@cyanheads/pubmed-mcp-server 2.10.13 → 2.10.14

package/changelog/2.9.x/2.9.6.md

@@ -0,0 +1,22 @@
+---
+summary: "Output cleanups: convert_ids accepts mixed PMC/bare-digit batches; europepmc_search and fetch_articles strip leaked markup and decode entities; europepmc_search splits its silent-rejection diagnosis from its recovery hint; lookup_mesh drops non-navigable SCR tree pointers"
+breaking: false
+security: false
+---
+
+# 2.9.6 — 2026-06-18
+
+## Fixed
+
+- **`pubmed_convert_ids` mixed PMCID batches** — `NcbiService.idConvert` now canonicalizes bare-digit PMCIDs to `PMC`+digits before the PMC ID Converter call, so a batch mixing `PMC3531190` and `3531190` resolves like a homogeneous one instead of being rejected wholesale (HTTP 400). The `pmcid` format hint (both `ID_CONVERT_FORMAT_HINTS` and the tool's `ids` `.describe()`) now states bare digits are accepted. ([#73](https://github.com/cyanheads/pubmed-mcp-server/issues/73))
+- **`pubmed_europepmc_search` `abstractSnippet`** — normalized to display-ready plain text via a new `toDisplayText` helper: strips structural JATS/HTML tags, decodes HTML entities, and removes soft hyphens (U+00AD) before truncation, so the snippet budget holds text rather than markup and stray soft hyphens don't corrupt token matching. ([#74](https://github.com/cyanheads/pubmed-mcp-server/issues/74))
+- **`pubmed_fetch_articles` `grantList`** — `extractGrants` now decodes the residual `&` that NCBI's double-encoding leaves after the XML parser's single decode pass, so `grantId`/`acronym`/`agency`/`country` surface as `CSR&D` rather than `CSR&D`. ([#74](https://github.com/cyanheads/pubmed-mcp-server/issues/74))
+- **`pubmed_europepmc_search` silent-rejection error** — the version-only-envelope throw now passes a distinct diagnosis as the message and an actionable next step as `recovery.hint`, instead of the same string for both. Previously the framework rendered byte-identical `Error:`/`Recovery:` blocks. ([#75](https://github.com/cyanheads/pubmed-mcp-server/issues/75))
+- **`pubmed_lookup_mesh` `treeNumbers`** — `extractTreeNumbers` now drops `@`-prefixed values, which supplementary concept records (SCRs) surface in the `TreeNum` field as non-navigable mapped-heading pointers (e.g. `@218176`). `treeNumbers` now holds only real tree numbers and is omitted for SCRs; its `.describe()` documents this. ([#76](https://github.com/cyanheads/pubmed-mcp-server/issues/76))
+
+## Dependencies
+
+- `defuddle` ^0.18.1 → ^0.19.0
+- `fast-xml-parser` ^5.8.0 → ^5.9.2
+- `vitest` ^4.1.8 → ^4.1.9
+- `@vitest/coverage-istanbul` ^4.1.8 → ^4.1.9

