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Can you double check that you are using the latest version from trunk - it sounds like you're running against #55 which has been fixed a couple of days ago.
I've tried replicating your bug (using Hive nevertheless) and I get the same result as in ES.
When Hadoop executes a Job using plugin with one query like the follow:
samples/test/_search?q=*
The Map input 136188 data to map. But in ElasticSearch execute the follow query:
samples/test/_count?q=*
The result is:
{"count": 68094, "_shards":{"total":5, "successful":5, "failed":0}}
My environment is:
Linux, Hadoop 1.2.0 (3 nodes), ES 0.90.1 (3 nodes).
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