[BioSQL-l] null title and CRC

[Hilmar Lapp]

I think I need to debug this. If bioperl-db stumbles over this, then  
it sounds like that's what needs to be fixed.

Can you or somebody else provide with two sample records that  
exemplify (i.e., replicate) the problem and which I can turn into a  
test case?

	-hilmar

On Aug 3, 2006, at 2:12 PM, Angel Pizarro wrote:

>  From hilmar:
>> The CRC for references uses the authors, title, and location
>> attributes in Bioperl-db, and empty (or null) strings default to the
>> string "<undef>".
>>
>> If title is empty and authors and location do not distinguish two
>> references, then why do you want to have two rows for those
>> references? Basically, there are identical for all intents and
>> purposes, or are they not?
>>
>> 	-hilmar
>
> Sorry for not replying to the original thread, but I just joined  
> this list.
> This was an issue for me with bioperl loading as well, since I was  
> using
> the same biosql instance to load two different biodatabases with the
> same entry. Specifically, I loaded IPI, which has no feature table in
> the entries, and the genbank equivalents to get the feature tables.
> Namely the constraint caused an error when the the genbank record was
> loaded.
>
> I think that this is primarily an issue with bioperl, but I raise it
> here to make the java folks aware of the potential pitfall and  
> maybe ask
> if whether the CRC should be calculated with the biodatabase in mind?
> Probably not, since as hilmar states, it's still the same reference.
>
> BTW - I solved the issue by dropping the constraint, since I really
> don't care about references. Not optimal, but certainly easiest  
> thing to
> do ;)
>
> -angel
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================