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Upgrading
PWM 1.7+ - You will need to define PWM_APPLICATIONPATH environment variable. You can set this within the setenv.sh script in tomcat when it start's up. Example, export PWM_APPLICATIONPATH=/opt/pwmdata , if you renamed the war to something else such as mypwm then it would read, export MYPWM_APPLICATIONPATH=/opt/mypwmdata
PWM 1.8+ - Your config files and LocalDB would be located where you defined PWM_APPLICATIONPATH and not necessarily in /WEB-INF/. For example, PWM_APPLICATIONPATH=/opt/pwmdata then /opt/pwmdata would replace /WEB-INF/ below.
JDK Version - Ensure you update your JDK if needed.
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Stop the tomcat service
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Copy your pwm application directory to a location outside of tomcat
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Additional measure: Copy /WEB-INF/PwmConfiguration.xml and /WEB-INF/LocalDB to a location outside of tomcat
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If you made other changes, such as sql drivers/jars, theme, copy those also. You can also add those to tomcats global lib directory so that you don't always have to copy them off.
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Delete the existing pwm directory and pwm.war from tomcats webapps directory
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Delete pwm directory from tomcats /work folder , such as /var/lib/tomcat7/work/Catalina/localhost/pwm which is a symlink to /var/cache/tomcat7/Catalina/localhost/pwm
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Copy the new pwm.war to tomcats webapps directory
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Start Tomcat and let it deploy the new application. Wait until it finishes and then Stop tomcat.
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Copy LocalDB and PwmConfiguration.xml back to webapps/pwm/WEB-INF/
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Start tomcat