This document contains instructions on how to upgrade your installation of VIVO from Version 1.5 (or 1.5.1, or 1.5.2) to Version 1.6. This and other documentation can be found on the support page at VIVOweb.org

Create backups of:

• The VIVO distribution directory (which contains the source for VIVO 1.5 or VIVO 1.5.1)

• 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)

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.
• When 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.

Noteworthy Changes

VIVO becomes more portable

• The VIVO build script now includes a distribute target that will produce a file called distribution.tar.gz. This compressed archive contains these files:
  1. vivo.war -- a WAR file for the main VIVO application.
  2. vivosolr.war -- a WAR file for the Solr application.
  3. solrhome.tar -- a Solr home directory that is configured for use with VIVO.
  These files can be used with Tomcat, or with any container that supports the Java Servlet 2.4 Specification.To permit this portability, the deploy.properties file has been split in two. build.properties contains only the properties that are required for building VIVO. runtime.properties, which must be created in the Vitro home directory, contains the properties that VIVO uses while running.If you are building to deploy to Tomcat (as with previous releases), then build.properties must contain these properties:
  • vitro.core.dir
  • webapp.name
  • tomcat.home
  • vitro.home-- note that this was vitro.home.directory in previous releases
  If you are building to distribute, the build.properties file requires only these properties:
  • vitro.core.dir
  • webapp.name

Solr is no longer secured

In previous releases, Solr was deployed to Tomcat with a RemoteAddrValve that would only permit access from certain IP addresses. Acceptable IP addresses were those which matched the regular expression pattern in the vitro.local.solr.ipaddress.mask property.This has been removed because:

• It caused repeated problems for sites who were experimenting with VIVO.
• It was not standards-based, but specific to Tomcat.
• It was redundant. Production instances of VIVO are usually hidden behind a firewall and accessed through an Apache Http server.

Sites that need to secure Solr are now left to their own devices.

Log4J properties file renamed

In previous releases, the properties file for the VIVO logging system was called default.log4j.properties. In release 1.6, this file has been renamed to log4j.properties. This is so the developers and implementers will know where to look for the file.Note that debug.log4j.properties, if present, will still override the default.

Property groups now displayed in a tab format, including a "View All" tab

With release 1.6, the property group menu bar that was used on profile pages has been replaced by java script enabled tabs. When clicked, each property group tab will display the properties within that group while the contents of the previously displayed group will be hidden. The array of tabs also includes a "View All" tab that, when clicked, displays the contents of all the property groups.

Class-specific SPARQL Query Data Getters

The VIVO software now supports the development of SPARQL query data getters that can be associated with specific ontological classes. These data getters, in turn, can be accessed within Freemarker templates to provide richer content on VIVO profile pages. For example, the profile page for an academic department lists only the names of the faculty within that department and their titles, but with a SPARQL query data getter it is now possible to extend the faculty information to display all of the faculty members' research areas. Refer to this wiki page for details on how to use class-specific SPARQL query data getters: https://wiki.duraspace.org/display/VIVO/Enriching+VIVO+Content+Using+SPARQL+Query+Data+Getters.

The foaf:Person template has been re-located

Multiple foaf:Person Profile Pages

VIVO now supports multiple profile pages for foaf:Persons. This feature, which is optional so installations can continue to use just the individual--foaf-person.ftl template, currently consists of two profile page types: a standard view, which is a redesigned version of the foaf:Person template in previous releases; and a quick view, which emphasizes the individual's own web page presence while providing summary VIVO information, such as current positions and research areas. The profile quick view requires the use of a web service that captures images of web pages. This web service is not included with the VIVO software. An installation will either have to develop their own service or use a third-party service, usually for a small fee depending on the number of images served. (Examples of these services include WebShotsPro, Thumbalizr and Websnapr.) For more information on how to implement multiple profile page views, refer to this wiki page: https://wiki.duraspace.org/display/VIVO/Multiple+foaf%3APerson+Profile+Pages.

Home Page Re-design

For Release 1.6 the VIVO Home Page has been redesigned. The Search field beneath the "welcome" text now allows the user to limit the results of a search to a specific class group, such as people, organizations, etc. In addition, the browse-by-class-group display has been removed from the Home Page and replaced by multiple features, which include: a list of four randomly selected faculty members, including their titles and thumbnail images; a display of statistical data about the VIVO installation, such as the number of people, activities and organizations; and, optionally a global map showing researchers' areas of geographic focus.

