@cyanheads/pubmed-mcp-server 2.10.1 → 2.10.3

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 (63) hide show
  1. package/AGENTS.md +8 -8
  2. package/CLAUDE.md +8 -8
  3. package/Dockerfile +9 -4
  4. package/LICENSE +1 -1
  5. package/README.md +1 -1
  6. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -1
  8. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +4 -1
  11. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +1 -0
  13. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +11 -2
  15. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +26 -7
  18. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +4 -1
  21. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  22. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  23. package/dist/mcp-server/tools/definitions/search-articles.tool.js +4 -1
  24. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  25. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  26. package/dist/services/europe-pmc/api-client.js +7 -4
  27. package/dist/services/europe-pmc/api-client.js.map +1 -1
  28. package/dist/services/europe-pmc/europe-pmc-service.d.ts +5 -3
  29. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  30. package/dist/services/europe-pmc/europe-pmc-service.js +24 -11
  31. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  32. package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
  33. package/dist/services/europe-pmc/request-queue.js +9 -5
  34. package/dist/services/europe-pmc/request-queue.js.map +1 -1
  35. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  36. package/dist/services/ncbi/api-client.js +8 -2
  37. package/dist/services/ncbi/api-client.js.map +1 -1
  38. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  39. package/dist/services/ncbi/ncbi-service.js +13 -11
  40. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  41. package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
  42. package/dist/services/ncbi/parsing/esummary-parser.js +9 -13
  43. package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
  44. package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
  45. package/dist/services/ncbi/parsing/text-helpers.js +15 -1
  46. package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
  47. package/dist/services/ncbi/request-queue.d.ts.map +1 -1
  48. package/dist/services/ncbi/request-queue.js +10 -6
  49. package/dist/services/ncbi/request-queue.js.map +1 -1
  50. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  51. package/dist/services/ncbi/response-handler.js +29 -23
  52. package/dist/services/ncbi/response-handler.js.map +1 -1
  53. package/dist/services/openalex/api-client.d.ts.map +1 -1
  54. package/dist/services/openalex/api-client.js +7 -5
  55. package/dist/services/openalex/api-client.js.map +1 -1
  56. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  57. package/dist/services/openalex/openalex-service.js +6 -6
  58. package/dist/services/openalex/openalex-service.js.map +1 -1
  59. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  60. package/dist/services/unpaywall/unpaywall-service.js +16 -10
  61. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  62. package/package.json +11 -11
  63. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,8 +1,8 @@
1
1
  # Agent Protocol
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3
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.10.1
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
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+ **Version:** 2.10.3
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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  > **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.
@@ -33,7 +33,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
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  - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
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  - **Use `ctx.log`** for request-scoped logging. No `console` calls.
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  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
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- - **Check `ctx.elicit`** for presence before calling (`if (ctx.elicit) { ... }` — defined only when the client advertised elicitation capability).
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+ - **Need input the caller didn't supply?** `return ctx.requestInput(...)` and read `ctx.inputs` when the handler is re-entered. Never `await` for user input mid-handler.
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  - **Secrets in env vars only** — never hardcoded.
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  - **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
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@@ -164,10 +164,10 @@ Handlers receive a unified `ctx` object. Key properties:
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  | Property | Description |
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  |:---------|:------------|
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- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
167
+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
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168
  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
169
- | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
170
- | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
169
+ | `ctx.requestInput` | Suspend and ask the caller for more input — `return ctx.requestInput({ inputRequests: { key: inputRequired.elicit({ message, requestedSchema }) } })`. Never returns; the handler is re-entered with the answers. Always present. |
170
+ | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. Empty on the first round. |
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  | `ctx.enrich` | Success-path agent context (empty-result notices, query echo, pagination totals) — `ctx.enrich(...)` or `.notice()` / `.total()` / `.echo()` / `.truncated()`. Reaches `structuredContent` and `content[]`; lands only when the definition declares an `enrichment` block (no-op otherwise). |
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  | `ctx.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
173
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  | `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
@@ -293,9 +293,9 @@ Available skills:
293
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  | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
294
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  | `api-auth` | Auth modes, scopes, JWT/OAuth |
295
295
  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
296
- | `api-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
296
+ | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
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  | `api-config` | AppConfig, parseConfig, env vars |
298
- | `api-context` | Context interface, logger, state, progress |
298
+ | `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
299
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  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
300
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  | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
301
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  | `api-services` | LLM, Speech, Graph services |
package/CLAUDE.md CHANGED
@@ -1,8 +1,8 @@
1
1
  # Agent Protocol
2
2
 
3
3
  **Server:** @cyanheads/pubmed-mcp-server
4
- **Version:** 2.10.1
5
- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
4
+ **Version:** 2.10.3
5
+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
6
6
  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
7
7
 
8
8
  > **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.
@@ -33,7 +33,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
33
33
  - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
34
34
  - **Use `ctx.log`** for request-scoped logging. No `console` calls.
35
35
  - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
36
- - **Check `ctx.elicit`** for presence before calling (`if (ctx.elicit) { ... }` — defined only when the client advertised elicitation capability).
36
+ - **Need input the caller didn't supply?** `return ctx.requestInput(...)` and read `ctx.inputs` when the handler is re-entered. Never `await` for user input mid-handler.
37
37
  - **Secrets in env vars only** — never hardcoded.
38
38
  - **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
39
39
 
@@ -164,10 +164,10 @@ Handlers receive a unified `ctx` object. Key properties:
164
164
 
165
165
  | Property | Description |
166
166
  |:---------|:------------|
167
- | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
167
+ | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
168
168
  | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.getMany(keys)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
169
- | `ctx.elicit` | Ask user for structured input — form call `(message, schema)` or `.url(message, url)` for an external link. **Check for presence first:** `if (ctx.elicit) { ... }` |
170
- | `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
169
+ | `ctx.requestInput` | Suspend and ask the caller for more input — `return ctx.requestInput({ inputRequests: { key: inputRequired.elicit({ message, requestedSchema }) } })`. Never returns; the handler is re-entered with the answers. Always present. |
170
+ | `ctx.inputs` | Reader over a retried request's responses — `.accepted(key, schema)`, `.view(key)`, `.state()`, `.dropped`. Empty on the first round. |
171
171
  | `ctx.enrich` | Success-path agent context (empty-result notices, query echo, pagination totals) — `ctx.enrich(...)` or `.notice()` / `.total()` / `.echo()` / `.truncated()`. Reaches `structuredContent` and `content[]`; lands only when the definition declares an `enrichment` block (no-op otherwise). |
172
172
  | `ctx.content` | Non-text content blocks — `.image(data, mimeType)`, `.audio(data, mimeType)`, or `ctx.content(block)` for a raw block. Prepended to `content[]` after `format()`; never enters `structuredContent`. |
173
173
  | `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
@@ -293,9 +293,9 @@ Available skills:
293
293
  | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
294
294
  | `api-auth` | Auth modes, scopes, JWT/OAuth |
295
295
  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
296
- | `api-mirror` | MirrorService: persistent, self-refreshing local SQLite mirror of bulk upstream datasets — Tier 3 opt-in, Node/Bun only |
296
+ | `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
297
297
  | `api-config` | AppConfig, parseConfig, env vars |
298
- | `api-context` | Context interface, logger, state, progress |
298
+ | `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
299
299
  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
300
300
  | `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
301
301
  | `api-services` | LLM, Speech, Graph services |
package/Dockerfile CHANGED
@@ -4,7 +4,7 @@
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4
  # This stage installs all dependencies (including dev), builds the TypeScript
5
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  # source code into JavaScript, and prepares the production assets.
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  # ==============================================================================
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- FROM oven/bun:1.3.14 AS build
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+ FROM oven/bun:1.4.0 AS build
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  WORKDIR /usr/src/app
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@@ -32,7 +32,7 @@ RUN bun run build
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  # application. It uses a slim base image and only includes production
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  # dependencies and build artifacts.
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  # ==============================================================================
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- FROM oven/bun:1.3.14-slim AS production
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+ FROM oven/bun:1.4.0-slim AS production
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  WORKDIR /usr/src/app
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@@ -51,8 +51,13 @@ COPY package.json bun.lock ./
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  # Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
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  # that are not needed in the final production image.
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+ # `--omit=peer` drops the framework's optional peer tiers (test runner, service
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+ # SDKs, parsers) that Bun would otherwise auto-install. Anything this server
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+ # actually imports belongs in its own `dependencies`, so nothing needed at
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+ # runtime is lost. The OTEL step below carries the same flag — without it, that
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+ # install re-resolves the graph and pulls every optional peer back in.
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  RUN --mount=type=cache,target=/root/.bun/install/cache \
55
- bun install --production --frozen-lockfile --ignore-scripts
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+ bun install --production --omit=peer --frozen-lockfile --ignore-scripts
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  # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
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  # These are not bundled by default to keep the base image lean. Enable at build time
@@ -60,7 +65,7 @@ RUN --mount=type=cache,target=/root/.bun/install/cache \
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  ARG OTEL_ENABLED=true
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  RUN --mount=type=cache,target=/root/.bun/install/cache \
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  if [ "$OTEL_ENABLED" = "true" ]; then \
