@cyanheads/pubmed-mcp-server 2.10.15 → 2.10.17

package/AGENTS.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.15
+**Version:** 2.10.17
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.15
+**Version:** 2.10.17
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.10.15-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.10.17-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 
@@ -44,9 +44,9 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 | `pubmed_fetch_fulltext` | Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs. |
 | `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM) |
 | `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
-| `pubmed_spell_check` | Spell-check a biomedical query via NCBI ESpell — returns the corrected query and whether a suggestion was found |
+| `pubmed_spell_check` | Spell-check a PubMed query via NCBI ESpell — every misspelled token corrected in one call; the recovery step after a zero-hit or thin search |
 | `pubmed_lookup_mesh` | Search MeSH by heading — tree numbers, scope notes, entry terms — for building controlled-vocabulary queries |
-| `pubmed_lookup_citation` | Resolve partial bibliographic references to PubMed IDs via ECitMatch |
+| `pubmed_lookup_citation` | Resolve partial bibliographic references — one citation or a batch of up to 25 — to PubMed IDs via ECitMatch |
 | `pubmed_convert_ids` | Convert between DOI, PMID, and PMCID using the PMC ID Converter API |
 
 ### Resources
@@ -68,14 +68,17 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 - Full PubMed boolean and field-tag syntax, plus structured filters: author, journal, MeSH terms, language, species, publication type, has-abstract, free-full-text
 - Date ranges by publication, modification, or Entrez date; sort by relevance, date, author, or journal; offset pagination
 - Optional brief summaries for the top N results via ESummary
-- NCBI Bookshelf hits carry `bookTitle`, `publisherName`, `docType`, and `editors` in place of the empty `source`
-- Echoes the original query, the fully applied PubMed query, and normalized filter metadata
+- NCBI Bookshelf hits carry `bookTitle`, `publisherName`, `docType`, and `editors` in place of the empty `source`; the rendered summary shows the doc type only for these, not for ordinary journal articles (`citation`)
+- Reports `totalCount`, stated in the header beside the page (`Returned: 3 of 2924`); echoes the original query, the fully applied PubMed query, and normalized filter metadata
+- A query with no search term — blank, markup only, a bare field tag like `[pdat]`, or empty `()` — is rejected as `blank_query` rather than sent upstream
+- `limit` is accepted for `maxResults`
 
 ---
 
 ### `pubmed_fetch_articles` <sub>tool</sub>
 
-- Up to 200 PMIDs per call (POST for batches of 100 or more)
+- Up to 200 PMIDs per call (POST for batches of 100 or more); `ids` is accepted for `pmids`
+- A zero-padded PMID (`00000001`) resolves as the PMID it spells; `unavailablePmids` lists misses as you sent them
 - Title, abstract, authors with deduplicated affiliations, journal info, DOI, PubMed/PMC links; optional MeSH terms, grants, and publication types
 - Tolerant of PubMed's inconsistent XML — structured abstracts, missing fields, varying date formats
 - Bookshelf chapters and books are first-class: `recordType` (`journal-article` / `book-chapter` / `book`) plus a `book` object (title, publisher, editors, ISBNs, Bookshelf accession); `journalInfo` is absent on them
@@ -86,20 +89,23 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 
 ### `pubmed_fetch_fulltext` <sub>tool</sub>
 
