First shot at fleshing out the upgrade document.
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j2blake
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V1.4 Upgrade Guide</h1>
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<small>
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Upgrading from Release 1 V1.3 to Release 1 V1.4
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December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4
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</small>
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<toc>
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<ul>
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<li>
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<a href="#announcement">Release announcement for V1.4</a>
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</li>
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<li>
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<a href="#upgrade">Upgrade process for V1.4</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 1.3 to Version 1.4.
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This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
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at <a href="http://vivoweb.org/">VIVOweb.org</a>
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</p>
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<p>
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If you need to do a fresh install, please consult the VIVO Release V1.4 Installation
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Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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or the install.html file located in the <code>doc</code>
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directory of the VIVO source code distribution. The installation document also has a
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list of the required software and versions (there are no new hardware
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or software requirements for V1.4).
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</p>
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<h3 id="announcement">Release Announcement for V1.4</h3>
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<!-- Release Announcement -->
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<p><em>TBD</em></p>
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<br>
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<hr><!-- Page break --><!-- Upgrade process for V1.4 --><h2 id="upgrade">Upgrade process for V1.4</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="#changes">Noteworthy Changes</a>
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<br>
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<ol class="roman2">
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<li>
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<a href="#template_changes">Template changes</a>
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</li>
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<li>
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<a href="#proxy_editing">Profile editing by Proxies</a>
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</li>
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<li>
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<a href="#tomcat_setup">Change to Tomcat configuration</a>
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</li>
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</ol>
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</li>
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<li>
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<a href="#upgrade_process">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="roman3">
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<li>
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<a href="#verify_ontology_upgrade">Verify
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Ontology upgrade process</a>
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</li>
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<li>
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<a href="#ontology_knowledge_base">Ontology
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knowledge
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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="#termsofuse">Review the VIVO Terms of Use</a>
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</li>
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</ol>
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</toc>
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<h2>Template changes</h2>
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<ul>
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<li><code>${stylesheets.list}</code>, <code>${scripts.list}</code>, and <code>${headscripts.list}</code> have changed to
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<code>${stylesheets.list()}</code>, <code>${scripts.list()}</code>, and <code>${headscripts.list()}</code>, respectively.
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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
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with
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the following EXCEPTIONS:
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</p>
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<ul>
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<li>
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If you are still in RDB mode, it is required that you move
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your
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triple store to SDB while still at V1.2 (see <a href="#triple_store">Triple
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Store</a>
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info 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.
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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 root account after the upgrade
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process is complete will use the password previously set, NOT the
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default password used on the first login after the initial
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installation.
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</li>
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<li>
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The first time Apache Tomcat starts up after the upgrade, 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="changes">II. Noteworthy Changes</h3>
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<h4 id="template_changes">i. Template changes
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</h4>
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<ul>
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<li><code>${stylesheets.list}</code>, <code>${scripts.list}</code>, and <code>${headscripts.list}</code> have changed to
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<code>${stylesheets.list()}</code>, <code>${scripts.list()}</code>, and <code>${headscripts.list()}</code>, respectively.
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</li>
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(ryounes)
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</ul>
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<h2>addition to deploy.properties</h2>
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<ul>
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<li> What types of individuals may have proxy editors?
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<pre>proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization</pre>
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</li>
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</ul>
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<h4 id="proxy_editing">ii. Profile editing by Proxies
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</h4>
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<ul>
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<li>addition to deploy.properties</li>
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<li> What types of individuals may have proxy editors?
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<pre>proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization</pre>
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</li>
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(jblake)
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</ul>
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</ul>
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<h2>changes to the build script</h2>
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<ul>
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<li> Incremental builds go much faster, but at some cost:
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<h4 id="tomcat_setup">iii. Change to Tomcat configuration
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</h4>
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<ul>
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<li>Tomcat configuration</hli>
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<li>Specify URI encoding
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</li>
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</ul>
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(jblake)
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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
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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).
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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vitro.core.dir
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</td>
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<td>
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./vitro-core
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where tomcat is installed.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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tomcat.home
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</td>
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<td>
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/usr/local/tomcat
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Name of your VIVO application.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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webapp.name
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</td>
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<td>
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vivo
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</td>
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</tr>
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<tr>
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<td colspan="2">
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URL of Solr context used in local VIVO search.
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Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
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In the standard installation, the Solr context will be on the same
|
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server as VIVO, and in the same Tomcat instance. The path will be the
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VIVO webapp.name (specified above) + "solr"
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</td>
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</tr>
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<tr class="odd_row">
|
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<td>
|
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vitro.local.solr.url
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</td>
|
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<td>
|
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http://localhost:8080/vivosolr
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</td>
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</tr>
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<tr>
|
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<td colspan="2">
|
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Restricts access to the Solr search platform.
|
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One or more regular expressions, separated by commas. When a request is
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made to Solr, the IP address of the requestor must match one of the
|
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patterns, or the request will be rejected.
