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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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@ -26,7 +26,7 @@
</li>
</ul>
</toc>
<p>
<p>
This document provides a short description of the steps involved in
upgrading your installation of VIVO from Release 1, Version 1.1 to
Version 1.2. This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
@ -41,95 +41,69 @@
</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>
@ -432,9 +406,9 @@
<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>
@ -566,11 +540,11 @@
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 your institution's tracking code, see
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 your institution's tracking code, see
the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
Google
Analytics
@ -587,299 +561,294 @@
</li>
</ul>
</blockquote>
</p>
<p>
4. If you had modified <code>web.xml</code>
to configure the Pellet Reasoner (as described
in the installation instructions), repeat that modification.
</p>
<p>
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
</p>
<p>
6. Start Apache Tomcat and log in to VIVO.
</p>
<h3 id="ontology">III. Ontology Changes</h3>
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
<p>
After Apache Tomcat is started, these files should be reviewed to
verify that the automated upgrade process was executed
successfully.&nbsp; The ontology alignment process will create the
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
</p>
<dl>
<dt>
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
</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 representative to see whether any
corrective action needs to be taken.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code>
</dt>
<dd>
A log of errors that were encountered during the upgrade process. This
file should be empty if the upgrade was successful.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/changedData/removedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were removed from the
knowledge base.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/changedData/addedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were added to the
knowledge base.
</dd>
</dl>
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual review</h4>
<p>
Changes to the VIVO core ontology may require corresponding
modifications of the knowledge base instance data and local ontology
extensions.
</p>
<p>
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 following
types of changes:
</p>
<dl>
<dt>
Class or Property renaming
</dt>
<dd>
All references to the class (in the subject or object position) will be
updated to the new name. References to the property will be updated to
the new name.
</dd>
</dl>
<dl>
<dt>
Class or Property deletion
</dt>
<dd>
All individuals in 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
directory.
</dd>
</dl>
<dl>
<dt>
Property addition
</dt>
<dd>
If a newly added property is the inverse of a previously existing
property, the inverse of any statements using the pre-existing property
will be asserted.
</dd>
</dl>
<dl>
<dt>
Annotation property default values
</dt>
<dd>
If a site has modified the value of a vitro annotation (such as
displayRankAnnot or displayLimitAnnot) so that it is no longer using
the default, then that setting will be left unchanged.
<br>
If a site is using the default value of a vitro annotation, and the
default has been changed in the new version of the ontology, then the
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>
Each uploaded file exists as an individual entity in VIVO. When the
browser requests an upload file from VIVO, the data model is queried to
find out where the file is actually stored, so it can be downloaded to
the browser.
</p>
<p>
In VIVO release 1.2 this storage location,
known as the "Alias URL" for the uploaded file,
is stored in the file entity.
That way, pages that contain many files can be displayed much more quickly.
</p>
<p>
When Apache Tomcat starts up after the upgrade,
it will initiate a process to calculate the "Alias URL"
for each existing file and store it in the data model for fast access.
</p>
<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
<p>
The File Storage upgrade process will create a log file in the
VIVO upload directory. You should review this file to ensure that
this upgrade worked properly.
</p>
<dl>
<dt>
<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
</dt>
<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>
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>
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
engine for generating web pages. The theme is located in /vivo/themes/wilma and
the FreeMarker files have an ftl (for FreeMarker Template Language) extension.
</p>
<p>
Follow step A or B below, whichever is applicable to your site:
</p>
<p>
A. If you did not create a customized theme for your site in V1.0 or V1.1, but used
the vivo-basic theme in its original directory, you need not take any
action in order to convert your site to the VIVO 1.1 theme.
</p>
<p>
B. If you created your own theme directory in VIVO 1.1, follow the steps below
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
theme to VIVO 1.2.
</p>
<dl>
<dt>
1. Templates
</dt>
<dd>
<dl>
<dt>
a. Copy the directory <code>/vivo/themes/vivo-basic/templates</code>
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
</dt>
<dd>
</dd>
<dt>
b. Follow step i or ii below, whichever is applicable to your theme.
