815 lines
40 KiB
HTML
815 lines
40 KiB
HTML
<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.4 Upgrade Guide</title>
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<link rel="stylesheet" href="./css/doc.css" media="screen">
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</head>
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<body>
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<div id="branding" role="banner">
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<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
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</div>
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V1.4 Upgrade Guide</h1>
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<small>
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December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4
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</small>
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<p>
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This document contains instructions on how to upgrade your
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installation of VIVO from Version 1.3 to Version 1.4.
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This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
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at <a href="http://vivoweb.org/">VIVOweb.org</a>
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</p>
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<p>
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If you need to do a fresh install, please consult the VIVO Release V1.4 Installation
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Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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or the install.html file located in the <code>doc</code>
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directory of the VIVO source code distribution. The installation document also has a
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list of the required software and versions (there are no new hardware
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or software requirements for V1.4).
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</p>
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<p>
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For a description of the release contents see the <a href="./release.html">Release announcement for V1.4</a>.
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</p>
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<hr/>
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<!-- Upgrade process for V1.4 --><h3 id="tableofcontents">Table of Contents</h3>
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<toc>
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<ol class="roman2">
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<li>
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<a href="#preparation">Before Performing the Upgrade</a>
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</li>
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<li>
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<a href="#changes">Noteworthy Changes</a>
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<br>
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<ol class="roman2">
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<li>
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<a href="#newproperty">New Property in deploy.properties</a>
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</li>
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<li>
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<a href="#changetoconfig">Change to tomcat configuration</a>
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</li>
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</ol>
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</li>
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<li>
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<a href="#upgrade_process">Upgrade Instructions</a>
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</li>
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<li>
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<a href="#kbm">Knowledge Base Migration</a>
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<ol class="roman3">
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<li>
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<a href="#verifymigration">Knowledge Base Migration Process</a>
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</li>
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<li>
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<a href="#reviewkbm">Knowledge Base Manual Review for Local Extensions</a>
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</li>
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</ol>
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</li>
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<li>
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<a href="#termsofuse">Review the VIVO Terms of Use</a>
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</li>
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<li>
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<a href="#nextsteps">Next Steps</a>
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</li>
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</ol>
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</toc>
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<hr/>
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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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<br/>
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Create backups of:
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<ul style="list-style-type: square;">
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<li>
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The VIVO distribution directory (which contains the source for VIVO 1.3)
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</li>
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<li>
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The VIVO home directory (pointed to by your deploy.properties file)
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</li>
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<li>
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The webapps directory in Tomcat
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</li>
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<li>
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MySQL database (most people use mysqldump to create the backup)
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</li>
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</ul>
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<p>
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The upgrade process is similar to the initial install process
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with
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the following exceptions:
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</p>
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<ul>
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<li>
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You do not need to reinstall MySQL or recreate the MySQL database. Please
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backup your MySQL database as noted above.
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</li>
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<li>
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First-time login of the root account after the upgrade
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process is complete will use the password previously set (not the
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default password used on the first login after the initial
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installation.)
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</li>
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<li>
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The first time Apache Tomcat starts up after the upgrade, an automated
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process will modify the knowledge base to align the
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data with any ontology updates made for the new release. See the section on the <a href="#kbm">Knowledge Base Migration</a>
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below for more information.
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</li>
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</ul>
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<h3 id="changes">II. Noteworthy Changes</h3>
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<ul>
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<li>
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<h4 id="newproperty">New property in deploy.properties</h4>
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<p>
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<code>proxy.eligibleTypeList</code> describes which classes of Individuals are
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eligible for "self-editing" by proxy.
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See the table in <a href="#upgrade_process">Section III</a> for more details.
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</p>
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</li>
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<li>
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<h4 id="changetoconfig">Change to Tomcat configuration</h4>
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<p>
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In order for VIVO to correctly handle international characters,
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you must configure Tomcat to conform to the URI standard by
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accepting percent-encoded UTF-8.
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</p>
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<p>
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Edit Tomcat's conf/server.xml and add the following attribute to each of the
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Connector elements: URIEncoding="UTF-8".
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</p>
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<pre>
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<Server ...>
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<Service ...>
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<Connector ... URIEncoding="UTF-8"/>
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...
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</Connector>
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</Service>
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</Server>
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</pre>
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</li>
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</ul>
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<h3 id="upgrade_process">III. Upgrade Instructions</h3>
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<p>
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1. Download the new distribution file and unpack it into a new
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source directory.
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</p>
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<p>
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2. Create a new deploy.properties using the same settings as in
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your previous installation and set values for the new variables as described
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below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
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vitro.home.directory, email.smptHost, email.replyTo,
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rootUser.emailAddress)
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<br>
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</p>
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<p>
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<!-- deploy.properties table from install.html -->
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</p>
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<table border='1' bordercolor="#CCCCCC" cellspacing="5">
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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 a
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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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URL of Solr context used in local VIVO search.
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Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
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In the standard installation, the Solr context will be on the same
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server as VIVO, and in the same Tomcat instance. The path will be the
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VIVO webapp.name (specified above) + "solr"
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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.local.solr.url
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</td>
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<td>
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http://localhost:8080/vivosolr
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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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Restricts access to the Solr search platform.
