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.

Table of Contents

  1. Before Performing the Upgrade
  2. Noteworthy Changes
    1. Ant version 1.8 is required
    2. Custom short views
    3. Support for OpenSocial gadgets
    4. Supported Browsers
  3. Upgrade Instructions
  4. Knowledge Base Migration
  5. Review the VIVO Terms of Use
  6. Next Steps

I. Before Performing the Upgrade


Create backups of:

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

II. Noteworthy Changes

III. Upgrade Instructions

1. Download the new distribution file and unpack it into a new source directory.

2. Create a new deploy.properties using the same settings as in your previous installation and set values for the new variables as described below:

Property Name Example Value
Show only the most appropriate data values based on the Accept-Language header supplied by the browser. Default is true if not set.
RDFService.languageFilter true
These values are used when deploying VIVO as an OpenSocial container and integrating with OpenSocial gadgets. For instructions, look at setting_up_orng.html, in this directory. If you are creating a VIVO installation that does not use OpenSocial gadgets, these values are omitted.
OpenSocial.shindigURL
OpenSocial.tokenService
OpenSocial.tokenKeyFile
OpenSocial.sandbox 		 

3. Apply any previous changes you have made to the new source directory.

Special notes regarding source files

5. Stop Apache Tomcat and from your VIVO source directory, run ant by typing: ant all

6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is completed. Depending on the size of your database, the migration process may take up to several hours. When it is complete, you will see a message in the catalina.log file that the server has started.

INFO: Server startup in XXXXX ms

7. As root or an administrator, request a rebuild of the Solr search index: Go to the "Site Admin" page and click on "Rebuild Search Index" under the heading "Refresh Content".

8. Review and save aside the knowledge base migration logs. The knowledge base migration process described in the next section will generate logs. These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since they may be a useful reference if questions come up about your 1.5 VIVO data after deployment, you should save them aside. The logs are created in the Tomcat webapps/vivo/WEB-INF directory:

ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log
A log of a summary of updates that were made to the knowledge base. This file should end with "Finished knowledge base migration". If this file contains any warnings they should be reviewed with your implementation team representative to see whether any corrective action needs to be taken.
ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log
A log of errors that were encountered during the upgrade process. This file should be empty if the upgrade was successful. If any errors are encountered you will need to rerun the knowledge base migration.

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.