2011-01-17 01:49:25 +00:00
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8" />
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2011-02-10 04:23:54 +00:00
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<title>VIVO Release 1 V1.2 Upgrade Guide</title>
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2011-02-10 02:22:37 +00:00
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<link rel="stylesheet" href="./css/doc.css" media="screen" />
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<link rel="stylesheet" href="./css/print.css" media="print" />
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2011-01-17 01:49:25 +00:00
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</head>
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<body>
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2011-02-03 21:28:27 +00:00
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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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2011-02-03 21:28:27 +00:00
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</div>
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2011-01-17 01:49:25 +00:00
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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2011-02-01 22:13:04 +00:00
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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
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v1.2
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</small>
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<toc>
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<ul>
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<li>
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<a href="#announcement">Release announcement for V1.2</a>
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</li>
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<li>
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<a href="#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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2011-02-10 02:22:37 +00:00
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<p>
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This document provides a short description of the steps involved in
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upgrading your installation of VIVO from Release 1, Version 1.1 to
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Version 1.2. 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 <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1 v1.2
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Installation Guide</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
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document also has a list of the required software and versions.
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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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2011-02-09 23:36:30 +00:00
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The VIVO 1.2 release incorporates major changes throughout the
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application - notably a new templating system to support more flexible
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display and navigation, plus improvements to address scalability. The
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release also features two new visualization options: temporal graphing
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for organizations, and personal visualizations extended to cover grants
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as well as publications. The VIVO Harvester library has also been
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significantly improved and expanded in scope for its 1.0 release
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through the VIVO SourceForge project at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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<h4>Templating system for page generation, navigation, and theming</h4>
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<p>
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A new installation of VIVO 1.2 looks strikingly different, with a
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new navigation and browse interface as well as a more modular page
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design that is easier to customize and brand for your local
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institution. Page displays now support inline navigation to streamline
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viewing of expanded personal and organizational profiles, as well as
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improved graphic layout and organization. New browsing controls on the
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home page and each menu page include interactive visual controls to
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provide an immediate overview of the size and range of content and
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quick access down to the individual person, organization, research
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feature, or event. VIVO's navigation has also been completely
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overhauled.
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</p>
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<h4>Storage model</h4>
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<p>
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While server memory capacity has increased significantly in recent
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years, VIVO's reliance on in-memory caching of RDF data had put limits
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on the ultimate scalability of VIVO instances and potentially increased
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the cost of servers required to support VIVO.
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<br>
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</p>
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<p>
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With version 1.2, VIVO has been converted to optionally use Jena's
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SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
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memory footprint, allowing VIVO installations to scale well beyond what
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has previously been possible.
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</p>
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<h4>New visualizations</h4>
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<p>
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VIVO continues to expand visualization options including all-new
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user-configurable temporal comparisons of publications and grants,
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grouped by organization or by affiliated person. Visualizations of
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networks of co-authors are now complemented by visualizations of
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co-investigators on grants, with a similar interactivity and options
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for export as images or data.
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</p>
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<h4>Ontology</h4>
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<p>
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VIVO 1.2 includes a new ontology module representing research
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resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
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is aligned with the top-level ontology classes and properties from the
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NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
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</p>
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<h3>Associated VIVO releases</h3>
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<h4>VIVO Harvester</h4>
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<p>
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The Harvester development team is releasing version 1.0 of the VIVO
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Harvester library, an extensible data ingest and updating framework
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with sample configurations for loading PubMed publication, grants, and
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human resources data. The Harvester is available at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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2011-02-01 22:13:04 +00:00
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</p>
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2011-02-09 23:36:30 +00:00
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
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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="#triple_store">Chose Triple Store</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
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process</a>
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</li>
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<li>
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<a href="#ontology_knowledge_base">Ontology knowledge base
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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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2011-02-02 04:01:34 +00:00
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<a href="#changes_to_storage">Changes to the File
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Storage System</a>
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</li>
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<li>
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2011-02-02 04:01:34 +00:00
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<a href="#verify_file_upgrade">Verify File Storage
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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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<li>
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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2011-02-01 22:13:04 +00:00
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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
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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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DO NOT reinstall MySQL or recreate the MySQL database. Please
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ensure that you back-up the MySQL database. Also note that VIVO 1.2 will
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not run on older versions of MySQL that may have worked with 1.1.1.
