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The install.html is up2date with the content in index.txt, so I will ask developers to edit install.html instead of install.txt if no outstanding changes.

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<!-- Start of content --> <!-- Start of content -->
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.2 Installation Guide</h1> <h1>VIVO Release 1 V1.2 Installation Guide</h1>
<div style="background: #EEEEEE">
<b>Missing pieces and fixes</b>
<ul>
<li>
SDB info, config changes any checks? (BL/SM)
</li>
<li>
Theme changes, file locations, branding issues (NC/MB)
</li>
<li>
Fix styles on file, dir, parameters name styles
</li>
</ul>
</div>
<toc> <toc>
<ul> <ul>
<li> <li>
@ -522,147 +536,222 @@
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> &lt;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"&gt;
xmlValidation="false" xmlNamespaceAware="false"&gt;
&lt;Alias&gt;example.com&lt;/Alias&gt; &lt;Alias&gt;example.com&lt;/Alias&gt;
&lt;Context path="" &lt;Context path=""
docBase="/usr/local/tomcat/webapps/vivo" docBase="/usr/local/tomcat/webapps/vivo"
reloadable="true" reloadable="true"
cookies="true" &gt; cookies="true" &gt;
&lt;Manager pathname="" /&gt; &lt;Manager pathname="" /&gt;
&lt;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; /&gt;
&lt;/Context&gt; &lt;/Context&gt;
... ...
</pre> </pre>
<h3 id="pellet">XI. Configure Pellet Reasoner </h3> <h3 id="pellet">XI. Configure Pellet Reasoner </h3>
<p><em>Do we need this section still? - elly</em></p> <p>
<p>VIVO uses the Pellet engine to perform reasoning, which runs in the <em>Do we need this section still? - elly</em>
</p>
<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.</p> VIVO is restarted.
<p>By default, Pellet is fed only an incomplete view of </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. </p> skip to the next step.
<p> </p>
To enable "complete" OWL inference (materialize <p>
all significant entailed statements), open To enable "complete" OWL inference (materialize
"vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup. all significant entailed statements), open
</p> "vitro-core/webapp/config/web.xml" and search for PelletReasonerSetup.
<p>Then change the name of the listener class to </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. </p> all inferences except owl:sameAs and owl:differentFrom.
<p>This is enabled </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. </p> improvements over the "complete" mode.
<p>Finally, a class called </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.</p> 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>
VIVO can be configured to work with an external authentication <p>
system VIVO can be configured to work with an external authentication system like
like Shibboleth or CUWebAuth. VIVO must be accessible only through an Shibboleth or CUWebAuth.
Apache HTTP server. The Apache server will be configured to invoke the </p>
external authentication system. When the user&nbsp; completes the <p>
authentication, the Apache server will pass a network ID to VIVO, to VIVO must be accessible only through an Apache HTTP server. The Apache server
identify the user. If VIVO has an account for that user, the user will will be configured to invoke the external authentication system. When the user
be logged in with the privileges of that account. In the absence of an completes the authentication, the Apache server will pass a network ID to VIVO,
account, VIVO will try to find&nbsp; a page associated with the user. to identify the user.
If such a page is found, the user can log in to edit his own profile </p>
information.---- Configuring the Apache server: Your institution will <p>
provide you with instructions for setting up the external If VIVO has an account for that user, the user will be logged in with the
authentication system. The Apache server must be configured to secure a privileges of that account. In the absence of an account, VIVO will try to find
page in&nbsp; VIVO. When a user reaches this secured page, the Apache a page associated with the user. If such a page is found, the user can log in
server will invoke the external authentication system.For VIVO, this to edit his own profile information.
secured page is named: /loginExternalAuthReturn When your instructions </p>
call for the location of the secured page, this is the value you should <h4>Configuring the Apache server</h4>
use.---- Configuring VIVO: To enable external authentication, VIVO <p>
requires three values in the deploy.properties file.* The name of the Your institution will provide you with instructions for setting up the external
HTTP header that will hold the external userâÃ&Ntilde;Ã&yen;s network authentication system. The Apache server must be configured to secure a page in
ID When a user completes the authentication process, the Apache server VIVO. When a user reaches this secured page, the Apache server will invoke the
will put the userâÃ&Ntilde;Ã&yen;s network ID into one of the headers external authentication system.
of the HTTP request.&nbsp; The instructions from your institution </p>
should tell you which header is used for this purpose.&nbsp; You need <p>
to tell VIVO the name of that HTTP header. Insert a line like this in For VIVO, this secured page is named:
the deploy.properties file:externalAuth.netIdHeaderName = [the header <code>
name]For example: externalAuth.netIdHeaderName = remote_userID * The /loginExternalAuthReturn
text for the Login button To start the authentication process, the user </code>
will click on a button in the VIVO login form. You need to tell VIVO </p>
what text should appear in that button.Put a line like this in the <p>
deploy.properties file:externalAuth.buttonText = [the text for your When your instructions call for the location of the secured page, this is the
login button]For example:externalAuth.buttonText = Log in using BearCat value you should use.
ShibbolethThe VIVO login form will display a button labelled </p>
âÃ&Ntilde;úLog in using BearCat ShibbolethâÃ&Ntilde;ù.* Associating a <h4>Configuring VIVO</h4>
User with a profile page If VIVO has an account for the user, the user <p>
will be given the privileges assigned to that account.In addition, VIVO To enable external authentication, VIVO requires three values in the
will try to associate the user with a profile page, so&nbsp; the user deploy.properties file.
may edit his own profile data. VIVO will search the data model for a </p>
person with a property that matches the UserâÃ&Ntilde;Ã&yen;s network <ul>
ID.You need to tell VIVO what property should be used for matching. <li>
Insert a line like this in the deploy.properties The name of the HTTP header that will hold the external user’s network ID
file:selfEditing.idMatchingProperty = [the URI of the property]For When a user completes the authentication process, the Apache server will
example:selfEditing.idMatchingProperty = put the user’s network ID into one of the headers of the HTTP request.
http://vivo.mydomain.edu/ns#networkId The instructions from your institution should tell you which header is
used for this purpose.
