chore: better connect tool guidance with Atlas MCP-48 (#349)

Co-authored-by: Copilot <[email protected]>

Author: nirinchev

README.md

@@ -285,7 +285,7 @@ The MongoDB MCP Server can be configured using multiple methods, with the follow
 | `connectionString` | MongoDB connection string for direct database connections. Optional, if not set, you'll need to call the `connect` tool before interacting with MongoDB data. |
 | `logPath`          | Folder to store logs.                                                                                                                                         |
 | `disabledTools`    | An array of tool names, operation types, and/or categories of tools that will be disabled.                                                                    |
-| `readOnly`         | When set to true, only allows read and metadata operation types, disabling create/update/delete operations.                                                   |
+| `readOnly`         | When set to true, only allows read, connect, and metadata operation types, disabling create/update/delete operations.                                         |
 | `indexCheck`       | When set to true, enforces that query operations must use an index, rejecting queries that perform a collection scan.                                         |
 | `telemetry`        | When set to disabled, disables telemetry collection.                                                                                                          |
 
@@ -318,10 +318,11 @@ Operation types:
 - `delete` - Tools that delete resources, such as delete document, drop collection, etc.
 - `read` - Tools that read resources, such as find, aggregate, list clusters, etc.
 - `metadata` - Tools that read metadata, such as list databases, list collections, collection schema, etc.
+- `connect` - Tools that allow you to connect or switch the connection to a MongoDB instance. If this is disabled, you will need to provide a connection string through the config when starting the server.
 
 #### Read-Only Mode
 
-The `readOnly` configuration option allows you to restrict the MCP server to only use tools with "read" and "metadata" operation types. When enabled, all tools that have "create", "update" or "delete" operation types will not be registered with the server.
+The `readOnly` configuration option allows you to restrict the MCP server to only use tools with "read", "connect", and "metadata" operation types. When enabled, all tools that have "create", "update" or "delete" operation types will not be registered with the server.
 
 This is useful for scenarios where you want to provide access to MongoDB data for analysis without allowing any modifications to the data or infrastructure.
 

src/server.ts

@@ -12,6 +12,7 @@ import { type ServerCommand } from "./telemetry/types.js";
 import { CallToolRequestSchema, CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import assert from "assert";
 import { detectContainerEnv } from "./common/container.js";
+import { ToolBase } from "./tools/tool.js";
 
 export interface ServerOptions {
     session: Session;
@@ -22,9 +23,10 @@ export interface ServerOptions {
 
 export class Server {
     public readonly session: Session;
-    private readonly mcpServer: McpServer;
+    public readonly mcpServer: McpServer;
     private readonly telemetry: Telemetry;
     public readonly userConfig: UserConfig;
+    public readonly tools: ToolBase[] = [];
     private readonly startTime: number;
 
     constructor({ session, mcpServer, userConfig, telemetry }: ServerOptions) {
@@ -141,8 +143,11 @@ export class Server {
     }
 
     private registerTools() {
-        for (const tool of [...AtlasTools, ...MongoDbTools]) {
-            new tool(this.session, this.userConfig, this.telemetry).register(this.mcpServer);
+        for (const toolConstructor of [...AtlasTools, ...MongoDbTools]) {
+            const tool = new toolConstructor(this.session, this.userConfig, this.telemetry);
+            if (tool.register(this)) {
+                this.tools.push(tool);
+            }
         }
     }
 

src/tools/atlas/atlasTool.ts

@@ -6,7 +6,7 @@ import { z } from "zod";
 import { ApiClientError } from "../../common/atlas/apiClientError.js";
 
 export abstract class AtlasToolBase extends ToolBase {
-    protected category: ToolCategory = "atlas";
+    public category: ToolCategory = "atlas";
 
     protected verifyAllowed(): boolean {
         if (!this.config.apiClientId || !this.config.apiClientSecret) {
@@ -29,7 +29,7 @@ export abstract class AtlasToolBase extends ToolBase {
                             type: "text",
                             text: `Unable to authenticate with MongoDB Atlas, API error: ${error.message}
 
-Hint: Your API credentials may be invalid, expired or lack permissions. 
+Hint: Your API credentials may be invalid, expired or lack permissions.
 Please check your Atlas API credentials and ensure they have the appropriate permissions.
 For more information on setting up API keys, visit: https://www.mongodb.com/docs/atlas/configure-api-access/`,
                         },
@@ -44,7 +44,7 @@ For more information on setting up API keys, visit: https://www.mongodb.com/docs
                         {
                             type: "text",
                             text: `Received a Forbidden API Error: ${error.message}
-                            
+
 You don't have sufficient permissions to perform this action in MongoDB Atlas
 Please ensure your API key has the necessary roles assigned.
 For more information on Atlas API access roles, visit: https://www.mongodb.com/docs/atlas/api/service-accounts-overview/`,

src/tools/atlas/metadata/connectCluster.ts renamed to src/tools/atlas/connect/connectCluster.ts

