I am using Lucene to index as well as to store complete source documents 
(typically few tens of thousands of documents, not millions). I would like 
to protect the source documents with encryption but have the following 
questions:
Is it possible to reconstruct a complete source document from the data 
stored in the index, even if the fields are only indexed but not stored? 

-- Don't think so, especially if you remove stop words or use a stemming 
analyzer, etc.

Because if the answer is "yes" there is no point in encrypting, unless the 
index itself can be encrypted. Is it feasible to encrypt the index?

-- I believe there are file-system level "things" that migt allow that (e.g. 
encrypt the directory with the index)

If some of the source document fields are also stored in the index, can they 
be encrypted after indexing (and decoded following a search) without any 
side effects?

-- I'll let somebody else answer that.

- Bill Clinton





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