npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.3.11 → 2.4.0 - Mend

@cyanheads/pubmed-mcp-server 2.3.11 → 2.4.0

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 (30) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.3.11
+**Version:** 2.4.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **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.
@@ -104,31 +104,36 @@ export const databaseInfoResource = resource('pubmed://database/info', {
 ```ts
 // src/config/server-config.ts — lazy-parsed, separate from framework config
+import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+const emptyAsUndefined = (v: unknown) => (v === '' ? undefined : v);
 const ServerConfigSchema = z.object({
-  apiKey: z.string().optional().describe('NCBI API key'),
-  toolIdentifier: z.string().describe('NCBI tool identifier'),
-  adminEmail: z.email().optional().describe('Admin contact email'),
+  apiKey: z.preprocess(emptyAsUndefined, z.string().optional()).describe('NCBI API key'),
+  toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
+  adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
   requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
-  maxRetries: z.coerce.number().min(0).max(10).default(3).describe('Max retry attempts'),
+  maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
   timeoutMs: z.coerce.number().min(1000).max(120000).default(30000).describe('Request timeout in ms'),
 });
 let _config: z.infer<typeof ServerConfigSchema> | undefined;
 export function getServerConfig(): z.infer<typeof ServerConfigSchema> {
-  if (!_config) {
-    _config = ServerConfigSchema.parse({
-      apiKey: process.env.NCBI_API_KEY || undefined,
-      toolIdentifier: process.env.NCBI_TOOL_IDENTIFIER ?? 'pubmed-mcp-server',
-      adminEmail: process.env.NCBI_ADMIN_EMAIL || undefined,
-      requestDelayMs: process.env.NCBI_REQUEST_DELAY_MS,
-      maxRetries: process.env.NCBI_MAX_RETRIES,
-      timeoutMs: process.env.NCBI_TIMEOUT_MS,
-    });
-  }
+  _config ??= parseEnvConfig(ServerConfigSchema, {
+    apiKey: 'NCBI_API_KEY',
+    toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
+    adminEmail: 'NCBI_ADMIN_EMAIL',
+    requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
+    maxRetries: 'NCBI_MAX_RETRIES',
+    timeoutMs: 'NCBI_TIMEOUT_MS',
+  });
   return _config;
 }
 ```
+`parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`NCBI_REQUEST_DELAY_MS` must be a number) rather than the internal path (`requestDelayMs: expected number`).
 ---
 ## Context

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![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) [![Version](https://img.shields.io/badge/Version-2.3.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-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) [![Version](https://img.shields.io/badge/Version-2.4.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)

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

@@ -6,9 +6,9 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 declare const ServerConfigSchema: z.ZodObject<{
-    apiKey: z.ZodOptional<z.ZodString>;
-    toolIdentifier: z.ZodString;
-    adminEmail: z.ZodOptional<z.ZodEmail>;
+    apiKey: z.ZodPipe<z.ZodTransform<unknown, unknown>, z.ZodOptional<z.ZodString>>;
+    toolIdentifier: z.ZodDefault<z.ZodString>;
+    adminEmail: z.ZodPipe<z.ZodTransform<unknown, unknown>, z.ZodOptional<z.ZodEmail>>;
     requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAE3C~~,QAAA,MAAM,kBAAkB;;;;;;;~~iBAkBtB~~,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,~~CAc9C~~"}
1	+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAU3C,QAAA,MAAM,kBAAkB;;;;;;;iBAYtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAqB9C"}

package/dist/config/server-config.js CHANGED Viewed

@@ -5,18 +5,19 @@
  * @module src/config/server-config
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+/**
+ * Treats an unset env var (`undefined`) and a set-but-empty env var (`""`)
+ * identically. Without this, `NCBI_ADMIN_EMAIL=` would fail `z.email()`
+ * validation instead of being interpreted as "no admin email configured".
+ */
+const emptyAsUndefined = (v) => (v === '' ? undefined : v);
 const ServerConfigSchema = z.object({
-    /** NCBI API key for higher rate limits. Optional but recommended. */
-    apiKey: z.string().optional().describe('NCBI API key'),
-    /** Tool identifier sent with every NCBI request (required by NCBI). */
-    toolIdentifier: z.string().describe('NCBI tool identifier'),
-    /** Admin email sent with every NCBI request (required by NCBI). */
-    adminEmail: z.email().optional().describe('Admin contact email'),
-    /** Minimum delay between NCBI requests in ms. NCBI requires ~334ms without API key. */
+    apiKey: z.preprocess(emptyAsUndefined, z.string().optional()).describe('NCBI API key'),
+    toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
+    adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
     requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
-    /** Maximum retry attempts for failed NCBI requests. */
     maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
-    /** Request timeout in ms. */
     timeoutMs: z.coerce
         .number()
         .min(1000)
@@ -27,16 +28,23 @@ const ServerConfigSchema = z.object({
 let _config;
 export function getServerConfig() {
     if (!_config) {
-        const env = process.env;
-        const hasApiKey = !!env.NCBI_API_KEY;
-        _config = ServerConfigSchema.parse({
-            apiKey: env.NCBI_API_KEY || undefined,
-            toolIdentifier: env.NCBI_TOOL_IDENTIFIER ?? 'pubmed-mcp-server',
-            adminEmail: env.NCBI_ADMIN_EMAIL || undefined,
-            requestDelayMs: env.NCBI_REQUEST_DELAY_MS ?? (hasApiKey ? 100 : 334),
-            maxRetries: env.NCBI_MAX_RETRIES,
-            timeoutMs: env.NCBI_TIMEOUT_MS,
+        const parsed = parseEnvConfig(ServerConfigSchema, {
+            apiKey: 'NCBI_API_KEY',
+            toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
+            adminEmail: 'NCBI_ADMIN_EMAIL',
+            requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
+            maxRetries: 'NCBI_MAX_RETRIES',
+            timeoutMs: 'NCBI_TIMEOUT_MS',
         });
+        /**
+         * An API key raises NCBI's rate ceiling from ~3 req/s to ~10 req/s. If the
+         * operator hasn't explicitly overridden the delay, tighten from the 334ms
+         * safe default to 100ms when a key is present.
+         */
+        _config =
+            parsed.apiKey && process.env.NCBI_REQUEST_DELAY_MS === undefined
+                ? { ...parsed, requestDelayMs: 100 }
+                : parsed;
     }
     return _config;
 }

package/dist/config/server-config.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,CAAC,CAAU,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAEpE,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC,CAAC,UAAU,CAAC,gBAAgB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,cAAc,CAAC;IACtF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IACxF,UAAU,EAAE,CAAC,CAAC,UAAU,CAAC,gBAAgB,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChG,cAAc,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;IAChG,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACtF,SAAS,EAAE,CAAC,CAAC,MAAM;SAChB,MAAM,EAAE;SACR,GAAG,CAAC,IAAI,CAAC;SACT,GAAG,CAAC,MAAM,CAAC;SACX,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,uBAAuB,CAAC;CACrC,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,MAAM,GAAG,cAAc,CAAC,kBAAkB,EAAE;YAChD,MAAM,EAAE,cAAc;YACtB,cAAc,EAAE,sBAAsB;YACtC,UAAU,EAAE,kBAAkB;YAC9B,cAAc,EAAE,uBAAuB;YACvC,UAAU,EAAE,kBAAkB;YAC9B,SAAS,EAAE,iBAAiB;SAC7B,CAAC,CAAC;QACH;;;;WAIG;QACH,OAAO;YACL,MAAM,CAAC,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,qBAAqB,KAAK,SAAS;gBAC9D,CAAC,CAAC,EAAE,GAAG,MAAM,EAAE,cAAc,EAAE,GAAG,EAAE;gBACpC,CAAC,CAAC,MAAM,CAAC;IACf,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/mcp-server/tools/definitions/_schemas.d.ts ADDED Viewed

