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DataCenter MCP Server with semantic search and operation execution","maintainers":[{"name":"guerchele","email":"guerchele@hotmail.com"}],"readme":"# Jira Data Center MCP Server\n\n[![CI](https://github.com/guercheLE/jira-dc-mcp/workflows/CI/badge.svg)](https://github.com/guercheLE/jira-dc-mcp/actions)\n[![npm version](https://badge.fury.io/js/jira-dc-mcp.svg)](https://www.npmjs.com/package/jira-dc-mcp)\n[![License: LGPL-3.0](https://img.shields.io/badge/License-LGPL%203.0-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0)\n[![Node.js Version](https://img.shields.io/badge/node-%3E%3D22-brightgreen)](https://nodejs.org)\n[![Contributing](https://img.shields.io/badge/Contributions-Welcome-blue.svg)](CONTRIBUTING.md)\n\n**Model Context Protocol (MCP) server for Atlassian Jira Data Center** with semantic search and AI-powered workflow automation.\n\nTransform natural language queries into precise Jira API operations. Built for LLMs (Claude, GPT-4, and other MCP-compatible clients) to interact intelligently with Jira Data Center through production-ready semantic search and operation execution.\n\n## Why This Exists\n\nWorking with Jira's REST API requires knowing exact endpoint names, HTTP methods, and complex JSON schemas. **This MCP server solves that problem**:\n\n- **Semantic Search**: Ask \"create an issue\" → get ranked Jira operations with >90% relevance\n- **Zero-Config Setup**: Interactive 5-minute wizard handles authentication, credentials, and database setup\n- **Production-Ready**: Circuit breakers, rate limiting, retry logic, and secure credential storage (OS keychains)\n- **Multi-Auth Support**: OAuth 2.0, Personal Access Tokens, OAuth 1.0a, or Basic Auth\n- **Security-First**: Automatic data sanitization in logs, sensitive information redaction, and structured logging\n\nPerfect for teams building AI assistants, automation workflows, or LLM integrations with Jira Data Center.\n\n---\n\n<!-- TODO: Add screenshots once available\n## Visual Overview\n\n### Setup Wizard\n![Setup Wizard](docs/images/setup-wizard.png)\n*Interactive setup wizard completes configuration in under 5 minutes*\n\n### Semantic Search in Action\n![Search Results](docs/images/search-results.png)\n*Natural language queries return ranked Jira operations with relevance scores*\n\n### Claude Desktop Integration\n![Claude Desktop](docs/images/claude-desktop-integration.png)\n*Claude Desktop using MCP tools to interact with Jira Data Center*\n-->\n\n---\n\n## Table of Contents\n\n- [Key Features](#key-features)\n- [Quick Start](#quick-start)\n  - [Docker (Recommended)](#docker-recommended)\n  - [npm Install](#npm-install)\n  - [From Source](#from-source)\n- [Usage](#usage)\n  - [MCP Tools](#mcp-tools)\n  - [Common Workflows](#common-workflows)\n- [Installation](#installation)\n- [Configuration](#configuration)\n- [MCP Client Configuration](#mcp-client-configuration)\n- [Project Structure](#project-structure)\n- [Documentation](#documentation)\n- [Development](#development)\n- [Contributing](#contributing)\n- [License](#license)\n - [Contributors](#contributors)\n\n## Key Features\n\n✅ **Semantic Search Engine** - Find Jira operations using natural language with >90% relevance (sqlite-vec embeddings)  \n✅ **Three MCP Tools** - `search_ids`, `get_id`, `call_id` for discovery, inspection, and execution  \n✅ **Multi-Authentication** - OAuth 2.0, Personal Access Tokens, OAuth 1.0a, Basic Auth with secure OS keychain storage  \n✅ **Production Resilience** - Circuit breaker pattern, rate limiting, exponential backoff, automatic retries  \n✅ **Zero-Config Setup** - Interactive CLI wizard completes full setup in <5 minutes  \n✅ **Structured Logging** - JSON logs with correlation IDs, automatic credential redaction, ELK/Datadog ready  \n✅ **Air-Gapped Support** - Local embeddings generation, no external API dependencies  \n✅ **Cross-Platform** - Linux, macOS, Windows with Node.js 22+\n\n## Quick Start\n\nGet up and running in under 5 minutes using Docker, npm, or source installation.\n\n### Docker (Recommended)\n\n**Fastest path** - One command to start the MCP server:\n\n```bash\n# Pull and run the official image\ndocker run -it \\\n  -e JIRA_URL=https://jira.example.com \\\n  -e JIRA_AUTH_METHOD=pat \\\n  -e JIRA_TOKEN=your-personal-access-token \\\n  ghcr.io/guercheLE/jira-dc-mcp:latest\n```\n\n**Or use docker-compose** for persistent configuration:\n\n```bash\n# Clone the repo\ngit clone https://github.com/guercheLE/jira-dc-mcp.git\ncd jira-datacenter-mcp-server\n\n# Configure environment variables in docker-compose.yml\n# Start the server\ndocker-compose up -d\n```\n\n**Expected Output:**\n```\n✅ MCP Server started successfully\n🔍 Semantic search ready (500+ Jira operations indexed)\n🔐 Authentication configured: Personal Access Token\n📡 Listening on stdio transport\n```\n\n**Troubleshooting:** If you see connection errors, verify your `JIRA_URL` and credentials. See [Docker Guide](docs/docker.md) for advanced configuration.