VIVO Release 1 V1.5 Upgrade Guide

February 15, 2012 - Upgrading from Release 1 V1.4 to Release 1 V1.5

This document contains instructions on how to upgrade your installation of VIVO from Version 1.4 (or 1.4.1) to Version 1.5. This and other documentation can be found on the support page at VIVOweb.org

If you need to do a fresh install, please consult the VIVO Release V1.5 Installation Guide found on vivoweb.org or the install.html file located in the doc directory of the VIVO source code distribution. The installation document also has a list of the required software and versions.

For a description of the release contents see the Release announcement for V1.5.

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Table of Contents

1. Before Performing the Upgrade
2. Noteworthy Changes
   
3. Upgrade Instructions
4. Knowledge Base Migration
5. Review the VIVO Terms of Use
6. Next Steps

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I. Before Performing the Upgrade

Create backups of:

• The VIVO distribution directory (which contains the source for VIVO 1.4 or VIVO 1.4.1)
• The VIVO home directory (pointed to by your deploy.properties file)
• The webapps directory in Tomcat
• MySQL database (most people use mysqldump to create the backup)

The upgrade process is similar to the initial install process with the following exceptions:

• You do not need to reinstall MySQL or recreate the MySQL database. Please backup your MySQL database as noted above.
• First-time login of the root account after the upgrade process is complete will use the password previously set (not the default password used on the first login after the initial installation.)
• The first time Apache Tomcat starts up after the upgrade, an automated process will modify the knowledge base to align the data with any ontology updates made for the new release. See the section on the Knowledge Base Migration below for more information.

BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY

II. Noteworthy Changes

• Ant version 1.8 required

  See J.Blake for details.

• Custom search views

  "Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism. If you have custom search views, you will need to re-configure them. See J.Blake for details.

• Support for OpenSocial gadgets

  You can now add OpenSocial support to your VIVO instance. Look at setting_up_orng.html for details. See J.Blake for details.

• Supported Browsers

  For this release, the following browsers are supported.

  Mac:

  • Chrome 8.0.552.237
  • FireFox 3.6.13
  • Opera 10.6.2
  • Safari 5.0.3

  PC:

  • Chrome 8.0.552.273
  • FireFox 10.0.2
  • Internet Explorer 7, 8, 9
  • Opera 10.6.2

BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY

III. Upgrade Instructions

BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY

IV .Knowledge Base Migration

Changes to the VIVO core ontology may require corresponding modifications to the knowledge base instance data and ontology annotations. When VIVO first starts up following the upgrade, it will initiate a process to examine the knowledge base and apply necessary changes. The knowledge base migration process for release 1.5 will make the following types of changes:

The vivo:ResearchLaboratory class has been removed. All instances of vivo:ResearchLaboratory will be retyped to its superclass vivo:Laboratory.

Annotation property default values

If a site has modified the value of a vitro annotation (such as displayRankAnnot or displayLimitAnnot) so that it is no longer using the default, then that setting will be left unchanged.
If a site is using the default value of a vitro annotation, and the default has been changed in the new version of the ontology, then the new default value will be propagated to the knowledge base.

In addition to the logs described in step 8 of the previous section, the knowledge base migration process will log copies of all additions and deletions that were made to the knowledge base in the following files:

webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3

An N3 file containing all the statements that were removed from the knowledge base.

webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3

An N3 file containing all the statements that were added to the knowledge base.

V. Review the VIVO Terms of Use

VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" you assign in the "Site Information" form under the Site Admin area will be inserted into the "Terms of Use" statement. If you want to edit the text content more than just the "Site Name", the file can be found here:

[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl

Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose your changes next time you deploy for another reason.

Next Steps

Now that you have VIVO up and running, please refer to the Site Administrator's Guide for information about its operation.