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- bun add --omit=dev --ignore-scripts @hono/otel \
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+ bun add --omit=dev --omit=peer --ignore-scripts @hono/otel \
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  @opentelemetry/instrumentation-http \
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  @opentelemetry/exporter-metrics-otlp-http \
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  @opentelemetry/exporter-trace-otlp-http \
package/LICENSE CHANGED
@@ -186,7 +186,7 @@ Apache License
186
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  same "printed page" as the copyright notice for easier
187
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  identification within third-party archives.
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- Copyright 2025 Casey Hand @cyanheads
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+ Copyright 2026 Casey Hand @cyanheads
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  Licensed under the Apache License, Version 2.0 (the "License");
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  you may not use this file except in compliance with the License.
package/README.md CHANGED
@@ -9,7 +9,7 @@
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- [![Version](https://img.shields.io/badge/Version-2.10.1-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-^1.29.0-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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-2.10.3-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/)
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  </div>
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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED
@@ -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;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2GzB,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;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA6GzB,CAAC"}
package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED
@@ -43,7 +43,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
43
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  doi: z
44
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  .string()
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  .optional()
46
- .describe('Digital Object Identifier; absent if no DOI is on record'),
46
+ .describe('Digital Object Identifier, cased as the PMC ID Converter reports it; absent if no DOI is on record. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively.'),
47
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  errmsg: z
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  .string()
49
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  .optional()
package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED
@@ -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;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAsK3F,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;AA8GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAsK3F,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -83,7 +83,10 @@ const FetchedArticleSchema = z
83
83
  affiliations: z.array(z.string()).optional().describe('Deduplicated author affiliations'),
84
84
  authors: z.array(AuthorSchema).optional().describe('Author list'),
85
85
  journalInfo: JournalInfoSchema.optional(),
86
- doi: z.string().optional().describe('DOI'),
86
+ doi: z
87
+ .string()
88
+ .optional()
89
+ .describe("DOI, cased as NCBI reports it (usually the publisher's mixed case). DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_europepmc_search` and `pubmed_europepmc_fetch` (NCBI `10.1056/NEJMoa2212948`, Europe PMC `10.1056/nejmoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch."),
87
90
  pmcId: z.string().optional().describe('PMC ID'),
88
91
  pubmedUrl: z.string().optional().describe('PubMed article URL'),
89
92
  pmcUrl: z.string().optional().describe('PMC full text URL'),
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED
@@ -234,5 +234,6 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
234
234
  readonly retryable: false;
235
235
  }], {
236
236
  readonly notice: z.ZodOptional<z.ZodString>;
237
+ readonly truncated: z.ZodOptional<z.ZodBoolean>;
237
238
  }>;
238
239
  //# sourceMappingURL=fetch-fulltext.tool.d.ts.map
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
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;AAmoB/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2rB5B,CAAC"}
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;AAwoB/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAosB5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -169,7 +169,10 @@ const PmcArticleSchema = z
169
169
  pmcUrl: z.string().optional().describe('PMC URL — derived from `pmcId` when present'),
170
170
  pmid: z.string().optional().describe('PubMed ID'),
171
171
  pubmedUrl: z.string().optional().describe('PubMed URL'),
172
- doi: z.string().optional().describe('DOI'),
172
+ doi: z
173
+ .string()
174
+ .optional()
175
+ .describe('DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.'),
173
176
  title: z.string().optional().describe('Article title'),
174
177
  abstract: z.string().optional().describe('Abstract'),
175
178
  authors: z.array(AuthorSchema).optional().describe('Authors'),
@@ -637,6 +640,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
637
640
  .string()
638
641
  .optional()
639
642
  .describe('Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A budgeted response names the characters returned versus carried and points at `truncation`. Absent when none of those applies.'),
643
+ truncated: z
644
+ .boolean()
645
+ .optional()
646
+ .describe('True when a character budget shortened at least one returned body. Absent when every returned article carries its full post-filter body. The per-article accounting is in `truncation`.'),
640
647
  },
641
648
  async handler(input, ctx) {
642
649
  ctx.log.info('Executing pubmed_fetch_fulltext', {
@@ -1154,8 +1161,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
1154
1161
  const unrecoveredBodyless = [...bodylessInputIds].filter((id) => !recoveredIds.has(id));
1155
1162
  if (unrecoveredBodyless.length > 0)
1156
1163
  notices.push(buildBodylessNotice(unrecoveredBodyless));
1157
- if (truncation)
1164
+ if (truncation) {
1158
1165
  notices.push(buildTruncationNotice(truncation));
1166
+ ctx.enrich({ truncated: true });
1167
+ }
1159
1168
  if (notices.length > 0)
1160
1169
  ctx.enrich.notice(notices.join(' '));
1161
1170
  return {