894 lines
47 KiB
HTML
894 lines
47 KiB
HTML
<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.6 Upgrade Guide</title>
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<link rel="stylesheet" href="./css/doc.css" media="screen">
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</head>
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<body>
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<div id="branding" role="banner">
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<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
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</div>
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V1.6 Upgrade Guide</h1>
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<small>
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BOGUS DATE, 2013 - Upgrading from Release 1 V1.5 to Release 1 V1.6
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</small>
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<p>
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This document contains instructions on how to upgrade your
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installation of VIVO from Version 1.5 (or 1.5.1) to Version 1.6.
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This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
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at <a href="http://vivoweb.org/">VIVOweb.org</a>
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</p>
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<p>
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If you need to do a fresh install, please consult the VIVO Release V1.6 Installation
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Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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or the install.html file located in the <code>doc</code>
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directory of the VIVO source code distribution. The installation document also has a
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list of the required software and versions.
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</p>
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<p>
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For a description of the release contents see the <a href="./release.html">Release announcement for V1.6</a>.
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</p>
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<hr/>
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<h3 id="tableofcontents">Table of Contents</h3>
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<toc>
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<ol class="roman2">
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<li><a href="#preparation">Before Performing the Upgrade</a></li>
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<li>
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<a href="#changes">Noteworthy Changes</a>
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<ol class="roman2">
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<li><a href="#more_portable">VIVO becomes more portable</a></li>
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<li><a href="#solr_insecure">Solr is no longer secured</a></li>
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<li><a href="#log4j_properties">Log4J properties file renamed</a></li>
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<li><a href="#tabMenu">Property groups now displayed in a tab format</a></li>
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<li><a href="#sparqlDataGetters">Class-specific SPARQL Query Data Getters</a></li>
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<li><a href="#foafPersonTemplate">The foaf:Person template has been re-located.</a></li>
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<li><a href="#multiple">Multiple foaf:Person Profile Pages</a></li>
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<li><a href="#homePage">Home Page Re-design</a></li>
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<li><a href="#rdffiles">Auto-loaded RDF files move to the Home directory</a></li>
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<li><a href="#language">Support for additional languages</a></li>
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<li><a href="#BOGUS">ANYTHING ELSE?</a></li>
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</ol>
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</li>
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<li><a href="#upgrade_process">Upgrade Instructions</a></li>
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<li><a href="#kbm">Knowledge Base Migration</a></li>
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<li><a href="#termsofuse">Review the VIVO Terms of Use</a></li>
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<li><a href="#nextsteps">Next Steps</a></li>
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</ol>
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</toc>
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<hr/>
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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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<br/>
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Create backups of:
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<ul style="list-style-type: square;">
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<li>
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The VIVO distribution directory (which contains the source for VIVO 1.5 or VIVO 1.5.1)
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</li>
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<li>
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The VIVO home directory (pointed to by your deploy.properties file)
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</li>
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<li>
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The webapps directory in Tomcat
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</li>
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<li>
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MySQL database (most people use mysqldump to create the backup)
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</li>
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</ul>
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<p>
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The upgrade process is similar to the initial install process
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with
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the following exceptions:
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</p>
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<ul>
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<li>
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You do not need to reinstall MySQL or recreate the MySQL database. Please
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backup your MySQL database as noted above.
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</li>
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<li>
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First-time login of the root account after the upgrade
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process is complete will use the password previously set (not the
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default password used on the first login after the initial
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installation.)
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</li>
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<li>
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The first time Apache Tomcat starts up after the upgrade, an automated
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process will modify the knowledge base to align the
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data with any ontology updates made for the new release. See the section on the <a href="#kbm">Knowledge Base Migration</a>
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below for more information.
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</li>
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</ul>
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<h3 id="changes">II. Noteworthy Changes</h3>
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<ul>
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<li>
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<h4 id="more_portable">VIVO becomes more portable</h4>
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<p>
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The VIVO build script now includes a <code>distribute</code> target that will produce
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a file called <code>distribution.tar.gz</code>. This compressed archive contains
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these files:
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<ol>
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<li><code>vivo.war</code> -- a WAR file for the main VIVO application.</li>
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<li><code>vivosolr.war</code> -- a WAR file for the Solr application.</li>
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<li><code>solrhome.tar</code> -- a Solr home directory that is configured for use with VIVO.</li>
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</ol>
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These files can be used with Tomcat, or with any container that supports
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the Java Servlet 2.4 Specification.
