npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.4 → 2.10.6 - Mend

@cyanheads/pubmed-mcp-server 2.10.4 → 2.10.6

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 (61) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.4
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
+**Version:** 2.10.6
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, 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.
@@ -181,7 +181,7 @@ 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`) bubble freely and don't need declaring.
+**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.
 ```ts
 errors: [
@@ -354,7 +354,7 @@ Directory-based, grouped by minor series via the `.x` semver-wildcard convention
 `agent-notes` is an optional free-form field consumed by agents running the `maintenance` skill downstream — adoption instructions that don't fit the human-facing sections. Omit entirely when there's nothing to say.
-**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries.
+**Section order:** the Keep a Changelog sequence — Added, Changed, Deprecated, Removed, Fixed, Security — then `Dependencies` last. Include only sections with entries.
 **Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.4
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
+**Version:** 2.10.6
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, 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.
@@ -181,7 +181,7 @@ 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`) bubble freely and don't need declaring.
+**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.
 ```ts
 errors: [
@@ -354,7 +354,7 @@ Directory-based, grouped by minor series via the `.x` semver-wildcard convention
 `agent-notes` is an optional free-form field consumed by agents running the `maintenance` skill downstream — adoption instructions that don't fit the human-facing sections. Omit entirely when there's nothing to say.
-**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries.
+**Section order:** the Keep a Changelog sequence — Added, Changed, Deprecated, Removed, Fixed, Security — then `Dependencies` last. Include only sections with entries.
 **Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@
-[![Version](https://img.shields.io/badge/Version-2.10.4-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-2.10.6-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>
@@ -136,6 +136,7 @@ Find articles related to a source article via ELink.
 - Three relationship types: `similar` (content similarity), `cited_by`, `references`
 - Results enriched with title, authors, publication date, and source via ESummary
 - Results returned in NCBI's relevance order
+- Falls back to Europe PMC, then OpenAlex, when NCBI cannot answer; the response names which provider served it. A request no provider can answer fails with a typed `all_providers_failed` error instead of an empty result
 ---
@@ -322,11 +323,12 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http` | `stdio` |
 | `MCP_HTTP_PORT` | HTTP server port | `3010` |
 | `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path where the MCP server is mounted | `/mcp` |
+| `MCP_SESSION_MODE` | HTTP session mode: `stateless`, `stateful`, or `auto` (resolves to `stateful`). This server ships `stateless` — it has no `ctx.requestInput` call sites. | `stateless` |
 | `MCP_PUBLIC_URL` | Public origin override for TLS-terminating reverse-proxy deployments (landing page, Server Card, RFC 9728 metadata). | none |
 | `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |
 | `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |
 | `MCP_GC_PRESSURE_INTERVAL_MS` | Opt-in Bun-only forced-GC pressure loop (ms). Drains the per-request `McpServer`/`McpSessionTransport` cycle under sustained low-traffic HTTP. Recommended starting point if heap growth is observed: `60000`. | `0` (disabled) |
-| `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
+| `LOGS_DIR` | Directory for log files (Node.js only). Relative paths resolve against the application root. | `<app-root>/logs` |
 | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
 | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
 | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |

package/dist/config/server-config.d.ts CHANGED Viewed

@@ -6,18 +6,18 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 declare const ServerConfigSchema: z.ZodObject<{
-    apiKey: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
+    apiKey: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
     toolIdentifier: z.ZodDefault<z.ZodString>;
-    adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
+    adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>, unknown>;
     requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxConcurrent: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    unpaywallEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
+    unpaywallEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>, unknown>;
     unpaywallTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     europepmcEnabled: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
-    europepmcEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
+    europepmcEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>, unknown>;
     europepmcRequestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     europepmcMaxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     europepmcTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;

