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Skeleton MCP Server

by nickweedon

Skeleton MCP Server

A template project for building Model Context Protocol (MCP) servers. This skeleton provides a solid foundation with best practices, Docker support, and example implementations.

Features

  • FastMCP framework for easy MCP server development

  • Docker and Docker Compose support for containerized deployment

  • VS Code Dev Container configuration for consistent development environments

  • Example CRUD API implementation to demonstrate patterns

  • Test suite with pytest

  • Claude Code integration with custom commands

Related MCP server: MCP Server Template

Quick Start

Prerequisites

  • Python 3.10 or higher

  • uv package manager (recommended)

  • Docker (optional, for containerized deployment)

Installation

  1. Clone this repository and rename it for your project:

git clone <this-repo> my-mcp-server
cd my-mcp-server
  1. Rename the package:

    • Rename src/skeleton_mcp to src/your_project_name

    • Update pyproject.toml with your project name and metadata

    • Update imports in all Python files

  2. Install dependencies:

uv sync
  1. Create your environment file:

cp .env.example .env
# Edit .env with your API credentials
  1. Run the server:

uv run skeleton-mcp

Project Structure

skeleton_mcp/
├── src/skeleton_mcp/
│   ├── __init__.py          # Package initialization
│   ├── server.py            # Main MCP server entry point
│   ├── client.py            # API client for backend communication
│   ├── types.py             # TypedDict definitions
│   ├── api/                  # API modules
│   │   ├── __init__.py
│   │   └── example.py       # Example CRUD operations
│   └── utils/               # Utility modules
│       └── __init__.py
├── tests/                   # Test suite
│   ├── conftest.py          # Pytest fixtures
│   ├── test_example_api.py  # API tests
│   └── test_server.py       # Server tests
├── docs/                    # Documentation
├── .claude/                 # Claude Code configuration
│   ├── commands/            # Custom slash commands
│   └── settings.local.json  # Permission settings
├── .devcontainer/           # VS Code dev container
├── Dockerfile               # Container image definition
├── docker-compose.yml       # Production compose file
├── docker-compose.devcontainer.yml  # Dev container compose
├── pyproject.toml           # Project configuration
├── CLAUDE.md               # Claude context documentation
└── README.md               # This file

Development

Running Tests

uv run pytest -v

Linting

uv run ruff check src/ tests/
uv run ruff format src/ tests/

Building

uv build

Adding Your Own Tools

  1. Create a new module in src/skeleton_mcp/api/:

# src/skeleton_mcp/api/my_api.py

async def my_tool(param1: str, param2: int = 10) -> dict:
    """
    Description of what this tool does.

    Args:
        param1: Description of param1
        param2: Description of param2

    Returns:
        Description of return value
    """
    # Your implementation here
    return {"result": "success"}
  1. Register the tool in server.py:

from .api import my_api

mcp.tool()(my_api.my_tool)
  1. Add types in types.py if needed:

class MyDataType(TypedDict):
    field1: str
    field2: int

Handling Large Files and Binary Data

For MCP servers that need to handle large file uploads, downloads, or binary blob storage, use the mcp-mapped-resource-lib library:

pip install mcp-mapped-resource-lib

This library provides:

  • Blob management with unique identifiers

  • Automatic TTL-based expiration and cleanup

  • Content deduplication

  • Security features (path traversal prevention, MIME validation)

  • Docker volume integration for shared storage

See CLAUDE.md for detailed usage examples.

