npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.18 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

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 (121) hide show

package/dist/mcp-server/tools/definitions/_text.js CHANGED Viewed

@@ -66,11 +66,16 @@ export function sliceAtWordBoundary(text, limit) {
 /** Any line break, including the Unicode line and paragraph separators. */
 const LINE_BREAK_RE = /[\r\n\u2028\u2029]+/g;
 /**
- * A `<` that opens something a Markdown renderer will read as raw HTML or an
- * autolink: a tag-name start, then a body carrying no further angle bracket,
- * then a closing `>`. Deliberately the same shape as `MARKUP_TAG_RE` in
- * `text-helpers.ts` — a `<` with no `>` after it (`n<N`) or one followed by a
- * digit (`P<0.001`) cannot open a tag and is left alone.
+ * A `<` that could open something a Markdown renderer reads as raw HTML or an
+ * autolink: a tag-name start (a letter, `/`, `!`, or `?`), then a body carrying
+ * no further angle bracket, then a closing `>`. Looser than `MARKUP_TAG_RE` in
+ * `text-helpers.ts` on purpose: that pattern deletes what it matches, so its tag
+ * name ends only at whitespace, `/`, or `>` to keep PubMed's `<or= 20 or > 20`
+ * as text, while an escape here costs only a backslash the renderer hides, so
+ * that `<` is escaped. The two agree that a `<` with no `>` after it (`n<N`) or
+ * one followed by a digit (`P<0.001`) cannot open a tag and is left alone. An
+ * entity-encoded tag (`&lt;i&gt;`), which `MARKUP_TAG_RE` also strips, is literal
+ * text to a renderer and is not escaped here.
  */
 const HTML_TAG_OPENER_RE = /<(?=[A-Za-z/!?][^<>]*>)/g;
 /** A character that makes an adjacent `_` intraword, where it cannot emphasize. */

package/dist/mcp-server/tools/definitions/_text.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/_visible-text.d.ts ADDED Viewed

@@ -0,0 +1,19 @@
+/**
+ * @fileoverview The one test every blank-input rejection shares: does a value
+ * hold any character a reader could see? `String.prototype.trim` is not enough —
+ * it keeps U+0085 (NEL), control characters such as U+0001 and U+007F (`\p{Cc}`),
+ * every format character (`\p{Cf}`: zero-width space, word joiner, soft
+ * hyphen, …), and the other default-ignorable code points (Hangul fillers such
+ * as U+3164, variation selectors, the combining grapheme joiner), so a value
+ * made only of those reads as nonblank and reaches the upstream as an invisible
+ * term. (#176)
+ * @module src/mcp-server/tools/definitions/_visible-text
+ */
+/**
+ * True when `value` has at least one character outside `\p{White_Space}`,
+ * `\p{Cc}`, `\p{Cf}`, and `\p{Default_Ignorable_Code_Point}`. Pure: it strips no
+ * markup and decodes no entities, so a caller that sanitizes input runs this on
+ * the sanitized copy.
+ */
+export declare function hasVisibleText(value: string): boolean;
+//# sourceMappingURL=_visible-text.d.ts.map

package/dist/mcp-server/tools/definitions/_visible-text.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"_visible-text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_visible-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAIH;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAErD"}

package/dist/mcp-server/tools/definitions/_visible-text.js ADDED Viewed

@@ -0,0 +1,22 @@
+/**
+ * @fileoverview The one test every blank-input rejection shares: does a value
+ * hold any character a reader could see? `String.prototype.trim` is not enough —
+ * it keeps U+0085 (NEL), control characters such as U+0001 and U+007F (`\p{Cc}`),
+ * every format character (`\p{Cf}`: zero-width space, word joiner, soft
+ * hyphen, …), and the other default-ignorable code points (Hangul fillers such
+ * as U+3164, variation selectors, the combining grapheme joiner), so a value
+ * made only of those reads as nonblank and reaches the upstream as an invisible
+ * term. (#176)
+ * @module src/mcp-server/tools/definitions/_visible-text
+ */
+const VISIBLE_CHARACTER = /[^\p{White_Space}\p{Cc}\p{Cf}\p{Default_Ignorable_Code_Point}]/u;
+/**
+ * True when `value` has at least one character outside `\p{White_Space}`,
+ * `\p{Cc}`, `\p{Cf}`, and `\p{Default_Ignorable_Code_Point}`. Pure: it strips no
+ * markup and decodes no entities, so a caller that sanitizes input runs this on
+ * the sanitized copy.
+ */
+export function hasVisibleText(value) {
+    return VISIBLE_CHARACTER.test(value);
+}
+//# sourceMappingURL=_visible-text.js.map

