Deprecated. This material represents early efforts and may be of interest to historians. It doe not describe current VIVO efforts.

  • Created by Unknown User (conlon), last modified on May 12, 2011

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Installation instructions for VIVO 1.1 on Debian OS.

Install Apache 2 and Tomcat 6

Add 'non-free' to end of deb and deb-src

nano /etc/apt/sources.list

Update and install java

apt-get update
apt-get install apache2 sun-java6-jdk sun-java6-jre libtcnative-1 sudo

Ensure that Java was installed

java -version

Set JAVA_HOME

nano ~/.bashrc

Add the following at the end of the file, making sure to check the version

export JAVA_HOME=/usr/lib/jvm/java-6-sun 
export CLASSPATH=$CLASSPATH:/usr/share/java/mysql-connector-java-5.1.6.jar
export CLASSPATH=$CLASSPATH:/usr/share/java/mysql-connector-java.jar

Install Tomcat 6 Note: get the cores tar.gz

wget http://people.apache.org/~remm/tomcat-6/v6.0.20/bin/apache-tomcat-6.0.20.tar.gz	
tar -zxvf apache-tomcat.....tar.gz
mv apache-tomcat-6.0.20/ /usr/local/tomcat

Create tomcat Group/user

groupadd tomcat
useradd -g tomcat -d /usr/local/tomcat tomcat
usermod -G www-data tomcat

Set Password

passwd tomcat VIVO123

Create the INIT File for Tomcat with the following text added:

nano /etc/init.d/tomcat
	
# Tomcat auto-start description: Auto-starts tomcat processname: tomcat pidfile: /var/run/tomcat.pid
	
	export JAVA_HOME=/usr/lib/jvm/java-6-sun
	case $1 in
	start)
	sh /usr/local/tomcat/bin/startup.sh
	;;
	stop)
	sh /usr/local/tomcat/bin/shutdown.sh
	;;
	restart)
	sh /usr/local/tomcat/bin/shutdown.sh
	sh /usr/local/tomcat/bin/startup.sh
	;;
	esac
	exit 0

Adjust permissions

	
chmod 755 /etc/init.d/tomcat

Add for auto-start on boot

update-rc.d tomcat defaults

Modify the default users file with the following:

nano /usr/local/tomcat/conf/tomcat-users.xml
		
	<tomcat-users>
	<role rolename="manager"/>
	<role rolename="admin"/>
	<user username="VIVO" password="VIVO123" roles="admin,manager"/> </tomcat-users>

Restart tomcat

/etc/init.d/apache2 stop
/etc/init.d/tomcat restart 
/etc/iinit.d/apache2 start

Test Admin

http://localhost:8080/manager/html/list

Enter username/password as shown here

	
Username: VIVO
Password: VIVO123

Install VIVO

Create a VIVO user for deployment

	
useradd vitro
passwd vitro

Enter new password:

	
vitro123

Add user to sudoers file

nano /etc/sudoers

Change the following line

root,vitro	ALL=(ALL) ALL

Stop Tomcat

/etc/init.d/tomcat stop

Install more required packages

apt-get update
apt-get install subversion-tools sudo ant mysql-server-5.0 libmysql-java

Mysql root password is set to

vitro123

Download latest repository of VIVO

cd /tmp
wget https://downloads.sourceforge.net/project/vivo/VIVO%20Application%20Source/rel-1.1.tar.gz
tar -zxvf rel-1.1.tar.gz

Move downloaded directory

mv vivo-rel-1.1 /usr/local/vivo

Edit deploy.properties

cd /usr/local/vivo
mv example.deploy.properties deploy.properties
nano deploy.properties
VIVO.defaultNamespace=http://localhost/vivo/
VIVOConnection.DataSource.url=jdbc:mysql://localhost/VIVOdb
VIVOConnection.DataSource.username=VIVO
VIVOConnection.DataSource.password=VIVO123

Create directories as required in deploy.properties

mkdir /usr/local/vivo/data
mkdir /usr/local/vivo/data/uploads
mkdir /usr/local/vivo/data/luceneIndex

chown tomcat:www-data /usr/local/vivo/data/uploads
chmod 775 /usr/local/vivo/data/uploads 

chown tomcat:www-data /usr/local/vivo/data/luceneIndex
chmod 775 /usr/local/vivo/data/luceneIndex

Edit globalbuild.properties in config

cd /usr/local/vivo/vitro-core/config
mv example.globalbuild.properties globalbuild.properties
nano globalbuild.properties 

java_api=/usr/lib/jvm/java-6-sun

Create the source.home directory as required in globalbuild.properties file

mkdir /usr/local/src/Vitro
chown tomcat:www-data /usr/local/src/Vitro
chmod 775 /usr/local/src/Vitro

Create an empty MySQL database (password vitro123)

mysql -u root -p
CREATE DATABASE vitrodb CHARACTER SET utf8;
CREATE USER 'VIVO'@'localhost' IDENTIFIED BY 'vitro123'; 
GRANT ALL ON *.* TO 'VIVO'@'localhost';
quit;

Deploy vivo and start tomcat

	
/etc/init.d/tomcat stop
cd /usr/local/vivo
ant all

After a successful build, start Tomcat

	
/etc/init.d/tomcat start

Test application at

	
http://localhost:8080/vivo

Installation of Mod_Proxy

Enable the following Modules in Apache

a2enmod proxy	
a2enmod proxy_http

Setup support in your servlet container

Note: Be careful that there is no direct HTTP listener opened by the servlet container. If, for example, there's an HTTP connector listening on port 8080 and no interceding firewall, users would be able to directly access the servlet on port 8080, which bypasses Apache. This also means they would bypass Shibboleth authentication and authorization.

nano /usr/local/tomcat/conf/server.xml

Make sure the following is in your server.xml file

	<!-- Set context path for access to 8080 over port 80 -->
	<Connector port="8080" maxHttpHeaderSize="8192"
	maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
	enableLookups="false" redirectPort="8443" acceptCount="100"
	connectionTimeout="10000" disableUploadTimeout="true"
	proxyName="YOUR.DOMAIN.EDU" proxyPort="80"/>

	<!-- Set context path for access over SSL -->
	<Connector port="8443" maxHttpHeaderSize="8192"
	maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
	enableLookups="false" disableUploadTimeout="true"
	acceptCount="100" scheme="https" secure="true"
	clientAuth="false" sslProtocol="TLS"
	proxyName="YOUR.DOMAIN.EDU" proxyPort="443" />
	
	<!-- Set docBase for root webserver application -->
	<Host name="localhost" appBase="webapps/vivo">
    	<Context path="" docBase="." />
    </Host>

Configure Apache to route requests to your servlet

Modify your default Apache site configuration to map requests on the proper virtual hosts to your application.

nano /etc/apache2/sites-available/default
	ProxyRequests On
	ProxyPreserveHost On
	ProxyStatus On
	
	<Proxy *>
	    Order deny,allow
	    Allow from all
	</Proxy>

	# Use proxy to restrict the need for a port in the URL
	ProxyPass /vivo/ http://localhost:8080/vivo/
	ProxyPassReverse /vivo/ http://localhost:8080/vivo/

	ProxyPass / http://localhost/vivo/
	ProxyPassReverse / http://localhost/vivo/

Now repeat if your virtual host will be SSL enabled.

nano /etc/apache2/sites-available/default-ssl

Add the following to your virtual host

	ProxyRequests On
	ProxyPreserveHost On
	ProxyStatus On
	
	<Proxy *>
	    Order deny,allow
	    Allow from all
	</Proxy>

	# Use proxy to restrict the need for a port in the URL
	ProxyPass /vivo/ http://localhost:8080/vivo/
	ProxyPassReverse /vivo/ http://localhost:8080/vivo/

