Obsidian MCP Server: Complete Project Analysis

Table of Contents

1. •What are MCPs
2. •Project Overview
3. •Architecture Analysis
4. •Key Components
5. •How It Works
6. •Security Features
7. •Use Cases
8. •Installation and Setup
9. •Technical Details

What are MCPs

Introduction to MCPs

MCP stands for Model Context Protocol. It is a standardized communication protocol that allows artificial intelligence assistants and other clients to interact with external systems, services, and data sources in a structured and safe way.

Core Purpose

The Model Context Protocol was created to solve a key problem in AI systems: how to safely give AI models access to tools and information beyond their training data, while maintaining security, clarity, and controlled behavior. Instead of building custom integrations for each AI tool or service, MCPs provide a unified interface.

How MCPs Work

MCPs operate on a client server architecture. Think of it like a plug and play system for AI applications. An MCP server exposes capabilities through a standard interface, and any MCP client can connect to that server to use those capabilities.

The protocol uses a transport mechanism called stdio. This means the server communicates with the client through standard input and output streams. This is simple, reliable, and works across different systems.

Key Components of MCP

MCPs have three main types of features that servers can expose:

Resources: These represent readable data that the AI can access. Resources are like documents or files the AI can look at. Each resource has a unique URI (similar to a web address), a name, a description, and a MIME type that describes what kind of data it is.

Tools: These are functions or actions that the AI can call. Unlike resources which are read only, tools can perform operations like creating, modifying, or deleting data. Tools have parameters that describe what inputs they need and what they expect to happen.

Prompts: These are templates or examples that help guide the AI on how to use the tools and resources effectively. They are like instruction guides built into the server.

Why MCPs Matter

Before MCPs existed, developers had to create custom integrations for each AI application. This was time consuming and led to security issues because each integration was different. MCPs standardize this process. Now a developer creates one MCP server for their service, and it can be used with any MCP compatible client like Claude Desktop or other AI applications.

Real World Example

Imagine you want Claude (an AI assistant) to read and edit your Obsidian notes. Without MCPs, Claude would need special integration code built just for Obsidian. With MCPs, an Obsidian MCP server is created once, and Claude can connect to it. If another AI tool wants to use Obsidian too, it can use the exact same server without any changes.

Project Overview

What is This Project

The Obsidian MCP Server is a specialized server that connects your Obsidian vault (a note taking and knowledge management system) to AI assistants through the Model Context Protocol. It enables AI systems like Claude to read, write, search, and edit your markdown notes directly.

Purpose and Goals

The primary goal is to give AI assistants safe, structured access to your personal knowledge base stored in Obsidian. This enables powerful workflows like:

• •Having Claude read your research notes and synthesize information
• •Creating new notes through AI assistance
• •Searching your vault for relevant information
• •Automatically organizing and updating notes
• •Using your personal knowledge as context for AI conversations

Project Creator

This project was created by Nattie Nkosi and is released under the MIT license, meaning it is free to use, modify, and distribute.

Technology Stack

The project is built with modern web technologies:

• •Language: TypeScript, a typed version of JavaScript that catches errors at compile time
• •Runtime: Node.js, which executes JavaScript outside of web browsers
• •MCP SDK: The official Model Context Protocol SDK from Anthropic
• •Environment Management: dotenv for handling configuration variables
• •Build Process: TypeScript compiler for converting TypeScript to JavaScript

Architecture Analysis

Design Philosophy

The codebase follows a clean architecture pattern with strong separation of concerns. This means each part of the code has one specific job and responsibilities are clearly divided. This approach makes the code easier to understand, test, and extend.

Directory Structure

src/
├── index.ts              # Entry point - starts the server
├── server.ts             # Server initialization and request handling
├── config.ts             # Configuration and environment variables
├── handlers/
│   ├── resources.ts      # Handles resource listing and reading
│   └── tools.ts          # Defines tools and handles tool execution
└── utils/
    ├── validation.ts     # Path and argument validation logic
    └── filesystem.ts     # File system operations

Layer Breakdown

Entry Layer: The index.ts file serves as the application entry point. It catches any errors during startup and exits gracefully if something goes wrong.

Server Layer: The server.ts file handles all MCP protocol setup. It creates the server instance, sets up transport (stdin/stdout), and registers handlers for different types of requests that clients send.

