571 lines
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HTML
571 lines
24 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> July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1
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v1.3 </small> <toc>
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<ul>
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<li> <a href="#announcement">Release announcement for V1.3</a> </li>
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<li> <a href="#upgrade">Upgrade process for V1.3</a> </li>
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</ul>
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</toc>
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<p> 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
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href="http://vivoweb.org/support">support page</a> at <a
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href="http://vivoweb.org/">VIVOweb.org</a> </p>
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<p> 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> 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. </p>
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<h3 id="announcement">Release Announcement for V1.3</h3>
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<p>https://confluence.cornell.edu/x/3B4DCQ - get content from the wiki
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page before final release.<br>
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</p>
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<!-- Release Announcement -->
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<hr><!-- Page break --><!-- Upgrade process for V1.2 -->
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<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> <a href="#preparation">Before Performing the Upgrade</a> </li>
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<li> <a href="#triple_store">Triple Store</a> (BL)</li>
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<li> <a href="#upgrade_process">The Upgrade Process</a> </li>
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<li> <a href="#ontology">Ontology Changes</a> (SM)
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<ol class="roman2">
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<li> <a href="#verify_ontology_upgrade">Verify Ontology upgrade
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process</a> </li>
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<li> <a href="#ontology_knowledge_base">Ontology knowledge base
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manual review</a></li>
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</ol>
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</li>
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<li><a href="template">Template Changes</a> (RY)</li>
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<li><a href="listview">List View Changes</a> (RY)</li>
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<li><a href="authorization">Authorization Changes</a> (JB)<br>
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</li>
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<li><a href="#setup_sdb">Set Up SDB Store in the Background
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(Optional)</a> </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> Please ensure that backups are created of the: </p>
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<ul style="list-style-type: square;">
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<li> Tomcat webapps directory </li>
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<li> Original source directory </li>
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<li> MySQL database (mysqldump) </li>
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</ul>
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<p> The upgrade process is similar to the original install process with
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the following EXCEPTIONS: </p>
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<ul>
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<li> 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. </li>
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<li> It is not necessary to add RDF data. </li>
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<li> 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. </li>
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<li> 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
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href="#ontology">Ontology Upgrade</a> below for more information. </li>
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</ul>
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<h3 id="triple_store">II. Triple Store</h3>
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<p> 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. A VIVO 1.2 system running
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in RDB mode ... [<span style="color: rgb(255, 102, 102);">WHAT HAPPENS
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IF THEY UPGRADE in RDB MODE? - elly</span>]</p>
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<p> 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 make 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, though they are generated as soon as data is
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edited rather than in a background process. </p>
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<p> This copying process can take a number of hours to complete if the
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installation contains a large amount of RDF data (roughly a million
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triples or more). See section <a href="#setup_sdb">Set Up SDB Store in
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the Background (Optional)</a> for instructions on how to run this
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lengthy conversion process in the background while an RDB system is
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operating. Doing this will reduce the time necessary to start VIVO the
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first time it is run in SDB mode. </p>
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<h3 id="upgrade_process">III. The Upgrade Process</h3>
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<p> 1. Download the new distribution file and unpack it into a new
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source directory. </p>
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<p> 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,
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email.smptHost, email.replyTo, rootUser.emailAddress)<br>
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</p>
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<p><!-- deploy.properties table from install.html --></p>
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<table>
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<tbody>
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<tr>
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<th> Property Name </th>
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<th> Example Value </th>
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</tr>
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<tr>
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<td colspan="2"> 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/"
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<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> Vitro.defaultNamespace </td>
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<td> http://vivo.mydomain.edu/individual/ </td>
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</tr>
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<tr>
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<td colspan="2"> 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">
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<td> vitro.core.dir </td>
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<td> ./vitro-core </td>
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</tr>
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<tr>
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<td colspan="2"> Directory where tomcat is installed. </td>
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</tr>
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<tr class="odd_row">
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<td> tomcat.home </td>
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<td> /usr/local/tomcat </td>
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</tr>
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<tr>
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<td colspan="2"> Name of your VIVO application. </td>
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</tr>
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<tr class="odd_row">
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<td> webapp.name </td>
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<td> vivo </td>
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</tr>
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<tr>
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<td colspan="2"> URL of Solr context used in local VIVO search.
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Should consist of:
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<pre> scheme + servername + port + vivocontextpath + "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" </td>
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</tr>
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<tr class="odd_row">
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<td> vitro.local.solr.url </td>
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<td> http://localhost:8080/vivosolr </td>
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</tr>
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<tr>
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<td colspan="2"> 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. <br>
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Examples:
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<ul>
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<li>vitro.local.solr.ipaddress.mask = 127\.0\.0\.1</li>
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<li>vitro.local.solr.ipaddress.mask =
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127\.0\.0\.1,0:0:0:0:0:0:0:1</li>
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<li>vitro.local.solr.ipaddress.mask = 169.254.*</li>
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</ul>
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</td>
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</tr>
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<tr class="odd_row">
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<td> vitro.local.solr.ipaddress.mask </td>
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<td> 127\.0\.0\.1,0:0:0:0:0:0:0:1 </td>
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</tr>
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<tr>
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<td colspan="2"> Directory where the VIVO application will store
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the data that it creates. This includes uploaded files (usually images)
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and the Solr search index. Be sure this directory exists and is
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writable by the user who the Tomcat service is running as. </td>
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</tr>
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<tr class="odd_row">
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<td> vitro.home.directory </td>
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<td> /usr/local/vivo/data </td>
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</tr>
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<tr>
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<td colspan="2"> Specify an SMTP host that the application will
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use for sending e-mail (Optional). If this is left blank, the contact
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form will be hidden and disabled, and users will not be notified of
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changes to their accounts. </td>
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</tr>
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<tr class="odd_row">
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<td> email.smtpHost </td>
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<td> smtp.servername.edu </td>
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</tr>
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<tr>
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<td colspan="2"> Specify an email address which will appear as
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the sender in e-mail notifications to users (Optional). If a user
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replies to the notification, this address will receive the reply. If a
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user's e-mail address is invalid, this address will receive the error
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notice. If this is left blank, users will not be notified of changes to
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their accounts. </td>
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</tr>
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<tr class="odd_row">
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<td> email.replyTo </td>
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<td> vivoAdmin@my.domain.edu </td>
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</tr>
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<tr>
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<td colspan="2"> Specify the JDBC URL of your database. Change
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the end of the URL to reflect your database name (if it is not "vivo").
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</td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.url </td>
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<td> jdbc:mysql://localhost/vivo </td>
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</tr>
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<tr>
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<td colspan="2"> Change the username to match the authorized user
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you created in MySQL. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.username </td>
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<td> username </td>
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</tr>
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<tr>
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<td colspan="2"> Change the password to match the password you
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created in MySQL. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.password </td>
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<td> password </td>
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</tr>
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<tr>
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<td colspan="2"> Specify the Jena triple store technology to use.
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SDB is Jena's SPARQL database; this setting allows RDF data to scale
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beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
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store with in-memory caching. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.tripleStoreType </td>
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<td> SDB </td>
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</tr>
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<tr>
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<td colspan="2"> Specify the maximum number of active connections
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in the database connection pool to support the anticipated number of
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concurrent page requests. It is not necessary to adjust this value when
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using the RDB configuration. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.pool.maxActive </td>
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<td> 40 </td>
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</tr>
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<tr>
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<td colspan="2"> Specify the maximum number of database
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connections that will be allowed to remain idle in the connection pool.
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Default is 25% of the maximum number of active connections. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.pool.maxIdle </td>
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<td> 10 </td>
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</tr>
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<tr>
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<td colspan="2"> Change the dbtype setting to use a database
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other than MySQL. Otherwise, leave this value unchanged. Possible
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values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
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SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
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for additional information. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.dbtype </td>
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<td> MySQL </td>
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</tr>
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<tr>
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<td colspan="2"> Specify a driver class name to use a database
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other than MySQL. Otherwise, leave this value unchanged. This JAR file
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for this driver must be added to the the webapp/lib directory within
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the vitro.core.dir specified above. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.driver </td>
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<td> com.mysql.jdbc.Driver </td>
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</tr>
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<tr>
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<td colspan="2"> Change the validation query used to test
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database connections only if necessary to use a database other than
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MySQL. Otherwise, leave this value unchanged. </td>
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</tr>
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<tr class="odd_row">
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<td> VitroConnection.DataSource.validationQuery </td>
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<td> SELECT 1 </td>
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</tr>
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<tr>
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<td colspan="2"> Specify the email address of the root user
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account for the VIVO application. This user will have an initial
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temporary password of 'rootPassword'. You will be prompted to create a
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new password on first login. </td>
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</tr>
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<tr class="odd_row">
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<td> rootUser.emailAddress </td>
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<td> vivoAdmin@my.domain.edu </td>
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</tr>
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<tr>
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<td colspan="2"> The URI of a property that can be used to
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associate an Individual with a user account. When a user logs in with a
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name that matches the value of this property, the user will be
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authorized to edit that Individual. </td>
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</tr>
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<tr class="odd_row">
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<td> selfEditing.idMatchingProperty </td>
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<td> http://vivo.mydomain.edu/ns#networkId </td>
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</tr>
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<tr>
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<td colspan="2"> The temporal graph visualization can require
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extensive machine resources. This can have a particularly noticable
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impact on memory usage if
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<ul>
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<li> VIVO is configured to use Jena SDB, </li>
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<li> The organization tree is deep, </li>
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<li> The number of grants and publications is large. </li>
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</ul>
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The VIVO developers are working to make this visualization more
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efficient. In the meantime, VIVO release 1.2 guards against this impact
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by disabling the temporal graph visualization unless the
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"visualization.temporal" flag is set to "enabled". To enable it,
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uncomment the line for this setting. </td>
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</tr>
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<tr class="odd_row">
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<td> visualization.temporal </td>
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<td> enabled </td>
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</tr>
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<tr>
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<td colspan="2"> The temporal graph visualization is used to
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compare different organizations/people within an organization on
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parameters like number of publications or grants. By default, the app
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will attempt to make its best guess at the top level organization in
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your instance. If you're unhappy with this selection, uncomment out the
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property below and set it to the URI of the organization individual you
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want to identify as the top level organization. It will be used as the
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default whenever the temporal graph visualization is rendered without
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being passed an explicit org. For example, to use "Ponce School of
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Medicine" as the top organization: <br>
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<span style="font-style: italic;">visualization.topLevelOrg =
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http://vivo.psm.edu/individual/n2862</span> <br>
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</td>
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</tr>
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<tr class="odd_row">
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<td> visualization.topLevelOrg </td>
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<td> http://vivo-trunk.indiana.edu/individual/topLevelOrgURI </td>
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</tr>
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</tbody>
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</table>
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<p> 3. Apply any previous changes you have made to the new source
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directory. </p>
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<blockquote> <strong>Special notes regarding source files</strong>
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<ul>
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<li> This process assumes any changes made to the application were
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made in the source directory and deployed, and were not made directly
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within the Tomcat webapps directory. </li>
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<li> In many cases, simply copying the modified files from your
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original source directory will not work since the files on which they
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are based have changed. It will be necessary to inspect the new source
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files and add any changes to them at that time. </li>
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<li> NIH-funded VIVO implementations will need to apply the Google
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Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code> in
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the theme:
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<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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A sample <code>googleAnalytics.ftl</code> is included in the built-in
