npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.8 → 2.10.10 - Mend

@cyanheads/pubmed-mcp-server 2.10.8 → 2.10.10

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 (67) hide show

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

@@ -14,6 +14,7 @@ import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { getOpenAlexServiceOptional } from '../../../services/openalex/openalex-service.js';
+import { OPENALEX_MAX_UPSTREAM_REQUESTS, } from '../../../services/openalex/types.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 import { escapeMarkdownInline } from './_text.js';
@@ -34,6 +35,11 @@ const PROVIDER_LABELS = {
 const PROVIDER_DISABLED = 'provider_disabled';
 /** A provider failure that carried no declared service-contract reason. */
 const UNCLASSIFIED_ERROR = 'unclassified_error';
+/** Declared retryability per reason the two coverage fallbacks can throw. */
+const RETRYABLE_BY_REASON = new Map([...EUROPEPMC_SERVICE_ERRORS, ...OPENALEX_SERVICE_ERRORS].map((entry) => [
+    entry.reason,
+    entry.retryable,
+]));
 // ─── NCBI provider ────────────────────────────────────────────────────────────
 async function ncbiProvider(pmid, relationship, signal) {
     const ncbi = getNcbiService();
@@ -143,7 +149,59 @@ async function openAlexProvider(pmid, relationship, maxNeeded, signal) {
             result = await oa.references(pmid, maxNeeded, signal);
             break;
     }
-    return { allPmids: result.pmids, totalCount: result.totalCount, source: 'openalex' };
+    return {
+        allPmids: result.pmids,
+        totalCount: result.totalCount,
+        source: 'openalex',
+        droppedNoPmid: result.droppedNoPmid,
+        reachCapped: result.reachCapped,
+    };
+}
+/**
+ * Record a coverage-fallback failure with its declared reason. A provider off by
+ * configuration never recovers on retry; an unclassified transport failure is
+ * treated as transient, matching how the fully-failed chain reports one.
+ */
+function coverageFailureFrom(provider, err) {
+    const { reason } = attemptFrom(provider, err);
+    const retryable = reason === PROVIDER_DISABLED ? false : (RETRYABLE_BY_REASON.get(reason) ?? true);
+    return { provider, reason, retryable };
+}
+/** "A", "A or B", "A, B, or C" — the providers a notice may claim answered. */
+function joinWithOr(labels) {
+    if (labels.length <= 1)
+        return labels[0] ?? '';
+    if (labels.length === 2)
+        return `${labels[0]} or ${labels[1]}`;
+    return `${labels.slice(0, -1).join(', ')}, or ${labels[labels.length - 1]}`;
+}
+/** One provider outcome per entry: `Europe PMC (provider_disabled), OpenAlex (openalex_unreachable)`. */
+function summarizeOutcomes(entries) {
+    return entries.map((e) => `${PROVIDER_LABELS[e.provider]} (${e.reason})`).join(', ');
+}
+/**
+ * Trailing clause naming the providers configuration turned off, which no retry
+ * brings back. Empty when every entry is a transient failure.
+ */
+function disabledClause(entries) {
+    const disabled = entries
+        .filter((e) => e.reason === PROVIDER_DISABLED)
+        .map((e) => PROVIDER_LABELS[e.provider]);
+    if (disabled.length === 0)
+        return '';
+    return ` ${disabled.join(' and ')} ${disabled.length > 1 ? 'are' : 'is'} turned off by server configuration and will not recover on retry.`;
+}
+/**
+ * Disclosure for a `references` answer whose coverage check came back short.
+ * Names each provider that failed and its reason, separates a
+ * configuration-disabled provider from the transient failures worth retrying,
+ * and never describes a failed provider as having answered.
+ */
+function coverageIncompleteNotice(failures) {
+    const retryClause = failures.some((f) => f.retryable)
+        ? ' Retry after a brief delay to complete the coverage check.'
+        : '';
+    return `Reference coverage could not be fully checked — ${summarizeOutcomes(failures)} did not answer.${retryClause}${disabledClause(failures)}`;
 }
 /** Compact, log-safe description of an unknown thrown value. */
 function describeError(err) {
@@ -167,14 +225,7 @@ function attemptFrom(provider, err) {
  * the transient failures worth retrying.
  */
 function allProvidersFailedHint(attempts) {
-    const summary = attempts.map((a) => `${PROVIDER_LABELS[a.provider]} (${a.reason})`).join(', ');
-    const disabled = attempts
-        .filter((a) => a.reason === PROVIDER_DISABLED)
-        .map((a) => PROVIDER_LABELS[a.provider]);
-    const disabledClause = disabled.length
-        ? ` ${disabled.join(' and ')} ${disabled.length > 1 ? 'are' : 'is'} turned off by server configuration and will not recover on retry.`
-        : '';
-    return `Providers attempted: ${summary}. Retry the transient failures after a brief delay.${disabledClause}`;
+    return `Providers attempted: ${summarizeOutcomes(attempts)}. Retry the transient failures after a brief delay.${disabledClause(attempts)}`;
 }
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const findRelatedTool = tool('pubmed_find_related', {
@@ -230,18 +281,35 @@ export const findRelatedTool = tool('pubmed_find_related', {
     enrichment: {
         totalCount: z
             .number()
-            .describe('Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned.'),
+            .describe('Total related articles found before windowing. A Europe PMC or OpenAlex total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned.'),
         source: z
             .enum(['ncbi', 'europepmc', 'openalex'])
             .describe('Provider that answered this request'),
         notice: z
             .string()
             .optional()
-            .describe('Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page.'),
+            .describe('Guidance when results are empty, a fallback provider answered, offset overshot, a fallback provider could not be reached, or upstream rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page.'),
+        coverageFailures: z
+            .array(z
+            .object({
+            provider: z
+                .enum(['europepmc', 'openalex'])
+                .describe('Reference-coverage provider that failed'),
+            reason: z
+                .string()
+                .describe('Declared failure reason, e.g. europepmc_unreachable or provider_disabled'),
+            retryable: z.boolean().describe('Whether a retry can reach this provider'),
+        })
+            .describe('One coverage provider that could not be checked'))
+            .optional()
+            .describe('Reference-coverage fallbacks that failed instead of answering, so the reference set is unverified rather than confirmed absent. Absent when every provider consulted answered.'),
     },
     enrichmentTrailer: {
         totalCount: { label: 'Total Found' },
         source: { label: 'Source' },
+        coverageFailures: {
+            render: (value = []) => `**Coverage not checked:** ${summarizeOutcomes(value)}`,
+        },
     },
     async handler(input, ctx) {
         const ncbi = getNcbiService();
@@ -265,6 +333,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
         // Records WHY a non-primary provider answered, so the provenance notice can
         // distinguish an NCBI outage from references coverage for a non-PMC source.
         let fallbackKind;
+        // Reference-coverage fallbacks that threw. NCBI answering successfully with
+        // an empty set is not the same fact as a provider never being reached, so a
+        // failure here is carried to the caller instead of logged and dropped.
+        const coverageFailures = [];
         // 1. NCBI (primary)
         try {
             providerResult = await ncbiProvider(input.pmid, input.relationship, ctx.signal);
@@ -369,20 +441,34 @@ export const findRelatedTool = tool('pubmed_find_related', {
             // likely a transient NCBI issue, not a real "no references".
             if (input.relationship === 'references' && sourceSummary?.title) {
                 let refFallback = null;
+                // Providers that actually answered — the only ones a "no references"
+                // notice may claim to have checked.
+                const coverageChecked = ['ncbi'];
                 const refAttempts = [
-                    () => epmcProvider(input.pmid, 'references', input.offset, input.maxResults, ctx.signal),
-                    () => openAlexProvider(input.pmid, 'references', input.offset + input.maxResults, ctx.signal),
+                    {
+                        provider: 'europepmc',
+                        run: () => epmcProvider(input.pmid, 'references', input.offset, input.maxResults, ctx.signal),
+                    },
+                    {
+                        provider: 'openalex',
+                        run: () => openAlexProvider(input.pmid, 'references', input.offset + input.maxResults, ctx.signal),
+                    },
                 ];
                 for (const attempt of refAttempts) {
                     try {
-                        const result = await attempt();
+                        const result = await attempt.run();
+                        coverageChecked.push(attempt.provider);
                         if (result.allPmids.length > 0) {
                             refFallback = result;
                             break;
                         }
                     }
                     catch (err) {
-                        ctx.log.warning('References fallback provider failed', { err: describeError(err) });
+                        ctx.log.warning('References fallback provider failed', {
+                            provider: attempt.provider,
+                            err: describeError(err),
+                        });
+                        coverageFailures.push(coverageFailureFrom(attempt.provider, err));
