clinicaltrialsgov-mcp-server 1.0.2 → 1.0.4

package/README.md

@@ -1,8 +1,8 @@
 # ClinicalTrials.gov MCP Server
 
 [![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg)](https://www.typescriptlang.org/)
-[![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.13.0-green.svg)](https://modelcontextprotocol.io/)
-[![Version](https://img.shields.io/badge/Version-1.0.2-blue.svg)](./CHANGELOG.md)
+[![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.13.1-green.svg)](https://modelcontextprotocol.io/)
+[![Version](https://img.shields.io/badge/Version-1.0.3-blue.svg)](./CHANGELOG.md)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 [![Status](https://img.shields.io/badge/Status-beta-orange.svg)](https://github.com/cyanheads/clinicaltrialsgov-mcp-server/issues)
 [![GitHub](https://img.shields.io/github/stars/cyanheads/clinicaltrialsgov-mcp-server?style=social)](https://github.com/cyanheads/clinicaltrialsgov-mcp-server)

package/dist/config/index.d.ts

@@ -31,7 +31,7 @@ export declare const config: {
     /** Logging level. From `MCP_LOG_LEVEL` env var. Default: "debug". */
     logLevel: string;
     /** Absolute path to the logs directory. From `LOGS_DIR` env var. */
-    logsPath: string;
+    logsPath: string | null;
     /** Runtime environment. From `NODE_ENV` env var. Default: "development". */
     environment: string;
     /** MCP transport type ('stdio' or 'http'). From `MCP_TRANSPORT_TYPE` env var. Default: "stdio". */
@@ -86,7 +86,7 @@ export declare const config: {
         serviceRoleKey: string | undefined;
     } | undefined;
     /** Absolute path to the ClinicalTrials.gov data directory. From `CLINICALTRIALS_DATA_PATH` env var. */
-    clinicalTrialsDataPath: string;
+    clinicalTrialsDataPath: string | null;
 };
 /**
  * Configured logging level for the application.

package/dist/config/index.js

@@ -226,21 +226,38 @@ const ensureDirectory = (dirPath, rootDir, dirName) => {
 };
 // --- End Directory Ensurance Function ---
 // --- Logs Directory Handling ---
-const validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
+let validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
 if (!validatedLogsPath) {
     if (process.stdout.isTTY) {
-        console.error("FATAL: Logs directory configuration is invalid or could not be created. Please check permissions and path. Exiting.");
+        console.warn(`Warning: Custom logs directory ('${env.LOGS_DIR}') is invalid or outside the project boundary. Falling back to default.`);
+    }
+    // Try again with the absolute default path
+    const defaultLogsDir = path.join(projectRoot, "logs");
+    validatedLogsPath = ensureDirectory(defaultLogsDir, projectRoot, "logs");
+    if (!validatedLogsPath) {
+        if (process.stdout.isTTY) {
+            // This is just a warning now, not fatal.
+            console.warn("Warning: Default logs directory could not be created. File logging will be disabled.");
+        }
+        // Do not exit. validatedLogsPath remains null, and the logger will handle it.
     }
-    process.exit(1); // Exit if logs directory is not usable
 }
 // --- End Logs Directory Handling ---
 // --- Data Directory Handling ---
-const validatedDataPath = ensureDirectory(env.CLINICALTRIALS_DATA_PATH, projectRoot, "data");
+let validatedDataPath = ensureDirectory(env.CLINICALTRIALS_DATA_PATH, projectRoot, "data");
 if (!validatedDataPath) {
     if (process.stdout.isTTY) {
-        console.error("FATAL: Data directory configuration is invalid or could not be created. Please check permissions and path. Exiting.");
+        console.warn(`Warning: Custom data directory ('${env.CLINICALTRIALS_DATA_PATH}') is invalid or outside the project boundary. Falling back to default.`);
+    }
+    // Try again with the absolute default path
+    const defaultDataDir = path.join(projectRoot, "data");
+    validatedDataPath = ensureDirectory(defaultDataDir, projectRoot, "data");
+    if (!validatedDataPath) {
+        if (process.stdout.isTTY) {
+            console.warn("Warning: Default data directory could not be created. Features requiring local data caching will be disabled.");
+        }
+        // Do not exit. validatedDataPath remains null.
     }
-    process.exit(1); // Exit if data directory is not usable
 }
 // --- End Data Directory Handling ---
 /**

package/dist/services/clinical-trials-gov/ClinicalTrialsGovService.d.ts

@@ -49,7 +49,7 @@ export declare class ClinicalTrialsGovService {
     }, context: RequestContext): Promise<any>;
     /**
      * A generic fetch method that handles backing up the response.
-     * It always fetches live data and writes it to a backup file.
+     * It always fetches live data and writes it to a backup file if the data path is configured.
      * @param url - The URL to fetch.
      * @param fileName - The file name to use for the backup.
      * @param context - The request context for logging.