Docker Deployment

Build and run with Docker Compose:

docker compose up --build

For development with VS Code Dev Containers:

  1. Open the project in VS Code

  2. Install the "Dev Containers" extension

  3. Click "Reopen in Container" when prompted

Claude Desktop Integration

Add to your Claude Desktop configuration (claude_desktop_config.json):

{
  "mcpServers": {
    "skeleton-mcp": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "--env-file",
        "/path/to/your/.env",
        "skeleton-mcp:latest"
      ]
    }
  }
}

Or for local development:

{
  "mcpServers": {
    "skeleton-mcp": {
      "command": "uv",
      "args": ["--directory", "/path/to/skeleton_mcp", "run", "skeleton-mcp"]
    }
  }
}

Available Tools

Tool

Description

health_check

Check server health and configuration status

list_items

List all items with filtering and pagination

get_item

Get a specific item by ID

create_item

Create a new item

update_item

Update an existing item

delete_item

Delete an item

Environment Variables

Variable

Description

Default

API_KEY

Your API key for authentication

(required)

API_BASE_URL

Base URL for the backend API

https://api.example.com/v1

API_TIMEOUT

Request timeout in seconds

30

DEBUG

Enable debug logging

false

License

MIT License - See LICENSE file for details.

Contributing

  1. Fork the repository

  2. Create a feature branch

  3. Make your changes

  4. Run tests and linting

  5. Submit a pull request

Available Tools

6 tools
create_itemB

Create a new item.

Args: name: The name of the item (required) description: Optional description metadata: Optional key-value metadata

Returns: The created item data including the generated ID

ParametersJSON Schema
NameRequiredDescriptionDefault
nameYes
descriptionNo
metadataNo

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

B3.2/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries full burden for behavioral disclosure. It states this is a creation operation but doesn't mention permission requirements, whether the operation is idempotent, potential side effects, rate limits, or error handling. The return statement is helpful but doesn't fully compensate for the lack of behavioral context in a mutation tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is perfectly structured with clear sections: a one-sentence purpose statement, organized parameter documentation, and a return value description. Every sentence earns its place, and the information is front-loaded with the most important details first. No wasted words or redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given this is a mutation tool with no annotations but with an output schema (implied by 'Returns' statement), the description covers the basics: purpose, parameters, and return value. However, for a creation operation, it lacks important context about authentication needs, error conditions, and behavioral constraints that would help the agent use it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description must compensate, and it does so effectively by documenting all 3 parameters with their purposes and requirements. It clearly distinguishes required vs optional parameters and provides meaningful context about what each parameter represents, going well beyond what the bare schema provides.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Create' and resource 'new item', making the purpose immediately understandable. It distinguishes from siblings like 'get_item' or 'update_item' by specifying creation rather than retrieval or modification. However, it doesn't specify what type of item or system this operates on, which prevents a perfect score.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives like 'update_item' or when not to use it. There's no mention of prerequisites, error conditions, or typical use cases. The agent must infer usage from the tool name alone, which is insufficient for optimal selection.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

delete_itemC

Delete an item.

Args: item_id: The unique identifier of the item to delete

Returns: A confirmation message

Raises: ValueError: If the item is not found

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

C2.9/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. While it mentions the destructive nature ('Delete') and error conditions, it doesn't address critical aspects like whether deletion is permanent, what permissions are required, rate limits, or side effects on related data. The 'Raises' section adds some value but doesn't fully compensate for the lack of annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with clear sections (Args, Returns, Raises) and uses minimal words to convey essential information. Every sentence earns its place, though the core 'Delete an item' could be slightly more specific about what 'item' refers to in this context.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given this is a destructive operation with no annotations, 0% schema coverage, but with an output schema (implied by 'Returns'), the description is moderately complete. It covers the basic operation, parameter, return value, and one error case, but lacks details on permissions, reversibility, and broader error handling that would be crucial for safe agent use.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It provides the parameter name and clarifies it's 'The unique identifier of the item to delete,' which adds meaningful context beyond the bare schema. However, it doesn't specify format requirements (UUID, integer, etc.) or validation rules, leaving gaps in parameter understanding.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb ('Delete') and resource ('an item'), making the purpose immediately understandable. However, it doesn't differentiate this destructive operation from its sibling 'update_item' which also modifies items, or explain what type of 'item' is being deleted (database record, file, etc.).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives like 'update_item' for modification or 'create_item' for recreation. It mentions raising ValueError if the item is not found, but doesn't specify prerequisites like authentication needs or whether deletion is reversible.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_itemA

Get a specific item by ID.

