648222cb47
Added in text for release announcement that Jon edited. Added print border for deploy.properties. Fixed typos found by Tim.
1165 lines
57 KiB
HTML
1165 lines
57 KiB
HTML
<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.3 Upgrade Guide</title>
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<link rel="stylesheet" href="./css/doc.css" media="screen">
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</head>
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<body>
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<div id="branding" role="banner">
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<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
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</div>
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 v1.3 Upgrade Guide</h1>
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<small>
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July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1 v1.3
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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 V1.3</a>
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</li>
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<li>
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<a href="#upgrade">Upgrade process for V1.3</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
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upgrading your installation of VIVO from Version 1.2+ to Version 1.3.
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This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
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at <a href="http://vivoweb.org/">VIVOweb.org</a>
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</p>
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<p>
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If you need to do a fresh install, please consult the VIVO Release
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1 v1.3 Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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or the install.html file located in the <code>doc</code>
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directory of
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the VIVO source code distribution. The installation document also has a
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list of the required software and versions (there are no new hardware
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or software requirements for V1.3).
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</p>
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<h3 id="announcement">Release Announcement for V1.3</h3>
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V<!-- Release Announcement -->IVO Release 1.3 incorporates changes to
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the search indexing, user
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accounts, menu management, ontology, and visualizations.
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<br>
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<h4>Search</h4>
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VIVO 1.3 will feature notable improvements to the local search,
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primarily to improve relevance ranking but also to boost the influence
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of semantic relationships in the search. This will improve recall by
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including text from related resources (e.g., adding a person’s grant
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and publication titles to his or her search entry) and by boosting
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overall relevance ranking based on the number and nature of connections
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from one individual to others.
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<br>
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
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of Apache Lucene to improve indexing and faceting of search results.
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The migration to Solr also aligns the local search with the VIVO
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multi-site search site under development for release prior to the 2011
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VIVO Conference.
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<br>
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<h4>Authorization</h4>
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Release 1.3 provides an entirely new model of authorization within the
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VIVO application to allow more granular control over system
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configuration and editing. The first phase of the new user account
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interface is included in V1.3. This interface provides a user search, a
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root acount, and password reset functionality where the password gets
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emailed to the user. The next phase will provide the ability to create
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new roles.
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<br>
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<h4>Menu management</h4>
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The menus across the top of the site (Home, People, Organizations,
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Research, Events) can now be managed in a web form instead of editing
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an RDF file. In addition to making site management much easier,
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form-based editing also allows more control over what classes of data
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are displayed and provides a mechanism to limit certain menu pages to
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content identified as internal to the institution.
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<br>
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<h4>FreeMaker template improvements</h4>
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While less directly visible to the public, version 1.3 also includes
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additional changes focused directly on supporting open source community
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involvement in extending and customizing VIVO. The development team
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began a year ago to transition VIVO’s code base away from Java Server
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Pages to the FreeMarker page templating system that much more cleanly
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separates internal application programming logic from page display.
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<br>
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<h4>Visualization</h4>
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The visualization team has implemented a Science Map visualization,
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which allows users to visually explore the scientific strengths of a
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university, school, department, or person in the VIVO instance. Users
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will be able to see where an organization or person’s interests lay
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across 13 major scientific disciplines or 554 sub-disciplines, and will
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be able to see how these disciplines and sub-disciplines interrelate
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with one another on the map of science. Wireframes and design
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documentation for upcoming enhanced versions of the Science Map
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visualization have already been developed; the Science Map
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visualization will most likely be in the form of a PDF that a user can
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download.
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<br>
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Several visualization also now provide a caching feature that improves
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performance after the initial processing.
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<br>
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<h4>QR Codes</h4>
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Pages for people in VIVO have the option of displaying QR codes.