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<br>
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Examples:<code>
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<ul>
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<li>
|
||||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
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</li>
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<li>
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vitro.local.solr.ipaddress.mask =
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127\.0\.0\.1,0:0:0:0:0:0:0:1
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</li>
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||||
<li>
|
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vitro.local.solr.ipaddress.mask = 169.254.*
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</li>
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</ul>
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||||
</code>
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</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
vitro.local.solr.ipaddress.mask
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||||
</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">
|
||||
<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">
|
||||
<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">
|
||||
<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 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.
|
||||
<p>
|
||||
NOTE: The root user account has access to all data and all
|
||||
operations in VIVO. Data views may be surprising when logged in as the
|
||||
root user. It is best to create a Site Admin account to use for every
|
||||
day administrative tasks.
|
||||
</p>
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<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
|
||||
(the value of the property must be either a String literal or an untyped literal).
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
selfEditing.idMatchingProperty
|
||||
</td>
|
||||
<td>
|
||||
http://vivo.mydomain.edu/ns#networkId
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
If an external authentication system like Shibboleth or CUWebAuth is to be
|
||||
used, these properties say how the login button should be labeled, and which
|
||||
HTTP header will contain the user ID from the authentication system. If such
|
||||
a system is not to be used, leave these commented out. Consult the installation
|
||||
instructions for more details.
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
externalAuth.buttonText
|
||||
<br/>
|
||||
externalAuth.netIdHeaderName
|
||||
</td>
|
||||
<td>
|
||||
Log in using BearCat Shibboleth
|
||||
<br/>
|
||||
remote_userID
|
||||
</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>
|
||||
The organization tree is deep,
|
||||
</li>
|
||||
<li>
|
||||
The number of grants and publications is large.
|
||||
</li>
|
||||
</ul>
|
||||
VIVO V1.4 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>
|
||||
<code>visualization.topLevelOrg =
|
||||
http://vivo.psm.edu/individual/n2862</code>
|
||||
<br>
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
visualization.topLevelOrg
|
||||
</td>
|
||||
<td>
|
||||
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
An absolute file path, pointing to the root directory of the Harvester utility.
|
||||
You must include the final slash.
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
harvester.location
|
||||
</td>
|
||||
<td>
|
||||
/usr/local/vivo/harvester/
|
||||
</td>
|
||||
</tr>
|
||||
</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>full builds go a little slower</li>
|
||||
<li>if you delete a source file, you must do a full build to really get rid of it.</li>
|
||||
<li>
|
||||
This process assumes any changes made to the application
|
||||
were
|
||||
made in the source directory and deployed, and were not made directly
|
||||
within the Tomcat webapps directory.
|
||||
</li>
|
||||
<li>
|
||||
In many cases, simply copying the modified files from your
|
||||
original source directory will not work since the files on which they
|
||||
are based have changed. It will be necessary to inspect the new source
|
||||
files and add any changes to them at that time.
|
||||
</li>
|
||||
<li>
|
||||
NIH-funded VIVO implementations will need to apply the
|
||||
Google
|
||||
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
|
||||
in
|
||||
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
||||
A sample <code>googleAnalytics.ftl</code>
|
||||
is included in the built-in
|
||||
theme. This file serves only as an example, and you must replace the
|
||||
tracking code shown with your institution's own tracking code. For
|
||||
additional information about the GATC for the NIH-funded VIVO
|
||||
implementation sites and a copy of your institution's tracking code,
|
||||
see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
||||
Google
|
||||
Analytics
|
||||
wiki
|
||||
page</a>.
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li> Changes to solr deploy.</li>
|
||||
(jblake)
|
||||
</ul>
|
||||
|
||||
<h2>Tomcat configuration</h2>
|
||||
<ul>
|
||||
<li>Specify URI encoding
|
||||
</li>
|
||||
(jblake)
|
||||
</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 into VIVO as the root user when the upgrade is
|
||||
completed. Depending on the size of your database, the migration process may
|
||||
take up to several hours. When it is complete, you will
|
||||
see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
|
||||
</p>
|
||||
<p>
|
||||
7. As root or an administrator, request a rebuild of the Solr search index:
|
||||
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
|
||||
heading "Refresh Content".
|
||||
</p>
|
||||
<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="termsofuse">V. Review the VIVO Terms of Use</h3>
|
||||
<p>
|
||||
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
|
||||
you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
||||
area will be
|
||||
inserted into the "Terms of Use" statement. If you want to edit the text content more than just
|
||||
the "Site Name", the file can be found here:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
|
||||
Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose
|
||||
your changes next time you deploy for another reason.
|
||||
</p>
|
||||
<h3>Next Step ...</h3>
|
||||
<p>
|
||||
Now that you have VIVO up and running, please go read the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<!-- #wrapper-content -->
|
||||
<div id="footer" role="contentinfo">
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue