957 lines
48 KiB
HTML
957 lines
48 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</title>
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<link rel="stylesheet" href="./css/doc.css" />
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</head>
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<body>
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<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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January 28, 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
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application - notably a new templating system to support more flexible
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display and navigation, plus improvements to address scalability. The
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release also features two new visualization options: temporal graphing
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for organizations, and personal visualizations extended to cover grants
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as well as publications. The VIVO Harvester library has also been
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significantly improved and expanded in scope for its 1.0 release
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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 new installation of VIVO 1.2 looks strikingly different, with a
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new navigation and browse interface as well as a more modular page
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design that is easier to customize and brand for your local
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institution. Page displays now support inline navigation to streamline
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viewing of expanded personal and organizational profiles, as well as
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improved graphic layout and organization. New browsing controls on the
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home page and each menu page include interactive visual controls to
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provide an immediate overview of the size and range of content and
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quick access down to the individual person, organization, research
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feature, or event. VIVO's navigation has also been completely
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overhauled.
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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
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years, VIVO's reliance on in-memory caching of RDF data had put limits
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on the ultimate scalability of VIVO instances and potentially increased
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the cost of servers required to support VIVO.
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<br>
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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
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SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
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memory footprint, allowing VIVO installations to scale well beyond what
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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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VIVO continues to expand visualization options including all-new
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user-configurable temporal comparisons of publications and grants,
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grouped by organization or by affiliated person. Visualizations of
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networks of co-authors are now complemented by visualizations of
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co-investigators on grants, with a similar interactivity and options
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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
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Harvester library, an extensible data ingest and updating framework
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with sample configurations for loading PubMed publication, grants, and
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human resources data. The Harvester is 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 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.txt 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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<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="#data_storage">SDB vs RDB</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 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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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 setup the environment variables for <code 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 web sites.
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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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<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>
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</h3>
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<p>
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Download the VIVO application source as either <code>rel-1.2.zip</code>
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or <code>rel-1.2.gz</code>
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file and unpack it on your web server:
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<br>
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<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
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</p>
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<h3 id="data_storage">IV. SDB vs RDB (title)</h3>
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<p>
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Content from Brian Lowe coming.
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</p>
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<h3 id="deploy_properties">V. Specify deployment properties </h3>
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<p>
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At the top level of the unpacked distribution, copy the file <code>example.deploy.properties</code>
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to a file named simply <code>deploy.properties</code>. This file sets
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several properties used in compilation and deployment.
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</p>
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<p>
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<em>Windows:</em>
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For those installing on Windows operating
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system, include the windows drive and use the forward slash "/" and not
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the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
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</p>
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<p>
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<em>External authentication:</em>
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If you want to use an external
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authentication system like Shibboleth or CUWebAuth, you will need to
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set two additional properties in this file. See the section below
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entitled <a href="#external_auth">Using an External Authentication
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System with VIVO</a>.
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</p>
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<table>
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<tbody>
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<tr>
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<th>
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Property Name
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</th>
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<th>
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Example Value
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</th>
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</tr>
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<tr>
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<td colspan="2">
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Default namespace: VIVO installations make their
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RDF resources available for harvest using linked data. Requests for RDF
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resource URIs redirect to HTML or RDF representations as specified by
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the client. To make this possible, VIVO's default namespace must have
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certain structure and begin with the public web address of the VIVO
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installation. For example, if the web address of a VIVO installation is
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"http://vivo.example.edu/" the default namespace must be set to
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"http://vivo.example.edu/individual/" in order to support linked data.
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Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
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default namespace must be set to
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"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with "individual/" (including the
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trailing slash).</h5>
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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Vitro.defaultNamespace
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</td>
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<td>
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http://vivo.mydomain.edu/individual/
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where Vitro code is located. In most
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deployments, this is set to ./vitro-core (It is not uncommon for this
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setting to point elsewhere in development environments).
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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vitro.core.dir
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</td>
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<td>
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./vitro-core
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where tomcat is installed.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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tomcat.home
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</td>
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<td>
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/usr/local/tomcat
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Name of your VIVO application.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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webapp.name
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</td>
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<td>
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vivo
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where uploaded files will be stored.
