[moby] Re: [MOBY-dev] how to handle errors in a biomoby service?

[Mark Wilkinson]

On Wed, 2005-08-17 at 13:12 +0200, David González Pisano wrote:

> We understand that the articleName attribute in Simple / Collection tags 
> is the "anchor point" we have to use to refer to that Simple / 
> Collection. Referring to Simples / Collections / Simples into collection 
> using articleNames give us more granularity than referring to mobyDatas 
> using queryIDs. There is no need to create another additional 
> "identifying" attribute if we can identify the entity we are reporting 
> an error for.

This is the only problematic part of the solution, since it requires a
potentially troublesome change to the API.  For this solution, you
require all of the Simples in a Collection to have a unique articleName
tag.  At present, they likely have no tag at all (since this is not
mandated by the API), and at best will all have the *same* tag even if
we mandate that all output parameters must have an article name.  If we
make the value of this tag auto-generated (like an auto-increment field
in a database), then it adds a new meaning to articleName, so let's just
not pursue this possibility any further :-)  Whatever solution we come
up with, it cannot use articleName as its primary means of identifying
the failed entity.


> - The error tag has to use an attribute to refer to the corresponding 
> failing simple / collection. We can call this attribute exceptionRef, 
> articleNameRef or something similar, to avoid using articleName again in 
> a different context, but

Super!


> - We are referring to the erroneus entity using its articleName, and 
> that's why the articleName has to be mandatory (note that this is a 
> significant change in the bioMOBY specification, but we can't figure out 
> any other way to report errors at this level)

I'm not sure why we need two ways of referring to the same entity?

M



-- 
"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
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