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doc/install.html
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doc/install.html
|
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@ -3,44 +3,43 @@
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<head>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
|
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<meta charset="utf-8">
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<title>VIVO Release 1 V1.4 Installation Guide</title>
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<title>VIVO Release V1.4 Installation Guide</title>
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<link rel="stylesheet" href="./css/doc.css" media="screen">
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||||
</head>
|
||||
<body>
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||||
<div id="branding" role="banner">
|
||||
<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
|
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<h1 class="vivo-logo"><a href="http://vivoweb.org"><span class="displace">VIVO</span></a></h1>
|
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</div>
|
||||
<!-- Start of content -->
|
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 V4 Installation Guide</h1>
|
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<small>
|
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December 9, 2011
|
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</small>
|
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<br>
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<hr><!-- Page break --><!-- Installation process for V1.4 --><h2 id="installation">Installation process for V1.4</h2>
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<h1>VIVO Release V1.4 Installation Guide</h1>
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<div>
|
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December 10, 2011
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</div>
|
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|
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<p>
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This document is a summary of the VIVO installation process. This
|
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and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
|
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at <a href="http://vivoweb.org">VIVOweb.org</a>
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This document is a summary of the VIVO installation
|
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process. For information about this release, consult
|
||||
the <a href="release.html">VIVO v1.4 Release
|
||||
Announcement</a>. This and other documentation can be found on
|
||||
the <a href="http://vivoweb.org/support">support
|
||||
page</a> at <a href="http://vivoweb.org">VIVOweb.org</a>.
|
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</p>
|
||||
<ul>
|
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<li>
|
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<p>
|
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These instructions assume that you are performing a clean
|
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install, including emptying an existing database, emptying the VIVO
|
||||
home directory, and removing a previous installation from the Tomcat
|
||||
webapps directory. Product functionality may not be as expected if you
|
||||
install over an existing installation of an earlier version.
|
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</li>
|
||||
<li>
|
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If you are going to upgrade an existing service, please consult
|
||||
the "upgrade" files in this directory.
|
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</li>
|
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</ul>
|
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<p>
|
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</p><p>
|
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If you are going to upgrade an existing deployment, please consult
|
||||
the <a href="upgrade-1.4.html">Release 1 V1.4 Upgrade Guide</a> in this directory.
|
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</p><p>
|
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VIVO Developers: If you are working on the VIVO source code from
|
||||
Subversion, the instructions are slightly different. Please consult
|
||||
developers.txt in this directory.
|
||||
</p>
|
||||
<a href="developers.txt">developers.txt</a> in this directory.
|
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<p>
|
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|
||||
<h3>Where does VIVO live on your computer?</h3>
|
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<p>
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Before beginning the installation, let's look at the four locations
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|
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@ -48,10 +47,10 @@
|
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</p>
|
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<h4>The VIVO distribution directory</h4>
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<p>
|
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This is created when you unpack the VIVO distribution file (see <a href="#download_code">Step III</a>, below). This is where you will
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This directory is created when you unpack the VIVO distribution file (see <a href="#download_code">Step III</a>, below). This directory is where you will
|
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create your deploy.properties file (see <a href="#deploy_properties">Step
|
||||
V</a>, below), and where you will make any modifications to the VIVO
|
||||
theme or code. You can create this wherever you choose.
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||||
theme or code. You can create this directory wherever you choose.
|
||||
</p>
|
||||
<h4>VIVO inside Tomcat</h4>
|
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<p>
|
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|
|
@ -66,25 +65,24 @@
|
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<h4>The VIVO home directory</h4>
|
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<p>
|
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VIVO will use this area to store some of the data it uses. Uploaded
|
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image files are stored here, and the search index is stored here also.
|
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image files are stored here, and the Solr home directory is stored here also.
|
||||
You can create this wherever you choose. Tell VIVO where to find the
|
||||
home directory by setting <code>vitro.home.directory</code>
|
||||
in the
|
||||
deploy.properties file (see <a href="#deploy_properties">Step V</a>,
|
||||
in the deploy.properties file (see <a href="#deploy_properties">Step V</a>,
|
||||
below). You must create this directory before starting VIVO, and you
|
||||
must ensure that Tomcat has permission to read and write to this
|
||||
directory when it runs.
