Merging 3394 to 3396 from maint-rel-1.3 branch
Cleaning up text inconsistencies and grammar corrections from Tobi.
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@ -1,4 +1,4 @@
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<!DOCTYPE html>
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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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@ -12,9 +12,9 @@
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</div>
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<!-- Start of content -->
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 v1.3 Upgrade Guide</h1>
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<h1>VIVO Release 1 V1.3 Upgrade Guide</h1>
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<small>
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July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1 v1.3
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July 28, 2011 - Upgrading from Release 1 V1.2 to Release 1 V1.3
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</small>
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<toc>
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<ul>
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|
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@ -33,77 +33,90 @@
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at <a href="http://vivoweb.org/">VIVOweb.org</a>
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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
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1 v1.3 Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
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If you need to do a fresh install, please consult the VIVO Release V1.3 Installation
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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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directory of the VIVO source code distribution. The installation document also has a
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list of the required software and versions (there are no new hardware
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or software requirements for V1.3).
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</p>
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<h3 id="announcement">Release Announcement for V1.3</h3>
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V<!-- Release Announcement -->IVO Release 1.3 incorporates changes to
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the search indexing, user accounts, menu management, ontology, and
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visualizations.
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<!-- Release Announcement -->VIVO Release V1.3 incorporates changes to the search
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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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<h4>Search</h4>
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VIVO 1.3 will feature notable improvements to the local search,
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primarily to improve relevance ranking but also to boost the influence
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of semantic relationships in the search. This will improve recall by
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including text from related resources (e.g., adding a person's grant
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and publication titles to his or her search entry) and by boosting
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overall relevance ranking based on the number and nature of connections
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from one individual to others.
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<br>
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
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of Apache Lucene to improve indexing and faceting of search results.
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The migration to Solr also aligns the local search with the VIVO
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multi-site search site under development for release prior to the 2011
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VIVO Conference.
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<br>
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<p>
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VIVO V1.3 will feature notable improvements to the local search, primarily to improve relevance
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ranking but also to boost the influence of semantic relationships in the search. This will
|
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improve recall by including text from related resources (e.g., adding a person's grant and
|
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publication titles to his or her search entry) and by boosting overall relevance ranking
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based on the number and nature of connections from one individual to others.
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</p>
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<p>
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of Apache Lucene to
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improve indexing and faceting of search results. The migration to Solr also aligns the
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local search with the VIVO multi-site search site under development for release prior to
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the 2011 VIVO Conference.
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</p>
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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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VIVO application to allow more granular control over system
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configuration and editing. The first phase of the new user account
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interface is included in V1.3. This interface provides a user search, a
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root acount, and password reset functionality where the password gets
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emailed to the user. The next phase will provide the ability to create
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new roles.
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<br>
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<p>
|
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Release V1.3 provides an entirely new model of authorization within the
|
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VIVO application to allow more granular control over system
|
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configuration and editing. The first phase of the new user account
|
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interface is included in V1.3. This interface provides a user search, a
|
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root acount, and password reset functionality where the password gets
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emailed to the user. The next phase will provide the ability to create
|
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new roles.
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</p>
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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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Research, Events) can now be managed in a web form instead of editing
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an RDF file. In addition to making site management much easier,
|
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form-based editing also allows more control over what classes of data
|
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are displayed and provides a mechanism to limit certain menu pages to
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content identified as internal to the institution.
|
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<br>
|
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<h4>FreeMaker template improvements</h4>
|
||||
While less directly visible to the public, version 1.3 also includes
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO's code base away from Java Server
|
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Pages to the FreeMarker page templating system that much more cleanly
|
||||
separates internal application programming logic from page display.
|
||||
<br>
|
||||
<p>
|
||||
The menus across the top of the site (Home, People, Organizations,
|
||||
Research, Events) can now be managed in a web form instead of editing
|
||||
an RDF file. In addition to making site management much easier,
|
||||
form-based editing also allows more control over what classes of data
|
||||
are displayed and provides a mechanism to limit certain menu pages to
|
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content identified as internal to the institution.
