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NIHVIVO-3103 corrections and reformatting.

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j2blake 2011-11-16 16:55:34 +00:00
parent 363f5a6d2a
commit 535bb3bbfc
3 changed files with 33 additions and 96 deletions
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@ -28,7 +28,7 @@ body{
margin: 0 auto; margin: 0 auto;
} }
body{ body{
background: #f3f3f0 url(../images/header-background.png) center 0 no-repeat; background: #fff url(../images/header-background.gif) center 0 repeat-x;
} }
/* h1,h2,h3,h4,h5,h6 ------> */ /* h1,h2,h3,h4,h5,h6 ------> */
h1 { h1 {

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doc/install.html
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@ -334,21 +334,6 @@
http://vivo.mydomain.edu/individual/ http://vivo.mydomain.edu/individual/
</td> </td>
</tr> </tr>
<tr>
<td colspan="2">
Directory where Vitro code is located. In most
deployments, this is set to ./vitro-core (It is not uncommon for this
setting to point elsewhere in development environments).
</td>
</tr>
<tr class="odd_row">
<td>
vitro.core.dir
</td>
<td>
./vitro-core
</td>
</tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where tomcat is installed. Directory where tomcat is installed.
@ -654,71 +639,12 @@
remote_userID remote_userID
</td> </td>
</tr> </tr>
<tr>
<td colspan="2">
The temporal graph visualization can require
extensive machine resources. This can have a particularly noticable
impact on memory usage if
<ul>
<li>
The organization tree is deep,
</li>
<li>
The number of grants and publications is large.
</li>
</ul>
VIVO V1.3 mitigates this problem by the way of a caching
mechanism and hence we can safely set this to be enabled by default.
</td>
</tr>
<tr class="odd_row">
<td>
visualization.temporal
</td>
<td>
enabled
</td>
</tr>
<tr>
<td colspan="2">
The temporal graph visualization is used to
compare different organizations/people within an organization on
parameters like number of publications or grants. By default, the app
will attempt to make its best guess at the top level organization in
your instance. If you're unhappy with this selection, uncomment out the
property below and set it to the URI of the organization individual you
want to identify as the top level organization. It will be used as the
default whenever the temporal graph visualization is rendered without
being passed an explicit org. For example, to use "Ponce School of
Medicine" as the top organization:
<br>
<code>visualization.topLevelOrg =
http://vivo.psm.edu/individual/n2862</code>
<br>
</td>
</tr>
<tr class="odd_row">
<td>
visualization.topLevelOrg
</td>
<td>
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
</td>
</tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
An absolute file path, pointing to the root directory of the Harvester utility. An absolute file path, pointing to the root directory of the Harvester utility.
You must include the final slash. You must include the final slash.
</td> </td>
</tr> </tr>
<tr class="odd_row">
<td>
harvester.location
</td>
<td>
/usr/local/vivo/harvester/
</td>
</tr>
</tbody> </tbody>
</table> </table>
<h3 id="deploy">V. Compile and deploy</h3> <h3 id="deploy">V. Compile and deploy</h3>
@ -733,12 +659,12 @@
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security <h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
limits</h3> limits</h3>
<p> <p>
Currently, VIVO copies the contents of your RDF database into VIVO copies small sections of your RDF database into
memory in order to serve Web requests quickly (the in-memory copy and memory in order to serve Web requests quickly (the in-memory copy and
the underlying database are kept in synch as edits are performed). the underlying database are kept in synch as edits are performed).
</p> </p>
<p> <p>
VIVO will require more memory than that allocated to Tomcat by VIVO may require more memory than that allocated to Tomcat by
default. With most installations of Tomcat, the "setenv.sh" or default. With most installations of Tomcat, the "setenv.sh" or
"setenv.bat" file in Tomcat's bin directory is a convenient place to "setenv.bat" file in Tomcat's bin directory is a convenient place to
set the memory parameters. <em>If this file does not exist in Tomcat's set the memory parameters. <em>If this file does not exist in Tomcat's
@ -746,14 +672,11 @@
<br> <br>
For example: For example:
</p> </p>
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre> <pre> export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"<br> </pre>
<p> <p>
This sets Tomcat to allocate an initial heap of 2048 megabytes, a This sets Tomcat to allocate an initial heap of 512 megabytes, a
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower
megabytes is a minimum practical heap size for production installations values may suffice, especially for small test installations.
storing data for large academic institutions, and additional heap space
is preferable. For testing with small sets of data, 256m to 512m should
be sufficient.
</p> </p>
<p> <p>
If an OutOfMemoryError is encountered during VIVO execution, it can If an OutOfMemoryError is encountered during VIVO execution, it can
@ -795,8 +718,8 @@
properties, data properties, and configure the display of data. properties, data properties, and configure the display of data.
Currently, any classes you wish to make visible on your website must be Currently, any classes you wish to make visible on your website must be
part of a class group, and there are a number of visibility and display part of a class group, and there are a number of visibility and display
options available for each ontology entity. VIVO comes with a core VIVO options available for each ontology entity. Vitro comes with a minimal
ontology, but you may also upload other ontologies from an RDF file. ontology. You will likely want to upload additional ontologies from an RDF file.
</p> </p>
<p> <p>
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
@ -810,10 +733,7 @@
Clicking the "Index" tab in the navigation bar at the top right of Clicking the "Index" tab in the navigation bar at the top right of
the page will show a simple index of the knowledge base. the page will show a simple index of the knowledge base.
</p> </p>
<p>
See more documentation for configuring VIVO, ingesting data, and
manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
</p>
<h3 id="contact_email">IX. Set the Contact Email Address (if using <h3 id="contact_email">IX. Set the Contact Email Address (if using
"Contact Us" form)</h3> "Contact Us" form)</h3>
<p> <p>
@ -875,7 +795,28 @@
directive directive
and update as follows: and update as follows:
</p> </p>
<pre> <br> &lt;Host name="localhost" appBase="webapps"<br> <br> DeployOnStartup="false"<br> <br> unpackWARs="true" autoDeploy="false"<br> <br> xmlValidation="false" xmlNamespaceAware="false"&gt;<br> <br> <br> &lt;Alias&gt;example.com&lt;/Alias&gt;<br> <br> &lt;Context path=""<br> <br> docBase="/usr/local/tomcat/webapps/vivo"<br> <br> reloadable="true"<br> <br> cookies="true" &gt;<br> <br> &lt;Manager pathname="" /&gt;<br> <br> &lt;Environment type="java.lang.String" override="false" <br> <br> name="path.configuration" <br> <br> value="deploy.properties"<br> <br> /&gt;<br> <br> &lt;/Context&gt;<br> <br> ...<br> </pre> <pre> &lt;Host name="localhost" appBase="webapps"
DeployOnStartup="false"
unpackWARs="true" autoDeploy="false"
xmlValidation="false" xmlNamespaceAware="false"&gt;
&lt;Alias&gt;example.com&lt;/Alias&gt;
&lt;Context path=""
docBase="/usr/local/tomcat/webapps/vivo"
reloadable="true"
cookies="true" &gt;
&lt;Manager pathname="" /&gt;
&lt;Environment type="java.lang.String" override="false"
name="path.configuration"
value="deploy.properties"
/&gt;
&lt;/Context&gt;
...
</pre>
<h3 id="external_auth">XI. Using an External Authentication System <h3 id="external_auth">XI. Using an External Authentication System
with VIVO </h3> with VIVO </h3>
<p> <p>
@ -954,11 +895,7 @@
<li> <li>
<h5>Associating a User with a profile page.</h5> <h5>Associating a User with a profile page.</h5>
<p> <p>
If VIVO has an account for the user, the user will be given the VIVO will try to associate the user with a profile
privileges assigned to that account.
</p>
<p>
In addition, VIVO will try to associate the user with a profile
page, so the user may edit his own profile data. VIVO will search the page, so the user may edit his own profile data. VIVO will search the
data model for a person with a property that matches the User’s network data model for a person with a property that matches the User’s network
ID (the value of the property must be either a String literal or an ID (the value of the property must be either a String literal or an