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Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using unsupported
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versions may result in strange error messages related to table formatting or
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other unexpected problems.
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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
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installation.
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2011-01-25 20:43:06 +00:00
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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
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will initiate a process that modifies the knowledge base to align the
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data 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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2011-02-10 04:23:54 +00:00
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<h3 id="triple_store">II. Choose Triple Store</h3>
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<p>
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VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
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Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was
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used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
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entire RDF model in the server's main memory. The memory available to VIVO limits the
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number of RDF statements that may be stored.
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</p>
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<p>
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SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
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against the underlying database. This allows VIVO installations to display data from large
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RDF models while requiring only a small amount of server memory to run the application.
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There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
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and performance will depend on the configuration parameters of the database server.
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Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
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in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
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generated, though they are generated as soon as data is edited rather than in a background process.
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</p>
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<p>
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Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
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a configuration property and redeploying the application, it is important to note that data
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added in one mode will not typically appear in the other. The exception is when a system is
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first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
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automatically migrated to SDB.
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</p>
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<p>
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A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
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receive required ontology updates. Attempting to run an upgraded system initially in SDB will
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result in a logged error message, and the application will not start. After the system starts
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up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
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Upon restart, the data in the RDB store will be copied to the SDB store.
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</p>
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<p>
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This copying process can take a number of hours to complete if the installation contains a large
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amount of RDF data (roughly a million triples or more). See section
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a> for instructions on how
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to run this lengthy conversion process in the background while an RDB system is operating.
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Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
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</p>
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<h3 id="upgrade_process">III. 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
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source 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
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previous installation and set values for the new variables. The
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following table shows the default properties for deploy.properties with
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new V1.2 properties in <span class="blue">blue</span>.<!-- deploy.properties table from install.html -->
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</p>
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<table>
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<tbody>
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<tr>
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<th>
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Property Name
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</th>
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<th>
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Example Value
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</th>
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</tr>
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<tr>
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<td colspan="2">
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Default namespace: VIVO installations make their
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RDF resources available for harvest using linked data. Requests for RDF
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resource URIs redirect to HTML or RDF representations as specified by
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the client. To make this possible, VIVO's default namespace must have
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certain structure and begin with the public web address of the VIVO
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installation. For example, if the web address of a VIVO installation is
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"http://vivo.example.edu/" the default namespace must be set to
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|
|
|
"http://vivo.example.edu/individual/" in order to support linked data.
|
|
|
|
|
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
|
|
|
|
|
default namespace must be set to
|
|
|
|
|
"http://www.example.edu/vivo/individual/"<h4>* The namespace must end with "individual/" (including the
|
|
|
|
|
trailing slash).</h4>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
Vitro.defaultNamespace
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
http://vivo.mydomain.edu/individual/
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Directory where Vitro code is located. In most
|
|
|
|
|
deployments, this is set to ./vitro-core (It is not uncommon for this
|
|
|
|
|
setting to point elsewhere in development environments).
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
vitro.core.dir
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
./vitro-core
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Directory where tomcat is installed.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
tomcat.home
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
/usr/local/tomcat
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Name of your VIVO application.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
webapp.name
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
vivo
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Directory where uploaded files will be stored.
|
|
|
|
|
Be sure this directory exists and is writable by the user that
|
|
|
|
|
the Tomcat service is running as.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
upload.directory
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
/usr/local/vivo/data/uploads
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Directory where the Lucene search index will be
|
|
|
|
|
built. Be sure this directory exists and is writable by the user that
|
|
|
|
|
the Tomcat service is running as.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
LuceneSetup.indexDir
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
/usr/local/vivo/data/luceneIndex
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify an SMTP host that the form will use for
|
|
|
|
|
sending e-mail (Optional). If this is left blank, the contact form will
|
|
|
|
|
be hidden and disabled.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
Vitro.smtpHost
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
smtp.servername.edu
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify the JDBC URL of your database. Change
|
|
|
|
|
the end of theURL to reflect your database name (if it is not "vivo").
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.url
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
jdbc:mysql://localhost/vivo
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Change the username to match the authorized user
|
|
|
|
|
you created in MySQL.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.username
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
username
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Change the password to match the password you
|
|
|
|
|
created in MySQL.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.password
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
password
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify the Jena triple store technology to use.
|
|
|
|
|
SDB is Jena's SPARQL database; this setting allows RDF data to scale
|
|
|
|
|
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
|
|
|
|
|
store with in-memory caching.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.tripleStoreType
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
SDB
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify the maximum number of active connections
|
|
|
|
|
in the database connection pool to support the anticipated number of
|
|
|
|
|
concurrent page requests. It is not necessary to adjust this value when
|
|
|
|
|
using the RDB configuration.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.pool.maxActive
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
40
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify the maximum number of database
|
|
|
|
|
connections that will be allowed to remain idle in the connection pool.
|
|
|
|
|
Default is 25% of the maximum number of active connections.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.pool.maxIdle
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
10
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Change the dbtype setting to use a database
|
2011-02-09 23:36:30 +00:00
|
|
|
other than MySQL. Otherwise, leave this value unchanged. Possible
|
|
|
|
|
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
|
|
|
|
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
2011-02-01 22:13:04 +00:00
|
|
|
for additional information.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.dbtype
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
MySQL
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify a driver class name to use a database
|
|
|
|
|
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
|
|
|
|
for this driver must be added to the the <code>webapp/lib</code>
|
|
|
|
|
directory within the vitro.core.dir specified above.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.driver
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
com.mysql.jdbc.Driver
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Change the validation query used to test
|
|
|
|
|
database connections only if necessary to use a database other than
|
|
|
|
|
MySQL. Otherwise, leave this value unchanged.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
VitroConnection.DataSource.validationQuery
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
SELECT 1
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
Specify the name of your first admin user for
|
|
|
|
|
the VIVO application. This user will have an initial temporary password
|
|
|
|
|
of 'defaultAdmin'. You will be prompted to create a new password on
|
|
|
|
|
first login.
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row">
|
|
|
|
|
<td>
|
|
|
|
|
initialAdminUser
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
defaultAdmin
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
The URI of a property that can be used to
|
|
|
|
|
associate an Individual with a user account. When a user logs in with a
|
|
|
|
|
name that matches the value of this property, the user will be
|
|
|
|
|
authorized to edit that Individual. For example, to use the netID
|
|
|
|
|
at Cornell University as the property:
|
|
|
|
|
<br>
|
|
|
|
|
<span style="font-style: italic;">seflEditing.idMatchingProperty
|
|
|
|
|
=
|
|
|
|
|
http://vivo.cornell.edu/ns/hr/0.9/hr.owl#netId</span>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
selfEditing.idMatchingProperty
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
http://vivo.mydomain.edu/ns#networkId
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr>
|
|
|
|
|
<td colspan="2">
|
|
|
|
|
The temporal graph visualization is used to
|
|
|
|
|
compare different
|
|
|
|
|
organizations/people within an organization on parameters like number
|
|
|
|
|
of publications or grants. By default, the app will attempt to make its
|
|
|
|
|
best guess at the top level organization in your instance. If you're
|
|
|
|
|
unhappy with this selection, uncomment out the property below and set
|
|
|
|
|
it to the URI of the organization individual you want to identify as
|
|
|
|
|
the top level organization. It will be used as the default whenever the
|
|
|
|
|
temporal graph visualization is rendered without being passed an
|
|
|
|
|
explicit org. For example, to use "Ponce School of Medicine" as the top
|
|
|
|
|
organization:
|
|
|
|
|
<br>
|
|
|
|
|
<span style="font-style: italic;">visualization.topLevelOrg =
|
|
|
|
|
http://vivo.psm.edu/individual/n2862</span>
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
<tr class="odd_row blue">
|
|
|
|
|
<td>
|
|
|
|
|
visualization.topLevelOrg
|
|
|
|
|
</td>
|
|
|
|
|
<td>
|
|
|
|
|
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
|
|
|
|
|
</td>
|
|
|
|
|
</tr>
|
|
|
|
|
</tbody>
|
2011-01-17 01:49:25 +00:00
|
|
|
</table>
|
2011-02-01 22:13:04 +00:00
|
|
|
<p>
|
|
|
|
|
3. Apply any previous changes you have made to the new source
|
|
|
|
|
directory.
