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Adding BrianL's note about MySql version.

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ejc12 2011-02-10 02:22:37 +00:00
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doc/upgrade-1.2.html
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<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>VIVO</title> <title>VIVO</title>
<link rel="stylesheet" href="./css/doc.css" /> <link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head> </head>
<body> <body>
<div id="branding" role="banner"> <div id="branding" role="banner">
@ -26,7 +27,7 @@
</li> </li>
</ul> </ul>
</toc> </toc>
<p> <p>
This document provides a short description of the steps involved in This document provides a short description of the steps involved in
upgrading your installation of VIVO from Release 1, Version 1.1 to upgrading your installation of VIVO from Release 1, Version 1.1 to
Version 1.2. This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a> 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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<h4>Storage model</h4> <h4>Storage model</h4>
<p> <p>
While server memory capacity has increased significantly in recent While server memory capacity has increased significantly in recent
years, VIVO's reliance on in-memory caching of RDF data had put limits years, VIVO's reliance on in-memory caching of RDF data had put limits
on the ultimate scalability of VIVO instances and potentially increased on the ultimate scalability of VIVO instances and potentially increased
the cost of servers required to support VIVO.&nbsp; the cost of servers required to support VIVO.&nbsp;
<br> <br>
</p> </p>
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<h4>Ontology</h4> <h4>Ontology</h4>
<p> <p>
VIVO 1.2 includes a new ontology module representing research VIVO 1.2 includes a new ontology module representing research
resources including biological specimens, human studies, instruments, resources including biological specimens, human studies, instruments,
organisms, protocols, reagents, and research opportunities. This module organisms, protocols, reagents, and research opportunities. This module
is aligned with the top-level ontology classes and properties from the is aligned with the top-level ontology classes and properties from the
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>. NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
</p> </p>
<h3>Associated VIVO releases</h3> <h3>Associated VIVO releases</h3>
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<ul> <ul>
<li> <li>
DO NOT reinstall MySQL or recreate the MySQL database. Please DO NOT reinstall MySQL or recreate the MySQL database. Please
ensure that you back-up the MySQL database. ensure that you back-up the MySQL database. Also note that VIVO 1.2 will
not run on older versions of MySQL that may have worked with 1.1.1.
Be sure to run VIVO 1.2 with MySQL 5.1 or higher. Using unsupported
versions may result in strange error messages related to table formatting or
other unexpected problems.
</li> </li>
<li> <li>
It is not necessary to add RDF data. It is not necessary to add RDF data.
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the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre> the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
A sample <code>googleAnalytics.ftl</code> A sample <code>googleAnalytics.ftl</code>
is included in the built-in is included in the built-in
theme. This file serves only as an example, and you must replace the theme. This file serves only as an example, and you must replace the
tracking code shown with your institution's own tracking code. For tracking code shown with your institution's own tracking code. For
additional information about the GATC for the NIH-funded VIVO additional information about the GATC for the NIH-funded VIVO
implementation sites and a copy your institution's tracking code, see implementation sites and a copy your institution's tracking code, see
the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
Google Google
Analytics Analytics
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</dt> </dt>
<dd> <dd>
A log of a summary of updates that were made to the knowledge base and 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 notes about some recommended manual reviews. This file should end with
"Finished knowledge base migration". "Finished knowledge base migration".
If this file contains any warnings they should be reviewed with If this file contains any warnings they should be reviewed with
your implementation team representative to see whether any your implementation team representative to see whether any
corrective action needs to be taken. corrective action needs to be taken.
</dd> </dd>
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<h3 id="fileSystem">IV. File Storage System Upgrade</h3> <h3 id="fileSystem">IV. File Storage System Upgrade</h3>
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4> <h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
<p> <p>
Each uploaded file exists as an individual entity in VIVO. When the Each uploaded file exists as an individual entity in VIVO. When the
browser requests an upload file from VIVO, the data model is queried to browser requests an upload file from VIVO, the data model is queried to
find out where the file is actually stored, so it can be downloaded to find out where the file is actually stored, so it can be downloaded to
the browser. the browser.
</p> </p>
<p> <p>
In VIVO release 1.2 this storage location, In VIVO release 1.2 this storage location,
known as the "Alias URL" for the uploaded file, known as the "Alias URL" for the uploaded file,
is stored in the file entity. is stored in the file entity.
That way, pages that contain many files can be displayed much more quickly. That way, pages that contain many files can be displayed much more quickly.
</p> </p>
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</dl> </dl>
</div> </div>
<!-- end of content --> <!-- end of content -->
<div role="contentinfo"> <div id="footer" role="contentinfo">
<p class="copyright"> <p class="copyright">
<small> <small>
&copy;2011 &copy;2011
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</small> </small>
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a> | Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
</p> </p>
<nav role="navigation"> <div id="nav" role="navigation">
<ul id="footer-nav" role="list"> <ul id="footer-nav" role="list">
<li role="listitem"> <li role="listitem">
<a href="http://vivoweb.org/about">About</a> <a href="http://vivoweb.org/about">About</a>
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<a href="http://www.vivoweb.org/support" target="blank">Support</a> <a href="http://www.vivoweb.org/support" target="blank">Support</a>
</li> </li>
</ul> </ul>
</nav> </div>
</div> </div>
</body> </body>
</html> </html>