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

Chris Fields cjfields at uiuc.edu
Thu Jun 26 16:41:08 EDT 2008


On Jun 26, 2008, at 1:47 PM, Sendu Bala wrote:

> 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.

Double-checked, DESTROY wouldn't be called unless all references to  
the root node were removed.  weaken() is really the best option; it  
might be possible to wrap everything in a proxy object if weaken  
doesn't work (though it's a bit of a hack):

http://www.perl.com/pub/a/2002/08/07/proxyobject.html?page=3

chris


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