Appendix J. Things to consider when updating an existing BASE installation

Table of Contents

J.1. BASE 3.2
J.2. BASE 3.0
J.3. All BASE 2.x releases

This document is a list of things that may have to be considered when updating a BASE installation to a newer version. The Section 20.1, “Upgrade instructions” section only include the most recent information that is needed for updating the previous BASE version to the current version.

J.1. BASE 3.2

Custom logging implementations must be updated

The plug-in functionality for custom logging has been converted to an extension point. The default database logging will continue to function, but custom logging implementations must be converted to an extension. See Section I.1, “BASE 3.2 release” and Section 26.8.9, “Logging managers” for more information.

J.2. BASE 3.0

[Note] Upgrading to BASE 3.0 is supported from BASE 2.17 only

If your BASE is an older 2.x version you'll need to upgrade to BASE 2.17 before an upgrade to BASE 3.0 is possible.

[Warning] Make sure that you have a recent backup of the BASE 2.17 database

Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you have a recent backup. If the upgrade fails you must restore the 2.17 database before you can try again. The upgrade only changes the 'static' part of the database, so you do not have to restore the 'dynamic' part or the uploaded files.

Old plug-ins and extensions may not work

The BASE API has changed in several places and it is not certain that plug-ins and extensions developed for BASE 2 works with BASE 3. The upgrade will disable all plug-ins and extensions that are currently installed. Before you upgrade we recommend that you go through all (external) plug-ins and check if there is an updated version. The recommended approach is to first upgrade BASE and then install updated versions of plug-ins and extensions following the instructions in Section 21.1, “Managing plug-ins and extensions”.

If there is no updated version of a specific plug-in you may try a manual re-installation of the old plug-ins. Follow the instructions in Section 21.1.2, “Manual plug-in registration”.

If there is no updated version and the old plug-in doesn't work with BASE 3, you'll need to decide if you really need the plug-in or if the upgrade should wait until a new version of the plug-in has been released.

Batch item importer changes

There are several changes to batch item importers that may affect current workflows and file templates used for importing data.

  • Sample and extract importers: The 'pooled' column is no longer used. Instead a 'parent type' column should be used with the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT). Existing importer configurations and file templates may have to be updated. If no parent type is specified the sample importer assumes a biosource and the extract importer assumes a sample.

  • Labeled extract importer: This has been deprecated and it is recommended that the Extract importer is used instead. We recommend that existing labeled extract importer configurations are re-created as extract importer configurations. The old labeled extract importer can be re-enabled, but note that the existing configurations still need to be changed due to the 'pooled' column is no longer used.

  • Hybridization importer: This has been deprecated and we recommend that the Physical bioassay importer is used instead. Existing hybridization importer configurations should be re-created as physical bioassay importer configurations.

  • Scan importer: This has been deprecated and it is recommended that the Derived bioassay importer is used instead. Existing scan importer configurations should be re-created as derived bioassay importer configurations.

[Note] Note
The deprecated importers can be re-enabled by an administrator from the AdministratePlug-ins & extensionsOverview page, but they are lacking features that are available in the new importers so this is not something that we recommend.

MySQL and PostgreSQL versions

We have only tested BASE 3 with PostgreSQL 9.1. If anyone experiences any issues with earlier PostgreSQL versions, we recommend an upgrade to PostgreSQL 9.1. This is a change since BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3 may work with older PostgreSQL versions, we don't have the resources needed to test and provide support for it.

We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2). If anyone experiences any issues with earlier (or later) MySQL versions, we recommend an upgrade/downgrade to MySQL 5.1.

J.3. All BASE 2.x releases

We only support updating to BASE 3 from BASE 2.17. If you have an older BASE version and wish to update to BASE 3, you first have to upgrade to BASE 2.17. BASE 2.17 can be downloaded from the BASE download page. Documentation for BASE 2.17 is available as part of the download and at http://base.thep.lu.se/chrome/site/2.17/html/index.html.