feat: allow reading config from a file and support toolMetadataOverrides MCP-292

scripts/generateArguments.ts

@@ -3,7 +3,7 @@
 /**
  * This script generates argument definitions and updates:
  * - server.json arrays
- * - README.md configuration table
+ * - CONFIGURATION.md configuration table
  *
  * It uses the Zod schema and OPTIONS defined in src/common/config.ts
  */
@@ -244,7 +244,7 @@ function updateServerJsonEnvVars(envVars: ArgumentInfo[]): void {
     console.log(`✓ Updated server.json (version ${version})`);
 }
 
-function generateReadmeConfigTable(argumentInfos: ArgumentInfo[]): string {
+function generateConfigurationTable(argumentInfos: ArgumentInfo[]): string {
     const rows = [
         "| CLI Option                             | Environment Variable                                | Default                                                                     | Description                                                                                                                                                                                             |",
         "| -------------------------------------- | --------------------------------------------------- | --------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |",
@@ -275,6 +275,10 @@ function generateReadmeConfigTable(argumentInfos: ArgumentInfo[]): string {
                     case "string":
                         defaultValueString = `\`"${defaultValue}"\``;
                         break;
+                    case "object": {
+                        defaultValueString = `\`"${JSON.stringify(defaultValue)}"\``;
+                        break;
+                    }
                     default:
                         throw new Error(`Unsupported default value type: ${typeof defaultValue}`);
                 }
@@ -290,31 +294,31 @@ function generateReadmeConfigTable(argumentInfos: ArgumentInfo[]): string {
     return rows.join("\n");
 }
 
-function updateReadmeConfigTable(envVars: ArgumentInfo[]): void {
-    const readmePath = join(__dirname, "..", "README.md");
-    let content = readFileSync(readmePath, "utf-8");
+function updateConfigurationTable(envVars: ArgumentInfo[]): void {
+    const configurationPath = join(__dirname, "..", "CONFIGURATION.md");
+    let content = readFileSync(configurationPath, "utf-8");
 
-    const newTable = generateReadmeConfigTable(envVars);
+    const newTable = generateConfigurationTable(envVars);
 
     // Find and replace the configuration options table
-    const tableRegex = /### Configuration Options\n\n\| CLI Option[\s\S]*?\n\n####/;
-    const replacement = `### Configuration Options\n\n${newTable}\n\n####`;
+    const tableRegex = /## Configuration Options\n\n\| CLI Option[\s\S]*?\n\n###/;
+    const replacement = `## Configuration Options\n\n${newTable}\n\n###`;
 
     content = content.replace(tableRegex, replacement);
 
-    writeFileSync(readmePath, content, "utf-8");
-    console.log("✓ Updated README.md configuration table");
+    writeFileSync(configurationPath, content, "utf-8");
+    console.log("✓ Updated CONFIGURATION.md configuration table");
 
-    // Run prettier on the README.md file
-    execSync("npx prettier --write README.md", { cwd: join(__dirname, "..") });
+    // Run prettier on the CONFIGURATION.md file
+    execSync("npx prettier --write CONFIGURATION.md", { cwd: join(__dirname, "..") });
 }
 
 function main(): void {
     const zodMetadata = extractZodDescriptions();
 
     const argumentInfo = getArgumentInfo(OPTIONS, zodMetadata);
     updateServerJsonEnvVars(argumentInfo);
-    updateReadmeConfigTable(argumentInfo);
+    updateConfigurationTable(argumentInfo);
 }
 
 main();

server.json

@@ -170,6 +170,13 @@
           "format": "string",
           "isSecret": false
         },
+        {
+          "name": "MDB_MCP_TOOL_METADATA_OVERRIDES",
+          "description": "A map of name of the MongoDB MCP server tool to the metadata that needs to be used for that tool. Example: `{ \"toolMetadataOverrides\": { \"find\": { \"name\": \"query\" } } }`",
+          "isRequired": false,
+          "format": "string",
+          "isSecret": false
+        },
         {
           "name": "MDB_MCP_TRANSPORT",
           "description": "Either 'stdio' or 'http'.",
@@ -323,6 +330,12 @@
           "description": "When set to disabled, disables telemetry collection.",
           "isRequired": false
         },
+        {
+          "type": "named",
+          "name": "--toolMetadataOverrides",
+          "description": "A map of name of the MongoDB MCP server tool to the metadata that needs to be used for that tool. Example: `{ \"toolMetadataOverrides\": { \"find\": { \"name\": \"query\" } } }`",
+          "isRequired": false
+        },
         {
           "type": "named",
           "name": "--transport",
@@ -498,6 +511,13 @@
           "format": "string",
           "isSecret": false
         },
+        {
+          "name": "MDB_MCP_TOOL_METADATA_OVERRIDES",
+          "description": "A map of name of the MongoDB MCP server tool to the metadata that needs to be used for that tool. Example: `{ \"toolMetadataOverrides\": { \"find\": { \"name\": \"query\" } } }`",
+          "isRequired": false,
+          "format": "string",
+          "isSecret": false
+        },
         {
           "name": "MDB_MCP_TRANSPORT",
           "description": "Either 'stdio' or 'http'.",
@@ -651,6 +671,12 @@
           "description": "When set to disabled, disables telemetry collection.",
           "isRequired": false
         },
+        {
+          "type": "named",
+          "name": "--toolMetadataOverrides",
+          "description": "A map of name of the MongoDB MCP server tool to the metadata that needs to be used for that tool. Example: `{ \"toolMetadataOverrides\": { \"find\": { \"name\": \"query\" } } }`",
+          "isRequired": false
+        },
         {
           "type": "named",
           "name": "--transport",

