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Installation instructions for VIVO 1.1 on Debian OS.

Warning

Obsolete: This page was written for VIVO 1.1 - it is no longer correct.

We will attempt to revise this page to work with newer releases. In the meantime, please check the current installation instructions: VIVO Installation Instructions

Install Apache 2 and Tomcat 6

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

No Format
nano /etc/apt/sources.list

Update and install java

No Format
apt-get update apt-get install apache2 sun-java6-jdk sun-java6-jre libtcnative-1 sudo

Ensure that Java was installed

No Format
java -version

Set JAVA_HOME

No Format
nano ~/.bashrc

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

No Format
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

No Format
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

No Format
groupadd tomcat useradd -g tomcat -d /usr/local/tomcat tomcat usermod -G www-data tomcat

Set Password

No Format
passwd tomcat VIVO123

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

No Format

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

No Format
chmod 755 /etc/init.d/tomcat

Add for auto-start on boot

No Format
update-rc.d tomcat defaults

Modify the default users file with the following:

No Format
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

No Format
/etc/init.d/apache2 stop /etc/init.d/tomcat restart /etc/iinit.d/apache2 start

Test Admin

No Format
http://localhost:8080/manager/html/list

Enter username/password as shown here

No Format
Username: VIVO Password: VIVO123

Install VIVO

Create a VIVO user for deployment

No Format
useradd vitro passwd vitro

Enter new password:

No Format
vitro123

Add user to sudoers file

No Format
nano /etc/sudoers

Change the following line

No Format
root,vitro ALL=(ALL) ALL

Stop Tomcat

No Format
/etc/init.d/tomcat stop

Install more required packages

No Format
apt-get update apt-get install subversion-tools sudo ant mysql-server-5.0 libmysql-java

Mysql root password is set to

No Format
vitro123

Download latest repository of VIVO

No Format
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

No Format
mv vivo-rel-1.1 /usr/local/vivo

Edit deploy.properties

No Format


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

No Format


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

No Format
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

No Format
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)

No Format
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

No Format
/etc/init.d/tomcat stop cd /usr/local/vivo ant all

After a successful build, start Tomcat

No Format
/etc/init.d/tomcat start

Test application at

No Format
http://localhost:8080/vivo

Installation of Mod_Proxy

Enable the following Modules in Apache

No Format
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.

No Format
nano /usr/local/tomcat/conf/server.xml

Make sure the following is in your server.xml file

No Format


	<!-- 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.

No Format


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.

No Format
nano /etc/apache2/sites-available/default-ssl

Add the following to your virtual host

No Format


	ProxyRequests On
	 ProxyPreserveHost On
	 ProxyStatus On
	
	 <Proxy *>
	 Order   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

No Format
/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

No Format
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

No Format
cd /usr/sbin/

Generate a key/certificate for Shibboleth

No Format
./shib-keygen -h shib.your.domain.edu

Make an SSL directory to store the certs

No Format
mkdir /etc/shibboleth/ssl

Copy certs and rename with your hostname

No Format
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

No Format
cd /etc/shibboleth mv shibboleth2.xml shibboleth2.xml.bak

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

No Format
wget http://YOUR.IDENTITYPROVIDER.EDU/linux.shibboleth2.xml

Rename the XML config file

No Format
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

No Format
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.

No Format

	
# 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

No Format
nano /etc/apache2/sites-available/default-ssl

Add the following to your virtual host

No Format


	<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:

No Format
uf_login_process.jsp webapp/src/edu/cornell/mannlib/VIVO/webapp/controller/edit/UfAuthenticate.java (Copy of Authenticate.java, Compiled)

Modify the following files:

No Format

	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<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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