@cyanheads/pubmed-mcp-server 2.10.16 → 2.10.18

package/AGENTS.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.16
+**Version:** 2.10.18
 **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
 
@@ -115,7 +115,7 @@ const ServerConfigSchema = z.object({
   apiKey: z.string().optional().describe('NCBI API key'),
   toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
   adminEmail: z.email().optional().describe('Admin contact email'),
-  requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
+  requestDelayMs: z.coerce.number().min(50).max(5000).default(400).describe('Request delay in ms'),
   maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
   timeoutMs: z.coerce.number().min(1000).max(120000).default(30000).describe('Request timeout in ms'),
 });

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.16
+**Version:** 2.10.18
 **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
 
@@ -115,7 +115,7 @@ const ServerConfigSchema = z.object({
   apiKey: z.string().optional().describe('NCBI API key'),
   toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
   adminEmail: z.email().optional().describe('Admin contact email'),
-  requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
+  requestDelayMs: z.coerce.number().min(50).max(5000).default(400).describe('Request delay in ms'),
   maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
   timeoutMs: z.coerce.number().min(1000).max(120000).default(30000).describe('Request timeout in ms'),
 });

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.10.16-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-2.10.18-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>
 
@@ -89,12 +89,14 @@ 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; a zero-padded PMID resolves as the PMID it spells, and `unavailable[].id` keeps your spelling
+- 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
 
 ---
 
@@ -321,7 +323,7 @@ Key environment variables:
 | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
 | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
 | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
-| `NCBI_REQUEST_DELAY_MS` | Minimum gap between NCBI request starts in ms | 334 (100 with key) |
+| `NCBI_REQUEST_DELAY_MS` | Minimum gap between NCBI request starts in ms | 400 (100 with key) |
 | `NCBI_MAX_CONCURRENT` | Max concurrent in-flight NCBI requests | `8` |
 | `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
 | `NCBI_TIMEOUT_MS` | Per-request HTTP timeout in ms | `30000` |

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 — 2026-09-22
+
+## 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/changelog/2.10.x/2.10.18.md

@@ -0,0 +1,14 @@
+---
+summary: "Moves Europe PMC's request queue onto the framework pacer with retries outside it, so a backoff no longer holds a concurrency slot and an upstream Retry-After is honored; also widens the unkeyed NCBI request delay to 400ms and limits openalex_unreachable to exhausted ServiceUnavailable errors."
+breaking: false
+security: false
+---
+
+# 2.10.18 — 2026-09-22
+
+## Fixed
+
+- **Europe PMC's request queue moves onto the framework pacer, with retries outside it.** A backoff no longer holds one of the four concurrency slots, and every attempt waits out the start gap from the last request any caller started. An upstream `Retry-After` now sets the retry wait; one over the 30 s backoff cap fails without another attempt, `retryAfter` included. [#163](https://github.com/cyanheads/pubmed-mcp-server/issues/163)
+- **The unkeyed `NCBI_REQUEST_DELAY_MS` default rises from 334ms to 400ms.** 334ms sat exactly at NCBI's 3 req/s ceiling, so small bursts drew 429s that closed the request queue's cooldown gate. The keyed 100ms default and an explicit override still apply. [#162](https://github.com/cyanheads/pubmed-mcp-server/issues/162)
+- **OpenAlex stamps `openalex_unreachable` only on an exhausted `ServiceUnavailable`.** An exhausted `Timeout` or `RateLimited` keeps its own code with no reason, and every exhausted error keeps its upstream `retryAfter`. [#160](https://github.com/cyanheads/pubmed-mcp-server/issues/160)
+- **`pubmed_find_related` names a provider failure that carries no reason by its code** — `rate_limited` or `timed_out`, not `unclassified_error` — in the coverage summary and the all-providers-failed `data.attempted`. The coverage summary takes such a failure's retryability from its own `retryable` flag. [#160](https://github.com/cyanheads/pubmed-mcp-server/issues/160)

package/dist/config/server-config.d.ts.map

@@ -1 +1 @@
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package/dist/config/server-config.js

