Merging from maint 1.3 (3420) for upgrade (3409) and install (3361).
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doc/install.html
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doc/install.html
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@ -16,7 +16,7 @@
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<div id="wrapper-content" role="main">
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V1.3 Installation Guide</h1>
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<h1>VIVO Release 1 V1.3 Installation Guide</h1>
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<small>
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<small>
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July 22, 2011
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July 29, 2011
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</small>
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</small>
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<toc>
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<toc>
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<ul>
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<ul>
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@ -29,68 +29,83 @@
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</ul>
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</ul>
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</toc>
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</toc>
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<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
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<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
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VIVO Release 1.3 incorporates changes to the search indexing, user
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<!-- Release Announcement -->VIVO Release 1.3 incorporates changes to the search
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accounts, menu management, ontology, and visualizations.
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indexing, user accounts, menu management, ontology, and visualizations, and begins
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integration of VIVO Harvester functions with VIVO's own ingest tools.
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<br>
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<br>
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<h4>Search</h4>
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<h4>Search</h4>
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VIVO 1.3 will feature notable improvements to the local search,
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<p>
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primarily to improve relevance ranking but also to boost the influence
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VIVO 1.3 will feature notable improvements to the local search, primarily to
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of semantic relationships in the search. This will improve recall by
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improve relevance ranking but also to boost the influence of semantic relationships
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including text from related resources (e.g., adding a person’s grant
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in the search. This will improve recall by including text from related resources
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and publication titles to his or her search entry) and by boosting
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(e.g., adding a person's grant and publication titles to his or her search entry)
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overall relevance ranking based on the number and nature of connections
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and by boosting overall relevance ranking based on the number and nature of
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from one individual to others.
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connections from one individual to others.
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<br>
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</p>
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
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<p>
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of Apache Lucene to improve indexing and faceting of search results.
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of
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The migration to Solr also aligns the local search with the VIVO
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Apache Lucene to improve indexing and faceting of search results. The migration
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multi-site search site under development for release prior to the 2011
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to Solr also aligns the local search with the VIVO multi-site search site under
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VIVO Conference.
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development for release prior to the 2011 VIVO Conference.
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<br>
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</p>
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<h4>Authorization</h4>
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<h4>Authorization</h4>
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Release 1.3 provides an entirely new model of authorization within the
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<p>
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VIVO application to allow more granular control over system
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Release 1.3 provides an entirely new model of authorization within the
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configuration and editing. The first phase of the new user account
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VIVO application to allow more granular control over system
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interface is included in V1.3. This interface provides a user search, a
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configuration and editing. The first phase of the new user account
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root acount, and password reset functionality where the password gets
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interface is included in V1.3. This interface provides a user search, a
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emailed to the user. The next phase will provide the ability to create
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root acount, and password reset functionality where the password gets
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new roles.
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emailed to the user. The next phase will provide the ability to create
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<br>
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new roles.
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</p>
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<h4>Menu management</h4>
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<h4>Menu management</h4>
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The menus across the top of the site (Home, People, Organizations,
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<p>
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Research, Events) can now be managed in a web form instead of editing
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The menus across the top of the site (Home, People, Organizations,
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an RDF file. In addition to making site management much easier,
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Research, Events) can now be managed in a web form instead of editing
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form-based editing also allows more control over what classes of data
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an RDF file. In addition to making site management much easier,
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are displayed and provides a mechanism to limit certain menu pages to
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form-based editing also allows more control over what classes of data
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content identified as internal to the institution.
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are displayed and provides a mechanism to limit certain menu pages to
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<br>
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content identified as internal to the institution.
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</p>
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<h4>FreeMaker template improvements</h4>
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<h4>FreeMaker template improvements</h4>
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While less directly visible to the public, version 1.3 also includes
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<p>
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additional changes focused directly on supporting open source community
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While less directly visible to the public, version 1.3 also includes
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involvement in extending and customizing VIVO. The development team
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additional changes focused directly on supporting open source community
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began a year ago to transition VIVO’s code base away from Java Server
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involvement in extending and customizing VIVO. The development team
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Pages to the FreeMarker page templating system that much more cleanly
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began a year ago to transition VIVO's code base away from Java Server
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separates internal application programming logic from page display.
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Pages to the FreeMarker page templating system that much more cleanly
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<br>
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separates internal application programming logic from page display.
