@djmima/pubmed-mcp 1.0.2 → 1.2.0

package/dist/tools/getFullTextArticle.js

@@ -8,12 +8,13 @@
  */
 import { z } from 'zod';
 import { IMPORTANT_LEGAL_NOTICE } from '../pubmed/types.js';
+import { pmcidSchema } from '../utils/ids.js';
 import { parsePmcEfetchXml } from '../utils/xml.js';
 /** PMCIDs per request; the CLI splits longer lists into batches of this size. */
 export const MAX_FULL_TEXT_IDS = 20;
 export const getFullTextArticleSchema = {
     pmc_ids: z
-        .array(z.string().min(1))
+        .array(pmcidSchema)
         .min(1)
         .max(MAX_FULL_TEXT_IDS)
         .describe('Array of PubMed Central IDs (PMCIDs) to retrieve full text for. ' +

package/dist/tools/getFullTextArticle.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getFullTextArticle.js","sourceRoot":"","sources":["../../src/tools/getFullTextArticle.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAGxB,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAC;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AAEpD,iFAAiF;AACjF,MAAM,CAAC,MAAM,iBAAiB,GAAG,EAAE,CAAC;AAEpC,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC,OAAO,EAAE,CAAC;SACP,KAAK,CAAC,WAAW,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,iBAAiB,CAAC;SACtB,QAAQ,CACP,kEAAkE;QAChE,6EAA6E;QAC7E,qEAAqE;QACrE,yBAAyB,CAC5B;CACJ,CAAC;AAMF,oEAAoE;AACpE,SAAS,cAAc,CAAC,EAAU;IAChC,MAAM,OAAO,GAAG,EAAE,CAAC,IAAI,EAAE,CAAC;IAC1B,OAAO,OAAO,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;AAC9E,CAAC;AAED,SAAS,cAAc,CAAC,EAAU;IAChC,OAAO,MAAM,cAAc,CAAC,EAAE,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC;AAClD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,MAAgC,EAChC,MAAkB;IAElB,iEAAiE;IACjE,MAAM,UAAU,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;IAEtD,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,MAAM,CAAC;QAC9B,EAAE,EAAE,KAAK;QACT,EAAE,EAAE,UAAU;QACd,OAAO,EAAE,KAAK;KACf,CAAC,CAAC;IAEH,IAAI,cAAiC,CAAC;IACtC,IAAI,CAAC;QACH,cAAc,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAC;IAC1C,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,wBAAwB,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC9D,OAAO;YACL,sBAAsB,EAAE,sBAAsB;YAC9C,QAAQ,EAAE,EAAE;YACZ,MAAM,EAAE,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;gBACrC,KAAK,EAAE,cAAc,CAAC,KAAK,CAAC;gBAC5B,KAAK,EAAE,0CAA0C;aAClD,CAAC,CAAC;YACH,KAAK,EAAE,CAAC;SACT,CAAC;IACJ,CAAC;IAED,MAAM,QAAQ,GAAsB,EAAE,CAAC;IACvC,MAAM,MAAM,GAAyC,EAAE,CAAC;IACxD,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IAEtC,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,cAAc,CAAC,OAAO,EAAE,EAAE,CAAC;QACxD,MAAM,KAAK,GAAG,OAAO,CAAC,WAAW,CAAC,KAAK;YACrC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC;YAC3C,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;QAChD,WAAW,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QAEvB,IAAI,OAAO,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC;YAC7B,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QACzB,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK;gBACL,KAAK,EAAE,8DAA8D;aACtE,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,KAAK,MAAM,KAAK,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,CAAC;QAChE,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5B,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK;gBACL,KAAK,EAAE,yCAAyC;aACjD,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,OAAO;QACL,sBAAsB,EAAE,sBAAsB;QAC9C,QAAQ;QACR,MAAM;QACN,KAAK,EAAE,QAAQ,CAAC,MAAM;KACvB,CAAC;AACJ,CAAC"}

package/dist/utils/ids.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Zod schemas for article IDs in tool arguments.
+ *
+ * Each value must be a single ID. NCBI reads commas as separators, so a value
+ * such as "1,2,3" would otherwise carry any number of IDs past a tool's
+ * per-request limit.
+ */
+import { z } from 'zod';
+export declare const pmidSchema: z.ZodString;
+/**
+ * With or without the "PMC" prefix, in any case. Spelled without the i flag,
+ * which the JSON Schema in tools/list cannot carry.
+ */
+export declare const pmcidSchema: z.ZodString;
+/** A PMID, PMCID, or DOI. */
+export declare const articleIdSchema: z.ZodString;
+//# sourceMappingURL=ids.d.ts.map

package/dist/utils/ids.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ids.d.ts","sourceRoot":"","sources":["../../src/utils/ids.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,UAAU,aAA4D,CAAC;AAEpF;;;GAGG;AACH,eAAO,MAAM,WAAW,aAE4C,CAAC;AAErE,6BAA6B;AAC7B,eAAO,MAAM,eAAe,aAE0C,CAAC"}

