Editorial changes. When updating from Nick's version, lost section VII re optional SDB store text.
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@ -35,7 +35,7 @@
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</p>
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</p>
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<p>
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<p>
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If you need to do a fresh install, please consult the VIVO Release 1 v1.2
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If you need to do a fresh install, please consult the VIVO Release 1 v1.2
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Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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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>
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or the install.html file located in the <code>doc</code>
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directory of the VIVO source code distribution. The installation
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directory of the VIVO source code distribution. The installation
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document also has a list of the required software and versions.
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document also has a list of the required software and versions.
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@ -48,8 +48,8 @@
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release also features two new visualization options: temporal graphing
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release also features two new visualization options: temporal graphing
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for organizations, and personal visualizations extended to cover grants
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for organizations, and personal visualizations extended to cover grants
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as well as publications. The VIVO Harvester library has also been
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as well as publications. The VIVO Harvester library has also been
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significantly improved and expanded in scope for its 1.0 release
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significantly improved and expanded in scope for its 1.0 release
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through the VIVO SourceForge project at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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</p>
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<h4>Templating system for page generation, navigation, and theming</h4>
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<h4>Templating system for page generation, navigation, and theming</h4>
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<p>
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<p>
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@ -101,8 +101,8 @@
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<p>
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<p>
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The Harvester development team is releasing version 1.0 of the VIVO
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The Harvester development team is releasing version 1.0 of the VIVO
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Harvester library, an extensible data ingest and updating framework
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Harvester library, an extensible data ingest and updating framework
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with sample configurations for loading PubMed publication, grants, and
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with sample configurations for loading PubMed publication, grants, and
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human resources data. The Harvester is available at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
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</p>
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</p>
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
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<toc>
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<toc>
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@ -110,7 +110,7 @@
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<li>
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<li>
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<a href="#preparation">Before Performing the Upgrade</a>
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<a href="#preparation">Before Performing the Upgrade</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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<a href="#triple_store">Chose Triple Store</a>
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<a href="#triple_store">Chose Triple Store</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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@ -145,7 +145,7 @@
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<li>
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<li>
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<a href="#theme">Theme Modifications</a>
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<a href="#theme">Theme Modifications</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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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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</li>
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</li>
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</ol>
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</ol>
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@ -197,7 +197,7 @@
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<h3 id="triple_store">II. Choose Triple Store</h3>
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<h3 id="triple_store">II. Choose Triple Store</h3>
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<p>
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<p>
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VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
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VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
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Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was
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Jena's legacy relational database store (RDB), and Jena's SPARQL database (SDB). RDB was
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used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
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used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
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entire RDF model in the server's main memory. The memory available to VIVO limits the
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entire RDF model in the server's main memory. The memory available to VIVO limits the
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number of RDF statements that may be stored.
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number of RDF statements that may be stored.
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@ -221,17 +221,17 @@
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</p>
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</p>
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<p>
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<p>
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A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
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A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
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receive required ontology updates. Attempting to run an upgraded system initially in SDB will
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to receive required ontology updates. Attempting to run an upgraded system initially in SDB will
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result in a logged error message, and the application will not start. After the system starts
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result in a logged error message, and the application will not start. After the system starts
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up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
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up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
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Upon restart, the data in the RDB store will be copied to the SDB store.
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Upon restart, the data in the RDB store will be copied to the SDB store.
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</p>
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</p>
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<p>
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<p>
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This copying process can take a number of hours to complete if the installation contains a large
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This copying process can take a number of hours to complete if the installation contains a large
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amount of RDF data (roughly a million triples or more). See section
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amount of RDF data (roughly a million triples or more). See section <a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
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<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a> for instructions on how
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for instructions on how
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to run this lengthy conversion process in the background while an RDB system is operating.
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to run this lengthy conversion process in the background while an RDB system is operating.
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Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
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Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
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</p>
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</p>
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<h3 id="upgrade_process">III. The Upgrade Process</h3>
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<h3 id="upgrade_process">III. The Upgrade Process</h3>
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<p>
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<p>
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@ -260,7 +260,7 @@
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RDF resources available for harvest using linked data. Requests for RDF
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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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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
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the client. To make this possible, VIVO's default namespace must have
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certain structure and begin with the public web address of the VIVO
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a 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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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/" 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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"http://vivo.example.edu/individual/" in order to support linked data.
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@ -322,7 +322,7 @@
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<tr>
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<tr>
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<td colspan="2">
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<td colspan="2">
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Directory where uploaded files will be stored.
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Directory where uploaded files will be stored.