package/changelog/2.9.x/2.9.7.md

@@ -0,0 +1,26 @@
+---
+summary: "Adopt mcp-ts-core 0.10.9: devcheck gains a Dependency Specifiers guard (floating latest/*/dist-tags) and plugin-manifest checks in lint:packaging; fresh-scaffold git guards; 14 skills re-synced; dependency refresh"
+breaking: false
+security: false
+---
+
+# 2.9.7 — 2026-06-20
+
+## Added
+
+- **`Dependency Specifiers` devcheck step** — new `scripts/check-dependency-specifiers.ts` (flag `--no-dep-specifiers`) hard-fails on floating specifiers (`latest`, `*`, `next`/`beta`/`canary`/`rc`) in `package.json`'s dependency sections and `bun.lock`'s `workspaces` map, catching the case where `bun update --latest` writes a literal `latest` dist-tag into the lock and lets the next `bun install` re-resolve past the manifest range. Static and local — runs in the default and `--fast` passes. ([mcp-ts-core#246](https://github.com/cyanheads/mcp-ts-core/issues/246))
+- **Plugin marketplace manifest checks in `lint:packaging`** — `scripts/lint-packaging.ts` check 10 validates `.claude-plugin/plugin.json`, `.codex-plugin/plugin.json`, and `.codex-plugin/mcp.json`: non-empty descriptions, display fields carrying the unscoped machine name, and the `npx -y` install arg carrying the full scoped package name. Gated by the new `devcheck.config.json` `packaging.pluginManifests` flag (default on; set here). ([mcp-ts-core#240](https://github.com/cyanheads/mcp-ts-core/issues/240))
+
+## Changed
+
+- **14 `skills/<name>/SKILL.md` re-synced** from mcp-ts-core 0.10.7–0.10.9 — `metadata.version` bumps and body drift: `add-tool` 2.14→2.15, `api-auth` 1.1→1.2, `api-canvas` 1.6→1.7, `api-config` 1.7→1.8, `api-context` 1.8→1.9, `api-errors` 1.6→1.7, `api-services` 1.3→1.4, `api-telemetry` 1.0→1.2, `field-test` 2.5→2.6, `git-wrapup` 1.2→1.4, `orchestrations` 1.3→1.4, `polish-docs-meta` 2.7→2.9, `report-issue-local` 1.5→1.6, `tool-defs-analysis` 1.2→1.3.
+
+## Fixed
+
+- **Fresh-scaffold devcheck guards** — `devcheck.ts` (TODOs/FIXMEs, Tracked Secrets, Framework Antipatterns), `check-framework-antipatterns.ts`, and `build-changelog.ts --check` now skip cleanly when `.git` is absent, and `check-skill-versions.ts` skips a `SKILL.md` deleted from the worktree, instead of exiting 128 / crashing with ENOENT. ([mcp-ts-core#242](https://github.com/cyanheads/mcp-ts-core/issues/242), [#243](https://github.com/cyanheads/mcp-ts-core/issues/243), [#237](https://github.com/cyanheads/mcp-ts-core/issues/237))
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` ^0.10.6 → ^0.10.9
+- `fast-xml-parser` ^5.9.2 → ^5.9.3
+- `@types/node` ^25.9.3 → ^26.0.0

package/changelog/2.9.x/2.9.8.md

@@ -0,0 +1,15 @@
+---
+summary: "pubmed_fetch_fulltext surfaces a recovery notice when a sections filter removes every body section from an article that had one — naming the requested terms and affected article ids, still returning the article; detected on both the PMC and Europe PMC paths. Adopts mcp-ts-core 0.10.10."
+breaking: false
+security: false
+---
+
+# 2.9.8 — 2026-06-30
+
+## Added
+
+- **`pubmed_fetch_fulltext` section-filter-miss notice** — when a `sections` filter removes every body section from an article that had sections upstream, the tool surfaces a recovery notice via a new `enrichment.notice` block (emitted through `ctx.enrich.notice`) instead of silently returning an empty body. The notice names the requested section terms and the affected article id(s), distinguishes a filtered-empty body from one absent upstream, and suggests retrying without `sections` or filtering on broader headings (Introduction, Methods, Results, Discussion). The article is still returned with its empty body — not an error — and the miss is detected on both the PMC EFetch and Europe PMC paths. ([#80](https://github.com/cyanheads/pubmed-mcp-server/issues/80))
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` ^0.10.9 → ^0.10.10 (framework js-yaml v4→v5 migration and biome 2.5.1; no consumer change — this server installs no js-yaml directly)