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</p>
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<p>
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To permit this portability, the <code>deploy.properties</code> file
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has been split in two. <code>build.properties</code> contains only the properties
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that are required for building VIVO. <code>runtime.properties</code>,
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which must be created in the Vitro home directory, contains the properties
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that VIVO uses while running.
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</p>
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<p>
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If you are building to <code>deploy</code> to Tomcat (as with previous releases),
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then <code>build.properties</code> must contain these properties:
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<ul>
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<li><code>vitro.core.dir</code></li>
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<li><code>webapp.name</code></li>
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<li><code>tomcat.home</code></li>
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<li><code>vitro.home</code> <em>-- note that this was <code>vitro.home.directory</code>
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in previous releases</em></li>
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</ul>
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</p>
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<p>
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If you are building to <code>distribute</code>, the <code>build.properties</code>
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file requires only these properties:
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<ul>
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<li><code>vitro.core.dir</code></li>
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<li><code>webapp.name</code></li>
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</ul>
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</p>
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<h4 id="solr_insecure">Solr is no longer secured</h4>
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<p>
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In previous releases, Solr was deployed to Tomcat with a <code>RemoteAddrValve</code>
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that would only permit access from certain IP addresses.
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Acceptable IP addresses were those which matched the regular expression pattern in
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the <code>vitro.local.solr.ipaddress.mask</code> property.
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</p>
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<p>
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This has been removed because:
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<ul>
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<li>It caused repeated problems for sites who were experimenting with VIVO.</li>
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<li>It was not standards-based, but specific to Tomcat.</li>
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<li>It was redundant. Production instances of VIVO are
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usually hidden behind a firewall and accessed through an Apache Http server.</li>
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</ul>
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</p>
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<p>
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Sites that need to secure Solr are now left to their own devices.
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</p>
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<h4 id="log4j_properties">Log4J properties file renamed</h4>
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<p>
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In previous releases, the properties file for the VIVO logging system
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was called <code>default.log4j.properties</code>. In release 1.6, this
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file has been renamed to <code>log4j.properties</code>. This is so the
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developers and implementers will know where to look for the file.
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</p>
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<p>
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Note that <code>debug.log4j.properties</code>, if present, will still
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override the default.
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</p>
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<h4 id="tabMenu">Property groups now displayed in a tab format, including a "View All" tab</h4>
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<p>
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With release 1.6, the property group menu bar that was used on profile pages has been replaced
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by java script enabled tabs. When clicked, each property group tab will display the properties
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within that group while the contents of the previously displayed group will be hidden. The array of
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tabs also includes a "View All" tab that, when clicked, displays the contents of all the property groups.
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</p>
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<h4 id="sparqlDataGetters">Class-specific SPARQL Query Data Getters</h4>
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<p>
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The VIVO software now supports the development of SPARQL query data getters that can be associated
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with specific ontological classes. These data getters, in turn, can be accessed within Freemarker
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templates to provide richer content on VIVO profile pages. For example, the profile page for an academic
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department lists only the names of the faculty within that department and their titles, but with a SPARQL
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query data getter it is now possible to extend the faculty information to display all of the faculty
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members' research areas. Refer to this wiki page for details on how to use class-specific SPARQL query
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data getters:
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<code>https://wiki.duraspace.org/display/VIVO/Enriching+VIVO+Content+Using+SPARQL+Query+Data+Getters</code>.
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</p>
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<h4 id="foafPersonTemplate">The foaf:Person template has been re-located.</h4>
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<p>
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The template individual--foaf-person.ftl has been moved to the "templates" subdirectory in the wilma
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theme directory (vivo/themes/wilma/templates). If your installation has a customized version of
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individual--foaf-person.ftl, ensure that it is located in the templates subdirectory in your installation's
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theme directory or, if your installation does not have it's own theme directory, in the
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<code>themes/wilma/templates subdirectory</code>.
