776 lines
33 KiB
HTML
776 lines
33 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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<header 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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</header>
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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 Upgrade Guide</h1>
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<small>
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January 28, 2011 - Upgrading from Release 1 v1.1 to Release 1 v1.2
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</small>
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<blockquote>
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<b>Missing pieces and fixes</b>
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<ul>
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<li>
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Link to install pdf online at SF
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</li>
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<li>
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Add config table from install d/t so many new vars.
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</li>
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<li>
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</li>
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</ul>
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</blockquote>
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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="#upgrade">Upgrade process for V1.2</a>
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</li>
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</ul>
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</toc>
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<p>
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This document provides a short description of the steps involved in upgrading your
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installation of VIVO from Release 1, Version 1.1 to Version 1.2. This and other
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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 <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1 v1.2 Installation Guide</a>
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or the install.html file located in the <code>doc</code>
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directoy of the VIVO source code distribution.
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</p>
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<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
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<p>
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Text from the wiki page
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</p>
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<!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
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</p>
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<toc>
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<ol class="roman1">
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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="#upgrade_process">The Upgrade Process</a>
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</li>
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<li>
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<a href="#ontology">Ontology Upgrade</a>
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<ol class="roman2">
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<li>
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<a href="#verify_ontology_upgrade">Verify Ontology upgrade process</a>
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</li>
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<li>
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<a href="#ontology_knowledge_base">Ontology knowledge base manual review</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="#fileSystem">File Storage System Upgrade</a>
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<ol class="roman2">
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<li>
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<a href="#verify_ontology_upgrade">Changes to the File Storage System</a>
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</li>
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<li>
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<a href="#verify_ontology_upgrade">Verify File Storage System upgrade process</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="#theme">Theme Modifications</a>
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</li>
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</ol>
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</toc>
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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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<p>
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Please ensure that backups are created of the:
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</p>
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<ul style="list-style-type:square;">
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<li>
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Tomcat webapps directory
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</li>
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<li>
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Original source directory
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</li>
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<li>
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MySQL database (mysqldump)
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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 original install process with the following
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EXCEPTIONS:
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</p>
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<ul>
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<li>
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DO NOT reinstall MySQL or recreate the MySQL database. Please ensure that
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you back-up the MySQL database.
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</li>
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<li>
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It is not necessary to add RDF data.
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</li>
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<li>
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First-time login of the administrator 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 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, it will
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initiate a process that modifies the knowledge base to align the data
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with the revised ontology. See the section on the <a href="ontology">Ontology Upgrade</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="upgrade_process">The Upgrade Process</h3>
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<p>
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1. Download the new distribution file and unpack it into a new source
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directory.
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</p>
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<p>
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2. Create deploy.properties, using the same values as in your previous
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installation and set values for the new variables. The following table
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shows the default properties for deploy.properties with new V1.2 properties in
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<span class="blue">blue</span>.
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<!-- deploy.properties table from install.html -->
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<table>
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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 RDF resources available
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for harvest using linked data. Requests for RDF resource URIs redirect to HTML
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or RDF representations as specified by the client. To make this possible,
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VIVO's default namespace must have certain structure and begin with the public
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web address of the VIVO installation. For example, if the web address of a VIVO
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installation is "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. Similarly,
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if VIVO is installed at "http://www.example.edu/vivo" the default namespace must be
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set to "http://www.example.edu/vivo/individual/"
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<h4>* The namespace must end with "individual/" (including the trailing slash).</h4>
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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 deployments, this is set to
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./vitro-core, but it commonly points elsewhere during development.
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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. You must create this directory ahead of time.
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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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<td colspan="2">
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Directory where the Lucene search index will be built. Depending on your
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permissions and who Tomcat is running as, you may need to create this directory
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ahead of time.
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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 sending e-mail (Optional). If
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this is left blank, the contact form will 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 the end of theURL to reflect
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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 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 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. SDB is Jena's
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SPARQL database; this setting allows RDF data to scale beyond the
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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 blue">
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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 in the database
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connection pool to support the anticipated number of concurrent
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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 blue">
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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 connections that will be
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allowed to remain idle in the connection pool. Default is
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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 blue">
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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 other than MySQL.
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Otherwise, leave this value unchanged.
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Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle,
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PostgreSQL, and SQLServer.
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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 blue">
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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 other than MySQL.
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Otherwise, leave this value unchanged.
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This JAR file for this driver must be added to the the <code>webapp/lib</code>
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directory within the vitro.core.dir specified above.
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</td>
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</tr>
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<tr class="odd_row blue">
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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 database connections
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only if necessary to use a database other than MySQL.
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Otherwise, leave this value unchanged.
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</td>
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</tr>
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<tr class="odd_row blue">
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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 the VIVO application.
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This user will have an initial temporary password of 'defaultAdmin'.
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You will be prompted to create a new password on first login.
