238 lines
11 KiB
HTML
238 lines
11 KiB
HTML
<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.5 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 V1.5 Upgrade Guide</h1>
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<small>
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February 15, 2012 - Upgrading from Release 1 V1.4 to Release 1 V1.5
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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 1.4 (or 1.4.1) to Version 1.5.
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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 V1.5 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 V1.5</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><a href="#changes">Noteworthy Changes</a> <br>
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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 1.4 or VIVO 1.4.1)
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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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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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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="upgradeAnt">Ant version 1.8 required</h4>
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<p>
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See J.Blake for details.
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</p>
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</li>
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<li>
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<h4 id="customSearchView">Custom search views</h4>
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<p>
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"Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism.
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If you have custom search views, you will need to re-configure them.
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See J.Blake for details.
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</p>
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</li>
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<li>
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<h4 id="openSocial">Support for OpenSocial gadgets</h4>
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<p>
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You can now add OpenSocial support to your VIVO instance. Look at setting_up_orng.html for details.
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See J.Blake for details.
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</p>
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</li>
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<li>
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<h4 id="openSocial">Supported Browsers</h4>
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<p>
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For this release, the following browsers are supported.
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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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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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<h3 id="#upgrade_process">III. Upgrade Instructions</h3>
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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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<h3 id="kbm">IV .Knowledge Base Migration</h3>
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<p>
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Changes to the VIVO core ontology may require corresponding
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modifications to the knowledge base instance data and ontology annotations.
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When VIVO first starts up following the upgrade, it will
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initiate a process to examine the knowledge base and apply necessary
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changes. The knowledge base migration process for release 1.5 will make
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the following types of changes:
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</p>
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<dl>
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<dt>
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The vivo:ResearchLaboratory class has been removed. All instances of vivo:ResearchLaboratory will be
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retyped to its superclass vivo:Laboratory.
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</dt>
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</dl>
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<dl>
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<dt>
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Annotation property default values
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</dt>
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<dd>
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If a site has modified the value of a vitro annotation (such
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as
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displayRankAnnot or displayLimitAnnot) so that it is no longer using
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the default, then that setting will be left unchanged.
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<br>
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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 the
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new default value will be propagated to the knowledge base.
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</dd>
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</dl>
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<p>
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In addition to the logs described in <strong>step 8</strong> of the <a href="#upgrade_process">previous section</a>, the knowledge base migration
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process will log copies of all additions and deletions that were made to the knowledge base in the following files:
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</p>
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<dl>
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<dt>
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<code>webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3</code>
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</dt>
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<dd>
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An N3 file containing all the statements that were removed from the knowledge base.
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</dd>
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</dl>
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<dl>
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<dt>
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<code>webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3</code>
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</dt>
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<dd>
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An N3 file containing all the statements that were added to the knowledge base.
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</dd>
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</dl>
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<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
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<p>
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VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
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you assign in the "Site Information" form under the <strong>Site Admin</strong>
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area will be
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inserted into the "Terms of Use" statement. If you want to edit the text content more than just
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the "Site Name", the file can be found here:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
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Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose
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your changes next time you deploy for another reason.
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</p>
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<h3 id="nextsteps">Next Steps</h3>
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<p>
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Now that you have VIVO up and running, please refer to the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>
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for information about its operation.
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</p>
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</div>
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<!-- #wrapper-content -->
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<div id="footer" role="contentinfo">
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<p class="copyright">
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<small>
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©2011 All Rights Reserved
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</small>
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| Powered
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by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
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<ul id="footer-nav" role="list">
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<li role="listitem">
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<a href="http://vivoweb.org/about">About</a>
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</li>
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<li role="listitem">
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<a href="http://vivoweb.org/contact">Contact Us</a>
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</li>
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<li role="listitem">
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<a href="http://www.vivoweb.org/support" target="blank">Support</a>
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</li>
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</ul>
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</div>
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</div>
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</div>
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