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<br>
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<h4>Ontology changes</h4>
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<ul>
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<li>
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support for certifications and licenses
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</li>
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<li>
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expanded support for intellectual property (patents) (it was
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there as stub before but didn't allow common things such as assignee
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and issuer)
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</li>
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<li>
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support for editorial, reviewing and organizing activities
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</li>
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<li>
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expanded shared geographical instance data vocabulary to include
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the 50 U.S. states
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</li>
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<li>
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representing specific types of EducationalTraining:
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PostdoctoralTraining, Internship, MedicalResidency
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</li>
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</ul>
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<h4>Linked open data</h4>
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Responses to linked data requests have been enhanced to include
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additional context about any individual, in working toward a goal of
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being able to provide all the data in a person's profile available as
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RDF via a single web request.
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<br>
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<br>
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</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">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 Changes</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="#template">Template Changes</a>
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</li>
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<li>
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<a href="#listview">List View Changes</a>
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</li>
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<li>
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<a href="#authorization">Authorization Changes</a>
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<ol class="roman2">
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<li>
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<a href="#accounts_created">User Accounts are created for
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externally authenticated users</a>
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</li>
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<li>
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<a href="#email_on_accounts">E-mail address becomes an
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important part of User Accounts</a>
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</li>
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<li>
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<a href="#root_account">Each VIVO installation will have a
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'root' account</a>
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</li>
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</ol>
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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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If you are still in RDB mode, it is required that you move your
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triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a>
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info
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below).
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<br>
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</li>
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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
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will not run on older versions of MySQL that may have worked with
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1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using
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unsupported versions may result in strange error messages related to
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table formatting or 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. With V1.3 there is also a new root user. Please see the
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section on <a href="#authorization">Authorization changes</a> for more information.
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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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<h3 id="triple_store">II. Triple Store</h3>
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<p>
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VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
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the triple store technology. Jena's legacy relational database
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store (RDB) was used by VIVO 1.1.1 and earlier. Both SDB and RDB
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were available in VIVO 1.2 and 1.2.1. It is required that you
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move your triple store to SDB while still at V1.2.
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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
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queries are issued directly against the underlying database. This
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allows VIVO installations to display data from large RDF models while
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requiring only a small amount of server memory to run the application.
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There is a tradeoff in response time: pages may take slightly longer
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to load in SDB mode, and performance will depend on the configuration
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parameters of the database server. Additionally, advanced OWL reasoning
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(not enabled by default in either mode) is not possible in SDB mode.
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With SDB, only the default set of inferences (inferred rdf:type
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statements) are generated, and they are generated as soon as data is
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edited rather than in a background process.
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</p>
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<p>
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A conversion from RDB to SDB mode can take a number of hours to
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complete if the installation contains a large amount of RDF data
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(roughly a million triples or more). You can start the conversion
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process in the background while the RDB system is running. This will
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reduce the delay in initial startup after the application is redeployed
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with deploy.properties set for SDB. <span style="font-weight: bold;">Note
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that
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it is important not to edit any data anywhere in the application
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while this background conversion is running</span>.
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</p>
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<p>
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To start the SDB conversion, log in as a system administrator and
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request /sdbsetup (For example, if your VIVO is installed at
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http://vivo.myuniversity.edu/ you would type
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http://vivo.myuniversity.edu/sdbsetup into your browser).
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</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
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a large database, subsequent requests to /sdbsetup will display a
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message that the operation is still in progress. When a request for
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this page shows a message that the SDB setup has completed
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successfully, shut down Tomcat, set deploy.properties to SDB mode,
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redeploy, and restart Tomcat. VIVO will now be running from the SDB
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store.