|
||||
</p>
|
||||
<h4>The MySQL database</h4>
|
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<p>
|
||||
Essentially all of the data that you store in VIVO will be given to
|
||||
MySQL for storage. The actual location of this data depends on what
|
||||
system you have, and on how you install MySQL (see <a href="#required_software">Step I</a>, below). but you won’t need to
|
||||
know the location. You will access the data through VIVO, or
|
||||
The data that you add into VIVO will be stored in a MySQL database. The
|
||||
actual location of this data depends on what
|
||||
system you have, and on how you install MySQL (see <a href="#required_software">Step I</a>, below).
|
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You will typically access the data through VIVO, or
|
||||
occasionally through the MySQL client application.
|
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</p>
|
||||
<toc>
|
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<h3>Steps to Installation</h3>
|
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<h3>Installation Instructions</h3>
|
||||
<ol class="roman1">
|
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<li>
|
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<a href="#required_software">Install required software</a>
|
||||
|
|
@ -136,17 +134,17 @@
|
|||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
Java (SE) 1.6 or higher, <a href="http://java.sun.com">http://java.sun.com</a>
|
||||
Java (SE) 1.6.x* <a href="http://java.sun.com">http://java.sun.com</a>
|
||||
(Not OpenJDK)
|
||||
</li>
|
||||
<li>
|
||||
Apache Tomcat 6.x, <a href="http://tomcat.apache.org">http://tomcat.apache.org</a>
|
||||
Apache Tomcat 6.x or 7.x <a href="http://tomcat.apache.org">http://tomcat.apache.org</a>
|
||||
</li>
|
||||
<li>
|
||||
Apache Ant 1.7 or higher, <a href="http://ant.apache.org">http://ant.apache.org</a>
|
||||
</li>
|
||||
<li>
|
||||
MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a>
|
||||
MySQL 5.1 or higher**, <a href="http://www.mysql.com">http://www.mysql.com</a>
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
|
|
@ -157,14 +155,12 @@
|
|||
support websites.
|
||||
</p>
|
||||
<p>
|
||||
* Note that VIVO V1.4 will not run on older versions of MySQL that
|
||||
may have worked with 1.1.1. Be sure to run VIVO 1.4 with MySQL 5.1 or
|
||||
** Note that from version V1.2 onward VIVO does
|
||||
not support older versions of MySQL that
|
||||
may have worked with 1.1.1. Be sure to use MySQL 5.1 or
|
||||
higher. Using unsupported versions may result in strange error messages
|
||||
related to table formatting or other unexpected problems.
|
||||
</p>
|
||||
<p>
|
||||
* Note that VIVO is not yet compatible with Tomcat 7.
|
||||
</p>
|
||||
<h3 id="create_database">II. Create an empty MySQL database </h3>
|
||||
<p>
|
||||
Decide on a database name, username, and password. Log into your
|
||||
|
|
@ -191,7 +187,7 @@
|
|||
<br>
|
||||
</h3>
|
||||
<p>
|
||||
Download the VIVO application source as either <code>rel-4.zip</code>
|
||||
Download the VIVO application source as either <code>rel-1.4.zip</code>
|
||||
or <code>rel-1.4.gz</code>
|
||||
file and unpack it on your web server:
|
||||
<br>
|
||||
|
|
@ -213,7 +209,7 @@
|
|||
<em>External authentication:</em>
|
||||
If you want to use an external
|
||||
authentication system like Shibboleth or CUWebAuth, you will need to
|
||||
set two additional properties in this file. See the section below
|
||||
set two additional properties in this file. See the step below
|
||||
entitled <a href="#external_auth">Using an External Authentication
|
||||
System with VIVO</a>.
|
||||
</p>
|
||||
|
|
@ -235,11 +231,11 @@
|
|||
the client. To make this possible, VIVO's default namespace must have a
|
||||
certain structure and begin with the public web address of the VIVO
|
||||
installation. For example, if the web address of a VIVO installation is
|
||||
"http://vivo.example.edu/" the default namespace must be set to
|
||||
"http://vivo.example.edu/", the default namespace must be set to
|
||||
"http://vivo.example.edu/individual/" in order to support linked data.
|
||||
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
|
||||
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
|
||||
"http://www.example.edu/vivo/individual/".<h5>* The namespace must end with "individual/" (including the
|
||||
trailing slash).</h5>
|
||||
</td>
|
||||
</tr>
|
||||
|
|
@ -635,6 +631,22 @@
|
|||
/usr/local/vivo/harvester/
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
<tr>
|
||||
<td colspan="2">
|
||||
Types of individual for which we can create proxy editors.