|
|
|
|
|
</p>
|
2011-01-17 01:49:25 +00:00
|
|
|
<blockquote>
|
|
|
|
|
<strong>Special notes regarding source files</strong>
|
|
|
|
|
<ul>
|
|
|
|
|
<li>
|
2011-02-01 22:13:04 +00:00
|
|
|
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.
|
2011-01-17 01:49:25 +00:00
|
|
|
</li>
|
|
|
|
|
<li>
|
2011-02-01 22:13:04 +00:00
|
|
|
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.
|
2011-01-17 01:49:25 +00:00
|
|
|
</li>
|
|
|
|
|
<li>
|
2011-02-10 14:19:58 +00:00
|
|
|
NIH-funded VIVO implementations will need to apply the Google
|
2011-02-01 22:13:04 +00:00
|
|
|
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
2011-02-10 14:19:58 +00:00
|
|
|
in the theme:
|
|
|
|
|
<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
2011-01-17 01:49:25 +00:00
|
|
|
A sample <code>googleAnalytics.ftl</code>
|
2011-02-10 14:19:58 +00:00
|
|
|
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 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>.
|
2011-01-17 01:49:25 +00:00
|
|
|
</li>
|
|
|
|
|
<li>
|
|
|
|
|
If you had used the <code>vivo/contrib/FLShibboleth</code>
|
2011-02-01 22:13:04 +00:00
|
|
|
code in your previous release, you should stop using it. Consult <code>install.html</code>
|
|
|
|
|
or <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1
|
|
|
|
|
v1.2 Installation Guide</a>
|
|
|
|
|
on "Using an External Authentication System
|
|
|
|
|
with VIVO".
|
2011-01-17 01:49:25 +00:00
|
|
|
</li>
|
|
|
|
|
</ul>
|
|
|
|
|
</blockquote>
|
2011-02-09 23:36:30 +00:00
|
|
|
<p>
|
|
|
|
|
4. If you had modified <code>web.xml</code>
|
|
|
|
|
to configure the Pellet Reasoner (as described
|
|
|
|
|
in the installation instructions), repeat that modification.
|
|
|
|
|
</p>
|
|
|
|
|
<p>
|
|
|
|
|
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
|
|
|
|
|
</p>
|
|
|
|
|
<p>
|
|
|
|
|
6. Start Apache Tomcat and log in to VIVO.
|
|
|
|
|
</p>
|
2011-02-10 14:19:58 +00:00
|
|
|
<h3 id="ontology">III. Ontology Changes</h3>
|
2011-02-09 23:36:30 +00:00
|
|
|
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
|
|
|
|
|
<p>
|
|
|
|
|
After Apache Tomcat is started, these files should be reviewed to
|
|
|
|
|
verify that the automated upgrade process was executed
|
|
|
|
|
successfully. The ontology alignment process will create the
|
|
|
|
|
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
|
|
|
|
</p>
|
|
|
|
|
<dl>
|
|
|
|
|
<dt>
|
|
|
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
|
|
|
|
|
</dt>
|
|
|
|
|
<dd>
|
2011-02-10 14:19:58 +00:00
|
|
|
A log of a summary of updates that were made to the knowledge base and
|
|
|
|
|
notes about some recommended manual reviews. 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
|
2011-02-09 23:36:30 +00:00
|
|
|
corrective action needs to be taken.
