BioCoRE - Biological Collaborative Research Environment

Upgrading Tomcat 5.0.x to 5.0.y

We are going to assume that you installed BioCoRE into $BIOCORE_HOME as discussed in the installation instructions and that you followed the installation instructions for installation.

This example upgrade upgrades from Tomcat 5.0.25 to Tomcat 5.0.28.

In the packages directory, find a subdirectory called tomcat. In the tomcat directory, uncompress the new Tomcat file that you downloaded. Use the GNU version of tar. This will create a directory called jakarta-tomcat-5.0.28 (to go along with the 5.0.25 directory that you already have) At this point, leave the symlink pointing to 5.0.25 until you are told to update it below.

IMPORTANT: In the new Tomcat directory make sure that the temp, work, and logs directories are owned by the user that will be running Tomcat.

Copy files over from older version of Tomcat

You will need to copy the server.xml file over from the older version of Tomcat to the newer. It is in the conf/ subdirectory. Note: It is wise to verify that formatting, etc hasn't changed in the file before you just copy the old one on top of the newer version. In addition, if you have modified or added any other files, those will need to be copied in. (If you modified tomcat-users.xml you will need to copy that over. (Check in webapps/ROOT and see if you have put any files in there. Also check to see if you have put the server certificates somewhere in the Tomcat tree) (Note, if you were using the favicon.ico file, be sure to add the following to the web.xml file in the conf directory: 
  <mime-mapping>
    <extension>ico</extension>
    <mime-type>image/x-icon</mime-type>
  </mime-mapping>

Copy over the biocore*.xml file(s) from current/conf/Catalina/localhost to the new conf/Catalina/localhost directory.

Copy mail.jar and activation.jar from current/common/lib to the new common/lib.

Shutdown the old Tomcat

Shutdown the old Tomcat server that is running.

Update current symlink

Delete the current symlink the Tomcat directory, and create a new one that points to the 5.0.28 version of Tomcat.

Install BioCoRE files

If you installed via:
  • BioCoRE distribution download:
    In the MySQL installation step you should have unpacked a biocore.war file.

    Change to the $BIOCORE_HOME/packages/tomcat/current/webapps directory and create a subdirectory called biocore. Change to the new directory you just created, and unpack the biocore.war file. 

    $BIOCORE_HOME/java/current/bin/jar xvf /PATH/TO/biocore.war
    This will uncompress the WAR file.

  • Source Distribution:
    do an 'ant deploy'.

Run install script

Run the install.sh script that came in the BioCoRE tar file that you originally downloaded. The script might not be executable. If this is the case you will need to chmod it first.

Delete unnecessary webapps

You don't need webdav/, tomcat-docs/, jsp-examples, balancer or servlets-examples/ in the webapps directory. You can delete these directories. In addition, you will need to delete the balancer.xml file from conf/Catalina/localhost (not for 5.5.x).

Restart Tomcat

You should be upgraded!

Feedback

The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.