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</p>
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<h4>Visualization</h4>
|
<h4>Visualization</h4>
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The visualization team has implemented a Science Map visualization,
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<p>
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which allows users to visually explore the scientific strengths of a
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The visualization team has implemented a Map of Science visualization,
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university, school, department, or person in the VIVO instance. Users
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which allows users to visually explore the scientific strengths of a
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will be able to see where an organization or person’s interests lay
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university, school, department, or person in the VIVO instance. Users
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across 13 major scientific disciplines or 554 sub-disciplines, and will
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will be able to see where an organization or person's interests lay
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be able to see how these disciplines and sub-disciplines interrelate
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across 13 major scientific disciplines or 554 sub-disciplines, and will
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with one another on the map of science. Wireframes and design
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be able to see how these disciplines and sub-disciplines interrelate
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documentation for upcoming enhanced versions of the Science Map
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with one another on the map of science. Wireframes and design
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visualization have already been developed; the Science Map
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documentation for upcoming enhanced versions of the Map of Science
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visualization will most likely be in the form of a PDF that a user can
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visualization have already been developed; the Map of Science
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download.
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visualization will most likely be in the form of a PDF that a user can
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<br>
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download.
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Several visualization also now provide a caching feature that improves
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</p>
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performance after the initial processing.
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<p>
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<br>
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Several visualization also now provide a caching feature that improves
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performance after the initial processing.
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</p>
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<h4>QR Codes</h4>
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<h4>QR Codes</h4>
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Pages for people in VIVO have the option of displaying QR codes.
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<p>
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<br>
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Pages for people in VIVO now have an icon for displaying QR codes to allow
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capturing names and available contact information on mobile devices.
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</p>
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<h4>Harvester Integration</h4>
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<p>
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VIVO sites have the option with Release 1.3 of coordinating the configuration
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of VIVO and the Harvester to enable many Harvester functions to be initiated
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from the VIVO Ingest Tools menu in support of more unified and centralized
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|
management for data ingest.
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</p>
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<h4>Ontology changes</h4>
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<h4>Ontology changes</h4>
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<ul>
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<ul>
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<li>
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<li>
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@ -114,11 +129,12 @@
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</li>
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</li>
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</ul>
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</ul>
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<h4>Linked open data</h4>
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<h4>Linked open data</h4>
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Responses to linked data requests have been enhanced to include
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<p>
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additional context about any individual, in working toward a goal of
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Responses to linked data requests have been enhanced to include
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being able to provide all the data in a person's profile available as
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additional context about any individual, in working toward a goal of
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RDF via a single web request.
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being able to provide all the data in a person's profile available as
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<br>
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RDF via a single web request.
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</p>
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<br>
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<br>
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<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
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<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
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<p>
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<p>
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@ -228,6 +244,9 @@
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<li>
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<li>
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<a href="#installation_check">Was the installation successful?</a>
|
<a href="#installation_check">Was the installation successful?</a>
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</li>
|
</li>
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<li>
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<a href="#termsofuse">Review the VIVO Terms of Use</a>
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</li>
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</ol>
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</ol>
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</toc>
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</toc>
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<h3 id="required_software">I. Install required software </h3>
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<h3 id="required_software">I. Install required software </h3>
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@ -258,7 +277,7 @@
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support websites.
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support websites.
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</p>
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</p>
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<p>
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<p>
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* Note that VIVO 1.2 will not run on older versions of MySQL that
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* Note that VIVO V1.2 or V1.3 will not run on older versions of MySQL that
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may have worked with 1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or
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may have worked with 1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or
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higher. Using unsupported versions may result in strange error messages
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higher. Using unsupported versions may result in strange error messages
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related to table formatting or other unexpected problems.
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related to table formatting or other unexpected problems.
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<br>
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<br>
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</h3>
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</h3>
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<p>
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<p>
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Download the VIVO application source as either <code>rel-1.2.zip</code>
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Download the VIVO application source as either <code>rel-1.3.zip</code>
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or <code>rel-1.2.gz</code>
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or <code>rel-1.3.gz</code>
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file and unpack it on your web server:
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file and unpack it on your web server:
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<br>
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<br>
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<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
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<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
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@ -417,20 +436,19 @@
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made to Solr, the IP address of the requestor must match one of the
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made to Solr, the IP address of the requestor must match one of the
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patterns, or the request will be rejected.
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patterns, or the request will be rejected.
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<br>
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<br>
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Examples:
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Examples:<code>
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<code>
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<ul>
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<ul>
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<li>
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<li>
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vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
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vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
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</li>
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</li>
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<li>
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<li>
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vitro.local.solr.ipaddress.mask =
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vitro.local.solr.ipaddress.mask =
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127\.0\.0\.1,0:0:0:0:0:0:0:1
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127\.0\.0\.1,0:0:0:0:0:0:0:1
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</li>
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</li>
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<li>
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<li>
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vitro.local.solr.ipaddress.mask = 169.254.*
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vitro.local.solr.ipaddress.mask = 169.254.*
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</li>
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</li>
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</ul>
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</ul>
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</code>
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</code>
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</td>
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</td>
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</tr>
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</tr>
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@ -534,22 +552,6 @@
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password
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password
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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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<td colspan="2">
|
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Specify the Jena triple store technology to use.
|
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SDB is Jena's SPARQL database; this setting allows RDF data to scale
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beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
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store with in-memory caching.