|
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</p>
|
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<h4>FreeMarker template improvements</h4>
|
||||
<p>
|
||||
While less directly visible to the public, V1.3 also includes
|
||||
additional changes focused directly on supporting open source community
|
||||
involvement in extending and customizing VIVO. The development team
|
||||
began a year ago to transition VIVO's code base away from Java Server
|
||||
Pages to the FreeMarker page templating system that much more cleanly
|
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separates internal application programming logic from page display.
|
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</p>
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<h4>Visualization</h4>
|
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The visualization team has implemented a Map of Science visualization,
|
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which allows users to visually explore the scientific strengths of a
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university, school, department, or person in the VIVO instance. Users
|
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will be able to see where an organization or person's interests lay
|
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across 13 major scientific disciplines or 554 sub-disciplines, and will
|
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be able to see how these disciplines and sub-disciplines interrelate
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with one another on the map of science. Wireframes and design
|
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documentation for upcoming enhanced versions of the Map of Science
|
||||
visualization have already been developed; 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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download.
|
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<br>
|
||||
Several visualization also now provide a caching feature that improves
|
||||
performance after the initial processing.
|
||||
<br>
|
||||
<p>
|
||||
The visualization team has implemented a Map of Science visualization,
|
||||
which allows users to visually explore the scientific strengths of a
|
||||
university, school, department, or person in the VIVO instance. Users
|
||||
will be able to see where an organization or person's interests lay
|
||||
across 13 major scientific disciplines or 554 sub-disciplines, and will
|
||||
be able to see how these disciplines and sub-disciplines interrelate
|
||||
with one another on the Map of Science. Wireframes and design
|
||||
documentation for upcoming enhanced versions of the Map of Science
|
||||
visualization have already been developed; the Map of Science
|
||||
visualization will most likely be in the form of a PDF that a user can
|
||||
download.
|
||||
</p>
|
||||
<p>
|
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Several visualizations 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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Pages for people in VIVO have the option of displaying QR codes.
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<br>
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<p>
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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>
|
||||
<h4>Harvester Integration</h4>
|
||||
<p>
|
||||
VIVO sites have the option with Release 1.3 of coordinating the configuration
|
||||
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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<ul>
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<li>
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@ -127,11 +140,12 @@
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</li>
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</ul>
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<h4>Linked open data</h4>
|
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Responses to linked data requests have been enhanced to include
|
||||
additional context about any individual, in working toward a goal of
|
||||
being able to provide all the data in a person's profile available as
|
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RDF via a single web request.
|
||||
<br>
|
||||
<p>
|
||||
Responses to linked data requests have been enhanced to include
|
||||
additional context about any individual, in working toward a goal of
|
||||
being able to provide all the data in a person's profile available as
|
||||
RDF via a single web request.
|
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</p>
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<br>
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2>
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<toc>
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|
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@ -164,20 +178,23 @@
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<a href="#upgrade_process">The Upgrade Process</a>
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</li>
|
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<li>
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<a href="upgrade-1.3.html#ontology">Ontology</a>
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<a href="#ontology">Ontology Changes</a>
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<ol class="roman3">
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<li>
|
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<a href="upgrade-1.3.html#verify_ontology_upgrade">Verify
|
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<a href="#verify_ontology_upgrade">Verify
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Ontology upgrade process</a>
|
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</li>
|
||||
<li>
|
||||
<a href="upgrade-1.3.html#ontology_knowledge_base">Ontology
|
||||
<a href="#ontology_knowledge_base">Ontology
|
||||
knowledge
|
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base
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manual review</a>
|
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</li>
|
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</ol>
|
||||
</li>
|
||||
<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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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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<p>
|
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|
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@ -209,22 +226,22 @@
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<br>
|
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</li>
|
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<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. 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
|
||||
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>
|
||||
It is not necessary to add RDF data.
|
||||
</li>
|
||||
<li>
|
||||
First-time login of the administrator account after the
|
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First-time login of the administrator account after the
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upgrade
|
||||
process is complete will use the password previously set, NOT the
|
||||
default password used on the first login after the initial
|
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installation. With V1.3 there is also a new root user. Please see the
|
||||
process is complete will use the password previously set, NOT the
|
||||
default password used on the first login after the initial
|
||||
installation. With V1.3 there is also a new root user. Please see the
|
||||
section on <a href="#authorization">Authorization changes</a>
|
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for more
|
||||
information.
|
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|
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@ -236,16 +253,15 @@
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below for more information.
