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Updating from most recent release announcement.

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Adding BrianL's note about MySql version.
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</toc> </toc>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2> <!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
<p> <p>
The VIVO 1.2 release incorporates major changes to the entire The VIVO 1.2 release incorporates major changes throughout the
application - theming and navigation changes that will be immediately application - notably a new templating system to support more flexible
evident to any user, and underlying changes to the system architecture display and navigation, plus improvements to address scalability. The
that are less visible but address important questions of scalability release also features two new visualization options: temporal graphing
and extensibility. for organizations, and personal visualizations extended to cover grants
as well as publications. The VIVO Harvester library has also been
significantly improved and expanded in scope for its 1.0 release
through the VIVO SourceForge project at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<h3>Theming and Navigation</h3> <h4>Templating system for page generation, navigation, and theming</h4>
<p> <p>
A new installation of VIVO 1.2 will look strikingly different - the A new installation of VIVO 1.2 looks strikingly different, with a
User Interface team has designed a new visual theme that incorporates a new navigation and browse interface as well as a more modular page
new navigation and browse structure as well as a much more modular design that is easier to customize and brand for your local
approach to page design. This theme is not only cosmetically different institution. Page displays now support inline navigation to streamline
but leverages entirely new page templates developed with the Freemarker viewing of expanded personal and organizational profiles, as well as
system, an open-source library for Java development that enables much improved graphic layout and organization. New browsing controls on the
cleaner separation of application logic from the actual page design. home page and each menu page include interactive visual controls to
These changes extend the available configuration options controlling provide an immediate overview of the size and range of content and
VIVO's appearance and navigation options while also simplifying the quick access down to the individual person, organization, research
process of local customization and branding. feature, or event. VIVO's navigation has also been completely
overhauled.
</p>
<h4>Storage model</h4>
<p>
While server memory capacity has increased significantly in recent
years, VIVO's reliance on in-memory caching of RDF data had put limits
on the ultimate scalability of VIVO instances and potentially increased
the cost of servers required to support VIVO.&nbsp;
<br>
</p> </p>
<p> <p>
For existing installations of VIVO, the upgrade will not immediately With version 1.2, VIVO has been converted to optionally use Jena's
transition to the new theme, navigation, or page templates. The current SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
default theme and "tabs" (top-level and secondary navigation controls) memory footprint, allowing VIVO installations to scale well beyond what
will be left intact on upgrade and will still function as they do in has previously been possible.
version 1.1.1, with the caveat that local modifications to the default
theme may conflict with internal application changes. We highly
recommend that current VIVO installations use the time between release
1.2 and the upcoming release of version 1.3 (targeted for June or July
2011) to migrate local theme branding and navigation to the new VIVO
template. Many legacy features such as the "tab" infrastructure have
been deprecated with version 1.2 and will no longer be supported as of
version 1.3.
</p> </p>
<h3>Browsing</h3> <h4>New visualizations</h4>
<p> <p>
In addition to changes in the top-level navigation, VIVO 1.2 VIVO continues to expand visualization options including all-new
introduces a number of new browsing controls that will be made more user-configurable temporal comparisons of publications and grants,
configurable and extensible in version 1.3 but which already offer grouped by organization or by affiliated person. Visualizations of
extensive functionality. networks of co-authors are now complemented by visualizations of
co-investigators on grants, with a similar interactivity and options
for export as images or data.
</p> </p>
<h4>Ontology</h4>
<p> <p>
A fresh installation of VIVO 1.2 will feature the new theme and VIVO 1.2 includes a new ontology module representing research
additional browsing options on other top-level navigation pages (Home, resources including biological specimens, human studies, instruments,
People, Research, Organizations, and Events). Primary among the new organisms, protocols, reagents, and research opportunities. This module
browsing options will be browsing by <b>type</b>, organized is aligned with the top-level ontology classes and properties from the
hierarchically with the same upper-level <b>class groups</b> NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
currently
visible in search results - people, courses, activities, topics,
events, organizations, and publications. Class groups combine the
similar types such as people or organizations into groups for browsing
and searching, and are locally configurable using the VIVO ontology
editor.
