mcp_server_development_guide_with_evaluation_harness.py

python
An MCP (Model Context Protocol) server evaluation harness that connects to MCP servers via stdio, SSE, or HTTP transports, runs test questions against them using Claude as the evaluating LLM, and generates accuracy reports with tool usage metrics and feedback.
20d ago777 lines
sickn33/antigravity-awesome-skills
Agent Votes
mcp_server_development_guide_with_evaluation_harness.py
# SKILL.md

---
name: mcp-builder
description: Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
license: Complete terms in LICENSE.txt
---

# MCP Server Development Guide

## Overview

Create MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. The quality of an MCP server is measured by how well it enables LLMs to accomplish real-world tasks.

---

# Process

## 🚀 High-Level Workflow

Creating a high-quality MCP server involves four main phases:

### Phase 1: Deep Research and Planning

#### 1.1 Understand Modern MCP Design

**API Coverage vs. Workflow Tools:**
Balance comprehensive API endpoint coverage with specialized workflow tools. Workflow tools can be more convenient for specific tasks, while comprehensive coverage gives agents flexibility to compose operations. Performance varies by client—some clients benefit from code execution that combines basic tools, while others work better with higher-level workflows. When uncertain, prioritize comprehensive API coverage.

**Tool Naming and Discoverability:**
Clear, descriptive tool names help agents find the right tools quickly. Use consistent prefixes (e.g., `github_create_issue`, `github_list_repos`) and action-oriented naming.

**Context Management:**
Agents benefit from concise tool descriptions and the ability to filter/paginate results. Design tools that return focused, relevant data. Some clients support code execution which can help agents filter and process data efficiently.

**Actionable Error Messages:**
Error messages should guide agents toward solutions with specific suggestions and next steps.

#### 1.2 Study MCP Protocol Documentation

**Navigate the MCP specification:**

Start with the sitemap to find relevant pages: `https://modelcontextprotocol.io/sitemap.xml`

Then fetch specific pages with `.md` suffix for markdown format (e.g., `https://modelcontextprotocol.io/specification/draft.md`).

Key pages to review:
- Specification overview and architecture
- Transport mechanisms (streamable HTTP, stdio)
- Tool, resource, and prompt definitions

#### 1.3 Study Framework Documentation

**Recommended stack:**
- **Language**: TypeScript (high-quality SDK support and good compatibility in many execution environments e.g. MCPB. Plus AI models are good at generating TypeScript code, benefiting from its broad usage, static typing and good linting tools)
- **Transport**: Streamable HTTP for remote servers, using stateless JSON (simpler to scale and maintain, as opposed to stateful sessions and streaming responses). stdio for local servers.

**Load framework documentation:**

- **MCP Best Practices**: [📋 View Best Practices](./reference/mcp_best_practices.md) - Core guidelines

**For TypeScript (recommended):**
- **TypeScript SDK**: Use WebFetch to load `https://raw.githubusercontent.com/modelcontextprotocol/typescript-sdk/main/README.md`
- [⚡ TypeScript Guide](./reference/node_mcp_server.md) - TypeScript patterns and examples

**For Python:**
- **Python SDK**: Use WebFetch to load `https://raw.githubusercontent.com/modelcontextprotocol/python-sdk/main/README.md`
- [🐍 Python Guide](./reference/python_mcp_server.md) - Python patterns and examples

#### 1.4 Plan Your Implementation

**Understand the API:**
Review the service's API documentation to identify key endpoints, authentication requirements, and data models. Use web search and WebFetch as needed.

**Tool Selection:**
Prioritize comprehensive API coverage. List endpoints to implement, starting with the most common operations.

