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$ mkdir /opt/shrine/upgrade-backups

Remove the old .war files with this command:

$ rm /opt/shrine/tomcat/webapps/*.war

Next, move the current SHRINE webapp folder to the backup location:

$ mv /opt/shrine/tomcat/webapps/shrine /opt/shrine/upgrade-backups/shrine

Make sure to also back up the other existing SHRINE components (shrine-proxy and steward), just in case:

$ mv /opt/shrine/tomcat/webapps/shrine-proxy /opt/shrine/upgrade-backups/shrine-proxy
$ mv /opt/shrine/tomcat/webapps/steward /opt/shrine/upgrade-backups/steward

Make especially sure that the shrine-webclient/ folder is backed up. Later on, we will be restoring important webclient configuration files Next, move the SHRINE webclient to that same backup location. Later on, we will be restoring i2b2_config_data.js from this backup. If you choose not to make any backups, make sure to at least keep a copy of i2b2_config_data.js and js-i2b2/cells/SHRINE/cell_config_data.js!

$ mv /opt/shrine/tomcat/webapps/shrine-webclient /opt/shrine/upgrade-backups/shrine-webclient

Modify Tomcat

You will need to create a file called setenv.sh in Tomcat's bin/ folder to increase the PermGen size given to it. This will prevent OutOfMemoryError messages caused by one of the underlying application libraries. Make sure this file is owned by the same user that runs SHRINE, and make sure it is executable:

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