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Tracking missing cobertura code coverage

I had recently plugged in code coverage tool cobertura in our startup and got X% of coverage and was happy because this is the first time we had testcases and code coverage working in jenkins.  I was happy and we were planning to steadily increase this code coverage but then one of the developer complained that some of the jersey tests were showing proper coverage but the server classes calling it were not showing any coverage at all.  When I had initially plugged in the coverage tool I had seen server classes showing coverage and those classes are still  showing coverage.  I thought this has to do with the grizzly rest container we were using for Jersey test.  Then while tracing missing code coverage like a detective I had an Aha moment.  Our code structure is something like

module
     server
          src
          src_test
     ui
          src
          src_test

The ui module depends on server module classes for testcase execution. I had a common_module.xml ant build file that is imported by both server  and ui module. The way I was calculating coverage is to run first instrument task and then run test and put build/instrumented_classes before the classpath.

Well it turns out the server classes were showing coverage for only code called by server/src_test and not by ui/src_test. The reason is that when I was running ui tests I was using only build/instrumented_classes whereas I also need to include ../server/build/instrumented_classes. 

Just adding that gave a solid 10% jump in code coverage :).

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