\n\n### npm Install\n\n**Recommended for local development** - Global CLI with interactive setup:\n\n```bash\n# Install globally\nnpm install -g jira-dc-mcp\n\n# Run setup wizard (interactive prompts)\njira-dc-mcp setup\n\n# Start the MCP server\njira-dc-mcp start\n```\n\nThe setup wizard will:\n1. Ask for your Jira URL (e.g., `https://jira.example.com`)\n2. Select authentication method (OAuth 2.0, PAT, OAuth 1.0a, Basic)\n3. Securely store credentials in OS keychain\n4. Download OpenAPI spec and generate embeddings database\n5. Validate connection with health check\n\n**Expected Output:**\n```\n🚀 Jira MCP Server Setup Wizard\n━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\n\n✓ Jira URL configured: https://jira.example.com\n✓ Authentication method: Personal Access Token\n✓ Credentials stored securely in system keychain\n✓ OpenAPI spec downloaded (500 operations)\n✓ Embeddings database generated (768-dim vectors)\n✓ Connection validated\n\nSetup complete! Start the server with: jira-dc-mcp start\n```\n\n**Troubleshooting:** See [Setup Issues](docs/troubleshooting.md#setup-wizard-errors) for common problems.\n\n### From Source\n\n**For contributors and developers** - Build from source:\n\n```bash\n# Clone repository\ngit clone https://github.com/guercheLE/jira-dc-mcp.git\ncd jira-datacenter-mcp-server\n\n# Install dependencies\nnpm install\n\n# Build TypeScript\nnpm run build\n\n# Run setup wizard\nnpm run setup\n\n# Start the server\nnpm start\n```\n\n**Expected Output:** Same as npm install method above.\n\n### What's Next?\n\n- **Test the connection:** Run `jira-dc-mcp test-connection` to verify connectivity and authentication\n- **Search for operations:** Run `jira-dc-mcp search \"create issue\"` to test semantic search\n- **Get operation details:** Run `jira-dc-mcp get <operationId>` to view operation schema and parameters\n- **Start the server:** Run `jira-dc-mcp start` to launch the MCP server\n- **Configure MCP client:** Follow [MCP Client Configuration](#mcp-client-configuration) to connect Claude Desktop, Cline, or other clients\n- **Explore MCP tools:** See [Usage Examples](#usage) below\n- **Configure advanced features:** Check [Configuration Guide](#configuration)\n\n---\n\n---\n\n## CLI Commands\n\nThe `jira-dc-mcp` CLI provides several commands for setup, testing, and running the MCP server:\n\n### Available Commands\n\n| Command | Description | Example |\n|---------|-------------|---------|\n| `setup` | Run interactive setup wizard | `jira-dc-mcp setup` |\n| `start` | Start the MCP server (stdio mode) | `jira-dc-mcp start` |\n| `test-connection` | Test Jira connectivity and authentication | `jira-dc-mcp test-connection` |\n| `search <query>` | Search for operations using semantic search | `jira-dc-mcp search \"create issue\"` |\n| `get <operationId>` | Get detailed info about a specific operation | `jira-dc-mcp get createIssue` |\n| `call <operationId>` | Execute a Jira operation | `jira-dc-mcp call createIssue --param ...` |\n| `config <action>` | Manage configuration (show, validate, path, reset) | `jira-dc-mcp config show` |\n| `version` | Show version information | `jira-dc-mcp version` |\n\n### Command Details\n\n#### `jira-dc-mcp setup`\n\nRun the interactive setup wizard to configure your Jira instance and credentials.\n\n**Options:**\n- `--force` - Overwrite existing config\n- `--non-interactive` - Use environment variables and defaults\n\n**Example:**\n```bash\njira-dc-mcp setup\n```\n\n#### `jira-dc-mcp start`\n\nStart the MCP server in stdio mode for use with MCP clients.\n\n**Example:**\n```bash\njira-dc-mcp start\n```\n\n**Note:** This is typically called by your MCP client (Claude Desktop, Cline, etc.) via the client's configuration file.\n\n#### `jira-dc-mcp test-connection`\n\nVerify connectivity and authentication to your Jira Data Center instance.\n\n**Example:**\n```bash\njira-dc-mcp test-connection\n```\n\n#### `jira-dc-mcp search <query>`\n\nSearch for Jira operations using natural language queries.\n\n**Options:**\n- `--limit <n>` - Maximum number of results (default: 5)\n- `--json` - Output results as JSON\n- `--verbose` - Show similarity scores\n\n**Example:**\n```bash\njira-dc-mcp search \"create issue\" --limit 3 --verbose\n```\n\n#### `jira-dc-mcp get <operationId>`\n\nGet detailed information about a specific Jira operation including schema, parameters, and examples.\n\n**Options:**\n- `--json` - Output results as JSON\n- `--verbose` - Show detailed schema and examples\n\n**Example:**\n```bash\njira-dc-mcp get createIssue --verbose\n```\n\n**Use case:** After using `search` to find operations, use `get` to inspect the operation's schema before calling it.\n\n#### `jira-dc-mcp call <operationId>`\n\nExecute a Jira operation with specified parameters.\n\n**Options:**\n- `--param <key=value>` - Operation parameters (can be repeated)\n- `--json` - Output raw JSON response\n- `--dry-run` - Validate parameters only, do not execute\n\n**Example:**\n```bash\njira-dc-mcp call createIssue \\\n  --param projectKey=TEST \\\n  --param summary=\"New bug report\" \\\n  --param issueType=Bug\n```\n\n#### `jira-dc-mcp config <action>`\n\nManage configuration settings.\n\n**Actions:**\n- `show` - Display current configuration\n- `validate` - Validate configuration file\n- `path` - Show config file path\n- `reset` - Reset configuration to defaults\n\n**Example:**\n```bash\njira-dc-mcp config show\njira-dc-mcp config validate\n```\n\n#### `jira-dc-mcp version`\n\nShow version information for the MCP server.\n\n**Options:**\n- `--check-updates` - Check for available updates\n\n**Example:**\n```bash\njira-dc-mcp version --check-updates\n```\n\n---\n\n## Database Regeneration\n\nIf you encounter issues with the embeddings database (corrupted data, outdated operations, or compatibility issues), you can regenerate it completely:\n\n### Quick Regeneration\n\n```bash\n# Complete database regeneration (recommended)\ncd jira-dc-mcp\nrm -f data/embeddings.db* && npm run build:all\n```\n\n### Step-by-Step Regeneration\n\n```bash\n# 1. Remove existing database and auxiliary files\nrm data/embeddings.db\nrm data/embeddings.db-wal 2>/dev/null || true\nrm data/embeddings.db-shm 2>/dev/null || true\n\n# 2. Regenerate from scratch\nnpm run download-openapi\nnpm run generate-schemas\nnpm run generate-embeddings  \nnpm run populate-db\n\n# 3. Compile the project\nnpm run build\n```\n\n### When to Regenerate\n\n- **Outdated data**: Database contains operations from old versions with incompatible IDs\n- **Data contamination**: Database contains operations from other MCP servers\n- **Corruption**: Database is corrupted or inaccessible\n- **API updates**: OpenAPI specification has been updated\n- **Server migration**: Switching between different server types\n\n### Verification\n\n```bash\n# Check database was created successfully\nls -lh data/embeddings.db\n\n# Validate database integrity\nnpm run validate-embeddings\n```\n\n**Estimated time**: \n- **MacBook Air M1**: ~3 minutes\n- **GitHub Actions**: ~3 hours (not recommended for CI/CD)\n- **Modern hardware**: 3-5 minutes\n\nFor detailed troubleshooting, see [docs/EMBEDDINGS_REGENERATION.md](docs/EMBEDDINGS_REGENERATION.md).\n\n---\n\n## Usage\n\nThe MCP server provides both **CLI commands** for direct interaction and **MCP tools** for integration with LLM clients.\n\n### CLI Commands\n\nThe `jira-dc-mcp` CLI provides several commands for setup, testing, and operation:\n\n#### Core Commands\n\n```bash\n# Setup wizard - Interactive configuration\njira-dc-mcp setup\n\n# Start the MCP server in stdio mode\njira-dc-mcp start\n\n# Test connection and authentication\njira-dc-mcp test-connection\n\n# Display version information\njira-dc-mcp version [--check-updates]\n```\n\n#### Operation Discovery Commands\n\n```bash\n# Search for operations using semantic search\njira-dc-mcp search \"create issue\" [--limit 5] [--json] [--verbose]\n\n# Get detailed information about a specific operation\njira-dc-mcp get <operationId> [--json] [--verbose]\n\n# Execute a Jira operation\njira-dc-mcp call <operationId> [--param key=value] [--json] [--dry-run]\n```\n\n#### Configuration Commands\n\n```bash\n# Show current configuration\njira-dc-mcp config show\n\n# Validate configuration file\njira-dc-mcp config validate\n\n# Show configuration file path\njira-dc-mcp config path\n\n# Reset configuration to defaults\njira-dc-mcp config reset\n```\n\n#### Examples\n\n```bash\n# Search for issue creation operations\njira-dc-mcp search \"create issue\" --limit 3\n\n# Get detailed schema for createIssue operation\njira-dc-mcp get createIssue --verbose\n\n# Execute an operation (dry-run mode)\njira-dc-mcp call createIssue --param projectKey=TEST --dry-run\n\n# Check for updates\njira-dc-mcp version --check-updates\n```\n\n**For comprehensive CLI usage, run:** `jira-dc-mcp --help`\n\n---\n\n### MCP Tools\n\nThe MCP server exposes **three tools** for interacting with Jira Data Center. Use these tools from any MCP client (Claude Desktop, custom LLM applications, etc.).\n\n#### 1. `search_ids` - Semantic Search for Operations\n\nFind relevant Jira API operations using natural language queries.\n\n**Input:**\n- `query` (string, required): Natural language description (e.g., \"create issue\", \"update assignee\")\n- `limit` (number, optional): Maximum results to return (1-20, default: 5)\n\n**Output:**\n- `operations` (array): Ranked list of matching operations with:\n  - `operation_id`: Jira API operation identifier\n  - `summary`: Human-readable description\n  - `similarity_score`: Relevance score (0.0-1.0, higher is better)\n\n**Example:**\n```json\n{\n  \"tool\": \"search_ids\",\n  \"input\": {\n    \"query\": \"create an issue\",\n    \"limit\": 3\n  }\n}\n```\n\n**Response:**\n```json\n{\n  \"operations\": [\n    {\n      \"operation_id\": \"createIssue\",\n      \"summary\": \"Create issue in Jira\",\n      \"similarity_score\": 0.94\n    },\n    {\n      \"operation_id\": \"createIssues\",\n      \"summary\": \"Create multiple issues (bulk)\",\n      \"similarity_score\": 0.89\n    },\n    {\n      \"operation_id\": \"createIssueLink\",\n      \"summary\": \"Create link between two issues\",\n      \"similarity_score\": 0.82\n    }\n  ]\n}\n```\n\n---\n\n#### 2. `get_id` - Retrieve Operation Details\n\nGet complete schema, documentation, and examples for a specific Jira operation.