-- Exactly one of `pmcids`, `pmids`, or `dois` (one id per element), up to 10 per request
+- Exactly one of `pmcids`, `pmids`, or `dois` (one id per element), up to 10 per request; a zero-padded PMID or PMC ID resolves as the ID it spells, DOIs match case-insensitively, and PMC IDs match with or without the `PMC` prefix in any case. Each record is fetched once however many spellings name it; `unavailable[].id` keeps your PMID or DOI spelling, and reports a PMC ID as `PMC<digits>`
 - Three-tier chain: NCBI PMC EFetch → Europe PMC `fullTextXML` (`EUROPEPMC_ENABLED`, default on) → Unpaywall (needs `UNPAYWALL_EMAIL`); `viaSource` names which tier served each article
 - Preprints, patents, and Agricola records have metadata via `pubmed_europepmc_search` but no full text through this chain — Europe PMC's `fullTextXML` is PMC-keyed
-- `source: "pmc"` returns structured sections plus `tables[]` (cells, caption, label, footnotes) and `assets[]` (figures and supplementary material, with `[Figure: <label>]` markers left in the body); `source: "unpaywall"` returns a best-effort body with `contentFormat` (`html-markdown` / `pdf-text`)
+- `source: "pmc"` returns structured sections plus `tables[]` (cells, caption, label, footnotes) and `assets[]` (figures and supplementary material, with `[Figure: <label>]` markers left in the body, and the file pointer read through `<alternatives>` when a figure offers several formats); `source: "unpaywall"` returns a best-effort body with `contentFormat` (`html-markdown` / `pdf-text`), a `title` from Unpaywall's record (else the Europe PMC record, else the HTML page), and `journalName` / `year` when Unpaywall has them
+- A titled list, definition list, or boxed text that sits in the body outside any section, or is the only content of an untitled section, such as an abbreviations list, becomes a section under its own title, and a figure or table inside it names that section; a section with no title is headed `untitled section`, the same name the `truncation` ledger gives it, and section titles in headings and ledger lines are Markdown-escaped
 - Unavailable entries carry a typed `reason` (`not-found`, `no-doi`, `doi-lookup-failed`, `no-oa`, `service-error`, …), `idType`, `triedTiers` (per-tier outcome in execution order), and `unqueriedTiers` when an unconfigured tier could have served the id
-- Filters and budgets: `sections` (case-insensitive title match), `maxSections`, `includeTables`, `includeAssets`, `maxCharacters`, `maxCharactersPerSection`, `overflowMode` (`truncate` / `outline`), and `maxResponseCharacters`, which defers whole articles past the ceiling to `deferred.ids`; a `truncation` object reports what was shortened or omitted
+- Filters and budgets: `sections` (case-insensitive title match), `maxSections`, `includeTables`, `includeAssets`, `maxCharacters`, `maxCharactersPerSection`, `overflowMode` (`truncate` / `outline`), and `maxResponseCharacters`, which defers whole articles past the ceiling to `deferred.ids`; a `truncation` object reports what was shortened or omitted, per section and subsection
+- A budget cut ends at a word boundary; `truncate` drops every section and subsection past the cut, while `outline` keeps each heading and marks one the budget left empty
 
 ---
 
 ### `pubmed_europepmc_search` <sub>tool</sub>
 
 - Reaches records PubMed can't: preprints (`PPR`), patents (`PAT`), Agricola (`AGR`), alongside `MED` and `PMC`; default `sources` is `["MED", "PMC", "PPR"]`
-- Cursor pagination via `cursorMark` — `*` for the first page, then `nextCursorMark`
+- Cursor pagination via `cursorMark` — `*` for the first page, then `nextCursorMark`; `pageSize` up to 100, with `max_results` and `limit` accepted for it
 - Hits carry `source` plus `pmid` / `pmcId` / `doi` when known; `abstractSnippet` is capped at 400 characters, with `abstractTruncated` flagging the cut
+- `totalCount` reports the full hit count, stated in the header beside the page; `searchUrl` opens the same source-filtered query on europepmc.org
 - Not registered when `EUROPEPMC_ENABLED=false`
 
 ---
@@ -117,7 +123,7 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 - APA 7th, MLA 9th, BibTeX, RIS, Vancouver (ICMJE/NLM); several styles per article in one call, up to 50 articles
 - Bookshelf chapters and books cite in each style's edited-book form; articles without a page range cite by electronic locator in each style's convention
 - Hand-rolled formatters — zero dependencies, Workers-compatible
-- Reports formatted counts and unavailable PMIDs
+- Reports formatted counts and unavailable PMIDs; `ids` is accepted for `pmids`, and a zero-padded PMID resolves as the PMID it spells
 
 ---
 
@@ -125,12 +131,15 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 
 - `similar`, `cited_by`, or `references` for a PMID, in NCBI relevance order, enriched with title, authors, date, and source (or Bookshelf book title and publisher)
 - Falls back to Europe PMC, then OpenAlex, when NCBI can't answer; the response names the provider. Fails with a typed `all_providers_failed` error rather than an empty result
+- `maxResults` up to 50 (`limit` also accepted) with offset pagination; `totalCount` reports the full match count, stated in the header beside the page
+- A zero-padded source PMID resolves as the PMID it spells and is never listed among its own related articles
 
 ---
 
 ### `pubmed_spell_check` <sub>tool</sub>
 
-- Runs a query through NCBI ESpell and returns `original`, `corrected`, and `hasSuggestion`
+- Runs a PubMed query through NCBI ESpell and returns `original`, `corrected`, and `hasSuggestion`; every misspelled token is corrected in one call (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`)
+- Reach for it after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled, then re-run the search with `corrected`
 - A blank or whitespace-only query is rejected rather than sent upstream
 
 ---
@@ -139,13 +148,14 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 
 - Looks up MeSH descriptors by name or free-text term, pinning the exact-heading match to the top of the first page
 - Records carry `meshId` (DescriptorUI), `entrezUid`, and, with `includeDetails` (default on), tree numbers, scope notes, and entry terms
-- `maxResults` up to 50 with offset pagination via `nextOffset`; `totalCount` reports the upstream match count
+- `maxResults` up to 50 (`limit` also accepted) with offset pagination via `nextOffset`; `totalCount` reports the upstream match count
 