package/changelog/2.9.x/2.9.9.md

@@ -0,0 +1,35 @@
+---
+summary: "pubmed_lookup_mesh gets true upstream totalCount plus offset/nextOffset pagination; pubmed_lookup_citation stops false-flagging authors ranked 4th or later; pubmed_spell_check threads ctx.signal into ESpell. Adopts mcp-ts-core 0.11.0."
+breaking: false
+security: false
+---
+
+# 2.9.9 — 2026-07-26
+
+## Added
+
+- **`pubmed_lookup_mesh` offset pagination** — new `offset` input (default `0`) and `nextOffset` output let callers page past the `maxResults` cap; `nextOffset` is omitted on the last page as the end-of-results signal. ([#84](https://github.com/cyanheads/pubmed-mcp-server/issues/84))
+
+## Changed
+
+- **`pubmed_lookup_mesh` `totalCount`** now reports the true upstream match count from `eSearch`'s `count` field instead of the number of records returned on the page. ([#82](https://github.com/cyanheads/pubmed-mcp-server/issues/82))
+
+## Fixed
+
+- **`pubmed_lookup_mesh` pinned exact-match double-serve** — the exact-descriptor match is now held back on every page it ranks into, not just the first; a page consisting solely of the already-served pinned match returns an explanatory `enrichment.notice` instead of an empty or duplicated result. ([#91](https://github.com/cyanheads/pubmed-mcp-server/issues/91))
+- **`pubmed_lookup_citation` false `author_mismatch` warning** — the mismatch check now verifies the queried author against the full author roster (`authorNames`) instead of the `authors` display string, which truncates to three names plus "et al." and was flagging genuine fourth-or-later authors as mismatches. `ESummaryDocumentSummary` parsing and `ParsedBriefSummary` gain an `authorNames: string[]` field alongside the existing `authors` display string. ([#87](https://github.com/cyanheads/pubmed-mcp-server/issues/87))
+- **`pubmed_spell_check` dropped `ctx.signal`** — the handler now passes `{ signal: ctx.signal }` into `eSpell`, so request cancellation reaches the NCBI ESpell call. Also fixes a stale `pubmed_spell` log message to `pubmed_spell_check`. ([#89](https://github.com/cyanheads/pubmed-mcp-server/issues/89))
+- **`pubmed_format_citations` description** — replaced "styles"/"style" with "formats"/"format" for accuracy.
+- **Noisy error-path telemetry on expected 404s** — `expectedStatuses` added to the `fetchWithTimeout` call sites in `src/services/europe-pmc/api-client.ts` (404), `src/services/openalex/api-client.ts` (404), and `src/services/unpaywall/unpaywall-service.ts` (404, 422), so upstream responses these services already treat as expected "not found" outcomes no longer classify as errors.
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` ^0.10.10 → ^0.11.0
+- `typescript` ^6.0.3 → ^7.0.2
+- `bun` (packageManager) 1.3.2 → 1.3.14; `engines.bun` floor relaxed `>=1.3.2` → `>=1.3.0`
+- `@biomejs/biome` ^2.5.0 → ^2.5.5, `@types/node` ^26.0.0 → ^26.1.1, `@vitest/coverage-istanbul`/`vitest` ^4.1.9 → ^4.1.10, `fast-check` ^4.8.0 → ^4.9.0, `ignore` ^7.0.5 → ^7.0.6, `tsc-alias` ^1.8.17 → ^1.9.1
+- `defuddle` ^0.19.0 → ^0.19.2, `fast-xml-parser` ^5.9.3 → ^5.10.1, `linkedom` ^0.18.12 → ^0.18.13, `sanitize-html` ^2.17.5 → ^2.17.6
+- Added `@socketsecurity/bun-security-scanner` ^1.1.2 as a dev dependency, wired as the `bunfig.toml` `[install.security]` scanner and a `devcheck.config.json` known-dep entry
+- New `package.json` `overrides` block pins nested transitive copies: `@hono/node-server` ^2.0.11, `brace-expansion` ^2.1.2, `fast-uri` ^3.1.4, `postcss` ^8.5.22
+- `Dockerfile` — `oven/bun:1.3` → `oven/bun:1.3.14` (build and production stages), `bun install` steps gain `--ignore-scripts` and a BuildKit cache mount on `/root/.bun/install/cache`
+- `bunfig.toml` — `install.minimumReleaseAge` set to 259200s (3 days), excluding `@cyanheads/mcp-ts-core`