                     }
                 }
                 if (refFallback) {
@@ -392,10 +478,16 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 else {
                     ctx.enrich({ source: 'ncbi' });
                     ctx.enrich.total(0);
+                    if (coverageFailures.length > 0)
+                        ctx.enrich({ coverageFailures });
                     const sourcePmcId = sourceSummary.pmcId;
-                    ctx.enrich.notice(sourcePmcId
-                        ? `No reference list found for PMID ${input.pmid} (PMCID ${sourcePmcId}) via NCBI, Europe PMC, or OpenAlex.`
-                        : `No reference list available for PMID ${input.pmid} via NCBI, Europe PMC, or OpenAlex. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`);
+                    const checked = joinWithOr(coverageChecked.map((p) => PROVIDER_LABELS[p]));
+                    const noReferences = sourcePmcId
+                        ? `No reference list found for PMID ${input.pmid} (PMCID ${sourcePmcId}) via ${checked}.`
+                        : `No reference list available for PMID ${input.pmid} via ${checked}. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
+                    ctx.enrich.notice(coverageFailures.length > 0
+                        ? `${noReferences} ${coverageIncompleteNotice(coverageFailures)}`
+                        : noReferences);
                     return {
                         sourcePmid: input.pmid,
                         relationship: input.relationship,
@@ -421,6 +513,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
         const { allPmids, totalCount, source, droppedNoPmid = 0, reachCapped = false } = providerResult;
         ctx.enrich({ source });
         ctx.enrich.total(totalCount);
+        // A provider that failed before another one answered still shapes how far
+        // this reference set was actually checked.
+        if (coverageFailures.length > 0)
+            ctx.enrich({ coverageFailures });
         // For NCBI the full neighbor set is in memory; for EPMC/OpenAlex the provider
         // pre-fetched enough PMID-addressable rows to cover the window.
         const window = allPmids.slice(input.offset, input.offset + input.maxResults);
@@ -443,15 +539,27 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 ? `NCBI has no PMC-indexed reference list for PMID ${input.pmid} — references served by ${providerName} (${detail}).`
                 : `NCBI eLink unavailable — related articles served by ${providerName} (${detail}).`);
         }
-        // Europe PMC counts every upstream record, but only MED-source rows carry a
-        // PubMed PMID. Disclose the gap so an empty or short window reads as an
+        // Both fallbacks count every upstream record, but only some rows carry a
+        // PubMed PMID — Europe PMC's non-MED sources, OpenAlex works with no PubMed
+        // record. Disclose the gap so an empty or short window reads as an
         // excluded-rows effect rather than an exhausted result set.
         if (droppedNoPmid > 0) {
-            notices.push(`Europe PMC served ${allPmids.length + droppedNoPmid} upstream rows for this request, ${droppedNoPmid} with no PubMed PMID (non-MED sources such as preprints); those rows cannot be returned here.`);
+            const excluded = source === 'europepmc'
+                ? 'non-MED sources such as preprints'
+                : 'works OpenAlex indexes with no PubMed record';
+            notices.push(`${PROVIDER_LABELS[source]} served ${allPmids.length + droppedNoPmid} upstream rows for this request, ${droppedNoPmid} with no PubMed PMID (${excluded}); those rows cannot be returned here.`);
         }
-        // The page cap bounds how far into Europe PMC's set one request can reach.
+        // The request cap bounds how far into a fallback's set one request can
+        // reach. It counts pages for Europe PMC and for OpenAlex's `cites:` filter,
+        // but OpenAlex serves `similar` and `references` from the source work's own
+        // ID list, which it resolves in batches — so the same cap names a different
+        // unit of work there.
         if (reachCapped) {
-            notices.push(`Europe PMC paging stopped after ${EPMC_MAX_PAGES} pages (${allPmids.length} PubMed-addressable rows) without reaching offset ${input.offset}; lower the offset.`);
+            const cap = source === 'europepmc' ? EPMC_MAX_PAGES : OPENALEX_MAX_UPSTREAM_REQUESTS;
+            const walk = source === 'europepmc' || input.relationship === 'cited_by'
+                ? `paging stopped after ${cap} pages`
+                : `ID resolution stopped after ${cap} batches`;
+            notices.push(`${PROVIDER_LABELS[source]} ${walk} (${allPmids.length} PubMed-addressable rows) without reaching offset ${input.offset}; lower the offset.`);
         }
         if (window.length === 0) {
             if (notices.length > 0)

