CLI Commands

Complete reference for all Aether CLI commands and options.

Global Options

All commands support these options:

aether [global-options] <command> [command-options]

Global Options:

• --config, -c FILE - Path to aether.yaml configuration file
• --jobs-dir DIR - Override jobs directory
• --help, -h - Show command help
• --version, -v - Show Aether version
• --debug - Enable debug logging

Commands

aether pipeline start

Start a new pipeline execution.

Syntax:

aether pipeline start [options] <input>

Arguments:

• <input> - Path to FHIR directory or CRTDL query file

Options:

• --config, -c FILE - Configuration file (default: aether.yaml)
• --jobs-dir DIR - Override jobs directory
• --steps STEP1,STEP2 - Override enabled steps

Examples:

# Start from local FHIR files
aether pipeline start /data/fhir/

# Start from CRTDL query
aether pipeline start my_cohort.crtdl

# Override configuration
aether pipeline start --config prod.yaml query.crtdl

# Run specific steps only
aether pipeline start --steps import,dimp /data/fhir/

aether pipeline status

Check the status of a running or completed pipeline.

Syntax:

aether pipeline status [options] <job-id>

Arguments:

• <job-id> - Job identifier

Options:

• --json - Output as JSON
• --jobs-dir DIR - Override jobs directory

Examples:

# Check job status
aether pipeline status abc123

# Get JSON output for scripting
aether pipeline status --json abc123

aether pipeline continue

Resume a failed pipeline from where it stopped.

Syntax:

aether pipeline continue [options] <job-id>

Arguments:

• <job-id> - Job identifier of failed pipeline

Options:

• --config, -c FILE - Configuration file
• --jobs-dir DIR - Override jobs directory

Examples:

# Resume failed job
aether pipeline continue abc123

# Resume with specific configuration
aether pipeline continue --config prod.yaml abc123

aether job list

List all jobs.

Syntax:

aether job list [options]

Options:

• --jobs-dir DIR - Override jobs directory
• --status STATUS - Filter by status (running, completed, failed)
• --json - Output as JSON
• --limit N - Show last N jobs (default: 10)

Examples:

# List all jobs
aether job list

# Show failed jobs only
aether job list --status failed

# Get as JSON for scripting
aether job list --json

aether job logs

View logs for a specific job.

Syntax:

aether job logs [options] <job-id>

Arguments:

• <job-id> - Job identifier

Options:

• --jobs-dir DIR - Override jobs directory
• --follow, -f - Stream logs continuously
• --step STEP - Show logs for specific step only
• --errors-only - Show only error lines

Examples:

# View job logs
aether job logs abc123

# Stream logs as they happen
aether job logs --follow abc123

# View only DIMP step logs
aether job logs --step dimp abc123

# Show only errors
aether job logs --errors-only abc123

aether job delete

Delete a completed job and its data.

Syntax:

aether job delete [options] <job-id>

Arguments:

• <job-id> - Job identifier

Options:

• --jobs-dir DIR - Override jobs directory
• --force, -f - Skip confirmation prompt

Examples:

# Delete job (with confirmation)
aether job delete abc123

# Force delete without confirmation
aether job delete --force abc123

aether completion

Generate shell completion scripts.

Syntax:

aether completion <shell>

Arguments:

• <shell> - Shell type: bash, zsh, fish, powershell

Examples:

# Generate bash completions
aether completion bash

# Install for zsh
aether completion zsh | sudo tee /etc/zsh/completions/_aether

# Install for bash
aether completion bash | sudo tee /etc/bash_completion.d/aether

aether version

Show Aether version and build information.

Syntax:

aether version

Output:

Aether v1.0.0
Build: abc123def456
Go: 1.21.0

aether help

Show help information.

Syntax:

aether help [command]

Arguments:

• [command] - Optional specific command to show help for

Examples:

# Show general help
aether help

# Show help for specific command
aether help pipeline start

Exit Codes

• 0 - Success
• 1 - General error
• 2 - Configuration error
• 3 - Invalid input
• 4 - Service unavailable
• 5 - Pipeline failed (retryable)
• 6 - Pipeline failed (fatal)

Output Formats

Default (Human-Readable)

Job: abc123
Status: running
Steps: torch, import, dimp
Progress: 45%
Elapsed: 2m 30s
ETA: 3m 15s

JSON Format

{
  "job_id": "abc123",
  "status": "running",
  "steps": ["torch", "import", "dimp"],
  "progress": 0.45,
  "elapsed_seconds": 150,
  "eta_seconds": 195
}

Environment Variables

• AETHER_CONFIG - Default configuration file path
• AETHER_JOBS_DIR - Default jobs directory
• AETHER_LOG_LEVEL - Logging level (debug, info, warn, error)
• TORCH_USERNAME - TORCH username
• TORCH_PASSWORD - TORCH password
• DIMP_URL - DIMP service URL

Next Steps

• Configuration Reference - Configuration file options
• Pipeline Steps - Pipeline architecture
• Troubleshooting - Common issues