Configuration Layer: The config.ts file manages environment variables and validates that the Obsidian vault path is valid before the server runs.

Handler Layer: Two handler files manage different aspects of the MCP protocol. Resources are handled in resources.ts which lists and reads notes. Tools are defined and executed in tools.ts.

Utility Layer: Two utility files provide common functionality. Validation utility checks that paths are safe and arguments are correct. Filesystem utility performs actual file operations like reading, writing, and searching.

Data Flow

When a client makes a request to the server:

1. •The request arrives through stdin transport
2. •The server.ts receives and identifies the request type
3. •The appropriate handler is called (either resources or tools)
4. •The handler uses utilities to validate inputs and perform operations
5. •Results are formatted according to MCP protocol
6. •Response is sent back through stdout

Key Components

1. Server Configuration (config.ts)

This file handles all setup and validation.

OBSIDIAN_VAULT_PATH: Reads the path to your Obsidian vault from environment variables or uses the current directory as default. This tells the server where to find your notes.

validateVaultPath(): Checks that the vault path actually exists on your system. If the path is invalid, it throws an error immediately during startup, preventing the server from running with a broken configuration.

SERVER_INFO: Contains metadata about the server including name (obsidian mcp) and version (1.0.0) that identify it to clients.

2. File System Utilities (utils/filesystem.ts)

This file provides all operations that interact with your actual files and folders.

getAllMarkdownFiles(): Recursively walks through your vault directory and collects all markdown files. It skips hidden files (starting with dot) and node modules folders. Returns an array of note information objects.

searchNotes(): Takes a search query and looks through all markdown files in your vault for matching text. The search is case insensitive, meaning it does not matter if you use uppercase or lowercase letters.

readNote(): Reads the complete content of a specific note file. Throws an error if the file does not exist.

writeNote(): Creates a new note or overwrites an existing one. Automatically creates directory folders if they do not exist yet.

appendToNote(): Adds new content to the end of an existing note. Automatically adds a newline before the new content if needed.

replaceInNote(): Finds specific text in a note and replaces it with new text. Throws an error if the text to find does not exist.

3. Validation Utilities (utils/validation.ts)

This file provides security and input checking.

validatePath(): The most important security function. It checks that any file path you try to access stays within your vault directory. This prevents a malicious client from trying to access files outside your vault. It uses path resolution to prevent tricks like using symbols to escape the vault.

validateToolArguments(): Checks that all required parameters are provided when a tool is called. If any required parameter is missing, it throws an error with a list of what is missing.

4. Resource Handlers (handlers/resources.ts)

Resources in MCP are read only data that clients can access. This handler exposes your notes as resources.

handleListResources(): Creates a list of all notes in your vault. Each note becomes a resource with a unique obsidian URI (like obsidian://folder/note.md), a name, and a MIME type indicating it is markdown.

handleReadResource(): Takes a resource URI, validates that it points to a real note in your vault, reads the note content, and returns it in the MCP format.

5. Tool Handlers (handlers/tools.ts)

Tools are functions that clients can call to perform operations. This file defines what tools are available and what happens when they are called.

TOOL_DEFINITIONS: An array of all available tools. Each tool has a name, description, and schema that describes what parameters it accepts.

The six available tools are:

write_note: Takes a path and content, then creates or overwrites a note with that content.

edit_note: Takes a path, text to find, and replacement text, then performs a search and replace operation.

append_note: Takes a path and content, then adds the content to the end of an existing note.

read_note: Takes a path and returns the content of that note.

list_notes: Takes no parameters and returns all notes in the vault as a list of paths.

search_notes: Takes a search query and returns all notes that contain that text.

handleToolCall(): This is a router function. When a client wants to call a tool, this function receives the tool name and arguments, then calls the appropriate handler function based on the tool name.

6. Server Setup (server.ts)

This file brings everything together and sets up the MCP server.

createServer(): Initializes a new MCP server with the name and version from config. It registers handlers for four types of MCP requests: listing resources, reading resources, listing tools, and calling tools.

startServer(): Creates the server, sets up stdio transport for communication, and connects everything together. Stdio transport means the server communicates through standard input and output streams.

How It Works

Step by Step Workflow

Initialization:

1. •The server starts by importing index.ts
2. •index.ts calls startServer() from server.ts
3. •startServer() calls createServer() which validates the vault path
4. •If the vault path is valid, the server is created with MCP capabilities
5. •Stdio transport is attached so the server can receive and send messages
6. •The server logs that it is running and waits for client requests

Client Connection:

1. •A client like Claude Desktop connects to the server using the configured path
2. •The client and server establish a stdio communication channel
3. •The client asks what resources and tools are available

Listing Resources:

1. •Client sends a list resources request
2. •Server calls handleListResources()
3. •getAllMarkdownFiles() scans the vault and finds all markdown notes
4. •Server returns a formatted list with obsidian URIs for each note
5. •Client receives the list and knows what notes are available

Reading a Resource:

1. •Client wants to read a specific note and sends a read request with the obsidian URI
2. •Server extracts the path from the URI
3. •validatePath() checks that the path stays within the vault
4. •readNote() reads the file content
5. •Server returns the markdown content with the resource URI and MIME type

Listing Tools:

1. •Client asks what tools are available
2. •Server returns the TOOL_DEFINITIONS array
3. •Client knows what operations it can perform

Calling a Tool:

1. •Client wants to perform an action (like write a note) and sends a tool call request
2. •handleToolCall() receives the tool name and arguments
3. •Based on the tool name, the appropriate handler is called
4. •The handler validates arguments using validateToolArguments()
5. •The handler builds the full file path
6. •validatePath() confirms the path is within the vault
7. •The file system operation is performed (read, write, append, or replace)
8. •A success message is returned to the client

Error Handling

Throughout the process, errors are caught and returned to the client with descriptive messages:

• •Vault path validation errors before the server even starts
• •File not found errors when reading non existent notes
• •Path security errors when trying to access outside the vault
• •Missing parameter errors when tool arguments are incomplete
• •Text not found errors when replacing text that does not exist

Security Features

Path Validation and Directory Traversal Protection

The most critical security feature is path validation. This prevents attackers from using tricks to escape the vault directory and access sensitive files on your computer.

The validatePath() function:

1. •Takes the file path being accessed
2. •Converts it to an absolute path (a complete path from the root)
3. •Gets the absolute path of the vault directory
4. •Checks that the file path starts with the vault path
5. •Throws an error if the file is outside the vault

Example: If your vault is at /Users/username/notes and someone tries to access /Users/username/sensitive/passwords.txt, the validation will fail and the access is denied.

Common tricks that are prevented:

Dot Dot Escaping: Trying to use ../ to go up directories will be resolved to the absolute path and caught.

Symbolic Links: On systems with symbolic links, the resolution process prevents following links outside the vault.

Absolute Paths: An absolute path like /etc/passwd will not start with the vault path and will be rejected.

Input Validation

Tool arguments are validated to ensure:

• •Required parameters are provided
• •Parameters are not undefined or empty
• •Errors are descriptive when validation fails

Vault Restriction

The entire server operates under the constraint of OBSIDIAN_VAULT_PATH. Every operation is restricted to this path:

• •Reading only returns notes from the vault
• •Writing only creates notes inside the vault
• •Searching only examines vault contents
• •Listing only shows vault notes

Error Handling

Errors do not expose internal paths or system information. Instead, they return user friendly messages:

• •"Access denied: Path outside vault" instead of revealing directory structures
• •"Note not found: filename" instead of system errors
• •"Text not found in note" instead of vague errors

Use Cases

Research and Knowledge Management

Store research notes in Obsidian and have Claude read and synthesize information across multiple notes. Ask questions like "What did I learn about machine learning last month" and have Claude search your vault, read relevant notes, and provide a summary.

Writing Assistance

Use Claude to help write notes. Ask it to expand on a topic, create outlines, or refactor existing content. The AI can read your current notes, understand context, and suggest improvements.

Automated Note Organization

Have Claude create new notes, organize information, and create connections between concepts. For example, automatically create summary notes from meeting transcripts or categorize articles you have saved.

Personal AI Assistant with Memory

Your Obsidian vault becomes your AI assistant's long term memory. Claude can remember important information about you, your projects, your preferences, and use this context in all conversations.

Integration with Workflows

Combine this server with other tools. For example, a workflow could capture highlights from articles, have Claude analyze them, and create organized notes in your vault.

Learning and Education

Students can have Claude help them learn by reading their course notes, explaining concepts, generating practice questions, and creating study guides.