---

### Phase 2: Implementation

#### 2.1 Set Up Project Structure

See language-specific guides for project setup:
- [⚡ TypeScript Guide](./reference/node_mcp_server.md) - Project structure, package.json, tsconfig.json
- [🐍 Python Guide](./reference/python_mcp_server.md) - Module organization, dependencies

#### 2.2 Implement Core Infrastructure

Create shared utilities:
- API client with authentication
- Error handling helpers
- Response formatting (JSON/Markdown)
- Pagination support

#### 2.3 Implement Tools

For each tool:

**Input Schema:**
- Use Zod (TypeScript) or Pydantic (Python)
- Include constraints and clear descriptions
- Add examples in field descriptions

**Output Schema:**
- Define `outputSchema` where possible for structured data
- Use `structuredContent` in tool responses (TypeScript SDK feature)
- Helps clients understand and process tool outputs

**Tool Description:**
- Concise summary of functionality
- Parameter descriptions
- Return type schema

**Implementation:**
- Async/await for I/O operations
- Proper error handling with actionable messages
- Support pagination where applicable
- Return both text content and structured data when using modern SDKs

**Annotations:**
- `readOnlyHint`: true/false
- `destructiveHint`: true/false
- `idempotentHint`: true/false
- `openWorldHint`: true/false

---

### Phase 3: Review and Test

#### 3.1 Code Quality

Review for:
- No duplicated code (DRY principle)
- Consistent error handling
- Full type coverage
- Clear tool descriptions

#### 3.2 Build and Test

**TypeScript:**
- Run `npm run build` to verify compilation
- Test with MCP Inspector: `npx @modelcontextprotocol/inspector`

**Python:**
- Verify syntax: `python -m py_compile your_server.py`
- Test with MCP Inspector

See language-specific guides for detailed testing approaches and quality checklists.

---

### Phase 4: Create Evaluations

After implementing your MCP server, create comprehensive evaluations to test its effectiveness.

**Load [✅ Evaluation Guide](./reference/evaluation.md) for complete evaluation guidelines.**

#### 4.1 Understand Evaluation Purpose

Use evaluations to test whether LLMs can effectively use your MCP server to answer realistic, complex questions.

#### 4.2 Create 10 Evaluation Questions

To create effective evaluations, follow the process outlined in the evaluation guide:

1. **Tool Inspection**: List available tools and understand their capabilities
2. **Content Exploration**: Use READ-ONLY operations to explore available data
3. **Question Generation**: Create 10 complex, realistic questions
4. **Answer Verification**: Solve each question yourself to verify answers

#### 4.3 Evaluation Requirements

Ensure each question is:
- **Independent**: Not dependent on other questions
- **Read-only**: Only non-destructive operations required
- **Complex**: Requiring multiple tool calls and deep exploration
- **Realistic**: Based on real use cases humans would care about
- **Verifiable**: Single, clear answer that can be verified by string comparison
- **Stable**: Answer won't change over time

#### 4.4 Output Format

Create an XML file with this structure:

```xml
<evaluation>
  <qa_pair>
    <question>Find discussions about AI model launches with animal codenames. One model needed a specific safety designation that uses the format ASL-X. What number X was being determined for the model named after a spotted wild cat?</question>
    <answer>3</answer>
  </qa_pair>
<!-- More qa_pairs... -->
</evaluation>
```

---

# Reference Files

## 📚 Documentation Library

Load these resources as needed during development:

### Core MCP Documentation (Load First)
- **MCP Protocol**: Start with sitemap at `https://modelcontextprotocol.io/sitemap.xml`, then fetch specific pages with `.md` suffix
- [📋 MCP Best Practices](./reference/mcp_best_practices.md) - Universal MCP guidelines including:
  - Server and tool naming conventions
  - Response format guidelines (JSON vs Markdown)
  - Pagination best practices
  - Transport selection (streamable HTTP vs stdio)
  - Security and error handling standards

### SDK Documentation (Load During Phase 1/2)
- **Python SDK**: Fetch from `https://raw.githubusercontent.com/modelcontextprotocol/python-sdk/main/README.md`
- **TypeScript SDK**: Fetch from `https://raw.githubusercontent.com/modelcontextprotocol/typescript-sdk/main/README.md`

### Language-Specific Implementation Guides (Load During Phase 2)
- [🐍 Python Implementation Guide](./reference/python_mcp_server.md) - Complete Python/FastMCP guide with:
  - Server initialization patterns
  - Pydantic model examples
  - Tool registration with `@mcp.tool`
  - Complete working examples
  - Quality checklist