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</p>
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<h4 id="multiple">Multiple foaf:Person Profile Pages</h4>
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<p>
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VIVO now supports multiple profile pages for foaf:Persons. This feature, which is optional so installations
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can continue to use just the individual--foaf-person.ftl template, currently consists of two profile page
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types: a standard view, which is a redesigned version of the foaf:Person template in previous releases; and
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a quick view, which emphasizes the individual's own web page presence while providing summary VIVO information,
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such as current positions and research areas. The profile quick view requires the use of a web service that
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captures images of web pages. <strong>This web service is not included with the VIVO software.</strong> An
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installation will either have to develop their own service or use a third-party service, usually for a small
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fee depending on the number of images served. (Examples of these services include WebShotsPro, Thumbalizr and
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Websnapr.) For more information on how to implement multiple profile page views, refer to this wiki page:
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<code>https://wiki.duraspace.org/display/VIVO/Multiple+foaf%3APerson+Profile+Pages</code>.
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</p>
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<h4 id="homePage">Home Page Re-design</h4>
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<p>
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For Release 1.6 the VIVO Home Page has been redesigned. The Search field beneath the "welcome" text now
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allows the user to limit the results of a search to a specific class group, such as people, organizations,
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etc. In addition, the browse-by-class-group display has been removed from the Home Page and replaced by
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multiple features, which include: a list of four randomly selected faculty members, including their titles
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and thumbnail images; a display of statistical data about the VIVO installation, such as the number of people,
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activities and organizations; and, <a href="#optionalMap">optionally</a> a global map showing researchers'
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areas of geographic focus.
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</p>
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<h4 id="rdffiles">Auto-loaded RDF files move to the Home directory</h4>
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<p>
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The RDF files that initialize the data model have moved, in both the distribution and
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the runtime locations.
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In the distribution, they have been collected in one place, and reorganized to use
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a more consistent naming scheme. During the build process, they are copied to a
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location within the VIVO home directory, instead of residing in the webapp itself.
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</p>
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<p>
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If you have modified these RDF files, or added files of your own, you must adjust to
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the new locations accordingly.
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</p>
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<h5>Old locations of RDF files</h5>
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<pre>/WEB-INF/ontologies/app/application.owl
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/WEB-INF/ontologies/app/aboutPage.n3
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/WEB-INF/ontologies/app/menu.n3
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/WEB-INF/ontologies/app/profilePageType.n3
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/WEB-INF/ontologies/app/loadedAtStartup/displayModelListViews.rdf
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/WEB-INF/ontologies/app/loadedAtStartup/homePageDataGetters.n3
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/WEB-INF/ontologies/app/loadedAtStartup/localeSelectionGUI.n3
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/WEB-INF/ontologies/app/loadedAtStartup/vivoListViewConfig.rdf
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/WEB-INF/ontologies/app/loadedAtStartup/vivoOrganizationDataGetters.n3
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/WEB-INF/ontologies/app/loadedAtStartup/vivoSearchProhibited.n3
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/WEB-INF/ontologies/app/menuload/displayTBOX.n3
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/WEB-INF/ontologies/app/menuload/displayDisplay.n3
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/WEB-INF/init-data/initialSiteConfig.rdf
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/WEB-INF/ontologies/user/abox/geopolitical.ver1.1-11-18-11-individual-labels.rdf
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/WEB-INF/ontologies/user/abox/vocabularySource-labels.n3
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/WEB-INF/ontologies/user/tbox/vitro-0.7-annotations.rdf
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/WEB-INF/ontologies/user/tbox/geopolitical-ver1.1-11-18-11-annotations.rdf
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/WEB-INF/ontologies/user/tbox/scires-1.5-annotations.rdf
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/WEB-INF/ontologies/user/tbox/vivo-core-1.5-annotations.rdf
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/WEB-INF/ontologies/user/tbox/isDefinedBy-1.5-annotations.rdf
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/WEB-INF/ontologies/user/applicationMetadata/propertygroups.rdf
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/WEB-INF/ontologies/user/applicationMetadata/classgroups.rdf
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/WEB-INF/filegraph/abox/us-states.rdf
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/WEB-INF/filegraph/abox/geopolitical.abox.ver1.1-11-18-11.owl
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/WEB-INF/filegraph/abox/academicDegree.rdf
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/WEB-INF/filegraph/abox/documentStatus.owl
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/WEB-INF/filegraph/abox/continents.n3
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/WEB-INF/filegraph/abox/vocabularySource.n3
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/WEB-INF/filegraph/abox/dateTimeValuePrecision.owl
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/WEB-INF/filegraph/tbox/vitroPublic.owl
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/WEB-INF/filegraph/tbox/vivo-dcterms-1.5.owl