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One or more regular expressions, separated by commas. When a request is
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made to Solr, the IP address of the requestor must match one of the
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patterns, or the request will be rejected.
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<br>
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Examples:<code>
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<ul>
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<li>
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vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
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</li>
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<li>
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vitro.local.solr.ipaddress.mask =
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127\.0\.0\.1,0:0:0:0:0:0:0:1
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</li>
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<li>
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vitro.local.solr.ipaddress.mask = 169.254.*
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</li>
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</ul>
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</code>
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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.local.solr.ipaddress.mask
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</td>
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<td>
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127\.0\.0\.1,0:0:0:0:0:0:0:1
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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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Directory where the VIVO application will store
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the data that it creates. This includes uploaded files (usually images)
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and the Solr search index. Be sure this directory exists and is
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writable by the user who 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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vitro.home.directory
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</td>
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<td>
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/usr/local/vivo/data
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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 application will
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use for sending e-mail (Optional). If this is left blank, the contact
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form will be hidden and disabled, and users will not be notified of
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changes to their accounts.
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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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email.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 an email address which will appear as
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the sender in e-mail notifications to users (Optional). If a user
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replies to the notification, this address will receive the reply. If a
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user's e-mail address is invalid, this address will receive the error
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notice. If this is left blank, users will not be notified of changes to
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their accounts.
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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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email.replyTo
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</td>
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<td>
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vivoAdmin@my.domain.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 the URL 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 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.
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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 email address of the root user
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account for the VIVO application. This user will have an initial
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temporary password of 'rootPassword'. You will be prompted to create a
|
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new password on first login.
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<p>
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NOTE: The root user account has access to all data and all
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operations in VIVO. Data views may be surprising when logged in as the
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root user. It is best to create a Site Admin account to use for every
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day administrative tasks.
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</p>
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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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rootUser.emailAddress
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</td>
|
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<td>
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|
vivoAdmin@my.domain.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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The URI of a property that can be used to
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associate an Individual with a user account. When a user logs in with a
|
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name that matches the value of this property, the user will be
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authorized to edit that Individual
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(the value of the property must be either a String literal or an untyped literal).
|
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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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selfEditing.idMatchingProperty
|
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</td>
|
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<td>
|
|
http://vivo.mydomain.edu/ns#networkId
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
If an external authentication system like Shibboleth or CUWebAuth is to be
|
|
used, these properties say how the login button should be labeled, and which
|
|
HTTP header will contain the user ID from the authentication system. If such
|
|
a system is not to be used, leave these commented out. Consult the installation
|
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instructions for more details.
|
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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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externalAuth.buttonText
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<br/>
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externalAuth.netIdHeaderName
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</td>
|
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<td>
|
|
Log in using BearCat Shibboleth
|
|
<br/>
|
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remote_userID
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</td>
|
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</tr>
|
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<tr>
|
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<td colspan="2">
|
|
The temporal graph visualization can require
|
|
extensive machine resources. This can have a particularly noticable
|
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impact on memory usage if
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<ul>
|
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<li>
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The organization tree is deep,
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</li>
|
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<li>
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The number of grants and publications is large.
|
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</li>
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</ul>
|
|
VIVO V1.4 mitigates this problem by the way of a caching
|
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mechanism and hence we can safely set this to be enabled by default.
|
|
</td>
|
|
</tr>
|
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<tr class="odd_row">
|
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<td>
|
|
visualization.temporal
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</td>
|
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<td>
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enabled
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</td>
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</tr>
|
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<tr>
|
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<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>
|
|
<code>visualization.topLevelOrg =
|
|
http://vivo.psm.edu/individual/n2862</code>
|
|
<br>
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
visualization.topLevelOrg
|
|
</td>
|
|
<td>
|
|
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
An absolute file path, pointing to the root directory of the Harvester utility.
|
|
You must include the final slash.
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row">
|
|
<td>
|
|
harvester.location
|
|
</td>
|
|
<td>
|
|
/usr/local/vivo/harvester/
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td colspan="2">
|
|
Types of individual for which we can create proxy editors.
|
|
If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
|
|
</td>
|
|
</tr>
|
|
<tr class="odd_row blue">
|
|
<td>
|
|
proxy.eligibleTypeList
|
|
</td>
|
|
<td>
|
|
http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
|
|
<p>
|
|
3. Apply any previous changes you have made to the new source
|
|
directory.
|
|
</p>
|
|
<blockquote>
|
|
<strong>Special notes regarding source files</strong>
|
|
<ul>
|
|
<li>
|
|
This process assumes any changes made to the application
|
|
were
|
|
made in the source directory and deployed, and were not made directly
|
|
within the Tomcat webapps directory.
|
|
</li>
|
|
<li>
|
|
In many cases, simply copying the modified files from your
|
|
original source directory will not work since the files on which they
|
|
are based have changed. It will be necessary to inspect the new source
|
|
files and add any changes to them at that time.
