Occasionally something may go wrong with your webapp - your webapp may fail to load in your browser, not reflect your most recent changes and so on. In our experience, following the steps listed here should fix ~99% of any problems you encounter.
Restarting Tomcat may fix your issue. If you find you have to restart Tomcat often, you may want to give Tomcat more memory.
Also, if in a deadlock, Tomcat may not shutdown successfully. Be sure to check the Tomcat process really is gone before starting a new one.
The base-url property must valid or else queries will not run properly.
This file must live in the .intermine directory.
If you are using Tomcat 7, please make sure you have configured it correctly. See Tomcat
Run this command in your webapp directory:
$ ant clean-all
Verify /build is gone from your webapp directory.
$ ant default remove-webapp release-webapp