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/WEB-INF/filegraph/tbox/scires-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-core-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-c4o-1.5.owl
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/WEB-INF/filegraph/tbox/geopolitical.tbox.ver1.1-11-18-11.owl
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/WEB-INF/filegraph/tbox/vivo-fabio-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-skos-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-event-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-foaf-1.5.owl
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/WEB-INF/filegraph/tbox/vitro-0.7.owl
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/WEB-INF/filegraph/tbox/vivo-pws-1.5.owl
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/WEB-INF/filegraph/tbox/isDefinedBy-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-dcelements-1.5.owl
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/WEB-INF/filegraph/tbox/vivo-bibo-1.5.owl</pre>
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<h5>New locations of RDF files</h5>
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<pre>rdf/display/firsttime/aboutPage.n3
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rdf/display/firsttime/application.owl
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rdf/display/firsttime/menu.n3
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rdf/display/firsttime/profilePageType.n3
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rdf/display/everytime/displayModelListViews.rdf
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rdf/display/everytime/homePageDataGetters.n3
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rdf/display/everytime/localeSelectionGUI.n3
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rdf/display/everytime/vivoListViewConfig.rdf
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rdf/display/everytime/vivoOrganizationDataGetters.n3
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rdf/display/everytime/vivoSearchProhibited.n3
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rdf/displayTbox/everytime/displayTBOX.n3
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rdf/displayDisplay/everytime/displayDisplay.n3
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rdf/applicationMetadata/firsttime/classgroups.rdf
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rdf/applicationMetadata/firsttime/initialSiteConfig.rdf
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rdf/applicationMetadata/firsttime/propertygroups.rdf
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rdf/abox/firsttime/geopolitical.ver1.1-11-18-11-individual-labels.rdf
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rdf/abox/firsttime/vocabularySource-labels.n3
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rdf/abox/filegraph/abox/academicDegree.rdf
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rdf/abox/filegraph/abox/continents.n3
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rdf/abox/filegraph/abox/dateTimeValuePrecision.owl
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rdf/abox/filegraph/abox/documentStatus.owl
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rdf/abox/filegraph/abox/geopolitical.abox.ver1.1-11-18-11.owl
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rdf/abox/filegraph/abox/us-states.rdf
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rdf/abox/filegraph/abox/vocabularySource.n3
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rdf/tbox/firsttime/geopolitical-ver1.1-11-18-11-annotations.rdf
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rdf/tbox/firsttime/isDefinedBy-1.5-annotations.rdf
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rdf/tbox/firsttime/scires-1.5-annotations.rdf
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rdf/tbox/firsttime/vitro-0.7-annotations.rdf
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rdf/tbox/firsttime/vivo-core-1.5-annotations.rdf
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rdf/tbox/filegraph/tbox/geopolitical.tbox.ver1.1-11-18-11.owl
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rdf/tbox/filegraph/tbox/isDefinedBy-1.5.owl
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rdf/tbox/filegraph/tbox/scires-1.5.owl
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rdf/tbox/filegraph/tbox/vitro-0.7.owl
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rdf/tbox/filegraph/tbox/vitroPublic.owl
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rdf/tbox/filegraph/tbox/vivo-bibo-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-c4o-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-core-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-dcelements-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-dcterms-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-event-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-fabio-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-foaf-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-pws-1.5.owl
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rdf/tbox/filegraph/tbox/vivo-skos-1.5.owl</pre>
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<p>
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If you are using a three-tier build process, you will need to add a single line
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to the build script so the RDF files will be merged properly across the tiers. So this:
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<pre><patternset id="appbase.patterns">
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<include name="src/**/*" />
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<include name="lib/**/*" />
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<include name="test/**/*" />
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<include name="themes/**/*" />
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<include name="config/*.properties" />
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<include name="config/*.txt" />
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<include name="config/jarlist/*.txt" />
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<include name="config/solr/*" />
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<include name="context.xml" />
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</patternset></pre>
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becomes this:
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<pre><patternset id="appbase.patterns">
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<include name="src/**/*" />
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<include name="lib/**/*" />
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<include name="rdf/**/*" />
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<include name="test/**/*" />
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<include name="themes/**/*" />
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<include name="config/*.properties" />
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<include name="config/*.txt" />
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<include name="config/jarlist/*.txt" />
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<include name="config/solr/*" />
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<include name="context.xml" />
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</patternset></pre>
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</p>
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<h4 id="language">Support for additional languages</h4>
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<p>
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VIVO 1.6 includes limited support for other languages, in addition to American English.
