VIVO-2 Modify the build so installers can create a container-neutral VIVO.
Split deploy.properties into build.properties and runtime.properties, with runtime.properties going into the Vitro home directory. Modify ConfigurationProperties to locate the Vitro home directory, either by System property or JNDI Environment variable, or from build.properties, and to read from both build.properties and runtime.properties. Revise the install and upgrade documents for VIVO and Vitro. Change comments and error messages that referred to deploy.properties by name.
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doc/upgrade-1.6.html
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doc/upgrade-1.6.html
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<!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="#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="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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|
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|
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<h3 id="#upgrade_process">III. Upgrade Instructions</h3>
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|
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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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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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<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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<tr>
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<td colspan="2">
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BOGUS: ANY NEW PROPERTIES TO ADD?
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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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BOGUS.PROPERTYNAME
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</td>
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<td>
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BOGUS EXAMPLE VALUE
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</td>
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</tr>
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</tbody>
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</table>
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<p>
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3. Apply any previous changes you have made to the new source
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directory.
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</p>
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<blockquote>
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<strong>Special notes regarding source files</strong>
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<ul>
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<li>
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This process assumes any changes made to the application were
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made in the source directory and deployed, and were not made directly
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within the Tomcat webapps directory.
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</li>
|
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<li>
|
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In many cases, simply copying the modified files from your
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original source directory will not work since the files on which they
|
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are based have changed. It will be necessary to inspect the new source
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||||
files and add any changes to them at that time.
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</li>
|
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<li>
|
||||
NIH-funded VIVO implementations will need to apply the
|
||||
Google Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
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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 -->
|
||||
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
Loading…
Add table
Add a link
Reference in a new issue