npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.19 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.19 → 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 (84) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.19
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.10`
+**Version:** 2.10.20
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.11`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -259,7 +259,7 @@ src/
       response-handler.ts              # XML response parsing
       types.ts                          # NCBI/PubMed domain types
       parsing/                          # XML parsers (article, esummary, PMC)
-      formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS)
+      formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS, Vancouver)
   mcp-server/
     tools/definitions/                  # 11 tool definitions (*.tool.ts)
     resources/definitions/              # database-info.resource.ts
@@ -343,10 +343,13 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run format` | Auto-fix formatting (safe fixes only) |
 | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
 | `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
+| `bun run test:corpus` | Run only the real-article corpus suite in `tests/corpus/` (`bun run test` includes it) |
+| `bun run corpus:snapshot` | Rewrite each corpus fixture's `expected.md` after an intended output change — review every rewritten snapshot against its `source.xml` before keeping it |
+| `bun run scripts/corpus-add.ts <PMCID>` | Add an openly licensed PMC article (`--kind pubmed <PMID>` for a PubMed record) to the corpus; refuses any license but CC BY, CC BY-SA, CC0, or public domain, and regenerates `tests/corpus/ATTRIBUTION.md` |
 | `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
 | `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 | `bun run lint:mcp` | Validate MCP definitions against spec |
-| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
+| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity, `server.json` npm launch shape, plugin manifests (run by devcheck) |
 | `bun run list-skills` | List skills in `framework-skills/` with name + description |
 | `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
 | `bun run release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.19
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.10`
+**Version:** 2.10.20
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.11`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -259,7 +259,7 @@ src/
       response-handler.ts              # XML response parsing
       types.ts                          # NCBI/PubMed domain types
       parsing/                          # XML parsers (article, esummary, PMC)
-      formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS)
+      formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS, Vancouver)
   mcp-server/
     tools/definitions/                  # 11 tool definitions (*.tool.ts)
     resources/definitions/              # database-info.resource.ts
@@ -343,10 +343,13 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run format` | Auto-fix formatting (safe fixes only) |
 | `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
 | `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
+| `bun run test:corpus` | Run only the real-article corpus suite in `tests/corpus/` (`bun run test` includes it) |
+| `bun run corpus:snapshot` | Rewrite each corpus fixture's `expected.md` after an intended output change — review every rewritten snapshot against its `source.xml` before keeping it |
+| `bun run scripts/corpus-add.ts <PMCID>` | Add an openly licensed PMC article (`--kind pubmed <PMID>` for a PubMed record) to the corpus; refuses any license but CC BY, CC BY-SA, CC0, or public domain, and regenerates `tests/corpus/ATTRIBUTION.md` |
 | `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
 | `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
 | `bun run lint:mcp` | Validate MCP definitions against spec |
-| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
+| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity, `server.json` npm launch shape, plugin manifests (run by devcheck) |
 | `bun run list-skills` | List skills in `framework-skills/` with name + description |
 | `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
 | `bun run release:github` | Create GitHub Release from an annotated tag — enforces `v<VERSION>: <subject>` title, attaches `.mcpb` bundle |

package/Dockerfile CHANGED Viewed

@@ -36,9 +36,10 @@ RUN bun run build
 #
 # Installs the production dependency tree for the target platform. Every step
 # here can run JavaScript — bunfig.toml's security scanner runs as a Bun
-# program, and so does the OTel script — so the stage runs on $BUILDPLATFORM
-# and cross-installs with `--os`/`--cpu`, which pick each platform-specific
-# optional dependency for the target. Only `node_modules` leaves this stage.
+# program, and so do the OTel and musl-prune scripts — so the stage runs on
+# $BUILDPLATFORM and cross-installs with `--os`/`--cpu`, which pick each
+# platform-specific optional dependency for the target. Only `node_modules`
+# leaves this stage.
 #
 # A clean image rather than `FROM build`: the build stage's node_modules holds
 # devDependencies.
@@ -90,6 +91,14 @@ RUN --mount=type=cache,target=/root/.bun/install/cache \
       bun scripts/install-otel.ts --os="$TARGETOS" --cpu="$(cat .bun-cpu)"; \
     fi
+# `--os`/`--cpu` have no libc counterpart, so a native dependency published in
+# glibc and musl variants installs both. The runtime image is Debian (glibc)
+# and never loads the musl copy; the script deletes every package whose own
+# `libc` admits only musl. It follows every install, since a later
+# `bun install` restores what it removes.
+COPY scripts/prune-musl-packages.ts ./scripts/
+RUN bun scripts/prune-musl-packages.ts
 # The seeded scanner served only the installs above; keep it out of the image.
 RUN rm -rf node_modules/@socketsecurity/bun-security-scanner

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-2.10.19-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-^2.1.0-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-v1.4.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.10.20-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-^2.2.0-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-v1.4.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -64,7 +64,7 @@ Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fe
 ### `pubmed_search_articles` <sub>tool</sub>
 - Full PubMed query syntax plus filters (author, journal, MeSH, publication type, language, species, abstract, free full text) and publication/modification/Entrez date ranges
-- Up to 1,000 results per page and offsets up to 9,998; `summaryCount` adds briefs for up to 50 hits
+- Up to 1,000 results per page and offsets up to 9,998, or `maxResults: 0` for the match count alone; `summaryCount` adds briefs for up to 50 hits
 - Reports `totalCount`, the `effectiveQuery` PubMed ran, and the `appliedFilters`
 - Rejects blank filter values, impossible dates, and reversed date ranges before PubMed is called
@@ -80,7 +80,7 @@ Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fe
 ### `pubmed_fetch_fulltext` <sub>tool</sub>
-- One of `pmcids`, `pmids`, or `dois`, up to 10 per call, tried against PMC, then Europe PMC, then Unpaywall (needs `UNPAYWALL_EMAIL`); `viaSource` names the tier that answered
+- `pmcids`, `pmids`, and `dois` in any mix, up to 10 distinct identifiers per call, tried against PMC, then Europe PMC, then Unpaywall (needs `UNPAYWALL_EMAIL`); an article several of them name is fetched and returned once, and `viaSource` names the tier that answered
 - `source: "pmc"` returns sections, tables, and figures; `source: "unpaywall"` returns a best-effort HTML or PDF text body
 - Misses carry a typed `reason` and `triedTiers`; `sections`, `maxCharacters`, `overflowMode`, and `maxResponseCharacters` bound the response, and `truncation` reports what was cut
@@ -96,7 +96,7 @@ Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fe
 ### `pubmed_europepmc_fetch` <sub>tool</sub>
-- Up to 25 records per call, addressed by a search hit's `source` + `epmcId`, with the full abstract; unresolved ids land in `notFound`
+- Up to 25 records per call, addressed by a search hit's `source` + `epmcId`, with the full abstract; unresolved ids land in `notFound`; opt-in `maxResponseCharacters` defers overflow to `deferred.records`
 - Not registered when `EUROPEPMC_ENABLED=false`
 ---
@@ -104,7 +104,7 @@ Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fe
 ### `pubmed_format_citations` <sub>tool</sub>
 - Up to 50 PMIDs per call, in any mix of `apa`, `mla`, `bibtex`, `ris`, and `vancouver`
-- Bookshelf records cite as edited books; PMIDs that can't be fetched are reported as unavailable
+- Bookshelf records cite as edited books, each chapter dated by its own last revision or contribution date; PMIDs that can't be fetched are reported as unavailable
 ---
@@ -131,8 +131,8 @@ Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fe
 ### `pubmed_lookup_citation` <sub>tool</sub>
-- Up to 25 partial citations per call; journal or year is required, and volume, first page, and author sharpen the match
-- Each comes back `matched`, `not_found`, or `ambiguous`, with recovery detail
+- Up to 25 partial citations per call; a journal or a four-digit year is required, and volume, first page, and author sharpen the match
+- Each is matched independently and comes back `matched`, `not_found`, or `ambiguous`, with recovery detail
 ---

