[MOBY-l] MOBY tutorial - Taverna

[Nassib Nassar]

(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