2011-11-15 22:11:20 +00:00
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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>Vitro Version 1.6 Installation Guide</title>
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2011-11-15 22:11:20 +00:00
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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="vitro-logo"><a href="/"><span class="displace">Vitro</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>Vitro Version 1.6. Installation Guide</h1>
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<small>
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2013-01-16 14:54:33 -05:00
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January 6, 2013
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2011-11-15 22:11:20 +00:00
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</small>
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<toc>
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<ul>
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<li>
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<a href="#introduction">Introduction to the Vitro installation</a>
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</li>
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<li>
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<a href="#installation">Installation process for Version 1.6</a>
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2011-11-15 22:11:20 +00:00
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</li>
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</ul>
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</toc>
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<br>
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<p>
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This document is a summary of the Vitro installation process.
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</p>
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<p>
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These instructions assume that you are performing a clean install,
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starting with an empty database, an empty Vitro home directory,
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and a Tomcat installation with no Vitro webapp.
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If you are upgrading a previous installation of Vitro,
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2011-12-13 19:05:03 +00:00
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you may need to adjust your procedure accordingly.
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2011-11-15 22:11:20 +00:00
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</p>
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2013-01-16 14:54:33 -05:00
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<p>
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Other servlet containers: If you want to use a servlet container
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other than Tomcat, please consult <a href="other_servlet_containers.html">
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instructions for other servlet containers</a> in this directory.
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</p>
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<hr><h2 id="introduction">Introduction to the Vitro installation</h2>
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2011-11-16 17:35:55 +00:00
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2011-11-15 22:11:20 +00:00
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<p>
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Before beginning the installation,
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let’s discuss some of the major concepts relating to the Vitro installation.
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</p>
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<h3>Where does Vitro live on your computer?</h3>
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<p>
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Vitro exists in four locations on your computer, from the distribution to the runtime to the data storage.
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</p>
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<h4>The Vitro distribution directory</h4>
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<p>
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This is created when you checkout the Vitro source code
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(see <a href="#checkout_code">installation step III</a>, below).
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This is where you will create your build.properties file
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(see <a href="#build_properties">installation step IV</a>, below),
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2011-11-15 22:11:20 +00:00
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and where you will make any modifications to the Vitro
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theme or code. You can create this wherever you choose.
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</p>
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<h4>Vitro inside Tomcat</h4>
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<p>
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When you run the build script to compile and deploy Vitro
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(see <a href="#deploy">installation step VI</a>, below),
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the files will be deployed to a
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directory inside Tomcat. This is the actual executing code for Vitro,
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but you won’t need to look at it or change it. If you need to change
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Vitro, make the changes in the distribution directory, and run the build
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script again. Tell the build script where to find Tomcat by setting <code>tomcat.home</code>
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in the build.properties file (see <a href="#build_properties">installation step IV</a>,
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below).
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</p>
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<h4>The Vitro home directory</h4>
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<p>
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This directory contains the runtime configuration properties for Vitro.
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Vitro will also use this area to store some of the data it uses. Uploaded
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image files are stored here, and the Solr home directory is stored here also.
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You can create this wherever you choose. Tell Vitro where to find the
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home directory by setting <code>vitro.home</code> in the
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build.properties file (see <a href="#build_properties">installation step IV</a>,
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below). You must create this directory before starting Vitro,
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you must create the <code>runtime.properties</code> file in this directory
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(see <a href="#runtime_properties">Step V</a>, below), and you
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must ensure that Tomcat has permission to read and write to this
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directory when it runs.
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</p>
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<h4>The MySQL database</h4>
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<p>
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Essentially all of the data that you store in Vitro will be given to
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MySQL for storage. The actual location of this data depends on what
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system you have, and on how you install MySQL
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(see <a href="#required_software">installation step I</a>, below).
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but you won’t need to
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know the location. You will access the data through Vitro, or
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occasionally through the MySQL client application.
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</p>
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<h3>The relationship between Vitro and VIVO</h3>
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<h4>“Vitro Inside”</h4>
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<p>
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Vitro was developed as a
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“general-purpose web-based ontology and instance editor with customizable public browsing.”
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It is useful on its own, but also serves as the basis for several products,
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including VIVO. [http://sourceforge.net/projects/vivo/]
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</p>
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<p>
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In 2009, the National Institutes of Health (NIH) awarded a major grant to advance the development of VIVO.
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Much of the recent development on Vitro has been in support of that grant.
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However, Vitro retains its own identity,
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and still serves as the core of many projects and products.
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Some of these are currently in use, and some are still in the planning stages.
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</p>
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<p>
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Because VIVO was so well funded, and because it is widely used,
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someone seeking help with Vitro might find information that applies to VIVO instead.
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In many cases, that information will apply to Vitro as well.
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However, there are some notable exceptions:
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<ul>
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<li>
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<h5>Ontology</h5>
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<p>
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Vitro is essentially a blank slate, and is suitable for use with almost any ontology.
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It is packaged with a minimal ontology, sufficient to run the application itself.
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</p>
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<p>
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VIVO is packaged with a rich ontology, tailored to scientists and educators.
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</p>
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</li>
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<li>
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<h5>Theme</h5>
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<p>
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Vitro and VIVO are each packaged with their own default theme.
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The VIVO theme is more extensive,
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since it includes custom pages and custom list views that apply to the VIVO ontology.
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</p>
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</li>
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<li>
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<h5>Visualizations</h5>
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<p>
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VIVO includes some rich visualization tools that are specific to the VIVO ontology.