package/changelog/template.md

@@ -0,0 +1,151 @@
+---
+# FORMAT REFERENCE — do not edit. Copy this file to
+# `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.8.x/0.8.6.md`)
+# to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
+# with a concrete date.
+
+# Required. One-line GitHub Release-style headline. 350 character cap — a
+# ceiling, not a target. Default short and scannable. Don't pad, don't stitch
+# unrelated changes with commas/semicolons into an inventory — pick the one
+# headline the release is about. Quotes required: unquoted YAML treats
+# `: ` inside the value as a key separator and fails GitHub's strict parser.
+summary: ""
+
+# Set `true` when consumers must change code to upgrade: API removals,
+# signature changes, config renames, behavior changes that break existing
+# usage. Flagged as `Breaking` in the rollup.
+breaking: false
+
+# Set `true` ONLY for a security fix in THIS project's own source code — a
+# vulnerability or hardening in code you ship. A dependency or transitive CVE
+# bump is routine maintenance, NOT a security release: record it under
+# `## Dependencies` (with the advisory ID) and leave this `false`. When true,
+# pairs with the `## Security` section below and flags `Security` in the rollup.
+security: false
+
+# Optional free-form notes for maintenance agents processing this release.
+# Not rendered in CHANGELOG — consumed by agents running `maintenance` on
+# downstream servers. ADOPTION STEPS ONLY — new files to create, fields to
+# populate, one-time migration steps. Never a second rendering of the body:
+# if a body bullet already says it, name the bullet's symbol instead of
+# re-explaining. Omit the field entirely when there's nothing to say.
+# agent-notes: |
+#   <instructions for downstream maintenance agents>
+---
+
+# <version> — YYYY-MM-DD
+
+<!--
+  AUTHORING GUIDE — applies to the new per-version file you create from this
+  template.
+
+  Audience: someone scanning release notes to decide what affects them. Lead
+  each bullet with the symbol or concept name in **bold** so they can skip
+  what's irrelevant and zoom in on what's not.
+
+  Tone: terse, fact-dense, not verbose. Bullet shape: **symbol** + what
+  changed + at most one consumer-facing caveat. One sentence by default, two
+  when the second carries weight — a bullet past ~40 words or three sentences
+  is wrong. The depth lives one hop away: the linked issue carries the why,
+  the commit diff carries the how. The changelog names what changed and what
+  a consumer does about it; a reader who wants mechanism opens the link.
+
+  Model length on THIS guide, never on the previous entry — entries modeled
+  on entries compound.
+
+  Cut (each has shipped as a wall of text; these are the cruft):
+  - History/justification narration — how the bug worked, why the old
+    behavior was wrong. One short clause at most; the issue carries the story.
+  - Design-rationale defense — "chosen over Y because…", "guarding the
+    getter is not enough…". That is the author arguing with a reviewer;
+    reviewers read the PR, not the changelog.
+  - Defensive unchanged-clauses — "X is unchanged", "byte-identical to
+    <prev>". Keep one only where its absence would cause a real misread,
+    as a short parenthetical.
+  - Edge-case inventories — marker lists, not-flagged lists, escape tables.
+    Tests and the issue carry those.
+  - Mechanism walkthroughs (JSDoc, CLAUDE.md/AGENTS.md, or the relevant
+    skill own those), ceremonial framings ("This release introduces…"),
+    backwards-compat paragraphs, file-by-file test enumerations. Prefer
+    code/symbol names over English re-explanations.
+
+  Verified ≠ included: the every-claim-verified-from-the-diff rule bounds
+  the TRUTH of what you write, never the AMOUNT.
+
+  Example — same fact, right size:
+
+    TOO LONG: **`fetchWithTimeout`'s `timeoutMs` bounds the whole exchange**
+    (#341). `fetch` resolves once headers arrive and the deadline was
+    cleared as the helper returned, so a peer that answered promptly and
+    then stalled the stream held the request open indefinitely. A 2xx
+    carrying a body now comes back as a passthrough wrapper that disarms
+    the deadline when the body closes, errors, or is cancelled; …
+    [+90 more words of mechanism and edge cases]
+
+    RIGHT: **`fetchWithTimeout`'s `timeoutMs` now bounds the whole
+    exchange, not just the headers** (#341). A stalled body aborts with
+    the same `Timeout` error; the returned `Response` is a wrapper, so
+    identity assertions (`toBe(response)`) no longer hold.
+
+  Narrative intro: skip by default. Add one short sentence only when the
+  release theme genuinely needs framing the bullets can't carry. When many
+  bullets share one upgrade consequence, state it ONCE — intro line or
+  agent-notes — never per bullet.
+
+  Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
+  Fixed, Security. Include only sections with entries; delete the rest
+  (including the commented-out scaffolding below). Don't ship empty headers.
+
+  Include: every distinct fact a reader needs to adopt or audit the release —
+  new exports, signatures, lint rule IDs, env vars, breaking changes, version
+  bumps on shipped skills. Nothing more.
+
+  Links: link issues, PRs, docs, or skills where they help a reader jump to
+  context. Once per item per entry — don't re-link the same issue in summary,
+  narrative, and bullet. Skip links for inline symbol names; code spans speak
+  for themselves.
+
+  Issue/PR URLs: use full URLs. GitHub's bare `#NN` auto-link only resolves
+  inside its own UI, not in npm reads or local editors.
+
+      [#38](https://github.com/cyanheads/mcp-ts-core/issues/38)   ← issue
+      [#42](https://github.com/cyanheads/mcp-ts-core/pull/42)     ← PR
+
+  Verify numbers exist before linking (`gh issue view NN`, `gh pr view NN`).
+  Never speculate on a future number — `#42` for an upcoming PR silently
+  resolves to whatever real item already owns 42, and timeline previews pull
+  in that unrelated item's metadata.
+
+  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
+  via `gh release create --notes-from-tag`. It is a condensed digest of this
+  entry, never a copy, and its format is owned by the `release-and-publish`
+  skill (step 4, "Create the annotated tag"): a short subject line without the
+  version, flat headline bullets — no Keep-a-Changelog section headers, no
+  gates line — at most one deps line, issue backlinks, and the changelog link
+  last. In release-PR mode the `git-wrapup` skill authors those bullets as the
+  PR body's `## Changes` and the tag copies them.
+-->
+
+## Added
+
+-
+
+## Changed
+
+-
+
+<!-- ## Deprecated
+
+- -->
+
+<!-- ## Removed
+
+- -->
+
+## Fixed
+
+-
+
+<!-- ## Security
+
+- -->

