VIVO Release 1 V1.4 Upgrade Guide

December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4

This document contains instructions on how to upgrade your installation of VIVO from Version 1.3 to Version 1.4. This and other documentation can be found on the support page at

If you need to do a fresh install, please consult the VIVO Release V1.4 Installation Guide found on 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 (there are no new hardware or software requirements for V1.4).

For a description of the release contents see the Release announcement for V1.4.

Table of Contents

  1. Before Performing the Upgrade
  2. Noteworthy Changes
    1. New Property in
    2. Change to tomcat configuration
  3. Upgrade Instructions
  4. Knowledge Base Migration
    1. Knowledge Base Migration Process
    2. Knowledge Base Manual Review for Local Extensions
  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 using the same settings as in your previous installation and set values for the new variables as described below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,, email.smptHost, email.replyTo, rootUser.emailAddress)

Property Name Example Value
Default namespace: VIVO installations make their RDF resources available for harvest using linked data. Requests for RDF resource URIs redirect to HTML or RDF representations as specified by the client. To make this possible, VIVO's default namespace must have a certain structure and begin with the public web address of the VIVO installation. For example, if the web address of a VIVO installation is "" the default namespace must be set to "" in order to support linked data. Similarly, if VIVO is installed at "" the default namespace must be set to ""
* The namespace must end with "individual/" (including the trailing slash).
Directory where Vitro code is located. In most deployments, this is set to ./vitro-core (It is not uncommon for this setting to point elsewhere in development environments).
vitro.core.dir ./vitro-core
Directory where tomcat is installed.
tomcat.home /usr/local/tomcat
Name of your VIVO application. vivo
URL of Solr context used in local VIVO search. Should consist of:
    scheme + servername + port + vivo_webapp_name + "solr"
In the standard installation, the Solr context will be on the same server as VIVO, and in the same Tomcat instance. The path will be the VIVO (specified above) + "solr"
vitro.local.solr.url http://localhost:8080/vivosolr
Restricts access to the Solr search platform. One or more regular expressions, separated by commas. When a request is made to Solr, the IP address of the requestor must match one of the patterns, or the request will be rejected.
  • vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
  • vitro.local.solr.ipaddress.mask = 127\.0\.0\.1,0:0:0:0:0:0:0:1
  • vitro.local.solr.ipaddress.mask = 169.254.*
vitro.local.solr.ipaddress.mask 127\.0\.0\.1,0:0:0:0:0:0:0:1
Directory where the VIVO application will store the data that it creates. This includes uploaded files (usually images) and the Solr search index. Be sure this directory exists and is writable by the user who the Tomcat service is running as. /usr/local/vivo/data
Specify an SMTP host that the application will use for sending e-mail (Optional). If this is left blank, the contact form will be hidden and disabled, and users will not be notified of changes to their accounts.
Specify an email address which will appear as the sender in e-mail notifications to users (Optional). If a user replies to the notification, this address will receive the reply. If a user's e-mail address is invalid, this address will receive the error notice. If this is left blank, users will not be notified of changes to their accounts.
Specify the JDBC URL of your database. Change the end of the URL to reflect your database name (if it is not "vivo").
VitroConnection.DataSource.url jdbc:mysql://localhost/vivo
Change the username to match the authorized user you created in MySQL.
VitroConnection.DataSource.username username
Change the password to match the password you created in MySQL.
VitroConnection.DataSource.password password
Specify the maximum number of active connections in the database connection pool to support the anticipated number of concurrent page requests.
VitroConnection.DataSource.pool.maxActive 40
Specify the maximum number of database connections that will be allowed to remain idle in the connection pool. Default is 25% of the maximum number of active connections.
VitroConnection.DataSource.pool.maxIdle 10
Change the dbtype setting to use a database other than MySQL. Otherwise, leave this value unchanged. Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and SQLServer. Refer to for additional information.
VitroConnection.DataSource.dbtype MySQL
Specify a driver class name to use a database other than MySQL. Otherwise, leave this value unchanged. This JAR file for this driver must be added to the the webapp/lib directory within the vitro.core.dir specified above.
VitroConnection.DataSource.driver com.mysql.jdbc.Driver
Change the validation query used to test database connections only if necessary to use a database other than MySQL. Otherwise, leave this value unchanged.
VitroConnection.DataSource.validationQuery SELECT 1
Specify the email address of the root user account for the VIVO application. This user will have an initial temporary password of 'rootPassword'. You will be prompted to create a new password on first login.

NOTE: The root user account has access to all data and all operations in VIVO. Data views may be surprising when logged in as the root user. It is best to create a Site Admin account to use for every day administrative tasks.

The URI of a property that can be used to associate an Individual with a user account. When a user logs in with a name that matches the value of this property, the user will be authorized to edit that Individual (the value of the property must be either a String literal or an untyped literal).
If an external authentication system like Shibboleth or CUWebAuth is to be used, these properties say how the login button should be labeled, and which HTTP header will contain the user ID from the authentication system. If such a system is not to be used, leave these commented out. Consult the installation instructions for more details.
Log in using BearCat Shibboleth
The temporal graph visualization can require extensive machine resources. This can have a particularly noticable impact on memory usage if
  • The organization tree is deep,
  • The number of grants and publications is large.
VIVO V1.4 mitigates this problem by the way of a caching mechanism and hence we can safely set this to be enabled by default.
visualization.temporal enabled
The temporal graph visualization is used to compare different organizations/people within an organization on parameters like number of publications or grants. By default, the app will attempt to make its best guess at the top level organization in your instance. If you're unhappy with this selection, uncomment out the property below and set it to the URI of the organization individual you want to identify as the top level organization. It will be used as the default whenever the temporal graph visualization is rendered without being passed an explicit org. For example, to use "Ponce School of Medicine" as the top organization:
visualization.topLevelOrg =
An absolute file path, pointing to the root directory of the Harvester utility. You must include the final slash.
harvester.location /usr/local/vivo/harvester/
Types of individual for which we can create proxy editors. If this is omitted, defaults to

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 1.4 VIVO data after deployment, you should save them aside. The logs are created in the Tomcat webapps/vivo/WEB-INF directory:

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

i.Knowledge Base Migration Process

For an description of changes to the VIVO ontology in version 1.4 see the sourceforge wiki page on ontology changes

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 will make the following types of changes:

Class or Property renaming
All references to the class (in the subject or object position) will be updated to the new name. References to the property will be updated to the new name.
Class or Property deletion
All type assertions of a deleted class will be removed.
All statements using a deleted property will be changed to use the nearest available superproperty. If there is no available superproperty then the statement will be deleted from the knowledge base. Note that all removed and added data is recorded in the files in the changedData directory.
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.
Structural changes
Changes in the way individuals (intances of classes) are related to other individuals.

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.

ii. Knowledge Base Manual Review for Local Extensions

Not all of the modifications that may be required are automated. If you have local extensions to areas of the ontology that have changed, a manual review of the knowledge base is recommended after the automated upgrade process.

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:

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.