\n\n**Input:**\n- `operation_id` (string, required): Jira operation ID (from `search_ids` results)\n\n**Output:**\n- `operation_id`: Operation identifier\n- `summary`: Brief description\n- `description`: Detailed documentation\n- `method`: HTTP method (GET, POST, PUT, DELETE)\n- `path`: API endpoint path\n- `parameters`: Request parameters schema (path, query, body)\n- `responses`: Response schemas by status code\n- `examples`: Request/response examples (if available)\n\n**Example:**\n```json\n{\n  \"tool\": \"get_id\",\n  \"input\": {\n    \"operation_id\": \"createIssue\"\n  }\n}\n```\n\n**Response:**\n```json\n{\n  \"operation_id\": \"createIssue\",\n  \"summary\": \"Create issue\",\n  \"method\": \"POST\",\n  \"path\": \"/rest/api/3/issue\",\n  \"parameters\": {\n    \"body\": {\n      \"type\": \"object\",\n      \"required\": [\"fields\"],\n      \"properties\": {\n        \"fields\": {\n          \"project\": { \"type\": \"object\" },\n          \"summary\": { \"type\": \"string\" },\n          \"issuetype\": { \"type\": \"object\" }\n        }\n      }\n    }\n  },\n  \"responses\": {\n    \"201\": {\n      \"description\": \"Returned if the request is successful\",\n      \"content\": {\n        \"id\": \"10000\",\n        \"key\": \"PROJ-123\",\n        \"self\": \"https://jira.example.com/rest/api/3/issue/10000\"\n      }\n    }\n  }\n}\n```\n\n---\n\n#### 3. `call_id` - Execute Jira Operation\n\nExecute a Jira API operation with validated parameters and error handling.\n\n**Input:**\n- `operation_id` (string, required): Jira operation ID\n- `parameters` (object, required): Operation parameters matching the schema from `get_id`\n  - `path`: Path parameters (e.g., `{ \"issueIdOrKey\": \"PROJ-123\" }`)\n  - `query`: Query parameters (e.g., `{ \"fields\": \"summary,status\" }`)\n  - `body`: Request body for POST/PUT operations\n\n**Output:**\n- API response from Jira (varies by operation)\n\n**Example - Create Issue:**\n```json\n{\n  \"tool\": \"call_id\",\n  \"input\": {\n    \"operation_id\": \"createIssue\",\n    \"parameters\": {\n      \"body\": {\n        \"fields\": {\n          \"project\": { \"key\": \"PROJ\" },\n          \"summary\": \"Bug: Login page not loading\",\n          \"issuetype\": { \"name\": \"Bug\" },\n          \"priority\": { \"name\": \"High\" }\n        }\n      }\n    }\n  }\n}\n```\n\n**Response:**\n```json\n{\n  \"id\": \"10042\",\n  \"key\": \"PROJ-123\",\n  \"self\": \"https://jira.example.com/rest/api/3/issue/10042\"\n}\n```\n\n**Example - Get Issue:**\n```json\n{\n  \"tool\": \"call_id\",\n  \"input\": {\n    \"operation_id\": \"getIssue\",\n    \"parameters\": {\n      \"path\": { \"issueIdOrKey\": \"PROJ-123\" },\n      \"query\": { \"fields\": \"summary,status,assignee\" }\n    }\n  }\n}\n```\n\n---\n\n### Common Workflows\n\n#### Workflow 1: Find and Create an Issue\n\n```\n1. search_ids({ query: \"create issue\" })\n   → Returns: operation_id = \"createIssue\"\n\n2. get_id({ operation_id: \"createIssue\" })\n   → Returns: Full schema with required fields\n\n3. call_id({\n     operation_id: \"createIssue\",\n     parameters: { body: { fields: { ... } } }\n   })\n   → Returns: Created issue with key PROJ-123\n```\n\n#### Workflow 2: Update Issue Assignee\n\n```\n1. search_ids({ query: \"assign issue to user\" })\n   → Returns: operation_id = \"assignIssue\"\n\n2. get_id({ operation_id: \"assignIssue\" })\n   → Returns: Schema showing accountId parameter required\n\n3. call_id({\n     operation_id: \"assignIssue\",\n     parameters: {\n       path: { issueIdOrKey: \"PROJ-123\" },\n       body: { accountId: \"5b10a2...\" }\n     }\n   })\n   → Returns: 204 No Content (success)\n```\n\n#### Workflow 3: Bulk Operations Discovery\n\n```\n1. search_ids({ query: \"bulk edit issues\", limit: 10 })\n   → Returns: Multiple bulk operations ranked by relevance\n\n2. get_id({ operation_id: \"bulkEditIssues\" })\n   → Returns: Schema for bulk edit payload\n\n3. call_id({ ... })\n   → Execute bulk operation\n```\n\n**See [Cookbook](docs/cookbook.md) for 20+ practical examples and advanced patterns.**\n\n---\n\n## Installation\n\n### Prerequisites\n\n- **Node.js 22+** (LTS recommended) - [Download](https://nodejs.org)\n- **npm 9+** (included with Node.js)\n- **Jira Data Center** instance with API access\n- **Valid credentials**: OAuth 2.0, Personal Access Token, OAuth 1.0a, or Basic Auth\n\n### Installation Methods\n\nChoose the installation method that fits your workflow:\n\n| Method | Best For | Time | Difficulty |\n|--------|----------|------|------------|\n| **Docker** | Production deployments, containerized environments | 2 min | Easy ⭐ |\n| **npm Global** | Local development, CLI usage | 5 min | Easy ⭐ |\n| **From Source** | Contributors, custom builds | 10 min | Moderate ⭐⭐ |\n\n**Detailed instructions:** See [Quick Start](#quick-start) section above.