Installation and Setup

Prerequisites

You need to have the following installed on your computer:

• •Node.js (version 14 or higher recommended, but version 20 or 18 is ideal)
• •npm (Node Package Manager, which comes with Node.js)
• •An Obsidian vault (a folder where you keep your markdown notes)

Installation Steps

1. Clone or Download the Project

If you have git installed, run:

git clone <repository-url>
cd obsidian-mcp-server

Or download the files directly and extract them.

2. Install Dependencies

Navigate to the project folder and run:

npm install

This downloads and installs the MCP SDK, TypeScript, and other required libraries.

3. Create Environment Configuration

Create a file named .env in the project root directory with your vault path:

OBSIDIAN_VAULT_PATH=/Users/username/Documents/ObsidianVault

On Windows:

OBSIDIAN_VAULT_PATH=C:\Users\username\Documents\ObsidianVault

Replace the path with your actual Obsidian vault location.

4. Build the Project

Convert TypeScript to JavaScript:

npm run build

This creates a dist folder with compiled JavaScript files.

5. Test the Server

Run the server:

npm start

The server should display: "Obsidian MCP Server running on stdio"

Press Ctrl+C to stop it.

Configuration for Claude Desktop

To use this server with Claude Desktop:

Mac: Create or edit the file at:

~/Library/Application Support/Claude/claude_desktop_config.json

Windows: Create or edit the file at:

%APPDATA%\Claude\claude_desktop_config.json

Add this configuration:

{
  "mcpServers": {
    "obsidian": {
      "command": "node",
      "args": ["/full/path/to/obsidian-mcp-server/dist/index.js"],
      "env": {
        "OBSIDIAN_VAULT_PATH": "/full/path/to/your/vault"
      }
    }
  }
}

Replace the paths with your actual paths (use absolute paths, not relative paths).

After saving, restart Claude Desktop. You should now be able to use the Obsidian tools.

Development Mode

During development, you can run the server directly from TypeScript without building:

npm run dev

This requires ts node to be installed globally or as a dev dependency.

Technical Details

TypeScript and Type Safety

The project uses TypeScript for several benefits:

Compile Time Error Detection: Errors are caught before running the code.

IntelliSense: Code editors provide better autocomplete and suggestions.

Self Documenting Code: Types act as inline documentation about what data types are expected.

Maintainability: Future developers understand what data flows through the code.

Module System

The project uses ES modules (ESM), the modern JavaScript module system. This is specified in package.json with "type": "module".

Benefits include:

• •Native import/export syntax instead of require
• •Better tree shaking (removing unused code)
• •Compatibility with modern JavaScript

File Operations

All file operations go through the filesystem.ts utility:

• •Uses Node.js fs module for file operations
• •All paths go through validation before use
• •Errors are caught and reported clearly
• •Directory creation is automatic when writing notes

Search Implementation

The search function:

1. •Gets all markdown files in the vault
2. •Reads each file content
3. •Performs case insensitive text matching
4. •Returns matching file paths
5. •Skips unreadable files gracefully

The search is simple but effective. For huge vaults with thousands of notes, a more sophisticated search might be needed.

Dependency Management

The project minimizes external dependencies:

Required Dependencies:

• •@modelcontextprotocol/sdk: Official MCP SDK for implementing the protocol
• •dotenv: Loads environment variables from .env file

Dev Dependencies:

• •@types/node: TypeScript types for Node.js APIs
• •typescript: The TypeScript compiler

This keeps the project lightweight and fast.

Build Output

When you run npm run build:

• •TypeScript files are compiled to JavaScript
• •Source maps are generated (*.js.map) for debugging
• •Declaration files are created (*.d.ts) for type checking
• •All output goes to the dist folder

Summary

The Obsidian MCP Server is a well architected, secure bridge between your personal knowledge base and AI assistants. It demonstrates excellent software engineering practices:

Clean Architecture: Clear separation of concerns with modular code

Security First: Path validation prevents unauthorized file access

Error Handling: Graceful errors with helpful messages

Extensibility: Easy to add new tools or resources

Type Safety: TypeScript ensures code reliability

Minimal Dependencies: Focused on core functionality

This server exemplifies how MCPs democratize AI access to personal information while maintaining security and control. As MCP technology matures, this pattern will become standard for integrating AI with personal productivity tools.