The only way to invoke anything on GAE is via a HTTP request. You can make HTTP requets from command line (OS-specific), for example.
To supplement Peter's answer above, if you're just trying to test and debug your code, you may want to use a unit test. This document explains local unit testing for Java App Engine. In particular, you'll be interested in writing datastore tests, which uses an in-memory implementation of the datastore (and flushes the contents between tests).
Because these tests are based on JUnit, you can run them from the command line, or through the IDE of your choice.
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