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

@@ -1,6 +1,7 @@
 /**
- * @fileoverview Text-cutting helper shared by the tool definitions that bound
- * returned text to a character budget.
+ * @fileoverview Text helpers shared by the tool definitions: the surrogate-safe
+ * character cut used to bound returned text to a budget, and the render-time
+ * Markdown escape applied to upstream strings interpolated into `format()`.
  * @module src/mcp-server/tools/definitions/_text
  */
 /**
@@ -19,4 +20,28 @@
  * than assume the allowance was spent exactly. (#93)
  */
 export declare function sliceCodeUnits(text: string, limit: number): string;
+/**
+ * Escape the Markdown-significant characters in an upstream string that is
+ * about to be interpolated *inline* into a `format()` line — a `### `/`#### `
+ * heading or a `**Label:** ` line. Render-time only: the escaped form must
+ * never be written back into `structuredContent`, which is a contract over the
+ * plain-text value. (#102)
+ *
+ * Minimal by design, judged on what the reader actually sees rendered. Every
+ * Markdown construct here needs a partner delimiter to form, so a delimiter is
+ * escaped only when its partner is present: a lone `*` in `5*g`, a lone `~` in
+ * `~250`, and an intraword `_` in `TP53_mutant` are inert and stay legible.
+ * Escaping them would cost a reader of the raw text a stray backslash and buy
+ * nothing. What is escaped: a tag-shaped `<` (raw HTML and autolinks),
+ * pairable `` ` ``/`*`/`~`/`_`, every `[` and `]`, and the backslash itself,
+ * without which a trailing one in the source would neutralize the escape after
+ * it. Brackets get no pairing test: sibling label lines render as one
+ * paragraph, so a lone `[` in one field and a lone `]` in the next would still
+ * form a link.
+ *
+ * Line breaks collapse to a space. That is what keeps the value inline, and
+ * with it the reason `#`, `>`, and `-` need no escaping: they are structural
+ * only at the start of a line, and the value never reaches one.
+ */
+export declare function escapeMarkdownInline(text: string): string;
 //# sourceMappingURL=_text.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"_text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA~~;;;;GAIG~~;AAKH;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAMlE"}
1	+ {"version":3,"file":"_text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAMlE;AA2CD;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAazD"}