|
||||
If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="odd_row">
|
||||
<td>
|
||||
proxy.eligibleTypeList
|
||||
</td>
|
||||
<td>
|
||||
http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization
|
||||
</td>
|
||||
</tr>
|
||||
|
||||
</tbody>
|
||||
</table>
|
||||
<h3 id="deploy">V. Compile and deploy</h3>
|
||||
|
|
@ -670,14 +682,16 @@
|
|||
<h4>Set security limits</h4>
|
||||
<p>
|
||||
VIVO is a multithreaded web application that may
|
||||
require more threads than are permitted under your Linux installation's
|
||||
default configuration. Ensure that your installation can support the
|
||||
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
|
||||
require more threads than are permitted under your
|
||||
Linux installation's default configuration. Ensure
|
||||
that your installation can support the required number
|
||||
of threads by making the following edits
|
||||
to <code>/etc/security/limits.conf</code>:
|
||||
</p>
|
||||
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
|
||||
<h4>Set URI encoding</h4>
|
||||
<p>
|
||||
In order for Solr to correctly search for international characters (>127),
|
||||
In order for VIVO to correctly handle international characters,
|
||||
you must configure Tomcat to conform to the URI standard by
|
||||
accepting percent-encoded UTF-8.
|
||||
</p>
|
||||
|
|
@ -696,58 +710,82 @@
|
|||
</pre>
|
||||
<h4>Take care when creating Context elements</h4>
|
||||
<p>
|
||||
Each of the webapps in the VIVO distribution (VIVO and Solr) includes a "context fragment" file,
|
||||
containing some of the deployment information for that webapp.
|
||||
Each of the webapps in the VIVO distribution (VIVO and
|
||||
Solr) includes a "context fragment" file, containing
|
||||
some of the deployment information for that webapp.
|
||||
</p>
|
||||
<p>
|
||||
Tomcat allows you to override these context fragments by adding Context elements to "server.xml".
|
||||
If you decide to do this, be sure that your new Context element includes the necessary
|
||||
deployment parameters from the overridden context fragment.
|
||||
Tomcat allows you to override these context fragments
|
||||
by adding Context elements to "server.xml". If you
|
||||
decide to do this, be sure that your new Context
|
||||
element includes the necessary deployment parameters
|
||||
from the overridden context fragment.
|
||||
</p>
|
||||
<p>
|
||||
See <a href="#tomcat_connector">Section X</a> below,
|
||||
See <a href="#tomcat_connector">Step X</a> below,
|
||||
for an example of overriding the VIVO context fragment.
|
||||
</p>
|
||||
|
||||
<h3 id="start_tomcat">VII. Start Tomcat </h3>
|
||||
<p>
|
||||
Most Tomcat installations can be started by running <code>startup.sh</code>
|
||||
or <code>startup.bat</code>
|
||||
in Tomcat's bin directory. Point your
|
||||
browser to "http://localhost:8080/vivo/" to test the application. If
|
||||
Tomcat does not start up, or the VIVO application is not visible, check
|
||||
the files in Tomcat's logs directory. Error messages are commonly found
|
||||
in <code>catalina.out</code>
|
||||
or <code>localhost.log</code>
|
||||
or <code>startup.bat</code> in Tomcat's bin directory. Point your
|
||||
browser to <a href="http://localhost:8080/vivo/">http://localhost:8080/vivo</a> (or the appropriate URL based on the <code>webapp.name</code> value in deploy.properties) to test the application.
|
||||
</p>
|
||||
<p>
|
||||
On start up VIVO will run some diagnostic tests. If a
|
||||
problem is detected, the normal VIVO pages will redirect
|
||||
to a startup status page describing the problem. You
|
||||
can stop tomcat, attempt to fix the problem and
|
||||
proceed from <a href="#deploy">Step V</a>. The
|
||||
startup status page may offer a continue link which
|
||||
will allow you to use VIVO inspite of the problems.
|
||||
|
||||
<p>
|
||||
If Tomcat does not start up, or the VIVO application
|
||||
is not visible, check the files in Tomcat's logs
|
||||
directory. Error messages are commonly found
|
||||
in <code>tomcat/logs/catalina.out</code>
|
||||
or <code>tomcat/logs/vivo.all.log</code>
|
||||
or <code>tomcat/logs/localhost.log.</code>
|
||||
</p>
|
||||
<h3 id="add_rdf">VIII. Log in and add RDF data </h3>
|
||||
<p>
|
||||
If the startup was successful, you will see a welcome message
|
||||
informing you that you have successfully installed VIVO. Click the "Log
|
||||
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
|
||||
you set up in Step IV. The initial password for the root account is
|
||||
"rootPassword" (without the quotes). On first login, you will be
|
||||
prompted to select a new password and verify it a second time. When login is
|
||||
complete, the search index is checked and, if it is empty,
|
||||
a full index build will be triggered in the background, in order to ensure
|
||||
complete functionality throughout the site.
|
||||
If the startup was successful, you will see a welcome
|
||||
message informing you that you have successfully
|
||||
installed VIVO. Click the "Log in" link near the upper
|
||||
right corner. Log in with
|
||||
the <code>rootUser.emailAddress</code> you set up in
|
||||
Step IV. The initial password for the root account is
|
||||
"rootPassword" (without the quotes). On first login,
|
||||
you will be prompted to select a new password and
|
||||
verify it a second time. When login is complete, the
|
||||
search index is checked and, if it is empty, a full
|
||||
index build will be triggered in the background in
|
||||
order to ensure complete functionality throughout the
|
||||
site.
|
||||
</p>
|
||||
<p>
|
||||
After logging in, you will be presented with a
|
||||
menu of editing options. Here you can create OWL classes, object
|
||||
properties, data properties, and configure the display of data.
|
||||
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
|
||||
options available for each ontology entity. VIVO comes with a core VIVO
|
||||
ontology, but you may also upload other ontologies from an RDF file.
|
||||
After logging in, you can navigate to the "Site Admin" page that presents a menu of
|
||||
editing options. Here you can create OWL classes,
|
||||
object properties, data properties, and configure the
|
||||
display of data. Currently, any classes you wish to
|
||||
make visible on your website must be part of a class
|
||||
group and any individual must have an rdfs:label.
|
||||
There are a number of visibility and display options
|
||||
available for classes and properites. VIVO comes with a
|
||||
core VIVO ontology, but you may also upload other
|
||||
ontologies from an RDF file.
|
||||
</p>
|
||||
<p>
|
||||
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
|
||||
that Vitro currently works best with OWL-DL ontologies and has only
|
||||
limited support for pure RDF data. You can enter a URL pointing to the
|
||||
RDF data you wish to load or upload from a file on your local machine.
|
||||
Ensure that the "add RDF" radio button is selected. You will also
|
||||
likely want to check "create classgroups automatically."
|
||||
Under the "Advanced Data Tools" section, click "Add/Remove RDF
|
||||
Data." Note that Vitro currently works best with
|
||||
OWL-DL ontologies and has only limited support for
|
||||
pure RDF data. You can enter a URL pointing to the
|
||||
RDF data you wish to load or upload the RDF data from a file on
|
||||
your local machine. Ensure that the "add RDF" radio
|
||||
button is selected. You will also likely want to check
|
||||
"create classgroups automatically."
|
||||
</p>
|
||||
<p>
|
||||
Clicking the "Index" tab in the navigation bar at the top right of
|
||||
|
|
@ -948,6 +986,11 @@
|
|||
account.
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
The startup status will indicate if the basic
|
||||
configuration of the system was successful. It can be
|
||||
accessed from <strong>siteAdmin -> Startup status</strong>.
|
||||
</p>
|
||||
<p>
|
||||
Here is a simple test to see whether the ontology files were
|
||||
loaded:
|
||||
|
|
@ -991,12 +1034,11 @@
|
|||
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>.
|
||||
In
|
||||
the
|
||||
pink
|
||||
box on that page enter the URI of the individual you
|
||||
created in the previous step and click "open."
|
||||
Open a new web browser or browser tab to the
|
||||
page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
|
||||
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
|
||||
|
|
@ -1012,11 +1054,14 @@
|
|||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
Type the word "Australia" into the search 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. To trigger the search index, you can log in as a site
|
||||
administrator and go to "http://your-vivo-url/SearchIndex".
|
||||
Type the word "Australia" into the search 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. To trigger the search index,
|
||||
you can log in as a site administrator and go
|
||||
to <strong> Site Admin -> Rebuild search
|
||||
index</strong>.
|
||||
</li>
|
||||
</ul>
|
||||
<h3 id="termsofuse">XIII. Review the VIVO Terms of Use</h3>
|
||||
|
|
@ -1038,10 +1083,8 @@
|
|||
<div id="footer" role="contentinfo">
|
||||
<p class="copyright">
|
||||
<small>
|
||||
©2011 All Rights Reserved
|
||||
All Rights Reserved <a href="license.txt">see license</a>
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</small>
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by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
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</p>
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<div id="nav" role="navigation">
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<ul id="footer-nav" role="list">
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Add table
Reference in a new issue