npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.14 → 2.10.15 - Mend

@cyanheads/pubmed-mcp-server 2.10.14 → 2.10.15

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Files changed (57) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.14
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.4`
+**Version:** 2.10.15
+**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
 > **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.
@@ -198,7 +198,7 @@ Handlers receive a unified `ctx` object. Key properties:
 Handlers throw — the framework catches, classifies, and formats.
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text unless the message already contains it verbatim, then closes the text with `(reason <reason> · not retryable)`); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Forwarding is lint-enforced per throw site (`error-contract-recovery-unforwarded`). A declared reason the handler never names warns as `error-contract-unthrown` — entries the service layer throws carry `thrownBy: 'service'` (lint-only metadata; every entry in `src/services/error-contracts.ts`'s service arrays has it), and a tool whose handler catches a service's failures doesn't spread that service's array at all. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
 ```ts
 errors: [
@@ -257,7 +257,7 @@ src/
     ncbi/
       ncbi-service.ts                   # NCBI E-utilities service (init/accessor)
       api-client.ts                     # HTTP client for NCBI API
-      request-queue.ts                  # Rate-limited request queue
+      request-queue.ts                  # Request queue (framework pacer, 429 cooldown)
       response-handler.ts              # XML response parsing
       types.ts                          # NCBI/PubMed domain types
       parsing/                          # XML parsers (article, esummary, PMC)

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.14
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.4`
+**Version:** 2.10.15
+**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
 > **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.
@@ -198,7 +198,7 @@ Handlers receive a unified `ctx` object. Key properties:
 Handlers throw — the framework catches, classifies, and formats.
-**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text unless the message already contains it verbatim, then closes the text with `(reason <reason> · not retryable)`); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Forwarding is lint-enforced per throw site (`error-contract-recovery-unforwarded`). A declared reason the handler never names warns as `error-contract-unthrown` — entries the service layer throws carry `thrownBy: 'service'` (lint-only metadata; every entry in `src/services/error-contracts.ts`'s service arrays has it), and a tool whose handler catches a service's failures doesn't spread that service's array at all. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
 ```ts
 errors: [
@@ -257,7 +257,7 @@ src/
     ncbi/
       ncbi-service.ts                   # NCBI E-utilities service (init/accessor)
       api-client.ts                     # HTTP client for NCBI API
-      request-queue.ts                  # Rate-limited request queue
+      request-queue.ts                  # Request queue (framework pacer, 429 cooldown)
       response-handler.ts              # XML response parsing
       types.ts                          # NCBI/PubMed domain types
       parsing/                          # XML parsers (article, esummary, PMC)

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@
-[![Version](https://img.shields.io/badge/Version-2.10.14-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-2.10.15-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -181,7 +181,7 @@ Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): s
 PubMed-specific:
 - Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
-- Sequential request queue with configurable delay for NCBI rate limit compliance
+- Shared NCBI request queue — paced request starts, capped concurrency, a cooldown that holds every caller after an NCBI 429, and one deadline covering queue wait and retries
 - NCBI-specific XML parser with `isArray` hints for PubMed's inconsistent XML structure
 - Hand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) — zero deps, Workers-compatible
@@ -316,7 +316,7 @@ Key environment variables:
 | `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` |
-| `NCBI_TOTAL_DEADLINE_MS` | Total deadline across all retry attempts for one NCBI call, in ms | `60000` |
+| `NCBI_TOTAL_DEADLINE_MS` | Total deadline for one NCBI call — queue wait, retry attempts, and backoff — in ms. A call the queue cannot start before it is rejected at once | `60000` |
 | `UNPAYWALL_EMAIL` | Contact email for Unpaywall. When set, `pubmed_fetch_fulltext` falls back to Unpaywall open-access copies for non-PMC DOIs | none |
 | `UNPAYWALL_TIMEOUT_MS` | Per-request HTTP timeout for Unpaywall lookups and content fetches, in ms | `20000` |
 | `EUROPEPMC_ENABLED` | Enable Europe PMC search tool and the `pubmed_fetch_fulltext` JATS fallback chain. Set `false` to disable all EPMC calls and skip tool registration. | `true` |