\n\n---\n\n## Configuration\n\nThe server supports **four configuration methods** (priority order):\n\n1. **CLI Flags** (highest priority)\n2. **Environment Variables**\n3. **Config File** (`~/.jira-dc-mcp/config.yml`)\n4. **Defaults**\n\n### Environment Variables\n\n```bash\n# Required\nJIRA_URL=https://jira.example.com              # Jira Data Center URL\nJIRA_AUTH_METHOD=pat                            # Auth method: oauth2, pat, oauth1, basic\nJIRA_TOKEN=your-token                           # Token (for PAT/Basic)\n\n# Optional - API Configuration\nJIRA_API_VERSION=3                              # API version: 2 (Jira 8.x), 3 (Jira 9.x+)\n                                                # Auto-detected during setup\n\n# Optional - Performance\nRATE_LIMIT_MAX_REQUESTS=100                     # Max requests per minute\nREQUEST_TIMEOUT_MS=30000                        # Request timeout (milliseconds)\nCIRCUIT_BREAKER_FAILURE_THRESHOLD=5             # Failures before circuit opens\n\n# Optional - Logging\nLOG_LEVEL=INFO                                  # DEBUG, INFO, WARN, ERROR\nLOG_OUTPUT=stdout                               # stdout, file, both\nLOG_FILE_PATH=./logs/jira-dc-mcp.log              # Log file location\n```\n\n### Config File Example\n\nCreate `~/.jira-dc-mcp/config.yml`:\n\n```yaml\njira:\n  url: https://jira.example.com\n  auth_method: oauth2\n  api_version: \"3\"  # Auto-detected during setup (2 for Jira 8.x, 3 for Jira 9.x+)\n  \nperformance:\n  rate_limit: 100\n  timeout: 30000\n  retry_max_attempts: 3\n  \nlogging:\n  level: INFO\n  output: stdout\n  \ncircuit_breaker:\n  failure_threshold: 5\n  timeout: 30000\n```\n\n**Run setup wizard to generate config automatically:** `jira-dc-mcp setup`\n\n**Full configuration reference:** See [Configuration Guide](docs/internal/architecture/backend-architecture.md#configuration)\n\n### API Version Detection\n\nThe server automatically detects which REST API version your Jira instance supports during setup:\n\n- **API v2**: Jira Server/Data Center 8.x and older\n- **API v3**: Jira Server/Data Center 9.x and newer\n\nThe detected version is saved to your configuration and used automatically for all API calls. You can override it using the `JIRA_API_VERSION` environment variable if needed.\n\n**For detailed information, see:**\n- [API Version Detection Guide](docs/api-version-detection.md) - Complete guide on API version detection\n- [API Version FAQ](docs/api-version-faq.md) - Frequently asked questions\n\n---\n\n## MCP Client Configuration\n\nConfigure the Jira MCP server in your MCP-compatible client (Claude Desktop, Cline, etc.).\n\n### Claude Desktop\n\nEdit your Claude Desktop configuration file:\n\n**macOS:** `~/Library/Application Support/Claude/claude_desktop_config.json`  \n**Windows:** `%APPDATA%\\Claude\\claude_desktop_config.json`  \n**Linux:** `~/.config/Claude/claude_desktop_config.json`\n\n#### Option 1: Using npx (Recommended)\n\n```json\n{\n  \"mcpServers\": {\n    \"jira-datacenter\": {\n      \"command\": \"npx\",\n      \"args\": [\n        \"-y\",\n        \"jira-dc-mcp@latest\",\n        \"start\"\n      ],\n      \"env\": {\n        \"JIRA_URL\": \"https://jira.example.com\",\n        \"JIRA_AUTH_METHOD\": \"pat\",\n        \"JIRA_TOKEN\": \"your-personal-access-token\"\n      }\n    }\n  }\n}\n```\n\n#### Option 2: Using Local Installation\n\n```json\n{\n  \"mcpServers\": {\n    \"jira-datacenter\": {\n      \"command\": \"node\",\n      \"args\": [\n        \"/usr/local/lib/node_modules/jira-dc-mcp/dist/index.js\"\n      ],\n      \"env\": {\n        \"JIRA_URL\": \"https://jira.example.com\",\n        \"JIRA_AUTH_METHOD\": \"pat\",\n        \"JIRA_TOKEN\": \"your-personal-access-token\"\n      }\n    }\n  }\n}\n```\n\n#### Option 3: Using Source (Development)\n\n```json\n{\n  \"mcpServers\": {\n    \"jira-datacenter-local\": {\n      \"command\": \"node\",\n      \"args\": [\n        \"/path/to/jira-dc-mcp/dist/index.js\"\n      ],\n      \"env\": {\n        \"JIRA_URL\": \"https://jira.example.com\",\n        \"JIRA_AUTH_METHOD\": \"pat\",\n        \"JIRA_TOKEN\": \"your-personal-access-token\",\n        \"LOG_LEVEL\": \"DEBUG\"\n      }\n    }\n  }\n}\n```\n\n### Cline (VS Code Extension)\n\nAdd to Cline's MCP settings:\n\n```json\n{\n  \"mcpServers\": {\n    \"jira-datacenter\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"jira-dc-mcp@latest\", \"start\"],\n      \"env\": {\n        \"JIRA_URL\": \"https://jira.example.com\",\n        \"JIRA_AUTH_METHOD\": \"pat\",\n        \"JIRA_TOKEN\": \"your-token\"\n      }\n    }\n  }\n}\n```\n\n### Other MCP Clients\n\nFor other MCP-compatible clients, use the stdio transport:\n\n**Command:** `npx -y jira-dc-mcp@latest start`  \n**Transport:** stdio  \n**Environment Variables:**\n- `JIRA_URL` - Your Jira Data Center URL\n- `JIRA_AUTH_METHOD` - Authentication method (pat, oauth2, oauth1, basic)\n- `JIRA_TOKEN` - Your authentication token\n- `LOG_LEVEL` - Optional: DEBUG, INFO, WARN, ERROR\n\n### Verifying Configuration\n\nAfter configuring your MCP client:\n\n1. **Restart the client** (Claude Desktop, Cline, etc.)