@@ -10,7 +10,7 @@ const ServerConfigSchema = z.object({
     apiKey: z.string().optional().describe('NCBI API key'),
     toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
     adminEmail: z.email().optional().describe('Admin contact email'),
-    requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
+    requestDelayMs: z.coerce.number().min(50).max(5000).default(400).describe('Request delay in ms'),
     maxConcurrent: z.coerce
         .number()
         .min(1)
@@ -89,9 +89,13 @@ export function getServerConfig() {
         });
         /**
          * An API key raises NCBI's rate ceiling from ~3 req/s to ~10 req/s. If the
-         * operator hasn't explicitly overridden the delay, tighten from the 334ms
-         * safe default to 100ms when a key is present. A set-but-blank delay counts
+         * operator hasn't explicitly overridden the delay, tighten from the 400ms
+         * keyless default to 100ms when a key is present. A set-but-blank delay counts
          * as not overridden, matching how `parseEnvConfig` reads it.
+         *
+         * The keyless default sits above the 334ms that 3 req/s works out to, leaving
+         * margin for arrival jitter: spaced at exactly the ceiling, a small burst of
+         * concurrent calls draws 429s.
          */
         _config =
             parsed.apiKey && !process.env.NCBI_REQUEST_DELAY_MS?.trim()

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@@ -1 +1 @@
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+{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;IACtD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IACxF,UAAU,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChE,cAAc,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChG,aAAa,EAAE,CAAC,CAAC,MAAM;SACpB,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,wCAAwC,CAAC;IACrD,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACtF,SAAS,EAAE,CAAC,CAAC,MAAM;SAChB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,gCAAgC,CAAC;IAC7C,eAAe,EAAE,CAAC,CAAC,MAAM;SACtB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,mEAAmE,CAAC;IAChF,cAAc,EAAE,CAAC;SACd,KAAK,EAAE;SACP,QAAQ,EAAE;SACV,QAAQ,CAAC,uEAAuE,CAAC;IACpF,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,2EAA2E,CAAC;IACxF,gBAAgB,EAAE,CAAC;SAChB,UAAU,EAAE;SACZ,OAAO,CAAC,IAAI,CAAC;SACb,QAAQ,CACP,uHAAuH,CACxH;IACH,cAAc,EAAE,CAAC;SACd,KAAK,EAAE;SACP,QAAQ,EAAE;SACV,QAAQ,CAAC,sDAAsD,CAAC;IACnE,uBAAuB,EAAE,CAAC,CAAC,MAAM;SAC9B,MAAM,EAAE;SACR,GAAG,CAAC,EAAE,CAAC;SACP,GAAG,CAAC,IAAI,CAAC;SACT,OAAO,CAAC,GAAG,CAAC;SACZ,QAAQ,CAAC,qDAAqD,CAAC;IAClE,mBAAmB,EAAE,CAAC,CAAC,MAAM;SAC1B,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,mDAAmD,CAAC;IAChE,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,sDAAsD,CAAC;CACpE,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,MAAM,GAAG,cAAc,CAAC,kBAAkB,EAAE;YAChD,MAAM,EAAE,cAAc;YACtB,cAAc,EAAE,sBAAsB;YACtC,UAAU,EAAE,kBAAkB;YAC9B,cAAc,EAAE,uBAAuB;YACvC,aAAa,EAAE,qBAAqB;YACpC,UAAU,EAAE,kBAAkB;YAC9B,SAAS,EAAE,iBAAiB;YAC5B,eAAe,EAAE,wBAAwB;YACzC,cAAc,EAAE,iBAAiB;YACjC,kBAAkB,EAAE,sBAAsB;YAC1C,gBAAgB,EAAE,mBAAmB;YACrC,cAAc,EAAE,iBAAiB;YACjC,uBAAuB,EAAE,4BAA4B;YACrD,mBAAmB,EAAE,uBAAuB;YAC5C,kBAAkB,EAAE,sBAAsB;SAC3C,CAAC,CAAC;QACH;;;;;;;;;WASG;QACH,OAAO;YACL,MAAM,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,qBAAqB,EAAE,IAAI,EAAE;gBACzD,CAAC,CAAC,EAAE,GAAG,MAAM,EAAE,cAAc,EAAE,GAAG,EAAE;gBACpC,CAAC,CAAC,MAAM,CAAC;IACf,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,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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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts

