Removing html dir to avoid confusion. It was my working directory.
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ejc12
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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<title>VIVO</title>
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<link rel="stylesheet" href="../css/doc.css" />
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</head>
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<body>
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<header 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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</header>
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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<!-- template --->
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<h1>Heading One</h1><div></div>
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<h2>Heading Two</h2>
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<h3>Heading Three</h3>
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<h4>Heading Four</h4>
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<p>A paragraph tag</p>
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<ul>
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<li>List item one</li>
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<li>List item two</li>
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</ul>
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<ol>
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<li>Ordered list item one</li>
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<li>Ordered list item two</li>
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</ol>
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</div>
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<!-- end of content -->
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<footer role="contentinfo">
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<p class="copyright"><small>©2011
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All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a></small> | Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
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</p>
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<nav role="navigation">
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<ul id="footer-nav" role="list">
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<li role="listitem"><a href="http://vivoweb.org/about">About</a></li>
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<li role="listitem"><a href="http://vivoweb.org/contact">Contact Us</a></li>
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<li role="listitem"><a href="http://www.vivoweb.org/support" target="blank">Support</a></li>
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</ul>
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</nav>
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||||||
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</footer>
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</body>
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</html>
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@ -1,365 +0,0 @@
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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<title>VIVO</title>
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<link rel="stylesheet" href="../css/doc.css" />
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</head>
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<body>
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<header 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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</header>
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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 v1.2 Upgrade Guide</h1>
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<small>January 28, 2011 - Upgrading from Release 1 v1.1 to Release 1 v1.2</small>
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<blockquote>
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<b>Missing pieces and fixes</b>
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<ul>
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<li>
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Link to install pdf online at SF
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</li>
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<li>
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</li>
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<li>
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</li>
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</ul>
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</blockquote>
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<toc>
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<ul>
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<li>
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<a href="#announcement">Release announcement for V1.2</a>
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</li>
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<li>
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<a href="#upgrade">Upgrade process for V1.2</a>
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</li>
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</ul>
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</toc>
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<p>
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This document provides a short description of the steps involved in upgrading your
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installation of VIVO from Release 1, Version 1.1 to Version 1.2. This and other
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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
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<a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1 v1.2 Installation Guide</a>
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or the install.html file located in the
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<code>
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doc
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</code>
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directoy of the VIVO source code distribution.
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</p>
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<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
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<p>
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Text from the wiki page
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</p>
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<!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
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</p>
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<toc>
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<ol class="roman1">
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<li>
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<a href="#preparation">Before Performing the Upgrade</a>
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</li>
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<li>
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<a href="#upgrade_process">The Upgrade Process</a>
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</li>
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<li>
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<a href="#ontology">Ontology Upgrade</a>
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</li>
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<ol class="roman2">
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<li>
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<a href="#verify_ontology_upgrade">Verify Ontology upgrade process</a>
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</li>
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<li>
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<a href="#ontology_knowledge_base">Ontology knowledge base manual review</a>
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</li>
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</ol>
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<li>
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<a href="#theme">Theme Modifications</a>
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</li>
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</ol>
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</toc>
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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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<p>
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Please ensure that backups are created of the:
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</p>
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<ul style="list-style-type:square;">
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<li>
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Tomcat webapps directory
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</li>
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<li>
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Original source directory
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</li>
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<li>
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MySQL database (mysqldump)
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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 original install process with the following
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EXCEPTIONS:
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</p>
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<ul>
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<li>
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DO NOT reinstall MySQL or recreate the MySQL database. Please ensure that
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you back-up the MySQL database.
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</li>
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<li>
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It is not necessary to add RDF data.
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</li>
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<li>
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First-time login of the administrator account after the upgrade process is
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complete will use the password previously set, NOT the default password used
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on the first login after the initial 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, it will initiate a process
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that modifies the knowledge base to align the data with the revised ontology. See the
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section on the <a href="ontology">Ontology Upgrade</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="upgrade_process">The Upgrade Process</h3>
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<ol class="arabic">
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<li>
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Download the new distribution file and unpack it into a new source
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directory.
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</li>
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<li>
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Create deploy.properties, using the same values as in your previous
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installation and set values for the new variables.
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</li>
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<li>
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Apply any previous changes you have made to the new source directory.
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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 made in
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the source directory and deployed, and were not made directly within
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the Tomcat webapps directory.