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theme. This file serves only as an example, and you must replace the
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tracking code shown with your institution's own tracking code. For
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additional information about the GATC for the NIH-funded VIVO
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implementation sites and a copy of your institution's tracking code,
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see the <a
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href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
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Google
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Analytics
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wiki
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page</a>. </li>
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<li> If you had used the <code>vivo/contrib/FLShibboleth</code>
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code in your previous release, you should stop using it. Consult <code>install.html</code>
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or <a href="VIVO_Release-1-v1.2_Installation_Guide.pdf">VIVO Release 1
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v1.2 Installation Guide</a> on "Using an External Authentication System
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with VIVO". </li>
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</ul>
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</blockquote>
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<p> 4. If you had modified <code>web.xml</code> to configure the
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Pellet Reasoner (as described in the installation instructions), repeat
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that modification. </p>
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<p> 5. Stop Apache Tomcat and run ant by typing: <code>ant all</code> </p>
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<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
|
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verify that the automated upgrade process was executed
|
|
successfully. The ontology alignment process will create the
|
|
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
|
</p>
|
|
<dl>
|
|
<dt> <code>ontologies/update/logs/knowledgeBaseUpdate.log</code> </dt>
|
|
<dd> 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.error.log</code>
|
|
</dt>
|
|
<dd> A log of errors that were encountered during the upgrade
|
|
process. This file should be empty if the upgrade was successful. </dd>
|
|
</dl>
|
|
<dl>
|
|
<dt> <code>ontologies/update/changedData/removedData.n3</code> </dt>
|
|
<dd> An N3 file containing all the statements that were removed from
|
|
the knowledge base. </dd>
|
|
</dl>
|
|
<dl>
|
|
<dt> <code>ontologies/update/changedData/addedData.n3</code> </dt>
|
|
<dd> An N3 file containing all the statements that were added to the
|
|
knowledge base. </dd>
|
|
</dl>
|
|
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual
|
|
review</h4>
|
|
<p> Changes to the VIVO core ontology may require corresponding
|
|
modifications of the knowledge base instance data and local ontology
|
|
extensions. </p>
|
|
<p> When Apache Tomcat starts up following the upgrade, it will
|
|
initiate a process to examine the knowledge base and apply necessary
|
|
changes. Not all of the modifications that may be required can be
|
|
automated, so manual review of the knowledge base is recommended after
|
|
the automated upgrade process. The automated process will make only the
|
|
following types of changes: </p>
|
|
<dl>
|
|
<dt> Class or Property renaming </dt>
|
|
<dd> All references to the class (in the subject or object position)
|
|
will be updated to the new name. References to the property will be
|
|
updated to the new name. </dd>
|
|
</dl>
|
|
<dl>
|
|
<dt> Class or Property deletion </dt>
|
|
<dd> All individuals in a deleted class will be removed. <br>
|
|
All statements using a deleted property will be changed to use the
|
|
nearest available superproperty. If there is no available superproperty
|
|
then the statement will be deleted from the knowledge base. Note that
|
|
all removed and added data is recorded in the files in the changedData
|
|
directory. </dd>
|
|
</dl>
|
|
<dl>
|
|
<dt> Property addition </dt>
|
|
<dd> If a newly added property is the inverse of a previously
|
|
existing property, the inverse of any statements using the pre-existing
|
|
property will be asserted. </dd>
|
|
</dl>
|
|
<dl>
|
|
<dt> Annotation property default values </dt>
|
|
<dd> If a site has modified the value of a vitro annotation (such as
|
|
displayRankAnnot or displayLimitAnnot) so that it is no longer using
|
|
the default, then that setting will be left unchanged. <br>
|
|
If a site is using the default value of a vitro annotation, and the
|
|
default has been changed in the new version of the ontology, then the
|
|
new default value will be propagated to the knowledge base. </dd>
|
|
</dl>
|
|
<blockquote> <strong>Please note:</strong> The vivo-basic theme has
|
|
been deprecated and is no longer supported </blockquote>
|
|
<p> For details on the new structure of themes in 1.2 and further
|
|
information regarding the development of your own custom theme, please
|
|
review the <a
|
|
href="http://www.vivoweb.org/support/user-guide/administration"
|
|
title="Download VIVO documentation" target="_blank">Site
|
|
Administrator's Guide</a>. This document will focus on updating an
|
|
existing pre 1.2 theme.<br>
|
|
</p>
|
|
<h3 id="template">V. Template changes [see RY for further details]</h3>
|
|
<ul>
|
|
<li>
|
|
<p>${stylesheets}, ${scripts}, and ${headScripts} add() methods now
|
|
take the full tag as an argument. This will require a change to all
|
|
calls to this method in the templates. This change allows for
|
|
specification of the media and other attributes. Example:</p>
|
|
<ul>
|
|
<li>1.2: ${stylesheets.add("/css/individual/individual.css")}</li>
|
|
<li>1.3: ${stylesheets.add('<link rel="stylesheet"
|
|
href="${urls.base}/css/individual/individual.css" />')}</li>
|
|
</ul>
|
|
</li>
|
|
<li>The addFromTheme() methods of the ${stylesheets}, ${scripts}, and
|
|
${headScripts} objects has been deleted.</li>
|
|
<li>propertyGroups.getPropertyAndRemoveFromList() has been
|
|
deprecated. The replacement method is propertyGroups.pullProperty(). No
|
|
change in functionality.</li>
|
|
</ul>
|
|
<h3 id="listview">VI. List view changes [see RY for further details]</h3>
|
|
<ul>
|
|
<li><query-base> and <query-collated> have been replaced
|
|
with a single query <query-select> that contains tags for
|
|
fragments to be used only in the collated version of the query. </li>
|
|
<li>This and other changes are documented in
|
|
vitro/doc/list_view_configuration_guidelines.txt.</li>
|
|
</ul>
|
|
<h3 id="authorization">VII. Authorization changes [see JB for further
|
|
details]</h3>
|
|
<ul>
|
|
<li>selfEditing.idMatchingProperty will now match String literals as
|
|
well as untyped literals.</li>
|
|
<li>'initialAdminUser' property is replaced by
|
|
'rootUser.emailAddress' - initial password is 'rootPassword'</li>
|
|
<li>Tell what happens to user accounts in the migration.</li>
|
|
</ul>
|
|
<h3 id="setup_sdb">VIII. Set Up SDB Store in the Background (Optional)</h3>
|
|
<p> If your VIVO installation is running in RDB mode, and you'd like to
|
|
convert to SDB, you can start the conversion process in the background
|
|
while the RDB system is running. This will reduce the delay in initial
|
|
startup after the application is redeployed with deploy.properties set
|
|
for SDB. Note that it is important not to edit any data anywhere in the
|
|
application while this background conversion is running. </p>
|
|
<p> To start the SDB conversion, log in as a system administrator and
|
|
request /sdbsetup (For example, if your VIVO is installed at
|
|
http://vivo.myuniversity.edu/ you would type
|
|
http://vivo.myuniversity.edu/sdbsetup into your browser). </p>
|
|
<p> Click the button that appears on this page. </p>
|
|
<p> During the course of the SDB setup, which may take several hours on
|
|
a large database, subsequent requests to /sdbsetup will display a
|
|
message that the operation is still in progress. When a request for
|
|
this page shows a message that the SDB setup has completed
|
|
successfully, shut down Tomcat, set deploy.properties to SDB mode,
|
|
redeploy, and restart Tomcat. VIVO will now be running from the SDB
|
|
store. </p>
|
|
</div>
|
|
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