aether

README

Aether

A command-line tool for processing FHIR healthcare data through configurable pipeline steps.

Aether is a Go command-line tool that orchestrates a configurable FHIR data pipeline for the Medizininformatik-Initiative (MII). It chains steps such as TORCH/CRTDL import, DIMP pseudonymization, bundle splitting, flattening to CSV, and send — with wait checkpoints for manual inspection and zstd compression between stages. Aether is built for data stewards and integration engineers who move MII FHIR data between research and clinical systems.

What Does Aether Do?

Aether helps you:

1. Extract patient data from a TORCH server using CRTDL query files
2. Pseudonymize the data using a DIMP service to protect patient privacy
3. Flatten FHIR data to CSV using SQL-on-FHIR ViewDefinitions
4. Send processed data to FHIR servers or DSF transfer systems

Installation

For Linux and macOS:

curl -sSfL https://raw.githubusercontent.com/medizininformatik-initiative/aether/main/install.sh | sh
sudo mv aether /usr/local/bin/

For manual installation or Windows, download the latest release.

Verify installation:

aether --help

Configuration

Create an aether.yaml file (any path is fine — pass it as the first positional arg):

services:
  torch:
    base_url: "https://your-torch-server.org"
    username: "your-username"
    password: "your-password"

  dimp:
    url: "http://your-dimp-server:32861"  # server root; /fhir appended by client

pipeline:
  enabled_steps:
    - torch
    - dimp

jobs_dir: "./jobs"

Usage

Every subcommand takes the path to your aether.yaml as the first positional argument.

Run a Pipeline

aether pipeline start aether.yaml your-crtdl.json

Check Status

aether job list aether.yaml
aether pipeline status aether.yaml <job-id>

Resume a Pipeline

aether pipeline continue aether.yaml <job-id>

More Information

• Full Documentation
• Configuration Options
• Pipeline Steps

License

Apache License 2.0 - see LICENSE