openbis/debian-openbis repository overview

⁠Decommissioned

This image has been decommissioned since it is not suited for any type of production use. We do not provide patches for this image either. Any tagged versions of this image are to be used for development purposes only.

Please use openbis/openbis-app⁠ instead, for which we provide unified support, consistent configuration and documentation for containerized and cloud native infrastructure environments.

⁠Migration

The docker image openbis/debian-openbis was specifically designed for development purposes and was not intended to use in production environments. Data persistence and simplicity of upgrades are not achievable trivially. Production environments should be migrated to openbis/openbis-app⁠.

⁠Prerequisites

Initial openbis-app container is set up and running as an empty instance. Procedure below assumes the both containers are running at the same host.

⁠Backup

The docker container "debian-openbis" should be running to create archives of database, data store, passwords, and configuration properties.

Dump all databases to a compressed archive.

$ docker exec debian-openbis pg_dumpall -U postgres -c --if-exists | gzip -c > debian-openbis.sql.gz;

Create a compressed archive file containing the data store.

$ docker exec debian-openbis tar --one-file-system -C /home/openbis/openbis_state -cf - dss_store | gzip -c > debian-openbis-data.tar.gz;

Create a compressed archive file containing the AS raw-store (containing files embedded in rich-text fields).

$ docker exec debian-openbis tar --one-file-system -C /home/openbis/openbis_state -cf - as_data | gzip -c > debian-openbis-as-data.tar.gz

Create a compressed archive file containing passwords of local file-authentication accounts.

$ docker exec debian-openbis tar --one-file-system -C /home/openbis/openbis_state/as_etc -cf - passwd | gzip -c > debian-openbis-passwd.tar.gz

Create a compressed archive file containing the application (AS and DSS) configuration.

$ docker exec debian-openbis tar --one-file-system -C /home/openbis/openbis_state/as_etc -cf - service.properties | gzip -c > debian-openbis-as-properties.tar.gz
$ docker exec debian-openbis tar --one-file-system -C /home/openbis/openbis_state/dss_etc -cf - service.properties | gzip -c > debian-openbis-dss-properties.tar.gz

⁠Restore

Restore user's password file into openbis-app container and verify if the user's list if correct.

$ gunzip -c debian-openbis-passwd.tar.gz | docker exec -i -u openbis openbis-app tar -xf - -C /etc/openbis/as;
$ docker exec -i openbis-app /home/openbis/servers/openBIS-server/jetty/bin/passwd.sh list;

Restore data store into openbis-app container.

$ gunzip -c debian-openbis-data.tar.gz | docker exec -i -u openbis openbis-app tar --strip-components=1 -xf - -C /data/openbis;

Restore raw-store into openbis-app container (AS property file-server.repository-path).

$ gunzip -c debian-openbis-as-data.tar.gz | docker exec -i -u openbis openbis-app tar --strip-components=1 -xf - -C /data/openbis/raw-store;

Restore database into openbis-db container. Application should not be running while restoration is in progress so stop openbis-app before and start after it is completed.

$ docker stop openbis-app;
$ gunzip -c debian-openbis.sql.gz | docker exec -i -u postgres openbis-db psql -w;
$ docker start openbis-app;

⁠Credentials

Set new admin password.

$ docker exec -i -u openbis openbis-app /home/openbis/servers/openBIS-server/jetty/bin/passwd.sh change admin -P;

Set new etlserver password. This username/password in DSS server settings are used to contact AS server. Make sure the password is correct in dss/service.properties.

$ docker exec -i -u openbis openbis-app /home/openbis/servers/openBIS-server/jetty/bin/passwd.sh change etlserver -P;
$ docker exec -i -u openbis openbis-app grep ^password /etc/openbis/dss/service.properties;

⁠Configuration

Application configuration, including core-plugins customization, is highly complex and we can thus not provide an easy recipe for migration. We advise to maintain all configuration items through a configuration management system to support individual use cases. The best approach is to review each item manually and follow the configuration documentation of the openbis/openbis-app⁠ container image and to refer to the main openBIS documentation⁠.

vimdiff can be used to visually compare configuration files.

$ vimdiff <(gunzip -c debian-openbis-as-properties.tar.gz) <(docker exec -i -u openbis openbis-app cat /etc/openbis/as/service.properties)
$ vimdiff <(gunzip -c debian-openbis-dss-properties.tar.gz) <(docker exec -i -u openbis openbis-app cat /etc/openbis/dss/service.properties)

⁠License

Copyright 2007-2025 ETH Zurich Scientific IT Services

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0⁠

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.