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</p>
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</li>
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<li>
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<h5>Harvester</h5>
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<p>
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VIVO includes an RDF Harvester tool for importing data from sources of record.
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The Harvester may be useful for Vitro as well, but it was developed for VIVO,
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and may have some dependencies on VIVO.
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</p>
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</li>
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</ul>
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</p>
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<h4>Release schedule and names</h4>
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<p>
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Currently, the Vitro release schedule is coordinated with the VIVO releases,
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so version 1.6 of Vitro forms the basis of version 1.6 of VIVO.
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In the Vitro code repository, the release tags illustrate this relationship.
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For example, the Vitro revision that was tagged for version 1.6 of VIVO is named “rel-vivo-1.6”
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</p>
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2013-07-10 11:16:43 -04:00
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<hr><!-- Page break --><!-- Installation process for Version 1.6 --><h2 id="installation">Installation process for Version 1.6</h2>
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2011-11-15 22:11:20 +00:00
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<p>
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2011-11-16 17:30:30 +00:00
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This document is a summary of the Vitro installation process.
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2011-11-15 22:11:20 +00:00
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</p>
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<toc>
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<h3>Steps to Installation</h3>
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<ol class="roman1">
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<li>
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<a href="#required_software">Install required software</a>
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</li>
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<li>
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<a href="#create_database">Create an empty MySQL database</a>
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</li>
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<li>
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<a href="#checkout_code">Check out the Vitro Source Code</a>
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</li>
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<li>
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<a href="#build_properties">Specify build properties</a>
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</li>
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<li>
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<a href="#runtime_properties">Specify runtime properties</a>
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</li>
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<li>
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<a href="#deploy">Compile and deploy</a>
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</li>
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<li>
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2011-11-23 16:04:51 +00:00
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<a href="#tomcat_settings">Configure Tomcat</a>
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</li>
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<li>
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<a href="#start_tomcat">Start Tomcat</a>
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</li>
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<li>
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<a href="#add_rdf">Log in and add RDF data</a>
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</li>
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<li>
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<a href="#contact_email">Set the Contact Email Address (if
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using "Contact Us" form)</a>
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</li>
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<li>
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<a href="#httpd">Set up Apache HTTPD</a>
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</li>
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<li>
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<a href="#external_auth">Using an External Authentication
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System with Vitro</a>
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</li>
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<li>
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<a href="#installation_check">Was the installation successful?</a>
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</li>
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<li>
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<a href="#termsofuse">Review the Vitro Terms of Use</a>
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</li>
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</ol>
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</toc>
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<h3 id="required_software">I. Install required software </h3>
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<p>
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Before installing Vitro, make sure that the following software is
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installed on the desired machine:
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</p>
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<ul>
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<li>
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Java (SE) 1.6 or higher, <a href="http://java.sun.com">http://java.sun.com</a>
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(Not OpenJDK)
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</li>
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<li>
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Apache Tomcat 6.x or higher, <a href="http://tomcat.apache.org">http://tomcat.apache.org</a>
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</li>
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<li>
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2012-10-08 16:45:32 +00:00
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Apache Ant 1.8 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
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</li>
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<li>
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MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a>
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</li>
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<li>
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Apache Subversion 1.6.x or higher*, <a href="http://subversion.apache.org/">http://subversion.apache.org/</a>
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</li>
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</ul>
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<p>
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Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code>
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and <code>ANT_HOME</code>
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and add the executables to your path per
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your operating system and installation directions from the software
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support websites.
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</p>
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2011-11-16 17:30:30 +00:00
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2011-11-15 22:11:20 +00:00
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<h3 id="create_database">II. Create an empty MySQL database </h3>
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<p>
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Decide on a database name, username, and password. Log into your
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MySQL server and create a new database in MySQL that uses <code>UTF-8
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encoding</code>. You will need these values for Step IV when you
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configure the deployment properties. At the MySQL command line you can
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create the database and user with these commands substituting your
|
|
|
|
|
|
values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
|
|
|
|
|
|
Most
|
|
|
|
|
|
of
|
|
|
|
|
|
the
|
|
|
|
|
|
time, the hostname will equal <code>localhost</code>.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Grant access to a database user. For example:
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br></pre>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Keep track of the database name, username, and password for Step
|
|
|
|
|
|
IV.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<h3 id="checkout_code">III. Check out the Vitro Source Code
|
|
|
|
|
|
<br>
|
|
|
|
|
|
</h3>
|
|
|
|
|
|
<p>
|
2011-12-16 20:59:56 +00:00
|
|
|
|
Download the latest stable release of Vitro from SourceForge:
|
|
|
|
|
|
go to
|
|
|
|
|
|
<pre> http://sourceforge.net/projects/vivo/files/Vitro%20Application%20Source/</pre>
|
2013-07-10 11:16:43 -04:00
|
|
|
|
and download either <code>vitro-rel-1.6.zip</code> or <code>vitro-rel-1.6.tar.gz</code>
|
2011-12-16 20:59:56 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If you want the very latest Vitro source, you can use subversion to check it out from SourceForge:
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<pre> svn checkout svn://svn.code.sf.net/p/vivo/vitro/code/trunk</code> <em>[Vitro_distribution_dir]</em></pre>
|
|
|
|
|
|
</p>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
|
|
|
|
|
|
<h3 id="build_properties">IV. Specify build properties </h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-12-13 19:05:03 +00:00
|
|
|
|
In the <code>webapp/config</code> directory of the Vitro distribution,
|
2013-01-16 14:54:33 -05:00
|
|
|
|
copy the file <code>example.build.properties</code>
|
|
|
|
|
|
to a file named simply <code>build.properties</code>.