package/dist/utils/ids.js

@@ -0,0 +1,21 @@
+/**
+ * Zod schemas for article IDs in tool arguments.
+ *
+ * Each value must be a single ID. NCBI reads commas as separators, so a value
+ * such as "1,2,3" would otherwise carry any number of IDs past a tool's
+ * per-request limit.
+ */
+import { z } from 'zod';
+export const pmidSchema = z.string().regex(/^\d+$/, 'must be a PMID (digits only)');
+/**
+ * With or without the "PMC" prefix, in any case. Spelled without the i flag,
+ * which the JSON Schema in tools/list cannot carry.
+ */
+export const pmcidSchema = z
+    .string()
+    .regex(/^([Pp][Mm][Cc])?\d+$/, 'must be a PMCID, e.g. PMC7984072');
+/** A PMID, PMCID, or DOI. */
+export const articleIdSchema = z
+    .string()
+    .regex(/^[^\s,]+$/, 'must be a single ID, without commas or spaces');
+//# sourceMappingURL=ids.js.map

package/dist/utils/ids.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ids.js","sourceRoot":"","sources":["../../src/utils/ids.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,MAAM,CAAC,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,OAAO,EAAE,8BAA8B,CAAC,CAAC;AAEpF;;;GAGG;AACH,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC;KACzB,MAAM,EAAE;KACR,KAAK,CAAC,sBAAsB,EAAE,kCAAkC,CAAC,CAAC;AAErE,6BAA6B;AAC7B,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,MAAM,EAAE;KACR,KAAK,CAAC,WAAW,EAAE,+CAA+C,CAAC,CAAC"}

package/dist/version.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Package version, read from package.json at runtime.
+ *
+ * package.json sits one directory above this module both in src/ (tsx) and in
+ * dist/ (build, npm package, Docker image), so a single relative path works
+ * everywhere. Reading it keeps the version in one place: `npm version` updates
+ * package.json only.
+ */
+/** The version field of the package's package.json, e.g. "1.1.0". */
+export declare function packageVersion(): string;
+//# sourceMappingURL=version.d.ts.map

package/dist/version.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"version.d.ts","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAcH,qEAAqE;AACrE,wBAAgB,cAAc,IAAI,MAAM,CASvC"}

package/dist/version.js

@@ -0,0 +1,25 @@
+/**
+ * Package version, read from package.json at runtime.
+ *
+ * package.json sits one directory above this module both in src/ (tsx) and in
+ * dist/ (build, npm package, Docker image), so a single relative path works
+ * everywhere. Reading it keeps the version in one place: `npm version` updates
+ * package.json only.
+ */
+import { readFileSync } from 'node:fs';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+const PACKAGE_JSON_PATH = path.join(path.dirname(fileURLToPath(import.meta.url)), '..', 'package.json');
+let cachedVersion;
+/** The version field of the package's package.json, e.g. "1.1.0". */
+export function packageVersion() {
+    if (cachedVersion === undefined) {
+        const pkg = JSON.parse(readFileSync(PACKAGE_JSON_PATH, 'utf8'));
+        if (typeof pkg.version !== 'string') {
+            throw new Error(`no version field in ${PACKAGE_JSON_PATH}`);
+        }
+        cachedVersion = pkg.version;
+    }
+    return cachedVersion;
+}
+//# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AAEzC,MAAM,iBAAiB,GAAG,IAAI,CAAC,IAAI,CACjC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAC5C,IAAI,EACJ,cAAc,CACf,CAAC;AAEF,IAAI,aAAiC,CAAC;AAEtC,qEAAqE;AACrE,MAAM,UAAU,cAAc;IAC5B,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,iBAAiB,EAAE,MAAM,CAAC,CAA0B,CAAC;QACzF,IAAI,OAAO,GAAG,CAAC,OAAO,KAAK,QAAQ,EAAE,CAAC;YACpC,MAAM,IAAI,KAAK,CAAC,uBAAuB,iBAAiB,EAAE,CAAC,CAAC;QAC9D,CAAC;QACD,aAAa,GAAG,GAAG,CAAC,OAAO,CAAC;IAC9B,CAAC;IACD,OAAO,aAAa,CAAC;AACvB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@djmima/pubmed-mcp",
-  "version": "1.0.2",
+  "version": "1.2.0",
   "description": "MCP server providing access to PubMed biomedical literature and citations",
   "license": "MIT",
   "author": "DJ MIMA",
@@ -45,10 +45,10 @@
     "prepublishOnly": "npm run typecheck && npm run lint && npm test && npm run build"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.12.0",
-    "axios": "^1.7.9",
+    "@modelcontextprotocol/sdk": "^1.32.2",
+    "axios": "^1.20.0",
     "dotenv": "^17.3.1",
-    "express": "^4.21.0",
+    "express": "^4.22.3",
     "fast-xml-parser": "^5.11.2",
     "jose": "^5.10.0",
     "zod": "^4.6.7"