[MOBY-l] MOBY tutorial - Taverna

['Nassib Nassar']

Hi Eddie,

Thanks.  Note that if you simulate this problem by setting
<moby:Simple moby:articleName=''> in the sample XML input (in_test),
it generates a very different kind of error - Taverna reports that the
process completed (not failed) and returns a MOBY object containing an
exception:

java.lang.IllegalArgumentException: While executing service: required
primary value "inseq" in job 1 is missing

So while that is a problem, the error I'm getting is different and
appears to be an even more basic problem.

Nassib


On Thu, Nov 02, 2006 at 12:23:00PM -0800, Edward Kawas wrote:
> Hi Nassar,
> 
> It seems that the articlename for the input isnt being set. I will look into
> this further.
> 
> Thanks,
> 
> Eddie
> 
> > -----Original Message-----
> > From: moby-l-bounces at lists.open-bio.org 
> > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Nassib Nassar
> > Sent: Thursday, November 02, 2006 11:58 AM
> > To: moby-l at lists.open-bio.org
> > Subject: [MOBY-l] MOBY tutorial - Taverna
> > 
> > (Thanks to Paul for the test client fix.)
> > 
> > I'm having trouble using the ConvertAAtoFASTA_AA servlet 
> > example from within Taverna.  I made a simple workflow to 
> > test this, and everything works perfectly if I send the 
> > biomoby service a fully formed XML input but not if I build 
> > the input using biomoby processor objects.  The workflow runs 
> > both cases in parallel:
> > 
> > Workflow:      http://nassar.europa.renci.org/biomoby_aa2fasta.xml
> > Inputs:        
> > http://nassar.europa.renci.org/biomoby_aa2fasta_input.xml
> > Error detail:  
> > http://nassar.europa.renci.org/biomoby_aa2fasta_error.xml
> > 
> > The error is "Task failed due to problem invoking biomoby service. /
> > SAXParseException: Premature end of file."  Tomcat's log 
> > reports non-XML in the SOAP message (and it actually appears 
> > to be non-ASCII).
> > I also see differences in the input XML constructed by the 
> > AminoAcidSequence object, such as missing articleName='inseq' 
> > in element moby:Simple.
> > 
> > I've tried this with the Taverna 1.4 release, the stable 
> > snapshot from October 2, and recent builds from cvs 
> > (hopefully including the newer biomoby plug-in module), and 
> > it seems I get the same results in all cases.
> > 
> > Maybe I'm building the input objects incorrectly?
> > 
> > Nassib
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