor('blank_query') });
+        //
+        // Invisible characters carry no term either, including those the sanitizer
+        // decodes from an entity (`&#8203;`). (#176)
+        if (!hasVisibleText(withoutTermlessMarkup(effectiveQuery))) {
+            throw ctx.fail('blank_query', 'The `query` carries no search term — it is blank once markup, bracketed field tags, parentheses, and invisible characters are disregarded.');
         }
-        // Build filters — capture normalized values for both query construction and appliedFilters
-        let normalizedDateRange;
         const { dateRange } = input;
         const minDate = dateRange?.minDate.trim() ?? '';
         const maxDate = dateRange?.maxDate.trim() ?? '';
+        const dateProblem = dateRangeProblem(minDate, maxDate);
+        if (dateProblem) {
+            throw ctx.fail('invalid_date_range', dateProblem.message, { fields: dateProblem.fields });
+        }
+        // Every filter is sanitized and checked before any clause is built, so a
+        // blank one fails the call instead of reaching PubMed as an empty field
+        // clause (`asthma AND    [Author]`). (#176)
+        const blankFilters = [];
+        const sanitizedPubTypes = await sanitizeFilterList(input.publicationTypes, 'publicationTypes', blankFilters);
+        const sanitizedAuthor = await sanitizeFilter(input.author, 'author', blankFilters);
+        const sanitizedJournal = await sanitizeFilter(input.journal, 'journal', blankFilters);
+        const sanitizedMeshTerms = await sanitizeFilterList(input.meshTerms, 'meshTerms', blankFilters);
+        const sanitizedLanguage = await sanitizeFilter(input.language, 'language', blankFilters);
+        if (blankFilters.length > 0) {
+            throw ctx.fail('blank_filter', `${quoteClauses(blankFilters)} ${blankFilters.length === 1 ? 'holds' : 'hold'} no term once markup, whitespace, invisible characters, parentheses, brackets, and double quotes are disregarded, so the field clause would carry no term.`, { fields: blankFilters });
+        }
+        // Build filters — capture normalized values for both query construction and appliedFilters
+        let normalizedDateRange;
         if (dateRange && minDate && maxDate) {
             normalizedDateRange = {
                 minDate: minDate.replace(/[-.]/g, '/'),
@@ -360,31 +523,18 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             : maxDate && !minDate
                 ? { name: 'maxDate', value: maxDate }
                 : undefined;
-        let sanitizedPubTypes;
-        if (input.publicationTypes?.length) {
-            sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
+        if (sanitizedPubTypes) {
             effectiveQuery += ` AND (${sanitizedPubTypes.map((pt) => `"${pt}"[Publication Type]`).join(' OR ')})`;
         }
-        let sanitizedAuthor;
-        if (input.author) {
-            sanitizedAuthor = await sanitization.sanitizeString(input.author, { context: 'text' });
+        if (sanitizedAuthor)
             effectiveQuery += ` AND ${sanitizedAuthor}[Author]`;
-        }
-        let sanitizedJournal;
-        if (input.journal) {
-            sanitizedJournal = await sanitization.sanitizeString(input.journal, { context: 'text' });
+        if (sanitizedJournal)
             effectiveQuery += ` AND "${sanitizedJournal}"[Journal]`;
-        }
-        let sanitizedMeshTerms;
-        if (input.meshTerms?.length) {
-            sanitizedMeshTerms = await Promise.all(input.meshTerms.map((term) => sanitization.sanitizeString(term, { context: 'text' })));
+        if (sanitizedMeshTerms) {
             effectiveQuery += ` AND (${sanitizedMeshTerms.map((term) => `"${term}"[MeSH Terms]`).join(' AND ')})`;
         }
-        let sanitizedLanguage;
-        if (input.language) {
-            sanitizedLanguage = await sanitization.sanitizeString(input.language, { context: 'text' });
+        if (sanitizedLanguage)
             effectiveQuery += ` AND ${sanitizedLanguage}[Language]`;
-        }
         if (input.hasAbstract)
             effectiveQuery += ' AND hasabstract[text word]';
         if (input.freeFullText)
@@ -439,10 +589,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         const searchUrl = `https://pubmed.ncbi.nlm.nih.gov/?term=${encodeURIComponent(effectiveQuery)}`;
         const appliedFilters = {
             ...(normalizedDateRange && { dateRange: normalizedDateRange }),
-            ...(sanitizedPubTypes?.length && { publicationTypes: sanitizedPubTypes }),
+            ...(sanitizedPubTypes && { publicationTypes: sanitizedPubTypes }),
             ...(sanitizedAuthor && { author: sanitizedAuthor }),
             ...(sanitizedJournal && { journal: sanitizedJournal }),
-            ...(sanitizedMeshTerms?.length && { meshTerms: sanitizedMeshTerms }),
+            ...(sanitizedMeshTerms && { meshTerms: sanitizedMeshTerms }),
             ...(sanitizedLanguage && { language: sanitizedLanguage }),
             ...(input.hasAbstract && { hasAbstract: true }),
             ...(input.freeFullText && { freeFullText: true }),

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts

@@ -21,15 +21,22 @@ export declare const spellCheckTool: 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';
 }, {
@@ -49,8 +56,8 @@ export declare const spellCheckTool: 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;
 }], undefined>;
 //# sourceMappingURL=spell-check.tool.d.ts.map

package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA+DzB,CAAC"}
+{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8DzB,CAAC"}

package/dist/mcp-server/tools/definitions/spell-check.tool.js

@@ -5,20 +5,21 @@
  * @module src/mcp-server/tools/definitions/spell-check.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 { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
+import { hasVisibleText } from './_visible-text.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
     description: 'Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled — every misspelled token is corrected in one call (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`), and `hasSuggestion` is false when NCBI has no change to offer. Re-run the search with `corrected`.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
-    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
+    errors: [...NCBI_SERVICE_ERRORS, ...QUERY_INPUT_ERRORS],
     input: z.object({
         query: z
             .string()
             .min(2)
-            .describe('PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell.'),
+            .describe('PubMed search query to spell-check. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than sent to ESpell.'),
     }),
     output: z.object({
         original: z.string().describe('Original query'),
@@ -30,11 +31,10 @@ export const spellCheckTool = tool('pubmed_spell_check', {
         // `min(2)` counts the spaces, so a whitespace-only query passes the schema.
         // ESpell answers a blank term with an empty `<ERROR/>` element the response
         // handler does not detect, and the tool would report the blank input as
-        // spell-checked. Reject before the call. (#133)
-        if (input.query.trim().length === 0) {
-            throw ctx.fail('blank_query', 'The `query` is blank — there is nothing to spell-check.', {
-                ...ctx.recoveryFor('blank_query'),
-            });
+        // spell-checked. Reject before the call — invisible characters such as a
+        // zero-width space included. (#133, #176)
+        if (!hasVisibleText(input.query)) {
+            throw ctx.fail('blank_query', 'The `query` is blank — there is nothing to spell-check.');
         }
         const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query }, { signal: ctx.signal });
         return {

package/dist/mcp-server/tools/definitions/spell-check.tool.js.map

@@ -1 +1 @@
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