1088 lines
55 KiB
HTML
1088 lines
55 KiB
HTML
<!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 Release 1 V1.2 Installation 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 V1.2 Installation Guide</h1>
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<small>
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February 16, 2011
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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="#announcement">Release announcement for V1.2</a>
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</li>
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<li>
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<a href="#installation">Installation process for V1.2</a>
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</li>
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</ul>
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</toc>
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<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
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<p>
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The VIVO 1.2 release incorporates major changes throughout the application -
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notably a new templating system to support more versatile page rendering, plus
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improvements to address scalability. The release also features a new personal
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visualization option covering grants as well as publications. The VIVO Harvester
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library has also been significantly improved and expanded in scope for its 1.0
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release through the VIVO SourceForge project at
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<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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<h4>Templating system for page generation, navigation, and theming</h4>
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<p>
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A fresh installation of VIVO 1.2 looks strikingly different, with the introduction
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of a new default theme which takes advantage of the navigation and browse features
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delivered by the templating system. Individual pages now offer inline navigation to
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streamline viewing of expanded personal and organizational profiles, as well as
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improved content layout and organization. New browse controls on the home page and
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menu pages help to provide an immediate overview of the size and range of content
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and quick access down to the individual person, organization, research feature, or
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event.
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</p>
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<h4>Storage model</h4>
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<p>
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While server memory capacity has increased significantly in recent years, VIVO's reliance
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on in-memory caching of RDF data had put limits on the ultimate scalability of VIVO instances
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and potentially increased the cost of servers required to support VIVO.
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</p>
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<p>
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With version 1.2, VIVO has been converted to optionally use Jena's SPARQL database (SDB)
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subsystem. SDB significantly reduces the baseline memory footprint, allowing VIVO installations
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to scale well beyond what has previously been possible.
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</p>
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<h4>New visualizations</h4>
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<p>
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Visualizations of networks of co-authors are now complemented by visualizations of co-investigators
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on grants, with similar interactivity and options for export as images or data.
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</p>
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<h4>Ontology</h4>
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<p>
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VIVO 1.2 includes a new ontology module representing research
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resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
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is aligned with the top-level ontology classes and properties from the
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NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
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</p>
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<h3>Associated VIVO releases</h3>
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<h4>VIVO Harvester</h4>
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<p>
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The Harvester development team is releasing version 1.0 of the VIVO Harvester library shortly
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following the release of VIVO 1.2. The Harvester is an extensible data ingest and updating
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framework with sample configurations for loading PubMed publication, grants, and human resources
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data. Pre-release versions of the Harvester are available at
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<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
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<p>
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This document is a summary of the VIVO installation process. This
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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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<ul>
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<li>
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These instructions assume that you are performing a clean
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install, including emptying an existing database,
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emptying the VIVO home directory, and removing a
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previous installation from the Tomcat webapps directory. Product
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functionality may not be as expected if you install over an existing
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installation of an earlier version.
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</li>
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<li>
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If you are going to upgrade an existing service, please consult
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the "upgrade" files in this directory.
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</li>
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</ul>
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<p>
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VIVO Developers: If you are working on the VIVO source code from
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Subversion, the instructions are slightly different. Please consult
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developers.txt in this directory.
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</p>
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<h3>Where does VIVO live on your computer?</h3>
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<p>
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Before beginning the installation, let's look at the four locations
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on your computer that will hold VIVO.
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</p>
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<h4>The VIVO distribution directory</h4>
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<p>
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This is created when you unpack the VIVO distribution file
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(see <a href="#download_code">Step III</a>, below).
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This is where you will create your deploy.properties file
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(see <a href="#deploy_properties">Step V</a>, below),
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and where you will make any modifications to the VIVO theme or code.
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You can create this wherever you choose.
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</p>
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<h4>VIVO inside Tomcat</h4>
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<p>
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When you run the build script to compile and deploy VIVO
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(see <a href="#deploy">Step VI</a>, below),
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the files will be deployed to a directory inside Tomcat.
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This is the actual executing code for VIVO,
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but you won’t need to look at it or change it.
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If you need to change VIVO,
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make the changes in the distribution directory,
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and run the build script again.