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Be sure this directory exists and is writable by the user that
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the Tomcat service is running as.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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upload.directory
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</td>
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<td>
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/usr/local/vivo/data/uploads
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where the Lucene search index will be
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built. Be sure this directory exists and is writable by the user that
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the Tomcat service is running as.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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LuceneSetup.indexDir
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</td>
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<td>
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/usr/local/vivo/data/luceneIndex
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify an SMTP host that the form will use for
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sending e-mail (Optional). If this is left blank, the contact form will
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be hidden and disabled.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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Vitro.smtpHost
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</td>
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<td>
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smtp.servername.edu
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify the JDBC URL of your database. Change
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the end of theURL to reflect your database name (if it is not "vivo").
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.url
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</td>
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<td>
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jdbc:mysql://localhost/vivo
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Change the username to match the authorized user
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you created in MySQL.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.username
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</td>
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<td>
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username
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Change the password to match the password you
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created in MySQL.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.password
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</td>
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<td>
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password
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify the Jena triple store technology to use.
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SDB is Jena's SPARQL database; this setting allows RDF data to scale
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beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
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store with in-memory caching.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.tripleStoreType
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</td>
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<td>
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SDB
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify the maximum number of active connections
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in the database connection pool to support the anticipated number of
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concurrent page requests. It is not necessary to adjust this value when
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using the RDB configuration.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.pool.maxActive
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</td>
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<td>
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40
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify the maximum number of database
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connections that will be allowed to remain idle in the connection pool.
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Default is 25% of the maximum number of active connections.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.pool.maxIdle
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</td>
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<td>
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10
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Change the dbtype setting to use a database
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other than MySQL. Otherwise, leave this value unchanged. Possible
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values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
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SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
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for additional information.
|
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</td>
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</tr>
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<tr class="odd_row">
|
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<td>
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VitroConnection.DataSource.dbtype
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</td>
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<td>
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MySQL
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify a driver class name to use a database
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other than MySQL. Otherwise, leave this value unchanged. This JAR file
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for this driver must be added to the the webapp/lib directory within
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the vitro.core.dir specified above.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.driver
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</td>
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<td>
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com.mysql.jdbc.Driver
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Change the validation query used to test
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database connections only if necessary to use a database other than
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MySQL. Otherwise, leave this value unchanged.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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VitroConnection.DataSource.validationQuery
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</td>
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<td>
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SELECT 1
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Specify the name of your first admin user for
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the VIVO application. This user will have an initial temporary password
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of 'defaultAdmin'. You will be prompted to create a new password on
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first login.
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</td>
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</tr>
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||
<tr class="odd_row">
|
||
<td>
|
||
initialAdminUser
|
||
</td>
|
||
<td>
|
||
defaultAdmin
|
||
</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 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 unpacked
|
||
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 databaseare 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.
|
||
<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 <code>catalina.out</code>
|
||
file in Tomcat's logs directory.
|
||
</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>initialAdminUser</code>
|
||
username you set up in Step IV. The initial password for the <code>initialAdminUser</code>
|
||
account is "defaultAdmin" (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 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 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>Vitro.smtpHost</code>), you will also need to
|
||
add an email address to the VIVO application. This is the email
|
||
that the contact form submits to. 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>Vitro.smtpHost</code>
|
||
in Step IV and do NOT
|
||
provide an email addressin 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> ...<br> </pre>
|
||
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
|
||
<p>
|
||
<em>Do we need this section still? - elly</em>
|
||
</p>
|
||
<p>
|
||
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>
|
||
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>
|
||
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>
|
||
For example:<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>
|
||
The VIVO login form will display a button labelled "Log in using
|
||
BearCat Shibboleth".
|
||
</li>
|
||
<li>
|
||
<h5>Associating a User with a profile page</h5>
|
||
If VIVO has an account for the user, the user will be given the
|
||
privileges assigned to that account.
|
||
<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. 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>
|
||
For example:<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>initialAdminUser</code>
|
||
username 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>
|
||
<!-- #wrapper-content -->
|
||
<div role="contentinfo">
|
||
<p class="copyright">
|
||
<small>
|
||
©2011
|
||
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
||
</small>
|
||
| Powered
|
||
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
||
</p>
|
||
<nav role="navigation">
|
||
<ul id="footer-nav" role="list">
|
||
<li role="listitem">
|
||
<a href="http://vivoweb.org/about">About</a>
|
||
</li>
|
||
<li role="listitem">
|
||
<a href="http://vivoweb.org/contact">Contact Us</a>
|
||
</li>
|
||
<li role="listitem">
|
||
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
|
||
</li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</body>
|
||
</html>
|