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In my own usage, I manage the secondary tables at the application level. This is faster but less safe.
I have plans to add a less safe, but fast server-side implementation of this in the future for my own purposes. But I also heard there's a chance OCC will be pluggable for the current implementation, in which case I'd just use that. Sign up to the mailing list, 0.20.0 release coming up soon and that will be determined for that release.
http://hadoop.apache.org/hbase/docs/current/api...
Which I'll look into and post about if it's useful.
Have you considered using a search server for the indexing/searching and hbase for storing?
You'd have to keep them in sync of course, but solr is quite useful. You can optimize for just returning ids, by indexing fields and not storing them and there is progress on sharding if you really need it. It doesn't scale to billions of rows of course, but it unlikely that will be a problem for users. You can do exact matches on any of the fields, and of course utilise full text searches where appropriate.
Thinking about it again, I may just look at both implementations in more depth because it may be a better way to go especially as indexes start to pile up.