- [⚡ TypeScript Implementation Guide](./reference/node_mcp_server.md) - Complete TypeScript guide with:
  - Project structure
  - Zod schema patterns
  - Tool registration with `server.registerTool`
  - Complete working examples
  - Quality checklist

### Evaluation Guide (Load During Phase 4)
- [✅ Evaluation Guide](./reference/evaluation.md) - Complete evaluation creation guide with:
  - Question creation guidelines
  - Answer verification strategies
  - XML format specifications
  - Example questions and answers
  - Running an evaluation with the provided scripts



# connections.py

```python
"""Lightweight connection handling for MCP servers."""

from abc import ABC, abstractmethod
from contextlib import AsyncExitStack
from typing import Any

from mcp import ClientSession, StdioServerParameters
from mcp.client.sse import sse_client
from mcp.client.stdio import stdio_client
from mcp.client.streamable_http import streamablehttp_client


class MCPConnection(ABC):
    """Base class for MCP server connections."""

    def __init__(self):
        self.session = None
        self._stack = None

    @abstractmethod
    def _create_context(self):
        """Create the connection context based on connection type."""

    async def __aenter__(self):
        """Initialize MCP server connection."""
        self._stack = AsyncExitStack()
        await self._stack.__aenter__()

        try:
            ctx = self._create_context()
            result = await self._stack.enter_async_context(ctx)

            if len(result) == 2:
                read, write = result
            elif len(result) == 3:
                read, write, _ = result
            else:
                raise ValueError(f"Unexpected context result: {result}")

            session_ctx = ClientSession(read, write)
            self.session = await self._stack.enter_async_context(session_ctx)
            await self.session.initialize()
            return self
        except BaseException:
            await self._stack.__aexit__(None, None, None)
            raise

    async def __aexit__(self, exc_type, exc_val, exc_tb):
        """Clean up MCP server connection resources."""
        if self._stack:
            await self._stack.__aexit__(exc_type, exc_val, exc_tb)
        self.session = None
        self._stack = None

    async def list_tools(self) -> list[dict[str, Any]]:
        """Retrieve available tools from the MCP server."""
        response = await self.session.list_tools()
        return [
            {
                "name": tool.name,
                "description": tool.description,
                "input_schema": tool.inputSchema,
            }
            for tool in response.tools
        ]

    async def call_tool(self, tool_name: str, arguments: dict[str, Any]) -> Any:
        """Call a tool on the MCP server with provided arguments."""
        result = await self.session.call_tool(tool_name, arguments=arguments)
        return result.content


class MCPConnectionStdio(MCPConnection):
    """MCP connection using standard input/output."""

    def __init__(self, command: str, args: list[str] = None, env: dict[str, str] = None):
        super().__init__()
        self.command = command
        self.args = args or []
        self.env = env

    def _create_context(self):
        return stdio_client(
            StdioServerParameters(command=self.command, args=self.args, env=self.env)
        )


class MCPConnectionSSE(MCPConnection):
    """MCP connection using Server-Sent Events."""

    def __init__(self, url: str, headers: dict[str, str] = None):
        super().__init__()
        self.url = url
        self.headers = headers or {}

    def _create_context(self):
        return sse_client(url=self.url, headers=self.headers)


class MCPConnectionHTTP(MCPConnection):
    """MCP connection using Streamable HTTP."""

    def __init__(self, url: str, headers: dict[str, str] = None):
        super().__init__()
        self.url = url
        self.headers = headers or {}

    def _create_context(self):
        return streamablehttp_client(url=self.url, headers=self.headers)


def create_connection(
    transport: str,
    command: str = None,
    args: list[str] = None,
    env: dict[str, str] = None,
    url: str = None,
    headers: dict[str, str] = None,
) -> MCPConnection:
    """Factory function to create the appropriate MCP connection.

    Args:
        transport: Connection type ("stdio", "sse", or "http")
        command: Command to run (stdio only)
        args: Command arguments (stdio only)
        env: Environment variables (stdio only)
        url: Server URL (sse and http only)
        headers: HTTP headers (sse and http only)

    Returns:
        MCPConnection instance
    """
    transport = transport.lower()

    if transport == "stdio":
        if not command:
            raise ValueError("Command is required for stdio transport")
        return MCPConnectionStdio(command=command, args=args, env=env)

    elif transport == "sse":
        if not url:
            raise ValueError("URL is required for sse transport")
        return MCPConnectionSSE(url=url, headers=headers)

    elif transport in ["http", "streamable_http", "streamable-http"]:
        if not url:
            raise ValueError("URL is required for http transport")
        return MCPConnectionHTTP(url=url, headers=headers)

    else:
        raise ValueError(f"Unsupported transport type: {transport}. Use 'stdio', 'sse', or 'http'")