\n2. **Check for errors** in the client's MCP server logs\n3. **Test the connection** by asking: \"Search for Jira operations to create an issue\"\n4. **Verify tools appear** in the client's available tools list:\n   - `search_ids` - Semantic search for Jira operations\n   - `get_id` - Get operation details and schema\n   - `call_id` - Execute Jira API operations\n\n### Troubleshooting MCP Client Issues\n\n**Server not appearing in client:**\n- Verify JSON syntax is valid (no trailing commas, proper quotes)\n- Check file path in configuration is correct\n- Restart the MCP client completely\n\n**Connection errors:**\n- Verify `JIRA_URL` is accessible from your machine\n- Check `JIRA_TOKEN` is valid and not expired\n- Review MCP server logs: Set `LOG_LEVEL=DEBUG` for detailed output\n\n**Tools not working:**\n- Ensure embeddings database exists: Run `npm run populate-db` if needed\n- Check permissions: Token must have READ and WRITE scopes\n- Verify operation IDs are valid: Use `search_ids` to find correct IDs\n\n**Full troubleshooting guide:** See [Troubleshooting](docs/troubleshooting.md)\n\n---\n\n## Project Structure\n\n```text\njira-dc-mcp/\n├── .github/workflows/    # GitHub Actions CI/CD workflows\n├── src/                  # Source code (TypeScript)\n│   ├── auth/            # Authentication strategies\n│   ├── core/            # Core services (config, logger, errors)\n│   ├── services/        # Business logic (semantic search, operations)\n│   ├── tools/           # MCP tool implementations\n│   └── cli/             # CLI utilities (setup wizard, search test)\n├── tests/                # Test suites (unit, integration, e2e)\n├── scripts/              # Build and automation scripts\n├── docs/                 # Project documentation\n├── data/                 # Generated data artifacts (gitignored)\n└── dist/                 # Compiled output (generated)\n```\n\n---\n\n## Documentation\n\nComprehensive guides and references:\n\n| Resource | Description |\n|----------|-------------|\n| **[Architecture Overview](docs/internal/architecture.md)** | System design, components, data flow |\n| **[Authentication Guide](docs/authentication.md)** | OAuth 2.0, PAT, OAuth 1.0a setup and troubleshooting |\n| **[API Version Detection](docs/api-version-detection.md)** | API version detection and configuration guide |\n| **[API Version FAQ](docs/api-version-faq.md)** | Frequently asked questions about API versions |\n| **[Cookbook](docs/cookbook.md)** | 20+ practical examples and code snippets |\n| **[Docker Deployment](docs/docker.md)** | Container setup, environment variables, docker-compose |\n| **[Troubleshooting Guide](docs/troubleshooting.md)** | Common issues and solutions |\n| **[API Reference](docs/internal/architecture/api-specification.md)** | Complete MCP tools specification |\n| **[Testing Strategy](docs/internal/architecture/testing-strategy.md)** | Unit, integration, E2E test patterns |\n| **[Observability](docs/observability.md)** | Logging, monitoring, alerting setup |\n\n### Getting Help\n\n- **🐛 Bug Reports:** [Open an issue](https://github.com/guercheLE/jira-dc-mcp/issues/new?template=bug_report.md)\n- **💡 Feature Requests:** [Request a feature](https://github.com/guercheLE/jira-dc-mcp/issues/new?template=feature_request.md)\n- **❓ Questions:** [Discussions](https://github.com/guercheLE/jira-dc-mcp/discussions)\n- **📧 Email:** Open a GitHub issue for fastest response\n\n---\n\n## Development\n\n### Development Commands\n\n```bash\nnpm run build          # Compile TypeScript to dist/\nnpm run dev            # Watch mode compilation\nnpm run test           # Execute Vitest test suite\nnpm run test:benchmark  # Run semantic search relevance benchmark suite\nnpm run test:coverage  # Generate coverage reports\nnpm run lint           # Run ESLint checks on src/\nnpm run format         # Apply Prettier formatting\nnpm run format:check   # Verify formatting without making changes\n```\n\n### CLI Commands (Post-Build)\n\nAfter building, you can test CLI commands locally:\n\n```bash\nnpm run setup          # Run setup wizard\nnpm run start          # Start MCP server\nnode dist/cli.js search \"create issue\"  # Test search command\nnode dist/cli.js get createIssue        # Test get command\nnode dist/cli.js test-connection        # Test connection\n```\n\n### OpenAPI Spec Processing\n\nDownload and process the Jira Data Center OpenAPI specification:\n\n```bash\nnpm run download-openapi                       # Download from default Atlassian URL\nnpm run download-openapi -- --url <url>        # Download from a custom URL\nnpm run download-openapi -- --local <path>     # Load a locally stored spec file\n```\n\nOutputs: `data/operations.json` and `data/schemas.json` with metadata.