The upgrade document does require discussion of the file system, after all.
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@ -65,7 +65,6 @@
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</li>
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<li>
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<a href="#ontology">Ontology Upgrade</a>
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</li>
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<ol class="roman2">
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<li>
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<a href="#verify_ontology_upgrade">Verify Ontology upgrade process</a>
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<a href="#ontology_knowledge_base">Ontology knowledge base 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="#fileSystem">File Storage System Upgrade</a>
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<ol class="roman2">
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<li>
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<a href="#verify_ontology_upgrade">Changes to the File Storage System</a>
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</li>
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<li>
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<a href="#verify_ontology_upgrade">Verify File Storage System upgrade process</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="#theme">Theme Modifications</a>
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</li>
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new default value will be propagated to the knowledge base.
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</dd>
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</dl>
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<h3>IV. Theme Changes</h3>
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<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
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<h4>A. 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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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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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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<p>
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When Apache Tomcat starts up after the upgrade,
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it will initiate a process to calculate the "Alias URL"
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for each existing file and store it in the data model for fast access.
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</p>
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<h4>B. Verify File Storage System upgrade process</h4>
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<p>
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The File Storage upgrade process will create a log file in the
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VIVO upload directory. You should review this file to ensure that
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this upgrade worked properly.
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</p>
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<dl>
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<dt>
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<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
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</dt>
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<dd>
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A log of the upgrade process. The actual filename includes a timestamp
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that tells when the upgrade executed.
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This file should end with
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<code>Finished adding alias URLs to FileByteStreams.</code>
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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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</dl>
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<h3>V. Theme Changes</h3>
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<p>
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VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
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engine for generating web pages. The theme is located in /vivo/themes/wilma and
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