```


# evaluation.py

```python
"""MCP Server Evaluation Harness

This script evaluates MCP servers by running test questions against them using Claude.
"""

import argparse
import asyncio
import json
import re
import sys
import time
import traceback
import xml.etree.ElementTree as ET
from pathlib import Path
from typing import Any

from anthropic import Anthropic

from connections import create_connection

EVALUATION_PROMPT = """You are an AI assistant with access to tools.

When given a task, you MUST:
1. Use the available tools to complete the task
2. Provide summary of each step in your approach, wrapped in <summary> tags
3. Provide feedback on the tools provided, wrapped in <feedback> tags
4. Provide your final response, wrapped in <response> tags

Summary Requirements:
- In your <summary> tags, you must explain:
  - The steps you took to complete the task
  - Which tools you used, in what order, and why
  - The inputs you provided to each tool
  - The outputs you received from each tool
  - A summary for how you arrived at the response

Feedback Requirements:
- In your <feedback> tags, provide constructive feedback on the tools:
  - Comment on tool names: Are they clear and descriptive?
  - Comment on input parameters: Are they well-documented? Are required vs optional parameters clear?
  - Comment on descriptions: Do they accurately describe what the tool does?
  - Comment on any errors encountered during tool usage: Did the tool fail to execute? Did the tool return too many tokens?
  - Identify specific areas for improvement and explain WHY they would help
  - Be specific and actionable in your suggestions

Response Requirements:
- Your response should be concise and directly address what was asked
- Always wrap your final response in <response> tags
- If you cannot solve the task return <response>NOT_FOUND</response>
- For numeric responses, provide just the number
- For IDs, provide just the ID
- For names or text, provide the exact text requested
- Your response should go last"""


def parse_evaluation_file(file_path: Path) -> list[dict[str, Any]]:
    """Parse XML evaluation file with qa_pair elements."""
    try:
        tree = ET.parse(file_path)
        root = tree.getroot()
        evaluations = []

        for qa_pair in root.findall(".//qa_pair"):
            question_elem = qa_pair.find("question")
            answer_elem = qa_pair.find("answer")

            if question_elem is not None and answer_elem is not None:
                evaluations.append({
                    "question": (question_elem.text or "").strip(),
                    "answer": (answer_elem.text or "").strip(),
                })

        return evaluations
    except Exception as e:
        print(f"Error parsing evaluation file {file_path}: {e}")
        return []


def extract_xml_content(text: str, tag: str) -> str | None:
    """Extract content from XML tags."""
    pattern = rf"<{tag}>(.*?)</{tag}>"
    matches = re.findall(pattern, text, re.DOTALL)
    return matches[-1].strip() if matches else None


async def agent_loop(
    client: Anthropic,
    model: str,
    question: str,
    tools: list[dict[str, Any]],
    connection: Any,
) -> tuple[str, dict[str, Any]]:
    """Run the agent loop with MCP tools."""
    messages = [{"role": "user", "content": question}]

    response = await asyncio.to_thread(
        client.messages.create,
        model=model,
        max_tokens=4096,
        system=EVALUATION_PROMPT,
        messages=messages,
        tools=tools,
    )

    messages.append({"role": "assistant", "content": response.content})

    tool_metrics = {}

    while response.stop_reason == "tool_use":
        tool_use = next(block for block in response.content if block.type == "tool_use")
        tool_name = tool_use.name
        tool_input = tool_use.input

        tool_start_ts = time.time()
        try:
            tool_result = await connection.call_tool(tool_name, tool_input)
            tool_response = json.dumps(tool_result) if isinstance(tool_result, (dict, list)) else str(tool_result)
        except Exception as e:
            tool_response = f"Error executing tool {tool_name}: {str(e)}\n"