@@ -3,19 +3,29 @@
  * three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
  * Accepts three mutually-exclusive input shapes:
  *
- *   - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
- *     EPMC by PMC ID, then to Unpaywall when the DOI is available.
+ *   - `pmcids` — fetch directly by PMC ID, once per record however it is
+ *     spelled (`PMC123`, `pmc123`, `123`, zero-padded `PMC0123`), and reported
+ *     in `PMC<digits>` form. Articles not in PMC fall through to EPMC by PMC ID,
+ *     then to Unpaywall when the DOI is available.
  *   - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
  *     A zero-padded PMID runs as the PMID it spells; `unavailable[]` and
  *     `deferred.ids` report it as the caller wrote it.
  *   - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
  *     then run the chain. DOIs with no PMC counterpart fall through to EPMC
  *     search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
+ *     DOIs are case-insensitive: every casing of one DOI runs the chain once,
+ *     and `unavailable[]` reports each casing as the caller wrote it.
  *
  * 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
- * DTD; `viaSource: 'europepmc'` distinguishes it from PMC EFetch output.
+ * DTD; `viaSource: 'europepmc'` distinguishes it from PMC EFetch output. An
+ * Unpaywall article takes its title from Unpaywall's record, else the Europe
+ * PMC record the chain searched, else (HTML only) the page itself.
+ *
+ * Europe PMC and Unpaywall failures are folded into each id's `triedTiers`
+ * rather than thrown, so the declared `errors[]` covers the NCBI ID routing
+ * alone.
  *
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
  */
@@ -137,6 +147,8 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
         doi: z.ZodString;
         sourceUrl: z.ZodString;
         title: z.ZodOptional<z.ZodString>;
+        journalName: z.ZodOptional<z.ZodString>;
+        year: z.ZodOptional<z.ZodNumber>;
         content: z.ZodString;
         wordCount: z.ZodOptional<z.ZodNumber>;
         totalPages: z.ZodOptional<z.ZodNumber>;
@@ -211,9 +223,17 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
             returnedCharacters: z.ZodNumber;
             sections: z.ZodOptional<z.ZodArray<z.ZodObject<{
                 title: z.ZodOptional<z.ZodString>;
+                label: z.ZodOptional<z.ZodString>;
                 originalCharacters: z.ZodNumber;
                 returnedCharacters: z.ZodNumber;
                 truncated: z.ZodBoolean;
+                subsections: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                    title: z.ZodOptional<z.ZodString>;
+                    label: z.ZodOptional<z.ZodString>;
+                    originalCharacters: z.ZodNumber;
+                    returnedCharacters: z.ZodNumber;
+                    truncated: z.ZodBoolean;
+                }, z.core.$strip>>>;
             }, z.core.$strip>>>;
             omittedTables: z.ZodOptional<z.ZodNumber>;
             omittedTableNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -268,34 +288,6 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     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: 'unpaywall_unreachable';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
-    readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
-    readonly retryable: true;
-    readonly thrownBy: 'service';
-}, {
-    readonly reason: 'europepmc_unreachable';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results.';
-    readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
-    readonly retryable: true;
-    readonly thrownBy: 'service';
-}, {
-    readonly reason: 'europepmc_invalid_response';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
-    readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
-    readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
-    readonly retryable: true;
-    readonly thrownBy: 'service';
-}, {
-    readonly reason: 'europepmc_invalid_input';
-    readonly code: import("@cyanheads/mcp-ts-core/errors").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 retryable: false;
-    readonly thrownBy: 'service';
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;

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

@@ -1 +1 @@
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