package/dist/mcp-server/tools/definitions/_visible-text.js.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"_visible-text.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_visible-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,MAAM,iBAAiB,GAAG,iEAAiE,CAAC;AAE5F;;;;;GAKG;AACH,MAAM,UAAU,cAAc,CAAC,KAAa;IAC1C,OAAO,iBAAiB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AACvC,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts CHANGED Viewed

@@ -34,15 +34,22 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
 }, {
     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 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: import("@cyanheads/mcp-ts-core/errors").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 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';
 }, {

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsDjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAuIzB,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED Viewed

@@ -103,7 +103,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             if (parsed.success)
                 continue;
             const shown = id.length > MAX_ECHOED_ID_LENGTH ? `${id.slice(0, MAX_ECHOED_ID_LENGTH)}…` : id;
-            throw ctx.fail('malformed_id', `Invalid ${input.idType} element "${shown}". ${parsed.error.issues[0]?.message}`, { ...ctx.recoveryFor('malformed_id') });
+            throw ctx.fail('malformed_id', `Invalid ${input.idType} element "${shown}". ${parsed.error.issues[0]?.message}`);
         }
         // The converter parses `0023193287` as PMID 23193287 yet answers "not found
         // in PMC" for it, so a PMID is sent in its canonical form. (#161)

package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED Viewed

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

@@ -1,8 +1,8 @@
 /**
  * @fileoverview PubMed fetch tool. Fetches full article metadata by PubMed IDs,
- * including abstracts, authors, journal info, and MeSH terms. A zero-padded
- * PMID is fetched and matched as the PMID it spells; `ids` is accepted as an
- * alias for `pmids`.
+ * including abstracts, authors, journal info, MeSH terms, and linked retraction
+ * and correction notices. A zero-padded PMID is fetched and matched as the PMID
+ * it spells; `ids` is accepted as an alias for `pmids`.
  * @module src/mcp-server/tools/definitions/fetch-articles.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -73,6 +73,12 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
         pubmedUrl: z.ZodOptional<z.ZodString>;
         pmcUrl: z.ZodOptional<z.ZodString>;
         publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        commentsCorrections: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            refType: z.ZodString;
+            refSource: z.ZodString;
+            pmid: z.ZodOptional<z.ZodString>;
+            note: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>>;
         keywords: z.ZodOptional<z.ZodArray<z.ZodString>>;
         meshTerms: z.ZodOptional<z.ZodArray<z.ZodObject<{
             descriptorName: z.ZodOptional<z.ZodString>;
@@ -116,15 +122,22 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
 }, {
     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 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: 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 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';
 }, {

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	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED Viewed