|
|
|
|
|
</dd>
|
|
|
|
|
</dl>
|
|
|
|
|
<dl>
|
|
|
|
|
<dt>
|
|
|
|
|
<code>ontologies/update/logs/knowledgeBaseUpdate.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.
|
|
|
|
|
</dd>
|
|
|
|
|
</dl>
|
|
|
|
|
<dl>
|
|
|
|
|
<dt>
|
|
|
|
|
<code>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>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="ontology_knowledge_base">ii. 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>
|
2011-02-10 14:19:58 +00:00
|
|
|
|
|
|
|
|
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
|
2011-02-09 23:36:30 +00:00
|
|
|
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
|
|
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
Each uploaded file exists as an individual in VIVO. When the browser
|
|
|
|
|
requests an uploaded 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.
|
2011-02-09 23:36:30 +00:00
|
|
|
</p>
|
|
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
In VIVO release 1.2 this storage location, known as the "Alias URL" for
|
|
|
|
|
the uploaded file, is stored in the file individual. That way, pages that
|
|
|
|
|
contain many files can be displayed much more quickly.
|
2011-02-09 23:36:30 +00:00
|
|
|
</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.
|
2011-02-10 14:19:58 +00:00
|
|
|
</p>
|
2011-02-09 23:36:30 +00:00
|
|
|
<h4 id="verify_file_upgrade">ii. 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.
|
2011-02-10 14:19:58 +00:00
|
|
|
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
|
2011-02-09 23:36:30 +00:00
|
|
|
corrective action needs to be taken.
|
|
|
|
|
</dd>
|
|
|
|
|
</dl>
|
2011-02-10 14:19:58 +00:00
|
|
|
|
|
|
|
|
<h3 id="theme">V. Theme Modifications</h3>
|
|
|
|
|
<h4 id="#newTheme">i. Introducing a New Default Theme</h4>
|
|
|
|
|
<p>
|
|
|
|
|
VIVO 1.2 includes a new default theme called <strong>wilma</strong> (located in
|
|
|
|
|
/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
|
|
|
|
|
create your own theme using wilma as a starting point, please review the
|
|
|
|
|
<a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">
|
|
|
|
|
Site Administrator's Guide</a>.
|
|
|
|
|
</p>
|
|
|
|
|
<blockquote id="vivoBasicDeprecated">
|
|
|
|
|
<h4>
|
|
|
|
|
The vivo-basic theme has been deprecated with the 1.2 release and is not
|
|
|
|
|
recommended for production instances.
|
|
|
|
|
</h4>
|
|
|
|
|
<p>
|
|
|
|
|
Since vivo-basic was the default theme for all previous releases, it is
|
|
|
|
|
included as part of VIVO 1.2 to help with the transition of upgrading
|
|
|
|
|
existing installations to the latest code, but all vivo-basic development
|
|
|
|
|
has ceased and it will not be distributed in future releases.
|
|
|
|
|
</p>
|
|
|
|
|
<p>
|
|
|
|
|
Please note that vivo-basic does not support all of the new 1.2 features.
|
|
|
|
|
Most notably, in choosing to use vivo-basic you will be missing out on the
|
|
|
|
|
following:
|
|
|
|
|
</p>
|
|
|
|
|
<ul>
|
|
|
|
|
<li>new primary menu for site navigation (replaces tabs)</li>
|
|
|
|
|
<li>home page with class group browse and visual graph</li>
|
|
|
|
|
<li>menu pages with class group and individual browse</li>
|
|
|
|
|
</ul>
|
|
|
|
|
</blockquote>
|
|
|
|
|
<h4 id="templateTransition">Templates</h4>
|
|
|
|
|
<p>
|
|
|
|
|
The 1.2 release continues the transition from JavaServer Pages (.jsp) to
|
|
|
|
|
Freemarker templates (.ftl) for generating web pages. While there are still
|
|
|
|
|
JSP files in action behind the scenes, as of 1.2 all theme templates
|
|
|
|
|
are of the Freemarker variety and are located in the "templates" directory
|
|
|
|
|
within a theme.