@@ -0,0 +1,14 @@
+/**
+ * @fileoverview Shared Zod schemas reused across tool definitions.
+ * @module src/mcp-server/tools/definitions/_schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Zod string schema for a single PubMed ID. Accepts only digit characters.
+ * The message is intentionally actionable so callers can self-correct without
+ * inspecting the regex — names the domain, shows an example, and lists the
+ * common failure modes we've seen in the wild (whitespace, comma-joined IDs,
+ * stray prefixes like "PMID:").
+ */
+export declare const pmidStringSchema: z.ZodString;
+//# sourceMappingURL=_schemas.d.ts.map

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C;;;;;;GAMG;AACH,eAAO,MAAM,gBAAgB,aAK1B,CAAC"}

package/dist/mcp-server/tools/definitions/_schemas.js ADDED Viewed

@@ -0,0 +1,16 @@
+/**
+ * @fileoverview Shared Zod schemas reused across tool definitions.
+ * @module src/mcp-server/tools/definitions/_schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Zod string schema for a single PubMed ID. Accepts only digit characters.
+ * The message is intentionally actionable so callers can self-correct without
+ * inspecting the regex — names the domain, shows an example, and lists the
+ * common failure modes we've seen in the wild (whitespace, comma-joined IDs,
+ * stray prefixes like "PMID:").
+ */
+export const pmidStringSchema = z
+    .string()
+    .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — provide each PMID separately.');
+//# sourceMappingURL=_schemas.js.map

package/dist/mcp-server/tools/definitions/_schemas.js.map ADDED Viewed

	@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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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;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBAkFzB,CAAC"}

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

@@ -53,21 +53,24 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
         return { records, totalConverted, totalSubmitted: input.ids.length };
     },
     format: (result) => {
+        const successful = result.records.filter((r) => !r.errmsg);
+        const errored = result.records.filter((r) => r.errmsg);
         const lines = [
             `## ID Conversion Results`,
             `**Converted:** ${result.totalConverted}/${result.totalSubmitted}`,
-            '',
-            '| Requested ID | PMID | PMCID | DOI |',
-            '|:---|:---|:---|:---|',
         ];
-        for (const r of result.records) {
-            if (r.errmsg) {
-                lines.push(`| ${r.requestedId} | - | - | Error: ${r.errmsg} |`);
-            }
-            else {
+        if (successful.length > 0) {
+            lines.push('', '| Requested ID | PMID | PMCID | DOI |', '|:---|:---|:---|:---|');
+            for (const r of successful) {
                 lines.push(`| ${r.requestedId} | ${r.pmid ?? '-'} | ${r.pmcid ?? '-'} | ${r.doi ?? '-'} |`);
             }
         }
+        if (errored.length > 0) {
+            lines.push('', '### Errors');
+            for (const r of errored) {
+                lines.push(`- **${r.requestedId}:** ${r.errmsg}`);
+            }
+        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });

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

	@@ -1 +1 @@
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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;AAOjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAuP5B,CAAC"}

