[MOBY-l] Problem with runGeneIDGFF code

[Carol Lushbough]

I was wondering if someone could help me figure out a problem I'm having 
with [genome.imim.es] runGeneIDGFF Web service.  I'm able to 
successfully execute it at http://www.inab.org/MOWServ/ but cannot 
successfully execute it through Dashboard or my Java program.  Through 
my Java program, I get the following error.  I've also included my 
code.  Any help would be greatly appreciated.  I'm sure I'm doing 
something dumb. I think I'm using the default endpoint.

ARNING: Unable to find required classes (javax.activation.DataHandler 
and javax.mail.internet.MimeMultipart). Attachment support is disabled.
Exception in thread "main" java.lang.IllegalArgumentException: Simple 
element has no MOBY child element, there is no instance to create
        at 
org.biomoby.shared.data.MobyDataObject.createInstanceFromDOM(MobyDataObject.java:118)
        at 
org.biomoby.shared.data.MobyContentInstance.parseDataGroup(MobyContentInstance.java:209)
        at 
org.biomoby.shared.data.MobyContentInstance.<init>(MobyContentInstance.java:115)
        at 
org.biomoby.shared.data.MobyDataUtils.fromXMLDocument(MobyDataUtils.java:84)
        at 
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:271)
        at testpackage.HelloMOBY.main(HelloMOBY.java:108)*
*
 ============================================================================= 
                        
        Central worker = new CentralImpl();
 
        MobyService templateService = new MobyService("runGeneIDGFF");
        MobyRequest mr = new MobyRequest(worker);
        MobyService[] validServices = worker.findService(templateService);
        mr.setService(validServices[0]);
          //      String sequence = getTestSequence();

                String sequence = "";
                sequence += 
"ctgagctgggcaggtgtcctgcaatcctggtgaatattcagcggtctgtgtccccttggctagctc";
                sequence += 
"tgcctatgcaaacagccacctgagaaggggaagcagagggtgcggtggaaacggctgtgtcaggggacagc";
                sequence += 
"aggggaaggaagatagccaaggcttactgaggctggtggagggagccactccatttccttg";

                MobyDataType dataType = new MobyDataType("DNASequence");
                MobyDataComposite dnaSequenceObject = new 
MobyDataComposite(dataType,"sequence");
                dnaSequenceObject.put("SequenceString", new 
MobyDataString(sequence));
                dnaSequenceObject.put("Length", new 
MobyDataInt(sequence.length()));

                mr.setInput(dnaSequenceObject); 
               
                MobyDataSecondaryInstance[] secondaryData = new 
MobyDataSecondaryInstance[5];
                MobySecondaryData p1 = new MobySecondaryData("strand");
                p1.setDataType("String");
                p1.setDefaultValue("Both");
                MobySecondaryData p2 = new MobySecondaryData("profile");
                p2.setDataType("String");
                p2.setDefaultValue("Homo sapiens (suitable for mammals)");
                MobySecondaryData p3 = new MobySecondaryData("engine");
                p3.setDataType("String");
                p3.setDefaultValue("Normal");
                MobySecondaryData p4 = new MobySecondaryData("signals");
                p4.setDataType("String");
                p4.setDefaultValue("None");
                MobySecondaryData p5 = new MobySecondaryData("exons");
                p5.setDataType("String");
                p5.setDefaultValue("None");

                secondaryData[0] = new 
MobyDataSecondaryInstance(p1);          
                secondaryData[1] = new 
MobyDataSecondaryInstance(p2);          
                secondaryData[2] = new 
MobyDataSecondaryInstance(p3);          
                secondaryData[3] = new 
MobyDataSecondaryInstance(p4);          
                secondaryData[4] = new 
MobyDataSecondaryInstance(p5);          
                mr.setSecondaryInput(secondaryData);          
 
             
        MobyContentInstance mobyContent = mr.invokeService();
        String response = mobyContent.toXML();

-- 
Carol Lushbough
Assistant Professor of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-6138