|
|
|
|
|
</p>
|
2011-02-09 23:36:30 +00:00
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
For details on the new structure of themes in 1.2 and further information
|
|
|
|
|
regarding the development of your own custom theme, please review the
|
|
|
|
|
<a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">
|
|
|
|
|
Site Administrator's Guide</a>. This document will focus on updating an existing
|
|
|
|
|
pre 1.2 theme.
|
2011-02-09 23:36:30 +00:00
|
|
|
</p>
|
2011-02-10 14:19:58 +00:00
|
|
|
<h4 id="updateTheme">Updating an Existing Theme</h4>
|
2011-02-09 23:36:30 +00:00
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
If you already have an existing pre 1.2 instance running, follow step A or B below,
|
|
|
|
|
whichever is applicable to your site:
|
2011-02-09 23:36:30 +00:00
|
|
|
</p>
|
|
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
A. If you did not create a custom theme for your site previously, but used
|
2011-02-09 23:36:30 +00:00
|
|
|
the vivo-basic theme in its original directory, you need not take any
|
2011-02-10 14:19:58 +00:00
|
|
|
action in order to remain using the vivo-basic theme in 1.2.
|
2011-02-09 23:36:30 +00:00
|
|
|
</p>
|
2011-02-10 14:19:58 +00:00
|
|
|
<blockquote>
|
|
|
|
|
<strong>Please note:</strong> The vivo-basic theme has been deprecated and is
|
|
|
|
|
<a href="#vivoBasicDeprecated">not recommended for production instances</a>.
|
|
|
|
|
</blockquote>
|
2011-02-09 23:36:30 +00:00
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
B. If you created your own theme in VIVO 1.1, follow the steps below under sections
|
|
|
|
|
"Templates," "Stylesheets," and "Site Icons" to upgrade your theme to VIVO 1.2.
|
|
|
|
|
</p>
|
|
|
|
|
<p style="color:#f00">
|
|
|
|
|
NC: Everything below up to Section VII still needs some work and is not ready for
|
|
|
|
|
prime time.
|
2011-02-09 23:36:30 +00:00
|
|
|
</p>
|
|
|
|
|
<dl>
|
|
|
|
|
<dt>
|
|
|
|
|
1. Templates
|
|
|
|
|
</dt>
|
|
|
|
|
<dd>
|
|
|
|
|
<dl>
|
|
|
|
|
<dt>
|
2011-02-10 14:19:58 +00:00
|
|
|
a. Copy the directory <code>/vivo/themes/vivo-basic/templates</code>
|
2011-02-09 23:36:30 +00:00
|
|
|
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>
|
2011-02-10 14:19:58 +00:00
|
|
|
If you did not make any customizations to the templates in your
|
|
|
|
|
VIVO 1.1 theme, then you do not need to apply any additional changes
|
|
|
|
|
to the new 1.2 theme templates during the upgrade process.
|
2011-02-09 23:36:30 +00:00
|
|
|
</li>
|
|
|
|
|
<li>
|
|
|
|
|
<p>
|
2011-02-10 14:19:58 +00:00
|
|
|
If you did make customizations to the templates in your VIVO 1.1
|
|
|
|
|
theme, you will need to hand-replicate those modifications in the
|
|
|
|
|
new theme templates.
|
2011-02-09 23:36:30 +00:00
|
|
|
</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>
|
2011-02-10 14:19:58 +00:00
|
|
|
identity.jsp => identity.ftl
|
|
|
|
|
menu.jsp => menu.ftl and search.ftl
|
|
|
|
|
footer.jsp => footer.ftl and googleAnalytics.ftl
|
|
|
|
|
</pre>
|
2011-02-09 23:36:30 +00:00
|
|
|
<p>
|
|
|
|
|
<code>googleAnalytics.ftl</code>
|
|
|
|
|
is the file to which you add your site's Google Analytics Tracking
|
|
|
|
|
Code (see section II).
