Basic configuration

Environment Variables

Variable

Default value

Description

OPENBIS_ADMIN_PASS

123456789

Administrator password to openBIS instance.

OPENBIS_DATA

/data/openbis

Directory for openBIS persistent data.

OPENBIS_DB_ADMIN_PASS

mysecretpassword

PostgreSQL superuser password.

OPENBIS_DB_ADMIN_USER

postgres

PostgreSQL superuser name.

OPENBIS_DB_APP_PASS

mysecretpassword

Password for application user connecting to the database.

OPENBIS_DB_APP_USER

openbis

Username for application user connecting to the database.

OPENBIS_DB_HOST

openbis-db

Name of container running PostgreSQL database.

OPENBIS_ETC

/etc/openbis

Directory for openBIS configuration files.

OPENBIS_HOME

/home/openbis

Directory for openBIS installation binaries.

OPENBIS_LOG

/var/log/openbis

Directory for openBIS log files.

OPENBIS_FQDN

openbis.domain

Full qualified domain name of openBIS service.

Configuration Files

openBIS offers the ability to pass in configuration files like, e.g., capabilities files. Those can be deployed in any directory mounted as a volume in the openBIS docker container. It needs to be ensured that the associated AS and DSS properties are pointing to the correct file paths.

Note

It is necessary to store any data files that needs to be preserved inside the openbis-app-data volume, or inside some other docker volume. Likewise, any configuration files should be stored within the openbis-app-etc volume. Failure to do so yields undesired behavior in the sense that changes made to the files within the container are being lost when the container goes down.

Examples

Suppy a json file for storing personal access tokens

  1. Enable the feature

Add the following line to the AS service.properties:

personal-access-tokens-enabled = true

  1. Ensure the AS property personal-access-tokens-file-path is pointing to the correct path to where the json file is located

Assuming the DSS root-dir points to the default dir, /data/openbis, then the personal-access-tokens.json could be stored in this directory:

personal-access-tokens-file-path = /data/openbis/personal-access-tokens.json

  1. Create a PAT and monitor the contents of the json file

personal-access-tokens.html#typical-application-workflow

Modify the AS capabilities file

For this, it is not needed to

Core Plugins

It is possible to make adjustments to core-plugins shipped with the openBIS installer. To do so, just start up openBIS at least once. This will copy the contents of the core-plugins directory to a sub-directory core-plugins which is stored within the docker volume openbis-app-etc. Any customizations made here will persist restarts of the application, as well as upgrades of the openbis-docker image.

Warning

Be careful when making changes to code of core-plugins since they might break when new releases are published. Please consider reading the Change Log published with each release.

If the application fails to start after changes to the core-plugins have been made, you can always revert to the original state of the core-plugins by removing the core-plugins folder within the openbis-app-etc volume.

Besides adjustments to existing plugins, it is also possible to create new plugins from scratch.

Examples

Customize the InstanceProfile.js

This file is part of the eln-lims core-plugin. It is located here: <openbis-app-etc>/core-plugins/eln-lims/1/as/webapps/eln-lims/html/etc/InstanceProfile.js

  1. Make any changes to this file

E.g., change this.showSemanticAnnotations = false; to this.showSemanticAnnotations = true;.

  1. Restart the container

Most changes made to the configuration of the openBIS application require a restart in order to be applied. Assuming the container running the openBIS application is named openbis-app, this is achieved as follows:

docker restart openbis-app