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

@@ -7,17 +7,12 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { pmidStringSchema } from './_schemas.js';
 export const fetchArticlesTool = tool('pubmed_fetch_articles', {
     description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     input: z.object({
-        pmids: z
-            .array(z
-            .string()
-            .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
-            .min(1)
-            .max(200)
-            .describe('PubMed IDs to fetch'),
+        pmids: z.array(pmidStringSchema).min(1).max(200).describe('PubMed IDs to fetch'),
         includeMesh: z.boolean().default(true).describe('Include MeSH terms'),
         includeGrants: z.boolean().default(false).describe('Include grant information'),
     }),
@@ -167,9 +162,9 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             }
             if (a.affiliations?.length) {
                 lines.push(`\n**Affiliations:**`);
-                a.affiliations.forEach((aff, i) => {
+                for (const [i, aff] of a.affiliations.entries()) {
                     lines.push(`${i + 1}. ${aff}`);
-                });
+                }
             }
             const ji = a.journalInfo;
             if (ji) {
@@ -212,19 +207,27 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             if (a.meshTerms?.length) {
                 lines.push(`\n#### MeSH Terms`);
                 for (const m of a.meshTerms) {
+                    const descriptor = m.descriptorUi
+                        ? `${m.descriptorName} [${m.descriptorUi}]`
+                        : m.descriptorName;
                     const major = m.isMajorTopic ? ' *' : '';
                     const qualifiers = m.qualifiers?.length
-                        ? ` (${m.qualifiers.map((q) => `${q.qualifierName}${q.isMajorTopic ? '*' : ''}`).join(', ')})`
+                        ? ` (${m.qualifiers
+                            .map((q) => {
+                            const name = q.qualifierUi
+                                ? `${q.qualifierName} [${q.qualifierUi}]`
+                                : q.qualifierName;
+                            return `${name}${q.isMajorTopic ? '*' : ''}`;
+                        })
+                            .join(', ')})`
                         : '';
-                    lines.push(`- ${m.descriptorName}${major}${qualifiers}`);
+                    lines.push(`- ${descriptor}${major}${qualifiers}`);
                 }
             }
             if (a.grantList?.length) {
                 lines.push(`\n#### Grants`);
                 for (const g of a.grantList) {
-                    const grantId = g.acronym
-                        ? `${g.grantId ?? g.acronym} (${g.acronym})`
-                        : (g.grantId ?? '');
+                    const grantId = g.grantId && g.acronym ? `${g.grantId} (${g.acronym})` : (g.grantId ?? g.acronym ?? '');
                     const parts = [grantId, g.agency, g.country].filter(Boolean);
                     lines.push(`- ${parts.join(' — ')}`);
                 }

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -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;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAgDjD~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAkO5B~~,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAiDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAmO5B,CAAC"}

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

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
 import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers.js';
+import { pmidStringSchema } from './_schemas.js';
 function normalizePmcId(id) {
     return id.replace(/^PMC/i, '');
 }
@@ -47,9 +48,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             .optional()
             .describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide this OR pmids, not both.'),
         pmids: z
-            .array(z
-            .string()
-            .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
+            .array(pmidStringSchema)
             .min(1)
             .max(10)
             .optional()
@@ -186,21 +185,29 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         for (const a of result.articles) {
             lines.push(`\n### ${a.title ?? a.pmcId}`);
             if (a.authors?.length) {
-                const fmtAuthor = (au) => au.collectiveName ??
-                    `${au.lastName ?? ''}${au.givenNames ? ` ${au.givenNames}` : ''}`.trim();
-                const first3 = a.authors.slice(0, 3).map(fmtAuthor).join(', ');
-                const authorStr = a.authors.length > 3 ? `${first3}, et al.` : first3;
-                lines.push(`**Authors:** ${authorStr}`);
+                lines.push(`\n**Authors (${a.authors.length}):**`);
+                for (const au of a.authors) {
+                    lines.push(`- ${formatPmcAuthor(au)}`);
+                }
+            }
+            if (a.affiliations?.length) {
+                lines.push(`\n**Affiliations:**`);
+                for (const [i, aff] of a.affiliations.entries()) {
+                    lines.push(`${i + 1}. ${aff}`);
+                }
             }
-            if (a.affiliations?.length)
-                lines.push(`**Affiliations:** ${a.affiliations.join('; ')}`);
             if (a.journal) {
-                const parts = [a.journal.title];
+                const parts = [];
+                if (a.journal.title)
+                    parts.push(a.journal.title);
                 if (a.journal.volume)
                     parts.push(`**${a.journal.volume}**${a.journal.issue ? `(${a.journal.issue})` : ''}`);
                 if (a.journal.pages)
                     parts.push(a.journal.pages);
-                lines.push(`**Journal:** ${parts.filter(Boolean).join(', ')}`);
+                if (a.journal.issn)
+                    parts.push(`ISSN ${a.journal.issn}`);
+                if (parts.length)
+                    lines.push(`\n**Journal:** ${parts.join(', ')}`);
             }
             if (a.articleType)
                 lines.push(`**Type:** ${a.articleType}`);
@@ -224,13 +231,13 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 lines.push(`\n#### Abstract\n${a.abstract}`);
             for (const sec of a.sections) {
                 if (sec.title)
-                    lines.push(`\n#### ${sec.title}`);
+                    lines.push(`\n#### ${formatHeading(sec.label, sec.title)}`);
                 if (sec.text)
                     lines.push(sec.text);
                 if (sec.subsections?.length) {
                     for (const sub of sec.subsections) {
                         if (sub.title)
-                            lines.push(`\n##### ${sub.title}`);
+                            lines.push(`\n##### ${formatHeading(sub.label, sub.title)}`);
                         if (sub.text)
                             lines.push(sub.text);
                     }
@@ -247,4 +254,13 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+function formatPmcAuthor(au) {
+    if (au.collectiveName)
+        return `${au.collectiveName} (collective)`;
+    const name = `${au.givenNames ? `${au.givenNames} ` : ''}${au.lastName ?? ''}`.trim();
+    return name || 'Unknown';
+}
+function formatHeading(label, title) {
+    return label ? `${label} ${title}` : title;
+}
 //# sourceMappingURL=fetch-fulltext.tool.js.map

