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Updating from most recent release announcement draft. Still needs Nick's theme documentation.

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doc/upgrade-1.2.html
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</p>
<!-- 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>
<!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
<toc>
<ol class="roman1">
<li>
@ -615,7 +589,6 @@
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 representative to see whether any
corrective action needs to be taken.
@ -710,7 +683,6 @@
new default value will be propagated to the knowledge base.
</dd>
</dl>
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
<p>
@ -743,15 +715,12 @@
<dd>
A log of the upgrade process. The actual filename includes a timestamp
that tells when the upgrade executed.
This file should end with
<code>Finished adding alias URLs to FileByteStreams.</code>
This file should end with<code>Finished adding alias URLs to FileByteStreams.</code>
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>
<h3 id="theme">V. Theme Changes</h3>
<h4 style="color:red">Need Nick to help with this section</h4>
<p>
@ -779,7 +748,7 @@
<dd>
<dl>
<dt>
a. Copy the directory <code>/vivo/themes/vivo-basic/templates</code>
a. Copy the directory <code>/vivo/themes/wilma/templates</code>
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
</dt>
<dd>