package/changelog/2.10.x/2.10.14.md CHANGED Viewed

@@ -23,6 +23,7 @@ security: true
 - `@cyanheads/mcp-ts-core` ^0.13.0 → ^0.13.4
 - `zod` ^4.6.1 → ^4.6.5
+- `vitest` ^5.0.0 → ^5.0.1
 - `@vitest/coverage-istanbul` ^5.0.0 → ^5.0.1
 - `fast-check` ^4.9.0 → ^4.10.0
 - `tsc-alias` ^1.9.4 → ^1.9.5

package/changelog/2.10.x/2.10.15.md ADDED Viewed

@@ -0,0 +1,28 @@
+---
+summary: "Retries NCBI's proxy_stream() backend relays and Europe PMC's empty-envelope and outage responses instead of surfacing them as caller errors, and closes the NCBI request queue on a 429 for every caller at once."
+breaking: false
+security: false
+---
+# 2.10.15 — 2026-09-22
+## Changed
+- **`pubmed_find_related` declares only `all_providers_failed` in its error contract.** Its handler catches every NCBI, Europe PMC, and OpenAlex failure and reports it inside `data.attempted` or the `coverageFailures` enrichment, so the service reasons it used to spread never reached the caller as `data.reason`.
+- **Tooling and docs:** every service-layer entry in `src/services/error-contracts.ts` carries `thrownBy: 'service'` for mcp-ts-core 0.13.6's `error-contract-unthrown` lint rule; `scripts/lint-mcp.ts` reads its rule options from the `lint` block of `devcheck.config.json`; the README and `.env.example` describe the new queue and deadline, and `.env.example` shows the actual `NCBI_MAX_RETRIES` default (6); `framework-skills/` synced to mcp-ts-core 0.13.6.
+## Fixed
+- **EFetch's `proxy_stream()` backend relays now retry as `ncbi_unreachable`** instead of a bare HTTP 400 — the same envelope NCBI's backend proxy prefixes onto a relayed 502 page or a "Failed to connect to PubOne service" message. [#155](https://github.com/cyanheads/pubmed-mcp-server/issues/155)
+- **An all-invalid EFetch ID list (`id=00000000`, `pubmed`/`pmc` only) now resolves as the empty set NCBI returns for a well-formed but unknown ID**, instead of an `ID list is empty!` error. [#155](https://github.com/cyanheads/pubmed-mcp-server/issues/155)
+- **The NCBI request queue is rebuilt on the framework pacer**, closing one shared cooldown gate for every queued caller on an NCBI 429 instead of each caller retrying independently into the same throttle. The gate holds one second, doubles per consecutive 429 up to 15 seconds, and resets on the first success; a `Retry-After` is honored within the same ceiling. Each retry attempt now re-queues and re-paces under one deadline covering queue wait, attempts, and backoff; a call that cannot start in time sheds as `queue_full` with `retryAfter`. [#157](https://github.com/cyanheads/pubmed-mcp-server/issues/157)
+- **A Europe PMC `/search` 404 now retries and ends as `ServiceUnavailable` with `europepmc_unreachable`** instead of a bare `NotFound` — a failed search is an outage, not "no match"; a genuine zero-hit query stays HTTP 200. A 500, 502, or 503 ends the same way. Only a `ServiceUnavailable` now carries that reason: a Europe PMC call whose retries run out on a `Timeout` (a 504) or a `RateLimited` (a 429) keeps its code with no reason, and a 429 keeps its `retryAfter`. [#152](https://github.com/cyanheads/pubmed-mcp-server/issues/152)
+- **Europe PMC's intermittent empty `{version}` envelope now retries as transient upstream noise** instead of failing fast as invalid input; one that persists through every attempt ends as retryable `europepmc_unreachable`. A `sort` with a key outside the four documented fields or without an `asc`/`desc` direction — each key of a comma-separated sort checked on its own — still fails fast as `europepmc_invalid_input` naming the sort. A non-default `cursorMark` whose envelope persists through the full retry budget ends as `europepmc_invalid_input` naming the cursor. The `pubmed_europepmc_search` `sort` description now covers multi-key sorts and undocumented fields. [#159](https://github.com/cyanheads/pubmed-mcp-server/issues/159)
+## Dependencies
+- `@cyanheads/mcp-ts-core` ^0.13.4 → ^0.13.6
+- `defuddle` ^0.19.3 → ^0.19.4
+- `@biomejs/biome` ^2.5.13 → ^2.5.14
+- `@types/node` ^26.5.1 → ^26.6.2
+- `fast-check` ^4.10.0 → ^4.10.2