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This limited support is described as <em>read-only</em> support on <em>public-facing</em>
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pages.
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</p>
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<p>
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<em>Read-only</em> 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.
|
|
</p>
|
|
<p>
|
|
<em>Public-facing</em> means that most of the pages used for site adminstration
|
|
are only presented in American English.
|
|
</p>
|
|
<p>
|
|
These two pages in the VIVO Wiki describe how to
|
|
<a href="https://wiki.duraspace.org/display/VIVO/Building+a+multi-language+VIVO+instance">
|
|
Build VIVO with multiple languages</a> and how to
|
|
<a href="https://wiki.duraspace.org/display/VIVO/Adding+a+language+to+VIVO">
|
|
Add a new language to VIVO</a>.
|
|
</p>
|
|
|
|
<h4 id="BOGUS">ANYTHING ELSE?</h4>
|
|
<p>
|
|
</p>
|
|
</li>
|
|
<li>
|
|
<h4 id="browsers">Supported Browsers</h4>
|
|
<p>
|
|
For this release, the following browsers are supported.
|
|
BOGUS IS THIS LIST CURRENT?
|
|
</p>
|
|
<p>
|
|
Mac:
|
|
</p>
|
|
<ul>
|
|
<li>Chrome 8.0.552.237</li>
|
|
<li>FireFox 3.6.13</li>
|
|
<li>Opera 10.6.2</li>
|
|
<li>Safari 5.0.3</li>
|
|
</ul>
|
|
<p>
|
|
PC:
|
|
</p>
|
|
<ul>
|
|
<li>Chrome 8.0.552.273</li>
|
|
<li>FireFox 10.0.2</li>
|
|
<li>Internet Explorer 7, 8, 9</li>
|
|
<li>Opera 10.6.2</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
|
|
<h3 id="upgrade_process">III. Upgrade Instructions</h3>
|
|
|
|
<p>
|
|
1. Download the new distribution file and unpack it into a new
|
|
source directory.
|
|
</p>
|
|
<p>
|
|
2. Separate your existing <code>deploy.properties</code> file into two files,
|
|
as described below. Store the new <code>build.properties</code> file in
|
|
the top level of the VIVO distribution directory. Store the new <code>runtime.properties</code>
|
|
file in your VIVO home directory.
|
|
<br>
|
|
</p>
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
<tbody>
|
|
<tr>
|
|
<th width="50%">
|
|
Properties in <code>build.properties</code>
|
|
</th>
|
|
<th>
|
|
Properties in <code>runtime.properties</code>
|
|
</th>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
<code>vitro.core.dir</code><br>
|
|
<code>vitro.home</code><br>
|
|
<code>tomcat.home</code><br>
|
|
<code>webapp.name</code><br>
|
|
</td>
|
|
<td>
|
|
All other properties from <code>deploy.properties</code>
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
<em>Note that <code>vitro.home</code> replaces <code>vitro.home.directory</code></em>
|
|
<br>
|
|
<em>Note that <code>vitro.local.solr.ipaddress.mask</code> is no longer used.</em>
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<br>
|
|
<p>
|
|
If you prefer, you may start with <code>example.build.properties</code>
|
|
and <code>example.runtime.properties</code>, make copies,
|
|
and edit them to suit your installation. Remember, the <code>runtime.properties</code> file
|
|
goes into your VIVO home directory.
|
|
</p>
|
|
|
|
<p>
|
|
The properties below are new to <code>build.properties</code>. They are optional,
|
|
so you need not add them unless you want a value other than the default.
|
|
</p>
|
|
<p>
|
|
<!-- runtime.properties table from install.html -->
|
|
</p>
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
<tbody>
|
|
<tr>
|
|
<th>
|
|
Property Name
|
|
</th>
|
|
<th>
|
|
Example Value
|
|
</th>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
Languages (in addition to American English) that will be built into your
|
|
VIVO site. The languages must be found in the
|
|
<code>languages</code> directory of the VIVO distribution.
