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

[Rebecca Ernst]

Hi Tom and others

This Taverna behaviour described below makes perfect sense to me! Does 
Taverna then check in MOBY-Central how this service is registered 
(taking simples or collections)?

I guess the way to go would be to:
1. change the Taverna behaviour back to how it is supposed to work (and 
did in 1.1)
2. - change the BioMoby Perl code to allow more than one simple in the 
MobyData AND
    - change almost all services that output collections to the way we 
discussed yesterday (only output collections if the objects build an 
entity. )

Either of the two changes solves the problems but I believe both are due 
to changes and should take place.

Best,
Rebecca





Tom Oinn wrote:

> That's kind of true, meaning actually not. There are three cases 
> involving collections (Taverna 1.1 behaviour) :
>
> 1) Consumer declares it consumes singles, Producer emits a collection. 
> In this context Taverna iteratively calls the Consumer with each item 
> from the collection. This is probably what you'd expect to happen, the 
> result is that the Consumer effectively emits a collection of whatever 
> it would emit normally.

> 2) Consumer declares it consumes a collection, Producer emits a 
> collection. In this case Taverna will indeed split the output 
> collection (because we always do) but it will be magically reassembled 
> before being given to the Consumer.
>
> 3) Consumer declares it consumes a collection, Producer emits a single 
> item. Taverna wraps the single item in a single element collection and 
> gives it to the Consumer.
>
> The intent is that as with the other plugin types Taverna guarantees 
> that the service sees the inputs it has asked for. Our experience with 
> other service types suggests that this is an extremely powerful 
> mechanism as it allows interoperability between services that would 
> otherwise mismatch - it's worth noting that our users expect these 
> services to match, while a CS perspective regards ProteinSequence and 
> ProteinSequence[] as completely different types most of our biologists 
> don't! Taverna behaves the way _they_ expect it to, remember who your 
> user are.
>
> Taverna data types are pretty much trivial, they're opaque data blobs 
> with the exception of collection structure which is exposed. We only 
> expose the collection structure to ensure the above properties, other 
> than that the framework is data agnostic (as it should be).
>
> Tom
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de