|
|
</li>
|
|
<li>
|
|
NIH-funded VIVO implementations will need to apply the
|
|
Google
|
|
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
|
in
|
|
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
|
A sample <code>googleAnalytics.ftl</code>
|
|
is included in the built-in
|
|
theme. This file serves only as an example, and you must replace the
|
|
tracking code shown with your institution's own tracking code. For
|
|
additional information about the GATC for the NIH-funded VIVO
|
|
implementation sites and a copy of your institution's tracking code,
|
|
see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
|
Google
|
|
Analytics
|
|
wiki
|
|
page</a>.
|
|
</li>
|
|
</ul>
|
|
</blockquote>
|
|
<p>
|
|
5. Stop Apache Tomcat and from your VIVO source directory, run
|
|
ant
|
|
by typing: <code>ant all</code>
|
|
</p>
|
|
<p>
|
|
6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is
|
|
completed. Depending on the size of your database, the migration process may
|
|
take up to several hours. When it is complete, you will
|
|
see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
|
|
</p>
|
|
<p>
|
|
7. As root or an administrator, request a rebuild of the Solr search index:
|
|
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
|
|
heading "Refresh Content".
|
|
</p>
|
|
<p>
|
|
8. Review and save aside the knowledge base migration logs.
|
|
The knowledge base migration process described in the next section will generate logs.
|
|
These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since
|
|
they may be a useful reference if questions come up about your 1.4 VIVO data after deployment, you should save them aside.
|
|
The logs are created in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log</code>
|
|
</dt>
|
|
<dd>
|
|
A log of a summary of updates that were made to the knowledge
|
|
base. This file should end with "Finished knowledge base migration".
|
|
If this file contains any warnings they should be reviewed with your
|
|
implementation team representative to see whether any corrective action needs to be taken.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
|
|
</dt>
|
|
<dd>
|
|
A log of errors that were encountered during the upgrade
|
|
process. This file should be empty if the upgrade was successful. If any errors are encountered
|
|
you will need to rerun the knowledge base migration.
|
|
</dd>
|
|
</dl>
|
|
|
|
<h3 id="kbm">IV. Knowledge Base Migration</h3>
|
|
<h4 id="kbmprocess">i.Knowledge Base Migration Process</h4>
|
|
<p>
|
|
For an description of changes to the VIVO ontology in version 1.4 see the <a href="https://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology_changes_from_version_1.3_to_1.4">sourceforge wiki page on ontology changes</a>
|
|
</p>
|
|
<p>
|
|
Changes to the VIVO core ontology may require corresponding
|
|
modifications to the knowledge base instance data and ontology annotations.
|
|
When VIVO first starts up following the upgrade, it will
|
|
initiate a process to examine the knowledge base and apply necessary
|
|
changes. The knowledge base migration process will make the following types of changes:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
Class or Property renaming
|
|
</dt>
|
|
<dd>
|
|
All references to the class (in the subject or object
|
|
position) will be updated to the new name. References to the property will be
|
|
updated to the new name.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Class or Property deletion
|
|
</dt>
|
|
<dd>
|
|
All type assertions of a deleted class will be removed.
|
|
<br>
|
|
All statements using a deleted property will be changed to use the
|
|
nearest available superproperty. If there is no available superproperty
|
|
then the statement will be deleted from the knowledge base. Note that
|
|
all removed and added data is recorded in the files in the changedData
|
|
directory.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Annotation property default values
|
|
</dt>
|
|
<dd>
|
|
If a site has modified the value of a vitro annotation (such
|
|
as
|
|
displayRankAnnot or displayLimitAnnot) so that it is no longer using
|
|
the default, then that setting will be left unchanged.
|
|
<br>
|
|
If a site is using the default value of a vitro annotation, and the
|
|
default has been changed in the new version of the ontology, then the
|
|
new default value will be propagated to the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
Structural changes
|
|
</dt>
|
|
<dd>
|
|
Changes in the way individuals (intances of classes) are related to other individuals.
|
|
</dd>
|
|
</dl>
|
|
<p>
|
|
In addition to the logs described in <strong>step 8</strong> of the <a href="#upgrade_process">previous section</a>, the knowledge base migration
|
|
process will log copies of all additions and deletions that were made to the knowledge base in the following files:
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were removed from the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<dl>
|
|
<dt>
|
|
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3</code>
|
|
</dt>
|
|
<dd>
|
|
An N3 file containing all the statements that were added to the knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<h4 id="reviewkbm">ii. Knowledge Base Manual Review for Local Extensions</h4>
|
|
Not all of the modifications that may be required are
|
|
automated. If you have local extensions to areas of the ontology that have changed, a manual review of the knowledge base is recommended after
|
|
the automated upgrade process.
|
|
<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
|
|
<p>
|
|
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
|
|
you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
|
area will be
|
|
inserted into the "Terms of Use" statement. If you want to edit the text content more than just
|
|
the "Site Name", the file can be found here:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
|
|
Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose
|
|
your changes next time you deploy for another reason.
|
|
</p>
|
|
<h3 id="nextsteps">Next Steps</h3>
|
|
<p>
|
|
Now that you have VIVO up and running, please refer to the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>
|
|
for information about its operation.
|
|
</p>
|
|
</div>
|
|
|
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<small>
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