 ---
 
 ### `pubmed_lookup_citation` <sub>tool</sub>
 
-- Match on journal, year, volume, first page, and/or author — at least one field, more fields for better precision; up to 25 per call
+- Match on journal, year, volume, first page, and/or author — journal or year required, more fields for better precision
+- `citations` takes an array of up to 25 or a single citation object; `citation` is accepted for it
 - Pipes and line breaks are rejected at the schema (ECitMatch's wire format is pipe-delimited); the free-form `key` label is exempt
 - Explicit `matched`, `not_found`, and `ambiguous` statuses with recovery detail
 
@@ -155,7 +165,8 @@ The biomedical literature via NCBI's E-utilities, PubMed Central, and Europe PMC
 
 - Up to 50 DOIs, PMIDs, or PMCIDs per call, all one type; only PMC-indexed articles resolve
 - One id per element — a packed `"23193287,37952131"` is rejected rather than expanded
-- Per-id success/error rows; a partial batch never fails as a whole
+- One success/error row per submitted element, in order, with `requestedId` exactly as sent — repeats, a bare-digit PMCID, and a DOI's casing included; a partial batch never fails as a whole
+- A zero-padded PMID resolves as the PMID it spells
 
 ---
 

package/changelog/2.10.x/2.10.16.md

@@ -0,0 +1,26 @@
+---
+summary: "Normalizes a zero-padded PMID to the PMID it spells across every ID-diffing tool, and adds snake_case/synonym parameter aliases (ids, limit, max_results, citation) across the tool surface."
+breaking: false
+security: false
+---
+
+# 2.10.16 — 2026-09-22
+
+## Added
+
+- **`inputAliases` accept snake_case and near-synonym parameter names**, rewritten to the canonical key before the schema parses and never advertised in `tools/list`: `ids` for `pmids` (`pubmed_fetch_articles`, `pubmed_format_citations`), `limit` for `maxResults`/`pageSize` (`pubmed_search_articles`, `pubmed_find_related`, `pubmed_lookup_mesh`, `pubmed_europepmc_search`), `max_results` for `pageSize` (`pubmed_europepmc_search`), and `citation` for `citations` (`pubmed_lookup_citation`). [#156](https://github.com/cyanheads/pubmed-mcp-server/issues/156)
+
+## Changed
+
+- **`pubmed_search_articles`, `pubmed_find_related`, and `pubmed_europepmc_search` state `totalCount` in the header** (`Returned: 3 of 2924`) instead of the enrichment trailer. It moves from `enrichment` into each tool's `output`, so `structuredContent.totalCount` keeps its value and type. [#147](https://github.com/cyanheads/pubmed-mcp-server/issues/147)
+- **`docType` is rendered only when it marks something other than an ordinary journal article (`citation`)** in `pubmed_search_articles` and `pubmed_find_related` summaries. [#146](https://github.com/cyanheads/pubmed-mcp-server/issues/146)
+- **`pubmed_lookup_citation`'s `citations` accepts a single citation object or an array of up to 25**, with a named error for a value that fits neither shape. [#156](https://github.com/cyanheads/pubmed-mcp-server/issues/156)
+- **`pubmed_europepmc_search`'s query description documents that identifier tokens may be quoted inside its source-filter wrapper**, and that a PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`. [#149](https://github.com/cyanheads/pubmed-mcp-server/issues/149)
+- **`pubmed_spell_check`'s description names PubMed and ESpell and states its role as the recovery step after a zero-hit or thin search**, with a worked correction example. [#151](https://github.com/cyanheads/pubmed-mcp-server/issues/151)
+
+## Fixed
+
+- **A zero-padded PMID (`00000001`) is no longer both returned and reported unavailable in the same response.** NCBI reads it as the PMID it spells; `pubmed_fetch_articles`, `pubmed_fetch_fulltext`, `pubmed_format_citations`, `pubmed_find_related`, and `pubmed_convert_ids` now send and compare the canonical form while reporting the caller's own spelling. [#161](https://github.com/cyanheads/pubmed-mcp-server/issues/161)
+- **`pubmed_convert_ids` gives every submitted element its own record, in submission order, under `requestedId` exactly as sent** — a repeated ID, including one DOI in two casings, gets a record per element instead of one shared record; a bare-digit PMCID is reported as sent rather than as `PMC<digits>`; and an element the converter returns nothing for gets an error row instead of disappearing. [#165](https://github.com/cyanheads/pubmed-mcp-server/issues/165)
+- **`pubmed_search_articles`'s blank-query guard now catches a bare field tag (`[pdat]`) or empty parentheses**, which previously passed the check: `[pdat]` reached NCBI as a zero-hit search pointing at `pubmed_spell_check`, and `()` drew NCBI's blank-term error, misread as a retryable outage. Only brackets holding a PubMed field tag are stripped for the check, so `[18F]` and `benzo[a]pyrene` are still searched as text. [#145](https://github.com/cyanheads/pubmed-mcp-server/issues/145)
+- **`pubmed_europepmc_search`'s `searchUrl` now carries the same source filter the search actually ran**, instead of opening an unfiltered query with a different hit count. The reported `query` falls back to that same source-filtered query when Europe PMC echoes none. [#150](https://github.com/cyanheads/pubmed-mcp-server/issues/150)

package/changelog/2.10.x/2.10.17.md

@@ -0,0 +1,19 @@
+---
+summary: "Fixes pubmed_fetch_fulltext body parsing (alternatives figures, titled body-level blocks), word-boundary truncation with per-subsection accounting, Unpaywall title/journal/year, and case-insensitive DOI and zero-padded PMC ID matching."
+breaking: false
+security: false
+---
+
+# 2.10.17 — 2026-09-23
+
+## Fixed
+
+- **`pubmed_fetch_fulltext` reads a figure's or supplementary file's pointer from `<alternatives>`** when it has no direct `<graphic>`/`<media>`, preferring the rendering whose `specific-use` names the web, else the first. Its `href`, and a label or caption hung on that pointer, are no longer lost. [#142](https://github.com/cyanheads/pubmed-mcp-server/issues/142)
+- **Character-budget cuts end at the last word boundary inside the allowance**, in sections and Unpaywall bodies alike; a single token longer than the allowance is still cut at it. In `truncate` mode every subsection past the cut is dropped and counted in `omittedSections`, where only whole top-level sections were before; `outline` mode keeps those headings and marks them in `content[]`. The `truncation` ledger lists a shortened section's `subsections` with their own accounting, and each entry carries its `label`. [#143](https://github.com/cyanheads/pubmed-mcp-server/issues/143)
+- **Unpaywall articles carry a `title`**, from Unpaywall's own DOI record, else the Europe PMC record the chain searched, else — for HTML content only — the page's own title, **plus `journalName` and `year`** when Unpaywall's record has them. [#144](https://github.com/cyanheads/pubmed-mcp-server/issues/144)
+- **A titled list, definition list, or boxed text sitting outside any `<sec>`, or alone inside an untitled one, becomes a section under its own title** instead of an untitled block with no heading to separate it from its neighbors. A figure or table inside a titled box names that section as its `sectionTitle`, so a `sections` filter on the box keeps them. [#148](https://github.com/cyanheads/pubmed-mcp-server/issues/148), [#169](https://github.com/cyanheads/pubmed-mcp-server/issues/169)
+- **Every section gets a heading in `content[]`**: an untitled one is headed `untitled section` and a label-only one by its label, the same name its truncation-ledger line uses, and section titles are Markdown-escaped in both places. [#148](https://github.com/cyanheads/pubmed-mcp-server/issues/148), [#169](https://github.com/cyanheads/pubmed-mcp-server/issues/169)
+- **A `<boxed-text>` caption's title and paragraph render as separate lines** instead of running together. [#169](https://github.com/cyanheads/pubmed-mcp-server/issues/169)
+- **DOI input matches case-insensitively**: every casing of one DOI runs the chain once, and `unavailable[]` reports each casing as submitted. Two different DOIs the ID Converter places on one PMC record also share one chain, and that record is fetched once. [#166](https://github.com/cyanheads/pubmed-mcp-server/issues/166)
+- **`errors[]` no longer declares Unpaywall or Europe PMC failure reasons the handler never throws** — both are folded into each id's `triedTiers` instead of propagated. [#168](https://github.com/cyanheads/pubmed-mcp-server/issues/168)
+- **A zero-padded PMC ID (`PMC0123`) resolves as the record it spells** instead of being returned and reported unavailable in the same response. Every spelling of one PMC ID — with or without the `PMC` prefix, in any case, zero-padded or not — is fetched once and reported in `PMC<digits>` form. [#170](https://github.com/cyanheads/pubmed-mcp-server/issues/170)

package/dist/mcp-server/tools/definitions/_schemas.d.ts

@@ -1,5 +1,6 @@
 /**
- * @fileoverview Shared Zod schemas reused across tool definitions.
+ * @fileoverview Shared Zod schemas reused across tool definitions, plus the
+ * normalizer for the PMID form {@link pmidStringSchema} accepts.
  * @module src/mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -11,6 +12,15 @@ import { z } from '@cyanheads/mcp-ts-core';
  * stray prefixes like "PMID:").
  */
 export declare const pmidStringSchema: z.ZodString;
+/**
+ * Canonical form of a PMID {@link pmidStringSchema} accepted: leading zeros
+ * stripped, `0` kept for an all-zero input. NCBI reads `00000001` as PMID 1 and
+ * answers with `<PMID>1</PMID>`, so a handler sends this form upstream and
+ * compares upstream PMIDs against it — the schema itself stays as advertised,
+ * since tool schemas carry no transforms. `0` is still no UID, so an all-zero
+ * list keeps NCBI's empty-list answer. (#161)
+ */
+export declare function normalizePmid(pmid: string): string;
 /**
  * Zod string schema for a single PMC ID. Digits, with the "PMC" prefix optional
  * and case-insensitive — both forms are accepted upstream.