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</li>
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<li> In many cases, simply copying the modified files from your original
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source directory will not work since the files on which they are based
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have changed. It will be necessary to inspect the new source files and
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add any changes to them at that time.</li>
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<li>
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NIH-funded VIVO Implmentations will need to apply the Google Analytics Tracking
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Code (GATC) to
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<code>
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googleAnalytics.ftl
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</code>
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in the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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A sample
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<code>
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googleAnalytics.ftl
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</code>
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is included in the built-in theme. This file
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serves only as an example, and you must replace the tracking code shown
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with your institution's own tracking code.
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For additional information about the GATC for the NIH-funded VIVO
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implementation sites and a copy your institution's tracking code, see the
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<a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO Google Analytics wiki page</a>.
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</li>
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<li>
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If you had used the <code>vivo/contrib/FLShibboleth</code> code in your previous release,
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you should stop using it. Consult <code>install.html</code> or <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1 v1.2 Installation Guide</a>
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on "Using an External Authentication System with VIVO".
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</li>
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</ul>
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</blockquote>
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</li>
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<li>
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If you had modified
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<code>
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web.xml
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</code>
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to configure the Pellet Reasoner (as described
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in the installation instructions), repeat that modification.
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</li>
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<li>
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Stop Apache Tomcat and run ant by typing:
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<code>
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ant all
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</code>
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</li>
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<li>
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|
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Start Apache Tomcat and log in to VIVO.
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</li>
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|
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</ol>
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<!-- TO BE FORMATTED --><pre>
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|
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|
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-------------------------------------------------------------------------------
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III. Ontology Changes
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A. Verify Ontology upgrade process
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After Apache Tomcat is started, these files should be reviewed to verify that
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the automated upgrade process was executed successfully. The ontology alignment
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process will create the following files in the Tomcat webapps/vivo/WEB-INF directory:
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ontologies/update/logs/knowledgeBaseUpdate.log
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A log of a summary of updates that were made to the knowledge base and notes
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about some recommended manual reviews. This file should end with
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"Successfully finished processing ontology changes".
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ontologies/update/logs/knowledgeBaseUpdate.error.log
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A log of errors that were encountered during the upgrade process. This file
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should be empty if the upgrade was successful.
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ontologies/update/changedData/removedData.n3
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An N3 file containing all the statements that were removed from the knowledge base.
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ontologies/update/changedData/addedData.n3
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An N3 file containing all the statements that were added to the knowledge base.
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B. Ontology knowledge base manual review
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Changes to the VIVO core ontology may require corresponding
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|
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modifications of the knowledge base instance data and local ontology
|
|
||||||
extensions.
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When Apache Tomcat starts up following the upgrade, it will initiate
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|
||||||
a process to examine the knowledge base and apply necessary changes.
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|
||||||
Not all of the modifications that may be required can be automated,
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|
||||||
so manual review of the knowledge base is recommended after the
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|
||||||
automated upgrade process. The automated process will make only
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the following types of changes:
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||||||
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|
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Class or Property renaming
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All references to the class (in the subject or object position) will
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be updated to the new name. References to the property will be
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|
||||||
updated to the new name.
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||||||
Class or Property deletion
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||||||
All individuals in a deleted class will be removed.
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||||||
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|
||||||
All statements using a deleted property will be changed
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|
||||||
to use the nearest available superproperty. If there is no available
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|
||||||
superproperty then the statement will be deleted from the
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|
||||||
knowledge base. Note that all removed and added data
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|
||||||
is recorded in the files in the changedData directory.
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|
||||||
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|
||||||
Property addition
|
|
||||||
If a newly added property is the inverse of a previously
|
|
||||||
existing property, the inverse of any statements using the
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|
||||||
pre-existing property will be asserted.
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|
||||||
|
|
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Annotation property default values
|
|
||||||
If a site has modified the value of a vitro annotation (such as
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|
||||||
displayRankAnnot or displayLimitAnnot) so that it is
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|
||||||
no longer using the default, then that setting will be left unchanged.
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|
||||||
If a site is using the default value of a vitro annotation, and the
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|
||||||
default has been changed in the new version of the ontology, then
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|
||||||
the new default value will be propagated to the knowledge base.
