@cyanheads/pubmed-mcp-server 2.10.14 → 2.10.16

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

@@ -1,6 +1,12 @@
 /**
  * @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`).
  * @module src/mcp-server/tools/definitions/search-articles.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -55,45 +61,50 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
         pubmedUrl: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     searchUrl: z.ZodString;
+    totalCount: z.ZodNumber;
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     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 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 retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
     readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
     readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
     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 thrownBy: 'service';
 }, {
     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 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 retryable: false;
 }], {
     readonly effectiveQuery: z.ZodString;
-    readonly totalCount: z.ZodNumber;
     readonly appliedFilters: z.ZodObject<{
         dateRange: z.ZodOptional<z.ZodObject<{
             minDate: z.ZodString;

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

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsa7B,CAAC"}
+{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8LjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmb7B,CAAC"}

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

@@ -1,6 +1,12 @@
 /**
  * @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`).
  * @module src/mcp-server/tools/definitions/search-articles.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -22,6 +28,48 @@ const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
  * still act on it. The limit is db-specific — it does not apply to db=mesh.
  */
 const OFFSET_MAX = 9998;
+/**
+ * PubMed search field tags, lowercased: the tags in PubMed's search-field help,
+ * their full names, and ESearch's own field names, each confirmed live to be
+ * read as a field tag — a bare `[pdat]` returns "No items found." PubMed searches
+ * the content of any other bracket as text (`[18F]`, `[cancer]`, `[smith j]`, and
+ * `[ab]` all return matches), so the blank-term check treats only these as
+ * carrying no term. A tag missing here fails safe: its bare form is sent and
+ * answered as an ordinary zero-hit search.
+ */
+const PUBMED_FIELD_TAGS = new Set([
+    '1au|ad|aid|all|au|auid|book|cn|cois|crdt|dcom|doi|dp|ed|edat|fau|filter|fir|gr|ip|ir',
+    'isbn|jid|la|lastau|lid|lr|majr|mh|mhda|nm|ot|pa|pg|pl|pmid|ps|pt|pubn|rn|sb|sh|si|so',
+    'ta|ti|tiab|tt|tw|vi|affl|aucl|auth|cdat|cnty|coln|ecno|eid|epdat|epdt|faut|filt|finv',
+    'full|grnt|iss|jour|lang|laut|mdat|mesh|otrm|page|papx|pdat|pid|ppdat|ppdt|ptyp|subh',
+    'subs|titl|vol|word|author|editor|issue|subset|title|volume',
+    'keyword|affiliation|all fields|author - corporate|author - first|author - identifier',
+    'author - last|author cluster id|completion date|conflict of interest statements',
+    'corporate author|create date|date - completion|date - create|date - entry|date - mesh',
+    'date - modification|date - publication|ec/rn number|electronic publication date',
+    'entry date|extended pmid|first author name|full author name|full investigator name',
+    'grants and funding|investigator|journal|language|last author name|location id',
+    'mesh date|mesh major topic|mesh subheading|mesh terms|modification date|other term',
+    'pagination|personal name as subject|pharmacological action|place of publication',
+    'print publication date|publication date|publication type|publisher|publisher id',
+    'secondary source id|subheading|subject - personal name|supplementary concept|text word',
+    'title/abstract|transliterated title',
+]
+    .join('|')
+    .split('|'));
+/**
+ * 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.
+ */
+function withoutTermlessMarkup(query) {
+    return query
+        .replace(/\[([^\]]*)\]/g, (bracket, content) => {
+        const tag = content.trim().toLowerCase();
+        return tag === '' || PUBMED_FIELD_TAGS.has(tag.replace(/\s*:.*$/, '')) ? '' : bracket;
+    })
+        .replace(/[()]/g, '');
+}
 /** Upper bound on brief summaries fetched per call; shared by the schema and the format() cap message. */
 const SUMMARY_COUNT_MAX = 50;
 /** Renders a diagnostic list as a comma-separated set of backticked clauses. */
@@ -117,11 +165,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     _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],
+    // 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' },
     input: z.object({
         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.'),
+            .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.'),
         maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
         offset: z
             .number()
@@ -218,16 +269,18 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             .describe('Brief article summary'))
             .describe('Brief summaries (empty array when summaryCount is 0)'),
         searchUrl: z.string().describe('PubMed search URL'),
+        // A domain field, not enrichment: format() sees only this payload, and the
+        // header states the total beside the returned count. (#147)
+        totalCount: z.number().describe('Total matching articles'),
     }),
     // Result-set context the agent reasons with — the query as PubMed parsed it, the
-    // total match count, the normalized filters, and recovery guidance for empty or
-    // overshot pages. Populated via ctx.enrich(...) so it reaches structuredContent and
-    // content[] alike; kept out of the domain return.
+    // normalized filters, and recovery guidance for empty or overshot pages.
+    // Populated via ctx.enrich(...) so it reaches structuredContent and content[]
+    // alike; kept out of the domain return.
     enrichment: {
         effectiveQuery: z
             .string()
             .describe('Sanitized query sent to PubMed after applying all active filters'),
-        totalCount: z.number().describe('Total matching articles'),
         appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
         notice: z
             .string()
@@ -238,7 +291,6 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     // carries the full structured value; this only shapes the human-facing trailer line.
     enrichmentTrailer: {
         effectiveQuery: { label: 'Effective Query' },
-        totalCount: { label: 'Total Found' },
         appliedFilters: {
             render: (filters) => {
                 const lines = [];
@@ -279,8 +331,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         // "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') });
+        //
+        // A bare field tag (`[pdat]`) or empty parentheses carry no term either, so
+        // the check runs on a copy with those removed; `effectiveQuery` itself is
+        // 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') });
         }
         // Build filters — capture normalized values for both query construction and appliedFilters
         let normalizedDateRange;
@@ -404,7 +462,6 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             ...(esResult.warningList && { warningList: esResult.warningList }),
         });
         ctx.enrich({ effectiveQuery, appliedFilters });
-        ctx.enrich.total(esResult.count);
         if (notice)
             ctx.enrich.notice(notice);
         return {
@@ -413,13 +470,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             pmids,
             summaries,
             searchUrl,
+            totalCount: esResult.count,
         };
     },
     format: (result) => {
         const lines = [
             `## PubMed Search Results`,
             `**Query:** ${result.query}`,
-            `**Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
+            `**Returned:** ${result.pmids.length} of ${result.totalCount} | **Offset:** ${result.offset}`,
             `**Search URL:** ${result.searchUrl}`,
         ];
         if (result.pmids.length > 0)
@@ -451,7 +509,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
                 if (s.bookTitle || s.publisherName) {
                     lines.push(`**Book:** ${[s.bookTitle, s.publisherName].filter(Boolean).join(' — ')}`);
                 }
-                if (s.docType)
+                // `citation` is every ordinary journal article; the line earns its
+                // place only when it flags a Bookshelf chapter or book. (#146)
+                if (s.docType && s.docType !== 'citation')
                     lines.push(`**Doc Type:** ${s.docType}`);
                 if (s.pubDate)
                     lines.push(`**Published:** ${s.pubDate}`);

