[MOBY-dev] MobyServices and Taverna workflow problems

[groscurt at mpiz-koeln.mpg.de]

Hi Eddie,

thanks for your answer. Unfortunately we cant send you currently an
example because we  *fixed* our problem... but we try to recreate the
error and then send you a copy.

I think your answer covers my problem, but then the questions is why does
the error occurred. The problem is that one service returns an object with
a specific articlename and the next service consumes the same object type
with a different articlename.

Like "I give you an AminoAcidSequence which is named sequence" - the other
response "I want an AminoAcidSequence which is named seq."

The second webservice then looks in the XML for something called seq and
does not find that because we have sequence -> nullpointerexception thrown
by the second webservice.

When I understand you correctly this should be handled by taverna - so
either there is a bug, or the problem is a total different one.

We try to recreate the situation and send you the workflow.

thanks
andreas

PS: we *fixed* this by naming all in- and outputs the same and then it
worked.....

> Hi Andreas,
>
>>From the first reading, I thought that you had a workflow that didnt
> work... From reading it again, it sounds like you are asking whether
> or not you have to worry about the article names in Taverna. Article
> names are automatically discovered and the correct one is used in
> Taverna. If you have a case where this might not be the case, then
> please let me know.
>
> The only things that a user of Taverna needs to take into account when
> using moby is to make sure that they supply the correct namespace and
> data for any particular service. Articlenames are taken care of, even
> though if you look in the intermediate input/output browser and the
> articlename is not what it's supposed to be.
>
> Does this answer your question?
>
> Thanks,
>
> Eddie
>
> On Nov 13, 2007 6:30 AM, Eddie Kawas <edward.kawas at gmail.com> wrote:
>> Hi Andreas,
>>
>> Can you send me an example workflow?
>>
>> Thanks,
>>
>> Eddie
>>
>>
>> On Nov 13, 2007 2:52 AM,  <groscurt at mpiz-koeln.mpg.de> wrote:
>> > Hi all,
>> >
>> > we have a problem concerning BioMoby webservices in taverna and we
>> hope
>> > one can help us out.
>> >
>> > We have two Webservices which e.g. one returns an object with the
>> > articlename 'sequence', the other has this object as input with the
>> > articlename 'seq' (as simple example).
>> >
>> > Now we tried to connect this services into a workflow and taverna
>> returned
>> > a NullPointerException apparently in the skeleton class of the second
>> > service, because it looks for 'seq' in the xml, but we only have
>> > 'sequence'.
>> >
>> > I'm not quite sure if this is the problem, but how is it possible to
>> > connect arbitrary services without taking care of the articlename ?
>> >
>> > What do we have to take into account when using a Biomoby webservice
>> for
>> > taverna ?
>> >
>> > the solution of having always the same articlename is working, but i
>> guess
>> > this is not intended...
>> >
>> > thanks in advance
>> > andreas
>> >
>> > _______________________________________________
>> > MOBY-dev mailing list
>> > MOBY-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/moby-dev
>> >
>>
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