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|
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|
|
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-------------------------------------------------------------------------------
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|
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|
|
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IV. Theme Changes
|
|
||||||
|
|
||||||
VIVO 1.1 introduces the first step in a transition from JavaServer Pages (JSPs)
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|
||||||
to the FreeMarker template engine for generating web pages. As part of this
|
|
||||||
process, the JSP files that were used for theme customization in earlier
|
|
||||||
versions of VIVO have been replaced by a set of FreeMarker templates.
|
|
||||||
In the 1.1 install package, these files are located in
|
|
||||||
/vivo/themes/vivo-basic/templates and have an ftl (for FreeMarker Template
|
|
||||||
Language) extension.
|
|
||||||
|
|
||||||
Follow step A or B below, whichever is applicable to your site:
|
|
||||||
|
|
||||||
A. If you did not create a customized theme for your site in VIVO 1.0, but used
|
|
||||||
the 1.0 vivo-basic theme in its original directory, you need not take any
|
|
||||||
action in order to convert your site to the VIVO 1.1 theme.
|
|
||||||
|
|
||||||
B. If you created your own theme directory in VIVO 1.0, follow the steps below
|
|
||||||
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
|
|
||||||
theme to VIVO 1.1.
|
|
||||||
|
|
||||||
1. Templates
|
|
||||||
|
|
||||||
a. Copy the directory /vivo/themes/vivo-basic/templates into your theme
|
|
||||||
directory /vivo/themes/<your-theme-name>.
|
|
||||||
|
|
||||||
b. Follow step i or ii below, whichever is applicable to your theme.
|
|
||||||
|
|
||||||
i. If you did not apply any customizations to the JSPs in your VIVO
|
|
||||||
1.0 theme, then you do not need to apply any additional changes
|
|
||||||
to the VIVO 1.1 theme templates during the upgrade process.
|
|
||||||
|
|
||||||
ii. If you did apply customizations to the JSPs in your VIVO 1.0
|
|
||||||
theme,you will need to hand-replicate those modifications in the
|
|
||||||
new theme template files.
|
|
||||||
|
|
||||||
The theme template content that was previously contained in
|
|
||||||
three JSP files is now contained in five FTL files. The
|
|
||||||
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
|
|
||||||
follows:
|
|
||||||
|
|
||||||
identity.jsp => identity.ftl
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|
||||||
menu.jsp => menu.ftl and search.ftl
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|
||||||
footer.jsp => footer.ftl and googleAnalytics.ftl
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|
||||||
|
|
||||||
googleAnalytics.ftl is a new file to which you will add
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|
||||||
your site's Google Analytics Tracking Code (see section II).
|
|
||||||
|
|
||||||
Because the FreeMarker Template Language uses many syntactic
|
|
||||||
conventions that will be familiar to template authors from JSP
|
|
||||||
or other common templating systems, the translation of your JSP
|
|
||||||
changes into the new FTLs should be relatively straightforward.
|
|
||||||
|
|
||||||
Consult the FreeMarker Template Author's Guide at
|
|
||||||
http://freemarker.org/docs/dgui.html and the Reference at
|
|
||||||
http://freemarker.org/docs/ref.html for complete documentation
|
|
||||||
of the syntax and available built-in constructs. Template
|
|
||||||
authors need not be concerned with the Programmer's Guide or
|
|
||||||
Java API documentation.
|
|
||||||
|
|
||||||
c. Remove the jsp directory from your themes directory.
|
|
||||||
|
|
||||||
2. Stylesheets
|
|
||||||
|
|
||||||
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
|
|
||||||
styles in your VIVO 1.0 theme, you will not be able to simply copy the
|
|
||||||
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
|
|
||||||
style upgrades that your theme should pick up. Instead, you should
|
|
||||||
use the vivo-basic 1.1 stylesheets as a starting point, and manually
|
|
||||||
merge your 1.0 style modifications in as needed.
|
|
||||||
|
|
||||||
3. Site Icons
|
|
||||||
|
|
||||||
Copy the site icons from your 1.0 theme into the site_icons folder in
|
|
||||||
your 1.1 theme.
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
</pre>
|
|
||||||
</div>
|
|
||||||
<!-- end of content -->
|
|
||||||
<footer role="contentinfo">
|
|
||||||
<p class="copyright">
|
|
||||||
<small>
|
|
||||||
©2011
|
|
||||||
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
|
||||||
</small>
|
|
||||||
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
|
||||||
</p>
|
|
||||||
<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>
|
|
||||||
</nav>
|
|
||||||
</footer>
|
|
||||||
</body>
|
|
||||||
</html>
|
|
||||||
Loading…
Add table
Reference in a new issue