Args: item_id: The unique identifier of the item

Returns: The item data if found

Raises: ValueError: If the item is not found

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

A3.7/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It discloses that the tool returns 'The item data if found' and raises 'ValueError: If the item is not found,' which adds useful context about success and error conditions. However, it lacks details on permissions, rate limits, or other behavioral traits like whether it's read-only or has side effects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured and front-loaded with the core purpose, followed by clear sections for Args, Returns, and Raises. Every sentence earns its place by providing essential information without redundancy. It is appropriately sized for a simple tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's low complexity (one parameter) and the presence of an output schema (which handles return values), the description is mostly complete. It covers the purpose, parameter meaning, and error conditions. However, it lacks context on when to use versus siblings and behavioral details like auth needs, which could be improved for a tool in a set with create/delete/update operations.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has 0% description coverage, but the description compensates by explaining the parameter: 'item_id: The unique identifier of the item.' This adds meaning beyond the schema's type definition. Since there is only one parameter, the description effectively covers it, though it could provide more details like format or examples.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'Get a specific item by ID.' It uses a specific verb ('Get') and resource ('item'), making it easy to understand. However, it does not explicitly differentiate from sibling tools like 'list_items' (which retrieves multiple items) or 'health_check' (which checks server status), though the specificity of 'by ID' implies a distinction.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage by stating 'Get a specific item by ID,' suggesting it should be used when you have a known item ID. However, it does not provide explicit guidance on when to use this tool versus alternatives like 'list_items' (for browsing items) or 'create_item' (for adding new items). No exclusions or prerequisites are mentioned.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

health_checkB

Check the health status of the MCP server.

Returns: A dictionary with the server status and configuration info.

ParametersJSON Schema
NameRequiredDescriptionDefault

No parameters

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

B3.3/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries full burden. It states what the tool does but doesn't disclose behavioral traits like whether this requires authentication, has rate limits, or what specific 'configuration info' is returned. The mention of return format is helpful but insufficient for a mutation-free tool with zero annotation coverage.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is appropriately sized with two sentences: one stating the purpose, one describing the return format. It's front-loaded with the core functionality. The second sentence about returns could potentially be omitted since there's an output schema, but it's still useful context.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given this is a simple health check tool with 0 parameters and an output schema, the description is adequate but has gaps. It explains what the tool does and the return format, but doesn't provide context about when to use it or behavioral considerations. With output schema handling return values, the description doesn't need to explain those details.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0 parameters and 100% schema description coverage, the baseline would be 4. The description correctly indicates this is a parameterless health check, which aligns perfectly with the empty input schema. No additional parameter information is needed or provided.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb ('Check') and resource ('health status of the MCP server'), making the purpose unambiguous. It doesn't explicitly differentiate from siblings like 'get_item' or 'list_items', but health checking is sufficiently distinct from CRUD operations that differentiation is implied rather than explicit.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies this should be used for health monitoring rather than data operations, but doesn't provide explicit guidance on when to use it versus alternatives. Given the sibling tools are all CRUD operations for 'item', the context suggests this is for server diagnostics rather than data manipulation, but this isn't explicitly stated.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

list_itemsA

List all items with optional filtering and pagination.

Args: page: Page number (1-indexed) page_size: Number of items per page filter_name: Optional filter by name (case-insensitive contains)

Returns: A dictionary containing: - items: List of item objects - total: Total number of items matching the filter - page: Current page number - page_size: Number of items per page

ParametersJSON Schema
NameRequiredDescriptionDefault
pageNo
page_sizeNo
filter_nameNo

