i2b2 Upgrade to Version 1.6

To upgrade an instance of i2b2 from version 1.5 to version 1.6 first you need to download the upgrade package from here (when I've put it there) and unzip it into a location on the appropriate server. The process is then as follows:

1. Back up existing system.
2. Change config values.
3. Run scripts and do manual processes.
4. Test upgrade.

These steps are laid out in more detail below.

1. Back up existing system

The following resources need packing up:

1. Databases:
   1. Common databases: hive and PM
   2. Project specific databases: data, work and meta
2. JBoss directory
3. Web client directory

2. Change config values

Config values have to be changed in 2 files in the i2b2-upgrade-1.6/procedures/config directory:

1. config.properties
2. defaults.sh

config.properties

These values are used to update the i2b2 config settings. Add the connection details for common databases and also the project specific databases.

defaults.sh

These values are used by the upgrade scripts. In order for the scripts to upgrade all the projects and their ontologies these should be provided as arrays in the form of space separated strings. For each project in the projects array create a dictionary item in the onotology dictionary containing a list of that project's ontologies (space separated).

3. Run scripts and do manual processes

In order to run the script you will need to become a super user:

sudo su

then cd into the base directory of the upgrade procedures i2b2-upgrade-1.6/procedures and run the following command:

export I2B2_INSTALL_HOME=$PWD

then cd into the script directory i2b2-upgrade-1.6/procedures/bin/installs and do the following procedure:

NB [run identifier] is used to create a working directory for the current run. It can be any valid directory name and must be the same for every script. E.g., 'Upgrade1'

1. Run the script ./1-acquisitions.sh [run identifier] - this downloads the i2b2 packages.
2. Run the script ./2-tailor-jboss.sh [run identifier] - it doesn't do anything, but on the up side it's unlikely that it will go wrong ;)
3. Run the script ./3-data-install.sh [run identifier] - this could go wrong so hold your hats. It runs SQL scripts to upgrade the databases.