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</td>
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</tr>
|
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<tr class="odd_row">
|
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<td>
|
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VitroConnection.DataSource.tripleStoreType
|
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</td>
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<td>
|
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SDB
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</td>
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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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Specify the maximum number of active connections
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Specify the maximum number of active connections
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@ -667,15 +669,33 @@
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http://vivo.mydomain.edu/ns#networkId
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http://vivo.mydomain.edu/ns#networkId
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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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<td colspan="2">
|
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|
If an external authentication system like Shibboleth or CUWebAuth is to be
|
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|
used, these properties say how the login button should be labeled, and which
|
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|
HTTP header will contain the user ID from the authentication system. If such
|
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|
a system is not to be used, leave these commented out. Consult the installation
|
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|
instructions for more details.
|
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|
</td>
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|
</tr>
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|
<tr class="odd_row">
|
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|
<td>
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|
externalAuth.buttonText
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|
<br/>
|
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|
externalAuth.netIdHeaderName
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|
</td>
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<td>
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|
Log in using BearCat Shibboleth
|
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|
<br/>
|
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|
remote_userID
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|
</td>
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</tr>
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<tr>
|
<tr>
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<td colspan="2">
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<td colspan="2">
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The temporal graph visualization can require
|
The temporal graph visualization can require
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extensive machine resources. This can have a particularly noticable
|
extensive machine resources. This can have a particularly noticable
|
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impact on memory usage if
|
impact on memory usage if
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<ul>
|
<ul>
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||||||
<li>
|
|
||||||
VIVO is configured to use Jena SDB,
|
|
||||||
</li>
|
|
||||||
<li>
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<li>
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The organization tree is deep,
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The organization tree is deep,
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</li>
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</li>
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@ -683,11 +703,8 @@
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The number of grants and publications is large.
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The number of grants and publications is large.
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</li>
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</li>
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</ul>
|
</ul>
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The VIVO developers are working to make this visualization more
|
VIVO V1.3 mitigates this problem by the way of a caching
|
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efficient. In the meantime, VIVO release 1.2 guards against this impact
|
mechanism and hence we can safely set this to be enabled by default.
|
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by disabling the temporal graph visualization unless the
|
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"visualization.temporal" flag is set to "enabled". To enable it,
|
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uncomment the line for this setting.
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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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|
|
@ -797,7 +814,7 @@
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or <code>localhost.log</code>
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or <code>localhost.log</code>
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</p>
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</p>
|
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<h3 id="add_rdf">VIII. Log in and add RDF data </h3>
|
<h3 id="add_rdf">VIII. Log in and add RDF data </h3>
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<p>
|
<p>
|
||||||
If the startup was successful, you will see a welcome message
|
If the startup was successful, you will see a welcome message
|
||||||
informing you that you have successfully installed VIVO. Click the "Log
|
informing you that you have successfully installed VIVO. Click the "Log
|
||||||
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
|
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
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|
|
@ -1077,12 +1094,26 @@
|
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administrator and go to "http://your-vivo-url/SearchIndex".
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administrator and go to "http://your-vivo-url/SearchIndex".
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</li>
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</li>
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</ul>
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</ul>
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|
<h3 id="termsofuse">XIII. Review the VIVO Terms of Use</h3>
|
||||||
|
<p>
|
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|
VIVO comes with a "Terms of Use" statement linked from the footer.
|
||||||
|
The "Site Name" you assign in the "Site Information" form under the <strong>Site Admin</strong>
|
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|
area will be inserted into the "Terms of Use"
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|
statement. If you want to edit the text content more than just the
|
||||||
|
"Site Name", the file can be found here:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
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||||||
|
Be sure to make the changes in your source files and deploy them to your
|
||||||
|
tomcat so you don't lose your changes next time you deploy for another reason.
