2013-01-16 14:52:35 -05:00
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<!DOCTYPE HTML>
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<html lang="en">
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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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<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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2013-06-21 15:39:27 -04:00
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<li><a href="#log4j_properties">Log4J properties file renamed</a></li>
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2013-01-16 14:52:35 -05:00
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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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2013-06-21 15:39:27 -04:00
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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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2013-01-16 14:52:35 -05:00
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<h4 id="BOGUS">ANYTHING ELSE?</h4>
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<p>
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</p>
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</li>
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<li>
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<h4 id="browsers">Supported Browsers</h4>
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<p>
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For this release, the following browsers are supported.
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BOGUS IS THIS LIST CURRENT?
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</p>
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<p>
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Mac:
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</p>
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<ul>
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<li>Chrome 8.0.552.237</li>
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<li>FireFox 3.6.13</li>
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<li>Opera 10.6.2</li>
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<li>Safari 5.0.3</li>
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</ul>
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<p>
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PC:
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</p>
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<ul>
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<li>Chrome 8.0.552.273</li>
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<li>FireFox 10.0.2</li>
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<li>Internet Explorer 7, 8, 9</li>
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<li>Opera 10.6.2</li>
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</ul>
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</li>
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</ul>
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<h3 id="#upgrade_process">III. Upgrade Instructions</h3>
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<p>
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1. Download the new distribution file and unpack it into a new
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source directory.
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</p>
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<p>
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2. Separate your existing <code>deploy.properties</code> file into two files,
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as described below. The new <code>build.properties</code> file is stored in
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the top level of the VIVO distribution directory. The new <code>runtime.properties</code>
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file is stored in your Vitro home directory.
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<br>
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</p>
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<table border='1' bordercolor="#CCCCCC" cellspacing="5">
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<tbody>
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<tr>
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<th width="50%">
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Properties in <code>build.properties</code>
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</th>
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<th>
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Properties in <code>runtime.properties</code>
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</th>
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</tr>
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<tr class="odd_row blue">
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<td>
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<code>vitro.core.dir</code><br>
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<code>vitro.home</code><br>
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<code>tomcat.home</code><br>
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<code>webapp.name</code><br>
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</td>
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<td>
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All other properties from <code>deploy.properties</code>
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</td>
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</tr>
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<tr>
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<td colspan="2">
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<em>Note that <code>vitro.home</code> replaces <code>vitro.home.directory</code></em>
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<br>
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<em>Note that <code>vitro.local.solr.ipaddress.mask</code> is no longer used.</em>
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</td>
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</tr>
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</tbody>
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</table>
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<br>
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2013-01-24 16:14:45 -05:00
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<p>
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2013-01-16 14:52:35 -05:00
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If you prefer, you may start with <code>example.build.properties</code>
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and <code>example.runtime.properties</code>, make copies,
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and edit them to suit your installation.
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2013-01-24 16:14:45 -05:00
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</p>
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<p>
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The properties below are new to <code>runtime.properties</code>. They are optional,
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so you need not add them, unless you want a value other than the default.
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</p>
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2013-01-16 14:52:35 -05:00
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<p>
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<!-- runtime.properties table from install.html -->
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</p>
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<table border='1' bordercolor="#CCCCCC" cellspacing="5">
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<tbody>
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<tr>
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<th>
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Property Name
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</th>
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<th>
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Example Value
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</th>
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</tr>
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2013-01-24 16:14:45 -05:00
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2013-06-03 15:44:35 -04:00
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<tr>
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<td colspan="2">
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Tell VIVO to generate HTTP headers on its responses to facilitate caching the
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profile pages that it creates. This can improve performance, but it can also
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result in serving stale data. Default is false if not set.
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For more information, see the VIVO wiki page:
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<a href="https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance">
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Use HTTP caching to improve performance </a>
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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http.createCacheHeaders
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</td>
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<td>
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true
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</td>
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</tr>
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2013-01-24 16:14:45 -05:00
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<tr>
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<td colspan="2">
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Force VIVO to use a specific language or Locale instead of those
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specified by the browser.
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This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
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This also affects the text of pages that have been modified to support multiple languages.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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languages.forceLocale
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</td>
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<td>
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en_US
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</td>
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</tr>
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<tr>
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<td colspan="2">
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A list of supported languages or Locales that the user may choose to
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use instead of the one specified by the browser. Selection images must
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be available in the i18n/images directory of the theme.
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This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
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This also affects the text of pages that have been modified to support multiple languages.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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languages.selectableLocales
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</td>
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<td>
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en, es, fr_FR
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</td>
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</tr>
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<tr>
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<td colspan="2">
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<b>For developers only.</b>
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Defeat the Freemarker template cache, so each template
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is read from disk on each request. This permits developers to immediately
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see the effect of changes to the template. The default is <code>false</code>, which
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means that a cached copy of each template will be used for 60 seconds
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before the disk is checked for a new version.
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<br/><b>Setting this option to "true" slows down VIVO performance.</b>
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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developer.defeatFreemarkerCache
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</td>
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<td>
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false
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</td>
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</tr>
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2013-01-16 14:52:35 -05:00
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<tr>
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<td colspan="2">
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2013-01-24 16:14:45 -05:00
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<b>For developers only.</b>
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Defeat the cache of language-specific text strings,
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so the language file is read from disk on each request.
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This permits developers to immediately
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|
|
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>
|
2013-01-16 14:52:35 -05:00
|
|
|
</td>
|
|
|
|
</tr>
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
<td>
|
2013-01-24 16:14:45 -05:00
|
|
|
developer.defeatI18nCache = true
|
2013-01-16 14:52:35 -05:00
|
|
|
</td>
|
|
|
|
<td>
|
2013-01-24 16:14:45 -05:00
|
|
|
false
|
2013-01-16 14:52:35 -05:00
|
|
|
</td>
|
|
|
|
</tr>
|
2013-01-24 16:14:45 -05:00
|
|
|
|
2013-01-25 16:29:30 -05:00
|
|
|
<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>
|
|
|
|
|
2013-06-17 10:44:31 -04:00
|
|
|
<tr>
|
|
|
|
<td colspan="2">
|
|
|
|
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>
|
|
|
|
|
2013-01-16 14:52:35 -05:00
|
|
|
</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>
|
|
|
|
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>
|
|
|
|
|
|
|
|
<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>
|
|
|
|
<li role="listitem">
|
|
|
|
<a href="http://vivoweb.org/contact">Contact Us</a>
|
|
|
|
</li>
|
|
|
|
<li role="listitem">
|
|
|
|
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
|
|
|
|
</li>
|
|
|
|
</ul>
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<!-- #footer -->
|
|
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|
|
|
|
|
</div>
|
|
|
|
</body>
|
|
|
|
</html>
|