|
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</li>
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</ul>
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<h3 id="changes">II. Noteworthy Changes
|
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</h3>
|
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<h4 id="triple_store">i. Triple store changes
|
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<h3 id="changes">II. Noteworthy Changes</h3>
|
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<h4 id="triple_store">i. Triple store
|
||||
<br>
|
||||
</h4>
|
||||
<p>
|
||||
VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
|
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the triple store technology. Jena's legacy relational database
|
||||
store (RDB) was used by VIVO 1.1.1 and earlier. Both SDB and RDB
|
||||
were available in VIVO 1.2 and 1.2.1. It is required that you
|
||||
the triple store technology. Jena's legacy relational database
|
||||
store (RDB) was used by VIVO 1.1.1 and earlier. Both SDB and RDB
|
||||
were available in VIVO 1.2 and 1.2.1. It is required that you
|
||||
move your triple store to SDB while still at V1.2.
|
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</p>
|
||||
<p>
|
||||
|
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@ -254,26 +270,26 @@
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|||
allows VIVO installations to display data from large RDF models while
|
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requiring only a small amount of server memory to run the application.
|
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There is a tradeoff in response time: pages may take slightly longer to
|
||||
load in SDB mode, and performance will depend on the configuration
|
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load in SDB mode, and performance will depend on the configuration
|
||||
parameters of the database server. Additionally, advanced OWL reasoning
|
||||
(not enabled by default in either mode) is not possible in SDB mode.
|
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With SDB, only the default set of inferences (inferred rdf:type
|
||||
statements) are generated, and they are generated as soon as data is
|
||||
(not enabled by default in either mode) is not possible in SDB mode.
|
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With SDB, only the default set of inferences (inferred rdf:type
|
||||
statements) are generated, and they are generated as soon as data is
|
||||
edited rather than in a background process.
|
||||
</p>
|
||||
<p>
|
||||
A conversion from RDB to SDB mode can take a number of hours to
|
||||
A conversion from RDB to SDB mode can take a number of hours to
|
||||
complete if the installation contains a large amount of RDF data
|
||||
(roughly a million triples or more). 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
|
||||
(roughly a million triples or more). 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. <span style="font-weight: bold;">Note
|
||||
that it is important not to edit any data anywhere in the application
|
||||
while this background conversion is running</span>.
|
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</p>
|
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<p>
|
||||
To start the SDB conversion, log in as a system administrator and
|
||||
request /sdbsetup (For example, if your VIVO is installed at
|
||||
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>
|
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|
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@ -283,37 +299,35 @@
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<p>
|
||||
During the course of the SDB setup, which may take several hours
|
||||
on
|
||||
a large database, subsequent requests to /sdbsetup will display a
|
||||
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
|
||||
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>
|
||||
<p>
|
||||
</p>
|
||||
<h4 id="theme">ii. Theme changes</h4>
|
||||
<h4 id="theme">ii. Theme</h4>
|
||||
<p>
|
||||
The vivo-basic theme was deprecated with VIVO V1.2 and is no longer
|
||||
present in the V1.3 release as it does not support V1.2 or V1.3
|
||||
features. It is highly recommended that you use the wilma theme or
|
||||
modify the wilma theme for branding or to create a custom look and
|
||||
present in the V1.3 release as it does not support V1.2 or V1.3
|
||||
features. It is highly recommended that you use the wilma theme or
|
||||
modify the wilma theme for branding or to create a custom look and
|
||||
feel. Please see the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administration Guide</a>
|
||||
for more information about customizing your
|
||||
theme.
|
||||
</p>
|
||||
</toc>
|
||||
<h4 id="template">iii. Template changes</h4>
|
||||
<h4 id="template">iii. Template</h4>
|
||||
<toc>
|
||||
<ul>
|
||||
<li>
|
||||
<p>
|
||||
The <code>${stylesheets}</code>, <code>${scripts}</code>,
|
||||
and<code>${headScripts}</code>
|
||||
<code>add()</code>
|
||||
methods now take the
|
||||
full tag as an argument.
|
||||
This will require a change to all calls to these methods in the
|
||||
The <code>${stylesheets}</code>, <code>${scripts}</code>,
|
||||
and <code>${headScripts} add()</code>
|
||||
methods now take the full tag as an argument.
