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Resolve "strange behaviour when retrieving objects from bob.bio.base filelist database query"

Merged Manuel Günther requested to merge 59-strange-behaviour-when-retrieving-objects-from-bob-bio-base-filelist-database-query into master

Closes #59 (closed)

I have implemented a way to create a ListReader object for each protocol. In this way, the #59 (closed) should be solved. However, I have not yet created a test case for that. Just the normal test cases still run (at least on my machine).

@heusch: Could you please test if your problem is solved with this implementation?

There are still several functions that rely on the internally stored self.protocol instead of taking the protocol as a parameter. I think the main reason for that is that some functions overwrite ZTBioDatabase base class functions that usually are not overwritten. Maybe, we can have an optional protocol parameter in these functions and use the same trick as in the others:

if protocol is None:
  protocol = self.protocol

(where self.protocol itself can be None).

@amohammadi: Do you think this is a reasonable approach?

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