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Tell the build script where to find Tomcat by setting
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<code>tomcat.home</code> in the deploy.properties file
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(see <a href="#deploy_properties">Step V</a>, below).
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</p>
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<h4>The VIVO home directory</h4>
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<p>
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VIVO will use this area to store some of the data it uses.
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Uploaded image files are stored here,
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and the search index is stored here also.
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You can create this wherever you choose.
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Tell VIVO where to find the home directory by setting
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<code>vitro.home.directory</code> in the deploy.properties file
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(see <a href="#deploy_properties">Step V</a>, below).
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You must create this directory before starting VIVO,
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and you must ensure that Tomcat has permission to read and write
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to this 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 VIVO will be
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given to MySQL for storage.
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The actual location of this data depends on what system you have,
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and on how you install MySQL
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(see <a href="#required_software">Step I</a>, below).
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but you won’t need to know the location.
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You will access the data through VIVO,
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or occasionally through the MySQL client application.
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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="#download_code">Download the VIVO Application Source</a>
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</li>
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<li>
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<a href="#triple_store">Choose Triple Store</a>
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</li>
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<li>
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<a href="#deploy_properties">Specify deployment 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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<a href="#tomcat_settings">Set Tomcat JVM parameters and
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security limits</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="#tomcat_connector">Setup Apache Tomcat Connector</a>
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</li>
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<li>
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<a href="#pellet">Configure Pellet Reasoner</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 VIVO</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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</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 VIVO, 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, <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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Apache Ant 1.7 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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</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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<p>
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* Note that VIVO 1.2 will not run on older versions of MySQL that may have worked
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with 1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using unsupported
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versions may result in strange error messages related to table formatting or other
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unexpected problems.
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</p>
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<p>
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* Note that VIVO is not yet compatible with Tomcat 7.
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</p>
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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
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values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
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Most
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of
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the time, the hostname will equal <code>localhost</code>.
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||
</p>
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<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
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<p>
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Grant access to a database user. For example:
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||
</p>
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<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br></pre>
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<p>
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Keep track of the database name, username, and password for Step
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IV.
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||
</p>
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||
<h3 id="download_code">III. Download the VIVO Application Source
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||
<br>
|
||
</h3>
|
||
<p>
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||
Download the VIVO application source as either <code>rel-1.2.zip</code>
|
||
or <code>rel-1.2.gz</code>
|
||
file and unpack it on your web server:
|
||
<br>
|
||
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
|
||
</p>
|
||
<h3 id="triple_store">IV. Choose Triple Store</h3>
|
||
<p>
|
||
VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
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Jena's legacy relational database store (RDB), and Jena's SPARQL database (SDB). RDB was
|
||
used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
|
||
entire RDF model in the server's main memory. The memory available to VIVO limits the
|
||
number of RDF statements that may be stored.
|
||
</p>
|
||
<p>
|
||
SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
|
||
against the underlying database. This allows VIVO installations to display data from large
|
||
RDF models while requiring only a small amount of server memory to run the application.
|
||
There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
|
||
and performance will depend on the configuration parameters of the database server.
|
||
Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
|
||
in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
|
||
generated, though they are generated as soon as data is edited rather than in a background process.
|
||
</p>
|
||
<p>
|
||
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
|
||
a configuration property and redeploying the application, it is important to note that data
|
||
added in one mode will not typically appear in the other. The exception is when a system is
|
||
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
|
||
automatically migrated to SDB.
|
||
</p>
|
||
<h3 id="deploy_properties">V. Specify deployment properties </h3>
|
||
<p>
|
||
At the top level of the VIVO distribution directory,
|
||
copy the file <code>example.deploy.properties</code>
|
||
to a file named simply <code>deploy.properties</code>. This file sets
|
||
several properties used in compilation and deployment.
|
||
</p>
|
||
<p>
|
||
<em>Windows:</em>
|
||
For those installing on Windows operating
|
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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 VIVO</a>.
|
||
</p>
|
||
<table>
|
||
<tbody>
|
||
<tr>
|
||
<th>
|
||
Property Name
|
||
</th>
|
||
<th>
|
||
Example Value
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Default namespace: VIVO 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, VIVO's default namespace must have
|
||
a certain structure and begin with the public web address of the VIVO
|
||
installation. For example, if the web address of a VIVO installation is
|
||
"http://vivo.example.edu/" the default namespace must be set to
|
||
"http://vivo.example.edu/individual/" in order to support linked data.
|
||
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
|
||
default namespace must be set to
|
||
"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with
|
||
"individual/" (including the trailing slash).</h5>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
Vitro.defaultNamespace
|
||
</td>
|
||
<td>
|
||
http://vivo.mydomain.edu/individual/
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Directory where Vitro code is located. In most
|
||
deployments, this is set to ./vitro-core (It is not uncommon for this
|
||
setting to point elsewhere in development environments).
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
vitro.core.dir
|
||
</td>
|
||
<td>
|
||
./vitro-core
|
||
</td>
|
||
</tr>
|
||
<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">
|
||
Name of your VIVO application.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
webapp.name
|
||
</td>
|
||
<td>
|
||
vivo
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Directory where the VIVO application will store the data that it creates.
|
||
This includes uploaded files (usually imageS) and the Lucene search index.
|
||
Be sure this directory exists and is writable by the user who
|
||
the Tomcat service is running as.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
vitro.home.directory
|
||
</td>
|
||
<td>
|
||
/usr/local/vivo/data
|
||
</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>
|
||
vivoAdmin@my.domain.edu
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the JDBC URL of your database. Change
|
||
the end of the URL to reflect your database name (if it is not "vivo").
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.url
|
||
</td>
|
||
<td>
|
||
jdbc:mysql://localhost/vivo
|
||
</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 Jena triple store technology to use.
|
||
SDB is Jena's SPARQL database; this setting allows RDF data to scale
|
||
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
|
||
store with in-memory caching.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.tripleStoreType
|
||
</td>
|
||
<td>
|
||
SDB
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the maximum number of active connections
|
||
in the database connection pool to support the anticipated number of
|
||
concurrent page requests. It is not necessary to adjust this value when
|
||
using the RDB configuration.
|
||
</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 account for
|
||
the VIVO application. This user will have an initial temporary password
|
||
of 'rootPassword'. You will be prompted to create a new password on
|
||
first login.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
rootUser.emailAddress
|
||
</td>
|
||
<td>
|
||
vivoAdmin@my.domain.edu
|
||
</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.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
selfEditing.idMatchingProperty
|
||
</td>
|
||
<td>
|
||
http://vivo.mydomain.edu/ns#networkId
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
The temporal graph visualization can require extensive machine resources.
|
||
This can have a particularly noticable impact on memory usage if
|
||
<ul>
|
||
<li>
|
||
VIVO is configured to use Jena SDB,
|
||
</li>
|
||
<li>
|
||
The organization tree is deep,
|
||
</li>
|
||
<li>
|
||
The number of grants and publications is large.
|
||
</li>
|
||
</ul>
|
||
The VIVO developers are working to make this visualization more efficient.
|
||
In the meantime, VIVO release 1.2 guards against this impact by disabling
|
||
the temporal graph visualization unless the "visualization.temporal" flag
|
||
is set to "enabled". To enable it, uncomment the line for this setting.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
visualization.temporal
|
||
</td>
|
||
<td>
|
||
enabled
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
The temporal graph visualization is used to
|
||
compare different organizations/people within an organization on
|
||
parameters like number of publications or grants. By default, the app
|
||
will attempt to make its best guess at the top level organization in
|
||
your instance. If you're unhappy with this selection, uncomment out the
|
||
property below and set it to the URI of the organization individual you
|
||
want to identify as the top level organization. It will be used as the
|
||
default whenever the temporal graph visualization is rendered without
|
||
being passed an explicit org. For example, to use "Ponce School of
|
||
Medicine" as the top organization:
|
||
<br>
|
||
<span style="font-style: italic;">visualization.topLevelOrg =
|
||
http://vivo.psm.edu/individual/n2862</span>
|
||
<br>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
visualization.topLevelOrg
|
||
</td>
|
||
<td>
|
||
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<h3 id="deploy">VI. Compile and deploy</h3>
|
||
<p>
|
||
At the command line,
|
||
from the top level of the VIVO distribution directory, type:
|
||
</p>
|
||
<pre> ant all<br> </pre>
|
||
<p>
|
||
to build VIVO and deploy to Tomcat's webapps directory.
|
||
</p>
|
||
<h3 id="tomcat_settings">VII. Set Tomcat JVM parameters and security
|
||
limits</h3>
|
||
<p>
|
||
Currently, VIVO copies the contents of your RDF database into
|
||
memory in order to serve Web requests quickly (the in-memory copy and
|
||
the underlying database are kept in synch as edits are performed).
|
||
</p>
|
||
<p>
|
||
VIVO will require more memory than that allocated to Tomcat by
|
||
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>
|
||
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
|
||
<p>
|
||
This sets Tomcat to allocate an initial heap of 2048 megabytes, a
|
||
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
|
||
megabytes is a minimum practical heap size for production installations
|
||
storing data for large academic institutions, and additional heap space
|
||
is preferable. For testing with small sets of data, 256m to 512m should
|
||
be sufficient.
|
||
</p>
|
||
<p>
|
||
If an OutOfMemoryError is encountered during VIVO execution, it can
|
||
be remedied by increasing the heap parameters and restarting Tomcat.
|
||
</p>
|
||
<p>
|
||
Security limits: VIVO is a multithreaded web application that may
|
||
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>
|
||
<h3 id="start_tomcat">VIII. Start Tomcat </h3>
|
||
<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
|
||
browser to "http://localhost:8080/vivo/" to test the application. If
|
||
Tomcat does not start up, or the VIVO application is not visible, check
|
||
the files in Tomcat's logs directory. Error messages are commonly
|
||
found in <code>catalina.out</code> or <code>localhost.log</code>
|
||
</p>
|
||
<h3 id="add_rdf">IX. Log in and add RDF data </h3>
|
||
<p>
|
||
If the startup was successful, you will see a welcome message
|
||
informing you that you have successfully installed VIVO. Click the "Log
|
||
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.
|
||
</p>
|
||
<p>
|
||
After verifying your new password, 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
|
||
options available for each ontology entity. VIVO comes with a core VIVO
|
||
ontology, but you may also upload other ontologies from an RDF file.
|
||
</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>
|
||
<p>
|
||
See more documentation for configuring VIVO, ingesting data, and
|
||
manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
|
||
</p>
|
||
<h3 id="contact_email">X. Set the Contact Email Address (if using
|
||
"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
|
||
add an email address to the VIVO application. This is the email
|
||
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>
|
||
<h3 id="tomcat_connector">XI. Set up Apache Tomcat Connector </h3>
|
||
<p>
|
||
It is recommended that a Tomcat Connector such as mod_jk be used to
|
||
ensure that the site address does not include the port number (e.g.
|
||
8080) and an additional reference to the Tomcat context name (e.g.
|
||
/vivo).
|
||
</p>
|
||
<p>
|
||
This will make VIVO available at "http://example.com" instead of
|
||
"http://example.com:8080/vivo"
|
||
</p>
|
||
<p>
|
||
Using the mod_jk connector allows for communication between Tomcat
|
||
and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick
|
||
Start
|
||
HowTo</a>
|
||
on the Apache site describes the minimum server
|
||
configurations for several popular web servers.
|
||
</p>
|
||
<p>
|
||
After setting up the mod_jk connector above, you will need to
|
||
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
|
||
to
|
||
respond
|
||
to requests from Apache via the connector. Look for the
|
||
<connector> directive and add the following properties:
|
||
</p>
|
||
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000" <br> </pre>
|
||
<p>
|
||
Note: the value for maxThreads (320) is equal to the value for
|
||
MaxClients in the apache's <code>httpd.conf</code>
|
||
file.
|
||
</p>
|
||
<p>
|
||
Locate the <code><Host name="localhost"...></code>
|
||
directive
|
||
and update as follows:
|
||
</p>
|
||
<pre>
|
||
<Host name="localhost" appBase="webapps"<br>
|
||
DeployOnStartup="false"<br>
|
||
unpackWARs="true" autoDeploy="false"<br>
|
||
xmlValidation="false" xmlNamespaceAware="false"><br> <br>
|
||
<Alias>example.com</Alias><br>
|
||
<Context path=""<br>
|
||
docBase="/usr/local/tomcat/webapps/vivo"<br>
|
||
reloadable="true"<br>
|
||
cookies="true" ><br>
|
||
<Manager pathname="" /><br>
|
||
<Environment type="java.lang.String" override="false" <br>
|
||
name="path.configuration" <br>
|
||
value="deploy.properties"<br>
|
||
/><br>
|
||
</Context><br>
|
||
...
