@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.10

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

@@ -4,7 +4,7 @@
  * @module src/mcp-server/tools/definitions/spell-check.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 { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
@@ -12,9 +12,12 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     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],
+    errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
     input: z.object({
-        query: z.string().min(2).describe('PubMed search query to spell-check'),
+        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.'),
     }),
     output: z.object({
         original: z.string().describe('Original query'),
@@ -23,6 +26,15 @@ export const spellCheckTool = tool('pubmed_spell_check', {
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
+        // `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'),
+            });
+        }
         const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query }, { signal: ctx.signal });
         return {
             original: result.original,

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

@@ -1 +1 @@
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+{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,uBAAuB,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAC7F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,EAAE,GAAG,uBAAuB,CAAU;IAErE,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iIAAiI,CAClI;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,4EAA4E;QAC5E,4EAA4E;QAC5E,wEAAwE;QACxE,gDAAgD;QAChD,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACpC,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,yDAAyD,EAAE;gBACvF,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC;aAClC,CAAC,CAAC;QACL,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAC1C,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,EACnC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;QACF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

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

@@ -1,6 +1,8 @@
 /**
- * @fileoverview Canonical service-layer error contracts. Single source of truth
- * for the failure modes both services throw and tools declare in `errors[]`.
+ * @fileoverview Canonical error contracts. Single source of truth for the
+ * failure modes services throw and tools declare in `errors[]`, plus the
+ * input rejections shared by the tools that forward a free-text query
+ * upstream.
  *
  * Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
  * `recoveryFor(reason)` from this module into the error factory's `data` arg.
@@ -50,6 +52,24 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
 }];
+/**
+ * Input failure the NCBI query tools reject before any call is made. Declared
+ * here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
+ * throw it advertise it — a tool that takes no free-text query can never
+ * produce it, and declaring it there would advertise a failure mode that
+ * cannot happen.
+ *
+ * Unlike the service arrays in this module, this one is thrown from a tool
+ * handler via `ctx.fail('blank_query', …)`, so its recovery hint resolves
+ * through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
+ */
+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 retryable: false;
+}];
 /**
  * Failure modes the Unpaywall service layer can surface. Tools that consume
  * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread

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

@@ -1 +1 @@
-{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,0CAA0C;aAChD,QAAQ,EAAE,qEAAqE;aAC/E,SAAS;;aAGT,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;;aAGT,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;;aAGT,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qEAAqE;aAC3E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,oDAAoD;aAC1D,QAAQ,EACN,4FAA4F;aAC9F,SAAS;;aAGT,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;EAEH,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,sDAAsD;aAC5D,QAAQ,EACN,iGAAiG;aACnG,SAAS;;aAGT,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,+FAA+F;aACrG,QAAQ,EACN,8GAA8G;aAChH,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
+{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,0CAA0C;aAChD,QAAQ,EAAE,qEAAqE;aAC/E,SAAS;;aAGT,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;;aAGT,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;;aAGT,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;;;;;;;GAUG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,yIAAyI;aAC/I,QAAQ,EACN,2GAA2G;aAC7G,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qEAAqE;aAC3E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,oDAAoD;aAC1D,QAAQ,EACN,4FAA4F;aAC9F,SAAS;;aAGT,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;EAEH,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,sDAAsD;aAC5D,QAAQ,EACN,iGAAiG;aACnG,SAAS;;aAGT,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,+FAA+F;aACrG,QAAQ,EACN,8GAA8G;aAChH,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}

package/dist/services/error-contracts.js

@@ -1,6 +1,8 @@
 /**
- * @fileoverview Canonical service-layer error contracts. Single source of truth
- * for the failure modes both services throw and tools declare in `errors[]`.
+ * @fileoverview Canonical error contracts. Single source of truth for the
+ * failure modes services throw and tools declare in `errors[]`, plus the
+ * input rejections shared by the tools that forward a free-text query
+ * upstream.
  *
  * Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
  * `recoveryFor(reason)` from this module into the error factory's `data` arg.
@@ -56,6 +58,26 @@ export const NCBI_SERVICE_ERRORS = [
         retryable: false,
     },
 ];
+/**
+ * Input failure the NCBI query tools reject before any call is made. Declared
+ * here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
+ * throw it advertise it — a tool that takes no free-text query can never
+ * produce it, and declaring it there would advertise a failure mode that
+ * cannot happen.
+ *
+ * Unlike the service arrays in this module, this one is thrown from a tool
+ * handler via `ctx.fail('blank_query', …)`, so its recovery hint resolves
+ * through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
+ */
+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.',
+        retryable: false,
+    },
+];
 /**
  * Failure modes the Unpaywall service layer can surface. Tools that consume
  * `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread

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

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

@@ -7,15 +7,22 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
+import type { ParsedPmcArticle, ParsedPmcAsset, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
 import { type JatsNode } from './pmc-xml-helpers.js';
 /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
 export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
 /**
  * Extract body sections from a `<body>` node, walking children in document order.
- * Consecutive bare `<p>` siblings are collected into an untitled section so
- * articles with mixed structure (direct paragraphs + trailing `<sec>`, common
- * in manuscript-submitted PMC deposits) preserve their main text.
+ * Consecutive bare `<p>` siblings — and any block element sitting directly under
+ * `<body>` — are collected into an untitled section so articles with mixed
+ * structure (direct paragraphs + trailing `<sec>`, common in
+ * manuscript-submitted PMC deposits) preserve their main text.
+ *
+ * A `<body>` whose whole content is one block and no `<sec>` therefore yields a
+ * section carrying that block's text, rather than the empty list the tool layer
+ * 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)
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
@@ -48,6 +55,19 @@ export declare function extractPmcTables(root: JatsNode | undefined): ParsedPmcT
  * source `<tr>` elements and needs no cap of its own. (#111)
  */
 export declare const MAX_TABLE_COLUMNS = 512;
+/**
+ * Extract every `<fig>` and `<supplementary-material>` under `root` in document
+ * order — pass the `<article>` node.
+ *
+ * Whole-article, for the reason the table walk is: 17% of figures and 23% of
+ * supplementary material sit outside `<body>` entirely — `<floats-group>`
+ * deposits, `<back>/<sec>` and `<app-group>/<app>` placements, and figures
+ * hanging off the abstract in `<front>`. Each asset names the innermost
+ * enclosing `<sec>` wherever that sits, an untitled one inheriting its parent's
+ * title, so the reader keeps a positional cue; an asset inside no `<sec>` at all
+ * carries no section name. (#130)
+ */
+export declare function extractPmcAssets(root: JatsNode | undefined): ParsedPmcAsset[];
 /**
  * Extract references from anywhere under `root` — pass the `<article>` node to
  * cover a whole document, or a `<back>` node to scope the search to it.

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

@@ -1 +1 @@
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