@@ -1,8 +1,8 @@
 /**
  * @fileoverview PubMed fetch tool. Fetches full article metadata by PubMed IDs,
- * including abstracts, authors, journal info, and MeSH terms. A zero-padded
- * PMID is fetched and matched as the PMID it spells; `ids` is accepted as an
- * alias for `pmids`.
+ * including abstracts, authors, journal info, MeSH terms, and linked retraction
+ * and correction notices. A zero-padded PMID is fetched and matched as the PMID
+ * it spells; `ids` is accepted as an alias for `pmids`.
  * @module src/mcp-server/tools/definitions/fetch-articles.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -149,11 +149,32 @@ const MeshTermSchema = z
 const GrantSchema = z
     .object({
     grantId: z.string().optional().describe('Grant identifier'),
-    acronym: z.string().optional().describe('Grant acronym'),
+    acronym: z
+        .string()
+        .optional()
+        .describe('Acronym of the funding institute or agency from `Grant/Acronym` (e.g. "EY" for the National Eye Institute) — it names the funder, never the grant, so it is no substitute for `grantId`.'),
     agency: z.string().optional().describe('Funding agency'),
     country: z.string().optional().describe('Agency country'),
 })
     .describe('Grant record');
+const CommentsCorrectionSchema = z
+    .object({
+    refType: z
+        .string()
+        .describe('Link type, verbatim from NCBI\'s `RefType` — e.g. "RetractionIn", "RetractionOf", "ErratumIn", "ErratumFor", "ExpressionOfConcernIn", "CommentIn", "CommentOn", "UpdateIn". The set is open: treat an unfamiliar value as opaque.'),
+    refSource: z
+        .string()
+        .describe('Citation of the linked record as NCBI writes it (e.g. "Lancet. 2010 Feb 6;375(9713):445. doi: 10.1016/S0140-6736(10)60175-4.").'),
+    pmid: z
+        .string()
+        .optional()
+        .describe('PMID of the linked record — pass it to `pubmed_fetch_articles` to read that record. Absent when the linked record has no PMID, as with many errata.'),
+    note: z
+        .string()
+        .optional()
+        .describe('NCBI\'s note on the link, e.g. what an erratum corrected ("Fuβer, Fabian [corrected to Fußer, Fabian]"). Absent unless NCBI supplies one.'),
+})
+    .describe('One record NCBI links to this article and published separately from it — for example a retraction notice, erratum, expression of concern, comment, update, or republication.');
 const ArticleDateSchema = z
     .object({
     dateType: z.string().optional().describe('Date type'),
@@ -188,10 +209,17 @@ const FetchedArticleSchema = z
     pubmedUrl: z.string().optional().describe('PubMed article URL'),
     pmcUrl: z.string().optional().describe('PMC full text URL'),
     publicationTypes: z.array(z.string()).optional().describe('Publication types'),
+    commentsCorrections: z
+        .array(CommentsCorrectionSchema)
+        .optional()
+        .describe("Records NCBI links to this article — for example retraction notices, errata, expressions of concern, comments, and updates — from `CommentsCorrectionsList`, in NCBI's order and uncapped. `Cites` entries are excluded: they list a bibliography, which `pubmed_find_related` covers with its `references` relationship. Read this alongside `publicationTypes`, not in place of it: that field describes the record itself, and a corrected or questioned article often carries no matching type. Absent when NCBI links nothing other than `Cites` entries, and never set on `book-chapter` or `book` records."),
     keywords: z.array(z.string()).optional().describe('Keywords'),
     meshTerms: z.array(MeshTermSchema).optional().describe('MeSH terms'),
     grantList: z.array(GrantSchema).optional().describe('Grant information'),
-    articleDates: z.array(ArticleDateSchema).optional().describe('Article dates'),
+    articleDates: z
+        .array(ArticleDateSchema)
+        .optional()
+        .describe("Dates of the record itself, each named by `dateType`. On a journal article, PubMed's `ArticleDate` entries (`Electronic` — the electronic publication date). On a Bookshelf record, its own `ContributionDate` (when the chapter was contributed) and `DateRevised` (when it was last updated), distinct from the containing book's dates in `book`; `pubmed_format_citations` cites a chapter by `DateRevised` when present, otherwise `ContributionDate`. Absent when NCBI supplies none."),
 })
     .describe('Parsed PubMed article');
 const DeferredSchema = z
@@ -214,7 +242,7 @@ const DeferredSchema = z
 })
     .describe('Continuation state for articles the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one article.');
 export const fetchArticlesTool = tool('pubmed_fetch_articles', {
-    description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms. Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.',
+    description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices. Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-articles.tool.ts',
@@ -273,7 +301,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
         const requested = [...new Set(input.pmids.map(normalizePmid))];
         const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: requested.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: requested.length >= 100, signal: ctx.signal });
         if (!xmlData || !('PubmedArticleSet' in xmlData)) {
-            throw ctx.fail('invalid_efetch_response', 'Invalid EFetch response from NCBI: missing PubmedArticleSet', { requestedPmids: input.pmids.length, ...ctx.recoveryFor('invalid_efetch_response') });
