Installation instructions for VIVO 1.1 on Debian OS.
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
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 »</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> |