\n\n### Semantic Search CLI\n\nUse the interactive CLI to validate semantic search behaviour without running the full benchmark suite:\n\n```bash\nnpm run search \"create issue\"              # Default settings (limit 5, threshold 0)\nnpm run search \"update assignee\" -- --limit 3\nnpm run search \"bulk update\" -- --threshold 0.85 --verbose\nnpm run search \"create project\" -- --benchmark\nnpm run search -- --batch queries.txt --limit 8 --benchmark\n```\n\nKey flags:\n\n- `--limit <n>` limits the maximum number of rows returned (1–100).\n- `--threshold <score>` filters out low-similarity matches (0.0–1.0).\n- `--verbose` adds the full operation description column.\n- `--benchmark` compares the results against precision targets from the benchmark suite and prints Precision@5.\n- `--batch <file>` executes multiple queries listed one per line, skipping blank lines automatically.\n\nScore colours highlight relevance: green ✅ for ≥0.85, yellow ⚠️ for 0.70–0.84, and red ❌ below 0.70. Example output:\n\n```text\nQuery: create issue\n┌──────┬────────────────────────────────────────┬────────────────────────────────────────┬────────────────┐\n│ Rank │ Operation ID                           │ Summary                                │ Score          │\n├──────┼────────────────────────────────────────┼────────────────────────────────────────┼────────────────┤\n│ 1    │ create_reciprocal_remote_issue_link     │ Summary for create issue 1             │ 0.95 ✅         │\n│ 2    │ create_issue_link_type                  │ Summary for create issue 2             │ 0.90 ✅         │\n└──────┴────────────────────────────────────────┴────────────────────────────────────────┴────────────────┘\nFound 5 result(s) matching \"create issue\" (limit 5, threshold 0.00)\n✅ Precision@5: 100.0% (required 85.0%)\n```\n\nTroubleshooting:\n\n- `Database not found. Run \"npm run populate-db\" first.` → Seed the embeddings database with `npm run populate-db`.\n- `sqlite-vec extension is required to query the embeddings database.` → Ensure the extension is installed and accessible to your SQLite build.\n\n---\n\n## Contributing\n\nWe welcome contributions! Here's how to get started:\n\nSee our full guidelines in [CONTRIBUTING.md](CONTRIBUTING.md) and please follow our [Code of Conduct](CODE_OF_CONDUCT.md).\n\nWhen opening an issue or pull request:\n- Use the [issue templates](.github/ISSUE_TEMPLATE) for bugs, features, and questions\n- Follow the [PR template](.github/PULL_REQUEST_TEMPLATE.md) and checklist\n\n### Quick Start\n\n1. **Fork** the repository\n2. **Create** a feature branch: `git checkout -b feature/my-feature`\n3. **Make** your changes following [Coding Standards](docs/internal/architecture/coding-standards.md)\n4. **Test** your changes: `npm test` (must pass)\n5. **Lint** your code: `npm run lint && npm run format:check`\n6. **Commit** with conventional commits: `feat: add feature` or `fix: resolve bug`\n7. **Push** and **open** a Pull Request\n\n### Development Setup\n\n```bash\ngit clone https://github.com/YOUR_USERNAME/jira-datacenter-mcp-server.git\ncd jira-datacenter-mcp-server\nnpm install\nnpm run build\nnpm test\n```\n\n### Coding Standards\n\n- ✅ TypeScript strict mode - No `any` without justification\n- ✅ Test coverage ≥80% - All features require tests\n- ✅ Conventional commits - Semantic commit messages\n- ✅ ESLint + Prettier - Run before committing\n- ❌ No console.log - Use Logger (pino)\n\n**Full guide:** [Coding Standards](docs/internal/architecture/coding-standards.md)\n\n### Testing Requirements\n\nThe project has a comprehensive test suite organized into different categories:\n\n**Test Types:**\n- **Unit Tests** (`tests/unit/`) - Fast, isolated tests (run by default)\n- **Integration Tests** (`tests/integration/`) - Service interactions (opt-in)\n- **E2E Tests** (`tests/e2e/`) - Full MCP protocol flows (opt-in)\n- **Benchmarks** (`tests/benchmarks/`) - Maintain >85% search precision\n\n**Running Tests:**\n```bash\n# Unit tests only (default, fast)\nnpm test\n\n# Unit tests (explicit)\nnpm run test:unit\n\n# Integration tests (requires Docker for some tests)\nnpm run test:integration\n\n# E2E tests (requires configured environment)\nnpm run test:e2e\n\n# All tests (unit + integration + e2e)\nnpm run test:all\n\n# With coverage\nnpm run test:coverage\n```\n\n**Environment Variables:**\n- `RUN_INTEGRATION_TESTS=true` - Enable integration tests\n- `RUN_E2E_TESTS=true` - Enable E2E tests\n- `E2E_USE_REAL_JIRA=true` - Use real Jira instance for E2E\n\n**For detailed testing documentation, see [tests/README.md](tests/README.md)**\n\n---\n\n## License\n\n**LGPL-3.0 License** - see [LICENSE](LICENSE) for details.\n\n✅ Commercial use, modification, distribution, private use, patent use  \n❌ No liability, no warranty  \n⚠️ License and copyright notice required, disclose source, state changes  \n📋 Must keep same license for library, but applications using it can use different licenses\n\n---\n\n## Contributors\n\nThanks to all our contributors! ✨\n\n- Read our [Contributing Guide](CONTRIBUTING.md) and follow our [Code of Conduct](CODE_OF_CONDUCT.md)\n- See everyone who has contributed on the [GitHub contributors page](https://github.com/guercheLE/jira-dc-mcp/graphs/contributors)\n\n---\n## Acknowledgments\n\nBuilt with excellent open-source tools:\n\n- [@modelcontextprotocol/sdk](https://github.com/anthropics/mcp) - MCP implementation by Anthropic\n- [sqlite-vec](https://github.com/asg017/sqlite-vec) - Vector search for SQLite\n- [@xenova/transformers](https://github.com/xenova/transformers.js) - Local embeddings\n- [Zod](https://github.com/colinhacks/zod) - TypeScript schema validation\n- [pino](https://github.com/pinojs/pino) - High-performance JSON logger\n- [Vitest](https://vitest.dev) - Testing framework\n\nSpecial thanks to the Jira Data Center team for comprehensive API documentation.