|
|
|
|
|
|
Edit the file to suit your installation, as described in the following table.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
These properties are used in compilation and deployment.
|
|
|
|
|
|
They will be incorporated into Vitro when it is compiled in
|
|
|
|
|
|
<a href="#deploy">Step VI</a>. If you want to change these properties at
|
|
|
|
|
|
a later date, you will need to stop Tomcat, repeat <a href="#deploy">Step VI</a>,
|
|
|
|
|
|
and restart Tomcat.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
<em>Windows:</em>
|
|
|
|
|
|
For those installing on Windows operating
|
|
|
|
|
|
system, include the windows drive and use the forward slash "/" and not
|
|
|
|
|
|
the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
|
|
|
|
<tbody>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Directory where tomcat is installed.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
tomcat.home
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
/usr/local/tomcat
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
2011-11-16 17:30:30 +00:00
|
|
|
|
Name of your Vitro application.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
webapp.name
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
vitro
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
2013-01-16 14:54:33 -05:00
|
|
|
|
Directory where the Vitro application will store
|
|
|
|
|
|
the data that it creates. This includes uploaded files (usually images)
|
|
|
|
|
|
and the Solr search index. Be sure this directory exists and is
|
|
|
|
|
|
writable by the user who the Tomcat service is running as.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
vitro.home
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
/usr/local/vitro/home
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
|
|
|
|
|
|
|
|
|
|
|
<h3 id="runtime_properties">V. Specify runtime properties </h3>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
In <a href="#build_properties">Step IV</a>, you defined the location of the Vitro home directory,
|
|
|
|
|
|
by specifying <code>vitro.home</code> in the <code>build.properties</code> file.
|
|
|
|
|
|
Create that directory now.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
In the <code>webapp/config</code> subdirectory of the Vitro distribution, you will find a file called
|
|
|
|
|
|
<code>example.runtime.properties</code>. Copy this to the Vitro home directory you have created,
|
|
|
|
|
|
renaming the copy to <code>runtime.properties</code>.
|
|
|
|
|
|
Edit the file to suit your installation, as described in the following table.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
These properties are loaded when Vitro starts up. If you want to change these
|
|
|
|
|
|
properties at a later date, you will need to restart Tomcat for them to take
|
|
|
|
|
|
effect. You will not need to repeat <a href="#deploy">Step VI</a>.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
<em>Windows:</em>
|
|
|
|
|
|
For those installing on Windows operating
|
|
|
|
|
|
system, include the windows drive and use the forward slash "/" and not
|
|
|
|
|
|
the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
<em>External authentication:</em>
|
|
|
|
|
|
If you want to use an external
|
|
|
|
|
|
authentication system like Shibboleth or CUWebAuth, you will need to
|
|
|
|
|
|
set two additional properties in this file. See the section below
|
|
|
|
|
|
entitled <a href="#external_auth">Using an External Authentication System with Vitro</a>.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
|
|
|
|
|
|
<tbody>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>
|
|
|
|
|
|
Property Name
|
|
|
|
|
|
</th>
|
|
|
|
|
|
<th>
|
|
|
|
|
|
Example Value
|
|
|
|
|
|
</th>
|
|
|
|
|
|
</tr>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
2013-01-16 14:54:33 -05:00
|
|
|
|
Default namespace: Vitro installations make their
|
|
|
|
|
|
RDF resources available for harvest using linked data. Requests for RDF
|
|
|
|
|
|
resource URIs redirect to HTML or RDF representations as specified by
|
|
|
|
|
|
the client. To make this possible, Vitro's default namespace must have a
|
|
|
|
|
|
certain structure and begin with the public web address of the Vitro
|
|
|
|
|
|
installation. For example, if the web address of a Vitro installation is
|
|
|
|
|
|
"http://vitro.example.edu/" the default namespace must be set to
|
|
|
|
|
|
"http://vitro.example.edu/individual/" in order to support linked data.
|
|
|
|
|
|
Similarly, if Vitro is installed at "http://www.example.edu/vitro" the
|
|
|
|
|
|
default namespace must be set to
|
|
|
|
|
|
"http://www.example.edu/vitro/individual/"
|
|
|
|
|
|
<h5>* The namespace must end with "individual/" (including the trailing slash).</h5>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
Vitro.defaultNamespace
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
http://vitro.mydomain.edu/individual/
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
2013-01-16 14:54:33 -05:00
|
|
|
|
URL of Solr context used in local Vitro search.
|
|
|
|
|
|
Should consist of:<pre> scheme + servername + port + vitro_webapp_name + "solr"</pre>
|
|
|
|
|
|
In the standard installation, the Solr context will be on the same
|
|
|
|
|
|
server as Vitro, and in the same Tomcat instance. The path will be the
|
|
|
|
|
|
Vitro webapp.name (specified above) + "solr"
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
vitro.local.solr.url
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
http://localhost:8080/vitrosolr
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify an SMTP host that the application will
|
|
|
|
|
|
use for sending e-mail (Optional). If this is left blank, the contact
|
|
|
|
|
|
form will be hidden and disabled, and users will not be notified of
|
|
|
|
|
|
changes to their accounts.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
email.smtpHost
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
smtp.servername.edu
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify an email address which will appear as
|
|
|
|
|
|
the sender in e-mail notifications to users (Optional). If a user
|
|
|
|
|
|
replies to the notification, this address will receive the reply. If a
|
|
|
|
|
|
user's e-mail address is invalid, this address will receive the error
|
|
|
|
|
|
notice. If this is left blank, users will not be notified of changes to
|
|
|
|
|
|
their accounts.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
email.replyTo
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
vitroAdmin@my.domain.edu
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify the JDBC URL of your database. Change
|
2011-11-16 17:30:30 +00:00
|
|
|
|
the end of the URL to reflect your database name (if it is not "vitro").
