[moby] [MOBY-dev] Re: Problems with Biomoby services in Taverna 1.2

[Heiko Schoof]

Well, if I understand you correctly, Mark, than I was right all along 
in that they way I see collections is the way they should be seen. Then 
the problem is that that is not clear enough to everybody else, and 
that possibly the examples in the API are misleading, because it's been 
used in such a different way. It's definitely something that needs to 
be fixed before release 1.0.

If I understand Tom correctly, the problem mainly appeared because the 
BioMoby support was rapidly and effectively incorporated into Taverna 
without proper integration, and what needs to happen is to define e.g. 
the iteration strategy for BioMoby: Taverna so far doesn't use the 
possibility to bundle multiple queries in a single BioMoby message, 
which is not a problem, but the Collection issue could point to a need 
for us BioMoby guys to look in more detail at Taverna data types and do 
a sound mapping.
Heiko

On 7. Jul 2005, at 22:07 Uhr, Mark Wilkinson wrote:

On Thu, 2005-07-07 at 17:34 +0200, Heiko Schoof wrote:

> I myself am confused about the use of collections. Originally I had in
> my mind that Collections were a construct to allow objects that
> inherently belong together to be "bagged".

You are 100% correct here.


> The confusion starts with the output of services. My understanding was
> that ONLY a service that is guaranteed to output exactly one object for
> each query (e.g. an averaging service that outputs the average of a
> list of inputs) is registered as outputting a Simple, all others have
> to output collections

No.

>  (as there must be exactly one mobyData matching
> the queryID of the input in the response,

Yes

>  and a mobyData may contain
> multiple Simple elements only if wrapped by a Collection).

No.  A mobyData element can wrap any number of outputs, and/or
combinations of simples, collections, and secondaries.



> In practice, the Collection tag has been used to indicate when more
> than one Simple occurs, with no "semantic" meaning. This imho is not
> necessary; when more than one Simple occurs, why not put more than one
> Simple? It's easy enough for everyone to figure that out. Then,
> Collection could be used to actually transfer meaning ;-)

I think a lot of people are using Collections incorrectly, yes.



> make things clearer, also to e.g. the Taverna developers: Getting back
> many Simple articles in response to a query very intuitively indicates
> to continue on with each one individually, whereas getting back a
> Collection indicates to put the whole thing as input into the next
> service, which is what they implemented. Makes perfect sense, as there
> can and will be services that consume Collections.

I don't think that Taverna handled collections correctly in the past,
and it would be a shame if that identical functionality was added back
in :-)  The functionality does need to go back into Taverna, but
correctly this time.



> Maybe I've made myself clear, maybe not. Anyway, the Collection issue
> has led to quite some discussions between Rebecca, Dirk and myself, and
> we are all not happy with the way they are currently handled.

I don't know if you are happier with them now that I have pointed out
where you are misinterpreting them...??

I agree, however, that their usage by many service providers is not
correct... but there's no way for MOBY Central to know that it isn't
correct, so we can't throw an error on registration of these "wonky"
services...

M



-- 
Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Vancouver, BC


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