+            throw ctx.fail('invalid_efetch_response', 'Invalid EFetch response from NCBI: missing PubmedArticleSet', { requestedPmids: input.pmids.length });
         }
         // Reads both members of the set. Taking `PubmedArticleSet.PubmedArticle`
         // alone discards every NCBI Bookshelf record, whose PMIDs then surface as
@@ -407,10 +435,11 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
                 if (bk.publisherLocation)
                     bookLines.push(`**Publisher Location:** ${bk.publisherLocation}`);
                 // A book published over several years carries a closed range
-                // (GeneReviews 1993–2026); otherwise the single publication year. A
-                // publication year that differs from the range's start is kept beside it.
-                const range = bk.beginningDate && bk.endingDate && bk.beginningDate !== bk.endingDate
-                    ? `${bk.beginningDate}–${bk.endingDate}`
+                // (GeneReviews 1993–2026), one still being updated an open one
+                // (Endotext 2000–); otherwise the single publication year. A publication
+                // year that differs from the range's start is kept beside it. (#189)
+                const range = bk.beginningDate && bk.beginningDate !== bk.endingDate
+                    ? `${bk.beginningDate}–${bk.endingDate ?? ''}`
                     : undefined;
                 const bookDate = range && bk.pubDate && bk.pubDate !== bk.beginningDate
                     ? `${bk.pubDate} (${range})`
@@ -447,6 +476,19 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             if (a.articleDates?.length) {
                 lines.push(`**Article Dates:** ${a.articleDates.map(formatArticleDate).join('; ')}`);
             }
+            // Ahead of the abstract, where PubMed itself shows "Retraction in" and
+            // "Erratum in": a notice qualifies how the rest of the record is read.
+            if (a.commentsCorrections?.length) {
+                lines.push(`\n#### Comments and Corrections (${a.commentsCorrections.length})`);
+                if (a.commentsCorrections.some((cc) => cc.pmid)) {
+                    lines.push('Fetch a linked record by its PMID with `pubmed_fetch_articles`.');
+                }
+                for (const cc of a.commentsCorrections) {
+                    const pmid = cc.pmid ? ` — PMID ${cc.pmid}` : '';
+                    const note = cc.note ? ` — Note: ${escapeMarkdownInline(cc.note)}` : '';
+                    lines.push(`- **${escapeMarkdownInline(cc.refType)}:** ${escapeMarkdownInline(cc.refSource)}${pmid}${note}`);
+                }
+            }
             if (a.abstractText)
                 lines.push(`\n#### Abstract\n${a.abstractText}`);
             if (a.keywords?.length)
@@ -474,8 +516,13 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             if (a.grantList?.length) {
                 lines.push(`\n#### Grants`);
                 for (const g of a.grantList) {
-                    const grantId = g.grantId && g.acronym ? `${g.grantId} (${g.acronym})` : (g.grantId ?? g.acronym ?? '');
-                    const parts = [grantId, g.agency, g.country].filter(Boolean);
+                    // The acronym names the funder, never the grant: without a GrantID it
+                    // follows the agency instead of taking the ID's slot. (#214)
+                    const grantId = g.grantId && g.acronym ? `${g.grantId} (${g.acronym})` : g.grantId;
+                    const agency = !g.grantId && g.acronym
+                        ? [g.agency, `(${g.acronym})`].filter(Boolean).join(' ')
+                        : g.agency;
+                    const parts = [grantId, agency, g.country].filter(Boolean);
                     lines.push(`- ${parts.join(' — ')}`);
                 }
             }
@@ -491,7 +538,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
  */
 function buildDeferralNotice(deferred) {
     const spent = deferred.returnedCharacters === 0
-        ? `No article fits the requested maxResponseCharacters of ${deferred.maxResponseCharacters}, so none were returned.`
+        ? `The first article alone exceeds the requested maxResponseCharacters of ${deferred.maxResponseCharacters}, so none were returned.`
         : `Response character budget reached: ${deferred.returnedCharacters} of ${deferred.maxResponseCharacters} characters returned.`;
     return `${spent} ${deferred.deferredCount} resolved article(s) were deferred whole: ${deferred.ids.join(', ')}. Re-call pubmed_fetch_articles with those PMIDs to retrieve them, or raise maxResponseCharacters to at least ${deferred.nextDeferredCharacters} — the size of the next deferred article.`;
 }
@@ -521,8 +568,14 @@ function formatPublicationDate(pd) {
         return `${pd.medlineDate} (${ymd})`;
     return pd.medlineDate || ymd || undefined;
 }
+/**
+ * `ContributionDate 2025-07-03`. A one-digit month or day is zero-padded for
+ * display only — the parser reads `<Month>07</Month>` as 7, and Bookshelf writes
+ * `<Month>7</Month>` outright — so structuredContent keeps the value as parsed.
+ */
 function formatArticleDate(ad) {
-    const datePart = [ad.year, ad.month, ad.day].filter(Boolean).join('-');
+    const pad = (part) => part?.length === 1 && part >= '0' && part <= '9' ? `0${part}` : part;
+    const datePart = [ad.year, pad(ad.month), pad(ad.day)].filter(Boolean).join('-');
     return ad.dateType ? `${ad.dateType} ${datePart}` : datePart;
 }
 //# sourceMappingURL=fetch-articles.tool.js.map