You need to tell VIVO the name of that HTTP header. Insert a line like
this in the deploy.properties file: <pre>externalAuth.netIdHeaderName = [the header name]</pre>
For example: <pre>externalAuth.netIdHeaderName = remote_userID</pre>
</li>
<li>
The text for the Login button
To start the authentication process, the user will click on a button in
the VIVO login form. You need to tell VIVO what text should appear in that
button.
Put a line like this in the deploy.properties file:
externalAuth.buttonText = [the text for your login button]
For example: <pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
The VIVO login form will display a button labelled “Log in using BearCat
Shibboleth”.
</li>
<li>
Associating a User with a profile page
If VIVO has an account for the user, the user will be given the privileges
assigned to that account.
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 data model
for a person with a property that matches the User’s network ID.
You need to tell VIVO what property should be used for matching. Insert
a line like this in the deploy.properties file:<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li>
</ul>
</p> </p>
<h3 id="installation_check">XIII. Was the installation successful? </h3> <h3 id="installation_check">XIII. Was the installation successful? </h3>
<p> <p>
If you have completed the previous steps, you have good indications If you have completed the previous steps, you have good indications that the
that the installation was successful.&nbsp; * Step VII showed that installation was successful.
Tomcat recognized the webapp, and that the webapp was able to present
the initial page.* Step VIII verified that you can log in to the
administrator account.Here is a simple test to see whether the ontology
files were loaded:* Click on the "Index" link on the upper left, below
the logo. You should seea "locations" section, with links for "Country"
and "Geographic Location."The index is built in a background thread, so
on your first login, you may see an empty index instead. Refresh the
page periodically to see whether the index will be populated. This may
take some time: with VIVO installed on a modest laptop computer,
loading the ontology files and building the index took more than 5
minutes from the time that Tomcat was started. * Click on the "Country"
link. You should see an alphabetical list of the countries of the
world.Here is a test to see whether your system is configured to serve
linked data: * Point your browser to the home page of your website, and
click the "Log in" link near the upper right corner. Log in with the
initialAdminUser username you set up in Step IV. If this is your first
time logging in, you will be prompted to change the password. * After
you have successfully logged in, click "site admin" in the upper right
corner.&nbsp; In the drop down under "Data Input" select "Faculty
Member(core)"and click the "Add individual of this class" button.*
Enter the name "test individual" under the field "Individual Name,"
scroll tothe 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. * Open a new web browser or
browser tab to the page http://marbles.sourceforge.net/.In the pink box
on that page enter the URI of the individual you created in theprevious
step and click "open." * In the resulting page search for the URI of
the "test individual." You should find it towards the bottom of the
page next to a red dot followed by "redirect (303)." This indicates
that you are successfully serving linked RDF data. If the URI of the
"test individual" is followed by "failed (400)" you are not
successfully serving linked data.Finally, test the search index. * The
search box is on the right side, directly opposite the "Index" link.
Type the word "Australia" into the box, and click on the "Search"
button.You should see a page of results, with links to countries that
border Australia, individuals that include Australia, and to Australia
itself.
</p> </p>
<ul>
<li>
Step VII showed that Tomcat recognized the webapp, and that the webapp was
able to present the initial page.
</li>
<li>
Step VIII verified that you can log in to the administrator account.
</li>
</ul>
<p>
Here is a simple test to see whether the ontology files were loaded:
</p>
<ul>
<li>
Click on the "Index" link on the upper left, below the logo. You should see
a "locations" section, with links for "Country" and "Geographic Location."
The index is built in a background thread, so on your first login, you may
see an empty index instead. Refresh the page periodically to see whether
the index will be populated. This may take some time: with VIVO installed
on a modest laptop computer, loading the ontology files and building the
index took more than 5 minutes from the time that Tomcat was started.
</li>
<li>
Click on the "Country" link. You should see an alphabetical list of the
countries of the world.
</li>
</ul>
<p>
Here is a test to see whether your system is configured to serve linked data:
</p>
<ul>
<li>
Point your browser to the home page of your website, and click the "Log in" link
near the upper right corner. Log in with the initialAdminUser username you
set up in Step IV. If this is your first time logging in, you will be
prompted to change the password.
</li>
<li>
After you have successfully logged in, click "site admin" in the upper right
corner. In the drop down under "Data Input" select "Faculty Member(core)"
and click the "Add individual of this class" button.
</li>
<li>
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.
</li>
<li>
Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
In the pink box on that page enter the URI of the individual you created in the
previous step and click "open."
</li>
<li>
In the resulting page search for the URI of the "test individual." You should
find it towards the bottom of the page next to a red dot followed by "redirect
(303)." This indicates that you are successfully serving linked RDF data.
If the URI of the "test individual" is followed by "failed (400)" you are not
successfully serving linked data.
</li>
</ul>
<p>
Finally, test the search index.
</p>
<ul>
<li>
The search box is on the right side, directly opposite the "Index" link.
Type the word "Australia" into the box, and click on the "Search"
button.You should see a page of results, with links to countries that
border Australia, individuals that include Australia, and to
Australia itself.
</li>
</ul>
</div> </div>
<!-- #wrapper-content --> <!-- #wrapper-content -->
<footer role="contentinfo"> <footer role="contentinfo">