|
||
</pre>
|
||
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
|
||
<p>
|
||
This optional configuration step is only applicable to VIVO installations
|
||
running in RDB mode (See section <a href="triple_store">Choose Triple Store</a>
|
||
for details).
|
||
VIVO uses the Pellet engine to perform reasoning, which runs in the
|
||
background at startup and also when the knowledge base is edited. VIVO
|
||
continues serving pages while the reasoner continues working; when the
|
||
reasoner finishes, the new inferences appear. Inferred statements are
|
||
cached in a database graph so that they are available immediately when
|
||
VIVO is restarted.
|
||
</p>
|
||
<p>
|
||
By default, Pellet is fed only an incomplete view of your ontology
|
||
and only certain inferences are materialized. These include rdf:type,
|
||
rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode
|
||
is typically suitable for ontologies with a lot of instance data. If
|
||
you would like to keep the default mode, skip to the next step.
|
||
</p>
|
||
<p>
|
||
To enable "complete" OWL inference (materialize all significant
|
||
entailed statements), open "vitro-core/webapp/config/web.xml" and
|
||
search for PelletReasonerSetup.
|
||
</p>
|
||
<p>
|
||
Then change the name of the listener class to
|
||
PelletReasonerSetupComplete. Because "complete" reasoning can be very
|
||
resource intensive, there is also an option to materialize nearly all
|
||
inferences except owl:sameAs and owl:differentFrom.
|
||
</p>
|
||
<p>
|
||
This is enabled by specifying PelletReasonerSetupPseudocomplete.
|
||
For ontologies with large numbers of individuals, this mode can offer
|
||
enormous performance improvements over the "complete" mode.
|
||
</p>
|
||
<p>
|
||
Finally, a class called
|
||
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
|
||
improve performance on ontologies with large literals where data
|
||
property entailments are not needed.
|
||
</p>
|
||
<h3 id="external_auth">XIII. Using an External Authentication System
|
||
with VIVO </h3>
|
||
<p>
|
||
</p>
|
||
<p>
|
||
VIVO can be configured to work with an external authentication
|
||
system like Shibboleth or CUWebAuth.
|
||
</p>
|
||
<p>
|
||
VIVO must be accessible only through an Apache HTTP server. The
|
||
Apache server will be configured to invoke the external authentication
|
||
system. When the user completes the authentication, the Apache server
|
||
will pass a network ID to VIVO, to identify the user.
|
||
</p>
|
||
<p>
|
||
If VIVO has an account for that user, the user will be logged in
|
||
with the privileges of that account. In the absence of an account, VIVO
|
||
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
|
||
configured to secure a page in VIVO. When a user reaches this secured
|
||
page, the Apache server will invoke the external authentication system.
|
||
</p>
|
||
<p>
|
||
For VIVO, this secured page is named: <code>/loginExternalAuthReturn</code>
|
||
</p>
|
||
<p>
|
||
When your instructions call for the location of the secured page,
|
||
this is the value you should use.
|
||
</p>
|
||
<h4>Configuring VIVO</h4>
|
||
<p>
|
||
To enable external authentication, VIVO requires three values in
|
||
the <code>deploy.properties</code>
|
||
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>
|
||
You need to tell VIVO the name of that HTTP header. Insert a
|
||
line like this in the deploy.properties file:
|
||
</p>
|
||
<pre>externalAuth.netIdHeaderName = [the header name]</pre>
|
||
<p>
|
||
For example:
|
||
</p>
|
||
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
|
||
</li>
|
||
<li>
|
||
<h5>The text for the Login button.</h5>
|
||
To start the authentication process, the user will click on a button in
|
||
the VIVO login form. You need to tell VIVO what text should appear in
|
||
that button.
|
||
<p>
|
||
Put a line like this in the deploy.properties file:
|
||
externalAuth.buttonText = [the text for your login button] For example:
|
||
</p>
|
||
<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
|
||
<p>
|
||
The VIVO login form will display a button labelled "Log in using
|
||
BearCat Shibboleth".
|
||
</p>
|
||
</li>
|
||
<li>
|
||
<h5>Associating a User with a profile page.</h5>
|
||
<p>
|
||
If VIVO has an account for the user, the user will be given the
|
||
privileges assigned to that account.
|
||
</p>
|
||
<p>
|
||
In addition, VIVO will try to associate the user with a profile
|
||
page, so the user may edit his own profile data. VIVO will search the
|
||
data model for a person with a property that matches the User’s network
|
||
ID
|
||
(the value of the property must be either a String literal or an untyped literal).
|
||
You need to tell VIVO what property should be used for matching.
|
||
Insert a line like this in the deploy.properties file:
|
||
</p>
|
||
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
|
||
<p>
|
||
For example:
|
||
</p>
|
||
<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
|
||
</li>
|
||
</ul>
|
||
<h3 id="installation_check">XIV. Was the installation successful? </h3>
|
||
<p>
|
||
If you have completed the previous steps, you have good indications
|
||
that the installation was successful.
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Step VII showed that Tomcat recognized the webapp, and that the
|
||
webapp was able to present the initial page.
|
||
</li>
|
||
<li>
|
||
Step VIII verified that you can log in to the administrator
|
||
account.
|
||
</li>
|
||
</ul>
|
||
<p>
|
||
Here is a simple test to see whether the ontology files were
|
||
loaded:
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Click on the "Index" link on the upper right, below the logo.
|
||
You should see a "locations" section, with links for "Country" and
|
||
"Geographic Location." The index is built in a background thread, so on
|
||
your first login, you may see an empty index instead. Refresh the page
|
||
periodically to see whether the index will be populated. This may take
|
||
some time: with VIVO installed on a modest laptop computer, loading the
|
||
ontology files and building the index took more than 5 minutes from the
|
||
time that Tomcat was started.
|
||
</li>
|
||
<li>
|
||
Click on the "Country" link. You should see an alphabetical list
|
||
of the countries of the world.
|
||
</li>
|
||
</ul>
|
||
<p>
|
||
Here is a test to see whether your system is configured to serve
|
||
linked data:
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Point your browser to the home page of your website, and click
|
||
the "Log in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
|
||
you set up in Step IV. If this is your first time logging in,
|
||
you will be prompted to change the password.
|
||
</li>
|
||
<li>
|
||
After you have successfully logged in, click "site admin" in the
|
||
upper right corner. In the drop down under "Data Input" select "Faculty
|
||
Member(core)" and click the "Add individual of this class" button.
|
||
</li>
|
||
<li>
|
||
Enter the name "test individual" under the field "Individual
|
||
Name," scroll to the bottom, and click "Create New Record." You will be
|
||
taken to the "Individual Control Panel." Make note of the value of the
|
||
field "URI" - it will be used in the next step.
|
||
</li>
|
||
<li>
|
||
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
|
||
In
|
||
the
|
||
pink box on that page enter the URI of the individual you
|
||
created in the previous step and click "open."
|
||
</li>
|
||
<li>
|
||
In the resulting page search for the URI of the "test
|
||
individual." You should find it towards the bottom of the page next to
|
||
a red dot followed by "redirect (303)." This indicates that you are
|
||
successfully serving linked RDF data. If the URI of the "test
|
||
individual" is followed by "failed (400)" you are not successfully
|
||
serving linked data.
|
||
</li>
|
||
</ul>
|
||
<p>
|
||
Finally, test the search index.
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Type the word "Australia" into the search box, and click on the
|
||
Search button.You should see a page of results, with links to countries
|
||
that border Australia, individuals that include Australia, and to
|
||
Australia itself. To trigger the search index, you can log in as a site
|
||
administrator and go to "http://your-vivo-url/SearchIndex".
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
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|
||
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|
||
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|
||
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|
||
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|
||
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
||
</small>
|
||
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|
||
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|
||
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|
||
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|
||
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|
||
<li role="listitem">
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|
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</li>
|
||
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|
||
<a href="http://vivoweb.org/contact">Contact Us</a>
|
||
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|
||
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|
||
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|
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