	ProxyPass / http://localhost/vivo/
	ProxyPassReverse / http://localhost/vivo/

// Stop and Restart Apache/Tomcat

/etc/init.d/apache2 stop
/etc/init.d/tomcat restart
/etc/init.d/apache2 start

Installing Shibboleth 2

Install the Shibboleth 2.0 Service Provider Packages

apt-get update
apt-get install shibboleth-sp2-schemas libshibsp-dev 
apt-get install libshibsp-doc libapache2-mod-shib2 opensaml2-tools

Enter Shibboleth config directory

cd /usr/sbin/

Generate a key/certificate for Shibboleth

./shib-keygen -h shib.your.domain.edu

Make an SSL directory to store the certs

mkdir /etc/shibboleth/ssl

Copy certs and rename with your hostname

cp -rp /etc/shibboleth/sp-cert.pem /etc/shibboleth/ssl/YOUR.DOMAIN.EDU.cert
cp -rp /etc/shibboleth/sp-key.pem /etc/shibboleth/ssl/YOUR.DOMAIN.EDU.pem

Rename the default XML file

cd /etc/shibboleth
mv shibboleth2.xml shibboleth2.xml.bak

Download the Linux XML config file from your Identity Provider (IDP) at your institution

wget http://YOUR.IDENTITYPROVIDER.EDU/linux.shibboleth2.xml

Rename the XML config file

mv linux.shibboleth2.xml shibboleth2.xml

Configure your XML file per your organizations Identity Provider

You will need to obtain a URN from your IDP.

Enabling Shibboleth Authentication

Add a line to your Apache configuration on the proper virtual host, such as
in httpd.conf, to trigger Shibboleth session initiation and authentication for
your application. The use of ShibUseHeaders On is important.

Edit virtual host

nano /etc/apache2/sites-available/default

Add the following to your virtual host.

You can enter anything to replace "shibauth". For example, you could use "/secure" or just "/" to secure the entire virtual host.

	
# Path for authentication
	<Location /shibauth>
	   AuthType shibboleth
	   ShibRequireSession On
	   ShibUseHeaders On
	   require valid-user
	</Location>

	# Shib Variables Available to entire web server
	<Location />
	  AuthType shibboleth
	  ShibRequireSession Off
	  require valid-user  
	  ShibUseHeaders On
	  require shibboleth
	</Location>

Repeat for SSL enabled site, edit virtual host

nano /etc/apache2/sites-available/default-ssl

Add the following to your virtual host

	<Location /shibauth>
	   AuthType shibboleth
	   ShibRequireSession On
	   ShibUseHeaders On
	   require valid-user
	</Location>

	# Shib Variables Available to entire web server
	<Location />
	  AuthType shibboleth
	  ShibRequireSession Off
	  require valid-user  
	  ShibUseHeaders On
	  require shibboleth
	</Location>

Installing Shibboleth Authentication Plugin

Create the following files:

uf_login_process.jsp
webapp/src/edu/cornell/mannlib/VIVO/webapp/controller/edit/UfAuthenticate.java (Copy of Authenticate.java, Compiled)

Modify the following files:

	about_body.jsp (Add html link to UF Shib Login)
	
		<strong>UF Shibboleth Login</strong><br/>
        <a href="http://vivotest.ctrip.ufl.edu/Shibboleth.sso/Login?
        target=<%= URLEncoder.encode("http://vivotest.ctrip.ufl.edu:8080/VIVO/uf_login_process.jsp" target="_self">Login &raquo;</a>
	
	webapp/WEB-INF/web.xml (Modified to reflect new class)
	
        <servlet> 
                <servlet-name>ufauthenticate</servlet-name> 
                <servlet-class>edu.cornell.mannlib.VIVO.webapp.controller.edit.UfAuthenticate</servlet-class>       
        </servlet> 
        <servlet-mapping> 
                <servlet-name>ufauthenticate</servlet-name> 
                <url-pattern>/ufauthenticate</url-pattern> 
        </servlet-mapping>
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Deprecated. This material represents early efforts and may be of interest to historians. It doe not describe current VIVO efforts.