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C;;;;;;GAMG;AACH,eAAO,MAAM,gBAAgB,aAK1B,CAAC;AAEJ;;;GAGG;AACH,eAAO,MAAM,iBAAiB,aAK3B,CAAC;AAEJ;;;;;;;;;GASG;AACH,eAAO,MAAM,eAAe,aAKzB,CAAC"}
+{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C;;;;;;GAMG;AACH,eAAO,MAAM,gBAAgB,aAK1B,CAAC;AAEJ;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAElD;AAED;;;GAGG;AACH,eAAO,MAAM,iBAAiB,aAK3B,CAAC;AAEJ;;;;;;;;;GASG;AACH,eAAO,MAAM,eAAe,aAKzB,CAAC"}

package/dist/mcp-server/tools/definitions/_schemas.js

@@ -1,5 +1,6 @@
 /**
- * @fileoverview Shared Zod schemas reused across tool definitions.
+ * @fileoverview Shared Zod schemas reused across tool definitions, plus the
+ * normalizer for the PMID form {@link pmidStringSchema} accepts.
  * @module src/mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -13,6 +14,17 @@ import { z } from '@cyanheads/mcp-ts-core';
 export const pmidStringSchema = z
     .string()
     .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — provide each PMID separately.');
+/**
+ * Canonical form of a PMID {@link pmidStringSchema} accepted: leading zeros
+ * stripped, `0` kept for an all-zero input. NCBI reads `00000001` as PMID 1 and
+ * answers with `<PMID>1</PMID>`, so a handler sends this form upstream and
+ * compares upstream PMIDs against it — the schema itself stays as advertised,
+ * since tool schemas carry no transforms. `0` is still no UID, so an all-zero
+ * list keeps NCBI's empty-list answer. (#161)
+ */
+export function normalizePmid(pmid) {
+    return pmid.replace(/^0+(?=\d)/, '');
+}
 /**
  * Zod string schema for a single PMC ID. Digits, with the "PMC" prefix optional
  * and case-insensitive — both forms are accepted upstream.

package/dist/mcp-server/tools/definitions/_schemas.js.map

@@ -1 +1 @@
-{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,gBAAgB,GAAG,CAAC;KAC9B,MAAM,EAAE;KACR,KAAK,CACJ,OAAO,EACP,6IAA6I,CAC9I,CAAC;AAEJ;;;GAGG;AACH,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,EAAE;KACR,KAAK,CACJ,gBAAgB,EAChB,2JAA2J,CAC5J,CAAC;AAEJ;;;;;;;;;GASG;AACH,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,MAAM,EAAE;KACR,KAAK,CACJ,wBAAwB,EACxB,0IAA0I,CAC3I,CAAC"}
+{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,gBAAgB,GAAG,CAAC;KAC9B,MAAM,EAAE;KACR,KAAK,CACJ,OAAO,EACP,6IAA6I,CAC9I,CAAC;AAEJ;;;;;;;GAOG;AACH,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,EAAE;KACR,KAAK,CACJ,gBAAgB,EAChB,2JAA2J,CAC5J,CAAC;AAEJ;;;;;;;;;GASG;AACH,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,MAAM,EAAE;KACR,KAAK,CACJ,wBAAwB,EACxB,0IAA0I,CAC3I,CAAC"}

package/dist/mcp-server/tools/definitions/_text.d.ts

@@ -1,8 +1,9 @@
 /**
  * @fileoverview Text helpers shared by the tool definitions: the surrogate-safe
- * character cut used to bound returned text to a budget, and the render-time
- * Markdown escapes applied to upstream strings interpolated into `format()` —
- * one for an inline position, one for a table cell.
+ * character cut and the word-boundary cut built on it, which bound returned text
+ * to a budget, and the render-time Markdown escapes applied to upstream strings
+ * interpolated into `format()` — one for an inline position, one for a table
+ * cell.
  * @module src/mcp-server/tools/definitions/_text
  */
 /**
@@ -21,6 +22,22 @@
  * than assume the allowance was spent exactly. (#93)
  */
 export declare function sliceCodeUnits(text: string, limit: number): string;
+/**
+ * Take at most `limit` UTF-16 code units from `text`, ending at the last word
+ * boundary inside the allowance rather than partway through a word.
+ *
+ * The cut is {@link sliceCodeUnits}' cut, backed off past the partial word it
+ * would end on — unless the character after it is whitespace, in which case
+ * the last word is already whole — with the whitespace before that word
+ * trimmed. A cut is therefore never mid-word and never ends in whitespace.
+ * `limit` stays a ceiling: the result can come back several units short of it,
+ * so callers reporting character counts measure the returned string. (#143)
+ *
+ * An allowance holding no boundary at all — one token longer than the
+ * allowance, such as a sequence or a URL — is cut at the allowance instead:
+ * backing off would return nothing, dropping a field that has text to give.
+ */
+export declare function sliceAtWordBoundary(text: string, limit: number): string;
 /**
  * Escape the Markdown-significant characters in an upstream string that is
  * about to be interpolated *inline* into a `format()` line — a `### `/`#### `