|
||||
This will require a change to all calls to these methods in the
|
||||
templates. This change allows for specification of attributes such as <code>media</code>
|
||||
directly in the tag. For example:
|
||||
</p>
|
||||
|
|
@ -333,8 +347,8 @@
|
|||
</li>
|
||||
<li>
|
||||
The <code>addFromTheme()</code>
|
||||
methods of the <code>${stylesheets}</code>,<code>${scripts}</code>,
|
||||
and<code>${headScripts}</code>
|
||||
methods of the <code>${stylesheets}</code>, <code>${scripts}</code>,
|
||||
and <code>${headScripts}</code>
|
||||
objects have been deleted. Substitute as
|
||||
shown in the preceding example.
|
||||
</li>
|
||||
|
|
@ -346,7 +360,7 @@
|
|||
</li>
|
||||
</ul>
|
||||
</toc>
|
||||
<h4 id="listview">v. List view changes</h4>
|
||||
<h4 id="listview">v. List view</h4>
|
||||
<toc>
|
||||
<code><query-base></code>
|
||||
and <code><query-collated></code>
|
||||
|
|
@ -356,20 +370,19 @@
|
|||
<br>
|
||||
<br>
|
||||
</toc>
|
||||
<h4 id="authorization">v. Authorization changes</h4>
|
||||
<h4 id="authorization">v. Authorization</h4>
|
||||
<toc>
|
||||
<p>
|
||||
In release 1.3, the VIVO authorization system has some extensive
|
||||
In V1.3, the VIVO authorization system has some extensive
|
||||
changes. In summary, these are:
|
||||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
Each user will have a user account, even if the user logs in
|
||||
by
|
||||
Shibboleth or some other external authentication system.
|
||||
with Shibboleth or some other external authentication system.
|
||||
</li>
|
||||
<li>
|
||||
E-mail is used to notify user's when an account is created for
|
||||
E-mail is used to notify users when an account is created for
|
||||
them, or when an administrator edits their account.
|
||||
</li>
|
||||
<li>
|
||||
|
|
@ -385,33 +398,28 @@
|
|||
<dl>
|
||||
<dd>
|
||||
<p style="margin-left: 40px;">
|
||||
With release 1.3, each authenticated
|
||||
user will have a user
|
||||
With V1.3, each authenticated user will have a user
|
||||
account. If someone logs in using an external authentication system,
|
||||
and no user account matches their external login credentials, an
|
||||
account will be created.
|
||||
</p>
|
||||
<p style="margin-left: 40px;">
|
||||
The user will be prompted to enter
|
||||
information for the
|
||||
account
|
||||
being created: first name, last name, and e-mail address.
|
||||
The user will be prompted to enter information for the
|
||||
account being created: first name, last name, and e-mail address.
|
||||
</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</toc>
|
||||
<toc>
|
||||
<h4 style="margin-left: 40px;" id="email_on_accounts">b. E-mail address
|
||||
becomes an important
|
||||
part
|
||||
of User Accounts</h4>
|
||||
becomes an important part of User Accounts</h4>
|
||||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
Prior to release 1.3, each user account was identified by a
|
||||
Username field. This field was labeled as "E-mail address" on some
|
||||
pages in VIVO, but no mail was ever sent. In release 1.3, this has
|
||||
changed, so the e-mail address is fully used, both for identification
|
||||
Prior to V1.3, each user account was identified by a
|
||||
Username field. This field was labeled as "E-mail address" on some
|
||||
pages in VIVO, but no mail was ever sent. In V1.3, this has
|
||||
changed, so the e-mail address is fully used, both for identification
|
||||
and for communication with the user.
|
||||
</p>
|
||||
</dd>
|
||||
|
|
@ -426,54 +434,48 @@
|
|||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
Prior to release 1.3, the Username field (also referred to as
|
||||
Prior to V1.3, the Username field (also referred to as
|
||||
'e-mail address') was used for several purposes:
|
||||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
Idenfiying the user account.
|
||||
Idenfiying the user account
|
||||
</li>
|
||||
<li>
|
||||
Part of the user's credentials when logging in (along with
|
||||
a
|
||||
password).