            tool_response += traceback.format_exc()
        tool_duration = time.time() - tool_start_ts

        if tool_name not in tool_metrics:
            tool_metrics[tool_name] = {"count": 0, "durations": []}
        tool_metrics[tool_name]["count"] += 1
        tool_metrics[tool_name]["durations"].append(tool_duration)

        messages.append({
            "role": "user",
            "content": [{
                "type": "tool_result",
                "tool_use_id": tool_use.id,
                "content": tool_response,
            }]
        })

        response = await asyncio.to_thread(
            client.messages.create,
            model=model,
            max_tokens=4096,
            system=EVALUATION_PROMPT,
            messages=messages,
            tools=tools,
        )
        messages.append({"role": "assistant", "content": response.content})

    response_text = next(
        (block.text for block in response.content if hasattr(block, "text")),
        None,
    )
    return response_text, tool_metrics


async def evaluate_single_task(
    client: Anthropic,
    model: str,
    qa_pair: dict[str, Any],
    tools: list[dict[str, Any]],
    connection: Any,
    task_index: int,
) -> dict[str, Any]:
    """Evaluate a single QA pair with the given tools."""
    start_time = time.time()

    print(f"Task {task_index + 1}: Running task with question: {qa_pair['question']}")
    response, tool_metrics = await agent_loop(client, model, qa_pair["question"], tools, connection)

    response_value = extract_xml_content(response, "response")
    summary = extract_xml_content(response, "summary")
    feedback = extract_xml_content(response, "feedback")

    duration_seconds = time.time() - start_time

    return {
        "question": qa_pair["question"],
        "expected": qa_pair["answer"],
        "actual": response_value,
        "score": int(response_value == qa_pair["answer"]) if response_value else 0,
        "total_duration": duration_seconds,
        "tool_calls": tool_metrics,
        "num_tool_calls": sum(len(metrics["durations"]) for metrics in tool_metrics.values()),
        "summary": summary,
        "feedback": feedback,
    }


REPORT_HEADER = """
# Evaluation Report

## Summary

- **Accuracy**: {correct}/{total} ({accuracy:.1f}%)
- **Average Task Duration**: {average_duration_s:.2f}s
- **Average Tool Calls per Task**: {average_tool_calls:.2f}
- **Total Tool Calls**: {total_tool_calls}

---
"""

TASK_TEMPLATE = """
### Task {task_num}

**Question**: {question}
**Ground Truth Answer**: `{expected_answer}`
**Actual Answer**: `{actual_answer}`
**Correct**: {correct_indicator}
**Duration**: {total_duration:.2f}s
**Tool Calls**: {tool_calls}

**Summary**
{summary}

**Feedback**
{feedback}

---
"""


async def run_evaluation(
    eval_path: Path,
    connection: Any,
    model: str = "claude-3-7-sonnet-20250219",
) -> str:
    """Run evaluation with MCP server tools."""
    print("🚀 Starting Evaluation")

    client = Anthropic()

    tools = await connection.list_tools()
    print(f"📋 Loaded {len(tools)} tools from MCP server")

    qa_pairs = parse_evaluation_file(eval_path)
    print(f"📋 Loaded {len(qa_pairs)} evaluation tasks")

    results = []
    for i, qa_pair in enumerate(qa_pairs):
        print(f"Processing task {i + 1}/{len(qa_pairs)}")
        result = await evaluate_single_task(client, model, qa_pair, tools, connection, i)
        results.append(result)

    correct = sum(r["score"] for r in results)
    accuracy = (correct / len(results)) * 100 if results else 0
    average_duration_s = sum(r["total_duration"] for r in results) / len(results) if results else 0
    average_tool_calls = sum(r["num_tool_calls"] for r in results) / len(results) if results else 0
    total_tool_calls = sum(r["num_tool_calls"] for r in results)

    report = REPORT_HEADER.format(
        correct=correct,
        total=len(results),
        accuracy=accuracy,
        average_duration_s=average_duration_s,
        average_tool_calls=average_tool_calls,
        total_tool_calls=total_tool_calls,
    )

    report += "".join([
        TASK_TEMPLATE.format(
            task_num=i + 1,
            question=qa_pair["question"],
            expected_answer=qa_pair["answer"],
            actual_answer=result["actual"] or "N/A",
            correct_indicator="✅" if result["score"] else "❌",
            total_duration=result["total_duration"],
            tool_calls=json.dumps(result["tool_calls"], indent=2),
            summary=result["summary"] or "N/A",
            feedback=result["feedback"] or "N/A",
        )
        for i, (qa_pair, result) in enumerate(zip(qa_pairs, results))
    ])

    return report


def parse_headers(header_list: list[str]) -> dict[str, str]:
    """Parse header strings in format 'Key: Value' into a dictionary."""
    headers = {}
    if not header_list:
        return headers

    for header in header_list:
        if ":" in header:
            key, value = header.split(":", 1)
            headers[key.strip()] = value.strip()
        else:
            print(f"Warning: Ignoring malformed header: {header}")
    return headers


def parse_env_vars(env_list: list[str]) -> dict[str, str]:
    """Parse environment variable strings in format 'KEY=VALUE' into a dictionary."""
    env = {}
    if not env_list:
        return env

    for env_var in env_list:
        if "=" in env_var:
            key, value = env_var.split("=", 1)
            env[key.strip()] = value.strip()
        else:
            print(f"Warning: Ignoring malformed environment variable: {env_var}")
    return env


async def main():
    parser = argparse.ArgumentParser(
        description="Evaluate MCP servers using test questions",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
Examples:
  # Evaluate a local stdio MCP server
  python evaluation.py -t stdio -c python -a my_server.py eval.xml

  # Evaluate an SSE MCP server
  python evaluation.py -t sse -u https://example.com/mcp -H "Authorization: Bearer token" eval.xml

  # Evaluate an HTTP MCP server with custom model
  python evaluation.py -t http -u https://example.com/mcp -m claude-3-5-sonnet-20241022 eval.xml
        """,
    )

    parser.add_argument("eval_file", type=Path, help="Path to evaluation XML file")
    parser.add_argument("-t", "--transport", choices=["stdio", "sse", "http"], default="stdio", help="Transport type (default: stdio)")
    parser.add_argument("-m", "--model", default="claude-3-7-sonnet-20250219", help="Claude model to use (default: claude-3-7-sonnet-20250219)")

    stdio_group = parser.add_argument_group("stdio options")
    stdio_group.add_argument("-c", "--command", help="Command to run MCP server (stdio only)")
    stdio_group.add_argument("-a", "--args", nargs="+", help="Arguments for the command (stdio only)")
    stdio_group.add_argument("-e", "--env", nargs="+", help="Environment variables in KEY=VALUE format (stdio only)")

    remote_group = parser.add_argument_group("sse/http options")
    remote_group.add_argument("-u", "--url", help="MCP server URL (sse/http only)")
    remote_group.add_argument("-H", "--header", nargs="+", dest="headers", help="HTTP headers in 'Key: Value' format (sse/http only)")

    parser.add_argument("-o", "--output", type=Path, help="Output file for evaluation report (default: stdout)")

    args = parser.parse_args()

    if not args.eval_file.exists():
        print(f"Error: Evaluation file not found: {args.eval_file}")
        sys.exit(1)

    headers = parse_headers(args.headers) if args.headers else None
    env_vars = parse_env_vars(args.env) if args.env else None

    try:
        connection = create_connection(
            transport=args.transport,
            command=args.command,
            args=args.args,
            env=env_vars,
            url=args.url,
            headers=headers,
        )
    except ValueError as e:
        print(f"Error: {e}")
        sys.exit(1)

    print(f"🔗 Connecting to MCP server via {args.transport}...")

    async with connection:
        print("✅ Connected successfully")
        report = await run_evaluation(args.eval_file, connection, args.model)

        if args.output:
            args.output.write_text(report)
            print(f"\n✅ Report saved to {args.output}")
        else:
            print("\n" + report)


if __name__ == "__main__":
    asyncio.run(main())

```