|
|
See <a href="https://wiki.duraspace.org/display/VIVO/Building+a+multi-language+VIVO+instance">
|
|
the VIVO Wiki</a> for more information.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
languages.addToBuild
|
|
</td>
|
|
<td>
|
|
es_MX
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
The properties below are new to <code>runtime.properties</code>. They are optional,
|
|
so you need not add them, unless you want a value other than the default.
|
|
</p>
|
|
<p>
|
|
<!-- runtime.properties table from install.html -->
|
|
</p>
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
<tbody>
|
|
<tr>
|
|
<th>
|
|
Property Name
|
|
</th>
|
|
<th>
|
|
Example Value
|
|
</th>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
Tell VIVO to generate HTTP headers on its responses to facilitate caching the
|
|
profile pages that it creates. This can improve performance, but it can also
|
|
result in serving stale data. Default is false if not set.
|
|
For more information, see the VIVO wiki page:
|
|
<a href="https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance">
|
|
Use HTTP caching to improve performance </a>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
http.createCacheHeaders
|
|
</td>
|
|
<td>
|
|
true
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
Force VIVO to use a specific language or Locale instead of those
|
|
specified by the browser.
|
|
This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
|
|
This also affects the text of pages that have been modified to support multiple languages.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
languages.forceLocale
|
|
</td>
|
|
<td>
|
|
en_US
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
A list of supported languages or Locales that the user may choose to
|
|
use instead of the one specified by the browser. Selection images must
|
|
be available in the i18n/images directory of the theme.
|
|
This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
|
|
This also affects the text of pages that have been modified to support multiple languages.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
languages.selectableLocales
|
|
</td>
|
|
<td>
|
|
en, es, fr_FR
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
<b>For developers only.</b>
|
|
Defeat the Freemarker template cache, so each template
|
|
is read from disk on each request. This permits developers to immediately
|
|
see the effect of changes to the template. The default is <code>false</code>, which
|
|
means that a cached copy of each template will be used for 60 seconds
|
|
before the disk is checked for a new version.
|
|
<br/><b>Setting this option to "true" slows down VIVO performance.</b>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
developer.defeatFreemarkerCache
|
|
</td>
|
|
<td>
|
|
false
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
<b>For developers only.</b>
|
|
Defeat the cache of language-specific text strings,
|
|
so the language file is read from disk on each request.
|
|
This permits developers to immediately
|
|
see the effect of changes to the text strings.
|
|
The default is <code>false</code>, which means that the language file is
|
|
read when VIVO starts up, or when a new theme is selected.
|
|
<br/><b>Setting this option to "true" slows down VIVO performance.</b>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
developer.defeatI18nCache = true
|
|
</td>
|
|
<td>
|
|
false
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
<b>For developers only.</b>
|
|
Add starting and ending delimiters to each Freemarker template, so you can see
|
|
which template were invoked by viewing the generated HTML.
|
|
The default is <code>false</code>.
|
|
<br/><b>Setting this option to "true" slows down VIVO performance.</b>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
developer.insertFreemarkerDelimiters = true
|
|
</td>
|
|
<td>
|
|
false
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2" id="optionalMap">
|
|
On the VIVO home page, display a global map highlighting the geographical focus
|
|
of foaf:person individuals. The default is <code>enabled</code>.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
homePage.geoFocusMaps = enabled
|
|
</td>
|
|
<td>
|
|
enabled
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td colspan="2">
|
|
<b>MultiViews for foaf:person profile pages.</b>
|
|
VIVO supports the simultaneous use of a full foaf:Person profile page view
|
|
and a "quick" page view that emphasizes the individual's own webpage presence.
|
|
<b>Implementing this feature requires an installation to develop a web service
|
|
that captures images of web pages or to use an existing service outside of VIVO,
|
|
usually for a small fee.</b>
|
|
The default is <code>disabled</code>.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
MultiViews.profilePageTypes=disabled
|
|
</td>
|
|
<td>
|
|
disabled
|
|
</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
|
|
<p>
|
|
3. Apply any previous changes you have made to the new source
|
|
directory.
|
|
</p>
|
|
<blockquote>
|
|
<strong>Special notes regarding source files</strong>
|
|
<ul>
|
|
<li>
|
|
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.