package/dist/mcp-server/tools/definitions/_text.js CHANGED Viewed

@@ -1,6 +1,7 @@
 /**
- * @fileoverview Text-cutting helper shared by the tool definitions that bound
- * returned text to a character budget.
+ * @fileoverview Text helpers shared by the tool definitions: the surrogate-safe
+ * character cut used to bound returned text to a budget, and the render-time
+ * Markdown escape applied to upstream strings interpolated into `format()`.
  * @module src/mcp-server/tools/definitions/_text
  */
 const HIGH_SURROGATE_FIRST = 0xd800;
@@ -29,4 +30,79 @@ export function sliceCodeUnits(text, limit) {
     const splitsPair = last >= HIGH_SURROGATE_FIRST && last <= HIGH_SURROGATE_LAST;
     return text.slice(0, splitsPair ? limit - 1 : limit);
 }
+/** Any line break, including the Unicode line and paragraph separators. */
+const LINE_BREAK_RE = /[\r\n\u2028\u2029]+/g;
+/**
+ * A `<` that opens something a Markdown renderer will read as raw HTML or an
+ * autolink: a tag-name start, then a body carrying no further angle bracket,
+ * then a closing `>`. Deliberately the same shape as `MARKUP_TAG_RE` in
+ * `text-helpers.ts` — a `<` with no `>` after it (`n<N`) or one followed by a
+ * digit (`P<0.001`) cannot open a tag and is left alone.
+ */
+const HTML_TAG_OPENER_RE = /<(?=[A-Za-z/!?][^<>]*>)/g;
+/** A character that makes an adjacent `_` intraword, where it cannot emphasize. */
+const WORD_CHAR_RE = /[0-9A-Za-z]/;
+function countOf(text, character) {
+    return text.split(character).length - 1;
+}
+function escapeEvery(text, pattern) {
+    return text.replace(pattern, (match) => `\\${match}`);
+}
+/**
+ * Positions of the `_` characters that could open or close emphasis. CommonMark
+ * forbids intraword `_` emphasis, so an underscore flanked by alphanumerics on
+ * both sides (`TP53_mutant`) is inert and stays unescaped.
+ */
+function pairableUnderscores(text) {
+    const positions = new Set();
+    for (let i = text.indexOf('_'); i !== -1; i = text.indexOf('_', i + 1)) {
+        const previous = text[i - 1];
+        const next = text[i + 1];
+        const intraword = previous !== undefined &&
+            next !== undefined &&
+            WORD_CHAR_RE.test(previous) &&
+            WORD_CHAR_RE.test(next);
+        if (!intraword)
+            positions.add(i);
+    }
+    return positions;
+}
+/**
+ * Escape the Markdown-significant characters in an upstream string that is
+ * about to be interpolated *inline* into a `format()` line — a `### `/`#### `
+ * heading or a `**Label:** ` line. Render-time only: the escaped form must
+ * never be written back into `structuredContent`, which is a contract over the
+ * plain-text value. (#102)
+ *
+ * Minimal by design, judged on what the reader actually sees rendered. Every
+ * Markdown construct here needs a partner delimiter to form, so a delimiter is
+ * escaped only when its partner is present: a lone `*` in `5*g`, a lone `~` in
+ * `~250`, and an intraword `_` in `TP53_mutant` are inert and stay legible.
+ * Escaping them would cost a reader of the raw text a stray backslash and buy
+ * nothing. What is escaped: a tag-shaped `<` (raw HTML and autolinks),
+ * pairable `` ` ``/`*`/`~`/`_`, every `[` and `]`, and the backslash itself,
+ * without which a trailing one in the source would neutralize the escape after
+ * it. Brackets get no pairing test: sibling label lines render as one
+ * paragraph, so a lone `[` in one field and a lone `]` in the next would still
+ * form a link.
+ *
+ * Line breaks collapse to a space. That is what keeps the value inline, and
+ * with it the reason `#`, `>`, and `-` need no escaping: they are structural
+ * only at the start of a line, and the value never reaches one.
+ */
+export function escapeMarkdownInline(text) {
+    let escaped = text.replace(LINE_BREAK_RE, ' ').replace(/\\/g, '\\\\');
+    escaped = escaped.replace(HTML_TAG_OPENER_RE, '\\<');
+    if (countOf(text, '`') >= 2)
+        escaped = escapeEvery(escaped, /`/g);
+    escaped = escapeEvery(escaped, /[[\]]/g);
+    if (countOf(text, '*') >= 2)
+        escaped = escapeEvery(escaped, /\*/g);
+    if (countOf(text, '~') >= 2)
+        escaped = escapeEvery(escaped, /~/g);
+    const pairable = pairableUnderscores(escaped);
+    if (pairable.size < 2)
+        return escaped;
+    return escaped.replace(/_/g, (underscore, index) => pairable.has(index) ? `\\${underscore}` : underscore);
+}
 //# sourceMappingURL=_text.js.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"_text.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_text.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,oBAAoB,GAAG,MAAM,CAAC;AACpC,MAAM,mBAAmB,GAAG,MAAM,CAAC;AAEnC;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,cAAc,CAAC,IAAY,EAAE,KAAa;IACxD,IAAI,KAAK,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC1B,IAAI,KAAK,IAAI,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,CAAC;IACtC,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IACxC,MAAM,UAAU,GAAG,IAAI,IAAI,oBAAoB,IAAI,IAAI,IAAI,mBAAmB,CAAC;IAC/E,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;AACvD,CAAC;AAED,2EAA2E;AAC3E,MAAM,aAAa,GAAG,sBAAsB,CAAC;AAC7C;;;;;;GAMG;AACH,MAAM,kBAAkB,GAAG,0BAA0B,CAAC;AACtD,mFAAmF;AACnF,MAAM,YAAY,GAAG,aAAa,CAAC;AAEnC,SAAS,OAAO,CAAC,IAAY,EAAE,SAAiB;IAC9C,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;AAC1C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAAe;IAChD,OAAO,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,CAAC;AACxD,CAAC;AAED;;;;GAIG;AACH,SAAS,mBAAmB,CAAC,IAAY;IACvC,MAAM,SAAS,GAAG,IAAI,GAAG,EAAU,CAAC;IACpC,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;QACvE,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;QACzB,MAAM,SAAS,GACb,QAAQ,KAAK,SAAS;YACtB,IAAI,KAAK,SAAS;YAClB,YAAY,CAAC,IAAI,CAAC,QAAQ,CAAC;YAC3B,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC1B,IAAI,CAAC,SAAS;YAAE,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,MAAM,UAAU,oBAAoB,CAAC,IAAY;IAC/C,IAAI,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;IACtE,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC;IACrD,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IAClE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzC,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,KAAK,CAAC,CAAC;IACnE,IAAI,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;QAAE,OAAO,GAAG,WAAW,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IAElE,MAAM,QAAQ,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC;IAC9C,IAAI,QAAQ,CAAC,IAAI,GAAG,CAAC;QAAE,OAAO,OAAO,CAAC;IACtC,OAAO,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,KAAa,EAAE,EAAE,CACzD,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC,CAAC,CAAC,UAAU,CACrD,CAAC;AACJ,CAAC"}

