Upgrading From The Old Version Of The Server To The New

This upgrade document assumes that you had installed a version of the BioCoRE server prior to August 2005, and are wanting to upgrade to a new version of BioCoRE.

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 at that time.

The new interface is nicer looking and more modern with more features, and this means that a lot changed "under the hood", and is going to require you to change several things to get the new server going. If you had installed a server but never really started using it, you might want to just follow the instructions to install a new server and skip the installation of packages that you've already got. That will get you a new setup with an empty database. When you get to the point where you create a maintenance account, simply enter the data that you were given in your initial email from before and the password that you set up.

If you want to upgrade your existing system:

  1. If you are running a really old version of the BioCoRE server, you need to upgrade the BioCoRE server to the newest old version for the database to be in a valid state to handle the upgrade to the new version. For this reason, the latest old version is available for download. (The latest old version is the June 30, 2005 version)
  2. Shut down Tomcat if it is running.
  3. We recommend backing up the BioCoRE database before proceeding. We've tried hard to make sure that the database won't get corrupted during the upgrade, but there is always the possibility of problems.
  4. Make sure that you are running version 5.0.x of Tomcat. Instructions are available to help upgrade if you aren't running Tomcat 5.0.x.
  5. Verify that you have at least Javamail 1.3.1. Look in $BIOCORE_HOME/packages/. You need to copy the mail.jar and activation.jar files into the $BIOCORE_HOME/packages/tomcat/current/common/lib/ directory. If you hadn't already done so.
  6. You might need to download JEP.
  7. Download the BioCoRE server files from our site. Do the steps to install the BioCoRE files and create the biocore.xml file. For the new version fo the server, the biocore.xml file contains the majority of the server configuration items. This file replaces the old collab.properties file, and you should see similarities in the contents of the two.
  8. If you had to install JEP in the earlier step, you will need to use the new version of the .biocoreInstallrc file described in the instructions and then do the install.sh.
  9. Restart Tomcat.
  10. Point your browser to the new admin pages. Previously they were at AdminServlet. Now they are at the location described in the install instructions. When you go to the new admin page, you should see the login page. If you see a page asking for maintenance account setup, that means that something isn't right with the database configuration for your new install. Browse that page if you are having problems.
  11. Assuming you see the login page, type in your old administration password and go to the Parameters page. From there, verify that the values look correct and add if necessary. The install instructions have the details. We were previously using something called webappBaseSecure and webappBaseNonSecure, but this has changed from 'webapp' to 'server'.

Restart Tomcat

You should be upgraded!


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.