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I've started playing around with mongodb and was trying to set up a field collection with the fields using mongodb field storage. What I have found is that while I am able to save the data without any issues, a render of the content brings up an EntityFieldQueryException (
No entity type).
Looking through the code, I see that field_collection.module calls on entityfieldquery but does not provide the type.
Will attach a patch in a followup post.