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</p>
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<p>
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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 a new deploy.properties using the same values as in your
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previous installation and set values for the new variables as described
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below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
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vitro.home.directory, email.smptHost, email.replyTo,
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rootUser.emailAddress)
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<br>
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</p>
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<p>
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<!-- deploy.properties table from install.html -->
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</p>
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<table border='1' bordercolor="#CCCCCC" cellspacing="5">
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<tbody>
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<tr>
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<th>
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Property Name
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</th>
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<th>
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Example Value
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</th>
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</tr>
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<tr>
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<td colspan="2">
|
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Default namespace: VIVO installations make their
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RDF resources available for harvest using linked data. Requests for RDF
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resource URIs redirect to HTML or RDF representations as specified by
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the client. To make this possible, VIVO's default namespace must have a
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certain structure and begin with the public web address of the VIVO
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installation. For example, if the web address of a VIVO installation is
|
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"http://vivo.example.edu/" the default namespace must be set to
|
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"http://vivo.example.edu/individual/" in order to support linked data.
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Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
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default namespace must be set to
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"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with "individual/" (including the
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trailing slash).</h5>
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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Vitro.defaultNamespace
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</td>
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<td>
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http://vivo.mydomain.edu/individual/
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</td>
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</tr>
|
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<tr>
|
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<td colspan="2">
|
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Directory where Vitro code is located. In most
|
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deployments, this is set to ./vitro-core (It is not uncommon for this
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setting to point elsewhere in development environments).
|
||
</td>
|
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</tr>
|
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<tr class="odd_row">
|
||
<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>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
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Directory where tomcat is installed.
|
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</td>
|
||
</tr>
|
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<tr class="odd_row">
|
||
<td>
|
||
tomcat.home
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</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">
|
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URL of Solr context used in local VIVO search.
|
||
Should consist of:<pre> scheme + servername + port + vivocontextpath + "solr"</pre>
|
||
In the standard installation, the Solr context will be on the same
|
||
server as VIVO, and in the same Tomcat instance. The path will be the
|
||
VIVO webapp.name (specified above) + "solr"
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
vitro.local.solr.url
|
||
</td>
|
||
<td>
|
||
http://localhost:8080/vivosolr
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Restricts access to the Solr search platform.
|
||
One or more regular expressions, separated by commas. When a request is
|
||
made to Solr, the IP address of the requestor must match one of the
|
||
patterns, or the request will be rejected.
|
||
<br>
|
||
Examples:
|
||
<ul>
|
||
<li>
|
||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
||
</li>
|
||
<li>
|
||
vitro.local.solr.ipaddress.mask =
|
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127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||
</li>
|
||
<li>
|
||
vitro.local.solr.ipaddress.mask = 169.254.*
|
||
</li>
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
vitro.local.solr.ipaddress.mask
|
||
</td>
|
||
<td>
|
||
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Directory where the VIVO application will store
|
||
the data that it creates. This includes uploaded files (usually images)
|
||
and the Solr search index. Be sure this directory exists and is
|
||
writable by the user who the Tomcat service is running as.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
vitro.home.directory
|
||
</td>
|
||
<td>
|
||
/usr/local/vivo/data
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify an SMTP host that the application will
|
||
use for sending e-mail (Optional). If this is left blank, the contact
|
||
form will be hidden and disabled, and users will not be notified of
|
||
changes to their accounts.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
email.smtpHost
|
||
</td>
|
||
<td>
|
||
smtp.servername.edu
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify an email address which will appear as
|
||
the sender in e-mail notifications to users (Optional). If a user
|
||
replies to the notification, this address will receive the reply. If a
|
||
user's e-mail address is invalid, this address will receive the error
|
||
notice. If this is left blank, users will not be notified of changes to
|
||
their accounts.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
email.replyTo
|
||
</td>
|
||
<td>
|
||
vivoAdmin@my.domain.edu
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the JDBC URL of your database. Change
|
||
the end of the URL to reflect your database name (if it is not "vivo").
