[MOBY-dev] Moby Collections in Taverna
Edward Kawas
edward.kawas at gmail.com
Wed Apr 19 14:50:52 UTC 2006
Hi Dirk,
You are right about the documentation and I plan on updating it today, but I
want to outline what the behaviour is now:
Service Output ----Connects to ---> Service Input
1 Simple Simple
2 Simple Collection
3 Collection Simple
4 Collection Collection
5 CollAsSimples Simples
6 CollAsSimples Collection
Note that CollAsSimples transforms a collection into a list of simples.
Case 1, 4 are straight forward - the output is passed to the input as is.
Case 2, 6 - the simple (or a 'taverna list' of simples) are placed in a
collection and passed to the service.
Case 3 - the collection is broken down and each simple in the collection is
passed to the downstream service one at a time (in a single invocation message).
i.e.
<MOBY>
<mobyContent>
<mobyData queryID="a0">
<Collection>
<Simple>1</Simple>
<Simple>2</Simple>
<Simple>3</Simple>
<Simple>4</Simple>
</Collection>
</mobyData>
</mobyContent>
</MOBY>
Becomes
<MOBY>
<mobyContent>
<mobyData queryID="a0_1">
<Simple>1</Simple>
</mobyData>
</mobyContent>
</MOBY>
<MOBY>
<mobyContent>
<mobyData queryID="a0_2">
<Simple>2</Simple>
</mobyData>
</mobyContent>
</MOBY>
<MOBY>
<mobyContent>
<mobyData queryID="a0_3">
<Simple>3</Simple>
</mobyData>
</mobyContent>
</MOBY>
<MOBY>
<mobyContent>
<mobyData queryID="a0_4">
<Simple>4</Simple>
</mobyData>
</mobyContent>
</MOBY>
Case 5 - The collection became a list of simples and this case becomes similar
to case 1.
Eddie
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase
> Sent: Wednesday, April 19, 2006 6:46 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Moby Collections in Taverna
>
> Hi Eddie,
>
> On Thursday 13 April 2006 15:56, Edward Kawas wrote:
> > Hi Dirk,
> >
> > The output port behaviour has been cloned for collections
> with a new
> > port, Collection 'As Simples'. So that port now takes the n
> items in a
> > collection and produces n simples that Taverna can iterate over.
>
> Wow, that's what I call a prompt fix!
>
> > However, if that port isn't used and a collection is passed to a
> > service that expects a simple, I transparently break apart the
> > collection with n items into n invocations containing a simple and
> > then invoke the service n times, rather than one time with a n
> > invocation message. This was done, because I noticed that
> there were
> > time out issues with very large collections.
>
> OK, I see this behavior when I use the 'output' port. For the
> old collection-type port 'Object(Collection -
> <outputArticleName>)' things are
> strange: it seems that only the first element in the
> collection is piped to the next service.
>
> However, I think this solution is very convenient. The
> drawback is that we now have three distinct types of output
> ports for moby services, this will confuse people. What I
> want to say is that good documentation is desperately needed ;-)
>
> Thanks,
> dirk
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