|
|
</li>
|
|
<li>
|
|
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.
|
|
</li>
|
|
<li>
|
|
NIH-funded VIVO implementations will need to apply the
|
|
Google Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
|
in the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
|
A sample <code>googleAnalytics.ftl</code> 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 <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
|
Google
|
|
Analytics
|
|
wiki
|
|
page</a>.
|
|
</li>
|
|
</ul>
|
|
</blockquote>
|
|
<p>
|
|
4. Apply any previous changes you have made to the RDF initialization files.
|
|
See the section on the <a href="#rdffiles">Auto-loaded RDF files</a>
|
|
above for more details.
|
|
</p>
|
|
<p>
|
|
5. Stop Apache Tomcat and from your VIVO source directory, run
|
|
ant
|
|
by typing: <code>ant all</code>
|
|
</p>
|
|
<p>
|
|
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.<pre>INFO: Server startup in XXXXX ms</pre>
|
|
</p>
|
|
<p>
|
|
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".
|
|
</p>
|
|
<p>
|
|
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 1.6 VIVO data after deployment,
|
|
you should save them aside.
|
|
The logs are created in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log</code>
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<p>
|
|
9. Load the About Page .N3 file (optional). Release 1.6 provides an "about VIVO" page that is editable
|
|
through the GUI, using the Page Management functionality. If your installation has a customized version
|
|
of the About Page and you do not need to have it accessible via Page Management, then skip this step.
|
|
Otherwise, here are the instructions for loading the About Page .N3 file:
|
|
<ol>
|
|
<li>
|
|
Once the VIVO application is running, go to the Site Admin page and click the "Ingest Tools"
|
|
link under Advanced Data Tools.
|
|
</li>
|
|
<li>
|
|
From the Ingest Menu click the "Manage Jena Tools" link, and then click the "RDB Models" button.
|
|
</li>
|
|
<li>
|
|
Locate the "vitro-kb-displayMetadata" model and click the "load RDF data" button.
|
|
</li>
|
|
<li>
|
|
Click the "Browse" button to upload the file from your computer and select the aboutPage.n3 file
|
|
located here in the VIVO source: <code>productMods/WEB-INF/ontologies/app/aboutPage.n3</code>.
|
|
</li>
|
|
<li>
|
|
Select N3 as the file type from the drop-down list and then click the "Load Data" button.
|
|
</li>
|
|
<li>
|
|
Restart tomcat.
|
|
</li>
|
|
</ol>
|
|
</p>
|
|
<p>
|
|
If your installation has a customized version of the About Page, but you would like to make its content
|
|
editable through the GUI, follow the above steps and then use Page Management to update the fixed HTML
|
|
content.
|
|
</p>
|
|
|
|
<h3 id="#kbm">IV. Knowledge Base Migration</h3>
|
|
|
|
<p>
|
|
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 1.6 will make
|
|
the following types of changes:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
BOGUS CHANGES
|
|
</dt>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Annotation property default values
|
|
</dt>
|
|
<dd>
|
|
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.
|
|
<br>
|
|
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.
|
|
</dd>
|
|
</dl>
|
|
<p>
|
|
In addition to the logs described in <strong>step 8</strong> of the <a href="#upgrade_process">previous section</a>, the knowledge base migration
|
|
process will log copies of all additions and deletions that were made to the knowledge base in the following files:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were removed from the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were added to the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
|
|
<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
|
|
<p>
|
|
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
|
|
you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
|
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:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
|
|
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.
|
|
</p>
|
|
<h3 id="nextsteps">Next Steps</h3>
|
|
<p>
|
|
Now that you have VIVO up and running, please refer to the
|
|
<a href="https://wiki.duraspace.org/display/VIVO/Site+Administrator+Guide">Site Administrator's Guide</a>
|
|
for information about its operation.
|
|
</p>
|
|
</div>
|
|
|
|
<!-- #wrapper-content -->
|
|
<div id="footer" role="contentinfo">
|
|
<p class="copyright">
|
|
<small>
|
|
©2013 All Rights Reserved
|
|
</small>
|
|
| Powered
|
|
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
|
</p>
|
|
<div id="nav" role="navigation">
|
|
<ul id="footer-nav" role="list">
|
|
<li role="listitem">
|
|
<a href="http://vivoweb.org/about">About</a>
|
|
</li>
|
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