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|
</p>
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|
<h3>Next Step ...</h3>
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|
<p>
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||||||
|
Now that you have VIVO up and running, please go read the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>.
|
||||||
|
</p>
|
||||||
</div>
|
</div>
|
||||||
<!-- #wrapper-content -->
|
<!-- #wrapper-content -->
|
||||||
<div id="footer" role="contentinfo">
|
<div id="footer" role="contentinfo">
|
||||||
<p class="copyright">
|
<p class="copyright">
|
||||||
<small>
|
<small>
|
||||||
©2011 All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
©2011 All Rights Reserved
|
||||||
</small>
|
</small>
|
||||||
| Powered
|
| Powered
|
||||||
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
||||||
|
|
|
||||||
|
|
@ -14,7 +14,7 @@
|
||||||
<div id="wrapper-content" role="main">
|
<div id="wrapper-content" role="main">
|
||||||
<h1>VIVO Release 1 V1.3 Upgrade Guide</h1>
|
<h1>VIVO Release 1 V1.3 Upgrade Guide</h1>
|
||||||
<small>
|
<small>
|
||||||
July 28, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3
|
July 29, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3
|
||||||
</small>
|
</small>
|
||||||
<toc>
|
<toc>
|
||||||
<ul>
|
<ul>
|
||||||
|
|
@ -364,21 +364,21 @@
|
||||||
<toc>
|
<toc>
|
||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
The file used to register list views has changed to a directory where new
|
The file used to register list views has changed to a directory where new<code>.rdf</code>
|
||||||
<code>.rdf</code> or <code>.n3</code> files can be placed:
|
or <code>.n3</code>
|
||||||
<code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required
|
files can be placed: <code>/vivo/productMods/WEB-INF/ontologies/app/loadedAtStartup</code>. The rdf required
|
||||||
to register a new view has not changed.
|
to register a new view has not changed.
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<code><query-base></code> and <code><query-collated></code>
|
<code><query-base></code>
|
||||||
|
and <code><query-collated></code>
|
||||||
have been replaced with a single query <code><query-select></code>
|
have been replaced with a single query <code><query-select></code>
|
||||||
that contains tags for fragments to be used only in the collated
|
that contains tags for fragments to be used only in the collated
|
||||||
version of the query.
|
version of the query.
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<p>
|
<p>
|
||||||
These and other changes are documented in greater detail in
|
These and other changes are documented in greater detail in<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
|
||||||
<code style="whitespace:nowrap;">/vitro/doc/list_view_configuration_guidelines.txt</code>.
|
|
||||||
</p>
|
</p>
|
||||||
</toc>
|
</toc>
|
||||||
<h4 id="authorization">v. Authorization</h4>
|
<h4 id="authorization">v. Authorization</h4>
|
||||||
|
|
@ -893,23 +893,6 @@
|
||||||
password
|
password
|
||||||
</td>
|
</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr>
|
|
||||||
<td colspan="2">
|
|
||||||
Specify the Jena triple store technology to
|
|
||||||
use.
|
|
||||||
SDB is Jena's SPARQL database; this setting allows RDF data to scale
|
|
||||||
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
|
|
||||||
store with in-memory caching.
|
|
||||||
</td>
|
|
||||||
</tr>
|
|
||||||
<tr class="odd_row">
|
|
||||||
<td>
|
|
||||||
VitroConnection.DataSource.tripleStoreType
|
|
||||||
</td>
|
|
||||||
<td>
|
|
||||||
SDB
|
|
||||||
</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
<tr>
|
||||||
<td colspan="2">
|
<td colspan="2">
|
||||||
Specify the maximum number of active
|
Specify the maximum number of active
|
||||||
|
|
@ -1022,15 +1005,33 @@
|
||||||
http://vivo.mydomain.edu/ns#networkId
|
http://vivo.mydomain.edu/ns#networkId
|
||||||
</td>
|
</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td colspan="2">
|
||||||
|
If an external authentication system like Shibboleth or CUWebAuth is to be
|
||||||
|
used, these properties say how the login button should be labeled, and which
|
||||||
|
HTTP header will contain the user ID from the authentication system. If such
|
||||||
|
a system is not to be used, leave these commented out. Consult the installation
|
||||||
|
instructions for more details.
|
||||||
|
</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd_row">
|
||||||
|
<td>
|
||||||
|
externalAuth.buttonText
|
||||||
|
<br/>
|
||||||
|
externalAuth.netIdHeaderName
|
||||||
|
</td>
|
||||||
|
<td>
|
||||||
|
Log in using BearCat Shibboleth
|
||||||
|
<br/>
|
||||||
|
remote_userID
|
||||||
|
</td>
|
||||||
|
</tr>
|
||||||
<tr>
|
<tr>
|
||||||
<td colspan="2">
|
<td colspan="2">
|
||||||
The temporal graph visualization can require
|
The temporal graph visualization can require
|
||||||
extensive machine resources. This can have a particularly noticable
|
extensive machine resources. This can have a particularly noticable
|
||||||
impact on memory usage if
|
impact on memory usage if
|
||||||
<ul>
|
<ul>
|
||||||
<li>
|
|
||||||
VIVO is configured to use Jena SDB,
|
|
||||||
</li>
|
|
||||||
<li>
|
<li>
|
||||||
The organization tree is deep,
|
The organization tree is deep,
|
||||||
</li>
|
</li>
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue