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Editorial changes. When updating from Nick's version, lost section VII re optional SDB store text.

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ejc12 2011-02-10 17:07:38 +00:00
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doc/upgrade-1.2.html
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@ -35,7 +35,7 @@
</p>
<p>
If you need to do a fresh install, please consult the VIVO Release 1 v1.2
Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
Installation Guide found on <a href="http://vivoweb.org/support">vivoweb.org</a>
or the install.html file located in the <code>doc</code>
directory of the VIVO source code distribution. The installation
document also has a list of the required software and versions.
@ -48,8 +48,8 @@
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>.
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>
<h4>Templating system for page generation, navigation, and theming</h4>
<p>
@ -101,8 +101,8 @@
<p>
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>.
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>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
<toc>
@ -110,7 +110,7 @@
<li>
<a href="#preparation">Before Performing the Upgrade</a>
</li>
<li>
<li>
<a href="#triple_store">Chose Triple Store</a>
</li>
<li>
@ -145,7 +145,7 @@
<li>
<a href="#theme">Theme Modifications</a>
</li>
<li>
<li>
<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
</li>
</ol>
@ -197,7 +197,7 @@
<h3 id="triple_store">II. Choose Triple Store</h3>
<p>
VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was
Jena's legacy relational database store (RDB), and Jena's SPARQL database (SDB). RDB was
used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
entire RDF model in the server's main memory. The memory available to VIVO limits the
number of RDF statements that may be stored.
@ -221,17 +221,17 @@
</p>
<p>
A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
receive required ontology updates. Attempting to run an upgraded system initially in SDB will
to receive required ontology updates. Attempting to run an upgraded system initially in SDB will
result in a logged error message, and the application will not start. After the system starts
up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
Upon restart, the data in the RDB store will be copied to the SDB store.
</p>
<p>
This copying process can take a number of hours to complete if the installation contains a large
amount of RDF data (roughly a million triples or more). See section
<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a> for instructions on how
to run this lengthy conversion process in the background while an RDB system is operating.
Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
amount of RDF data (roughly a million triples or more). See section <a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
for instructions on how
to run this lengthy conversion process in the background while an RDB system is operating.
Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
</p>
<h3 id="upgrade_process">III. The Upgrade Process</h3>
<p>
@ -260,7 +260,7 @@
RDF resources available for harvest using linked data. Requests for RDF
resource URIs redirect to HTML or RDF representations as specified by
the client. To make this possible, VIVO's default namespace must have
certain structure and begin with the public web address of the VIVO
a certain structure and begin with the public web address of the VIVO
installation. For example, if the web address of a VIVO installation is
"http://vivo.example.edu/" the default namespace must be set to
"http://vivo.example.edu/individual/" in order to support linked data.
@ -322,7 +322,7 @@
<tr>
<td colspan="2">
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 who
the Tomcat service is running as.
</td>
</tr>
@ -337,7 +337,7 @@
<tr>
<td colspan="2">
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 who
the Tomcat service is running as.
</td>
</tr>
@ -367,7 +367,7 @@
<tr>
<td colspan="2">
Specify the JDBC URL of your database. Change
the end of theURL to reflect your database name (if it is not "vivo").
the end of the URL to reflect your database name (if it is not "vivo").
</td>
</tr>
<tr class="odd_row">
@ -543,12 +543,18 @@
The temporal graph visualization can require extensive machine resources.
This can have a particularly noticable impact on memory usage if
<ul>
<li> VIVO is configured to use Jena SDB, </li>
<li> The organization tree is deep, </li>
<li> The number of grants and publications is large. </li>
<li>
VIVO is configured to use Jena SDB,
</li>
<li>
The organization tree is deep,
</li>
<li>
The number of grants and publications is large.
</li>
</ul>
The VIVO developers are working to make this visualization more efficient.
In the meantime, VIVO release 1.2 guards against this impact by disabling
The VIVO developers are working to make this visualization more efficient.
In the meantime, VIVO release 1.2 guards against this impact by disabling
temporal graph visualization unless the "visualization.temporal" flag is
set to "enabled".
</td>
@ -610,15 +616,13 @@
<li>
NIH-funded VIVO implementations will need to apply the Google
Analytics Tracking Code (GATC) to <code>googleAnalytics.ftl</code>
in the theme:
<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
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 theme. This file serves only as an example,
and you must replace the tracking code shown with your institution's own
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
the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">
VIVO Google Analytics wiki page</a>.
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 wiki page</a>.
</li>
<li>
If you had used the <code>vivo/contrib/FLShibboleth</code>
@ -656,10 +660,9 @@
<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
"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>
@ -752,17 +755,16 @@
new default value will be propagated to the knowledge base.
