Exception: org.xml.sax.SAXException: No deserializer defined for array type {htt

[Alex Bond]

Hi,

I am implementing a connector to the KEGGAPI web service using JAVA and 
APACHE AXIS 1.1.  However I am getting the following error when I get back 
data other than a String eg, SSDBResult object or GENESResult object.

Exception:
org.xml.sax.SAXException: No deserializer defined for array type 
{http://xml.apache.org/xml-soap}SOAPStruct
       at 
org.apache.axis.encoding.ser.ArrayDeserializer.onStartElement(ArrayDeserializer.java:304)
       at 
org.apache.axis.encoding.DeserializerImpl.startElement(DeserializerImpl.java:428)
       at 
org.apache.axis.encoding.DeserializationContextImpl.startElement(DeserializationContextImpl.java:976)
       at 
org.apache.axis.message.SAX2EventRecorder.replay(SAX2EventRecorder.java:198)
       at 
org.apache.axis.message.MessageElement.publishToHandler(MessageElement.java:722)
       at 
org.apache.axis.message.RPCElement.deserialize(RPCElement.java:233)
       at org.apache.axis.message.RPCElement.getParams(RPCElement.java:347)
       at org.apache.axis.client.Call.invoke(Call.java:2272)
       at org.apache.axis.client.Call.invoke(Call.java:2171)
       at org.apache.axis.client.Call.invoke(Call.java:1691)
       at 
org.apache.axis.client.AxisClientProxy.invoke(AxisClientProxy.java:186)
       at $Proxy0.get_all_neighbors_by_gene(Unknown Source)
       at 
KEGG.KEGGConnector.get_all_neighbors_by_gene(KEGGConnector.java:75)
       at KEGG.KEGGConnectorTest.main(KEGGConnectorTest.java:87)
; nested exception is:
       org.xml.sax.SAXException: No deserializer defined for array type 
{http://xml.apache.org/xml-soap}SOAPStruct

I was wondering if you know what is causing this error.  The code 
implementation is below.

KEGGConnector class:

public class KEGGConnector implements KEGGPortType{

   private KEGGPortType dynamicProxy;

   /** Creates a new instance of KEGGConnector */
   public KEGGConnector()
   {
       dynamicProxy = createDynamicProxy();
   }
   private KEGGPortType createDynamicProxy()
   {
       String urlString;
       String nameSpaceURI;
       String serviceName;
       String portName;
       URL keggWSDLURL;
       ServiceFactory serviceFactory;
       Service keggService;
       KEGGPortType proxy;
       urlString = "http://soap.genome.ad.jp/KEGG.wsdl";;
       nameSpaceURI = "SOAP/KEGG";
       serviceName = "KEGG";
       portName = "KEGGPort";
       keggWSDLURL = null;
       serviceFactory = null;
       keggService = null;
       proxy = null;
       try
       {
           keggWSDLURL = new URL(urlString);
           serviceFactory = serviceFactory.newInstance();
           keggService = serviceFactory.createService
               (keggWSDLURL, new QName(nameSpaceURI, serviceName));
           proxy = (KEGGPortType) keggService.getPort
               (new QName(nameSpaceURI, portName), KEGGPortType.class);
       }
       catch (MalformedURLException murle)
       {
           System.out.println(murle.getMessage());
       }
       catch (ServiceException se)
       {
           System.out.println(se.getMessage());
       }
       return proxy;
   }
   public SSDBResult[] get_all_neighbors_by_gene
       (String kid, int threshold, String[] orgs) throws RemoteException
   {
       return dynamicProxy.get_all_neighbors_by_gene(kid, threshold, orgs);
   }
}
KEGGConnectorTest class:

public class KEGGConnectorTest {

   /** Creates a new instance of KEGGMain */
   public KEGGConnectorTest()
   {
   }

   static private void printSSDBResults(SSDBResult[] ssdbResults)
   {
       for (int i = 0; i < ssdbResults.length; i++)
       {
           System.out.println("SSDB Result " + i + ":\tkid1 -\t" + 
ssdbResults[i].getKid1());
           System.out.println("             \tkid2 -\t" + 
ssdbResults[i].getKid2());
           System.out.println("             \tsw_score -\t" + 
ssdbResults[i].getSw_score());
           System.out.println("             \tident -\t" + 
ssdbResults[i].getIdent());
           System.out.println("             \toverlap -\t" + 
ssdbResults[i].getOverlap());
           System.out.println("             \ts1_start -\t" + 
ssdbResults[i].getS1_start());
           System.out.println("             \ts1_end -\t" + 
ssdbResults[i].getS1_end());
           System.out.println("             \ts2_start -\t" + 
ssdbResults[i].getS2_start());
           System.out.println("             \ts2_end -\t" + 
ssdbResults[i].getS2_end());
           System.out.println("             \tb1 -\t" + 
ssdbResults[i].getB1());
           System.out.println("             \tb2 -\t" + 
ssdbResults[i].getB2());
           System.out.println("             \tdefinition1 -\t" + 
ssdbResults[i].getDefinition1());
           System.out.println("             \tdefinition2 -\t" + 
ssdbResults[i].getDefinition2());
           System.out.println("             \tlength1 -\t" + 
ssdbResults[i].getLength1());
           System.out.println("             \tlength2 -\t" + 
ssdbResults[i].getLength2());
        }
   }

public static void main(String[] args)
   {
       KEGGConnector keggConnector;
       SSDBResult[] ssdbResults;
       String databases;
       String dbinfo;
       String[] genes;
       String[] enzymes;
       String[] pathways;
       String[] organisms;
       keggConnector =  new KEGGConnector();
       try
       {
           System.out.println("TEST :");
           System.out.println("Search all the homologous genes for E. coli 
gene 'b0002', over the default threshold score 100.");
           
System.out.println("keggConnector.get_all_neighbors_by_gene(\"eco:b0002\", 
100, null)\n");
           System.out.println("RESULTS:");
           organisms = new String[2];
           organisms[0] = "ece";
           organisms[1] = "hin";
           ssdbResults = 
keggConnector.get_all_neighbors_by_gene("eco:b0002", 500, organisms);
           printSSDBResults(ssdbResults);

I would be grateful if you could give me some help on this.

Thanks,

Alex Bond

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