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Adding the text from Brian about SDB to install.html (one section) and upgrade-1.2.html (2 sections).

Browse source 
Also added a new intro sentence to Pellet reasoner section.
Completes Jira NIHVIVO-1782
This commit is contained in:
ejc12 2011-02-10 04:23:54 +00:00
parent 6e65e2bb83
commit a500f980e8
2 changed files with 203 additions and 97 deletions
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115
doc/install.html
View file

@ -2,9 +2,9 @@
<html lang="en">
<head>
<meta charset="utf-8" />
<title>VIVO</title>
<title>VIVO Release 1 V1.2 Installation Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head>
<body>
<div id="branding" role="banner">
@ -35,8 +35,7 @@
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>.
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>
@ -89,8 +88,7 @@
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>.
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 --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p>
@ -129,7 +127,7 @@
<a href="#download_code">Download the VIVO Application Source</a>
</li>
<li>
<a href="#data_storage">SDB vs RDB</a>
<a href="#triple_store">Choose Triple Store</a>
</li>
<li>
<a href="#deploy_properties">Specify deployment properties</a>
@ -211,11 +209,11 @@
of
the time, the hostname will equal <code>localhost</code>.
</p>
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br> </pre>
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
<p>
Grant access to a database user. For example:
</p>
<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br> </pre>
<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br></pre>
<p>
Keep track of the database name, username, and password for Step
IV.
@ -230,9 +228,30 @@
<br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</p>
<h3 id="data_storage">IV. SDB vs RDB (title)</h3>
<h3 id="triple_store">IV. Choose Triple Store</h3>
<p>
Content from Brian Lowe coming.
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
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.
</p>
<p>
SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
against the underlying database. This allows VIVO installations to display data from large
RDF models while requiring only a small amount of server memory to run the application.
There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
and performance will depend on the configuration parameters of the database server.
Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
generated, though they are generated as soon as data is edited rather than in a background process.
</p>
<p>
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
a configuration property and redeploying the application, it is important to note that data
added in one mode will not typically appear in the other. The exception is when a system is
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
automatically migrated to SDB.
</p>
<h3 id="deploy_properties">V. Specify deployment properties </h3>
<p>
@ -276,8 +295,8 @@
"http://vivo.example.edu/individual/" in order to support linked data.
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
default namespace must be set to
"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with "individual/" (including the
trailing slash).</h5>
"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with
"individual/" (including the trailing slash).</h5>
</td>
</tr>
<tr class="odd_row">
@ -719,13 +738,29 @@
directive
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>
<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>
...
</pre>
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
<p>
<em>Do we need this section still? - elly</em>
</p>
<p>
VIVO uses the Pellet engine to perform reasoning, which runs in the
This optional configuration step is only applicable to VIVO installations
running in RDB mode (See section <a href="triple_store">Choose Triple Store</a> for details).
VIVO uses the Pellet engine to perform reasoning, which runs in the
background at startup and also when the knowledge base is edited. VIVO
continues serving pages while the reasoner continues working; when the
reasoner finishes, the new inferences appear. Inferred statements are
@ -932,27 +967,27 @@
</div>
<!-- #wrapper-content -->
<div id="footer" 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>
<div id="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 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>
<div id="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>
</body>
</html>

81
doc/upgrade-1.2.html
View file

@ -2,7 +2,7 @@
<html lang="en">
<head>
<meta charset="utf-8" />
<title>VIVO</title>
<title>VIVO Release 1 V1.2 Upgrade Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head>
@ -109,6 +109,9 @@
<ol class="roman1">
<li>
<a href="#preparation">Before Performing the Upgrade</a>
</li>
<li>
<a href="#triple_store">Chose Triple Store</a>
</li>
<li>
<a href="#upgrade_process">The Upgrade Process</a>
@ -141,6 +144,9 @@
</li>
<li>
<a href="#theme">Theme Modifications</a>
</li>
<li>
<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
</li>
</ol>
</toc>
@ -188,7 +194,46 @@
below for more information.
</li>
</ul>
<h3 id="upgrade_process">II. The Upgrade Process</h3>
<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
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.
</p>
<p>
SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
against the underlying database. This allows VIVO installations to display data from large
RDF models while requiring only a small amount of server memory to run the application.
There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
and performance will depend on the configuration parameters of the database server.
Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
generated, though they are generated as soon as data is edited rather than in a background process.
</p>
<p>
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
a configuration property and redeploying the application, it is important to note that data
added in one mode will not typically appear in the other. The exception is when a system is
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
automatically migrated to SDB.
</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
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.
</p>
<h3 id="upgrade_process">III. The Upgrade Process</h3>
<p>
1. Download the new distribution file and unpack it into a new
source directory.
@ -578,7 +623,7 @@
<p>
6. Start Apache Tomcat and log in to VIVO.
</p>
<h3 id="ontology">III. Ontology Changes</h3>
<h3 id="ontology">IV. 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
@ -688,7 +733,7 @@
new default value will be propagated to the knowledge base.
</dd>
</dl>
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
<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 entity in VIVO. When the
@ -726,7 +771,7 @@
corrective action needs to be taken.
</dd>
</dl>
<h3 id="theme">V. Theme Changes</h3>
<h3 id="theme">VI. 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
@ -831,6 +876,32 @@
your 1.2 theme.
</dd>
</dl>
<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">