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

@@ -1,6 +1,7 @@
 /**
- * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service
- * to suggest corrections for search queries.
+ * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
+ * every misspelled token of a PubMed search query in one call — the recovery
+ * step after a zero-hit or thin `pubmed_search_articles` result.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -13,38 +14,43 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     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 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 retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
     readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
     readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_resource_not_found';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
     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 thrownBy: 'service';
 }, {
     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 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 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;;;;GAIG;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;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA+DzB,CAAC"}

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

@@ -1,6 +1,7 @@
 /**
- * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service
- * to suggest corrections for search queries.
+ * @fileoverview PubMed spell-check tool. Uses NCBI's ESpell service to correct
+ * every misspelled token of a PubMed search query in one call — the recovery
+ * step after a zero-hit or thin `pubmed_search_articles` result.
  * @module src/mcp-server/tools/definitions/spell-check.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -8,7 +9,7 @@ import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
-    description: "Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.",
+    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',

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

@@ -1 +1 @@
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package/dist/services/error-contracts.d.ts

@@ -12,45 +12,55 @@
  *
  * Tool definitions import the contract arrays directly and spread them into
  * their `errors: [...]` declarations to surface the failure modes to the LLM.
+ * Every service-array entry carries `thrownBy: 'service'` so the linter's
+ * `error-contract-unthrown` check skips it while still checking the handler's
+ * own reasons. Spread a service array only into a tool whose handler lets that
+ * service's errors propagate — a tool that catches them all never produces
+ * those reasons.
  *
  * @module src/services/error-contracts
  */
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 /**
- * Failure modes the NCBI service layer can surface. Tools that consume
- * `getNcbiService()` should spread these into their own `errors[]` so the
- * declared contract matches what actually reaches the wire.
+ * Failure modes the NCBI service layer can surface. Tools whose handler lets
+ * `getNcbiService()` failures propagate spread these into their own `errors[]`
+ * so the declared contract matches what actually reaches the wire.
  */
 export declare const NCBI_SERVICE_ERRORS: readonly [{
     readonly reason: 'queue_full';
     readonly code: JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: 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 retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: 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 retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
     readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_resource_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
     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 thrownBy: 'service';
 }];
 /**
  * Input failure the NCBI query tools reject before any call is made. Declared
@@ -66,8 +76,8 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
 export declare const NCBI_QUERY_INPUT_ERRORS: readonly [{
     readonly reason: 'blank_query';
     readonly code: 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 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 retryable: false;
 }];
 /**
@@ -98,11 +108,12 @@ export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
     readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
     readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }];
 /**
- * Failure modes the OpenAlex service layer can surface. Tools that consume
- * `getOpenAlexService()` / `getOpenAlexServiceOptional()` should spread
- * these into their `errors[]`.
+ * Failure modes the OpenAlex service layer can surface. Tools whose handler
+ * lets `getOpenAlexService()` / `getOpenAlexServiceOptional()` failures
+ * propagate spread these into their `errors[]`.
  */
 export declare const OPENALEX_SERVICE_ERRORS: readonly [{
     readonly reason: 'openalex_unreachable';
@@ -110,35 +121,41 @@ export declare const OPENALEX_SERVICE_ERRORS: readonly [{
     readonly when: 'OpenAlex was unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'openalex_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: 'OpenAlex returned a body that could not be parsed (invalid JSON).';
     readonly recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }];
 /**
- * Failure modes the Europe PMC service layer can surface. Tools that consume
- * `getEuropePmcService()` should spread these into their `errors[]`.
+ * Failure modes the Europe PMC service layer can surface. Tools whose handler
+ * lets `getEuropePmcService()` failures propagate spread these into their
+ * `errors[]`.
  */
 export declare const EUROPEPMC_SERVICE_ERRORS: readonly [{
     readonly reason: 'europepmc_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'Europe PMC was unreachable after all retry attempts.';
+    readonly when: 'Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results.';
     readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'europepmc_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
     readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
-    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
+    readonly when: 'Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt.';
+    readonly recovery: 'Adjust the input — the query, the sort, or the cursorMark — before retrying; the same input will be rejected again.';
     readonly retryable: false;
+    readonly thrownBy: 'service';
 }];
 /**
  * Reason identifier union for type-safe authoring on the service layer.

package/dist/services/error-contracts.d.ts.map

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