[moby] [MOBY-dev] Re: API Change/Recommendation/Best-Practice/Meme Proposal

[Mark Wilkinson]

The "virtual decomposition" of objects that MOBY does during service
discovery can be switched on/off.  Switching it off will prevent this
behaviour also if it is an immediate concern.

M


On Wed, 2005-07-13 at 14:27 +0200, Heiko Schoof wrote:
> Hi Paul,
> thanks for the nice writeup. I agree.
> 
> I just want to stress that I find one of the consequences you mention a 
> very important argument for doing this: Services that act on Strings 
> will no longer automatically be discovered starting from e.g. 
> NCBI_BLAST_OUTPUT or DNA_SEQUENCE, but only when using object 
> decomposition.
> 
> Best, Heiko
> 
> On 8. Jul 2005, at 20:26 Uhr, Paul Gordon wrote:
> 
> Hi everyone,
> 
>     At long last after our discussions at the last MOBY meeting in 
> Vancouver, I have written a little document explaining the reason for 
> and consequences of not inheriting from "primitive" objects such as 
> String and Integer.  I think that this is a distruptive change for only 
> a few services, but is of great benefit.  Please see
> 
> http://coe02.ucalgary.ca/gordonp/moby_primitives.html
> 
> Mark has suggested that this not be a formal change to the API, but 
> that this new way of doing things be encouraged in all of the 
> documentation, and the old method explicitly deprecated but not 
> disabled.  Hopefully most of you agree, and we can just make temporary 
> exceptions in our code for the current non-compliant classes.  Or even 
> better, if most people agree, we can force the affected services to 
> change over. :-)
> 
> P.S.  Yan, your object browser came in quite handy while I was writing 
> this, nice work!  One suggestion though, arranging the objects 
> alphabetically in the tree (when within the same branch and level) 
> would help ease navigation.
> 
> P.P.S. Our Web server will be down briefly this afternoon, so you may 
> get a timeout/cannot connect on the link.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274