Merge pull request #10 from genomoncology/health_check

Health check

Author: imaurer

.gitignore

@@ -143,3 +143,4 @@ llms/
 vault/
 
 .DS_Store
+/node_modules/

docs/cli/health.md

@@ -0,0 +1,100 @@
+# Health Check CLI Documentation
+
+The Health Check CLI module provides commands for checking the health of API endpoints and system resources used by BioMCP.
+
+> **Tip**: Use the `--help` flag with any command (e.g., `biomcp health check --help`) to see the most up-to-date options directly from the tool.
+
+## Check Command (`check`)
+
+Run a comprehensive health check on API endpoints and system resources.
+
+### Usage
+
+```bash
+biomcp health check [OPTIONS]
+```
+
+#### Options
+
+- `--api-only`: Check only API endpoints. [default: False]
+- `--system-only`: Check only system health. [default: False]
+- `-v, --verbose`: Show detailed error information and API responses. [default: False]
+- `--help`: Show help message and exit.
+
+### API Endpoints Checked
+
+The health check command tests connectivity and responses from all external APIs that BioMCP depends on:
+
+1. **PubTator3 API**:
+
+   - Autocomplete endpoint
+   - Publications export endpoint
+   - Search endpoint
+
+2. **ClinicalTrials.gov API**:
+
+   - Studies search endpoint
+   - Individual study retrieval endpoint
+
+3. **MyVariant.info API**:
+   - Query endpoint
+   - Variant retrieval endpoint
+
+### System Health Checks
+
+When checking system health, the command evaluates:
+
+- **Network connectivity**: Tests basic internet connectivity
+- **System resources**: Monitors CPU usage, memory availability, and disk space
+- **Python environment**: Reports Python version and critical dependencies
+
+> **Note**: For full system resource checks, the `psutil` package is required. If not installed, the command will still run but will indicate that `psutil` is missing.
+
+### Examples
+
+Run a complete health check (API endpoints and system resources):
+
+```bash
+biomcp health check
+```
+
+Check only API endpoints:
+
+```bash
+biomcp health check --api-only
+```
+
+Check only system resources:
+
+```bash
+biomcp health check --system-only
+```
+
+Show detailed error information for any failing checks:
+
+```bash
+biomcp health check --verbose
+```
+
+Combine options as needed:
+
+```bash
+biomcp health check --api-only --verbose
+```
+
+### Output
+
+The command displays results in formatted tables:
+
+1. **API Endpoints Health**: Shows the status of each API endpoint (200 OK or error code)
+2. **System Resources**: Displays CPU, memory, and disk usage statistics
+3. **Network & Environment**: Shows network connectivity status and Python environment details
+
+In verbose mode, detailed error information is displayed for any failing endpoints, which can help diagnose API-related issues.
+
+### Exit Status
+
+The command provides a summary of overall health status:
+
+- "✓ All systems operational!" when all checks pass
+- "⚠ Some health checks failed." when one or more checks fail

pyproject.toml

@@ -21,7 +21,9 @@ dependencies = [
     "httpx>=0.28.1",
     "mcp[cli]>=1.3.0",
     "platformdirs>=4.3.6",
+    "psutil>=7.0.0",
     "pydantic>=2.10.6",
+    "rich>=14.0.0",
     "typer>=0.15.2",
 ]