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.url
|
||
</td>
|
||
<td>
|
||
jdbc:mysql://localhost/vivo
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Change the username to match the authorized user
|
||
you created in MySQL.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.username
|
||
</td>
|
||
<td>
|
||
username
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Change the password to match the password you
|
||
created in MySQL.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.password
|
||
</td>
|
||
<td>
|
||
password
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the Jena triple store technology to use.
|
||
SDB is Jena's SPARQL database; this setting allows RDF data to scale
|
||
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
|
||
store with in-memory caching.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.tripleStoreType
|
||
</td>
|
||
<td>
|
||
SDB
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the maximum number of active connections
|
||
in the database connection pool to support the anticipated number of
|
||
concurrent page requests. It is not necessary to adjust this value when
|
||
using the RDB configuration.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.pool.maxActive
|
||
</td>
|
||
<td>
|
||
40
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the maximum number of database
|
||
connections that will be allowed to remain idle in the connection pool.
|
||
Default is 25% of the maximum number of active connections.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.pool.maxIdle
|
||
</td>
|
||
<td>
|
||
10
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Change the dbtype setting to use a database
|
||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||
for additional information.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.dbtype
|
||
</td>
|
||
<td>
|
||
MySQL
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify a driver class name to use a database
|
||
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
||
for this driver must be added to the the webapp/lib directory within
|
||
the vitro.core.dir specified above.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.driver
|
||
</td>
|
||
<td>
|
||
com.mysql.jdbc.Driver
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Change the validation query used to test
|
||
database connections only if necessary to use a database other than
|
||
MySQL. Otherwise, leave this value unchanged.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
VitroConnection.DataSource.validationQuery
|
||
</td>
|
||
<td>
|
||
SELECT 1
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
Specify the email address of the root user
|
||
account for the VIVO application. This user will have an initial
|
||
temporary password of 'rootPassword'. You will be prompted to create a
|
||
new password on first login.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row blue">
|
||
<td>
|
||
rootUser.emailAddress
|
||
</td>
|
||
<td>
|
||
vivoAdmin@my.domain.edu
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
The URI of a property that can be used to
|
||
associate an Individual with a user account. When a user logs in with a
|
||
name that matches the value of this property, the user will be
|
||
authorized to edit that Individual.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
selfEditing.idMatchingProperty
|
||
</td>
|
||
<td>
|
||
http://vivo.mydomain.edu/ns#networkId
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
The temporal graph visualization can require
|
||
extensive machine resources. This can have a particularly noticable
|
||
impact on memory usage if
|
||
<ul>
|
||
<li>
|
||
VIVO is configured to use Jena SDB,
|
||
</li>
|
||
<li>
|
||
The organization tree is deep,
|
||
</li>
|
||
<li>
|
||
The number of grants and publications is large.
|
||
</li>
|
||
</ul>
|
||
VIVO 1.3 release mitigates this problem by the way of a caching
|
||
mechanism and hence we can safely set this to be enabled by default.
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
visualization.temporal
|
||
</td>
|
||
<td>
|
||
enabled
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td colspan="2">
|
||
The temporal graph visualization is used to
|
||
compare different organizations/people within an organization on
|
||
parameters like number of publications or grants. By default, the app
|
||
will attempt to make its best guess at the top level organization in
|
||
your instance. If you're unhappy with this selection, uncomment out the
|
||
property below and set it to the URI of the organization individual you
|
||
want to identify as the top level organization. It will be used as the
|
||
default whenever the temporal graph visualization is rendered without
|
||
being passed an explicit org. For example, to use "Ponce School of
|
||
Medicine" as the top organization:
|
||
<br>
|
||
<span style="font-style: italic;">visualization.topLevelOrg =
|
||
http://vivo.psm.edu/individual/n2862</span>
|
||
<br>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd_row">
|
||
<td>
|
||
visualization.topLevelOrg
|
||
</td>
|
||
<td>
|
||
http://vivo.mydomain.edu/individual/topLevelOrgURI
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>
|
||
3. Apply any previous changes you have made to the new source
|
||
directory.
|
||
</p>
|
||
<blockquote>
|
||
<strong>Special notes regarding source files</strong>
|
||
<ul>
|
||
<li>
|
||
This process assumes any changes made to the application were
|
||
made in the source directory and deployed, and were not made directly
|
||
within the Tomcat webapps directory.