package/dist/mcp-server/tools/definitions/_text.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"_text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAMlE;AA2CD;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAazD;AAED;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAE5D"}
+{"version":3,"file":"_text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAKH;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAMlE;AAQD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAUvE;AA2CD;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAazD;AAED;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAE5D"}

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

@@ -1,8 +1,9 @@
 /**
  * @fileoverview Text helpers shared by the tool definitions: the surrogate-safe
- * character cut used to bound returned text to a budget, and the render-time
- * Markdown escapes applied to upstream strings interpolated into `format()` —
- * one for an inline position, one for a table cell.
+ * character cut and the word-boundary cut built on it, which bound returned text
+ * to a budget, and the render-time Markdown escapes applied to upstream strings
+ * interpolated into `format()` — one for an inline position, one for a table
+ * cell.
  * @module src/mcp-server/tools/definitions/_text
  */
 const HIGH_SURROGATE_FIRST = 0xd800;
@@ -31,6 +32,37 @@ export function sliceCodeUnits(text, limit) {
     const splitsPair = last >= HIGH_SURROGATE_FIRST && last <= HIGH_SURROGATE_LAST;
     return text.slice(0, splitsPair ? limit - 1 : limit);
 }
+/** A whitespace character — the boundary a word-boundary cut backs off to. */
+const WHITESPACE_RE = /\s/;
+const isWhitespace = (text, index) => WHITESPACE_RE.test(text.charAt(index));
+/**
+ * Take at most `limit` UTF-16 code units from `text`, ending at the last word
+ * boundary inside the allowance rather than partway through a word.
+ *
+ * The cut is {@link sliceCodeUnits}' cut, backed off past the partial word it
+ * would end on — unless the character after it is whitespace, in which case
+ * the last word is already whole — with the whitespace before that word
+ * trimmed. A cut is therefore never mid-word and never ends in whitespace.
+ * `limit` stays a ceiling: the result can come back several units short of it,
+ * so callers reporting character counts measure the returned string. (#143)
+ *
+ * An allowance holding no boundary at all — one token longer than the
+ * allowance, such as a sequence or a URL — is cut at the allowance instead:
+ * backing off would return nothing, dropping a field that has text to give.
+ */
+export function sliceAtWordBoundary(text, limit) {
+    const cut = sliceCodeUnits(text, limit);
+    if (cut.length === text.length)
+        return cut;
+    let end = cut.length;
+    if (!isWhitespace(text, end)) {
+        while (end > 0 && !isWhitespace(cut, end - 1))
+            end -= 1;
+    }
+    while (end > 0 && isWhitespace(cut, end - 1))
+        end -= 1;
+    return end > 0 ? cut.slice(0, end) : cut.trimEnd();
+}
 /** Any line break, including the Unicode line and paragraph separators. */
 const LINE_BREAK_RE = /[\r\n\u2028\u2029]+/g;
 /**

