VIVO Release 1 V1.5 Upgrade GuideFebruary 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
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
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.
II. Noteworthy Changes
Ant version 1.8 is required
The VIVO build script has been revised, and now requires features from version 1.8 of Apache Ant. Version 1.8 has been available since February, 2010. The current version of Apache Ant is 1.8.4.
You can find recent versions of Apache Ant at http://ant.apache.org
Custom short views
"Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism. If you have implemented custom search views, you will need to re-configure them to fit the new framework. For an explanation of how to use custom search views, consult the SourceForge Wiki page on custom search views
Support for OpenSocial gadgets
VIVO can now be configured to support Open Research Networking Gadgets, an extension of OpenSocial gadgets. For a description of this, and instructions for configuring VIVO, look at setting_up_orng.html, in this directory.
For this release, the following browsers are supported.
- Chrome 8.0.552.237
- FireFox 3.6.13
- Opera 10.6.2
- Safari 5.0.3
- Chrome 8.0.552.273
- FireFox 10.0.2
- Internet Explorer 7, 8, 9
- Opera 10.6.2
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
|Property Name||Example Value|
|Show only the most appropriate data values based on the Accept-Language header supplied by the browser. Default is false if not set.|
|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.|
3. Apply any previous changes you have made to the new source directory.
Special notes regarding source files
- This process assumes any changes made to the application were made in the source directory and deployed, and were not made directly within the Tomcat webapps directory.
- In many cases, simply copying the modified files from your original source directory will not work since the files on which they are based have changed. It will be necessary to inspect the new source files and add any changes to them at that time.
- NIH-funded VIVO implementations will need to apply the Google Analytics Tracking Code (GATC) to
googleAnalytics.ftlin the theme:[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA sample
googleAnalytics.ftlis included in the built-in theme. This file serves only as an example, and you must replace the tracking code shown with your institution's own tracking code. For additional information about the GATC for the NIH-funded VIVO implementation sites and a copy of your institution's tracking code, see the VIVO Google Analytics wiki page.
5. Stop Apache Tomcat and from your VIVO source directory, run
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
- 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.
- 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
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:
- An N3 file containing all the statements that were removed from the knowledge base.
- An N3 file containing all the statements that were added to the knowledge base.
[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftlBe 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.
Now that you have VIVO up and running, please refer to the Site Administrator's Guide for information about its operation.