|
||||
a password)
|
||||
</li>
|
||||
<li>
|
||||
Connecting the user account to an external authentication
|
||||
system, like Shibboleth or CUWebAuth.
|
||||
system, like Shibboleth or CUWebAuth
|
||||
</li>
|
||||
<li>
|
||||
Connecting the user account to a personal Profile page.
|
||||
Connecting the user account to a personal Profile page
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
With release 1.3, these functions are handled by two separate
|
||||
With V1.3, these functions are handled by two separate
|
||||
fields called EmailAddress field and ExternalAuthId.
|
||||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
EmailAddress is used when logging in (along with a
|
||||
password).
|
||||
password)
|
||||
</li>
|
||||
<li>
|
||||
EmailAddress is used to send notifications to the user
|
||||
about
|
||||
changes to his/her account (see below).
|
||||
about changes to his/her account (see below)
|
||||
</li>
|
||||
<li>
|
||||
The ExternalAuthId is used when logging in using an
|
||||
external
|
||||
authentication system.
|
||||
external authentication system
|
||||
</li>
|
||||
<li>
|
||||
The ExternalAuthId is used to connect the user account to
|
||||
a
|
||||
personal Profile page.
|
||||
a personal Profile page
|
||||
<blockquote>
|
||||
<strong>Note:</strong>
|
||||
With release 1.3, the
|
||||
ExternalAuthId can now be matched against either an untyped literal or
|
||||
a string literal in the Profile page.
|
||||
With V1.3, the ExternalAuthId can now be matched against either an untyped literal or a string literal in the Profile page.
|
||||
</blockquote>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -494,24 +496,24 @@
|
|||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
If you are upgrading to VIVO release 1.3 from an existing
|
||||
VIVO
|
||||
If you are upgrading to VIVO V1.3 from an existing
|
||||
VIVO
|
||||
installation, the user accounts in your system will be migrated into
|
||||
the new data structures. When migrating an account, both the
|
||||
EmailAddress field and the ExternalAuthId field will be set to the
|
||||
value of the Username field in the old account. The new account should
|
||||
the new data structures. When migrating an account, both the
|
||||
EmailAddress field and the ExternalAuthId field will be set to the
|
||||
value of the Username field in the old account. The new account should
|
||||
behave as the old account did.
|
||||
</p>
|
||||
<p>
|
||||
When creating a new user account, or editing an existing one,
|
||||
the system requires that your e-mail address be in a valid form, like <code>somebody@somewhere.edu</code>.
|
||||
You
|
||||
should
|
||||
should
|
||||
plan
|
||||
for
|
||||
this
|
||||
as
|
||||
part of your migration to release 1.3
|
||||
for
|
||||
this
|
||||
as
|
||||
part of your migration to V1.3
|
||||
</p>
|
||||
</dd>
|
||||
</dl>
|
||||
|
|
@ -526,7 +528,7 @@
|
|||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
With release 1.3, VIVO users receive e-mail notifications
|
||||
With V1.3, VIVO users receive e-mail notifications
|
||||
when
|
||||
an account is created or modified for them or by them.
|
||||
</p>
|
||||
|
|
@ -538,11 +540,11 @@
|
|||
</p>
|
||||
<blockquote>
|
||||
<strong>Note:</strong>
|
||||
when creating the account,
|
||||
when creating the account,
|
||||
the
|
||||
administrator may indicate that it will only be used with an external
|
||||
authentication system like Shibboleth or CUWebAuth. In this case, the
|
||||
account will not require a password, and the e-mail notification
|
||||
administrator may indicate that it will only be used with an external
|
||||
authentication system like Shibboleth or CUWebAuth. In this case, the
|
||||
account will not require a password, and the e-mail notification
|
||||
message to the user will not provide a password link.
|
||||
</blockquote>
|
||||
<p>
|
||||
|
|
@ -565,15 +567,15 @@
|
|||
</toc>
|
||||
<div style="margin-left: 40px;">
|
||||
<toc>
|
||||
<h5 style="margin-left: 40px;">4. Disabling e-mail notificiation</h5>
|
||||
<h5 style="margin-left: 40px;">4. Disabling e-mail notification</h5>
|
||||
</toc>
|
||||
</div>
|
||||
<toc>
|
||||
<dl style="margin-left: 40px;">
|
||||
<dd>
|
||||
<p>
|
||||
The e-mail notification relies on two configuration
|
||||
properties:<code>email.smtpHost</code>
|
||||
The e-mail notification relies on two configuration
|
||||
properties: <code>email.smtpHost</code>
|
||||
and <code>email.replyTo</code>. If either of these properties is
|
||||
missing or empty, VIVO will not attempt to send e-mail notifications to
|
||||
users.
