[Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Apr 6 23:17:03 EDT 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2337





------- Comment #3 from cjfields at uiuc.edu  2008-04-06 23:17 EST -------
(In reply to comment #2)
> Naohisa is right, the spec says that some meta-data should go into a BerkeleyDB
> db. But it looks like what Lincoln did was to put information on primary and
> secondary namespaces in a human-readable file called config.dat. He did not put
> it into a BerkeleyDB db. His decision was the correct one, this information
> should be human-readable. Of course for OBDA to work across platforms Bioperl
> has to do what the other platforms do, even if it's not the right approach.
> Hmm.

I agree the namespace info should be human-readable.  Maybe the best solution
is to require BDB  storage as stated in the OBDA spec, and modify the spec to
(optionally) allow adding human-readable data to config.dat.  

Might be something to bring up at BOSC, to see how other OBDA implementations
in other Bio* langs are doing this.


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