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How secondary index works with Phoenix. I have an HBASE database setup, which is updated via direct insertion in HBASE and not via Phoenix insert queries. But all the select will be done via Phoenix select queries. Will Phoenix secondary indexes still work in those select queries?

Saurabh
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You need to use Phoenix API to write data to Phoenix tables for your secondary index to have the correct state. If you skip Phoenix api then it would not know when to update secondary index. Skipping Phoenix api is a bad design

Basically, Phoenix uses some client side logic and Coprocessors to accomplish most of the advance features of Secondary Indexing.

Anil Gupta
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