package/dist/services/clinical-trials-gov/ClinicalTrialsGovService.js

@@ -132,14 +132,13 @@ export class ClinicalTrialsGovService {
     }
     /**
      * A generic fetch method that handles backing up the response.
-     * It always fetches live data and writes it to a backup file.
+     * It always fetches live data and writes it to a backup file if the data path is configured.
      * @param url - The URL to fetch.
      * @param fileName - The file name to use for the backup.
      * @param context - The request context for logging.
      * @returns A promise that resolves with the fetched data.
      */
     async fetchAndBackup(url, fileName, context) {
-        const filePath = path.join(config.clinicalTrialsDataPath, fileName);
         logger.debug(`[API] Fetching from ${url}`, context);
         const fetchOptions = {
             headers: { Accept: "application/json" },
@@ -160,15 +159,21 @@ export class ClinicalTrialsGovService {
             });
         }
         const data = (await response.json());
-        try {
-            writeFileSync(filePath, JSON.stringify(data, null, 2));
-            logger.debug(`[Backup] Wrote to ${filePath}`, context);
+        if (config.clinicalTrialsDataPath) {
+            const filePath = path.join(config.clinicalTrialsDataPath, fileName);
+            try {
+                writeFileSync(filePath, JSON.stringify(data, null, 2));
+                logger.debug(`[Backup] Wrote to ${filePath}`, context);
+            }
+            catch (error) {
+                logger.error(`Failed to write backup file: ${filePath}`, {
+                    ...context,
+                    error,
+                });
+            }
         }
-        catch (error) {
-            logger.error(`Failed to write backup file: ${filePath}`, {
-                ...context,
-                error,
-            });
+        else {
+            logger.debug("[Backup] Skipping backup because data path is not configured.", context);
         }
         return data;
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "clinicaltrialsgov-mcp-server",
-  "version": "1.0.2",
+  "version": "1.0.4",
   "description": "A Model Context Protocol (MCP) Server providing LLM tools for the official ClinicalTrials.gov REST API. Search and retrieve clinical trial data, including study details and more",
   "main": "dist/index.js",
   "files": [
@@ -35,21 +35,19 @@
     "db:duckdb-example": "MCP_LOG_LEVEL=debug tsc && node dist/storage/duckdbExample.js"
   },
   "dependencies": {
-    "@hono/node-server": "^1.14.4",
-    "@modelcontextprotocol/sdk": "^1.13.0",
-    "@supabase/supabase-js": "^2.50.0",
-    "@types/jsonwebtoken": "^9.0.10",
-    "@types/node": "^24.0.3",
+    "@hono/node-server": "^1.15.0",
+    "@modelcontextprotocol/sdk": "^1.15.0",
+    "@supabase/supabase-js": "^2.50.3",
+    "@types/node": "^24.0.10",
     "@types/sanitize-html": "^2.16.0",
     "@types/validator": "13.15.2",
     "chrono-node": "^2.8.0",
     "dotenv": "^16.5.0",
-    "hono": "^4.8.2",
+    "hono": "^4.8.4",
     "ignore": "^7.0.5",
     "jose": "^6.0.11",
-    "jsonwebtoken": "^9.0.2",
     "npm": "^11.4.2",
-    "openai": "^5.6.0",
+    "openai": "^5.8.2",
     "partial-json": "^0.1.7",
     "sanitize-html": "^2.17.0",
     "tiktoken": "^1.0.21",
@@ -58,7 +56,8 @@
     "validator": "13.15.15",
     "winston": "^3.17.0",
     "winston-transport": "^4.9.0",
-    "zod": "^3.25.67"
+    "js-yaml": "^4.1.0",
+    "zod": "^3.25.74"
   },
   "keywords": [
     "typescript",
@@ -92,8 +91,7 @@
     "@types/js-yaml": "^4.0.9",
     "axios": "^1.10.0",
     "depcheck": "^1.4.7",
-    "js-yaml": "^4.1.0",
-    "prettier": "^3.5.3",
-    "typedoc": "^0.28.5"
+    "prettier": "^3.6.2",
+    "typedoc": "^0.28.7"
   }
 }