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

@@ -1 +1 @@
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+{"version":3,"file":"_text.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,MAAM,oBAAoB,GAAG,MAAM,CAAC;AACpC,MAAM,mBAAmB,GAAG,MAAM,CAAC;AAEnC;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,cAAc,CAAC,IAAY,EAAE,KAAa;IACxD,IAAI,KAAK,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC1B,IAAI,KAAK,IAAI,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,CAAC;IACtC,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IACxC,MAAM,UAAU,GAAG,IAAI,IAAI,oBAAoB,IAAI,IAAI,IAAI,mBAAmB,CAAC;IAC/E,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;AACvD,CAAC;AAED,8EAA8E;AAC9E,MAAM,aAAa,GAAG,IAAI,CAAC;AAE3B,MAAM,YAAY,GAAG,CAAC,IAAY,EAAE,KAAa,EAAW,EAAE,CAC5D,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;AAEzC;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,mBAAmB,CAAC,IAAY,EAAE,KAAa;IAC7D,MAAM,GAAG,GAAG,cAAc,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACxC,IAAI,GAAG,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM;QAAE,OAAO,GAAG,CAAC;IAE3C,IAAI,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC;IACrB,IAAI,CAAC,YAAY,CAAC,IAAI,EAAE,GAAG,CAAC,EAAE,CAAC;QAC7B,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,EAAE,GAAG,GAAG,CAAC,CAAC;YAAE,GAAG,IAAI,CAAC,CAAC;IAC1D,CAAC;IACD,OAAO,GAAG,GAAG,CAAC,IAAI,YAAY,CAAC,GAAG,EAAE,GAAG,GAAG,CAAC,CAAC;QAAE,GAAG,IAAI,CAAC,CAAC;IACvD,OAAO,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;AACrD,CAAC;AAED,2EAA2E;AAC3E,MAAM,aAAa,GAAG,sBAAsB,CAAC;AAC7C;;;;;;GAMG;AACH,MAAM,kBAAkB,GAAG,0BAA0B,CAAC;AACtD,mFAAmF;AACnF,MAAM,YAAY,GAAG,aAAa,CAAC;AAEnC,SAAS,OAAO,CAAC,IAAY,EAAE,SAAiB;IAC9C,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;AAC1C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAAe;IAChD,OAAO,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,CAAC;AACxD,CAAC;AAED;;;;GAIG;AACH,SAAS,mBAAmB,CAAC,IAAY;IACvC,MAAM,SAAS,GAAG,IAAI,GAAG,EAAU,CAAC;IACpC,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;QACvE,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QACzB,MAAM,SAAS,GACb,QAAQ,KAAK,SAAS;YACtB,IAAI,KAAK,SAAS;YAClB,YAAY,CAAC,IAAI,CAAC,QAAQ,CAAC;YAC3B,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC1B,IAAI,CAAC,SAAS;YAAE,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,MAAM,UAAU,oBAAoB,CAAC,IAAY;IAC/C,IAAI,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;IACtE,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC;IACrD,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IAClE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzC,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,KAAK,CAAC,CAAC;IACnE,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IAElE,MAAM,QAAQ,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC;IAC9C,IAAI,QAAQ,CAAC,IAAI,GAAG,CAAC;QAAE,OAAO,OAAO,CAAC;IACtC,OAAO,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,KAAa,EAAE,EAAE,CACzD,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC,CAAC,CAAC,UAAU,CACrD,CAAC;AACJ,CAAC;AAED;;;;;;;;;;;;;;;;;;;GAmBG;AACH,MAAM,UAAU,uBAAuB,CAAC,IAAY;IAClD,OAAO,oBAAoB,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;AAC1D,CAAC"}

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

@@ -1,6 +1,9 @@
 /**
  * @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
  * using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
+ * Every submitted element gets its own record, in submission order, with the
+ * caller's own spelling as `requestedId`; a zero-padded PMID is converted as the
+ * PMID it spells.
  * @module src/mcp-server/tools/definitions/convert-ids.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';

