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Updated with viz changes.

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ejc12 2011-01-14 17:02:11 +00:00
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@ -66,12 +66,13 @@ h5{
} }
a { a {
text-decoration: underline text-decoration: underline;
color: #2485ae;
} }
code { a:visited {
padding: 0 0 0 20px; text-decoration: underline;
margin: 10px; color: #5e6363;
} }
/* HEADER ------> */ /* HEADER ------> */

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@ -127,16 +127,16 @@
your values for "dbname", "username", and "password". Most of the time, your values for "dbname", "username", and "password". Most of the time,
the "hostname" will equal "localhost". the "hostname" will equal "localhost".
</p> </p>
<code> <pre>
CREATE DATABASE dbname CHARACTER SET utf8; CREATE DATABASE dbname CHARACTER SET utf8;
</code> </pre>
<p> <p>
Grant access to a database user. Grant access to a database user.
For example: For example:
</p> </p>
<code> <pre>
GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password'; GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
</code> </pre>
<p> <p>
Keep track of the database name, username, and password for Step IV. Keep track of the database name, username, and password for Step IV.
</p> </p>
@ -351,15 +351,33 @@
http://vivo.mydomain.edu/ns#networkId http://vivo.mydomain.edu/ns#networkId
</td> </td>
</tr> </tr>
<tr>
<td>
Temporal Graph Visualization is used to compare different organizations/people within
an organization on different parameters like number of publications, grants. This parameter will be
used as a default in case a URI is not provided. It will be also used whenever this visualization is to be rendered for top level organization.
In absence of this parameter a SPARQL query will be fired which will attempt to provide a top level organization.The name of a property
that can be used to associate an Individual with a user account. When a user logs in with a name that matches the value of this property,
the user will be authorized to edit that Individual.
</td>
</tr>
<tr class="odd_row">
<td>
visualization.topLevelOrg
</td>
<td>
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
</td>
</tr>
</table> </table>
<h3 id="deploy">V. Compile and deploy</h3> <h3 id="deploy">V. Compile and deploy</h3>
<p> <p>
At the command line, from the top level of the unpacked distribution At the command line, from the top level of the unpacked distribution
directory, type: directory, type:
</p> </p>
<code> <pre>
ant all ant all
</code> </pre>
<p> <p>
to build VIVO and deploy to Tomcat's webapps to build VIVO and deploy to Tomcat's webapps
directory. directory.
@ -367,7 +385,7 @@
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security limits</h3> <h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security limits</h3>
<p> <p>
Currently, VIVO copies the contents of your RDF database into memory Currently, VIVO copies the contents of your RDF database into memory
in order to serve Web requests quickly (the in-memory copy and the in order to serve Web requests quickly (the in-memory copy and the
underlying databaseare kept in synch as edits are performed). underlying databaseare kept in synch as edits are performed).
<p> <p>
VIVO will VIVO will
@ -377,9 +395,9 @@
<br/> <br/>
For example: For example:
</p> </p>
<code> <pre>
export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m" export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"
</code> </pre>
<p> <p>
This sets Tomcat to allocate an initial heap of 2048 megabytes, a This sets Tomcat to allocate an initial heap of 2048 megabytes, a
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
@ -400,13 +418,10 @@
that your installation can support the required number of threads that your installation can support the required number of threads
by making the following edits to "/etc/security/limits.conf": by making the following edits to "/etc/security/limits.conf":
</p> </p>
<code> <pre>
apache hard nproc 400 apache hard nproc 400
</code> tomcat6 hard nproc 1500
<br> </pre>
<code>
tomcat6 hard nproc 1500
</code>
<h3 id="start_tomcat">VII. Start Tomcat </h3> <h3 id="start_tomcat">VII. Start Tomcat </h3>
<p> <p>
Most Tomcat installations can be started by running "startup.sh" or Most Tomcat installations can be started by running "startup.sh" or
@ -427,11 +442,11 @@
<p> <p>
After verifying your new password, you will be presented with a menu of After verifying your new password, you will be presented with a menu of
editing options. Here you can create OWL classes, object properties, editing options. Here you can create OWL classes, object properties,
data properties, and configure the display of data. Currently, data properties, and configure the display of data. Currently,
any classes you wish to make visible on your website must be part of a any classes you wish to make visible on your website must be part of a
class group, and there a number of visibility and display options class group, and there a number of visibility and display options
available for each ontology entity. VIVO comes with a core VIVO available for each ontology entity. VIVO comes with a core VIVO
ontology, but you may also upload other ontologies from an RDF ontology, but you may also upload other ontologies from an RDF
file. file.
</p> </p>
<p> <p>
@ -442,8 +457,10 @@
machine. Ensure that the "add RDF" radio button is selected. You machine. Ensure that the "add RDF" radio button is selected. You
will also likely want to check "create classgroups automatically." will also likely want to check "create classgroups automatically."
</p> </p>
Clicking the "Index" tab in the navigation bar at the top left of <p>
the page will show a simple index of the knowledge base. Clicking the "Index" tab in the navigation bar at the top left of
the page will show a simple index of the knowledge base.
</p>
<p> <p>
See more See more
documentation for configuring VIVO, ingesting data, and manually adding documentation for configuring VIVO, ingesting data, and manually adding
@ -483,9 +500,9 @@
</p> </p>
<p> <p>
Using the mod_jk connector allows for communication between Tomcat Using the mod_jk connector allows for communication between Tomcat
and the primary web server. The and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick
<a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick Start HowTo</a>
Start HowTo</a> on the Apache site describes the minimum server configurations on the Apache site describes the minimum server configurations
for several popular web servers. for several popular web servers.
</p> </p>
<p> <p>
@ -494,9 +511,9 @@
requests from Apache via the connector. Look for the requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties: &lt;connector&gt; directive and add the following properties:
</p> </p>
<code> <pre>
connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp;
</code> </pre>
<p> <p>
Note: the value for maxThreads (320) is equal to the value for MaxClients Note: the value for maxThreads (320) is equal to the value for MaxClients
in the apache's "httpd.conf" file. in the apache's "httpd.conf" file.
@ -505,51 +522,57 @@
Locate the &lt;Host name="localhost"...&gt; directive and update as Locate the &lt;Host name="localhost"...&gt; directive and update as
follows: follows:
</p> </p>
<!-- ELLY IS WORKING HERE. -->
<!-- ELLY IS WORKING HERE. -->
<pre> <pre>
<Host name="localhost" appBase="webapps" &lt;Host name="localhost" appBase="webapps"
DeployOnStartup="false" DeployOnStartup="false"
unpackWARs="true" autoDeploy="false" unpackWARs="true" autoDeploy="false"
xmlValidation="false" xmlNamespaceAware="false"> xmlValidation="false" xmlNamespaceAware="false"&gt;
<Alias>example.com</Alias>
<Context path="" &lt;Alias&gt;example.com&lt;/Alias&gt;
&lt;Context path=""
docBase="/usr/local/tomcat/webapps/vivo" docBase="/usr/local/tomcat/webapps/vivo"
reloadable="true" reloadable="true"
cookies="true" > cookies="true" &gt;
<Manager pathname="" /> &lt;Manager pathname="" /&gt;
<Environment type="java.lang.String" override="false" &lt;Environment type="java.lang.String" override="false"
name="path.configuration" name="path.configuration"
value="deploy.properties" value="deploy.properties"
/> /&gt;
</Context> &lt;/Context&gt;
</pre> ...
</pre>
<h3 id="pellet">XI. Configure Pellet Reasoner </h3> <h3 id="pellet">XI. Configure Pellet Reasoner </h3>
<p> <p><em>Do we need this section still? - elly</em></p>
VIVO uses the Pellet engine to perform reasoning, which runs in the <p>VIVO uses the Pellet engine to perform reasoning, which runs in the
background at startup and also when the knowledge base is edited. VIVO background at startup and also when the knowledge base is edited. VIVO
continues serving pages while the reasoner continues working; when the continues serving pages while the reasoner continues working; when the
reasoner finishes, the new inferences appear. Inferred statements are reasoner finishes, the new inferences appear. Inferred statements are
cached in a database graph so that they are available immediately when cached in a database graph so that they are available immediately when
VIVO is restarted. By default, Pellet is fed only an incomplete view of VIVO is restarted.</p>
<p>By default, Pellet is fed only an incomplete view of
your ontology and only certain inferences are materialized. These your ontology and only certain inferences are materialized. These
include rdf:type,&nbsp; rdfs:subClassOf,owl:equivalentClass, and include rdf:type,&nbsp; rdfs:subClassOf,owl:equivalentClass, and
owl:disjointWith. This mode is typically suitable for ontologies with a owl:disjointWith. This mode is typically suitable for ontologies with a
lot of instance data.&nbsp; If you would like to keep the default mode, lot of instance data.&nbsp; If you would like to keep the default mode,
skip to the next step. To enable "complete" OWL inference (materialize skip to the next step. </p>
all significant entailed statements), open <p>
"vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup. To enable "complete" OWL inference (materialize
Then change the name of the listener class to all significant entailed statements), open
"vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup.
</p>
<p>Then change the name of the listener class to
PelletReasonerSetupComplete. Because "complete" reasoning can be very PelletReasonerSetupComplete. Because "complete" reasoning can be very
resource intensive, there is also an&nbsp; option to materialize nearly resource intensive, there is also an&nbsp; option to materialize nearly
all inferences except owl:sameAs and owl:differentFrom. This is enabled all inferences except owl:sameAs and owl:differentFrom. </p>
<p>This is enabled
by specifying PelletReasonerSetupPseudocomplete. For ontologies with by specifying PelletReasonerSetupPseudocomplete. For ontologies with
large numbers of individuals, this mode can offer enormous performance large numbers of individuals, this mode can offer enormous performance
improvements over the "complete" mode. Finally, a class called improvements over the "complete" mode. </p>
<p>Finally, a class called
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
improve performance on ontologies with large literals where data improve performance on ontologies with large literals where data
property entailments are not needed. property entailments are not needed.</p>
</p> </p>
<h3 id="external_auth">XII. Using an External Authentication System with VIVO </h3> <h3 id="external_auth">XII. Using an External Authentication System with VIVO </h3>
<p> <p>