NIHVIVO-3845 update the Upgrade document for 1.5
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j2blake
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3 changed files with 180 additions and 18 deletions
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Apache Tomcat 6.x or 7.x <a href="http://tomcat.apache.org">http://tomcat.apache.org</a>
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Apache Tomcat 6.x or 7.x <a href="http://tomcat.apache.org">http://tomcat.apache.org</a>
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</li>
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</li>
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<li>
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<li>
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Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
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Apache Ant 1.8 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
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</li>
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</li>
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<li>
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<li>
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MySQL 5.1 or higher, <a href="http://www.mysql.com">http://www.mysql.com</a>
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MySQL 5.1 or higher, <a href="http://www.mysql.com">http://www.mysql.com</a>
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@ -684,10 +684,7 @@
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you will need to rerun the knowledge base migration.
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you will need to rerun the knowledge base migration.
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</dd>
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</dd>
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</dl>
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</dl>
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<p>
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</p>
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</p>
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<h3 id="kbm">IV. Knowledge Base Migration</h3>
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<h3 id="kbm">IV. Knowledge Base Migration</h3>
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<h4 id="kbmprocess">i.Knowledge Base Migration Process</h4>
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<h4 id="kbmprocess">i.Knowledge Base Migration Process</h4>
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<p>
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<p>
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@ -37,7 +37,15 @@
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<toc>
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<toc>
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<ol class="roman2">
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<ol class="roman2">
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<li><a href="#preparation">Before Performing the Upgrade</a></li>
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<li><a href="#preparation">Before Performing the Upgrade</a></li>
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<li><a href="#changes">Noteworthy Changes</a> <br>
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<li>
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<a href="#changes">Noteworthy Changes</a>
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<ol class="roman2">
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<li><a href="#upgradeAnt">Ant version 1.8 is required</a></li>
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<li><a href="#customShortView">Custom short views</a></li>
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<li><a href="#openSocial">Support for OpenSocial gadgets</a></li>
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<li><a href="#browsers">Supported Browsers</a></li>
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</ol>
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</li>
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<li><a href="#upgrade_process">Upgrade Instructions</a></li>
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<li><a href="#upgrade_process">Upgrade Instructions</a></li>
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<li><a href="#kbm">Knowledge Base Migration</a></li>
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<li><a href="#kbm">Knowledge Base Migration</a></li>
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<li><a href="#termsofuse">Review the VIVO Terms of Use</a></li>
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<li><a href="#termsofuse">Review the VIVO Terms of Use</a></li>
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@ -86,32 +94,41 @@
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</li>
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</li>
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</ul>
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</ul>
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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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<h3 id="changes">II. Noteworthy Changes</h3>
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<h3 id="changes">II. Noteworthy Changes</h3>
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<ul>
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<ul>
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<li>
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<li>
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<h4 id="upgradeAnt">Ant version 1.8 required</h4>
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<h4 id="upgradeAnt">Ant version 1.8 is required</h4>
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<p>
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<p>
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See J.Blake for details.
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The VIVO build script has been revised, and now requires features from
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version 1.8 of Apache Ant. Version 1.8 has been available since February, 2010.
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The current version of Apache Ant is 1.8.4.
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</p>
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<p>
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You can find recent versions of Apache Ant at
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<a href="http://ant.apache.org">http://ant.apache.org</a>
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</p>
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</p>
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</li>
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</li>
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<li>
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<li>
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<h4 id="customSearchView">Custom search views</h4>
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<h4 id="customSearchView">Custom short views</h4>
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<p>
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<p>
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"Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism.
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"Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism.
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If you have custom search views, you will need to re-configure them.
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If you have implemented custom search views, you will need to re-configure them to fit the new framework.
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See J.Blake for details.
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For an explanation of how to use custom search views, consult the
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<a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Using_Short_Views_in_Release_1.5">
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SourceForge Wiki page on custom search views
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</a>
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</p>
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</p>
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</li>
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</li>
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<li>
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<li>
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<h4 id="openSocial">Support for OpenSocial gadgets</h4>
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<h4 id="openSocial">Support for OpenSocial gadgets</h4>
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<p>
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<p>
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You can now add OpenSocial support to your VIVO instance. Look at setting_up_orng.html for details.
