Adding BrianL's note about MySql version.
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<head>
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<meta charset="utf-8" />
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<title>VIVO</title>
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<link rel="stylesheet" href="./css/doc.css" />
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<link rel="stylesheet" href="./css/doc.css" media="screen" />
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<link rel="stylesheet" href="./css/print.css" media="print" />
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</head>
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<body>
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<div id="branding" role="banner">
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@ -26,7 +27,7 @@
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</li>
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</ul>
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</toc>
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<p>
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<p>
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This document provides a short description of the steps involved in
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upgrading your installation of VIVO from Release 1, Version 1.1 to
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Version 1.2. This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
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@ -67,8 +68,8 @@
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<h4>Storage model</h4>
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<p>
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While server memory capacity has increased significantly in recent
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years, VIVO's reliance on in-memory caching of RDF data had put limits
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on the ultimate scalability of VIVO instances and potentially increased
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years, VIVO's reliance on in-memory caching of RDF data had put limits
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on the ultimate scalability of VIVO instances and potentially increased
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the cost of servers required to support VIVO.
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<br>
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</p>
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@ -90,9 +91,9 @@
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<h4>Ontology</h4>
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<p>
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VIVO 1.2 includes a new ontology module representing research
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resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
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is aligned with the top-level ontology classes and properties from the
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resources including biological specimens, human studies, instruments,
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organisms, protocols, reagents, and research opportunities. This module
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is aligned with the top-level ontology classes and properties from the
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NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
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</p>
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<h3>Associated VIVO releases</h3>
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@ -165,7 +166,11 @@
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<ul>
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<li>
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DO NOT reinstall MySQL or recreate the MySQL database. Please
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ensure that you back-up the MySQL database.
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ensure that you back-up the MySQL database. Also note that VIVO 1.2 will
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not run on older versions of MySQL that may have worked with 1.1.1.
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Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using unsupported
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versions may result in strange error messages related to table formatting or
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other unexpected problems.
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</li>
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<li>
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It is not necessary to add RDF data.
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@ -541,10 +546,10 @@
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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 your institution's tracking code, see
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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 your institution's tracking code, see
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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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@ -587,9 +592,9 @@
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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 base and
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notes about some recommended manual reviews. This file should end with
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"Finished knowledge base migration".
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If this file contains any warnings they should be reviewed with
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notes about some recommended manual reviews. This file should end with
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"Finished knowledge base migration".
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If this file contains any warnings they should be reviewed with
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your implementation team representative to see whether any
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corrective action needs to be taken.
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</dd>
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@ -686,14 +691,14 @@
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<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
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<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
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<p>
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Each uploaded file exists as an individual entity in VIVO. When the
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browser requests an upload file from VIVO, the data model is queried to
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Each uploaded file exists as an individual entity in VIVO. When the
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browser requests an upload file from VIVO, the data model is queried to
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find out where the file is actually stored, so it can be downloaded to
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the browser.
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</p>
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<p>
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In VIVO release 1.2 this storage location,
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known as the "Alias URL" for the uploaded file,
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known as the "Alias URL" for the uploaded file,
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is stored in the file entity.
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That way, pages that contain many files can be displayed much more quickly.
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</p>
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@ -828,7 +833,7 @@
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</dl>
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</div>
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<!-- end of content -->
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<div role="contentinfo">
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<div id="footer" role="contentinfo">
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<p class="copyright">
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<small>
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©2011
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@ -836,7 +841,7 @@
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</small>
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| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
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</p>
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<nav role="navigation">
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<div id="nav" role="navigation">
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<ul id="footer-nav" role="list">
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<li role="listitem">
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<a href="http://vivoweb.org/about">About</a>
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@ -848,7 +853,7 @@
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<a href="http://www.vivoweb.org/support" target="blank">Support</a>
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</li>
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</ul>
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</nav>
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</div>
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</div>
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</body>
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</html>
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