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAkCjD~~,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;~~kBAoK1B~~,CAAC"}
1	+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBA8J1B,CAAC"}

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

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { pmidStringSchema } from './_schemas.js';
 function extractValue(field) {
     if (field === undefined || field === null)
         return '';
@@ -19,10 +20,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
     description: 'Find articles related to a source article — similar content, citing articles, or references.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     input: z.object({
-        pmid: z
-            .string()
-            .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace or non-digit characters.')
-            .describe('Source PubMed ID'),
+        pmid: pmidStringSchema.describe('Source PubMed ID'),
         relationship: z
             .enum(['similar', 'cited_by', 'references'])
             .default('similar')

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

	@@ -1 +1 @@
1	- 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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;~~AAUjD~~,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;~~kBAkG9B~~,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;AAWjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBAuF9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -8,17 +8,12 @@ import { formatCitations, } from '../../../services/ncbi/formatting/citation-for
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { pmidStringSchema } from './_schemas.js';
 export const formatCitationsTool = tool('pubmed_format_citations', {
     description: 'Get formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     input: z.object({
-        pmids: z
-            .array(z
-            .string()
-            .regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
-            .min(1)
-            .max(50)
-            .describe('PubMed IDs to cite'),
+        pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
         styles: z
             .array(z.enum(['apa', 'mla', 'bibtex', 'ris']))
             .default(['apa'])

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

	@@ -1 +1 @@
1	- {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;~~AAGrE~~,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC~~;aACL~~,~~KAAK,CACJ,~~CAAC~~;aACE~~,~~MAAM,EAAE;aACR,~~KAAK,~~CACJ~~,~~OAAO~~,~~EACP~~,~~2JAA2J~~,~~CAC5J,CACJ;aACA,~~GAAG,CAAC,CAAC,CAAC~~;aACN~~,GAAG,CAAC,EAAE,CAAC~~;aACP~~,QAAQ,CAAC,oBAAoB,CAAC;~~QACjC~~,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
1	+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

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

	@@ -1 +1 @@
1	- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsEjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAuS7B~~,CAAC"}
1	+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsEjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAwS7B,CAAC"}

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

@@ -317,6 +317,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
                     lines.push(`**Published:** ${s.pubDate}`);
                 if (s.doi)
                     lines.push(`**DOI:** ${s.doi}`);
+                if (s.pmcId)
+                    lines.push(`**PMCID:** ${s.pmcId}`);
                 if (s.pubmedUrl)
                     lines.push(`**PubMed:** ${s.pubmedUrl}`);
                 if (s.pmcUrl)

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

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.3.11",
+  "version": "2.4.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -67,7 +67,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.4.1",
+    "@cyanheads/mcp-ts-core": "^0.5.0",
     "fast-xml-parser": "^5.7.1",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.3"

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.3.11",
+  "version": "2.4.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.11",
+      "version": "2.4.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.11",
+      "version": "2.4.0",
       "packageArguments": [
         {
           "type": "positional",