|
||||
|
|
@ -584,9 +586,9 @@
|
|||
</p>
|
||||
<p>
|
||||
If e-mail notifications are disabled, an administrator must
|
||||
set
|
||||
a password on each new account, since the user will have no way of
|
||||
setting it. When the user logs in for the first time, VIVO will require
|
||||
set
|
||||
a password on each new account, since the user will have no way of
|
||||
setting it. When the user logs in for the first time, VIVO will require
|
||||
them to change their password to one of their own choosing.
|
||||
</p>
|
||||
</dd>
|
||||
|
|
@ -597,10 +599,10 @@
|
|||
<dl>
|
||||
<dd>
|
||||
<p style="margin-left: 40px;">
|
||||
Prior to release 1.3, each VIVO
|
||||
installation was created with
|
||||
a
|
||||
default administrator's account. In release 1.3, there is no such
|
||||
Prior to V1.3, each VIVO
|
||||
installation was created with
|
||||
a
|
||||
default administrator's account. In V1.3, there is no such
|
||||
account. Instead, each VIVO installation will have a "root" account.
|
||||
</p>
|
||||
<p style="margin-left: 40px;">
|
||||
|
|
@ -613,34 +615,34 @@
|
|||
The password for this account is
|
||||
automatically set to <code>rootPassword</code>,
|
||||
but
|
||||
you
|
||||
you
|
||||
will
|
||||
be
|
||||
required
|
||||
to change the password the first time you log
|
||||
be
|
||||
required
|
||||
to change the password the first time you log
|
||||
in.
|
||||
</div>
|
||||
<blockquote style="margin-left: 40px;">
|
||||
<strong>Note:</strong>
|
||||
the<code>initialAdminUser</code>
|
||||
the <code>initialAdminUser</code>
|
||||
is no longer use.
|
||||
</blockquote>
|
||||
<p style="margin-left: 40px;">
|
||||
The root account is not a site
|
||||
administrator's account — it
|
||||
is
|
||||
more powerful than a site administrator's acocunt. The root account is
|
||||
more powerful than a site administrator's account. The root account is
|
||||
permitted to visit any page in a VIVO application. It is permitted to
|
||||
see any data property, and to enter data into any field. As such, the
|
||||
root account can be very useful and rather dangerous. It can also give
|
||||
see any data property, and to enter data into any field. As such, the
|
||||
root account can be very useful and rather dangerous. It can also give
|
||||
you a distorted view of what your VIVO site looks like, since data is
|
||||
shown which other accounts cannot see.
|
||||
shown here which ins not visible to other accounts.
|
||||
</p>
|
||||
<p style="margin-left: 40px;">
|
||||
The root account is not intended for
|
||||
routine, every day use.
|
||||
The best way to use the root account is to create a site
|
||||
administrator's account. After that, use the root account only when
|
||||
routine, everyday use.
|
||||
The best way to use the root account is to create a site
|
||||
administrator's account. After that, use the root account only when
|
||||
necessary.
|
||||
</p>
|
||||
</dd>
|
||||
|
|
@ -651,11 +653,11 @@
|
|||
source directory.
|
||||
</p>
|
||||
<p>
|
||||
2. Create a new deploy.properties using the same values as in
|
||||
2. Create a new deploy.properties using the same values as in
|
||||
your
|
||||
previous installation and set values for the new variables as described
|
||||
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
|
||||
vitro.home.directory, email.smptHost, email.replyTo,
|
||||
previous installation and set values for the new variables as described
|
||||
below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
|
||||
vitro.home.directory, email.smptHost, email.replyTo,
|
||||
rootUser.emailAddress)
|
||||
<br>
|
||||
</p>
|
||||
|
|
@ -762,20 +764,19 @@
|
|||
made to Solr, the IP address of the requestor must match one of the
|
||||
patterns, or the request will be rejected.
|
||||
<br>
|
||||
Examples:
|
||||
<code>
|
||||
<ul>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask =
|
||||
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 169.254.*
|
||||
</li>
|
||||
</ul>
|
||||
Examples:<code>
|
||||
<ul>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask =
|
||||
127\.0\.0\.1,0:0:0:0:0:0:0:1
|
||||
</li>
|
||||
<li>
|
||||
vitro.local.solr.ipaddress.mask = 169.254.*
|
||||
</li>
|
||||
</ul>
|
||||
</code>
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -790,9 +791,9 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
Directory where the VIVO application will
|
||||
store
|
||||
the data that it creates. This includes uploaded files (usually images)
|
||||
and the Solr search index. Be sure this directory exists and is
|
||||
store
|
||||
the data that it creates. This includes uploaded files (usually images)
|
||||
and the Solr search index. Be sure this directory exists and is
|
||||
writable by the user who the Tomcat service is running as.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -822,11 +823,11 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Specify an email address which will appear as
|
||||
Specify an email address which will appear as
|
||||
the sender in e-mail notifications to users (Optional). If a user
|
||||
replies to the notification, this address will receive the reply. If a
|
||||
user's e-mail address is invalid, this address will receive the error
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
replies to the notification, this address will receive the reply. If a
|
||||
user's e-mail address is invalid, this address will receive the error
|
||||
notice. If this is left blank, users will not be notified of changes to
|
||||
their accounts.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -884,9 +885,9 @@
|
|||
<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
|
||||
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>
|
||||
|
|
@ -901,9 +902,9 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
Specify the maximum number of active
|
||||
connections
|
||||
in the database connection pool to support the anticipated number of
|
||||
concurrent page requests. It is not necessary to adjust this value when
|
||||
connections
|
||||
in the database connection pool to support the anticipated number of
|
||||
concurrent page requests. It is not necessary to adjust this value when
|
||||
using the RDB configuration.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -933,9 +934,9 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
Change the dbtype setting to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||||
for additional information.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -950,7 +951,7 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
Specify a driver class name to use a database
|
||||
other than MySQL. Otherwise, leave this value unchanged. This JAR file
|
||||
other than MySQL. Otherwise, leave this value unchanged. The JAR file
|
||||
for this driver must be added to the the webapp/lib directory within
|
||||
the vitro.core.dir specified above.
|
||||
</td>
|
||||
|
|
@ -1026,7 +1027,7 @@
|
|||
The number of grants and publications is large.
|
||||
</li>
|
||||
</ul>
|
||||
VIVO 1.3 release mitigates this problem by the way of a caching
|
||||
VIVO V1.3 mitigates this problem by the way of a caching
|
||||
mechanism and hence we can safely set this to be enabled by default.
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -1044,11 +1045,11 @@
|
|||
compare different organizations/people within an organization on
|
||||
parameters like number of publications or grants. By default, the app
|
||||
will attempt to make its best guess at the top level organization in
|
||||
your instance. If you're unhappy with this selection, uncomment out the
|
||||
your instance. If you're unhappy with this selection, uncomment out the
|
||||
property below and set it to the URI of the organization individual you
|
||||
want to identify as the top level organization. It will be used as the
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
want to identify as the top level organization. It will be used as the
|
||||
default whenever the temporal graph visualization is rendered without
|
||||
being passed an explicit org. For example, to use "Ponce School of
|
||||
Medicine" as the top organization:
|
||||
<br>
|
||||
<code>visualization.topLevelOrg =
|
||||
|
|
@ -1067,7 +1068,7 @@
|
|||
<tr>
|
||||
<td colspan="2">
|
||||
An absolute file path, pointing to the root directory of the Harvester utility.
|
||||
You must include the final slash.
|
||||
You must include the final slash.
|
||||
Setting a value for harvester.location indicates that the Harvester is installed at
|
||||
this path. This will enable the Harvester functions in the Ingest Tools page.