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

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

@@ -52,6 +52,12 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
+}, {
+    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 any markup the tool strips first, are removed — so NCBI would receive a blank term.';
+    readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
+    readonly retryable: false;
 }], {
     readonly totalCount: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;

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

	@@ -1 +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~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwLzB~~,CAAC"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsMzB,CAAC"}

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

@@ -5,7 +5,7 @@
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
-import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_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';
@@ -100,9 +100,12 @@ 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],
+    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
     input: z.object({
-        query: z.string().min(1).describe('MeSH descriptor name or free-text term to look up'),
+        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.'),
         maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
         offset: z
             .number()
@@ -158,6 +161,14 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         const { query, maxResults, offset, includeDetails } = input;
         const ncbi = getNcbiService();
         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'),
+            });
+        }
         const hasFieldTag = /\[.+\]/.test(query);
         const callOpts = { signal: ctx.signal };
         const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults, retstart: offset }, callOpts);

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

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

@@ -81,6 +81,12 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
+}, {
+    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 any markup the tool strips first, are removed — so NCBI would receive a blank term.';
+    readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
+    readonly retryable: false;
 }], {
     readonly effectiveQuery: z.ZodString;
     readonly totalCount: z.ZodNumber;

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;AAgJjD,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkW7B~~,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;AAgJjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqX7B,CAAC"}

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

@@ -5,7 +5,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { sanitization } from '@cyanheads/mcp-ts-core/utils';
-import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { NCBI_QUERY_INPUT_ERRORS, 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_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
@@ -116,9 +116,12 @@ 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],
+    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
     input: z.object({
-        query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
+        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 is stripped is rejected rather than sent to PubMed as an empty term.'),
         maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
         offset: z
             .number()
@@ -248,6 +251,15 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         ctx.log.info('Executing pubmed_search', { query: input.query });
         const ncbi = getNcbiService();
         let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
+        // `min(1)` counts whitespace, and the sanitizer reduces markup with no text
+        // content to an empty string, so both reach here as a blank term. NCBI
+        // answers a blank term with HTTP 200 and an embedded <ERROR> reading
+        // "Search is temporarily unavailable", which classifies as a retryable
+        // outage — the caller would spend the whole retry deadline on a
+        // deterministic input mistake. Reject before the call instead. (#122)
+        if (effectiveQuery.trim().length === 0) {
+            throw ctx.fail('blank_query', 'The `query` carries no search term — it is blank after markup is stripped.', { ...ctx.recoveryFor('blank_query') });
+        }
         // Build filters — capture normalized values for both query construction and appliedFilters
         let normalizedDateRange;
         const { dateRange } = input;

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

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

@@ -40,5 +40,11 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
+}, {
+    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 any markup the tool strips first, are removed — so NCBI would receive a blank term.';
+    readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same 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 CHANGED Viewed

	@@ -1 +1 @@
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