</dd>
</dl>
<h3 id="fileSystem">V. 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 in VIVO. When the browser
requests an uploaded file from VIVO, the data model is queried to find
requests an uploaded 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
In VIVO 1.2 this storage location, known as the "Alias URL" for
the uploaded file, is stored in the file individual. That way, pages that
contain many files can be displayed much more quickly.
</p>
@ -770,7 +772,7 @@
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>
</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
@ -784,32 +786,26 @@
<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
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">VI. Theme Modifications</h3>
<h3 id="theme">VI. Theme Changes</h3>
<h4 id="#newTheme">Introducing a New Default Theme</h4>
<p>
VIVO 1.2 includes a new default theme called <strong>wilma</strong> (located in
/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
create your own theme using wilma as a starting point, please review the
<a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">
Site Administrator's Guide</a>.
VIVO 1.2 includes a new default theme called <strong>wilma</strong>
(located in
/vivo/themes/wilma) which fully supports all 1.2 features. For details on how to
create your own theme using wilma as a starting point, please review the <a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">Site Administrator's Guide</a>.
</p>
<blockquote id="vivoBasicDeprecated">
<h4>
The vivo-basic theme has been deprecated with the 1.2 release and is not
recommended for production instances.
</h4>
<h4>The vivo-basic theme has been deprecated with the 1.2 release and is not
recommended for production instances.</h4>
<p>
Since vivo-basic was the default theme for all previous releases, it is
included as part of VIVO 1.2 to help with the transition of upgrading
included as part of VIVO 1.2 to help with the transition of upgrading
existing installations to the latest code, but all vivo-basic development
has ceased and it will not be distributed in future releases.
</p>
@ -819,15 +815,21 @@
following:
</p>
<ul>
<li>new primary menu for site navigation (replaces tabs)</li>
<li>home page with class group browse and visual graph</li>
<li>menu pages with class group and individual browse</li>
<li>
new primary menu for site navigation (replaces tabs)
</li>
<li>
home page with class group browse and visual graph
</li>
<li>
menu pages with class group and individual browse
</li>
</ul>
</blockquote>
<h4 id="templateTransition">Templates</h4>
<p>
The 1.2 release continues the transition from JavaServer Pages (.jsp) to
Freemarker templates (.ftl) for generating web pages. While there are still
Freemarker templates (.ftl) for generating web pages. While there are still
JSP files in action behind the scenes, as of 1.2 all theme templates
are of the Freemarker variety and are located in the "templates" directory
within a theme.
@ -837,19 +839,45 @@
the vivo-basic theme in its original directory, you need not take any
action in order to remain using the vivo-basic theme in 1.2.
</p>
<p>If you did make changes to the vivo-basic theme, you will need to reapply those changes.
We recommend you apply these changes to the wilma theme.</p>
<p>
If you did make changes to the vivo-basic theme, you will need to reapply those changes.
We recommend you apply these changes to the wilma theme.
</p>
<blockquote>
<strong>Please note:</strong> The vivo-basic theme has been deprecated and is
<a href="#vivoBasicDeprecated">not recommended for production instances</a>.
<strong>Please note:</strong>
The vivo-basic theme has been deprecated and is <a href="#vivoBasicDeprecated">not recommended for production instances</a>.
</blockquote>
<p>
<p>
For details on the new structure of themes in 1.2 and further information
regarding the development of your own custom theme, please review the
<a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">
Site Administrator's Guide</a>. This document will focus on updating an existing
regarding the development of your own custom theme, please review the <a href="http://www.vivoweb.org/support/user-guide/administration" title="Download VIVO documentation" target="_blank">Site Administrator's Guide</a>. This document will focus on updating an existing
pre 1.2 theme.
</p>
<h3 id="setup_sdb">VII. Set Up SDB Store in the Background (Optional)</h3>
<p>
If your VIVO installation is running in RDB mode, and you'd like to convert
to SDB, you can start the conversion process in the background while the RDB
system is running. This will reduce the delay in initial startup after the
application is redeployed with deploy.properties set for SDB. Note that it
is important not to edit any data anywhere in the application while this
background conversion is running.
</p>
<p>
To start the SDB conversion, log in as a system
administrator and request /sdbsetup (For example, if your VIVO is installed
at http://vivo.myuniversity.edu/ you would type
http://vivo.myuniversity.edu/sdbsetup into your browser).
</p>
<p>
Click the button that appears on this page.
</p>
<p>
During the course of the SDB setup, which may take several hours on a
large database, subsequent requests to /sdbsetup will display a
message that the operation is still in progress. When a request for this
page shows a message that the SDB setup has completed successfully, shut down
Tomcat, set deploy.properties to SDB mode, redeploy, and restart Tomcat.
VIVO will now be running from the SDB store.
</p>
</div>
<!-- end of content -->
<div id="footer" role="contentinfo">
@ -875,4 +903,4 @@
</div>
</div>
</body>
</html>
</html>