src/common/config/argsParserOptions.ts

@@ -55,6 +55,11 @@ export const OPTIONS = {
         "exportTimeoutMs",
         "exportCleanupIntervalMs",
         "voyageApiKey",
+        // Note: toolMetadataOverrides expects a JSON object but we mention it
+        // as a string only to let yargs-parser know that this key needs to be
+        // parsed. The internal handling of the key as an object is done within
+        // yargs-parser itself.
+        "toolMetadataOverrides",
     ],
     boolean: [
         "apiDeprecationErrors",

src/common/config/createUserConfig.ts

@@ -95,6 +95,10 @@ function parseUserConfigSources(cliArguments: string[]): {
         ...OPTIONS,
         // This helps parse the relevant environment variables.
         envPrefix: "MDB_MCP_",
+        // This is the name of key that yargs-parser will look up in CLI
+        // arguments (--config) and ENV variables (MDB_MCP_CONFIG) to load an
+        // initial configuration from.
+        config: "config",
         configuration: {
             ...OPTIONS.configuration,
             // Setting this to true will populate `_` variable which is

src/common/config/userConfig.ts

@@ -167,4 +167,16 @@ export const UserConfigSchema = z4.object({
         )
         .default([])
         .describe("An array of preview features that are enabled."),
+    toolMetadataOverrides: z4
+        .record(
+            z4.string().describe("Original name of the MongoDB MCP server tool that needs to be overridden."),
+            z4.object({
+                name: z4.string().nonempty().optional().describe("New name to be used for the tool."),
+                description: z4.string().nonempty().optional().describe("New description to be used for the tool."),
+            })
+        )
+        .default({})
+        .describe(
+            'A map of name of the MongoDB MCP server tool to the metadata that needs to be used for that tool. Example: `{ "toolMetadataOverrides": { "find": { "name": "query" } } }`'
+        ),
 });

src/server.ts

@@ -240,13 +240,27 @@ export class Server {
     }
 
     private registerTools(): void {
+        const toolsToRegister: ToolBase[] = [];
+        const usedNames = new Set<string>();
+
         for (const toolConstructor of this.toolConstructors) {
             const tool = new toolConstructor({
                 session: this.session,
                 config: this.userConfig,
                 telemetry: this.telemetry,
                 elicitation: this.elicitation,
             });
+
+            if (usedNames.has(tool.name)) {
+                throw new Error(
+                    `Tool name collision detected: '${tool.name}'. This might be due to toolMetadataOverrides configuration.`
+                );
+            }
+            usedNames.add(tool.name);
+            toolsToRegister.push(tool);
+        }
+
+        for (const tool of toolsToRegister) {
             if (tool.register(this)) {
                 this.tools.push(tool);
             }

src/tools/atlas/connect/connectCluster.ts

@@ -30,8 +30,8 @@ export const ConnectClusterArgs = {
 };
 
 export class ConnectClusterTool extends AtlasToolBase {
-    public name = "atlas-connect-cluster";
-    protected description = "Connect to MongoDB Atlas cluster";
+    public internalName = "atlas-connect-cluster";
+    protected internalDescription = "Connect to MongoDB Atlas cluster";
     public operationType: OperationType = "connect";
     protected argsShape = {
         ...ConnectClusterArgs,

src/tools/atlas/create/createAccessList.ts

@@ -17,8 +17,8 @@ export const CreateAccessListArgs = {
 };
 
 export class CreateAccessListTool extends AtlasToolBase {
-    public name = "atlas-create-access-list";
-    protected description = "Allow Ip/CIDR ranges to access your MongoDB Atlas clusters.";
+    public internalName = "atlas-create-access-list";
+    protected internalDescription = "Allow Ip/CIDR ranges to access your MongoDB Atlas clusters.";
     public operationType: OperationType = "create";
     protected argsShape = {
         ...CreateAccessListArgs,