[Bioperl-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl

Sendu Bala bix at sendu.me.uk
Thu Jun 26 14:47:18 EDT 2008


Chris Fields wrote:
>> As for a fall-back mechanism, I'm not really sure how that would work. 
>> The easiest thing to do would be to just not deal with the species 
>> lines if Bio::Species doesn't work. Is that an acceptable fall-back? 
>> If not, more thought and discussion is needed. Make a proposal: what 
>> would you want to happen?
> 
> Skipping the Species isn't an option; it's an integral part of the main 
> BioPerl core and would be a PITA to deal with in bioperl-live, let alone 
> bioperl-db.  We would have to wrap every Species-related call in an 
> eval{} and fallback to something else.  Could we just set DESTROY or a 
> root cleanup callback to delete the child/parent node references?

Just to remind everyone, this all first came up here:
http://thread.gmane.org/gmane.comp.lang.perl.bio.general/13623
And the associated bug report is here:
http://bugzilla.open-bio.org/show_bug.cgi?id=2149

I really can't remember now, but there might be problems with your 
suggestion. But by all means try your idea and see if it works. I'll 
take a look at it myself soon.


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