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Claude Desktop Integration Setup

This guide configures Claude Desktop to use the Health MCP server, enabling the complete Health Analyst Agent workflow.

Prerequisites

✅ MCP tools tested: Both test_import.py and test_query.py should pass
✅ Semantic model uploaded: health_intelligence_semantic_model.yaml in Snowflake @RAW_DATA stage
✅ Health data imported: Sample data imported via snowflake_import_analyze_health_records_v2
✅ Environment variables: All Snowflake credentials configured

Step 1: Locate Claude Desktop Config Directory

macOS:

~/Library/Application Support/Claude/

Windows:

%APPDATA%\Claude\

Linux:

~/.config/Claude/

Step 2: Configure Claude Desktop

  1. Copy the configuration file:

    # Navigate to your project directory
cd /Users/aju/Dropbox/Development/Git/multi-agent-health-insight-system-test-run-1

# Copy config to Claude Desktop directory (macOS)
cp claude_desktop_config.json ~/Library/Application\ Support/Claude/claude_desktop_config.json

  2. Update the configuration with your details:

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

    {
  "mcpServers": {
    "health-analysis-server": {
      "command": "/opt/homebrew/bin/uv",
      "args": [
        "--directory",
        "/Users/aju/Dropbox/Development/Git/multi-agent-health-insight-system-test-run-1/tools/health-mcp",
        "run",
        "src/health_mcp.py"
      ],
      "env": {
        "SNOWFLAKE_USER": "YOUR_ACTUAL_USERNAME",
        "SNOWFLAKE_ACCOUNT": "YOUR_ACTUAL_ACCOUNT",
        "SNOWFLAKE_PRIVATE_KEY_PATH": "~/.ssh/snowflake/snowflake_key.p8",
        "SNOWFLAKE_WAREHOUSE": "COMPUTE_WH",
        "SNOWFLAKE_DATABASE": "HEALTH_INTELLIGENCE",
        "SNOWFLAKE_SCHEMA": "HEALTH_RECORDS",
        "SNOWFLAKE_ROLE": "ACCOUNTADMIN",
        "SNOWFLAKE_SEMANTIC_MODEL_FILE": "health_intelligence_semantic_model.yaml"
      }
    }
  }
}

  3. Verify uv path (if needed):

    which uv
# Update the "command" path in config if different

Step 3: Update Project Path

IMPORTANT: Update the absolute path in the config file to match your system:

Replace:

"/Users/aju/Dropbox/Development/Git/multi-agent-health-insight-system-test-run-1/tools/health-mcp"

With your actual project path:

# Find your current path
pwd
# Should output something like: /Users/YOUR_USERNAME/path/to/multi-agent-health-insight-system-test-run-1

Step 4: Restart Claude Desktop

  1. Quit Claude Desktop completely
  2. Restart Claude Desktop
  3. Look for MCP connection indicator (usually shows connected servers in UI)

Step 5: Test Health Analyst Agent

Open a new conversation in Claude Desktop and test these scenarios:

Test 1: Agent Introduction

What can you do?

Expected: Health Analyst welcome message with capabilities overview

Test 2: Data Import

I have health data extracted from Apple Health PDFs. The files are located in:
/Users/aju/Dropbox/Development/Git/multi-agent-health-insight-system-test-run-1/example/extraction

Please import and analyze this data.

Expected:

  • Import statistics dashboard
  • Visual breakdown by category (Lab Results, Medications, Vitals, Clinical Data)
  • Timeline coverage chart
  • Data quality indicators
  • Key insights

Test 3: Natural Language Queries

What's my cholesterol trend over time?

Expected: Cholesterol data with trend analysis and visualizations

What medications am I currently taking?

Expected: Current medication list with dosages and frequencies

Show my abnormal lab results from this year

Expected: Filtered abnormal results with reference ranges

Step 6: Advanced Testing

Complex Analytical Query:

Analyze cholesterol relevant medication adherence patterns over that time period and how do they correlate with these cholesterol lab results

Expected: Multi-factor correlation analysis between medications and lab values

Multi-Provider Analysis:

Compare results across different doctors and healthcare systems

Expected: Provider-based analysis with insights

Troubleshooting

MCP Server Not Connecting

  1. Check Claude Desktop Developer Console for errors
  2. Verify all file paths are absolute and correct
  3. Ensure uv is installed and accessible
  4. Test MCP server independently: 
    cd tools/health-mcp
uv run src/health_mcp.py

Environment Variable Issues

  1. Verify all Snowflake credentials in config
  2. Test credentials with standalone tools: 
    cd tools/health-mcp
uv run test_import.py
uv run test_query.py

Semantic Model Not Found

  1. Verify semantic model is uploaded: 
    LIST @HEALTH_INTELLIGENCE.HEALTH_RECORDS.RAW_DATA;
  2. Check file name matches config exactly

Query Failures

  1. Ensure health data is imported first
  2. Check Cortex Analyst permissions
  3. Verify semantic model validates in Snowflake UI

Configuration Notes

  • Security: Never commit actual credentials to version control
  • Path handling: Use absolute paths for reliability
  • Environment isolation: MCP server runs in isolated uv environment
  • Logging: Check Claude Desktop logs for detailed debugging

Success Indicators

✅ MCP Connection: Claude Desktop shows connected health-analysis-server
✅ Agent Response: Welcome message displays correctly
✅ Import Works: Dashboard visualizations generate
✅ Queries Work: Natural language questions return health data
✅ Visualizations: Charts and trends display properly

Next Steps

Once working, you can:

  • Demo the system: Show complete health analytics workflow
  • Add more data: Import additional patient data
  • Extend queries: Test more complex analytical questions
  • Customize agent: Modify agent instructions for specific use cases

The Health Analyst Agent is now fully operational in Claude Desktop! 🎉