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.url
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
jdbc:mysql://localhost/vitro
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Change the username to match the authorized user
|
|
|
|
|
|
you created in MySQL.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.username
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
username
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Change the password to match the password you
|
|
|
|
|
|
created in MySQL.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.password
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
password
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify the maximum number of active connections
|
|
|
|
|
|
in the database connection pool to support the anticipated number of
|
2011-12-12 17:05:39 +00:00
|
|
|
|
concurrent page requests.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.pool.maxActive
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
40
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify the maximum number of database
|
|
|
|
|
|
connections that will be allowed to remain idle in the connection pool.
|
|
|
|
|
|
Default is 25% of the maximum number of active connections.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.pool.maxIdle
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
10
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Change the dbtype setting to use a database
|
|
|
|
|
|
other than MySQL. Otherwise, leave this value unchanged. Possible
|
|
|
|
|
|
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
|
|
|
|
|
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
|
|
|
|
|
for additional information.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.dbtype
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
MySQL
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify a driver class name to use a database
|
|
|
|
|
|
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
|
|
|
|
|
for this driver must be added to the the webapp/lib directory within
|
|
|
|
|
|
the vitro.core.dir specified above.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.driver
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
com.mysql.jdbc.Driver
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Change the validation query used to test
|
|
|
|
|
|
database connections only if necessary to use a database other than
|
|
|
|
|
|
MySQL. Otherwise, leave this value unchanged.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
VitroConnection.DataSource.validationQuery
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
SELECT 1
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Specify the email address of the root user
|
2011-11-16 17:30:30 +00:00
|
|
|
|
account for the Vitro application. This user will have an initial
|
2011-11-15 22:11:20 +00:00
|
|
|
|
temporary password of 'rootPassword'. You will be prompted to create a
|
|
|
|
|
|
new password on first login.
|
|
|
|
|
|
<p>
|
|
|
|
|
|
NOTE: The root user account has access to all data and all
|
2011-11-16 17:30:30 +00:00
|
|
|
|
operations in Vitro. Data views may be surprising when logged in as the
|
2011-11-15 22:11:20 +00:00
|
|
|
|
root user. It is best to create a Site Admin account to use for every
|
|
|
|
|
|
day administrative tasks.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
rootUser.emailAddress
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
vitroAdmin@my.domain.edu
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
The URI of a property that can be used to
|
|
|
|
|
|
associate an Individual with a user account. When a user logs in with a
|
|
|
|
|
|
name that matches the value of this property, the user will be
|
|
|
|
|
|
authorized to edit that Individual
|
|
|
|
|
|
(the value of the property must be either a String literal or an untyped literal).
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
selfEditing.idMatchingProperty
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
http://vitro.mydomain.edu/ns#networkId
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
If an external authentication system like Shibboleth or CUWebAuth is to be
|
|
|
|
|
|
used, these properties say how the login button should be labeled, and which
|
|
|
|
|
|
HTTP header will contain the user ID from the authentication system. If such
|
|
|
|
|
|
a system is not to be used, leave these commented out. Consult the installation
|
|
|
|
|
|
instructions for more details.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
externalAuth.buttonText
|
|
|
|
|
|
<br/>
|
|
|
|
|
|
externalAuth.netIdHeaderName
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
Log in using BearCat Shibboleth
|
|
|
|
|
|
<br/>
|
|
|
|
|
|
remote_userID
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
2013-06-03 15:44:17 -04:00
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
Tell Vitro to generate HTTP headers on its responses to facilitate caching the
|
|
|
|
|
|
profile pages that it creates. This can improve performance, but it can also
|
|
|
|
|
|
result in serving stale data. Default is false if not set.
|
|
|
|
|
|
For more information, see the VIVO wiki page:
|
|
|
|
|
|
<a href="https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance">
|
|
|
|
|
|
Use HTTP caching to improve performance </a>
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
http.createCacheHeaders
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
true
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
2013-01-24 16:21:36 -05:00
|
|
|
|
Force VIVO to use a specific language or Locale instead of those
|
|
|
|
|
|
specified by the browser.
|
|
|
|
|
|
This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
|
|
|
|
|
|
This also affects the text of pages that have been modified to support multiple languages.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
2013-01-24 16:21:36 -05:00
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
languages.forceLocale
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
en_US
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
A list of supported languages or Locales that the user may choose to
|
|
|
|
|
|
use instead of the one specified by the browser. Selection images must
|
|
|
|
|
|
be available in the i18n/images directory of the theme.
|
|
|
|
|
|
This affects RDF data retrieved from the model, if RDFService.languageFilter is true.
|
|
|
|
|
|
This also affects the text of pages that have been modified to support multiple languages.