|
||
</li>
|
||
<li>
|
||
In many cases, simply copying the modified files from your
|
||
original source directory will not work since the files on which they
|
||
are based have changed. It will be necessary to inspect the new source
|
||
files and add any changes to them at that time.
|
||
</li>
|
||
<li>
|
||
NIH-funded VIVO implementations will need to apply the Google
|
||
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
||
in
|
||
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
||
A sample <code>googleAnalytics.ftl</code>
|
||
is included in the built-in
|
||
theme. This file serves only as an example, and you must replace the
|
||
tracking code shown with your institution's own tracking code. For
|
||
additional information about the GATC for the NIH-funded VIVO
|
||
implementation sites and a copy of your institution's tracking code,
|
||
see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
||
Google
|
||
Analytics wiki page</a>.
|
||
</li>
|
||
<li>
|
||
If you had used the <code>vivo/contrib/FLShibboleth</code>
|
||
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".
|
||
</li>
|
||
</ul>
|
||
</blockquote>
|
||
<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 from your VIVO source directory, run ant by typing: <code>ant all</code>
|
||
</p>
|
||
<p>
|
||
6. Start Apache Tomcat and log in to VIVO.
|
||
</p>
|
||
<h3 id="ontology">IV. Ontology Changes</h3>
|
||
<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.(timestamp).log</code>
|
||
</dt>
|
||
<dd>
|
||
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 corrective action needs to be taken.
|
||
</dd>
|
||
</dl>
|
||
<dl>
|
||
<dt>
|
||
<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
|
||
</dt>
|
||
<dd>
|
||
A log of errors that were encountered during the upgrade
|
||
process. This file should be empty if the upgrade was successful.
|
||
</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 type assertions of a deleted class will be removed.
|
||
<br>
|
||
All statements using a deleted property will be changed to use the
|
||
nearest available superproperty. If there is no available superproperty
|
||
then the statement will be deleted from the knowledge base. Note that
|
||
all removed and added data is recorded in the files in the changedData
|
||
directory.
|
||
</dd>
|
||
</dl>
|
||
<dl>
|
||
<dt>
|
||
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="template">V. Template changes</h3>
|
||
<ul>
|
||
<li>
|
||
<p>
|
||
The <code>${stylesheets}</code>, <code>${scripts}</code>, and<code>${headScripts}</code>
|
||
<code>add()</code>
|
||
methods now take
|
||
the full tag as an argument. This will require a change to all calls to
|
||
these methods in the templates. This change allows for specification of
|
||
attributes such as <code>media</code>
|
||
directly in the tag. For
|
||
example:
|
||
</p>
|
||
<blockquote>
|
||
1.2: <code>${stylesheets.add("/css/individual/individual.css")}</code>
|
||
<br>
|
||
1.3: <code>${stylesheets.add('<link rel="stylesheet"
|
||
href="${urls.base}/css/individual/individual.css" />')}</code>
|
||
</blockquote>
|
||
<p>
|
||
Note the inclusion of <code>${urls.base}</code>
|
||
in the 1.3
|
||
example. The <code>add()</code>
|
||
method no longer prefixes the context
|
||
path to the url, so the full url must be specified in the tag.
|
||
</p>
|
||
</li>
|
||
<li>
|
||
The <code>addFromTheme()</code>
|
||
methods of the <code>${stylesheets}</code>,<code>${scripts}</code>,
|
||
and<code>${headScripts}</code>
|
||
objects have been deleted. Substitute as
|
||
shown in the preceding example.
|
||
</li>
|
||
<li>
|
||
<code>propertyGroups.getPropertyAndRemoveFromList()</code>
|
||
in
|
||
the individual templates has been deprecated. The replacement method is<code>propertyGroups.pullProperty()</code>. There is no change in
|
||
functionality.
