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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>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
<p>
The VIVO 1.2 release incorporates major changes to the entire
application - theming and navigation changes that will be immediately
evident to any user, and underlying changes to the system architecture
that are less visible but address important questions of scalability
and extensibility.
The VIVO 1.2 release incorporates major changes throughout the
application - notably a new templating system to support more flexible
display and navigation, plus improvements to address scalability. The
release also features two new visualization options: temporal graphing
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>
<h3>Theming and Navigation</h3>
<h4>Templating system for page generation, navigation, and theming</h4>
<p>
A new installation of VIVO 1.2 will look strikingly different - the
User Interface team has designed a new visual theme that incorporates a
new navigation and browse structure as well as a much more modular
approach to page design. This theme is not only cosmetically different
but leverages entirely new page templates developed with the Freemarker
system, an open-source library for Java development that enables much
cleaner separation of application logic from the actual page design.
These changes extend the available configuration options controlling
VIVO's appearance and navigation options while also simplifying the
process of local customization and branding.
A new installation of VIVO 1.2 looks strikingly different, with a
new navigation and browse interface as well as a more modular page
design that is easier to customize and brand for your local
institution. Page displays now support inline navigation to streamline
viewing of expanded personal and organizational profiles, as well as
improved graphic layout and organization. New browsing controls on the
home page and each menu page include interactive visual controls to
provide an immediate overview of the size and range of content and
quick access down to the individual person, organization, research
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>
For existing installations of VIVO, the upgrade will not immediately
transition to the new theme, navigation, or page templates. The current
default theme and "tabs" (top-level and secondary navigation controls)
will be left intact on upgrade and will still function as they do in
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.
With version 1.2, VIVO has been converted to optionally use Jena's
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
memory footprint, allowing VIVO installations to scale well beyond what
has previously been possible.
</p>
<h3>Browsing</h3>
<h4>New visualizations</h4>
<p>
In addition to changes in the top-level navigation, VIVO 1.2
introduces a number of new browsing controls that will be made more
configurable and extensible in version 1.3 but which already offer
extensive functionality.
VIVO continues to expand visualization options including all-new
user-configurable temporal comparisons of publications and grants,
grouped by organization or by affiliated person. Visualizations of
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>
<h4>Ontology</h4>
<p>
A fresh installation of VIVO 1.2 will feature the new theme and
additional browsing options on other top-level navigation pages (Home,
People, Research, Organizations, and Events). Primary among the new
browsing options will be browsing by <b>type</b>, organized
hierarchically with the same upper-level <b>class groups</b>
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.
VIVO 1.2 includes a new ontology module representing research
resources including biological specimens, human studies, instruments,
organisms, protocols, reagents, and research opportunities. This module
is aligned with the top-level ontology classes and properties from the
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
</p>
<h3>Associated VIVO releases</h3>
<h4>VIVO Harvester</h4>
<p>
Once a group has been selected, browsing can continue to the very
specific, at the level of individual people, organizations, events, or
publications via A ... Z listing featuring thumbnail pictures where
available. Sites will be able to configure which groups and which types
within a group are exposed in search results and for browsing.
The Harvester development team is releasing version 1.0 of the VIVO
Harvester library, an extensible data ingest and updating framework
with sample configurations for loading PubMed publication, grants, and
human resources data. The Harvester is available at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p>
<h3>Data Storage</h3>
<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>
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p>
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>
@ -151,6 +127,9 @@
<li>
<a href="#download_code">Download the VIVO Application Source</a>
</li>
<li>
<a href="#data_storage">SDB vs RDB</a>
</li>
<li>
<a href="#deploy_properties">Specify deployment properties</a>
</li>
@ -203,7 +182,7 @@
Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
</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>
</ul>
<p>
@ -213,6 +192,12 @@
your operating system and installation directions from the software
support web sites.
</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>
<p>
Decide on a database name, username, and password. Log into your
@ -244,7 +229,11 @@
<br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</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>
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
@ -581,7 +570,7 @@
</tr>
</tbody>
</table>
<h3 id="deploy">V. Compile and deploy</h3>
<h3 id="deploy">VI. Compile and deploy</h3>
<p>
At the command line, from the top level of the unpacked
distribution directory, type:
@ -590,7 +579,7 @@
<p>
to build VIVO and deploy to Tomcat's webapps directory.
</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>
<p>
Currently, VIVO copies the contents of your RDF database into
@ -625,7 +614,7 @@
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
</p>
<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>
Most Tomcat installations can be started by running <code>startup.sh</code>
or <code>startup.bat</code>
@ -635,7 +624,7 @@
the <code>catalina.out</code>
file in Tomcat's logs directory.
</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>
If the startup was successful, you will see a welcome message
informing you that you have successfully installed VIVO. Click the "Log
@ -669,7 +658,7 @@
See more documentation for configuring VIVO, ingesting data, and
manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
</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>
<p>
If you have configured your application to use the "Contact Us"
@ -691,7 +680,7 @@
provide an email addressin this step, your users will receive a java
error in the interface.
</p>
<h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3>
<h3 id="tomcat_connector">XI. Set up Apache Tomcat Connector </h3>
<p>
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.
@ -730,7 +719,7 @@
and update as follows:
</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>
<h3 id="pellet">XI. Configure Pellet Reasoner </h3>
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
<p>
<em>Do we need this section still? - elly</em>
</p>
@ -771,7 +760,7 @@
improve performance on ontologies with large literals where data
property entailments are not needed.
</p>
<h3 id="external_auth">XII. Using an External Authentication System
<h3 id="external_auth">XIII. Using an External Authentication System
with VIVO </h3>
<p>
</p>
@ -854,7 +843,7 @@
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li>
</ul>
<h3 id="installation_check">XIII. Was the installation successful? </h3>
<h3 id="installation_check">XIV. Was the installation successful? </h3>
<p>
If you have completed the previous steps, you have good indications
that the installation was successful.