|
|
|
|
|
</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>
|
|
|
|
|
</dl>
|
|
|
|
|
</dd>
|
|
|
|
|
<dt>
|
|
|
|
|
2. Stylesheets
|
|
|
|
|
</dt>
|
|
|
|
|
<dd>
|
2011-02-10 14:19:58 +00:00
|
|
|
VIVO 1.2 includes changes to vivo-basic stylesheets. If you modified
|
|
|
|
|
styles in your VIVO 1.1 theme, you will not be able to simply copy the
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1.1 stylesheets into your 1.2 theme, because you will then lose 1.2
|
2011-02-09 23:36:30 +00:00
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style upgrades that your theme should pick up. Instead, you should
|
2011-02-10 14:19:58 +00:00
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use the vivo-basic 1.2 stylesheets as a starting point, and manually
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merge your 1.1 style modifications in as needed.
|
2011-02-09 23:36:30 +00:00
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</dd>
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<dt>
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3. Site Icons
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</dt>
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<dd>
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Copy the site icons from your 1.1 theme into the site_icons folder in
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your 1.2 theme.
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</dd>
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</dl>
|
2011-02-10 04:23:54 +00:00
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<h3 id="setup_sdb">VII. Set Up SDB Store in the Background (Optional)</h3>
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<p>
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If your VIVO installation is running in RDB mode, and you'd like to convert
|
2011-02-10 14:19:58 +00:00
|
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to SDB, you can start the conversion process in the background while the RDB
|
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|
|
system is running. This will reduce the delay in initial startup after the
|
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|
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application is redeployed with deploy.properties set for SDB. Note that it
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|
is important not to edit any data anywhere in the application while this
|
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background conversion is running.
|
2011-02-10 04:23:54 +00:00
|
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</p>
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<p>
|
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To start the SDB conversion, log in as a system
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|
|
administrator and request /sdbsetup. (For example, if your VIVO is installed
|
2011-02-10 14:19:58 +00:00
|
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|
at http://vivo.myuniversity.edu/ you would type
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|
|
http://vivo.myuniversity.edu/sdbsetup into your browser.)
|
2011-02-10 04:23:54 +00:00
|
|
|
</p>
|
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|
|
<p>
|
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|
|
Click the button that appears on this page.
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|
</p>
|
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|
|
<p>
|
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|
During the course of the SDB setup, which may take several hours on a
|
|
|
|
|
large database, subsequent requests to /sdbsetup will display a
|
|
|
|
|
message that the operation is still in progress. When a request for this
|
2011-02-10 14:19:58 +00:00
|
|
|
page shows a message that the SDB setup has completed successfully, shut down
|
|
|
|
|
Tomcat, set deploy.properties to SDB mode, redeploy, and restart Tomcat.
|
|
|
|
|
VIVO will now be running from the SDB store.
|
2011-02-10 04:23:54 +00:00
|
|
|
</p>
|
2011-02-09 23:36:30 +00:00
|
|
|
</div>
|
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|
|
|
<!-- end of content -->
|
2011-02-10 02:22:37 +00:00
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|
|
<div id="footer" role="contentinfo">
|
2011-02-09 23:36:30 +00:00
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|
|
<p class="copyright">
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|
|
|
|
<small>
|
|
|
|
|
©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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|
|
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
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</p>
|
2011-02-10 02:22:37 +00:00
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|
<div id="nav" role="navigation">
|
2011-02-09 23:36:30 +00:00
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|
|
<ul id="footer-nav" role="list">
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<li role="listitem">
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<a href="http://vivoweb.org/about">About</a>
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</li>
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|
|
<li role="listitem">
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<a href="http://vivoweb.org/contact">Contact Us</a>
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</li>
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|
|
<li role="listitem">
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|
|
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
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|
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</li>
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|
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</ul>
|
2011-02-10 02:22:37 +00:00
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|
|
</div>
|
2011-02-09 23:36:30 +00:00
|
|
|
</div>
|
2011-01-17 01:49:25 +00:00
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|
|
</body>
|
2011-02-10 14:19:58 +00:00
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</html>
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