package/changelog/2.10.x/2.10.20.md ADDED Viewed

@@ -0,0 +1,63 @@
+---
+summary: "Text-fidelity fixes across full-text JATS, PubMed record, and Europe PMC parsing, with Bookshelf chapters dated by their own dates and pubmed_fetch_fulltext taking pmcids, pmids, and dois in one call."
+breaking: false
+security: false
+---
+# 2.10.20 — 2026-10-04
+## Added
+- **`pubmed_fetch_fulltext` takes `pmcids`, `pmids`, and `dois` together** ([#192](https://github.com/cyanheads/pubmed-mcp-server/issues/192)) — up to 10 distinct identifiers across the three; an article several of them name is fetched and returned once. `deferred.idType` is now optional: a deferral spanning fields lists its ids under `deferred.pmcids` / `pmids` / `dois`.
+- **`pubmed_europepmc_fetch` `maxResponseCharacters`** ([#188](https://github.com/cyanheads/pubmed-mcp-server/issues/188)) — opt-in ceiling for the whole response; records past it are deferred whole, listed in `deferred.records`, and flagged `truncated: true`.
+- **`pubmed_search_articles` `maxResults: 0`** ([#191](https://github.com/cyanheads/pubmed-mcp-server/issues/191)) — a count-only search returning `totalCount` alone.
+- **Input aliases** ([#190](https://github.com/cyanheads/pubmed-mcp-server/issues/190)) — E-utilities and sibling-tool parameter names (`retmax`, `retstart`, `term`, `pageSize`, `maxResults`, and others) are rewritten to each tool's canonical key on `pubmed_search_articles`, `pubmed_lookup_mesh`, `pubmed_find_related`, `pubmed_europepmc_search`, and `pubmed_spell_check`.
+- **Real-article test corpus** — `tests/corpus/` runs openly licensed PMC and PubMed records against reviewed expected output under `bun run test`; `bun run test:corpus`, `bun run corpus:snapshot`, and `scripts/corpus-add.ts` maintain it.
+## Changed
+- **Input tightening, deliberate:** `pubmed_lookup_citation` rejects a blank or whitespace-only `journal`, `year`, `volume`, `firstPage`, or `authorName`, and a `year` that is not four digits, with -32602 naming the field ([#187](https://github.com/cyanheads/pubmed-mcp-server/issues/187)). Some of these used to return a match, such as a whitespace `year` beside a full journal citation.
+- **Input tightening, deliberate:** `pubmed_fetch_fulltext` rejects a `sections` element of only whitespace or invisible characters with `blank_filter`, and trims surrounding spaces from the terms it keeps ([#186](https://github.com/cyanheads/pubmed-mcp-server/issues/186)). An exactly-empty element is skipped.
+- **PMC ID Converter HTTP 400** surfaces as `invalidParams` (-32602) instead of -32007.
+- **`pubmed_search_articles` `dateRange`** — the `minDate`/`maxDate` descriptions say an empty bound drops the whole range, and the partial-range notice suggests the open lower bound `minDate: "1000"` instead of `"1800"`.
+- **Zero-fit deferral notice** — `pubmed_fetch_articles`, `pubmed_fetch_fulltext`, and `pubmed_europepmc_fetch` name the first record as the one that exceeds `maxResponseCharacters`.
+- **Output descriptions** — `pubmed_fetch_articles` `grants[].acronym` names the funding institute, never the grant; `pubmed_lookup_citation` describes its citation as needing a journal or a four-digit year.
+- **`server.json` npm entries** launch the package bin through `npx` without the `run start:*` arguments, and the `streamable-http` entry sets `MCP_TRANSPORT_TYPE` to `http`.
+- **`.mcpb` bundle** — `.mcpbignore` excludes the build-only root directories `/src/`, `/scripts/`, `/tests/`, `/docs/`, `/coverage/`, `/.github/`, `/.vscode/`, and `/.cache/`, so the bundle drops from 11.7 MB to 10.7 MB and carries no corpus fixtures. The scaffold gap is tracked in [cyanheads/mcp-ts-core#508](https://github.com/cyanheads/mcp-ts-core/issues/508).
