@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.19

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

@@ -4,9 +4,11 @@
  * and EPMC-only OA articles. Uses EPMC's cursor-based pagination
  * (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
  * because EPMC's search API doesn't support offset. `max_results` and `limit`
- * are accepted as aliases for `pageSize`. The total hit count rides in
- * `output` so `format()` can state it in the header, and `searchUrl` opens the
- * source-filtered query Europe PMC actually ran.
+ * are accepted as aliases for `pageSize`. A `query` with no search term (`()`,
+ * `<b></b>`) or a blank `cursorMark` is rejected before Europe PMC is called.
+ * The total hit count rides in `output` so `format()` can state it in the
+ * header, and `searchUrl` opens the source-filtered query Europe PMC actually
+ * ran.
  *
  * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
  * fails fast with a configuration error if the service is unset, since the
@@ -78,10 +80,22 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    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 when: 'Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
+    readonly recovery: "Fix the rejected input before retrying — the query, the sort, or the cursorMark (pass the previous response's `nextCursorMark` verbatim, or `*` to restart); the same input will most likely be rejected again.";
     readonly retryable: false;
     readonly thrownBy: 'service';
+}, {
+    readonly reason: 'blank_query';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    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;
+}, {
+    readonly reason: 'blank_cursor';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: 'The `cursorMark` holds only whitespace or invisible characters such as a zero-width space. Europe PMC cannot read it and answers with the HTTP 503 it also uses for an outage.';
+    readonly recovery: "Omit `cursorMark` or pass `*` for the first page, or pass the previous response's `nextCursorMark` verbatim for the next page.";
+    readonly retryable: false;
 }, {
     readonly reason: 'europepmc_disabled';
     readonly code: JsonRpcErrorCode.ConfigurationError;

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

@@ -1 +1 @@
-{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;EAwSjG,CAAC"}
+{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgCjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAYxB,cAAc;;mBAEhB,gLAAgL;uBAEpL,gIAAgI;;;qBAI1H,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;EA+TjG,CAAC"}