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

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

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

@@ -1,13 +1,16 @@
 /**
  * @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
  * using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
+ * Every submitted element gets its own record, in submission order, with the
+ * caller's own spelling as `requestedId`; a zero-padded PMID is converted as the
+ * PMID it spells.
  * @module src/mcp-server/tools/definitions/convert-ids.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { NCBI_ID_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { conceptMeta, EDAM_ACCESSION, EDAM_ID_MAPPING } from './_concepts.js';
-import { doiStringSchema, pmcidStringSchema, pmidStringSchema } from './_schemas.js';
+import { doiStringSchema, normalizePmid, pmcidStringSchema, pmidStringSchema } from './_schemas.js';
 /**
  * NCBI's PMC ID Converter returns this exact wording for any non-PMC ID — even
  * articles that exist in PubMed and have a recoverable DOI. Rewrite to point
@@ -31,6 +34,24 @@ const ID_ELEMENT_SCHEMAS = {
 };
 /** Cap the offending value echoed back so an oversized element can't bloat the error. */
 const MAX_ECHOED_ID_LENGTH = 120;
+/** A submitted element the converter's answer carries no record for. */
+const NO_RECORD_ERRMSG = 'The PMC ID Converter returned no record for this ID. Article may still exist in PubMed — try pubmed_search_articles.';
+/**
+ * The form the PMC ID Converter echoes an identifier in, so each element can be
+ * matched to its answer: a PMID's canonical digits, a PMCID PMC-prefixed and
+ * upper-cased, a DOI lower-cased — DOIs are case-insensitive, and the converter
+ * echoes one casing for DOIs that differ only in case.
+ */
+function matchKey(id, idType) {
+    switch (idType) {
+        case 'pmid':
+            return normalizePmid(id);
+        case 'pmcid':
+            return (/^\d+$/.test(id) ? `PMC${id}` : id).toUpperCase();
+        case 'doi':
+            return id.toLowerCase();
+    }
+}
 export const convertIdsTool = tool('pubmed_convert_ids', {
     description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
@@ -84,29 +105,40 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             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') });
         }
-        const raw = await getNcbiService().idConvert(input.ids, input.idType, { signal: ctx.signal });
+        // 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)
+        const ids = input.idType === 'pmid' ? [...new Set(input.ids.map(normalizePmid))] : input.ids;
+        const raw = await getNcbiService().idConvert(ids, input.idType, { signal: ctx.signal });
         // NCBI returns pmid as a number in JSON — coerce all ID fields to strings
-        const records = raw.map((r) => {
-            const requestedId = String(r['requested-id']);
+        const conversions = new Map();
+        for (const r of raw) {
+            const requested = String(r['requested-id']);
             let errmsg;
             if (r.errmsg !== undefined) {
                 const original = String(r.errmsg);
                 if (PMC_NOT_FOUND_RE.test(original)) {
-                    ctx.log.debug('Rewriting PMC-not-found errmsg', { requestedId, original });
+                    ctx.log.debug('Rewriting PMC-not-found errmsg', { requestedId: requested, original });
                     errmsg = PMC_NOT_FOUND_REWRITE;
                 }
                 else {
                     errmsg = original;
                 }
             }
-            return {
-                requestedId,
+            conversions.set(matchKey(requested, input.idType), {
                 ...(r.pmid !== undefined && { pmid: String(r.pmid) }),
                 ...(r.pmcid !== undefined && { pmcid: String(r.pmcid) }),
                 ...(r.doi !== undefined && { doi: String(r.doi) }),
                 ...(errmsg !== undefined && { errmsg }),
-            };
-        });
+            });
+        }
+        // The converter answers a repeated identifier once and echoes the form it
+        // was sent in — PMC-prefixed, upper-cased, or with another element's DOI
+        // casing — so each element is matched to its answer by that key and
+        // reported under its own spelling. (#165)
+        const records = input.ids.map((requestedId) => ({
+            requestedId,
+            ...(conversions.get(matchKey(requestedId, input.idType)) ?? { errmsg: NO_RECORD_ERRMSG }),
+        }));
         const totalConverted = records.filter((r) => !r.errmsg).length;
         ctx.log.info('pubmed_convert_ids completed', {
             totalConverted,

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

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

@@ -1,6 +1,8 @@
 /**
  * @fileoverview PubMed fetch tool. Fetches full article metadata by PubMed IDs,
- * including abstracts, authors, journal info, and MeSH terms.
+ * 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`.
  * @module src/mcp-server/tools/definitions/fetch-articles.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';

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

@@ -1 +1 @@
-{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwRjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;;EAkR3F,CAAC"}
+{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwRjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;;EA0R3F,CAAC"}

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

@@ -1,6 +1,8 @@
 /**
  * @fileoverview PubMed fetch tool. Fetches full article metadata by PubMed IDs,
- * including abstracts, authors, journal info, and MeSH terms.
+ * 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`.
  * @module src/mcp-server/tools/definitions/fetch-articles.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -10,7 +12,7 @@ import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseArticleSet } from '../../../services/ncbi/parsing/article-parser.js';
 import { fitWholeItems } from './_budget.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
-import { pmidStringSchema } from './_schemas.js';
+import { normalizePmid, pmidStringSchema } from './_schemas.js';
 import { escapeMarkdownInline } from './_text.js';
 const AuthorSchema = z
     .object({
@@ -225,6 +227,8 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             recovery: 'Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.',
         },
     ],
+    // Never advertised; rewritten to the canonical key before the schema parses. (#156)
+    inputAliases: { ids: 'pmids' },
     input: z.object({
         pmids: z.array(pmidStringSchema).min(1).max(200).describe('PubMed IDs to fetch'),
         includeMesh: z.boolean().default(true).describe('Include MeSH terms'),
@@ -263,7 +267,11 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
     },
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
-        const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
+        // NCBI reads `00000001` as PMID 1 and answers with `<PMID>1</PMID>`, so the
+        // request and the unavailability diff below both use the canonical form;
+        // `unavailablePmids` still reports the caller's own spelling. (#161)
+        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') });
         }
@@ -281,7 +289,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             }),
         }));
         const returnedPmids = new Set(articles.map((a) => a.pmid).filter(Boolean));
-        const unavailable = input.pmids.filter((id) => !returnedPmids.has(id));
+        const unavailable = input.pmids.filter((id) => !returnedPmids.has(normalizePmid(id)));
         // Whole-response budget: fill with complete records in response order and
         // hand the remainder back as PMIDs the caller can re-submit. Without
         // `maxResponseCharacters` nothing is measured and the response is exactly