Auto-loaded RDF files move to the Home directory

The RDF files that initialize the data model have moved, in both the distribution and the runtime locations. In the distribution, they have been collected in one place, and reorganized to use a more consistent naming scheme. During the build process, they are copied to a location within the VIVO home directory, instead of residing in the webapp itself.If you have modified these RDF files, or added files of your own, you must adjust to the new locations accordingly.

If you are using a three-tier build process, you will need to add two lines to the build script to accomodate the RDF files, and the language support (see below) So this:

<patternset id="appbase.patterns">
  <include name="src/**/*" />
  <include name="lib/**/*" />
  <include name="test/**/*" />
  <include name="themes/**/*" />
  <include name="config/*.properties" />
  <include name="config/*.txt" />
  <include name="config/jarlist/*.txt" />
  <include name="config/solr/*" />
  <include name="context.xml" />
</patternset>

becomes this:

<patternset id="appbase.patterns">
  <include name="src/**/*" />
  <include name="lib/**/*" />
  <include name="rdf/**/*" /> 
  <include name="languages/**/*" />
  <include name="test/**/*" />
  <include name="themes/**/*" />
  <include name="config/*.properties" />
  <include name="config/*.txt" />
  <include name="config/jarlist/*.txt" />
  <include name="config/solr/*" />
  <include name="context.xml" />
</patternset>

Support for additional languages

VIVO 1.6 includes limited support for other languages, in addition to American English. This limited support is described as read-only support on public-facing pages.Read-only means that there is no provision for editing multi-language data or displays. Property values, ontology labels, etc. must all be provided in RDF files and ingested or otherwise inserted into the data model. The Page Management user interface does not support maintaining pages in multiple languages.Public-facing means that most of the pages used for site adminstration are only presented in American English.These two pages in the VIVO Wiki describe how to Build VIVO with multiple languages and how to Add a new language to VIVO.

More compact responses to Linked data requests

• Data properties of the individual
• Object relationships to and from the individual
• The RDF types and RDFS labels for any object that directly relates to the individual

• Data properties of the individual
• Object relationships from the individual
• All properties of the context nodes (positions, roles, etc.) that are associated with the individual.
• Labels of objects that are joined to the individual through context nodes.
• Full details of time intervals that are attached to context nodes: start, end, precision.

Changes to default types for Google Refine

The list of default types for Google Refine has changed, to accommodate changes in the ontology. If you are using Google Refine, you may need to change your runtime properties accordingly. The new defaults appear in example.runtime.properties.

Special runtime settings for developers

This release includes several settings to help developers by instrumenting the Freemarker templates and the SPARQL queries on the RDFService. Check the wiki for details, or look in the home directory in example.developer.properties.

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
    • Opera 12.02
    • Safari 5.0.3
  • PC:
    • Chrome 25.1364.2 and above
    • FireFox 10.0.12, 24
    • Internet Explorer 8, 9, 10
    • Opera 12.02

Upgrade Instructions

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

Separate your existing deploy.properties file into two files, as described below.

Store the new build.properties file in the top level of the VIVO distribution directory. Store the new runtime.properties file in your VIVO home directory.

external_login_text = Log in using BearCat Shibboleth

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.ftl

  A sample googleAnalytics.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

Start VIVO

INFO: Server startup in XXXXX ms

Rebuild the search index

Review the knowledge base migration logs.

Load the About Page .N3 file (optional).

1. Once the VIVO application is running, go to the Site Admin page and click the "Ingest Tools" link under Advanced Data Tools.
2. From the Ingest Menu click the "Manage Jena Tools" link, and then click the "RDB Models" button.
3. Locate the "vitro-kb-displayMetadata" model and click the "load RDF data" button.
4. Click the "Browse" button to upload the file from your computer and select the aboutPage.n3 file located here in the VIVO source: productMods/WEB-INF/ontologies/app/aboutPage.n3.
5. Select N3 as the file type from the drop-down list and then click the "Load Data" button.
6. Restart tomcat.

Knowledge Base Migration

• Instance data changes to align with VIVO-ISF

Review the VIVO Terms of Use

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

Next Steps