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Be sure this directory exists and is writable by the user that
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Be sure this directory exists and is writable by the user who
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the Tomcat service is running as.
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the Tomcat service is running as.
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</td>
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</td>
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</tr>
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</tr>
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<tr>
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<tr>
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<td colspan="2">
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<td colspan="2">
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Directory where the Lucene search index will be
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Directory where the Lucene search index will be
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built. Be sure this directory exists and is writable by the user that
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built. Be sure this directory exists and is writable by the user who
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the Tomcat service is running as.
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the Tomcat service is running as.
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</td>
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</td>
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</tr>
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</tr>
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@ -367,7 +367,7 @@
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<tr>
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<tr>
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<td colspan="2">
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<td colspan="2">
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Specify the JDBC URL of your database. Change
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Specify the JDBC URL of your database. Change
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the end of theURL to reflect your database name (if it is not "vivo").
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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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</td>
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</tr>
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</tr>
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<tr class="odd_row">
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<tr class="odd_row">
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The temporal graph visualization can require extensive machine resources.
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The temporal graph visualization can require extensive machine resources.
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This can have a particularly noticable impact on memory usage if
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This can have a particularly noticable impact on memory usage if
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<ul>
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<ul>
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<li> VIVO is configured to use Jena SDB, </li>
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<li>
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<li> The organization tree is deep, </li>
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VIVO is configured to use Jena SDB,
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<li> The number of grants and publications is large. </li>
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</li>
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<li>
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The organization tree is deep,
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</li>
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<li>
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The number of grants and publications is large.
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</li>
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</ul>
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</ul>
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The VIVO developers are working to make this visualization more efficient.
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The VIVO developers are working to make this visualization more efficient.
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In the meantime, VIVO release 1.2 guards against this impact by disabling
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In the meantime, VIVO release 1.2 guards against this impact by disabling
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temporal graph visualization unless the "visualization.temporal" flag is
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temporal graph visualization unless the "visualization.temporal" flag is
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set to "enabled".
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set to "enabled".
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</td>
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</td>
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<li>
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<li>
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NIH-funded VIVO implementations will need to apply the Google
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NIH-funded VIVO implementations will need to apply the Google
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Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
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Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
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in the theme:
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in the theme: <pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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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>
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A sample <code>googleAnalytics.ftl</code>
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is included in the built-in theme. This file serves only as an example,
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is included in the built-in theme. This file serves only as an example,
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and you must replace the tracking code shown with your institution's own
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and you must replace the tracking code shown with your institution's own
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tracking code. For additional information about the GATC for the NIH-funded
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tracking code. For additional information about the GATC for the NIH-funded
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VIVO implementation sites and a copy your institution's tracking code, see
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VIVO 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">
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the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO Google Analytics wiki page</a>.
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VIVO Google Analytics wiki page</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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If you had used the <code>vivo/contrib/FLShibboleth</code>
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If you had used the <code>vivo/contrib/FLShibboleth</code>
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<dd>
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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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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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notes about some recommended manual reviews. This file should end with
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"Finished knowledge base migration".
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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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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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your implementation team representative to see whether any
|
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corrective action needs to be taken.
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corrective action needs to be taken.
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</dd>
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</dd>
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</dl>
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</dl>
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new default value will be propagated to the knowledge base.
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new default value will be propagated 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="fileSystem">V. File Storage System Upgrade</h3>
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<h3 id="fileSystem">V. 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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<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
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<p>
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<p>
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Each uploaded file exists as an individual in VIVO. When the browser
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Each uploaded file exists as an individual in VIVO. When the browser
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requests an uploaded file from VIVO, the data model is queried to find
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requests an uploaded file from VIVO, the data model is queried to find
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out where the file is actually stored, so it can be downloaded to the
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out where the file is actually stored, so it can be downloaded to the
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browser.
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browser.
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</p>
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</p>
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<p>
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<p>
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In VIVO release 1.2 this storage location, known as the "Alias URL" for
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In VIVO 1.2 this storage location, known as the "Alias URL" for
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the uploaded file, is stored in the file individual. That way, pages that
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the uploaded file, is stored in the file individual. That way, pages that
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contain many files can be displayed much more quickly.
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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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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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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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for each existing file and store it in the data model for fast access.
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</p>
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</p>
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<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
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<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
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<p>
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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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The File Storage upgrade process will create a log file in the
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<dd>
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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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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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that tells when the upgrade executed.
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This file should end with
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This file should end with<code>Finished adding alias URLs to FileByteStreams.</code>
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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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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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corrective action needs to be taken.
