npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.15 → 2.10.17 - Mend

@cyanheads/pubmed-mcp-server 2.10.15 → 2.10.17

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 (77) hide show

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

@@ -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';
@@ -48,8 +49,8 @@ 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 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 CHANGED Viewed

	@@ -1 +1 @@
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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"}

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

@@ -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 CHANGED Viewed

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

@@ -76,8 +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;
 }];
 /**
@@ -98,9 +98,11 @@ export declare const NCBI_ID_INPUT_ERRORS: readonly [{
     readonly retryable: false;
 }];
 /**
- * Failure modes the Unpaywall service layer can surface. Tools that consume
- * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread
- * these into their `errors[]`.
+ * Failure modes the Unpaywall service layer can surface. A tool whose handler
+ * lets `getUnpaywallService()` failures propagate spreads these into its
+ * `errors[]`. None does today: `pubmed_fetch_fulltext`, the only consumer,
+ * folds every Unpaywall failure into its tier chain, so the entries serve the
+ * service's own `recoveryFor` hints.
  */
 export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
     readonly reason: 'unpaywall_unreachable';

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

	@@ -1 +1 @@
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package/dist/services/error-contracts.js CHANGED Viewed

@@ -83,8 +83,8 @@ export const NCBI_QUERY_INPUT_ERRORS = [
     {
         reason: 'blank_query',
         code: JsonRpcErrorCode.ValidationError,
-        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.',
-        recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.',
+        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.',
+        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.',
         retryable: false,
     },
 ];
@@ -108,9 +108,11 @@ export const NCBI_ID_INPUT_ERRORS = [
     },
 ];
 /**
- * Failure modes the Unpaywall service layer can surface. Tools that consume
- * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread
- * these into their `errors[]`.
+ * Failure modes the Unpaywall service layer can surface. A tool whose handler
+ * lets `getUnpaywallService()` failures propagate spreads these into its
+ * `errors[]`. None does today: `pubmed_fetch_fulltext`, the only consumer,
+ * folds every Unpaywall failure into its tier chain, so the entries serve the
+ * service's own `recoveryFor` hints.
  */
 export const UNPAYWALL_SERVICE_ERRORS = [
     {

package/dist/services/error-contracts.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/api-client.d.ts CHANGED Viewed

@@ -1,9 +1,11 @@
 /**
- * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs,
- * injects the optional contact email, and exposes single-attempt search,
- * fullTextXML, and citation-link calls. Classifies each endpoint's HTTP
- * failures — a failed search as `europepmc_unreachable`, a missing fullTextXML
- * as `not-available` — while retry logic lives in `EuropePmcService`.
+ * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs and
+ * the source-filtered search query (`buildSearchQuery`, shared with the service
+ * so it can report the query it sent), injects the optional contact email, and
+ * exposes single-attempt search, fullTextXML, and citation-link calls.
+ * Classifies each endpoint's HTTP failures — a failed search as
+ * `europepmc_unreachable`, a missing fullTextXML as `not-available` — while
+ * retry logic lives in `EuropePmcService`.
  * @module src/services/europe-pmc/api-client
  */
 import { type EuropePmcSearchParams } from './types.js';
@@ -76,11 +78,12 @@ export declare class EuropePmcApiClient {
     /** Helper: fetch a links (citations/references) JSON URL and return the body. */
     private fetchLinksJson;
     private buildSearchUrl;
-    /**
-     * Combine the caller's query with an optional source filter. EPMC's query
-     * syntax supports `SRC:"X"` field tokens — we OR-join the requested sources
-     * into a parenthesized clause and AND it with the user's query.
-     */
-    private buildQueryString;
 }
+/**
+ * The query string a search sends: the caller's query combined with an
+ * optional source filter. EPMC's query syntax supports `SRC:"X"` field tokens —
+ * the requested sources are OR-joined into a parenthesized clause and ANDed
+ * with the caller's query.
+ */
+export declare function buildSearchQuery(params: Pick<EuropePmcSearchParams, 'query' | 'sources'>): string;
 //# sourceMappingURL=api-client.d.ts.map

package/dist/services/europe-pmc/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAMH,OAAO,EAAsB,KAAK,qBAAqB,EAAE,MAAM,YAAY,CAAC;AAI5E,MAAM,WAAW,wBAAwB;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,MAAM,MAAM,4BAA4B,GACpC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAC9B;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAE9C;;;;;;;;GAQG;AACH,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,wBAAwB,EAAI;IAEjE;;;;;;;;;;;;;;OAcG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC,CA4C3D;IAED;;;;;;;;;OASG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC,CA4C7F;IAED;;;;OAIG;IACH,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAG7F;IAED;;;;OAIG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAG9F;IAED,iFAAiF;YACnE,cAAc;IA8B5B,OAAO,CAAC,cAAc;CAavB;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,IAAI,CAAC,qBAAqB,EAAE,OAAO,GAAG,SAAS,CAAC,GAAG,MAAM,CAKjG"}