</p> </p>
<h3>Associated VIVO releases</h3>
<h4>VIVO Harvester</h4>
<p> <p>
Once a group has been selected, browsing can continue to the very The Harvester development team is releasing version 1.0 of the VIVO
specific, at the level of individual people, organizations, events, or Harvester library, an extensible data ingest and updating framework
publications via A ... Z listing featuring thumbnail pictures where with sample configurations for loading PubMed publication, grants, and
available. Sites will be able to configure which groups and which types human resources data. The Harvester is available at
within a group are exposed in search results and for browsing. <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<h3>Data Storage</h3> <hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p>
Before this release, VIVO has used the Jena (<a href="http://jena.sourceforge.net/" rel="nofollow">http://jena.sourceforge.net</a>)
relational
database (RDB) subsystem for the storage of RDF data. The
performance of this persistence layer has never been fast enough for an
interactivity at any significant scale, so VIVO has also maintained a
complete copy of data in memory. While server memory capacity has
increased significantly in recent years, this requirement has put
limits on the ultimate scalability of VIVO instances and also increased
the cost of servers required to support VIVO.
</p>
<p>
With version 1.2 VIVO uses the SPARQL database (SDB) subsystem of
Jena, specifically designed to support scalable storage and query of
RDF datasets while still using standard relational database technology.
This transition will significantly reduce the initial memory footprint
of a VIVO application, and while the application will still require
adequate processor and memory resources to generate pages from so many
individual RDF statements, the scalability of VIVO installations is
greatly improved.
</p>
<p>
The transition to retrieving all data via SPARQL queries also
enables additional features important for tracking data provenance and
access to data outside the immediate local VIVO instance. These
features will be more fully explored and developed for version 1.3.
</p>
<!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p> <p>
This document is a summary of the VIVO installation process. This This document is a summary of the VIVO installation process. This
and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a> and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
@ -123,9 +99,9 @@
</p> </p>
<ul> <ul>
<li> <li>
These instructions assume that you are performing a clean These instructions assume that you are performing a clean
install, including emptying an existing database and removing a install, including emptying an existing database and removing a
previous installation from the Tomcat webapps directory. Product previous installation from the Tomcat webapps directory. Product
functionality may not be as expected if you install over an existing functionality may not be as expected if you install over an existing
installation of an earlier version. installation of an earlier version.
</li> </li>
@ -135,8 +111,8 @@
</li> </li>
</ul> </ul>
<p> <p>
VIVO Developers: If you are working on the VIVO source code from VIVO Developers: If you are working on the VIVO source code from
Subversion, the instructions are slightly different. Please consult Subversion, the instructions are slightly different. Please consult
developers.txt in this directory. developers.txt in this directory.
</p> </p>
<toc> <toc>
@ -151,6 +127,9 @@
<li> <li>
<a href="#download_code">Download the VIVO Application Source</a> <a href="#download_code">Download the VIVO Application Source</a>
</li> </li>
<li>
<a href="#data_storage">SDB vs RDB</a>
</li>
<li> <li>
<a href="#deploy_properties">Specify deployment properties</a> <a href="#deploy_properties">Specify deployment properties</a>
</li> </li>
@ -203,25 +182,31 @@
Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a> Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
</li> </li>
<li> <li>
MySQL 5.1 or higher, <a href="http://www.mysql.com">http://www.mysql.com</a> MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a>
</li> </li>
</ul> </ul>
<p> <p>
Be sure to setup the environment variables for <code java_home=""></code> Be sure to setup the environment variables for <code java_home=""></code>
and <code>ANT_HOME</code> and <code>ANT_HOME</code>
and add the executables to your path per and add the executables to your path per
your operating system and installation directions from the software your operating system and installation directions from the software
support web sites. support web sites.