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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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initialAdminUser
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</td>
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<td>
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defaultAdmin
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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 name of a property that can be used to associate an Individual
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with a user account. When a user logs in with a name that matches
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the value of this property, the user will be authorized to editthat Individual.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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selfEditing.idMatchingProperty
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</td>
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<td>
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http://vivo.mydomain.edu/ns#networkId
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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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Temporal Graph Visualization is used to compare different
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organizations/people within an organization on different parameters like
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number of publications, grants. This parameter will be used as a default
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in case a URI is not provided. It will be also used whenever this
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visualization is to be rendered for top level organization.
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In absence of this parameter a SPARQL query will be fired which will
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attempt to provide a top level organization. The name of a property that
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can be used to associate an Individual with a user account. When a user
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logs in with a name that matches the value of this property, the user
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will be authorized to edit that Individual.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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visualization.topLevelOrg
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</td>
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<td>
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http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
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</td>
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</tr>
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</table>
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</p>
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<p>
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3. Apply any previous changes you have made to the new source directory.
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<blockquote>
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<strong>Special notes regarding source files</strong>
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<ul>
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<li>
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This process assumes any changes made to the application were made in
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the source directory and deployed, and were not made directly within
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the Tomcat webapps directory.
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</li>
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<li>
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In many cases, simply copying the modified files from your original
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source directory will not work since the files on which they are based
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have changed. It will be necessary to inspect the new source files and
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add any changes to them at that time.
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</li>
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<li>
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NIH-funded VIVO Implmentations will need to apply the Google Analytics Tracking
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Code (GATC) to <code>googleAnalytics.ftl</code>
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in the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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A sample <code>googleAnalytics.ftl</code>
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is included in the built-in theme. This file
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serves only as an example, and you must replace the tracking code shown
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with your institution's own tracking code.
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For additional information about the GATC for the NIH-funded VIVO
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implementation sites and a copy 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>.
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</li>
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<li>
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If you had used the <code>vivo/contrib/FLShibboleth</code>
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code in your previous release,
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you should stop using it. Consult <code>install.html</code>
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or <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1 v1.2 Installation Guide</a>
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on "Using an External Authentication System with VIVO".
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</li>
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</ul>
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</blockquote>
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</p>
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<p>
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4. If you had modified <code>web.xml</code>
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to configure the Pellet Reasoner (as described
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in the installation instructions), repeat that modification.
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</p>
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<p>
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5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
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</p>
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<p>
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6. Start Apache Tomcat and log in to VIVO.
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</p>
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<h3 id="ontology">III. Ontology Changes</h3>
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<h4>A. Verify Ontology upgrade process</h4>
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<p>
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After Apache Tomcat is started, these files should be reviewed to
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verify that the automated upgrade process was executed
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successfully. The ontology alignment process will create the
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following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
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</p>
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<dl>
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<dt>
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<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
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</dt>
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<dd>
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A log of a summary of updates that were made to the knowledge base and
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notes about some recommended manual reviews. This file should end with
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"Finished knowledge base migration".
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If this file contains any warnings they should be reviewed with
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your implementation team representative to see whether any
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corrective action needs to be taken.
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</dd>
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</dl>
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<dl>
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<dt>
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<code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code>
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</dt>
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<dd>
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A log of errors that were encountered during the upgrade process. This
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file should be empty if the upgrade was successful.
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</dd>
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</dl>
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<dl>
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<dt>
|
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<code>ontologies/update/changedData/removedData.n3</code>
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</dt>
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<dd>
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An N3 file containing all the statements that were removed from the
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knowledge base.
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</dd>
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</dl>
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<dl>
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<dt>
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<code>ontologies/update/changedData/addedData.n3</code>
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</dt>
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<dd>
|
|
An N3 file containing all the statements that were added to the
|
|
knowledge base.
|
|
</dd>
|
|
</dl>
|
|
<h4>B. Ontology knowledge base manual review</h4>
|
|
<p>
|
|
Changes to the VIVO core ontology may require corresponding
|
|
modifications of the knowledge base instance data and local ontology
|
|
extensions.
|
|
</p>
|
|
<p>
|
|
When Apache Tomcat starts up following the upgrade, it will initiate a
|
|
process to examine the knowledge base and apply necessary changes. Not
|
|
all of the modifications that may be required can be automated, so
|
|
manual review of the knowledge base is recommended after the automated
|
|
upgrade process. The automated process will make only 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 individuals in 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>
|
|
Property addition
|
|
</dt>
|
|
<dd>
|
|
If a newly added property is the inverse of a previously existing
|
|
property, the inverse of any statements using the pre-existing property
|
|
will be asserted.
|
|
</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>
|
|
|
|
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
|
|
<h4>A. Changes to the File Storage System</h4>
|
|
<p>
|
|
Each uploaded file exists as an individual entity in VIVO. When the
|
|
browser requests an upload file from VIVO, the data model is queried to
|
|
find out where the file is actually stored, so it can be downloaded to
|
|
the browser.
|
|
</p>
|
|
<p>
|
|
In VIVO release 1.2 this storage location,
|
|
known as the "Alias URL" for the uploaded file,
|
|
is stored in the file entity.
|
|
That way, pages that contain many files can be displayed much more quickly.
|
|
</p>
|
|
<p>
|
|
When Apache Tomcat starts up after the upgrade,
|
|
it will initiate a process to calculate the "Alias URL"
|
|
for each existing file and store it in the data model for fast access.
|
|
</p>
|
|
<h4>B. Verify File Storage System upgrade process</h4>
|
|
<p>
|
|
The File Storage upgrade process will create a log file in the
|
|
VIVO upload directory. You should review this file to ensure that
|
|
this upgrade worked properly.
