README.md

Table of contents

• Introduction
• Quick Start for local development
  • Prerequisites
• Monitoring
  • Healthcheck
  • Long Term Monitoring
• Backup
  • VM
  • Database
• FAQ
  • I want to change a workflow/script for import
  • I want to deploy a new version

Introduction

This documentation is intended for admins of the OMERO server (omero.intranet.ufz.de). The prerequisite is SSH access (ideally with Publickey) and the password for the Vault keystore. The installation of the OS, required packages, as well as user configuration etc. for the server takes place in the repo https://git.ufz.de/rdm/ansible.

Only the deployment of the OMERO server software components and the associated configuration is provided here.

Quick Start for local development

Prerequisites

• Docker & Docker-Compose
• Python 3.9 (there are still some issues with 3.10 (May 2022))
• Packages
  • python3.9-dev
  • openssl
  • libssl-dev
  • libbz2-dev

Generate local dev-environment simply type make - after this you can switch into the environment via pipenv shell

Test with:

(omero) hannes@t490:~/code/omero$ python docker/omero-import/scripts/biotox/omero-import.py --username root --password test
Namespace(username='root', password='test', group='', host='omero.intranet.ufz.de', port=4064, import_path='/home/omero/mnt')
2022-05-03 16:33:27,218 - biotox - INFO - Importing from folder /home/omero/mnt
2022-05-03 16:33:27,219 - biotox - INFO - Importing 0 files

Monitoring

Healthcheck

Is done via Nagios-Plugins and aggregated in SnagView

Long Term Monitoring

In Grafana

Backup

There two separate automatic backup-processes which backups the VM itself including all mounted devices and the database with metadata.

VM

The Omero-VM including OS, User-Data and Image-Data is backuped once a week (Thursday) and Snapshots are stored for 3 weeks.

• Image-Date is stored in ESX-Storage mounted on /mnt (max. 10 TB, July 22).

Recovery needs to be done with the VMWare-Admins (e.g. Andrea Müller or Gundula)

Database

Metadata from the images is stored in a Postgres-DB omero_prod on postgres.intranet.ufz.de. There is a weekly physical backup + the transaction log, so that a restore is possible to every point in time until 4 weeks ago.

Restore needs to be done with Postgres-Admin (Conrad Ostertag)

FAQ

I want to change a workflow/script for import

I want to deploy a new version