</p> </p>
<p>
* 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 table formatting or other
unexpected problems.
</p>
<h3 id="create_database">II. Create an empty MySQL database </h3> <h3 id="create_database">II. Create an empty MySQL database </h3>
<p> <p>
Decide on a database name, username, and password. Log into your Decide on a database name, username, and password. Log into your
MySQL server and create a new database in MySQL that uses <code>UTF-8 MySQL server and create a new database in MySQL that uses <code>UTF-8
encoding</code>. You will need these values for Step IV when you encoding</code>. You will need these values for Step IV when you
configure the deployment properties. At the MySQL command line you can configure the deployment properties. At the MySQL command line you can
create the database and user with these commands substituting your create the database and user with these commands substituting your
values for <code>dbname</code>, <code>username</code>, and <code>password</code>. values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
Most Most
of of
the time, the hostname will equal <code>localhost</code>. the time, the hostname will equal <code>localhost</code>.
</p> </p>
@ -244,7 +229,11 @@
<br> <br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a> <a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</p> </p>
<h3 id="deploy_properties">IV. Specify deployment properties </h3> <h3 id="data_storage">IV. SDB vs RDB (title)</h3>
<p>
Content from Brian Lowe coming.
</p>
<h3 id="deploy_properties">V. Specify deployment properties </h3>
<p> <p>
At the top level of the unpacked distribution, copy the file <code>example.deploy.properties</code> At the top level of the unpacked distribution, copy the file <code>example.deploy.properties</code>
to a file named simply <code>deploy.properties</code>. This file sets to a file named simply <code>deploy.properties</code>. This file sets
@ -252,14 +241,14 @@
</p> </p>
<p> <p>
<em>Windows:</em> <em>Windows:</em>
For those installing on Windows operating For those installing on Windows operating
system, include the windows drive and use the forward slash "/" and not system, include the windows drive and use the forward slash "/" and not
the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>. the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
</p> </p>
<p> <p>
<em>External authentication:</em> <em>External authentication:</em>
If you want to use an external If you want to use an external
authentication system like Shibboleth or CUWebAuth, you will need to authentication system like Shibboleth or CUWebAuth, you will need to
set two additional properties in this file. See the section below set two additional properties in this file. See the section below
entitled <a href="#external_auth">Using an External Authentication entitled <a href="#external_auth">Using an External Authentication
System with VIVO</a>. System with VIVO</a>.
@ -300,8 +289,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where Vitro code is located. In most Directory where Vitro code is located. In most
deployments, this is set to ./vitro-core (It is not uncommon for this deployments, this is set to ./vitro-core (It is not uncommon for this
setting to point elsewhere in development environments). setting to point elsewhere in development environments).
</td> </td>
</tr> </tr>
@ -341,8 +330,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where uploaded files will be stored. Directory where uploaded files will be stored.
Be sure this directory exists and is writable by the user that Be sure this directory exists and is writable by the user that
the Tomcat service is running as. the Tomcat service is running as.
</td> </td>
</tr> </tr>
@ -356,8 +345,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where the Lucene search index will be Directory where the Lucene search index will be
built. Be sure this directory exists and is writable by the user that built. Be sure this directory exists and is writable by the user that
the Tomcat service is running as. the Tomcat service is running as.
</td> </td>
</tr> </tr>
@ -371,8 +360,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify an SMTP host that the form will use for Specify an SMTP host that the form will use for
sending e-mail (Optional). If this is left blank, the contact form will sending e-mail (Optional). If this is left blank, the contact form will
be hidden and disabled. be hidden and disabled.
</td> </td>
</tr> </tr>
@ -428,8 +417,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the Jena triple store technology to use. Specify the Jena triple store technology to use.
SDB is Jena's SPARQL database; this setting allows RDF data to scale 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 beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
store with in-memory caching. store with in-memory caching.
</td> </td>
@ -444,8 +433,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the maximum number of active connections Specify the maximum number of active connections
in the database connection pool to support the anticipated number of in the database connection pool to support the anticipated number of
concurrent page requests. It is not necessary to adjust this value when concurrent page requests. It is not necessary to adjust this value when
using the RDB configuration. using the RDB configuration.
</td> </td>
@ -460,8 +449,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the maximum number of database Specify the maximum number of database
connections that will be allowed to remain idle in the connection pool. connections that will be allowed to remain idle in the connection pool.
Default is 25% of the maximum number of active connections. Default is 25% of the maximum number of active connections.
</td> </td>
</tr> </tr>
@ -475,9 +464,9 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Change the dbtype setting to use a database Change the dbtype setting to use a database
other than MySQL. Otherwise, leave this value unchanged. Possible other than MySQL. Otherwise, leave this value unchanged. Possible
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
for additional information. for additional information.
</td> </td>
@ -492,8 +481,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify a driver class name to use a database 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. This JAR file
for this driver must be added to the the webapp/lib directory within for this driver must be added to the the webapp/lib directory within
the vitro.core.dir specified above. the vitro.core.dir specified above.
</td> </td>
@ -508,8 +497,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Change the validation query used to test Change the validation query used to test
database connections only if necessary to use a database other than database connections only if necessary to use a database other than
MySQL. Otherwise, leave this value unchanged. MySQL. Otherwise, leave this value unchanged.
</td> </td>
</tr> </tr>
@ -523,8 +512,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the name of your first admin user for Specify the name of your first admin user for
the VIVO application. This user will have an initial temporary password the VIVO application. This user will have an initial temporary password
of 'defaultAdmin'. You will be prompted to create a new password on of 'defaultAdmin'. You will be prompted to create a new password on
first login. first login.
</td> </td>
@ -539,8 +528,8 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
The URI of a property that can be used to The URI of a property that can be used to
associate an Individual with a user account. When a user logs in with a associate an Individual with a user account. When a user logs in with a
name that matches the value of this property, the user will be name that matches the value of this property, the user will be
authorized to edit that Individual. authorized to edit that Individual.
</td> </td>
@ -581,7 +570,7 @@
</tr> </tr>
</tbody> </tbody>
</table> </table>
<h3 id="deploy">V. Compile and deploy</h3> <h3 id="deploy">VI. Compile and deploy</h3>
<p> <p>
At the command line, from the top level of the unpacked At the command line, from the top level of the unpacked
distribution directory, type: distribution directory, type:
@ -590,16 +579,16 @@
<p> <p>
to build VIVO and deploy to Tomcat's webapps directory. to build VIVO and deploy to Tomcat's webapps directory.
</p> </p>
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security <h3 id="tomcat_settings">VII. Set Tomcat JVM parameters and security
limits</h3> limits</h3>
<p> <p>
Currently, VIVO copies the contents of your RDF database into Currently, VIVO copies the contents of your RDF database into
memory in order to serve Web requests quickly (the in-memory copy and memory in order to serve Web requests quickly (the in-memory copy and
the underlying databaseare kept in synch as edits are performed). the underlying databaseare kept in synch as edits are performed).
</p> </p>
<p> <p>
VIVO will require more memory than that allocated to Tomcat by VIVO will require more memory than that allocated to Tomcat by
default. With most installations of Tomcat, the "setenv.sh" or default. With most installations of Tomcat, the "setenv.sh" or
"setenv.bat" file in Tomcat's bin directory is a convenient place to "setenv.bat" file in Tomcat's bin directory is a convenient place to
set the memory parameters. set the memory parameters.
<br> <br>
@ -608,9 +597,9 @@
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre> <pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
<p> <p>
This sets Tomcat to allocate an initial heap of 2048 megabytes, a This sets Tomcat to allocate an initial heap of 2048 megabytes, a
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
megabytes is a minimum practical heap size for production installations megabytes is a minimum practical heap size for production installations
storing data for large academic institutions, and additional heap space storing data for large academic institutions, and additional heap space
is preferable. For testing with small sets of data, 256m to 512m should is preferable. For testing with small sets of data, 256m to 512m should
be sufficient. be sufficient.
</p> </p>
@ -619,26 +608,26 @@
be remedied by increasing the heap parameters and restarting Tomcat. be remedied by increasing the heap parameters and restarting Tomcat.
</p> </p>
<p> <p>
Security limits: VIVO is a multithreaded web application that may Security limits: VIVO is a multithreaded web application that may
require more threads than are permitted under your Linux installation's require more threads than are permitted under your Linux installation's
default configuration. Ensure that your installation can support the default configuration. Ensure that your installation can support the
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>: required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
</p> </p>
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre> <pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
<h3 id="start_tomcat">VII. Start Tomcat </h3> <h3 id="start_tomcat">VIII. Start Tomcat </h3>
<p> <p>
Most Tomcat installations can be started by running <code>startup.sh</code> Most Tomcat installations can be started by running <code>startup.sh</code>
or <code>startup.bat</code> or <code>startup.bat</code>
in Tomcat's bin directory. Point your in Tomcat's bin directory. Point your
browser to "http://localhost:8080/vivo/" to test the application. If browser to "http://localhost:8080/vivo/" to test the application. If
Tomcat does not start up, or the VIVO application is not visible, check Tomcat does not start up, or the VIVO application is not visible, check
the <code>catalina.out</code> the <code>catalina.out</code>
file in Tomcat's logs directory. file in Tomcat's logs directory.
</p> </p>
<h3 id="add_rdf">VIII. Log in and add RDF data </h3> <h3 id="add_rdf">IX. Log in and add RDF data </h3>
<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>initialAdminUser</code> in" link near the upper right corner. Log in with the <code>initialAdminUser</code>
username you set up in Step IV. The initial password for the <code>initialAdminUser</code> username you set up in Step IV. The initial password for the <code>initialAdminUser</code>
account is "defaultAdmin" (without the quotes). On first login, you account is "defaultAdmin" (without the quotes). On first login, you
@ -647,17 +636,17 @@
<p> <p>
After verifying your new password, you will be presented with a After verifying your new password, you will be presented with a
menu of editing options. Here you can create OWL classes, object menu of editing options. Here you can create OWL classes, object
properties, data properties, and configure the display of data. properties, data properties, and configure the display of data.
Currently, any classes you wish to make visible on your website must be Currently, any classes you wish to make visible on your website must be
part of a class group, and there a number of visibility and display part of a class group, and there a number of visibility and display
options available for each ontology entity. VIVO comes with a core VIVO options available for each ontology entity. VIVO comes with a core VIVO
ontology, but you may also upload other ontologies from an RDF file. ontology, but you may also upload other ontologies from an RDF file.
</p> </p>
<p> <p>
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
that Vitro currently works best with OWL-DL ontologies and has only that Vitro currently works best with OWL-DL ontologies and has only
limited support for pure RDF data. You can enter a URL pointing to the limited support for pure RDF data. You can enter a URL pointing to the
RDF data you wish to load or upload a file on your local machine. RDF data you wish to load or upload a file on your local machine.
Ensure that the "add RDF" radio button is selected. You will also Ensure that the "add RDF" radio button is selected. You will also
likely want to check "create classgroups automatically." likely want to check "create classgroups automatically."
</p> </p>
@ -669,32 +658,32 @@
See more documentation for configuring VIVO, ingesting data, and See more documentation for configuring VIVO, ingesting data, and
manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>. manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
</p> </p>
<h3 id="contact_email">IX. Set the Contact Email Address (if using <h3 id="contact_email">X. Set the Contact Email Address (if using
"Contact Us" form)</h3> "Contact Us" form)</h3>
<p> <p>
If you have configured your application to use the "Contact Us" If you have configured your application to use the "Contact Us"
feature in Step IV (<code>Vitro.smtpHost</code>), you will also need to feature in Step IV (<code>Vitro.smtpHost</code>), you will also need to
add an email address to the VIVO application.&nbsp; This is the email add an email address to the VIVO application.&nbsp; This is the email
that the contact form submits to. It can be a list server or an that the contact form submits to. It can be a list server or an
individual's email address. individual's email address.
</p> </p>
<p> <p>
Log in as a system administrator. Navigate to the "Site Admin" Log in as a system administrator. Navigate to the "Site Admin"
table of contents (link in the right side of the header). Go to "Site table of contents (link in the right side of the header). Go to "Site
Information" (under "Site Configuration"). In the "Site Information Information" (under "Site Configuration"). In the "Site Information
Editing Form," enter a functional email address in the field "Contact Editing Form," enter a functional email address in the field "Contact
Email Address." and submit the change. Email Address." and submit the change.
</p> </p>
<p> <p>
If you set the<code>Vitro.smtpHost</code> If you set the<code>Vitro.smtpHost</code>
in Step IV and do NOT in Step IV and do NOT
provide an email addressin this step, your users will receive a java provide an email addressin this step, your users will receive a java
error in the interface. error in the interface.
</p> </p>
<h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3> <h3 id="tomcat_connector">XI. Set up Apache Tomcat Connector </h3>
<p> <p>
It is recommended that a Tomcat Connector such as mod_jk be used to It is recommended that a Tomcat Connector such as mod_jk be used to
ensure that the site address does not include the port number (e.g. ensure that the site address does not include the port number (e.g.
8080) and an additional reference to the Tomcat context name (e.g. 8080) and an additional reference to the Tomcat context name (e.g.
/vivo). /vivo).
</p> </p>
@ -712,9 +701,9 @@
</p> </p>
<p> <p>
After setting up the mod_jk connector above, you will need to After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>) modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
to to
respond respond
to requests from Apache via the connector. Look for the to requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties: &lt;connector&gt; directive and add the following properties:
</p> </p>
@ -730,48 +719,48 @@
and update as follows: and update as follows:
</p> </p>
<pre> &lt;Host name="localhost" appBase="webapps"<br> DeployOnStartup="false"<br> unpackWARs="true" autoDeploy="false"<br> xmlValidation="false" xmlNamespaceAware="false"&gt;<br> <br> &lt;Alias&gt;example.com&lt;/Alias&gt;<br> &lt;Context path=""<br> docBase="/usr/local/tomcat/webapps/vivo"<br> reloadable="true"<br> cookies="true" &gt;<br> &lt;Manager pathname="" /&gt;<br> &lt;Environment type="java.lang.String" override="false" <br> name="path.configuration" <br> value="deploy.properties"<br> /&gt;<br> &lt;/Context&gt;<br> ...<br> </pre> <pre> &lt;Host name="localhost" appBase="webapps"<br> DeployOnStartup="false"<br> unpackWARs="true" autoDeploy="false"<br> xmlValidation="false" xmlNamespaceAware="false"&gt;<br> <br> &lt;Alias&gt;example.com&lt;/Alias&gt;<br> &lt;Context path=""<br> docBase="/usr/local/tomcat/webapps/vivo"<br> reloadable="true"<br> cookies="true" &gt;<br> &lt;Manager pathname="" /&gt;<br> &lt;Environment type="java.lang.String" override="false" <br> name="path.configuration" <br> value="deploy.properties"<br> /&gt;<br> &lt;/Context&gt;<br> ...<br> </pre>
<h3 id="pellet">XI. Configure Pellet Reasoner </h3> <h3 id="pellet">XII. Configure Pellet Reasoner </h3>
<p> <p>
<em>Do we need this section still? - elly</em> <em>Do we need this section still? - elly</em>
</p> </p>
<p> <p>
VIVO uses the Pellet engine to perform reasoning, which runs in the VIVO uses the Pellet engine to perform reasoning, which runs in the
background at startup and also when the knowledge base is edited. VIVO background at startup and also when the knowledge base is edited. VIVO
continues serving pages while the reasoner continues working; when the continues serving pages while the reasoner continues working; when the
reasoner finishes, the new inferences appear. Inferred statements are reasoner finishes, the new inferences appear. Inferred statements are
cached in a database graph so that they are available immediately when cached in a database graph so that they are available immediately when
VIVO is restarted. VIVO is restarted.
</p> </p>
<p> <p>
By default, Pellet is fed only an incomplete view of your ontology By default, Pellet is fed only an incomplete view of your ontology
and only certain inferences are materialized. These include rdf:type, and only certain inferences are materialized. These include rdf:type,
rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode
is typically suitable for ontologies with a lot of instance data. If is typically suitable for ontologies with a lot of instance data. If
you would like to keep the default mode, skip to the next step. you would like to keep the default mode, skip to the next step.
</p> </p>
<p> <p>
To enable "complete" OWL inference (materialize all significant To enable "complete" OWL inference (materialize all significant
entailed statements), open "vitro-core/webapp/config/web.xml" and entailed statements), open "vitro-core/webapp/config/web.xml" and
search for PelletReasonerSetup. search for PelletReasonerSetup.
</p> </p>
<p> <p>
Then change the name of the listener class to Then change the name of the listener class to
PelletReasonerSetupComplete. Because "complete" reasoning can be very PelletReasonerSetupComplete. Because "complete" reasoning can be very
resource intensive, there is also an option to materialize nearly all resource intensive, there is also an option to materialize nearly all
inferences except owl:sameAs and owl:differentFrom. inferences except owl:sameAs and owl:differentFrom.
</p> </p>
<p> <p>
This is enabled by specifying PelletReasonerSetupPseudocomplete. This is enabled by specifying PelletReasonerSetupPseudocomplete.
For ontologies with large numbers of individuals, this mode can offer For ontologies with large numbers of individuals, this mode can offer
enormous performance improvements over the "complete" mode. enormous performance improvements over the "complete" mode.
</p> </p>
<p> <p>
Finally, a class called Finally, a class called
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
improve performance on ontologies with large literals where data improve performance on ontologies with large literals where data
property entailments are not needed. property entailments are not needed.
</p> </p>
<h3 id="external_auth">XII. Using an External Authentication System <h3 id="external_auth">XIII. Using an External Authentication System
with VIVO </h3> with VIVO </h3>
<p> <p>
</p> </p>
@ -780,14 +769,14 @@
system like Shibboleth or CUWebAuth. system like Shibboleth or CUWebAuth.
</p> </p>
<p> <p>
VIVO must be accessible only through an Apache HTTP server. The VIVO must be accessible only through an Apache HTTP server. The
Apache server will be configured to invoke the external authentication Apache server will be configured to invoke the external authentication
system. When the user completes the authentication, the Apache server system. When the user completes the authentication, the Apache server
will pass a network ID to VIVO, to identify the user. will pass a network ID to VIVO, to identify the user.
</p> </p>
<p> <p>
If VIVO has an account for that user, the user will be logged in If VIVO has an account for that user, the user will be logged in
with the privileges of that account. In the absence of an account, VIVO with the privileges of that account. In the absence of an account, VIVO
will try to find a page associated with the user. If such a page is will try to find a page associated with the user. If such a page is
found, the user can log in to edit his own profile information. found, the user can log in to edit his own profile information.
</p> </p>
@ -844,9 +833,9 @@
If VIVO has an account for the user, the user will be given the If VIVO has an account for the user, the user will be given the
privileges assigned to that account. privileges assigned to that account.
<p> <p>
In addition, VIVO will try to associate the user with a profile In addition, VIVO will try to associate the user with a profile
page, so the user may edit his own profile data. VIVO will search the page, so the user may edit his own profile data. VIVO will search the
data model for a person with a property that matches the User’s network data model for a person with a property that matches the User’s network
ID. You need to tell VIVO what property should be used for matching. ID. You need to tell VIVO what property should be used for matching.
Insert a line like this in the deploy.properties file: Insert a line like this in the deploy.properties file:
</p> </p>
@ -854,7 +843,7 @@
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre> For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li> </li>
</ul> </ul>
<h3 id="installation_check">XIII. Was the installation successful? </h3> <h3 id="installation_check">XIV. Was the installation successful? </h3>
<p> <p>
If you have completed the previous steps, you have good indications If you have completed the previous steps, you have good indications
that the installation was successful. that the installation was successful.
@ -878,9 +867,9 @@
Click on the "Index" link on the upper right, below the logo. Click on the "Index" link on the upper right, below the logo.
You should see a "locations" section, with links for "Country" and You should see a "locations" section, with links for "Country" and
"Geographic Location." The index is built in a background thread, so on "Geographic Location." The index is built in a background thread, so on
your first login, you may see an empty index instead. Refresh the page your first login, you may see an empty index instead. Refresh the page
periodically to see whether the index will be populated. This may take periodically to see whether the index will be populated. This may take
some time: with VIVO installed on a modest laptop computer, loading the some time: with VIVO installed on a modest laptop computer, loading the
ontology files and building the index took more than 5 minutes from the ontology files and building the index took more than 5 minutes from the
time that Tomcat was started. time that Tomcat was started.
</li> </li>
@ -901,28 +890,28 @@
you will be prompted to change the password. you will be prompted to change the password.
</li> </li>
<li> <li>
After you have successfully logged in, click "site admin" in the After you have successfully logged in, click "site admin" in the
upper right corner. In the drop down under "Data Input" select "Faculty upper right corner. In the drop down under "Data Input" select "Faculty
Member(core)" and click the "Add individual of this class" button. Member(core)" and click the "Add individual of this class" button.
</li> </li>
<li> <li>
Enter the name "test individual" under the field "Individual Enter the name "test individual" under the field "Individual
Name," scroll to the bottom, and click "Create New Record." You will be Name," scroll to the bottom, and click "Create New Record." You will be
taken to the "Individual Control Panel." Make note of the value of the taken to the "Individual Control Panel." Make note of the value of the
field "URI" it will be used in the next step. field "URI" it will be used in the next step.
</li> </li>
<li> <li>
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>. Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
In In
the the
pink box on that page enter the URI of the individual you pink box on that page enter the URI of the individual you
created in the previous step and click "open." created in the previous step and click "open."
</li> </li>
<li> <li>
In the resulting page search for the URI of the "test In the resulting page search for the URI of the "test
individual." You should find it towards the bottom of the page next to individual." You should find it towards the bottom of the page next to
a red dot followed by "redirect (303)." This indicates that you are a red dot followed by "redirect (303)." This indicates that you are
successfully serving linked RDF data. If the URI of the "test successfully serving linked RDF data. If the URI of the "test
individual" is followed by "failed (400)" you are not successfully individual" is followed by "failed (400)" you are not successfully
serving linked data. serving linked data.
</li> </li>
@ -932,9 +921,9 @@
</p> </p>
<ul> <ul>
<li> <li>
Type the word "Australia" into the search box, and click on the Type the word "Australia" into the search box, and click on the
Search button.You should see a page of results, with links to countries Search button.You should see a page of results, with links to countries
that border Australia, individuals that include Australia, and to that border Australia, individuals that include Australia, and to
Australia itself. To trigger the search index, you can log in as a site Australia itself. To trigger the search index, you can log in as a site
administrator and go to "http://your-vivo-url/SearchIndex". administrator and go to "http://your-vivo-url/SearchIndex".
</li> </li>