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
|
|
</dt>
|
|
<dd>
|
|
A log of the upgrade process. The actual filename includes a timestamp
|
|
that tells when the upgrade executed.
|
|
This file should end with
|
|
<code>Finished adding alias URLs to FileByteStreams.</code>
|
|
|
|
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>
|
|
|
|
<h3>V. Theme Changes</h3>
|
|
<p>
|
|
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
|
|
engine for generating web pages. The theme is located in /vivo/themes/wilma and
|
|
the FreeMarker files have an ftl (for FreeMarker Template Language) extension.
|
|
</p>
|
|
<p>
|
|
Follow step A or B below, whichever is applicable to your site:
|
|
</p>
|
|
<p>
|
|
A. If you did not create a customized theme for your site in V1.0 or V1.1, but used
|
|
the vivo-basic theme in its original directory, you need not take any
|
|
action in order to convert your site to the VIVO 1.1 theme.
|
|
</p>
|
|
<h1>I THINK THIS SECTION NEEDS MAJOR CHANGING AND I NEED HELP WITH IT, Por Favor</h1>
|
|
<p>
|
|
B. If you created your own theme directory in VIVO 1.1, follow the steps below
|
|
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
|
|
theme to VIVO 1.2.
|
|
</p>
|
|
<dl>
|
|
<dt>
|
|
1. Templates
|
|
</dt>
|
|
<dd>
|
|
<dl>
|
|
<dt>
|
|
a. Copy the directory <code>/vivo/themes/vivo-basic/templates</code>
|
|
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
|
|
</dt>
|
|
<dd>
|
|
</dd>
|
|
<dt>
|
|
b. Follow step i or ii below, whichever is applicable to your theme.
|
|
</dt>
|
|
<dd>
|
|
<ol class="roman2">
|
|
<li>
|
|
If you did not apply any customizations to the JSPs in your VIVO
|
|
1.0 theme, then you do not need to apply any additional changes
|
|
to the VIVO 1.1 theme templates during the upgrade process.
|
|
</li>
|
|
<li>
|
|
<p>
|
|
If you did apply customizations to the JSPs in your VIVO 1.0
|
|
theme,you will need to hand-replicate those modifications in the
|
|
new theme template files.
|
|
</p>
|
|
<p>
|
|
The theme template content that was previously contained in
|
|
three JSP files is now contained in five FTL files. The
|
|
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
|
|
follows:
|
|
</p>
|
|
<pre>
|
|
identity.jsp => identity.ftl
|
|
menu.jsp => menu.ftl and search.ftl
|
|
footer.jsp => footer.ftl and googleAnalytics.ftl
|
|
</pre>
|
|
<p>
|
|
<code>googleAnalytics.ftl</code>
|
|
is the file to which you add your site's Google Analytics Tracking
|
|
Code (see section II).
|
|
</p>
|
|
<p>
|
|
Because the FreeMarker Template Language uses many syntactic
|
|
conventions that will be familiar to template authors from JSP
|
|
or other common templating systems, the translation of your JSP
|
|
changes into the new FTLs should be relatively straightforward.
|
|
</p>
|
|
<p>
|
|
Consult the FreeMarker Template Author's Guide at <a href="http://freemarker.org/docs/dgui.html">http://freemarker.org/docs/dgui.html</a>
|
|
and the Reference at <a href="http://freemarker.org/docs/ref.html">http://freemarker.org/docs/ref.html</a>
|
|
for complete documentation of the syntax and available built-in constructs. Template
|
|
authors need not be concerned with the Programmer's Guide or Java API documentation.
|
|
</p>
|
|
</li>
|
|
</ol>
|
|
</dd>
|
|
<dt>
|
|
c. Remove the jsp directory from your themes directory.
|
|
</dt>
|
|
<dd>
|
|
</dd>
|
|
</dl>
|
|
</dd>
|
|
<dt>
|
|
2. Stylesheets
|
|
</dt>
|
|
<dd>
|
|
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
|
|
styles in your VIVO 1.0 theme, you will not be able to simply copy the
|
|
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
|
|
style upgrades that your theme should pick up. Instead, you should
|
|
use the vivo-basic 1.1 stylesheets as a starting point, and manually
|
|
merge your 1.0 style modifications in as needed.
|
|
</dd>
|
|
<dt>
|
|
3. Site Icons
|
|
</dt>
|
|
<dd>
|
|
Copy the site icons from your 1.1 theme into the site_icons folder in
|
|
your 1.2 theme.
|
|
</dd>
|
|
</dl>
|
|
</div>
|
|
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<footer role="contentinfo">
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<p class="copyright">
|
|
<small>
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©2011
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All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
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</small>
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