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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="theme">VI. Theme Changes</h3>
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<h3 id="theme">VI. Theme Modifications</h3>
|
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<h4 id="#newTheme">Introducing a New Default Theme</h4>
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<h4 id="#newTheme">Introducing a New Default Theme</h4>
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<p>
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<p>
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VIVO 1.2 includes a new default theme called <strong>wilma</strong> (located in
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VIVO 1.2 includes a new default theme called <strong>wilma</strong>
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/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
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(located in
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create your own theme using wilma as a starting point, please review the
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/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
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<a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">
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create your own theme using wilma as a starting point, please review the <a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">Site Administrator's Guide</a>.
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Site Administrator's Guide</a>.
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</p>
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</p>
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<blockquote id="vivoBasicDeprecated">
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<blockquote id="vivoBasicDeprecated">
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<h4>
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<h4>The vivo-basic theme has been deprecated with the 1.2 release and is not
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The vivo-basic theme has been deprecated with the 1.2 release and is not
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recommended for production instances.</h4>
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recommended for production instances.
|
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</h4>
|
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<p>
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<p>
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Since vivo-basic was the default theme for all previous releases, it is
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Since vivo-basic was the default theme for all previous releases, it is
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included as part of VIVO 1.2 to help with the transition of upgrading
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included as part of VIVO 1.2 to help with the transition of upgrading
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existing installations to the latest code, but all vivo-basic development
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existing installations to the latest code, but all vivo-basic development
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has ceased and it will not be distributed in future releases.
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has ceased and it will not be distributed in future releases.
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</p>
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</p>
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following:
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following:
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</p>
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</p>
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<ul>
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<ul>
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<li>new primary menu for site navigation (replaces tabs)</li>
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<li>
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<li>home page with class group browse and visual graph</li>
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new primary menu for site navigation (replaces tabs)
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<li>menu pages with class group and individual browse</li>
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</li>
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<li>
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home page with class group browse and visual graph
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</li>
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<li>
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menu pages with class group and individual browse
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</li>
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</ul>
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</ul>
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</blockquote>
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</blockquote>
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<h4 id="templateTransition">Templates</h4>
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<h4 id="templateTransition">Templates</h4>
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<p>
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<p>
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The 1.2 release continues the transition from JavaServer Pages (.jsp) to
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The 1.2 release continues the transition from JavaServer Pages (.jsp) to
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Freemarker templates (.ftl) for generating web pages. While there are still
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Freemarker templates (.ftl) for generating web pages. While there are still
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JSP files in action behind the scenes, as of 1.2 all theme templates
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JSP files in action behind the scenes, as of 1.2 all theme templates
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are of the Freemarker variety and are located in the "templates" directory
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are of the Freemarker variety and are located in the "templates" directory
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within a theme.
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within a theme.
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|
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@ -837,19 +839,45 @@
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the vivo-basic theme in its original directory, you need not take any
|
the vivo-basic theme in its original directory, you need not take any
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action in order to remain using the vivo-basic theme in 1.2.
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action in order to remain using the vivo-basic theme in 1.2.
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</p>
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</p>
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<p>If you did make changes to the vivo-basic theme, you will need to reapply those changes.
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<p>
|
||||||
We recommend you apply these changes to the wilma theme.</p>
|
If you did make changes to the vivo-basic theme, you will need to reapply those changes.
|
||||||
|
We recommend you apply these changes to the wilma theme.
|
||||||
|
</p>
|
||||||
<blockquote>
|
<blockquote>
|
||||||
<strong>Please note:</strong> The vivo-basic theme has been deprecated and is
|
<strong>Please note:</strong>
|
||||||
<a href="#vivoBasicDeprecated">not recommended for production instances</a>.
|
The vivo-basic theme has been deprecated and is <a href="#vivoBasicDeprecated">not recommended for production instances</a>.
|
||||||
</blockquote>
|
</blockquote>
|
||||||
<p>
|
<p>
|
||||||
For details on the new structure of themes in 1.2 and further information
|
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
|
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
|
||||||
<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.
|
pre 1.2 theme.
|
||||||
</p>
|
</p>
|
||||||
|
<h3 id="setup_sdb">VII. 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>
|
</div>
|
||||||
<!-- end of content -->
|
<!-- end of content -->
|
||||||
<div id="footer" role="contentinfo">
|
<div id="footer" role="contentinfo">
|
||||||
|
|
@ -875,4 +903,4 @@
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
</body>
|
</body>
|
||||||
</html>
|
</html>
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue