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Updating version references and content from V1.2 to V1.3.
2011-07-18 03:07:32 +00:00
<!DOCTYPE htmlL>
The install.html is up2date with the content in index.txt, so I will ask developers to edit install.html instead of install.txt.
2011-01-14 19:11:35 +00:00
<html lang="en">
Adding in release announcement text from wiki.
2011-07-18 20:35:57 +00:00
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<title>VIVO Release 1 V1.3 Installation Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen">
<meta charset="utf-8">
<title>VIVO Release 1 V1.2 Installation Guide</title>
</head>
<body>
<div id="branding" role="banner">
<h1 class="vivo-logo"><a href="/"><span class="displace">VIVO</span></a></h1>
</div>
<!-- Start of content -->
<div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.3 Installation Guide</h1>
<small>
July 22, 2011
</small>
<toc>
<ul>
<li>
<a href="#announcement">Release announcement for V1.3</a>
</li>
<li>
<a href="#installation">Installation process for V1.3</a>
</li>
</ul>
</toc>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.3</h2>
VIVO Release 1.3 incorporates changes to the search indexing, user
accounts, menu management, ontology, and visualizations.
<br>
<h4>Search</h4>
VIVO 1.3 will feature notable improvements to the local search,
primarily to improve relevance ranking but also to boost the influence
of semantic relationships in the search. This will improve recall by
including text from related resources (e.g., adding a person’s grant
and publication titles to his or her search entry) and by boosting
overall relevance ranking based on the number and nature of connections
from one individual to others.
<br>
VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
of Apache Lucene to improve indexing and faceting of search results.
The migration to Solr also aligns the local search with the VIVO
multi-site search site under development for release prior to the 2011
VIVO Conference.
<br>
<h4>Authorization</h4>
Release 1.3 provides an entirely new model of authorization within the
VIVO application to allow more granular control over system
configuration and editing. The first phase of the new user account
interface is included in V1.3. This interface provides a user search, a
root acount, and password reset functionality where the password gets
emailed to the user. The next phase will provide the ability to create
new roles.
<br>
<h4>Menu management</h4>
The menus across the top of the site (Home, People, Organizations,
Research, Events) can now be managed in a web form instead of editing
an RDF file. In addition to making site management much easier,
form-based editing also allows more control over what classes of data
are displayed and provides a mechanism to limit certain menu pages to
content identified as internal to the institution.
<br>
<h4>FreeMaker template improvements</h4>
While less directly visible to the public, version 1.3 also includes
additional changes focused directly on supporting open source community
involvement in extending and customizing VIVO. The development team
began a year ago to transition VIVO’s code base away from Java Server
Pages to the FreeMarker page templating system that much more cleanly
separates internal application programming logic from page display.
<br>
<h4>Visualization</h4>
The visualization team has implemented a Science Map visualization,
which allows users to visually explore the scientific strengths of a
university, school, department, or person in the VIVO instance. Users
will be able to see where an organization or person’s interests lay
across 13 major scientific disciplines or 554 sub-disciplines, and will
be able to see how these disciplines and sub-disciplines interrelate
with one another on the map of science. Wireframes and design
documentation for upcoming enhanced versions of the Science Map
visualization have already been developed; the Science Map
visualization will most likely be in the form of a PDF that a user can
download.
<br>
Several visualization also now provide a caching feature that improves
performance after the initial processing.
<br>
<h4>QR Codes</h4>
Pages for people in VIVO have the option of displaying QR codes.
<br>
<h4>Ontology changes</h4>
<ul>
<li>
support for certifications and licenses
</li>
<li>
expanded support for intellectual property (patents) (it was
there as stub before but didn't allow common things such as assignee
and issuer)
</li>
<li>
support for editorial, reviewing and organizing activities
</li>
<li>
expanded shared geographical instance data vocabulary to include
the 50 U.S. states
</li>
<li>
representing specific types of EducationalTraining:
PostdoctoralTraining, Internship, MedicalResidency
</li>
</ul>
<h4>Linked open data</h4>
Responses to linked data requests have been enhanced to include
additional context about any individual, in working toward a goal of
being able to provide all the data in a person's profile available as
RDF via a single web request.
<br>
<br>
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.3</h2>
<p>
This document is a summary of the VIVO installation process. 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>
</p>
<ul>
<li>
These instructions assume that you are performing a clean
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.
</li>
<li>
If you are going to upgrade an existing service, please consult
the "upgrade" files in this directory.
</li>
</ul>
<p>
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>
<h3>Where does VIVO live on your computer?</h3>
<p>
Before beginning the installation, let's look at the four locations
on your computer that will hold VIVO.
</p>
<h4>The VIVO distribution directory</h4>
<p>
This is created when you unpack the VIVO distribution file (see <a href="#download_code">Step III</a>, below). This is where you will
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.
</p>
<h4>VIVO inside Tomcat</h4>
<p>
When you run the build script to compile and deploy VIVO (see <a href="#deploy">Step VI</a>, below), the files will be deployed to a
directory inside Tomcat. This is the actual executing code for VIVO,
but you won’t need to look at it or change it. If you need to change
VIVO, make the changes in the distribution directory, and run the build
script again. Tell the build script where to find Tomcat by setting <code>tomcat.home</code>
in the deploy.properties file (see <a href="#deploy_properties">Step V</a>,
below).
</p>
<h4>The VIVO home directory</h4>
<p>
VIVO will use this area to store some of the data it uses. Uploaded
image files are stored here, and the search index 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>,
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>
<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
occasionally through the MySQL client application.
</p>
<toc>
<h3>Steps to Installation</h3>
<ol class="roman1">
<li>
<a href="#required_software">Install required software</a>
</li>
<li>
<a href="#create_database">Create an empty MySQL database</a>
</li>
<li>
<a href="#download_code">Download the VIVO Application Source</a>
</li>
<li>
<a href="#deploy_properties">Specify deployment properties</a>
</li>
<li>
<a href="#deploy">Compile and deploy</a>
</li>
<li>
<a href="#tomcat_settings">Set Tomcat JVM parameters and
security limits</a>
</li>
<li>
<a href="#start_tomcat">Start Tomcat</a>
</li>
<li>
<a href="#add_rdf">Log in and add RDF data</a>
</li>
<li>
<a href="#contact_email">Set the Contact Email Address (if
using "Contact Us" form)</a>
</li>
<li>
<a href="#tomcat_connector">Setup Apache Tomcat Connector</a>
</li>
<li>
<a href="#external_auth">Using an External Authentication
System with VIVO</a>
</li>
<li>
<a href="#installation_check">Was the installation successful?</a>
</li>
</ol>
</toc>
<h3 id="required_software">I. Install required software </h3>
<p>
Before installing VIVO, make sure that the following software is
installed on the desired machine:
</p>
<ul>
<li>
Java (SE) 1.6 or higher, <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>
</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>
</li>
</ul>
<p>
Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code>
and <code>ANT_HOME</code>
and add the executables to your path per
your operating system and installation directions from the software
support websites.
</p>
<p>
* Note that VIVO 1.2 will not run on older versions of MySQL that
may have worked with 1.1.1. Be sure to run VIVO 1.2 with 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
MySQL server and create a new database in MySQL that uses <code>UTF-8
encoding</code>. You will need these values for Step IV when you
configure the deployment properties. At the MySQL command line you can
create the database and user with these commands substituting your
values for <code>dbname</code>, <code>username</code>, and <code>password</code>.
Most
of
the
time, the hostname will equal <code>localhost</code>.
</p>
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
<p>
Grant access to a database user. For example:
</p>
<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br></pre>
<p>
Keep track of the database name, username, and password for Step
IV.
</p>
<h3 id="download_code">III. Download the VIVO Application Source
<br>
</h3>
<p>
Download the VIVO application source as either <code>rel-1.2.zip</code>
or <code>rel-1.2.gz</code>
file and unpack it on your web server:
<br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</p>
<h3 id="deploy_properties">IV. Specify deployment properties </h3>
<p>
At the top level of the VIVO distribution directory, copy the file <code>example.deploy.properties</code>
to a file named simply <code>deploy.properties</code>. This file sets
several properties used in compilation and deployment.
</p>
<p>
<em>Windows:</em>
For those installing on Windows operating
system, include the windows drive and use the forward slash "/" and not
the back slash "\" in the directory locations, e.g. <code>c:/tomcat</code>.
</p>
<p>
<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
entitled <a href="#external_auth">Using an External Authentication
System with VIVO</a>.
</p>
Trying to get table border to print.
2011-07-18 20:56:58 +00:00
<table border='1' bordercolor="#CCCCCC" cellspacing="5">
Adding in release announcement text from wiki.
2011-07-18 20:35:57 +00:00
<tbody>
<tr>
<th>
Property Name
</th>
<th>
Example Value
</th>
</tr>
<tr>
<td colspan="2">
Default namespace: VIVO installations make their
RDF resources available for harvest using linked data. Requests for RDF
resource URIs redirect to HTML or RDF representations as specified by
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/individual/" in order to support linked data.
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
trailing slash).</h5>
</td>
</tr>
<tr class="odd_row">
<td>
Vitro.defaultNamespace
</td>
<td>
http://vivo.mydomain.edu/individual/
</td>
</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>
<td colspan="2">
Directory where tomcat is installed.
</td>
</tr>
<tr class="odd_row">
<td>
tomcat.home
</td>
<td>
/usr/local/tomcat
</td>
</tr>
<tr>
<td colspan="2">
Name of your VIVO application.
</td>
</tr>
<tr class="odd_row">
<td>
webapp.name
</td>
<td>
vivo
</td>
</tr>
<tr>
<td colspan="2">
URL of Solr context used in local VIVO search.
NIHVIVO-2936 Update to doc on vitro.local.solr.url to reflect changes to example.deploy.properties
2011-07-18 21:12:46 +00:00
Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre>
Adding in release announcement text from wiki.
2011-07-18 20:35:57 +00:00
In the standard installation, the Solr context will be on the same
server as VIVO, and in the same Tomcat instance. The path will be the
VIVO webapp.name (specified above) + "solr"
</td>
</tr>
<tr class="odd_row">
<td>
vitro.local.solr.url
</td>
<td>
http://localhost:8080/vivosolr
</td>
</tr>
<tr>
<td colspan="2">
Restricts access to the Solr search platform.
One or more regular expressions, separated by commas. When a request is
made to Solr, the IP address of the requestor must match one of the
patterns, or the request will be rejected.
<br>
Examples:
<ul>
<li>
vitro.local.solr.ipaddress.mask = 127\.0\.0\.1
</li>
<li>
vitro.local.solr.ipaddress.mask =
127\.0\.0\.1,0:0:0:0:0:0:0:1
</li>
<li>
vitro.local.solr.ipaddress.mask = 169.254.*
</li>
</ul>
</td>
</tr>
<tr class="odd_row">
<td>
vitro.local.solr.ipaddress.mask
</td>
<td>
127\.0\.0\.1,0:0:0:0:0:0:0:1
</td>
</tr>
<tr>
<td colspan="2">
Directory where the VIVO application will store
the data that it creates. This includes uploaded files (usually images)
and the Solr search index. Be sure this directory exists and is
writable by the user who the Tomcat service is running as.
</td>
</tr>
<tr class="odd_row">
<td>
vitro.home.directory
</td>
<td>
/usr/local/vivo/data
</td>
</tr>
<tr>
<td colspan="2">
Specify an SMTP host that the application will
use for sending e-mail (Optional). If this is left blank, the contact
form will be hidden and disabled, and users will not be notified of
changes to their accounts.
</td>
</tr>
<tr class="odd_row">
<td>
email.smtpHost
</td>
<td>
smtp.servername.edu
</td>
</tr>
<tr>
<td colspan="2">
Specify an email address which will appear as
the sender in e-mail notifications to users (Optional). If a user
replies to the notification, this address will receive the reply. If a
user's e-mail address is invalid, this address will receive the error
notice. If this is left blank, users will not be notified of changes to
their accounts.
</td>
</tr>
<tr class="odd_row">
<td>
email.replyTo
</td>
<td>
vivoAdmin@my.domain.edu
</td>
</tr>
<tr>
<td colspan="2">
Specify the JDBC URL of your database. Change
the end of the URL to reflect your database name (if it is not "vivo").
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.url
</td>
<td>
jdbc:mysql://localhost/vivo
</td>
</tr>
<tr>
<td colspan="2">
Change the username to match the authorized user
you created in MySQL.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.username
</td>
<td>
username
</td>
</tr>
<tr>
<td colspan="2">
Change the password to match the password you
created in MySQL.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.password
</td>
<td>
password
</td>
</tr>
<tr>
<td colspan="2">
Specify the Jena triple store technology to use.
SDB is Jena's SPARQL database; this setting allows RDF data to scale
beyond the limits of the JVM heap. Set to RDB to use the older Jena RDB
store with in-memory caching.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.tripleStoreType
</td>
<td>
SDB
</td>
</tr>
<tr>
<td colspan="2">
Specify the maximum number of active connections
in the database connection pool to support the anticipated number of
concurrent page requests. It is not necessary to adjust this value when
using the RDB configuration.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.pool.maxActive
</td>
<td>
40
</td>
</tr>
<tr>
<td colspan="2">
Specify the maximum number of database
connections that will be allowed to remain idle in the connection pool.
Default is 25% of the maximum number of active connections.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.pool.maxIdle
</td>
<td>
10
</td>
</tr>
<tr>
<td colspan="2">
Change the dbtype setting to use a database
other than MySQL. Otherwise, leave this value unchanged. Possible
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
for additional information.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.dbtype
</td>
<td>
MySQL
</td>
</tr>
<tr>
<td colspan="2">
Specify a driver class name to use a database
other than MySQL. Otherwise, leave this value unchanged. This JAR file
for this driver must be added to the the webapp/lib directory within
the vitro.core.dir specified above.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.driver
</td>
<td>
com.mysql.jdbc.Driver
</td>
</tr>
<tr>
<td colspan="2">
Change the validation query used to test
database connections only if necessary to use a database other than
MySQL. Otherwise, leave this value unchanged.
</td>
</tr>
<tr class="odd_row">
<td>
VitroConnection.DataSource.validationQuery
</td>
<td>
SELECT 1
</td>
</tr>
<tr>
<td colspan="2">
Specify the email address of the root user
account for the VIVO application. This user will have an initial
temporary password of 'rootPassword'. You will be prompted to create a
new password on first login.
<p>
NOTE: The root user account has access to all data and all
operations in VIVO. Data views may be surprising when logged in as the
root user. It is best to create a Site Admin account to use for every
day administrative tasks.
</p>
</td>
</tr>
<tr class="odd_row">
<td>
rootUser.emailAddress
</td>
<td>
vivoAdmin@my.domain.edu
</td>
</tr>
<tr>
<td colspan="2">
The URI 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>
selfEditing.idMatchingProperty
</td>
<td>
http://vivo.mydomain.edu/ns#networkId
</td>
</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>
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. In the meantime, VIVO release 1.2 guards against this impact
by disabling the temporal graph visualization unless the
"visualization.temporal" flag is set to "enabled". To enable it,
uncomment the line for this setting.
</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>
<span style="font-style: italic;">visualization.topLevelOrg =
http://vivo.psm.edu/individual/n2862</span>
<br>
</td>
</tr>
<tr class="odd_row">
<td>
visualization.topLevelOrg
</td>
<td>
http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
</td>
</tr>
</tbody>
</table>
<h3 id="deploy">V. Compile and deploy</h3>
<p>
At the command line, from the top level of the VIVO distribution
directory, type:
</p>
<pre> ant all<br> </pre>
<p>
to build VIVO and deploy to Tomcat's webapps directory.
</p>
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
limits</h3>
<p>
Currently, VIVO copies the contents of your RDF database into
memory in order to serve Web requests quickly (the in-memory copy and
the underlying database are kept in synch as edits are performed).
</p>
<p>
VIVO will require more memory than that allocated to Tomcat by
default. With most installations of Tomcat, the "setenv.sh" or
"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
bin directory, you can create it.</em>
<br>
For example:
</p>
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
<p>
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
megabytes is a minimum practical heap size for production 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>
If an OutOfMemoryError is encountered during VIVO execution, it can
be remedied by increasing the heap parameters and restarting Tomcat.
</p>
<p>
Security limits: 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>:
</p>
<pre> apache hard nproc 400<br> tomcat6 hard nproc 1500 <br> </pre>
<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>
</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.
</p>
<p>
After verifying your new password, 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.
</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."
</p>
<p>
Clicking the "Index" tab in the navigation bar at the top right of
the page will show a simple index of the knowledge base.
</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
"Contact Us" form)</h3>
<p>
If you have configured your application to use the "Contact Us"
feature in Step IV (<code>email.smtpHost</code>), you will also need to
add an email address to the VIVO application.&nbsp; This is the email
to which the contact form will submit. It can be a list server or an
individual's email address.
</p>
<p>
Log in as a system administrator. Navigate to the "Site Admin"
table of contents (link in the right side of the header). Go to "Site
Information" (under "Site Configuration"). In the "Site Information
Editing Form," enter a functional email address in the field "Contact
Email Address" and submit the change.
</p>
<p>
If you set the <code>email.smtpHost</code>
in Step IV and do NOT
provide an email address in this step, your users will receive a java
error in the interface.
</p>
<h3 id="tomcat_connector">X. Set up Apache Tomcat Connector </h3>
<p>
It is recommended that a Tomcat Connector such as mod_jk be used to
ensure that the site address does not include the port number (e.g.
8080) and an additional reference to the Tomcat context name (e.g.
/vivo).
</p>
<p>
This will make VIVO available at "http://example.com" instead of
"http://example.com:8080/vivo"
</p>
<p>
Using the mod_jk connector allows for communication between Tomcat
and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick
Start
HowTo</a>
on the Apache site describes the minimum server
configurations for several popular web servers.
</p>
<p>
After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
to
respond
to
requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties:
</p>
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; <br> </pre>
<p>
Note: the value for maxThreads (320) is equal to the value for
MaxClients in the apache's <code>httpd.conf</code>
file.
</p>
<p>
Locate the <code>&lt;Host name="localhost"...&gt;</code>
directive
and update as follows:
</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>
<h3 id="external_auth">XI. Using an External Authentication System
with VIVO </h3>
<p>
</p>
<p>
VIVO can be configured to work with an external authentication
system like Shibboleth or CUWebAuth.
</p>
<p>
VIVO must be accessible only through an Apache HTTP server. The
Apache server will be configured to invoke the external authentication
system. When the user completes the authentication, the Apache server
will pass a network ID to VIVO, to identify the user.
</p>
<p>
If VIVO has an account for that user, the user will be logged in
with the privileges of that account. In the absence of an account, VIVO
will try to find a page associated with the user. If such a page is
found, the user can log in to edit his own profile information.
</p>
<h4>Configuring the Apache server</h4>
<p>
Your institution will provide you with instructions for setting up
the external authentication system. The Apache server must be
configured to secure a page in VIVO. When a user reaches this secured
page, the Apache server will invoke the external authentication system.
</p>
<p>
For VIVO, this secured page is named: <code>/loginExternalAuthReturn</code>
</p>
<p>
When your instructions call for the location of the secured page,
this is the value you should use.
</p>
<h4>Configuring VIVO</h4>
<p>
To enable external authentication, VIVO requires three values in
the <code>deploy.properties</code>
file.
</p>
<ul>
<li>
<h5>The name of the HTTP header that will hold the external user's
network ID.</h5>
<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:
</p>
<pre>externalAuth.netIdHeaderName = [the header name]</pre>
<p>
For example:
</p>
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
</li>
<li>
<h5>The text for the Login button.</h5>
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.
<p>
Put a line like this in the deploy.properties file:
externalAuth.buttonText = [the text for your login button] For example:
</p>
<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
<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>
<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
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
untyped literal). You need to tell VIVO what property should be used
for matching. Insert a line like this in the deploy.properties file:
</p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
<p>
For example:
</p>
<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li>
</ul>
<h3 id="installation_check">XII. Was the installation successful? </h3>
<p>
If you have completed the previous steps, you have good indications
that the installation was successful.
</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 right, 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 <code>rootUser.emailAddress</code>
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 <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
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>
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".
</li>
</ul>
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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.
2011-01-14 19:11:35 +00:00
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