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

	@@ -1 +1 @@
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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;AA+GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAwK3F,CAAC"}

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

@@ -11,6 +11,7 @@ import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
+import { escapeMarkdownInline } from './_text.js';
 const AuthorSchema = z
     .object({
     lastName: z.string().optional().describe('Last name'),
@@ -176,7 +177,9 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
         }
         for (const a of result.articles) {
-            lines.push(`\n### ${a.title ?? a.pmid ?? 'Unknown'}`);
+            // Render-time only — `structuredContent.articles[].title` keeps the
+            // plain-text value the NCBI parser produced. (#102)
+            lines.push(`\n### ${escapeMarkdownInline(a.title ?? a.pmid ?? 'Unknown')}`);
             if (a.authors?.length) {
                 lines.push(`\n**Authors (${a.authors.length}):**`);
                 for (const au of a.authors) {

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

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

@@ -30,7 +30,7 @@ import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { getUnpaywallService, } from '../../../services/unpaywall/unpaywall-service.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
-import { sliceCodeUnits } from './_text.js';
+import { escapeMarkdownInline, sliceCodeUnits } from './_text.js';
 function normalizePmcId(id) {
     return id.replace(/^PMC/i, '');
 }
@@ -1683,7 +1683,9 @@ function truncationNote(t) {
     return `\n> Body shortened to fit the requested character budget — ${t.returnedCharacters} of ${t.originalCharacters} characters returned. See \`truncation\` for per-section counts.`;
 }
 function formatPmcArticle(a, lines, truncation) {
-    lines.push(`### ${a.title ?? a.pmcId}`);
+    // Render-time only — `structuredContent.articles[].title` keeps the
+    // plain-text value the JATS parser produced. (#102)
+    lines.push(`### ${escapeMarkdownInline(a.title ?? articleDisplayId(a))}`);
     const sourceLabel = a.viaSource === 'europepmc'
         ? `Europe PMC (structured JATS${a.epmcSource ? `, source: ${a.epmcSource}` : ''})`
         : 'PMC (structured JATS)';
@@ -1765,7 +1767,7 @@ function formatUnpaywallArticle(a, lines, truncation) {
     const formatLabel = a.contentFormat === 'html-markdown'
         ? 'Unpaywall (HTML → Markdown, best-effort)'
         : 'Unpaywall (PDF → plain text)';
-    lines.push(`### ${heading}`);
+    lines.push(`### ${escapeMarkdownInline(heading)}`);
     lines.push(`**Source:** ${formatLabel}`);
     if (a.pmcId)
         lines.push(`**PMCID:** ${a.pmcId}`);