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
languages.selectableLocales
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
en, es, fr_FR
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
<b>For developers only.</b>
|
|
|
|
|
|
Defeat the Freemarker template cache, so each template
|
|
|
|
|
|
is read from disk on each request. This permits developers to immediately
|
|
|
|
|
|
see the effect of changes to the template. The default is <code>false</code>, which
|
|
|
|
|
|
means that a cached copy of each template will be used for 60 seconds
|
|
|
|
|
|
before the disk is checked for a new version.
|
2013-01-25 16:29:17 -05:00
|
|
|
|
<br/><b>Setting this option to "true" slows down Vitro performance.</b>
|
2013-01-24 16:21:36 -05:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
developer.defeatFreemarkerCache
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
false
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
|
<b>For developers only.</b>
|
|
|
|
|
|
Defeat the cache of language-specific text strings,
|
|
|
|
|
|
so the language file is read from disk on each request.
|
|
|
|
|
|
This permits developers to immediately
|
|
|
|
|
|
see the effect of changes to the text strings.
|
|
|
|
|
|
The default is <code>false</code>, which means that the language file is
|
|
|
|
|
|
read when VIVO starts up, or when a new theme is selected.
|
2013-01-25 16:29:17 -05:00
|
|
|
|
<br/><b>Setting this option to "true" slows down Vitro performance.</b>
|
2013-01-24 16:21:36 -05:00
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
developer.defeatI18nCache = true
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
false
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
2013-01-25 16:29:17 -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 Vitro performance.</b>
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
|
<td>
|
|
|
|
|
|
developer.insertFreemarkerDelimiters = true
|
|
|
|
|
|
</td>
|
|
|
|
|
|
<td>
|
|
|
|
|
|
false
|
|
|
|
|
|
</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
<h3 id="deploy">VI. Compile and deploy</h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-12-13 19:05:03 +00:00
|
|
|
|
At the command line, change to the <code>webapp</code> directory inside the Vitro distribution
|
|
|
|
|
|
directory. Then type:
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
<pre> ant all<br> </pre>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
to build Vitro and deploy to Tomcat's webapps directory.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
2013-08-01 17:18:06 -04:00
|
|
|
|
<p>
|
|
|
|
|
|
The build script may run for as much as five minutes,
|
|
|
|
|
|
and creates more than 100 lines of output.
|
|
|
|
|
|
The process comprises several steps:
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>collecting the source files from the distribution directory,</li>
|
|
|
|
|
|
<li>compiling the Java source code,</li>
|
|
|
|
|
|
<li>compiling and running unit tests,</li>
|
|
|
|
|
|
<li>preparing the Solr search engine,</li>
|
|
|
|
|
|
<li>deploying Vitro and Solr to Tomcat.</li>
|
|
|
|
|
|
</ul>
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
The output of the build may include a variety of warning messages.
|
|
|
|
|
|
The Java compiler may warn of code that is outdated.
|
|
|
|
|
|
Unit tests may produce warning messages,
|
|
|
|
|
|
and some tests may be ignored if they do not produce consistent results.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<table align="center"><tr><td>
|
|
|
|
|
|
BUILD SUCCESSFUL<br>Total time: 1 minute 49 seconds
|
|
|
|
|
|
</td></tr></table>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If the output ends with a success message, the build was successful.
|
|
|
|
|
|
Proceed to the next step.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<table align="center"><tr><td>
|
|
|
|
|
|
BUILD FAILED<br>Total time: 35 seconds
|
|
|
|
|
|
</td></tr></table>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If the output ends with a failure message, the build has failed.
|
|
|
|
|
|
Find the cause of the failure, fix the problem, and run the script again.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
|
2013-01-16 14:54:33 -05:00
|
|
|
|
<h3 id="tomcat_settings">VII. Configure Tomcat</h3>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
<h4>Set JVM parameters</h4>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
Vitro may require more memory than that allocated to Tomcat by
|
2011-11-15 22:11:20 +00:00
|
|
|
|
default. With most installations of Tomcat, the "setenv.sh" or
|
|
|
|
|
|
"setenv.bat" file in Tomcat's bin directory is a convenient place to
|
|
|
|
|
|
set the memory parameters. <em>If this file does not exist in Tomcat's
|
|
|
|
|
|
bin directory, you can create it.</em>
|
|
|
|
|
|
<br>
|
|
|
|
|
|
For example:
|
|
|
|
|
|
</p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
<pre> export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"<br> </pre>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-11-16 16:55:34 +00:00
|
|
|
|
This sets Tomcat to allocate an initial heap of 512 megabytes, a
|
|
|
|
|
|
maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower
|
|
|
|
|
|
values may suffice, especially for small test installations.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
If an OutOfMemoryError is encountered during Vitro execution, it can
|
2011-11-15 22:11:20 +00:00
|
|
|
|
be remedied by increasing the heap parameters and restarting Tomcat.
|
|
|
|
|
|
</p>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
<h4>Set security limits</h4>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
Vitro is a multithreaded web application that may
|
2011-11-15 22:11:20 +00:00
|
|
|
|
require more threads than are permitted under your Linux installation's
|
|
|
|
|
|
default configuration. Ensure that your installation can support the
|
|
|
|
|
|
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
<h4>Set URI encoding</h4>
|
|
|
|
|
|
<p>
|
2011-12-13 20:31:25 +00:00
|
|
|
|
In order for VIVO to correctly handle international characters,
|
2011-11-23 16:04:51 +00:00
|
|
|
|
you must configure Tomcat to conform to the URI standard by
|
|
|
|
|
|
accepting percent-encoded UTF-8.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
Edit Tomcat's <code>conf/server.xml</code> and add the following attribute to each of the
|
2011-11-23 16:04:51 +00:00
|
|
|
|
Connector elements: URIEncoding="UTF-8".