+- **Framework 0.13.11 adoption** — the Docker image prunes musl-only packages (`scripts/prune-musl-packages.ts`); devcheck's TODO and tracked-secret scans, `lint:packaging` check 16, per-language CodeQL jobs, `.env*` ignore rules, and the `framework-skills/` sync follow the framework.
+- **Docs** — the README MCP SDK badge reads `^2.2.0` (was `^2.1.0`), and the `CLAUDE.md`/`AGENTS.md` Commands table gains the corpus commands and describes `lint:packaging`'s current checks.
+## Fixed
+- **Europe PMC text** ([#181](https://github.com/cyanheads/pubmed-mcp-server/issues/181), [#195](https://github.com/cyanheads/pubmed-mcp-server/issues/195)) — entity-encoded formatting tags (`&lt;i&gt;`) are stripped; a formatting tag right after `.`, `:`, `!`, or `?` reads as a space, so bold or italic abstract headings no longer fuse into the next sentence; PubMed's `<or=` notation is kept as text.
+- **`openalex_invalid_response`** survives exhausted retries instead of being re-stamped `openalex_unreachable` ([#182](https://github.com/cyanheads/pubmed-mcp-server/issues/182)).
+- **Bookshelf chapter dates** ([#189](https://github.com/cyanheads/pubmed-mcp-server/issues/189)) — `pubmed_format_citations` dates a chapter by its last revision, else its contribution, never the book's start year; Vancouver prints both, RIS adds `DA`, and a book still being updated prints an open range (`2000-`), as `pubmed_fetch_articles` `content[]` does (`2000–`). A publisher name that ends in a period (`MDText.com, Inc.`) gains no second one.
+- **Bookshelf chapter summaries** ([#199](https://github.com/cyanheads/pubmed-mcp-server/issues/199)) — `pubDate` on `pubmed_search_articles` and `pubmed_find_related` chapter rows, and the `pubmed_lookup_citation` verification date, come from the chapter's own ESummary `DocDate`.
+- **`pubmed_fetch_articles` Article Dates** — `content[]` zero-pads them for every record (`Electronic 2021-6-8` → `2021-06-08`); `structuredContent` is unchanged.
+- **Nested inline markup** in PubMed titles, abstracts, and keywords — nested `<sup>`/`<sub>`, emphasis inside scripts, and MathML — no longer deletes text or fuses words ([#211](https://github.com/cyanheads/pubmed-mcp-server/issues/211)).
+- **Collective authors** keep their affiliations ([#212](https://github.com/cyanheads/pubmed-mcp-server/issues/212)).
+- **Absent journal fields** are omitted rather than returned as `""` ([#213](https://github.com/cyanheads/pubmed-mcp-server/issues/213)); for a record with no ISO journal abbreviation, `pubmed_format_citations` Vancouver now prints the full journal title where nothing printed before.
+- **A grant with no `GrantID`** shows its acronym beside the agency rather than as the ID ([#214](https://github.com/cyanheads/pubmed-mcp-server/issues/214)).
+- **`pubmed_lookup_citation`** — a journal-less citation ECitMatch cannot match no longer drops every later citation; the rest are re-requested within the call's one deadline and retry budget ([#193](https://github.com/cyanheads/pubmed-mcp-server/issues/193)).
+- **`pubmed_lookup_citation`** reads an integer `year` in a lone citation object as its decimal string ([#198](https://github.com/cyanheads/pubmed-mcp-server/issues/198)), and verification reads ESummary 2.0, so consortium authors join the roster ([#201](https://github.com/cyanheads/pubmed-mcp-server/issues/201)).
+- **JATS table cells and footnotes** keep their line breaks as `\n`, one line per footnote with its label leading, and inline markup is never spaced (`0.108a`); `content[]` joins those lines with ` · ` ([#185](https://github.com/cyanheads/pubmed-mcp-server/issues/185)). In titles, captions, affiliations, and section prose, a `<break/>`, a sibling `<p>` or `<fn>`, or a `<label>` beside its text reads as one space (`1 Division of …`, not `1Division of …`), and a `simple` list keeps each item's label.