|
||
</li>
|
||
</ul>
|
||
<h3 id="listview">VI. List view changes</h3>
|
||
<code><query-base></code>
|
||
and <code><query-collated></code>
|
||
have been replaced with a single query <code><query-select></code>
|
||
that contains tags for fragments to be used only in the collated
|
||
version of the query. This and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
|
||
<p>
|
||
In release 1.3, the VIVO authorization system has some extensive
|
||
changes. In summary, these are:
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Each user will have a user account, even if the user logs in by
|
||
Shibboleth or some other external authentication system.
|
||
</li>
|
||
<li>
|
||
E-mail is used to notify user's when an account is created for
|
||
them, or when an administrator edits their account.
|
||
</li>
|
||
<li>
|
||
A "root" user account exists which has access to all pages and
|
||
all data fields. This is a powerful tool that can hold some surprises.
|
||
</li>
|
||
</ul>
|
||
<h4 id="accounts_created">i. User Accounts are created for externally
|
||
authenticated users</h4>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
With release 1.3, each authenticated user will have a user
|
||
account. If someone logs in using an external authentication system,
|
||
and no user account matches their external login credentials, an
|
||
account will be created.
|
||
</p>
|
||
<p>
|
||
The user will be prompted to enter information for the account
|
||
being created: first name, last name, and e-mail address.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h4 id="email_on_accounts">ii. E-mail address becomes an important part
|
||
of User Accounts</h4>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
Prior to release 1.3, each user account was identified by a
|
||
Username field. This field was labeled as “E-mail address” on some
|
||
pages in VIVO, but no mail was ever sent. In release 1.3, this has
|
||
changed, so the e-mail address is fully used, both for identification
|
||
and for communication with the user.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h5>a. User Account data is restructured</h5>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
Prior to release 1.3, the Username field (also referred to as
|
||
'e-mail address') was used for several purposes:
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
Idenfiying the user account.
|
||
</li>
|
||
<li>
|
||
Part of the user’s credentials when logging in (along with a
|
||
password).
|
||
</li>
|
||
<li>
|
||
Connecting the user account to an external authentication
|
||
system, like Shibboleth or CUWebAuth.
|
||
</li>
|
||
<li>
|
||
Connecting the user account to a personal Profile page.
|
||
</li>
|
||
</ul>
|
||
<p>
|
||
With release 1.3, these functions are handled by two separate
|
||
fields called EmailAddress field and ExternalAuthId.
|
||
</p>
|
||
<ul>
|
||
<li>
|
||
EmailAddress is used when logging in (along with a
|
||
password).
|
||
</li>
|
||
<li>
|
||
EmailAddress is used to send notifications to the user about
|
||
changes to his/her account (see below).
|
||
</li>
|
||
<li>
|
||
The ExternalAuthId is used when logging in using an external
|
||
authentication system.
|
||
</li>
|
||
<li>
|
||
The ExternalAuthId is used to connect the user account to a
|
||
personal Profile page.
|
||
<blockquote>
|
||
<strong>Note:</strong>
|
||
With release 1.3, the
|
||
ExternalAuthId can now be matched against either an untyped literal or
|
||
a string literal in the Profile page.
|
||
</blockquote>
|
||
</li>
|
||
</ul>
|
||
<p>
|
||
There are other changes to the internal structure of the user
|
||
accounts data, but they are important mostly to the VIVO software
|
||
developers, and you are not likely to notice them.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h5>b. Existing User Accounts are migrated</h5>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
If you are upgrading to VIVO release 1.3 from an existing VIVO
|
||
installation, the user accounts in your system will be migrated into
|
||
the new data structures. When migrating an account, both the
|
||
EmailAddress field and the ExternalAuthId field will be set to the
|
||
value of the Username field in the old account. The new account should
|
||
behave as the old account did.
|
||
</p>
|
||
<p>
|
||
When creating a new user account, or editing an existing one,
|
||
the system requires that your e-mail address be in a valid form, like <code>somebody@somewhere.edu</code>.