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VIVO can now be configured to support Open Research Networking Gadgets,
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See J.Blake for details.
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an extension of OpenSocial gadgets. For a description of this, and instructions
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for configuring VIVO, look at <a href="./setting_up_orng.html">setting_up_orng.html</a>, in this directory.
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</p>
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</p>
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</li>
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</li>
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<li>
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<li>
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<h4 id="openSocial">Supported Browsers</h4>
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<h4 id="browsers">Supported Browsers</h4>
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<p>
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<p>
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For this release, the following browsers are supported.
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For this release, the following browsers are supported.
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</p>
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</p>
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@ -137,11 +154,158 @@
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</ul>
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</ul>
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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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<h3 id="#upgrade_process">III. Upgrade Instructions</h3>
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<h3 id="#upgrade_process">III. Upgrade Instructions</h3>
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<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
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<p>
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<h3 id="kbm">IV .Knowledge Base Migration</h3>
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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 settings as in
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your previous installation and set values for the new variables as described
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below:
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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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Show only the most appropriate data values based on the Accept-Language
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header supplied by the browser. Default is true if not set.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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RDFService.languageFilter
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</td>
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<td>
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true
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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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These values are used when deploying VIVO as an OpenSocial container
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and integrating with OpenSocial gadgets.
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For instructions, look at <a href="./setting_up_orng.html">setting_up_orng.html</a>, in this directory.
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If you are creating
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a VIVO installation that does not use OpenSocial gadgets, these values are omitted.
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</td>
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</tr>
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<tr class="odd_row blue">
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<td>
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OpenSocial.shindigURL<br>
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OpenSocial.tokenService<br>
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OpenSocial.tokenKeyFile<br>
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OpenSocial.sandbox
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</td>
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<td>
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</td>
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</tr>
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</tbody>
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</table>
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<p>
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3. Apply any previous changes you have made to the new source
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directory.
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</p>
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<blockquote>
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<strong>Special notes regarding source files</strong>
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<ul>
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<li>
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This process assumes any changes made to the application
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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.
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</li>
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<li>
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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.
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</li>
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<li>
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NIH-funded VIVO implementations will need to apply the
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Google
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Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
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in
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the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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A sample <code>googleAnalytics.ftl</code>
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is included in the built-in
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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 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>.
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</li>
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</ul>
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</blockquote>
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<p>
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5. Stop Apache Tomcat and from your VIVO source directory, run
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ant
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by typing: <code>ant all</code>
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</p>
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<p>
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6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is
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completed. Depending on the size of your database, the migration process may
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take up to several hours. When it is complete, you will
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see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
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</p>
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<p>
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7. As root or an administrator, request a rebuild of the Solr search index:
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Go to the "Site Admin" page and click on "Rebuild Search Index" under the
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heading "Refresh Content".
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</p>
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<p>
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8. Review and save aside the knowledge base migration logs.
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The knowledge base migration process described in the next section will generate logs.
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These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since
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they may be a useful reference if questions come up about your 1.5 VIVO data after deployment,
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you should save them aside.
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The logs are created in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
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</p>
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<dl>
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<dt>
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<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log</code>
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</dt>
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<dd>
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A log of a summary of updates that were made to the knowledge
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base. This file should end with "Finished knowledge base migration".
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If this file contains any warnings they should be reviewed with your
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implementation team representative to see whether any corrective action needs to be taken.
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</dd>
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</dl>
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<dl>
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<dt>
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<code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
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</dt>
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<dd>
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A log of errors that were encountered during the upgrade
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process. This file should be empty if the upgrade was successful. If any errors are encountered
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you will need to rerun the knowledge base migration.
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</dd>
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</dl>
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<h3 id="#kbm">IV. Knowledge Base Migration</h3>
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<p>
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<p>
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Changes to the VIVO core ontology may require corresponding
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Changes to the VIVO core ontology may require corresponding
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modifications to the knowledge base instance data and ontology annotations.
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modifications to the knowledge base instance data and ontology annotations.
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@ -191,6 +355,7 @@
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An N3 file containing all the statements that were added to the knowledge base.
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An N3 file containing all the statements that were added to the knowledge base.
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</dd>
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</dd>
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</dl>
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</dl>
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<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
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<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
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<p>
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<p>
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VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
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VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
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