|
2011-11-25 17:20:16 +00:00
|
|
|
|
</p>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
<pre>
|
2011-11-25 17:20:16 +00:00
|
|
|
|
<Server ...>
|
|
|
|
|
|
<Service ...>
|
|
|
|
|
|
<Connector ... URIEncoding="UTF-8"/>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
...
|
2011-11-25 17:20:16 +00:00
|
|
|
|
</Connector>
|
|
|
|
|
|
</Service>
|
|
|
|
|
|
</Server>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
</pre>
|
2011-11-25 17:20:16 +00:00
|
|
|
|
<p>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
Note: some versions of Tomcat already include this attribute as the default.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
|
2011-11-25 17:20:16 +00:00
|
|
|
|
<h4>Take care when creating Context elements</h4>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Each of the webapps in the Vitro distribution (Vitro and Solr) includes a "context fragment" file,
|
|
|
|
|
|
containing some of the deployment information for that webapp.
|
2011-11-23 16:04:51 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-25 17:20:16 +00:00
|
|
|
|
Tomcat allows you to override these context fragments by adding Context elements to "server.xml".
|
|
|
|
|
|
If you decide to do this, be sure that your new Context element includes the necessary
|
|
|
|
|
|
deployment parameters from the overridden context fragment.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
See <a href="#httpd">Section XI</a> below,
|
2011-12-13 19:05:03 +00:00
|
|
|
|
for an example of overriding the Vitro context fragment.
|
2011-11-25 17:20:16 +00:00
|
|
|
|
</p>
|
2011-11-23 16:04:51 +00:00
|
|
|
|
|
2013-01-16 14:54:33 -05:00
|
|
|
|
<h3 id="start_tomcat">VIII. Start Tomcat </h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
|
|
|
|
|
Most Tomcat installations can be started by running <code>startup.sh</code>
|
|
|
|
|
|
or <code>startup.bat</code>
|
|
|
|
|
|
in Tomcat's bin directory. Point your
|
2013-01-16 14:54:33 -05:00
|
|
|
|
browser to "http://localhost:8080/vitro/" to test the application.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
On start up Vitro will run some diagnostic tests. If a
|
|
|
|
|
|
problem is detected, the normal Vitro pages will redirect
|
|
|
|
|
|
to a startup status page describing the problem. You
|
|
|
|
|
|
can stop tomcat, attempt to fix the problem and
|
|
|
|
|
|
proceeded from <a href="#deploy">Step VI</a>. The
|
|
|
|
|
|
startup status page may offer a continue link which
|
|
|
|
|
|
will allow you to use VIVO in spite of the problems.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If Tomcat does not start up, or the Vitro application is not visible, check
|
|
|
|
|
|
the files in Tomcat's <code>logs</code> directory. Error messages are commonly found
|
2011-11-15 22:11:20 +00:00
|
|
|
|
in <code>catalina.out</code>
|
|
|
|
|
|
or <code>localhost.log</code>
|
|
|
|
|
|
</p>
|
2013-01-16 14:54:33 -05:00
|
|
|
|
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<h3 id="add_rdf">IX. Log in and add RDF data </h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
|
|
|
|
|
If the startup was successful, you will see a welcome message
|
2011-11-16 17:30:30 +00:00
|
|
|
|
informing you that you have successfully installed Vitro. Click the "Log
|
2011-11-15 22:11:20 +00:00
|
|
|
|
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
|
|
|
|
|
|
you set up in Step IV. The initial password for the root account is
|
|
|
|
|
|
"rootPassword" (without the quotes). On first login, you will be
|
|
|
|
|
|
prompted to select a new password and verify it a second time. When login is
|
|
|
|
|
|
complete, the search index is checked and, if it is empty,
|
|
|
|
|
|
a full index build will be triggered in the background, in order to ensure
|
|
|
|
|
|
complete functionality throughout the site.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
After logging in, you will be presented with a
|
|
|
|
|
|
menu of editing options. Here you can create OWL classes, object
|
|
|
|
|
|
properties, data properties, and configure the display of data.
|
|
|
|
|
|
Currently, any classes you wish to make visible on your website must be
|
|
|
|
|
|
part of a class group, and there are a number of visibility and display
|
2011-11-16 16:55:34 +00:00
|
|
|
|
options available for each ontology entity. Vitro comes with a minimal
|
|
|
|
|
|
ontology. You will likely want to upload additional ontologies from an RDF file.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
|
|
|
|
|
|
that Vitro currently works best with OWL-DL ontologies and has only
|
|
|
|
|
|
limited support for pure RDF data. You can enter a URL pointing to the
|
|
|
|
|
|
RDF data you wish to load or upload from a file on your local machine.
|
|
|
|
|
|
Ensure that the "add RDF" radio button is selected. You will also
|
|
|
|
|
|
likely want to check "create classgroups automatically."
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Clicking the "Index" tab in the navigation bar at the top right of
|
|
|
|
|
|
the page will show a simple index of the knowledge base.
|
|
|
|
|
|
</p>
|
2011-11-16 16:55:34 +00:00
|
|
|
|
|
2013-01-16 14:54:33 -05:00
|
|
|
|
<h3 id="contact_email">X. Set the Contact Email Address (if using
|
2011-11-15 22:11:20 +00:00
|
|
|
|
"Contact Us" form)</h3>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If you have configured your application to use the "Contact Us"
|
|
|
|
|
|
feature in Step IV (<code>email.smtpHost</code>), you will also need to
|
2011-11-16 17:30:30 +00:00
|
|
|
|
add an email address to the Vitro application. This is the email
|
2011-11-15 22:11:20 +00:00
|
|
|
|
to which the contact form will submit. It can be a list server or an
|
|
|
|
|
|
individual's email address.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Log in as a system administrator. Navigate to the "Site Admin"
|
|
|
|
|
|
table of contents (link in the right side of the header). Go to "Site
|
|
|
|
|
|
Information" (under "Site Configuration"). In the "Site Information
|
|
|
|
|
|
Editing Form," enter a functional email address in the field "Contact
|
|
|
|
|
|
Email Address" and submit the change.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
If you set the <code>email.smtpHost</code>
|
|
|
|
|
|
in Step IV and do NOT
|
|
|
|
|
|
provide an email address in this step, your users will receive a java
|
|
|
|
|
|
error in the interface.
|
|
|
|
|
|
</p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
<h3 id="httpd">XI. Set up Apache HTTPD </h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
It is recommended to run an Apache HTTPD web server to accept requests
|
|
|
|
|
|
and then proxy them to the VIVO Tomcat context. This will make Vitro
|
|
|
|
|
|
available at "http://example.com" instead of "http://example.com:8080/vitro".
|
|
|
|
|
|
It will also allow the use of external authentication.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
Setup HTTPD to send all of the requests that it receives to Tomcat's AJP
|
|
|
|
|
|
connector. This can be done in HTTPD 2.x with a simple directive in httpd.conf:
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
<pre> ProxyPass / ajp://localhost:8009/ <br><br></pre>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
Modify the <Host> in Tomcat server.xml (located in <code>[tomcat root]/conf/</code>)
|
|
|
|
|
|
so that the context path is empty to allow VIVO to be servred from the root path.
|
|
|
|
|
|
Locate the <code><Host name="localhost"...></code> directive and update as follows:
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
2011-11-16 16:55:34 +00:00
|
|
|
|
<pre> <Host name="localhost" appBase="webapps"
|
|
|
|
|
|
DeployOnStartup="false"
|
|
|
|
|
|
unpackWARs="true" autoDeploy="false"
|
|
|
|
|
|
xmlValidation="false" xmlNamespaceAware="false">
|
|
|
|
|
|
|
|
|
|
|
|
<Alias>example.com</Alias>
|
|
|
|
|
|
|
|
|
|
|
|
<Context path=""
|
2011-11-16 17:30:30 +00:00
|
|
|
|
docBase="/usr/local/tomcat/webapps/vitro"
|
2011-11-16 16:55:34 +00:00
|
|
|
|
reloadable="true"
|
|
|
|
|
|
cookies="true" >
|
|
|
|
|
|
|
|
|
|
|
|
<Manager pathname="" />
|
|
|
|
|
|
</Context>
|
|
|
|
|
|
|
|
|
|
|
|
...
|
|
|
|
|
|
</pre>
|
2013-07-10 11:14:00 -04:00
|
|
|
|
<p>
|
|
|
|
|
|
After setting up the above, it is recommended that you modify the Tomcat AJP connector
|
|
|
|
|
|
parameters in server.xml. Look for the <connector> directive and add the
|
|
|
|
|
|
following properties:
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000" <br><br></pre>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Note: the value for maxThreads (320) is equal or greater than the value for
|
|
|
|
|
|
MaxClients in the apache's <code>httpd.conf</code> file.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
|
2013-01-16 14:54:33 -05:00
|
|
|
|
<h3 id="external_auth">XII. Using an External Authentication System
|
2011-11-16 17:30:30 +00:00
|
|
|
|
with Vitro </h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
Vitro can be configured to work with an external authentication
|
2011-11-15 22:11:20 +00:00
|
|
|
|
system like Shibboleth or CUWebAuth.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
Vitro must be accessible only through an Apache HTTP server. The
|
2011-11-15 22:11:20 +00:00
|
|
|
|
Apache server will be configured to invoke the external authentication
|
|
|
|
|
|
system. When the user completes the authentication, the Apache server
|
2011-11-16 17:30:30 +00:00
|
|
|
|
will pass a network ID to Vitro, to identify the user.
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
If Vitro has an account for that user, the user will be logged in
|
|
|
|
|
|
with the privileges of that account. In the absence of an account, Vitro
|
2011-11-15 22:11:20 +00:00
|
|
|
|
will try to find a page associated with the user. If such a page is
|
|
|
|
|
|
found, the user can log in to edit his own profile information.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<h4>Configuring the Apache server</h4>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
Your institution will provide you with instructions for setting up
|
|
|
|
|
|
the external authentication system. The Apache server must be
|
2011-11-16 17:30:30 +00:00
|
|
|
|
configured to secure a page in Vitro. When a user reaches this secured
|
2011-11-15 22:11:20 +00:00
|
|
|
|
page, the Apache server will invoke the external authentication system.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
For Vitro, this secured page is named: <code>/loginExternalAuthReturn</code>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
When your instructions call for the location of the secured page,
|
|
|
|
|
|
this is the value you should use.
|
|
|
|
|
|
</p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
<h4>Configuring Vitro</h4>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
To enable external authentication, Vitro requires three values in
|
2013-01-16 14:54:33 -05:00
|
|
|
|
the <code>runtime.properties</code>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
file.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
<h5>The name of the HTTP header that will hold the external user's
|
|
|
|
|
|
network ID.</h5>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
When a user completes the authentication process, the Apache
|
|
|
|
|
|
server will put the user's network ID into one of the headers of the
|
|
|
|
|
|
HTTP request. The instructions from your institution should tell you
|
|
|
|
|
|
which header is used for this purpose.
