I have recently published a code example for using the Kafka Spout that is now part of Storm 0.9.3. After wasting a day fighting with incompatible logging frameworks between Kafka and Storm, I found an example project in Scala that had the necessary exclusions to get the uber-jar to run in Storm cluster mode. I've converted that example to Java and Maven, rather than Scala and sbt, and considerably simplified the examples so you can focus on just one thing: getting Kafka hooked up to Storm using the KafkaSpout.
The code repo is here: https://github.com/quux00/kstorm
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