package/dist/index.js

@@ -38,6 +38,7 @@ const tools = [
 await createApp({
     name: 'pubmed-mcp-server',
     title: 'pubmed-mcp-server',
+    sessionMode: 'stateless',
     tools,
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],

package/dist/index.js.map

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package/dist/services/europe-pmc/europe-pmc-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAgBH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAGzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAkDpB;;;;;;;;;GASG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM,EAQpC;IAED;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA6F1E;IAED;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CAgBlC;IAED;;;;;;;;;;OAUG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;;OAUG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;OAKG;YACW,iBAAiB;IAsE/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;OAIG;YACW,SAAS;CAoDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAyB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
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package/dist/services/europe-pmc/europe-pmc-service.js

@@ -13,23 +13,16 @@
  *
  * @module src/services/europe-pmc/europe-pmc-service
  */
-import { internalError, JsonRpcErrorCode, McpError, serializationError, validationError, } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { internalError, McpError, serializationError, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
 import { XMLParser, XMLValidator } from 'fast-xml-parser';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
-import { isTransient } from '../retry-policy.js';
 import { EuropePmcApiClient } from './api-client.js';
 import { EuropePmcRequestQueue } from './request-queue.js';
-/** Retryable transient codes — same set NCBI uses. */
-const RETRYABLE_CODES = new Set([
-    JsonRpcErrorCode.ServiceUnavailable,
-    JsonRpcErrorCode.Timeout,
-    JsonRpcErrorCode.RateLimited,
-]);
 const MAX_BACKOFF_MS = 30_000;
 function abortableSleep(ms, signal) {
     if (!signal)
@@ -352,7 +345,7 @@ export class EuropePmcService {
                     throw signal.reason;
                 if (!(error instanceof McpError))
                     throw error;
-                if (!isTransient(error, RETRYABLE_CODES))
+                if (!defaultIsTransient(error))
                     throw error;
                 if (attempt < this.maxRetries) {
                     const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);

package/dist/services/europe-pmc/europe-pmc-service.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/ncbi-service.d.ts

@@ -43,8 +43,6 @@ export declare class NcbiService {
      * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
      */
     idConvert(ids: string[], idtype?: string, options?: NcbiCallOptions): Promise<IdConvertRecord[]>;
-    /** Error codes that are transient and worth retrying with backoff. */
-    private static readonly RETRYABLE_CODES;
     /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
     private static readonly MAX_BACKOFF_MS;
     /**

package/dist/services/ncbi/ncbi-service.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAA2B,MAAM,uBAAuB,CAAC;AACrF,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgFpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC,CAIZ;IAED,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CA+BxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;;;;;;;OASG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAmE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CA+E5B;IAED,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA4BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA8BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}

package/dist/services/ncbi/ncbi-service.js

@@ -5,10 +5,9 @@
  * @module src/services/ncbi/ncbi-service
  */
 import { internalError, JsonRpcErrorCode, McpError, serializationError, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
-import { isTransient } from '../retry-policy.js';
 import { NcbiApiClient } from './api-client.js';
 import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler, reclassifyNcbiHttpError } from './response-handler.js';
@@ -294,12 +293,6 @@ export class NcbiService {
         }
         return parsed.records ?? [];
     }
-    /** Error codes that are transient and worth retrying with backoff. */
-    static RETRYABLE_CODES = new Set([
-        JsonRpcErrorCode.ServiceUnavailable,
-        JsonRpcErrorCode.Timeout,
-        JsonRpcErrorCode.RateLimited,
-    ]);
     /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
     static MAX_BACKOFF_MS = 30_000;
     /**
@@ -350,7 +343,7 @@ export class NcbiService {
                 if (!(error instanceof McpError)) {
                     throw error;
                 }
-                if (!isTransient(error, NcbiService.RETRYABLE_CODES)) {
+                if (!defaultIsTransient(error)) {
                     throw error;
                 }
                 if (attempt < this.maxRetries) {

package/dist/services/ncbi/ncbi-service.js.map

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package/dist/services/openalex/openalex-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAQH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AAmFpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
+{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAOH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}

package/dist/services/openalex/openalex-service.js

@@ -17,19 +17,12 @@
  *
  * @module src/services/openalex/openalex-service
  */
-import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { internalError, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
-import { isTransient } from '../retry-policy.js';
 import { OpenAlexApiClient } from './api-client.js';
 import { OPENALEX_MAX_FILTER_VALUES, OPENALEX_MAX_PAGE_SIZE, OPENALEX_MAX_UPSTREAM_REQUESTS, } from './types.js';
-/** Transient codes eligible for retry. */
-const RETRYABLE_CODES = new Set([
-    JsonRpcErrorCode.ServiceUnavailable,
-    JsonRpcErrorCode.Timeout,
-    JsonRpcErrorCode.RateLimited,
-]);
 const MAX_BACKOFF_MS = 30_000;
 /** Strip the `https://openalex.org/` prefix an OA ID may carry. */
 function bareOaId(id) {
@@ -218,7 +211,7 @@ export class OpenAlexService {
                     throw signal.reason;
                 if (!(error instanceof McpError))
                     throw error;
-                if (!isTransient(error, RETRYABLE_CODES))
+                if (!defaultIsTransient(error))
                     throw error;
                 if (attempt < this.maxRetries) {
                     const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);

package/dist/services/openalex/openalex-service.js.map

@@ -1 +1 @@
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