package/dist/services/europe-pmc/api-client.js CHANGED Viewed

@@ -1,9 +1,11 @@
 /**
- * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs,
- * injects the optional contact email, and exposes single-attempt search,
- * fullTextXML, and citation-link calls. Classifies each endpoint's HTTP
- * failures — a failed search as `europepmc_unreachable`, a missing fullTextXML
- * as `not-available` — while retry logic lives in `EuropePmcService`.
+ * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs and
+ * the source-filtered search query (`buildSearchQuery`, shared with the service
+ * so it can report the query it sent), injects the optional contact email, and
+ * exposes single-attempt search, fullTextXML, and citation-link calls.
+ * Classifies each endpoint's HTTP failures — a failed search as
+ * `europepmc_unreachable`, a missing fullTextXML as `not-available` — while
+ * retry logic lives in `EuropePmcService`.
  * @module src/services/europe-pmc/api-client
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
@@ -163,7 +165,7 @@ export class EuropePmcApiClient {
     }
     buildSearchUrl(params) {
         const finalParams = {
-            query: this.buildQueryString(params),
+            query: buildSearchQuery(params),
             format: 'json',
             resultType: params.resultType ?? 'core',
             pageSize: String(params.pageSize ?? 25),
@@ -175,17 +177,18 @@ export class EuropePmcApiClient {
             finalParams.email = this.config.email;
         return `${EUROPEPMC_API_BASE}/search?${new URLSearchParams(finalParams).toString()}`;
     }
-    /**
-     * Combine the caller's query with an optional source filter. EPMC's query
-     * syntax supports `SRC:"X"` field tokens — we OR-join the requested sources
-     * into a parenthesized clause and AND it with the user's query.
-     */
-    buildQueryString(params) {
-        const base = params.query.trim();
-        if (!params.sources || params.sources.length === 0)
-            return base;
-        const sourceClause = params.sources.map((s) => `SRC:"${s}"`).join(' OR ');
-        return `(${base}) AND (${sourceClause})`;
-    }
+}
+/**
+ * The query string a search sends: the caller's query combined with an
+ * optional source filter. EPMC's query syntax supports `SRC:"X"` field tokens —
+ * the requested sources are OR-joined into a parenthesized clause and ANDed
+ * with the caller's query.
+ */
+export function buildSearchQuery(params) {
+    const base = params.query.trim();
+    if (!params.sources || params.sources.length === 0)
+        return base;
+    const sourceClause = params.sources.map((s) => `SRC:"${s}"`).join(' OR ');
+    return `(${base}) AND (${sourceClause})`;
 }
 //# sourceMappingURL=api-client.js.map

package/dist/services/europe-pmc/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/europe-pmc/europe-pmc-service.d.ts CHANGED Viewed

@@ -10,6 +10,8 @@
  * A search's retry boundary covers fetch and response classification, so
  * Europe PMC's intermittent empty `{ version }` envelope is retried like an
  * HTTP outage; only a sort or cursor that explains it is reported as bad input.
+ * A search reports the effective query Europe PMC echoes back, or — with no
+ * echo — the source-filtered query it sent.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/europe-pmc-service.js CHANGED Viewed

@@ -10,6 +10,8 @@
  * A search's retry boundary covers fetch and response classification, so
  * Europe PMC's intermittent empty `{ version }` envelope is retried like an
  * HTTP outage; only a sort or cursor that explains it is reported as bad input.
+ * A search reports the effective query Europe PMC echoes back, or — with no
+ * echo — the source-filtered query it sent.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so
@@ -25,7 +27,7 @@ import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
-import { EuropePmcApiClient } from './api-client.js';
+import { buildSearchQuery, EuropePmcApiClient } from './api-client.js';
 import { EuropePmcRequestQueue } from './request-queue.js';
 const MAX_BACKOFF_MS = 30_000;
 function abortableSleep(ms, signal) {
@@ -206,7 +208,9 @@ export class EuropePmcService {
             throw serviceUnavailable('Europe PMC returned an empty response with no hit count or result list.', { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') });
         }
         const hits = ensureArray(parsed.resultList?.result);
-        const echoed = parsed.request?.queryString ?? params.query;
+        // Without an echo, report the query actually sent — source filter included —
+        // not the caller's bare query, which searches every source. (#150)
+        const echoed = parsed.request?.queryString ?? buildSearchQuery(params);
         // EPMC's `request.cursorMark` echo is URL-encoded (the wire form), while
         // `nextCursorMark` in the JSON body is raw. Use the caller's input as the
         // current cursor so the echo is consistent and the equality check below

package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED Viewed

@@ -23,6 +23,14 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  * reads as an article with no body at all. Legacy
  * `<preformat preformat-type="pmc-ocr-text">` deposits, which put the entire
  * article in one such element, are the case that matters. (#130)
+ *
+ * A body-level block that carries a title of its own — a `<def-list>` or
+ * `<list>` `<title>`, a `<boxed-text>` `<caption>` title — forms a section of
+ * its own under that title, and the title leaves the block's text. PMC13546078
+ * opens its `<body>` with its abbreviations `<def-list>` this way; reporting it
+ * as an untitled section left `content[]` with no heading to separate the list
+ * from the abstract above it. Untitled blocks on either side of it are not its
+ * content and stay in untitled sections of their own. (#148)
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED Viewed

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