|
||||
</td>
|
||||
|
|
@ -1108,11 +1109,11 @@
|
|||
in
|
||||
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
||||
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
|
||||
tracking code shown with your institution's own tracking code. For
|
||||
additional information about the GATC for the NIH-funded VIVO
|
||||
implementation sites and a copy of your institution's tracking code,
|
||||
tracking code shown with your institution's own tracking code. For
|
||||
additional information about the GATC for the NIH-funded VIVO
|
||||
implementation sites and a copy of your institution's tracking code,
|
||||
see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
||||
Google
|
||||
Analytics
|
||||
|
|
@ -1142,17 +1143,16 @@
|
|||
</p>
|
||||
<p>
|
||||
6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is
|
||||
completed. Depending on the size of your database, the migration process may
|
||||
take up to several hours. When it is complete, you will
|
||||
see a message in the catalina.log file that the server has started.
|
||||
<pre>INFO: Server startup in XXXXX ms</pre>
|
||||
completed. Depending on the size of your database, the migration process may
|
||||
take up to several hours. When it is complete, you will
|
||||
see a message in the catalina.log file that the server has started.<pre>INFO: Server startup in XXXXX ms</pre>
|
||||
</p>
|
||||
<p>
|
||||
7. As root or an administrator, request a rebuild of the Solr search index:
|
||||
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
|
||||
heading "Refresh Content". You can check on the
|
||||
rebuild status by looking at the vivo.all.log in the tomcat logs.
|
||||
</p>
|
||||
<p>
|
||||
7. As root or an administrator, request a rebuild of the Solr search index:
|
||||
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
|
||||
heading "Refresh Content". You can check on the
|
||||
rebuild status by looking at the vivo.all.log in the tomcat logs.
|
||||
</p>
|
||||
<h3 id="ontology">IV. Ontology Changes</h3>
|
||||
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
|
||||
<p>
|
||||
|
|
@ -1167,9 +1167,9 @@
|
|||
</dt>
|
||||
<dd>
|
||||
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 "Finished knowledge base migration". If this file contains any
|
||||
warnings they should be reviewed with your implementation team
|
||||
base and notes about some recommended manual reviews. This file should
|
||||
end with "Finished knowledge base migration". If this file contains any
|
||||
warnings they should be reviewed with your implementation team
|
||||
representative to see whether any corrective action needs to be taken.
|
||||
</dd>
|
||||
</dl>
|
||||
|
|
@ -1210,11 +1210,11 @@
|
|||
extensions.
|
||||
</p>
|
||||
<p>
|
||||
When Apache Tomcat starts up following the upgrade, it will
|
||||
When Apache Tomcat starts up following the upgrade, it will
|
||||
initiate a process to examine the knowledge base and apply necessary
|
||||
changes. Not all of the modifications that may be required can be
|
||||
automated, so manual review of the knowledge base is recommended after
|
||||
the automated upgrade process. The automated process will make only the
|
||||
changes. Not all of the modifications that may be required can be
|
||||
automated, so manual review of the knowledge base is recommended after
|
||||
the automated upgrade process. The automated process will make only the
|
||||
following types of changes:
|
||||
</p>
|
||||
<dl>
|
||||
|
|
@ -1236,9 +1236,9 @@
|
|||
All type assertions of a deleted class will be removed.
|
||||
<br>
|
||||
All statements using a deleted property will be changed to use the
|
||||
nearest available superproperty. If there is no available superproperty
|
||||
then the statement will be deleted from the knowledge base. Note that
|
||||
all removed and added data is recorded in the files in the changedData
|
||||
nearest available superproperty. If there is no available superproperty
|
||||
then the statement will be deleted from the knowledge base. Note that
|
||||
all removed and added data is recorded in the files in the changedData
|
||||
directory.
|
||||
</dd>
|
||||
</dl>
|
||||
|
|
@ -1267,11 +1267,26 @@
|
|||
new default value will be propagated to the knowledge base.
|
||||
</dd>
|
||||
</dl>
|
||||
<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
|
||||
<p>
|
||||
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>
|
||||
area will be
|
||||
inserted into the "Terms of Use" 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>
|
||||
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.
|
||||
</p>
|
||||
<h3>Next Step ...</h3>
|
||||
<p>
|
||||
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>
|
||||
<!-- #wrapper-content -->
|
||||
<div id="footer" role="contentinfo">
|
||||
<p class="copyright">
|
||||
<small>
|
||||
©2011 All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
||||
©2011 All Rights Reserved
|
||||
</small>
|
||||
| Powered
|
||||
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
||||
|
|
|
|||
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Add table
Reference in a new issue