10.9 Upgrade to OpenClinica 3.2 on Linux

The following process describes how to upgrade Java and Tomcat to work with OpenClinica 3.2 on Linux. Be sure to back up your database before starting the upgrade process.

Before you begin, the following packages should be installed with your Linux operating system:
•    vim
•    unzip
•    tar
(eg:~# apt-get install vim)

You will require "root" user access to your operating system. Run all commands in this guide with a user account possessing root-level permissions.

9.3.1 Upgrade Java 6 to Java 7

9.3.1.1 Preconditions for Upgrading Java

  1. Access OpenClinica at the following URL:
    http://localhost:8080/OpenClinica
    The Login page should display.
  2. Verify the current version of Java is Java 6 by running this command:

    /usr/local/java/jre/bin# ./java –version

 9.3.1.2 Upgrade Java 6 to Java 7

a. For 32-bit operating systems, to get the files from OpenClinica, run:

    wget https://dev.openclinica.com/oc/software/OpenClinica-3.2/linux/jdk-7u51-linux-i586.gz

b. For 64-bit operating systems, to get the files from OpenClinca, run:

    wget https://dev.openclinica.com/oc/software/OpenClinica-3.2/linux/jdk-7u51-linux-x64.gz

The OpenClinica software is written in the Java programming language, so you must have Java installed on your system in order to run the OpenClinica application.

  1. Install Java by running:

    ar -xvf jdk-7u51-linux-x64.tar.gz       (This command is to unzip gz)

    chown –R root:root jdk1.7.0_51            ( to change owner)

    chmod a+x jdk-7*     

  2.  To install the Java in operating system by running
            
    mv jdk1.7* /usr/local/
            
    ln -s /usr/local/jdk1.7* /usr/local/java

    Java is now installed in the correct location. 

9.3.1.3 Verify Java 7 is installed

  1. Verify the current version of the Java is Java 7 by running these commands in root:

    Goto: cd /usr/local/java/jre/bin

    Run:  ./java –version
    (for example: root@bagel:/usr/local/java/jre/bin# ./java –version)

  2. Access OpenClinica at the following URL:
    http://localhost:8080/OpenClinica
    The Login page should display.

 9.3.2 Upgrade Tomcat 6 to Tomcat 7

9.3.2.1 Preconditions for Upgrading Tomcat

  1. Access OpenClinica at the following URL:
    http://localhost:8080/OpenClinica
    The Login page should display.
  2. Stop Tomcat 6 by running the following command:

    /etc/init.d/tomcat stop

  3. Uninstall Tomcat 6 from your system (including all the configuration files) but Before running this command make sure that ,  cd /usr/local.

    rm –rf tomcat

    rm –rf apache-tomcat-6.0.32

9.3.2.2 Install Tomcat 7

  1. The OpenClinica software uses the Apache Tomcat Java application server. Download Tomcat 7 from one of the following sites and copy it into the local folder /usr/local/oc/install/
    Download it from the Tomcat website: http://tomcat.apache.org/download-70.cgi
    - or -
    Download it from the OpenClinica website:  https://dev.openclinica.com/oc/software/OpenClinica-3.2/linux/apache-tom...
    Run the following command in /usr/local/oc/install/ to install Tomcat 7.
    wget https://dev.openclinica.com/oc/software/OpenClinica-3.2/linux/apache-tomcat-7.0.52.tar.gz
  2. The current directory on your system should be /usr/local/oc/install. If it is not, make it the current directory by running:
    cd /usr/local/oc/install
  3. Install Tomcat by running the following:

    tar -zxvf apache-tomcat-7*

    mv apache-tomcat-7.0.52 /usr/local/

    ln -s /usr/local/apache-tomcat-7.0.52 /usr/local/tomcat

    (Note: The system will prompt you to enter your UNIX password. Use “tomcat” as the password, and press enter for all the default value for the full name, room number, phone, home phone and other. Is the info correct? Type Y and enter.)

  4. Move the web apps provided with Tomcat that are not needed by OpenClinica to another location by running:

    mkdir /usr/local/tomcat/oldwebapps

    mv /usr/local/tomcat/webapps/* /usr/local/tomcat/oldwebapps

    Tomcat is now installed and you can set Tomcat to automatically start when you start your system, or you can start Tomcat manually by issuing commands.

    To set Tomcat to start automatically on system startup, run the following: (Note: Before running the command install the OpenClinica 3.2 on your install folder)

    cp /usr/local/oc/install/OpenClinica-3.2*/install-docs/linux/tomcat /etc/init.d/

    cd /etc/init.d

    chmod a+x /etc/init.d/tomcat

    /sbin/chkconfig --add tomcat

    (Note: This command is only for Red Hat Linux. For other operating systems, see the operating system instructions for adding an init script.)

  5. Update the File Path parameter to the correct value

    chown -R tomcat /usr/local/tomcat/*

    chown -R tomcat /usr/local/apache-*

9.3.2.3 Deploy the OpenClinica Software Package

        First, make sure Tomcat is stopped:

  1. Stop Tomcat 7 by running:
    /etc/init.d/tomcat stop
  2. The current directory on your system should be /usr/local/oc/install. If it is not, make it the current directory by running:
    cd /usr/local/oc/install
  3. Run each of the following commands:

    unzip OpenClinica 3.2*

    cd OpenClinica 3.2*/distribution

    unzip OpenClinica.war -d OpenClinica

    cp -rf OpenClinica* /usr/local/tomcat/webapps

    rm -f /usr/local/tomcat/webapps/OpenClinica.war

    OpenClinica is now deployed for use with the database.

9.3.2.4 Verify Tomcat 7 is Started and the Application is Running

  1. Start Tomcat:
    /etc/init.d/tomcat start
    (Note: Replace start with stop to stop the Tomcat service)
  2. Verify Tomcat 7 is running with the following commands. You should see a similar message as shown in the bracket().
    /etc/init.d/tomcat status  (Tomcat is running…)
  3. Access OpenClinica at the following URL:
    http://localhost:8080/OpenClinica
    The Login page should display.

Approved for publication by Benjamin Baumann (bbaumann), Principal. Signed on 2014-03-27 6:45PM

Not valid unless obtained from the OpenClinica document management system on the day of use.