\n\n---\n\n## Security\n\n### Secure Credential Storage\n\nCredentials are **never stored in plaintext**. The server uses OS-native keychains for secure storage:\n\n- **macOS**: Keychain Services via Security framework\n- **Windows**: Credential Manager\n- **Linux**: Secret Service API (libsecret)\n\nWhen OS keychain is unavailable, credentials are encrypted using AES-256-GCM with machine-specific keys before being stored locally.\n\nAll credential operations automatically redact sensitive data from logs and error messages.\n\nFor authentication setup and credential management details, see:\n- [Authentication Guide](docs/authentication.md) - Comprehensive security features and troubleshooting\n- [Cookbook](docs/cookbook.md) - Practical examples for credential management\n\n## Resilience & Fault Tolerance\n\n### Circuit Breaker Pattern\n\nThe server implements a **circuit breaker pattern** to protect against cascading failures when Jira Data Center is experiencing issues:\n\n- **Automatic failure detection**: Opens circuit after 5 consecutive failures OR 50% failure rate in 10-second window\n- **Fail-fast behavior**: When circuit is OPEN, requests are rejected immediately without calling Jira\n- **Self-healing**: After 30-second timeout, circuit attempts health check to automatically recover\n- **Observable**: Comprehensive structured logging and metrics for monitoring circuit state\n\nThis prevents overwhelming Jira during outages and enables graceful degradation of service.\n\n**Configuration**: Circuit breaker thresholds can be tuned via environment variables:\n```bash\nCIRCUIT_BREAKER_FAILURE_THRESHOLD=5     # Consecutive failures before opening\nCIRCUIT_BREAKER_FAILURE_RATE=0.5        # Failure rate threshold (0-1)\nCIRCUIT_BREAKER_WINDOW_SIZE=10000       # Time window in milliseconds\nCIRCUIT_BREAKER_TIMEOUT=30000           # Reset timeout in milliseconds\n```\n\nFor detailed architecture and troubleshooting, see [Backend Architecture - Circuit Breaker](docs/internal/architecture/backend-architecture.md#circuit-breaker-pattern).\n\n## Logging & Observability\n\nThe server provides **structured JSON logging** with correlation IDs for request tracing and comprehensive observability:\n\n- **Structured logs**: All logs are JSON with consistent schema for log aggregation tools (ELK, Datadog, Splunk)\n- **Correlation IDs**: Every MCP request gets a unique UUID that propagates through all related logs\n- **Sensitive data protection**: Automatic redaction of passwords, tokens, credentials (replaced with `***`)\n- **Audit trail**: All mutations (POST/PUT/DELETE) automatically logged with user, timestamp, and parameters\n- **Performance metrics**: Request latency, cache hit rates, circuit breaker states\n\n**Configuration**:\n```bash\n# Log level (DEBUG, INFO, WARN, ERROR)\nLOG_LEVEL=INFO                       # Default: INFO\n\n# Log output destination\nLOG_OUTPUT=stdout                    # Options: stdout, file, both\n\n# File output settings (when LOG_OUTPUT=file or both)\nLOG_FILE_PATH=./logs/jira-dc-mcp.log   # Log file location\nLOG_ROTATION=daily                   # Options: daily, hourly, size-based\nLOG_MAX_SIZE=100                     # Max file size in MB before rotation\nLOG_MAX_FILES=7                      # Number of rotated files to keep\n```\n\n**Example log entry**:\n```json\n{\n  \"level\": \"info\",\n  \"time\": 1705320000000,\n  \"correlation_id\": \"req-abc-123\",\n  \"service\": \"jira-dc-mcp\",\n  \"version\": \"1.0.0\",\n  \"event\": \"call_id.execution_success\",\n  \"tool_name\": \"call_id\",\n  \"operation_id\": \"create_issue\",\n  \"method\": \"POST\",\n  \"path\": \"/rest/api/3/issue\",\n  \"status\": 201,\n  \"latency_ms\": 342,\n  \"msg\": \"Operation executed successfully\"\n}\n```\n\n**Quick troubleshooting**:\n```bash\n# Find all logs for a specific request\ncat logs/jira-dc-mcp.log | jq 'select(.correlation_id == \"req-abc-123\")'\n\n# Find all errors\ncat logs/jira-dc-mcp.log | jq 'select(.level == \"error\")'\n\n# Find slow operations (>1 second)\ncat logs/jira-dc-mcp.log | jq 'select(.latency_ms > 1000)'\n\n# View audit trail\ncat logs/jira-dc-mcp.log | jq 'select(.audit_type == \"mutation\")'\n```\n\nFor comprehensive logging setup, integration with log aggregators, and alert recommendations, see:\n- [Observability Guide](docs/observability.md) - Complete logging, monitoring, and alerting setup\n- [Cookbook](docs/cookbook.md) - Practical logging examples and troubleshooting\n\n","readmeFilename":"README.md"}