+- **JATS affiliations** inside `<contrib-group>` or `<contrib>` are read ([#196](https://github.com/cyanheads/pubmed-mcp-server/issues/196)), and `content[]` lists them as `- ` bullets instead of a numbered list, so a deposited label isn't numbered twice.
+- **Adjacent citation markers** read `[1,2,3,4]`, not `[1234]` ([#197](https://github.com/cyanheads/pubmed-mcp-server/issues/197)).
+- **Nested lists** sit below their parent item, and prose after a nested list keeps its place ([#200](https://github.com/cyanheads/pubmed-mcp-server/issues/200), [#203](https://github.com/cyanheads/pubmed-mcp-server/issues/203)).
+- **Abstracts** — a list starts on its own line ([#202](https://github.com/cyanheads/pubmed-mcp-server/issues/202)), text beside a `<sec>` is kept ([#204](https://github.com/cyanheads/pubmed-mcp-server/issues/204)), and a section title with its own closing punctuation gains no second colon ([#205](https://github.com/cyanheads/pubmed-mcp-server/issues/205)).
+- **Institution ids** (ROR, GRID, Funder DOIs) no longer fuse onto institution names in affiliations and funding statements ([#208](https://github.com/cyanheads/pubmed-mcp-server/issues/208)).
+- **References** — unseparated author names gain `, `, an empty `<etal/>` reads `et al.`, page ranges read `56–71`, and volume and issue `16(1)`; `references[].label` drops its enclosing brackets (`[19]` → `19`) ([#209](https://github.com/cyanheads/pubmed-mcp-server/issues/209)).
+- **Boxed text** opens with a `[Box: …]` line and closes with `[End of box]` ([#210](https://github.com/cyanheads/pubmed-mcp-server/issues/210)).
+## Dependencies
+- `@cyanheads/mcp-ts-core` ^0.13.10 → ^0.13.11
+- `fast-xml-parser` ^5.11.1 → ^5.11.2
+- `sanitize-html` ^2.17.7 → ^2.18.0
+- `@biomejs/biome` ^2.5.14 → ^2.5.15 (dev)
+- `@types/node` ^26.6.2 → ^26.6.3 (dev)
+- `@types/sanitize-html` ^2.16.1 → ^2.16.2 (dev)
+- `@vitest/coverage-istanbul` ^5.0.1 → ^5.0.3 (dev)
+- `ignore` ^7.0.10 → ^7.0.11 (dev)
+- `tsc-alias` ^1.9.5 → ^1.9.7 (dev)
+- `vitest` ^5.0.1 → ^5.0.3 (dev)

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

	@@ -1 +1 @@
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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. */

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

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

@@ -149,7 +149,10 @@ 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'),
 })
@@ -213,7 +216,10 @@ const FetchedArticleSchema = z
     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
@@ -429,10 +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} (${range})`
@@ -509,8 +516,13 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             if (a.grantList?.length) {
                 lines.push(`\n#### Grants`);
                 for (const g of a.grantList) {
-                    const grantId = g.grantId && g.acronym ? `${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(' — ')}`);
                 }
             }
@@ -526,7 +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 ${deferred.nextDeferredCharacters} — the size of the next deferred article.`;
 }
@@ -556,8 +568,14 @@ function formatPublicationDate(pd) {
         return `${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

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

	@@ -1 +1 @@
1	- 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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`)
@@ -245,56 +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 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: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
+    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 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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