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Motivation

Since version S126 for DSS and S134 for AS the concept of core plugins has been introduced. It allows to split the monolithic service.properties into one service.properties file and several plugin.properties files. The later ones defining the core plugins. The openBIS Installer for Standard Technologies contains allready defined core plugins for the technologies (i.e. modules) screening, proteomics and Illumina NGS. For old openBIS installations some of these core plugins might be in conflict with stuff configured in service.properties. This guide explains how to migrate old service.properties file to avoid those conflicts and make use of core plugins shipped by the distribution.

Migration

  • The migration has to be done for all technologies enabled during upgrading the old openBIS instance by using the openBIS Installer for Standard Technologies.
  • Note, that the migration has to be done after upgrading and before starting the servers (by executing <installation path>/bin/allup.sh).
  • The general procedure for migration is the following:
    1. Compare plugin.properties of each core plugins of all enabled technologies with definitions in service.properties.
    2. Remove identical definitions from service.properties.
    3. Keep non-identical definitions in service.properties but disable the different core plugins in property disabled-core-plugins of core-plugins/core-plugins.properties.
    4. Disable core plugins which are not needed. That also includes disabling of master data initialization.
  • DSS core plugins of type drop-boxes are mostly meant to be examples. In a real productive openBIS instance they should probably be disabled. This can be done in property disabled-core-plugins by the term <module name>:drop-boxes which disables all drop boxes of specified module.

The following sections describe technology specific consideration.

Screening

Imaging Database: The DSS core-plugins for the imaging database (data-sources:imaging-db and maintenance-tasks:imaging-db-clean-up) have to be used and the corresponding entries in service.properties should be removed. If the name of the property imaging-db.databaseKind was not 'prod' the property should be still kept but renamed to imaging-database.kind. It will be used as a parameter inside the core plugin data-sources:imaging-db.

Proteomics

Proteomics Database: The DSS core-plugins for the proteomic database (data-sources:proteomics-db and maintenance-tasks:proteomics-db-clean-up) have to be used and the corresponding entries in service.properties should be removed. If the name of the property data-source.databaseKind was not 'productive' the property should be still kept but renamed to proteomics-database-kind. It will be used as a parameter inside the core plugin data-sources:proteomics-db.

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