SODAR Taskflow

The SODAR Taskflow component executes taskflows on the iRODS and SODAR databases. It also handles project locking and unlocking using tooz and Redis.

PLEASE NOTE: From SODAR v0.11.0 onwards this functionality will be merged into the sodar-server repository. This separate service will be archived and no longer developed.

Requirements

• Linux (Ubuntu 20.04 recommended)
• Python 3.8+
• Redis
• Access to two dedicated iRODS iCAT servers (one for running tests)

Installation

• Set up and activate a virtualenv environment for Python 3
• Execute pip install -r requirements.txt

• Set up required components

  • DEFAULT iRODS iCAT Server
  • TEST iRODS iCAT Server
  • Redis-server

• Execute utility/run_dev.sh for development/debug mode

Local Development Environment

The sodar-docker-compose setup runs a redis-server and two iRODS servers as Docker containers. It is the easiest way to get the required servers running. See the repository for installation instructions.

Make sure to set up your environment variables with the correct iRODS host, zone and admin user login data, both for the default and test iRODS servers. See config/base.py for the variables and their default values.

The default configuration assumes a local DEFAULT iRODS server, while the TEST iRODS server and Redis are accessed from sodar-docker-compose.

WARNING: Never set a production server as the TEST server in your configuration, as this may result in data loss!

Production Deployment

SODAR Taskflow can be deployed together with the main SODAR Server using Docker Compose.

NOTE: Due to the TASKFLOW_SODAR_SECRET variable having to match between SODAR and SODAR Taskflow, only one SODAR instance may be used with one SODAR Taskflow instance!