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-11-16 17:30:30 +00:00
|
|
|
|
You need to tell Vitro the name of that HTTP header. Insert a
|
2013-01-16 14:54:33 -05:00
|
|
|
|
line like this in the runtime.properties file:
|
2011-11-15 22:11:20 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<pre>externalAuth.netIdHeaderName = [the header name]</pre>
|
|
|
|
|
|
<p>
|
|
|
|
|
|
For example:
|
|
|
|
|
|
</p>
|
|
|
|
|
|
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
|
|
|
|
|
|
</li>
|
|
|
|
|
|
<li>
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<h5>The text for the Login button.</h5>
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To start the authentication process, the user will click on a button in
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the Vitro login form. You need to tell Vitro what text should appear in
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that button.
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<p>
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Put a line like this in the runtime.properties file:
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externalAuth.buttonText = [the text for your login button] For example:
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</p>
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<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
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<p>
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The Vitro login form will display a button labelled "Log in
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using BearCat Shibboleth".
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</p>
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</li>
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<li>
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<h5>Associating a User with a profile page.</h5>
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<p>
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Vitro will try to associate the user with a profile
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page, so the user may edit his own profile data. Vitro will search the
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data model for a person with a property that matches the User’s network
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ID (the value of the property must be either a String literal or an
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untyped literal). You need to tell Vitro what property should be used
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for matching. Insert a line like this in the runtime.properties file:
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</p>
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<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
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<p>
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For example:
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</p>
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<pre>selfEditing.idMatchingProperty = http://vitro.mydomain.edu/ns#networkId</pre>
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</li>
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</ul>
|
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<h3 id="installation_check">XIII. Was the installation successful? </h3>
|
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<p>
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If you have completed the previous steps, you have good indications
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that the installation was successful.
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</p>
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<ul>
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<li>
|
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Step VIII showed that Tomcat recognized the webapp, and that the
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2011-11-15 22:11:20 +00:00
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webapp was able to present the initial page.
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</li>
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<li>
|
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Step IX verified that you can log in to the administrator
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2011-11-15 22:11:20 +00:00
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account.
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</li>
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</ul>
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<p>
|
2013-01-16 14:54:33 -05:00
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Step VIII also shows that the Vitro self-tests ran successfully.
|
2011-12-13 19:05:03 +00:00
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When Tomcat starts the Vitro webapp, it runs several tests.
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If any of these tests produce warnings or error message,
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you would see them instead of the Vitro home page.
|
2011-11-15 22:11:20 +00:00
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</p>
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<p>
|
2011-12-13 19:05:03 +00:00
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Among other things, the self-tests check
|
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<ul>
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<li>The Vitro home directory exists and Vitro can write to it.</li>
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<li>Vitro can connect to the database.</li>
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<li>Vitro can connect to the Solr search application.</li>
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</ul>
|
2011-12-13 19:05:03 +00:00
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If you saw the Vitro home page in Step VII, you know that your installation passed all of these tests.
|
2011-11-15 22:11:20 +00:00
|
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|
</p>
|
2011-12-13 19:05:03 +00:00
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|
2013-01-16 14:54:33 -05:00
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|
<h3 id="termsofuse">XIV. Review the Vitro Terms of Use</h3>
|
2011-11-15 22:11:20 +00:00
|
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|
<p>
|
2011-11-16 17:30:30 +00:00
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|
Vitro comes with a "Terms of Use" statement linked from the footer.
|
2011-11-15 22:11:20 +00:00
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|
The "Site Name" you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
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|
area will be inserted into the "Terms of Use"
|
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statement. If you want to edit the text content more than just the
|
2011-11-16 17:30:30 +00:00
|
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|
"Site Name", the file can be found here:<pre>[vitro_source_dir]/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
Be sure to make the changes in your source files and deploy them to your
|
|
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|
|
tomcat so you don't lose your changes next time you deploy for another reason.
|
|
|
|
|
|
</p>
|
2011-12-16 20:59:56 +00:00
|
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|
<h3>Next Steps</h3>
|
2011-11-15 22:11:20 +00:00
|
|
|
|
<p>
|
2011-12-16 20:59:56 +00:00
|
|
|
|
For more information about Vitro see the <a href="http://vitro.mannlib.cornell.edu/">Vitro public website</a>.
|
|
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|
|
In addition, you may find helpful information in the
|
|
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|
|
<a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">VIVO Site Administrator's Guide</a>.
|
2011-11-16 17:30:30 +00:00
|
|
|
|
</p>
|
|
|
|
|
|
<p>
|
2011-12-16 20:59:56 +00:00
|
|
|
|
Send questions or comments to Vitro developers and designers at <strong>vivo-dev-all@lists.sourceforge.net</strong>.
|
2011-11-16 17:30:30 +00:00
|
|
|
|
</p>
|
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|
<p>
|
2011-11-15 22:11:20 +00:00
|
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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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©2013 All Rights Reserved
|
2011-11-15 22:11:20 +00:00
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</small>
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</p>
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</div>
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</body>
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</html>
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