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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 /**
  * @fileoverview Full-text fetch tool. Resolves full-text articles through a
  * three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
- * Accepts three mutually-exclusive input shapes:
+ * Accepts three input fields, alone or together, naming at most 10 distinct
+ * identifiers between them:
  *
  *   - `pmcids` — fetch directly by PMC ID, once per record however it is
  *     spelled (`PMC123`, `pmc123`, `123`, zero-padded `PMC0123`), and reported
@@ -16,6 +17,13 @@
  *     DOIs are case-insensitive: every casing of one DOI runs the chain once,
  *     and `unavailable[]` reports each casing as the caller wrote it.
  *
+ * Routing runs `pmcids`, then `pmids`, then `dois`. Every tier keys its work on
+ * the record — PMC on the PMCID, Europe PMC on the search hit's `source` + `id`,
+ * Unpaywall on the lowercased DOI — and the first id to reach a record owns it:
+ * a later id naming the same article joins the owner's chain as another caller
+ * id, so the article is fetched and returned once. Each `unavailable[]` entry
+ * and deferred id carries the field its id was sent in.
+ *
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
  * extra `viaSource` discriminator that records which layer produced the
  * content. EPMC's JATS reuses the `pmc` schema shape because it's the same
@@ -30,6 +38,7 @@
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 /**
  * Compose the tool description for the fallback tiers enabled in this
  * deployment. PMC EFetch is always present; Europe PMC (`EUROPEPMC_ENABLED`)
@@ -245,49 +254,65 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
         maxResponseCharacters: z.ZodNumber;
         returnedCharacters: z.ZodNumber;
         deferredCount: z.ZodNumber;
-        idType: z.ZodEnum<{
+        idType: z.ZodOptional<z.ZodEnum<{
             doi: "doi";
             pmcid: "pmcid";
             pmid: "pmid";
-        }>;
+        }>>;
         ids: z.ZodArray<z.ZodString>;
+        pmcids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        pmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        dois: z.ZodOptional<z.ZodArray<z.ZodString>>;
         nextDeferredCharacters: z.ZodNumber;
     }, z.core.$strip>>;
 }, z.core.$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_filter';
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: 'A `sections` element holds no visible character — only whitespace, or invisible characters such as a zero-width space — so it names no heading. An exactly-empty element is not blank here; it is skipped.';
+    readonly recovery: 'Give each named `sections` element a heading term such as Methods, or make it an empty string, which is skipped; omit `sections` for no filter. The same blank element will be rejected again.';
+    readonly retryable: false;
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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