[MOBY-l] MOBY tutorial - Taverna

[Paul Gordon]

Hi all,

I finally found some time to look at this Taverna/MobyServlet 
incompatability. 

It seems that Taverna does not include an XML declaration (<?xml...?>) 
at the start of the MOBY payload.  Because the payload did not have 
this, MobyServlet tried as a last ditch effort to Base64 decode the 
contents (some old servers sent data this way).  That's why you got 
garbage.  Now, between not finding the XML declaration and attempting a 
base64 decoding, I've inserted a check for the MOBY root tag.  Now 
Taverna jobs work, and will produce the following message in the 
catalina log:

Warning: The MOBY contents was missing an XML declaration, but it is 
required by the MOBY API, and may stop working in the future without 
it.  Please contact the client's provider to correct this.

Perhaps I am wrong, but the MOBY API specifically says that this 
declaration is required, no?  That's why we have to string-encode or 
base64 encode, etc. the SOAP contents (since processing instructions 
starting with "xml" are not allowed in the contents of an XML 
document)?  If not, I'll get rid of the warning message...

With kind regards,

Paul

P.S. It may take a few hours for the Web site MobyServlet.war to be 
mirrored, but the one from CVS is updated.
> (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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