|
||
You
|
||
should plan for this as part of your migration to release 1.3
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h5>c. E-mail is incorporated into the workflow for User Accounts</h5>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
With release 1.3, VIVO users receive e-mail notifications when
|
||
an account is created or modified for them or by them.
|
||
</p>
|
||
<p>
|
||
When an administrator creates a user account, the user will
|
||
receive an e-mail notification, telling them that the account has been
|
||
created, and providing a link to VIVO that will allow them to set a
|
||
password on the account.
|
||
</p>
|
||
<blockquote>
|
||
<strong>Note:</strong>
|
||
when creating the account, the
|
||
administrator may indicate that it will only be used with an external
|
||
authentication system like Shibboleth or CUWebAuth. In this case, the
|
||
account will not require a password, and the e-mail notification
|
||
message to the user will not provide a password link.
|
||
</blockquote>
|
||
<p>
|
||
When an administrator edits a user account, he may choose to
|
||
reset the password. As with a new account, the user will receive
|
||
notification with a link to VIVO that will allow them to set a new
|
||
password.
|
||
</p>
|
||
<p>
|
||
If a user changes the e-mail address on his account, he will
|
||
receive a notification message to that effect.
|
||
</p>
|
||
<p>
|
||
If a user account is auto-created for a user with external
|
||
authentication credentials, the user will receive a notification
|
||
message.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h5>d. Disabling e-mail notificiation</h5>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
The e-mail notification relies on two configuration properties:<code>email.smtpHost</code>
|
||
and <code>email.replyTo</code>. If either of these properties is
|
||
missing or empty, VIVO will not attempt to send e-mail notifications to
|
||
users.
|
||
</p>
|
||
<p>
|
||
This can be useful for small or experimental installations of
|
||
VIVO, or where e-mail notification is not desired.
|
||
</p>
|
||
<p>
|
||
If e-mail notifications are disabled, an administrator must set
|
||
a password on each new account, since the user will have no way of
|
||
setting it. When the user logs in for the first time, VIVO will require
|
||
them to change their password to one of their own choosing.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
<h4 id="root_account">iii. Each VIVO installation will have a 'root'
|
||
account.</h4>
|
||
<dl>
|
||
<dd>
|
||
<p>
|
||
Prior to release 1.3, each VIVO installation was created with a
|
||
default administrator’s account. In release 1.3, there is no such
|
||
account. Instead, each VIVO installation will have a “root” account.
|
||
</p>
|
||
<p>
|
||
The email address for the root account is specified in
|
||
deploy.properties, like this:
|
||
</p>
|
||
<pre>rootUser.emailAddress = vivo_root@mydomain.edu</pre>
|
||
The password for this account is automatically set to <code>rootPassword</code>,
|
||
but
|
||
you will be required to change the password the first time you log
|
||
in.
|
||
<blockquote>
|
||
<strong>Note:</strong>
|
||
the <code>initialAdminUser</code>
|
||
is no longer use.
|
||
</blockquote>
|
||
<p>
|
||
The root account is not a site administrator’s account – it is
|
||
more powerful than a site administrator’s acocunt. The root account is
|
||
permitted to visit any page in a VIVO application. It is permitted to
|
||
see any data property, and to enter data into any field. As such, the
|
||
root account can be very useful and rather dangerous. It can also give
|
||
you a distorted view of what your VIVO site looks like, since data is
|
||
shown which other accounts cannot see.
|
||
</p>
|
||
<p>
|
||
The root account is not intended for routine, every day use.
|
||
The best way to use the root account is to create a site
|
||
administrator’s account. After that, use the root account only when
|
||
necessary.
|
||
</p>
|
||
</dd>
|
||
</dl>
|
||
</div>
|
||
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|
||
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|
||
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|
||
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|
||
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|
||
</small>
|
||
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|
||
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|
||
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|
||
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|
||
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|
||
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|
||
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|
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|
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|
||
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|
||
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|
||
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|
||
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|
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|
||
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|
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|
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||
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||
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