@@ -13,9 +13,9 @@ function sleep(ms: number): Promise<void> {
 }
 
 export class ConnectClusterTool extends AtlasToolBase {
-    protected name = "atlas-connect-cluster";
+    public name = "atlas-connect-cluster";
     protected description = "Connect to MongoDB Atlas cluster";
-    protected operationType: OperationType = "metadata";
+    public operationType: OperationType = "connect";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID"),
         clusterName: z.string().describe("Atlas cluster name"),

src/tools/atlas/create/createAccessList.ts

@@ -6,9 +6,9 @@ import { ToolArgs, OperationType } from "../../tool.js";
 const DEFAULT_COMMENT = "Added by Atlas MCP";
 
 export class CreateAccessListTool extends AtlasToolBase {
-    protected name = "atlas-create-access-list";
+    public name = "atlas-create-access-list";
     protected description = "Allow Ip/CIDR ranges to access your MongoDB Atlas clusters.";
-    protected operationType: OperationType = "create";
+    public operationType: OperationType = "create";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID"),
         ipAddresses: z

src/tools/atlas/create/createDBUser.ts

@@ -6,9 +6,9 @@ import { CloudDatabaseUser, DatabaseUserRole } from "../../../common/atlas/opena
 import { generateSecurePassword } from "../../../common/atlas/generatePassword.js";
 
 export class CreateDBUserTool extends AtlasToolBase {
-    protected name = "atlas-create-db-user";
+    public name = "atlas-create-db-user";
     protected description = "Create an MongoDB Atlas database user";
-    protected operationType: OperationType = "create";
+    public operationType: OperationType = "create";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID"),
         username: z.string().describe("Username for the new user"),

src/tools/atlas/create/createFreeCluster.ts

@@ -5,9 +5,9 @@ import { ToolArgs, OperationType } from "../../tool.js";
 import { ClusterDescription20240805 } from "../../../common/atlas/openapi.js";
 
 export class CreateFreeClusterTool extends AtlasToolBase {
-    protected name = "atlas-create-free-cluster";
+    public name = "atlas-create-free-cluster";
     protected description = "Create a free MongoDB Atlas cluster";
-    protected operationType: OperationType = "create";
+    public operationType: OperationType = "create";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID to create the cluster in"),
         name: z.string().describe("Name of the cluster"),

src/tools/atlas/create/createProject.ts

@@ -5,9 +5,9 @@ import { ToolArgs, OperationType } from "../../tool.js";
 import { Group } from "../../../common/atlas/openapi.js";
 
 export class CreateProjectTool extends AtlasToolBase {
-    protected name = "atlas-create-project";
+    public name = "atlas-create-project";
     protected description = "Create a MongoDB Atlas project";
-    protected operationType: OperationType = "create";
+    public operationType: OperationType = "create";
     protected argsShape = {
         projectName: z.string().optional().describe("Name for the new project"),
         organizationId: z.string().optional().describe("Organization ID for the new project"),

src/tools/atlas/read/inspectAccessList.ts

@@ -4,9 +4,9 @@ import { AtlasToolBase } from "../atlasTool.js";
 import { ToolArgs, OperationType } from "../../tool.js";
 
 export class InspectAccessListTool extends AtlasToolBase {
-    protected name = "atlas-inspect-access-list";
+    public name = "atlas-inspect-access-list";
     protected description = "Inspect Ip/CIDR ranges with access to your MongoDB Atlas clusters.";
-    protected operationType: OperationType = "read";
+    public operationType: OperationType = "read";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID"),
     };

src/tools/atlas/read/inspectCluster.ts

@@ -5,9 +5,9 @@ import { ToolArgs, OperationType } from "../../tool.js";
 import { Cluster, inspectCluster } from "../../../common/atlas/cluster.js";
 
 export class InspectClusterTool extends AtlasToolBase {
-    protected name = "atlas-inspect-cluster";
+    public name = "atlas-inspect-cluster";
     protected description = "Inspect MongoDB Atlas cluster";
-    protected operationType: OperationType = "read";
+    public operationType: OperationType = "read";
     protected argsShape = {
         projectId: z.string().describe("Atlas project ID"),
         clusterName: z.string().describe("Atlas cluster name"),