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

@@ -4,9 +4,11 @@
  * and EPMC-only OA articles. Uses EPMC's cursor-based pagination
  * (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
  * because EPMC's search API doesn't support offset. `max_results` and `limit`
- * are accepted as aliases for `pageSize`. The total hit count rides in
- * `output` so `format()` can state it in the header, and `searchUrl` opens the
- * source-filtered query Europe PMC actually ran.
+ * are accepted as aliases for `pageSize`. A `query` with no search term (`()`,
+ * `<b></b>`) or a blank `cursorMark` is rejected before Europe PMC is called.
+ * The total hit count rides in `output` so `format()` can state it in the
+ * header, and `searchUrl` opens the source-filtered query Europe PMC actually
+ * ran.
  *
  * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
  * fails fast with a configuration error if the service is unset, since the
@@ -16,12 +18,14 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { EUROPEPMC_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { sanitization } from '@cyanheads/mcp-ts-core/utils';
+import { EUROPEPMC_SERVICE_ERRORS, QUERY_INPUT_ERRORS } from '../../../services/error-contracts.js';
 import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
 import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
 import { escapeMarkdownInline, sliceCodeUnits } from './_text.js';
+import { hasVisibleText } from './_visible-text.js';
 const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
 /**
  * Character budget for `abstractSnippet`. Keeps a search page bounded no matter
@@ -39,6 +43,14 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts',
     errors: [
         ...EUROPEPMC_SERVICE_ERRORS,
+        ...QUERY_INPUT_ERRORS,
+        {
+            reason: 'blank_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The `cursorMark` holds only whitespace or invisible characters such as a zero-width space. Europe PMC cannot read it and answers with the HTTP 503 it also uses for an outage.',
+            recovery: "Omit `cursorMark` or pass `*` for the first page, or pass the previous response's `nextCursorMark` verbatim for the next page.",
+            retryable: false,
+        },
         {
             reason: 'europepmc_disabled',
             code: JsonRpcErrorCode.ConfigurationError,
@@ -53,7 +65,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         query: z
             .string()
             .min(1)
-            .describe('Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords.'),
+            .describe('Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords. A query with no search term — blank once HTML entities are decoded and markup, parentheses, and invisible characters are disregarded, such as `()` or `<b></b>` — is rejected; any other query is sent as written.'),
         pageSize: z
             .number()
             .int()
@@ -64,7 +76,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         cursorMark: z
             .string()
             .default('*')
-            .describe("Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` for subsequent pages."),
+            .describe("Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` verbatim for subsequent pages. A whitespace-only cursor, invisible characters included, is rejected before the request, and a cursor Europe PMC cannot read fails with `europepmc_invalid_input` once a retry of it fails again while the first page of the same query is served."),
         sources: z
             .array(SourceEnum)
             .min(1)
@@ -164,9 +176,27 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
     },
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_europepmc_search', { query: input.query });
+        // `min(1)` counts whitespace, and the source wrapper trims a blank query to
+        // `() AND (SRC:"MED")`, which Europe PMC answers with every record of that
+        // source. The check runs on the caller's query, before the wrapper, and
+        // applies pubmed_search_articles' rule: markup stripped, entities decoded,
+        // parentheses and invisible characters disregarded. Europe PMC would search
+        // `<b></b>` as the word `b`, but that is no term the caller wrote. The
+        // sanitized copy only decides blankness; the query is sent as written. (#176)
+        const checkedQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
+        if (!hasVisibleText(checkedQuery.replace(/[()]/g, ''))) {
+            throw ctx.fail('blank_query', 'The `query` contains no search term — it is blank once HTML entities are decoded and markup, parentheses, and invisible characters are disregarded.');
+        }
+        // Europe PMC answers a blank cursor — whitespace or invisible characters —
+        // with the HTTP 503 it uses for an outage, which would be retried as one.
+        // An exactly-empty cursor reads as the first page upstream and passes
+        // through. (#180)
+        if (input.cursorMark !== '' && !hasVisibleText(input.cursorMark)) {
+            throw ctx.fail('blank_cursor', 'The `cursorMark` holds only whitespace or invisible characters, which Europe PMC cannot read as a page position.');
+        }
         const epmc = getEuropePmcService();
         if (!epmc) {
-            throw ctx.fail('europepmc_disabled', 'Europe PMC service is not available. Set EUROPEPMC_ENABLED=true to use this tool.', { ...ctx.recoveryFor('europepmc_disabled') });
+            throw ctx.fail('europepmc_disabled', 'Europe PMC service is not available. Set EUROPEPMC_ENABLED=true to use this tool.');
         }
         const sources = (input.sources ?? EUROPEPMC_DEFAULT_SOURCES);
         const result = await epmc.search({

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

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

@@ -1,15 +1,18 @@
 /**
  * @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 { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     query: z.ZodString;
     maxResults: z.ZodDefault<z.ZodNumber>;
@@ -64,44 +67,63 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     totalCount: z.ZodNumber;
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
+    readonly code: JsonRpcErrorCode.RateLimited;
     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 code: JsonRpcErrorCode.ServiceUnavailable;
+    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: 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 code: JsonRpcErrorCode.Timeout;
+    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';
 }, {
     readonly reason: 'ncbi_invalid_response';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
+    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: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    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';
 }, {
     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 code: JsonRpcErrorCode.ValidationError;
+    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;
+}, {
+    readonly reason: 'invalid_date_range';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly 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.';
+    readonly 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.';
+    readonly retryable: false;
+}, {
+    readonly reason: 'blank_filter';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly 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.';
+    readonly 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.';
     readonly retryable: false;
 }], {
     readonly effectiveQuery: z.ZodString;

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

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+{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiUjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAYjB,oBAAoB;;mBAEtB,2RAA2R;uBAE/R,oJAAoJ;;;qBAI9I,cAAc;;mBAEhB,mZAAmZ;uBAEvZ,gIAAgI;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuctI,CAAC"}