VIVO Documentation
Old Release
This documentation relates to an old version of VIVO, version 1.8.x. Looking for another version? See all documentation.
This document contains instructions on how to upgrade your installation of VIVO from Version 1.7 to Version 1.8.1. 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 Installation Instructions, found on vivoweb.org, or the VIVO Installation Instructions.pdf 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 V1.8.
Before Performing the Upgrade
Create backups of:
The VIVO distribution directory (which contains the source for VIVO 1.7
The VIVO home directory (pointed to by your build.properties file)
The webapps directory in Tomcat
MySQL database (most people use mysqldump to create the backup)
If you have used temporary models in the database to stage ingested data, you will want to clear out any unneeded models that remain listed on the Manage Jena Models
page (under Ingest tools
). This step is especially important if these temporary models contain blank nodes, as this may cause unwanted or duplicate data to appear following the upgrade.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.
- The root account will keep the password that was previously set on it. It will not return to the default password. Any user accounts that you have created will also be preserved.
Noteworthy Changes
Editing faux properties
There is now a GUI for editing faux properties. In previous releases, PropertyConfig.n3
contained the faux property configuration, now it will contain the initial configuration.
In v1.8, PropertyConfig.n3
has moved from rdf/display/evertime
to rdf/display/firsttime
. It will be read in once, in order to pick up the version changes.
If you have local modifications for PropertyConfig.n3
, you can ingest those changes or use the GUI to enter them into v1.8.
Configuration changes
Before starting VIVO 1.8, you must create config/applicationSetup.n3
in your VIVO home directory. For most installations this is simply a copy of config/example.applicationSetup.n3
.
If you have created a developer.properties
file in your VIVO home directory, you should move it to the config
sub-directory of the VIVO home directory.
Alternative triple stores
If you are using an external triple store on a SPARQL endpoint, you must change how it is configured. This configuration is no longer made in runtime.properties
; instead, it is done in config/applicationSetup.n3
.
For more details, consult the Installation Instructions, in the section titled "Using a Different Datastore".
Supported versions of Java
VIVO 1.8 supports Oracle Java 1.8 as well as Oracle Java 1.7.
Supported Browsers
For this release, the following browsers are supported.
- Mac:
- Chrome 30.0.1599.69 and above
- Firefox 3.6.28, 10.0.12, 24, 30
- Opera 12.15
- Safari 5.0.3 and above
- PC:
- Chrome 25.1364.2 and above
- Firefox 10.0.12, 24, 30
- Internet Explorer 8 (see compatibility note), 9, 10
- Opera 12.02
Compatibility Note
1.8.1 introduces new D3-based visualizations for the Co-Author and Co-Investigator networks. These do not work on IE 8, however, they do increase compatibility to mobile browsers that do not have Flash.
If you require the traditional Flash visualizations for IE 8 compatibility (providing Adobe Flash has been installed), then you can use them by setting the following in your runtime.properties:
visualization.d3 = disabled
It is expected that the Flash visualizations will be removed from version 1.9.0 onwards.
Upgrade Instructions
Download the new distribution file and unpack it into a new source directory.
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.ftl
in the theme:[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA samplegoogleAnalytics.ftl
is 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.
Apply any previous changes you have made to the RDF initialization files.
Run the build script
ant all
Create configuration files
In the config
sub-directory of your VIVO home directory (specified by vitro.home
in the build.properties
file), rename or copy example.applicationSetup.n3
to applicationSetup.n3
. For most installations, changes to this file are not needed.
If you have been using a SPARQL endpoint as your triple store, you will need to edit this file. See Using a different data store for more information.
If you have been using a developer.properties
file, you must move it to the config
sub-directory of your VIVO home directory.
Start VIVO
INFO: Server startup in XXXXX ms
Review the knowledge base migration logs.
This is usually an important step in VIVO upgrades. However, the upgrade from VIVO 1.7 to VIVO 1.8 does not require a knowledge base migration.
Knowledge Base Migration
This is usually an important step in VIVO upgrades. However, the upgrade from VIVO 1.7 to VIVO 1.8 does not require a knowledge base migration.
Review the VIVO Terms of Use
[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl