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doc/install.html
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@ -16,7 +16,7 @@
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.3 Installation Guide</h1> <h1>VIVO Release 1 V1.3 Installation Guide</h1>
<small> <small>
July 22, 2011 July 29, 2011
</small> </small>
<toc> <toc>
<ul> <ul>
@ -29,25 +29,27 @@
</ul> </ul>
</toc> </toc>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2> <!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
VIVO Release 1.3 incorporates changes to the search indexing, user <!-- Release Announcement -->VIVO Release 1.3 incorporates changes to the search
accounts, menu management, ontology, and visualizations. indexing, user accounts, menu management, ontology, and visualizations, and begins
integration of VIVO Harvester functions with VIVO's own ingest tools.
<br> <br>
<h4>Search</h4> <h4>Search</h4>
VIVO 1.3 will feature notable improvements to the local search, <p>
primarily to improve relevance ranking but also to boost the influence VIVO 1.3 will feature notable improvements to the local search, primarily to
of semantic relationships in the search. This will improve recall by improve relevance ranking but also to boost the influence of semantic relationships
including text from related resources (e.g., adding a person’s grant in the search. This will improve recall by including text from related resources
and publication titles to his or her search entry) and by boosting (e.g., adding a person's grant and publication titles to his or her search entry)
overall relevance ranking based on the number and nature of connections and by boosting overall relevance ranking based on the number and nature of
from one individual to others. connections from one individual to others.
<br> </p>
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place <p>
of Apache Lucene to improve indexing and faceting of search results. VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place of
The migration to Solr also aligns the local search with the VIVO Apache Lucene to improve indexing and faceting of search results. The migration
multi-site search site under development for release prior to the 2011 to Solr also aligns the local search with the VIVO multi-site search site under
VIVO Conference. development for release prior to the 2011 VIVO Conference.
<br> </p>
<h4>Authorization</h4> <h4>Authorization</h4>
<p>
Release 1.3 provides an entirely new model of authorization within the Release 1.3 provides an entirely new model of authorization within the
VIVO application to allow more granular control over system VIVO application to allow more granular control over system
configuration and editing. The first phase of the new user account configuration and editing. The first phase of the new user account
@ -55,42 +57,55 @@
root acount, and password reset functionality where the password gets root acount, and password reset functionality where the password gets
emailed to the user. The next phase will provide the ability to create emailed to the user. The next phase will provide the ability to create
new roles. new roles.
<br> </p>
<h4>Menu management</h4> <h4>Menu management</h4>
<p>
The menus across the top of the site (Home, People, Organizations, The menus across the top of the site (Home, People, Organizations,
Research, Events) can now be managed in a web form instead of editing Research, Events) can now be managed in a web form instead of editing
an RDF file. In addition to making site management much easier, an RDF file. In addition to making site management much easier,
form-based editing also allows more control over what classes of data form-based editing also allows more control over what classes of data
are displayed and provides a mechanism to limit certain menu pages to are displayed and provides a mechanism to limit certain menu pages to
content identified as internal to the institution. content identified as internal to the institution.
<br> </p>
<h4>FreeMaker template improvements</h4> <h4>FreeMaker template improvements</h4>
<p>
While less directly visible to the public, version 1.3 also includes While less directly visible to the public, version 1.3 also includes
additional changes focused directly on supporting open source community additional changes focused directly on supporting open source community
involvement in extending and customizing VIVO. The development team involvement in extending and customizing VIVO. The development team
began a year ago to transition VIVO’s code base away from Java Server began a year ago to transition VIVO&#39;s code base away from Java Server
Pages to the FreeMarker page templating system that much more cleanly Pages to the FreeMarker page templating system that much more cleanly
separates internal application programming logic from page display. separates internal application programming logic from page display.
<br> </p>
<h4>Visualization</h4> <h4>Visualization</h4>
The visualization team has implemented a Science Map visualization, <p>
The visualization team has implemented a Map of Science visualization,
which allows users to visually explore the scientific strengths of a which allows users to visually explore the scientific strengths of a
university, school, department, or person in the VIVO instance. Users university, school, department, or person in the VIVO instance. Users
will be able to see where an organization or person’s interests lay will be able to see where an organization or person&#39;s interests lay
across 13 major scientific disciplines or 554 sub-disciplines, and will across 13 major scientific disciplines or 554 sub-disciplines, and will
be able to see how these disciplines and sub-disciplines interrelate be able to see how these disciplines and sub-disciplines interrelate
with one another on the map of science. Wireframes and design with one another on the map of science. Wireframes and design
documentation for upcoming enhanced versions of the Science Map documentation for upcoming enhanced versions of the Map of Science
visualization have already been developed; the Science Map visualization have already been developed; the Map of Science
visualization will most likely be in the form of a PDF that a user can visualization will most likely be in the form of a PDF that a user can
download. download.
<br> </p>
<p>
Several visualization also now provide a caching feature that improves Several visualization also now provide a caching feature that improves
performance after the initial processing. performance after the initial processing.
<br> </p>
<h4>QR Codes</h4> <h4>QR Codes</h4>
Pages for people in VIVO have the option of displaying QR codes. <p>
<br> Pages for people in VIVO now have an icon for displaying QR codes to allow
capturing names and available contact information on mobile devices.
</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
from the VIVO Ingest Tools menu in support of more unified and centralized
management for data ingest.
</p>
<h4>Ontology changes</h4> <h4>Ontology changes</h4>
<ul> <ul>
<li> <li>
@ -114,11 +129,12 @@
</li> </li>
</ul> </ul>
<h4>Linked open data</h4> <h4>Linked open data</h4>
<p>
Responses to linked data requests have been enhanced to include Responses to linked data requests have been enhanced to include
additional context about any individual, in working toward a goal of 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 being able to provide all the data in a person's profile available as
RDF via a single web request. RDF via a single web request.
<br> </p>
<br> <br>
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2> <hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
<p> <p>
@ -228,6 +244,9 @@
<li> <li>
<a href="#installation_check">Was the installation successful?</a> <a href="#installation_check">Was the installation successful?</a>
</li> </li>
<li>
<a href="#termsofuse">Review the VIVO Terms of Use</a>
</li>
</ol> </ol>
</toc> </toc>
<h3 id="required_software">I. Install required software </h3> <h3 id="required_software">I. Install required software </h3>
@ -258,7 +277,7 @@
support websites. support websites.
</p> </p>
<p> <p>
* Note that VIVO 1.2 will not run on older versions of MySQL that * Note that VIVO V1.2 or V1.3 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 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 higher. Using unsupported versions may result in strange error messages
related to table formatting or other unexpected problems. related to table formatting or other unexpected problems.
@ -292,8 +311,8 @@
<br> <br>
</h3> </h3>
<p> <p>
Download the VIVO application source as either <code>rel-1.2.zip</code> Download the VIVO application source as either <code>rel-1.3.zip</code>
or <code>rel-1.2.gz</code> or <code>rel-1.3.gz</code>
file and unpack it on your web server: file and unpack it on your web server:
<br> <br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a> <a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
@ -417,8 +436,7 @@
made to Solr, the IP address of the requestor must match one of the made to Solr, the IP address of the requestor must match one of the
patterns, or the request will be rejected. patterns, or the request will be rejected.
<br> <br>
Examples: Examples:<code>
<code>
<ul> <ul>
<li> <li>
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1 vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
@ -534,22 +552,6 @@
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 connections Specify the maximum number of active connections
@ -667,15 +669,33 @@
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>
@ -683,11 +703,8 @@
The number of grants and publications is large. The number of grants and publications is large.
</li> </li>
</ul> </ul>
The VIVO developers are working to make this visualization more VIVO V1.3 mitigates this problem by the way of a caching
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.
by disabling the temporal graph visualization unless the
"visualization.temporal" flag is set to "enabled". To enable it,
uncomment the line for this setting.
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -1077,12 +1094,26 @@
administrator and go to "http://your-vivo-url/SearchIndex". administrator and go to "http://your-vivo-url/SearchIndex".
</li> </li>
</ul> </ul>
<h3 id="termsofuse">XIII. 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> </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>

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doc/upgrade-1.3.html
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@ -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>&lt;query-base&gt;</code> and <code>&lt;query-collated&gt;</code> <code>&lt;query-base&gt;</code>
and <code>&lt;query-collated&gt;</code>
have been replaced with a single query <code>&lt;query-select&gt;</code> have been replaced with a single query <code>&lt;query-select&gt;</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>