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Minor editorial changes applied to the docs.

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ejc12 2011-02-10 18:37:48 +00:00
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78
doc/install.html
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@ -33,7 +33,7 @@
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
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>
@ -77,16 +77,16 @@
<h4>Ontology</h4>
<p>
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
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>
The Harvester development team is releasing version 1.0 of the VIVO
Harvester library, an extensible data ingest and updating framework
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>
@ -567,13 +567,19 @@
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.
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
temporal graph visualization unless the "visualization.temporal" flag is
set to "enabled".
</td>
</tr>
@ -782,12 +788,13 @@
<h3 id="pellet">XII. Configure Pellet Reasoner </h3>
<p>
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
cached in a database graph so that they are available immediately when
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
cached in a database graph so that they are available immediately when
VIVO is restarted.
</p>
<p>
@ -863,17 +870,21 @@
<li>
<h5>The name of the HTTP header that will hold the external user's
network ID.</h5>
When a user completes the authentication process, the Apache server
will put the user's network ID into one of the headers of the HTTP
request. The instructions from your institution should tell you which
header is used for this purpose.
<p>
When a user completes the authentication process, the Apache server
will put the user's network ID into one of the headers of the HTTP
request. The instructions from your institution should tell you which
header is used for this purpose.
</p>
<p>
You need to tell VIVO the name of that HTTP header. Insert a
line like this in the deploy.properties file:
line like this in the deploy.properties file:
</p>
<pre>externalAuth.netIdHeaderName = [the header name]</pre>
<p>For example:</p>
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
<p>
For example:
</p>
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
</li>
<li>
<h5>The text for the Login button.</h5>
@ -885,13 +896,17 @@
externalAuth.buttonText = [the text for your login button] For example:
</p>
<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
The VIVO login form will display a button labelled "Log in using
BearCat Shibboleth".
<p>
The VIVO login form will display a button labelled "Log in using
BearCat Shibboleth".
</p>
</li>
<li>
<h5>Associating a User with a profile page</h5>
If VIVO has an account for the user, the user will be given the
privileges assigned to that account.
<h5>Associating a User with a profile page.</h5>
<p>
If VIVO has an account for the user, the user will be given the
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
@ -900,7 +915,10 @@
Insert a line like this in the deploy.properties file:
</p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
<p>
For example:
</p>
<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li>
</ul>
<h3 id="installation_check">XIV. Was the installation successful? </h3>
@ -958,7 +976,7 @@
Enter the name "test individual" under the field "Individual
Name," scroll to the bottom, and click "Create New Record." You will be
taken to the "Individual Control Panel." Make note of the value of the
field "URI" it will be used in the next step.
field "URI" - it will be used in the next step.
</li>
<li>
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.

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doc/upgrade-1.2.html
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@ -117,7 +117,7 @@
<a href="#upgrade_process">The Upgrade Process</a>
</li>
<li>
<a href="#ontology">Ontology Upgrade</a>
<a href="#ontology">Ontology Changes</a>
<ol class="roman2">
<li>
<a href="#verify_ontology_upgrade">Verify Ontology upgrade
@ -143,7 +143,7 @@
</ol>
</li>
<li>
<a href="#theme">Theme Modifications</a>
<a href="#theme">Theme Changes</a>
</li>
<li>
<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
@ -621,7 +621,7 @@
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
VIVO implementation sites and a copy of 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>