</dt>
<dd>
<ol class="roman2">
<li>
If you did not apply any customizations to the JSPs in your VIVO
1.0 theme, then you do not need to apply any additional changes
to the VIVO 1.1 theme templates during the upgrade process.
</li>
<li>
<p>
If you did apply customizations to the JSPs in your VIVO 1.0
theme,you will need to hand-replicate those modifications in the
new theme template files.
</p>
<p>
The theme template content that was previously contained in
three JSP files is now contained in five FTL files. The
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
follows:
</p>
<pre>
</p>
<p>
4. If you had modified <code>web.xml</code>
to configure the Pellet Reasoner (as described
in the installation instructions), repeat that modification.
</p>
<p>
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
</p>
<p>
6. Start Apache Tomcat and log in to VIVO.
</p>
<h3 id="ontology">III. Ontology Changes</h3>
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
<p>
After Apache Tomcat is started, these files should be reviewed to
verify that the automated upgrade process was executed
successfully.&nbsp; The ontology alignment process will create the
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
</p>
<dl>
<dt>
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
</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 representative to see whether any
corrective action needs to be taken.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code>
</dt>
<dd>
A log of errors that were encountered during the upgrade process. This
file should be empty if the upgrade was successful.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/changedData/removedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were removed from the
knowledge base.
</dd>
</dl>
<dl>
<dt>
<code>ontologies/update/changedData/addedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were added to the
knowledge base.
</dd>
</dl>
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual review</h4>
<p>
Changes to the VIVO core ontology may require corresponding
modifications of the knowledge base instance data and local ontology
extensions.
</p>
<p>
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 following
types of changes:
</p>
<dl>
<dt>
Class or Property renaming
</dt>
<dd>
All references to the class (in the subject or object position) will be
updated to the new name. References to the property will be updated to
the new name.
</dd>
</dl>
<dl>
<dt>
Class or Property deletion
</dt>
<dd>
All individuals in 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
directory.
</dd>
</dl>
<dl>
<dt>
Property addition
</dt>
<dd>
If a newly added property is the inverse of a previously existing
property, the inverse of any statements using the pre-existing property
will be asserted.
</dd>
</dl>
<dl>
<dt>
Annotation property default values
</dt>
<dd>
If a site has modified the value of a vitro annotation (such as
displayRankAnnot or displayLimitAnnot) so that it is no longer using
the default, then that setting will be left unchanged.
<br>
If a site is using the default value of a vitro annotation, and the
default has been changed in the new version of the ontology, then the
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>
Each uploaded file exists as an individual entity in VIVO. When the
browser requests an upload file from VIVO, the data model is queried to
find out where the file is actually stored, so it can be downloaded to
the browser.
</p>
<p>
In VIVO release 1.2 this storage location,
known as the "Alias URL" for the uploaded file,
is stored in the file entity.
That way, pages that contain many files can be displayed much more quickly.
</p>
<p>
When Apache Tomcat starts up after the upgrade,
it will initiate a process to calculate the "Alias URL"
for each existing file and store it in the data model for fast access.
</p>
<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
<p>
The File Storage upgrade process will create a log file in the
VIVO upload directory. You should review this file to ensure that
this upgrade worked properly.
</p>
<dl>
<dt>
<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
</dt>
<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>
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>
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
engine for generating web pages. The theme is located in /vivo/themes/wilma and
the FreeMarker files have an ftl (for FreeMarker Template Language) extension.
</p>
<p>
Follow step A or B below, whichever is applicable to your site:
</p>
<p>
A. If you did not create a customized theme for your site in V1.0 or V1.1, but used
the vivo-basic theme in its original directory, you need not take any
action in order to convert your site to the VIVO 1.1 theme.
</p>
<p>
B. If you created your own theme directory in VIVO 1.1, follow the steps below
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
theme to VIVO 1.2.
</p>
<dl>
<dt>
1. Templates
</dt>
<dd>
<dl>
<dt>
a. Copy the directory <code>/vivo/themes/wilma/templates</code>
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
</dt>
<dd>
</dd>
<dt>
b. Follow step i or ii below, whichever is applicable to your theme.
</dt>
<dd>
<ol class="roman2">
<li>
If you did not apply any customizations to the JSPs in your VIVO
1.0 theme, then you do not need to apply any additional changes
to the VIVO 1.1 theme templates during the upgrade process.
</li>
<li>
<p>
If you did apply customizations to the JSPs in your VIVO 1.0
theme,you will need to hand-replicate those modifications in the
new theme template files.
</p>
<p>
The theme template content that was previously contained in
three JSP files is now contained in five FTL files. The
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
follows:
</p>
<pre>
identity.jsp => identity.ftl
menu.jsp => menu.ftl and search.ftl
footer.jsp => footer.ftl and googleAnalytics.ftl
</pre>
<p>
<code>googleAnalytics.ftl</code>
is the file to which you add your site's Google Analytics Tracking
Code (see section II).
</p>
<p>
Because the FreeMarker Template Language uses many syntactic
conventions that will be familiar to template authors from JSP
or other common templating systems, the translation of your JSP
changes into the new FTLs should be relatively straightforward.
</p>
<p>
Consult the FreeMarker Template Author's Guide at <a href="http://freemarker.org/docs/dgui.html">http://freemarker.org/docs/dgui.html</a>
and the Reference at <a href="http://freemarker.org/docs/ref.html">http://freemarker.org/docs/ref.html</a>
for complete documentation of the syntax and available built-in constructs. Template
authors need not be concerned with the Programmer's Guide or Java API documentation.
</p>
</li>
</ol>
</dd>
<dt>
c. Remove the jsp directory from your themes directory.
</dt>
<dd>
</dd>
</dl>
</dd>
<dt>
2. Stylesheets
</dt>
<dd>
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
styles in your VIVO 1.0 theme, you will not be able to simply copy the
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
style upgrades that your theme should pick up. Instead, you should
use the vivo-basic 1.1 stylesheets as a starting point, and manually
merge your 1.0 style modifications in as needed.
</dd>
<dt>
3. Site Icons
</dt>
<dd>
Copy the site icons from your 1.1 theme into the site_icons folder in
your 1.2 theme.
</dd>
</dl>
</div>
<!-- end of content -->
<div role="contentinfo">
<p class="copyright">
<small>
&copy;2011
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
</small>
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
</p>
<nav role="navigation">
<ul id="footer-nav" role="list">
<li role="listitem">
<a href="http://vivoweb.org/about">About</a>
</li>
<li role="listitem">
<a href="http://vivoweb.org/contact">Contact Us</a>
</li>
<li role="listitem">
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
</li>
</ul>
</nav>
</div>
<p>
<code>googleAnalytics.ftl</code>
is the file to which you add your site's Google Analytics Tracking
Code (see section II).
</p>
<p>
Because the FreeMarker Template Language uses many syntactic
conventions that will be familiar to template authors from JSP
or other common templating systems, the translation of your JSP
changes into the new FTLs should be relatively straightforward.
</p>
<p>
Consult the FreeMarker Template Author's Guide at <a href="http://freemarker.org/docs/dgui.html">http://freemarker.org/docs/dgui.html</a>
and the Reference at <a href="http://freemarker.org/docs/ref.html">http://freemarker.org/docs/ref.html</a>
for complete documentation of the syntax and available built-in constructs. Template
authors need not be concerned with the Programmer's Guide or Java API documentation.
</p>
</li>
</ol>
</dd>
<dt>
c. Remove the jsp directory from your themes directory.
</dt>
<dd>
</dd>
</dl>
</dd>
<dt>
2. Stylesheets
</dt>
<dd>
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
styles in your VIVO 1.0 theme, you will not be able to simply copy the
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
style upgrades that your theme should pick up. Instead, you should
use the vivo-basic 1.1 stylesheets as a starting point, and manually
merge your 1.0 style modifications in as needed.
</dd>
<dt>
3. Site Icons
</dt>
<dd>
Copy the site icons from your 1.1 theme into the site_icons folder in
your 1.2 theme.
</dd>
</dl>
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