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

@@ -24,33 +24,38 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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: 'malformed_id';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;

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

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

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

@@ -107,33 +107,38 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    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: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     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: 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: 'invalid_efetch_response';
     readonly code: JsonRpcErrorCode.SerializationError;

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

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

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

@@ -234,57 +234,66 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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: '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 was unreachable after all retry attempts.';
+    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 (empty query, unknown sort field, malformed parameter).';
-    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
+    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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAu0C/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CAiCT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+2B5B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED Viewed

@@ -37,66 +37,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         pubDate: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: 'queue_full';
-    readonly code: JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
-    readonly retryable: true;
-}, {
-    readonly reason: 'ncbi_unreachable';
-    readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
-    readonly retryable: true;
-}, {
-    readonly reason: 'ncbi_deadline_exceeded';
-    readonly code: JsonRpcErrorCode.Timeout;
-    readonly when: 'Total request deadline expired before NCBI returned a response.';
-    readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
-    readonly retryable: true;
-}, {
-    readonly reason: 'ncbi_invalid_response';
-    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 reason: 'ncbi_resource_not_found';
-    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 reason: 'europepmc_unreachable';
-    readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'Europe PMC was unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
-    readonly retryable: true;
-}, {
-    readonly reason: 'europepmc_invalid_response';
-    readonly code: 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 reason: 'europepmc_invalid_input';
-    readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
-    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
-    readonly retryable: false;
-}, {
-    readonly reason: 'openalex_unreachable';
-    readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: 'OpenAlex was unreachable after all retry attempts.';
-    readonly recovery: 'Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.';
-    readonly retryable: true;
-}, {
-    readonly reason: 'openalex_invalid_response';
-    readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: 'OpenAlex returned a body that could not be parsed (invalid JSON).';
-    readonly recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.';
-    readonly retryable: true;
-}, {
     readonly reason: 'all_providers_failed';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'Every provider eligible for the requested relationship failed; none answered.';

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAsB,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AA4U/F,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAad,sBAAsB;;mBAExB,+EAA+E;uBAEnF,qMAAqM;;;;;;;;;;;;;;;;;;EA6f3M,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -8,7 +8,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { configurationError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { EUROPEPMC_SERVICE_ERRORS, NCBI_SERVICE_ERRORS, OPENALEX_SERVICE_ERRORS, } from '../../../services/error-contracts.js';
+import { EUROPEPMC_SERVICE_ERRORS, OPENALEX_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
@@ -233,10 +233,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/find-related.tool.ts',
+    // The handler catches every provider and ESummary failure, so no service
+    // reason reaches the caller as the top-level `data.reason`; each surfaces
+    // nested in `data.attempted` or the `coverageFailures` enrichment instead.
     errors: [
-        ...NCBI_SERVICE_ERRORS,
-        ...EUROPEPMC_SERVICE_ERRORS,
-        ...OPENALEX_SERVICE_ERRORS,
         {
             reason: 'all_providers_failed',
             code: JsonRpcErrorCode.ServiceUnavailable,

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

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

@@ -31,33 +31,38 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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 notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA2H9B,CAAC"}
1	+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2H9B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts CHANGED Viewed

@@ -42,32 +42,37 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
 }, z.core.$strip>, readonly [{
     readonly reason: 'queue_full';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: import("@cyanheads/mcp-ts-core/errors").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 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';
 }], undefined>;
 //# sourceMappingURL=lookup-citation.tool.d.ts.map