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

A3.8/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries full burden. It discloses pagination behavior (1-indexed page, returns metadata) and filtering (case-insensitive contains), but doesn't mention rate limits, authentication needs, error conditions, or whether this is a read-only operation (though 'List' implies safe read).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Well-structured with a clear summary sentence followed by Args/Returns sections. Every sentence adds value, though the Returns section could be slightly more concise given the output schema exists.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Good completeness for a list tool: purpose, parameters, and return structure are documented. With output schema present, the Returns description is somewhat redundant but helpful. Missing behavioral aspects like error handling or performance characteristics keep it from a 5.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description fully compensates by explaining all 3 parameters: page (1-indexed), page_size (items per page), and filter_name (case-insensitive contains, optional). It adds crucial semantic details not in the bare schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'List' and resource 'items', specifying optional filtering and pagination. It distinguishes from siblings like get_item (single item) and create_item/update_item/delete_item (mutations), but doesn't explicitly contrast with search or other list variants that might exist.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for retrieving multiple items with filtering/pagination, but doesn't explicitly state when to use this vs. get_item (single item) or when filtering/pagination is appropriate. No alternatives or exclusions are mentioned.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

update_itemB

Update an existing item.

Args: item_id: The unique identifier of the item to update name: New name (optional) description: New description (optional) metadata: New metadata (optional, replaces existing)

Returns: The updated item data

Raises: ValueError: If the item is not found

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes
nameNo
descriptionNo
metadataNo

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

TDQS

B3.4/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries full burden. It discloses that this is a mutation operation ('Update'), mentions the 'ValueError' for not found items, and notes that metadata 'replaces existing'. However, it lacks details about permissions, side effects, rate limits, or what 'updated item data' contains, leaving behavioral gaps.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with sections for Args, Returns, and Raises, making it easy to scan. Every sentence adds value—no fluff or repetition. It's appropriately sized for a tool with 4 parameters and clear output.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 4 parameters, 0% schema coverage, no annotations, but an output schema exists, the description is moderately complete. It covers basic parameter meanings and error handling, but lacks context on sibling differentiation, permissions, or detailed behavioral traits, making it adequate but with gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It adds meaningful semantics: 'item_id' is 'unique identifier', parameters are optional with 'new' values, and metadata 'replaces existing'. This clarifies beyond the schema's types and defaults, though it doesn't cover all parameter nuances like format constraints.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Update' and resource 'existing item', making the purpose immediately understandable. However, it doesn't differentiate from sibling tools like 'create_item' or 'delete_item' beyond the basic verb difference, which prevents a perfect score.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives like 'create_item' or 'delete_item'. It mentions that 'item_id' is required and parameters are optional, but offers no context about prerequisites, error conditions beyond 'ValueError', or comparison to siblings.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 6 tool updates
    • First observedcreate_item
    • First observeddelete_item
    • First observedget_item
    • First observedhealth_check
    • First observedlist_items
    • First observedupdate_item

TDQS

A3.7/5.0

Scored across 6 tools

Disambiguation5/5

Every tool has a clearly distinct purpose with no ambiguity. The five item-related tools (create_item, delete_item, get_item, list_items, update_item) form a complete CRUD set for a single resource type, while health_check serves a completely different operational purpose. The descriptions reinforce these distinct roles, making tool selection straightforward.

Naming Consistency5/5

All tools follow a consistent verb_noun naming pattern with snake_case throughout. The item-related tools use standard CRUD verbs (create, delete, get, list, update) followed by the resource name 'item', while health_check maintains the same pattern. There are no deviations in style or convention across the toolset.

Tool Count5/5

Six tools is perfectly appropriate for this server's purpose. The five item management tools provide complete CRUD operations with pagination and filtering, while health_check adds necessary operational functionality. This is a well-scoped set where each tool clearly earns its place without being overwhelming or insufficient.

Completeness5/5

The tool surface provides complete coverage for the item management domain with full CRUD operations (create, read, update, delete) plus listing with filtering and pagination. The health_check tool adds operational monitoring. There are no obvious gaps - agents can perform all expected lifecycle operations on items without dead ends or workarounds.

Maintenance

ActivityInactive
ResponsivenessNo issues

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