Hi Wei,
Its a document / literal type service so its correct the xsi:type is not included (unlike RPC/encoded). I've tried this using SoapUI which suggests a soap message that looks like:

<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:prep="http://mage.preprocessdataset.service.cagrid.genepattern.org/PreprocessDatasetMAGEService" xmlns:gov="gme://caArray.caBIG/1.1/gov.nih.nci.mageom.domain.BioAssay" xmlns:grid="gme://GenePattern.caBIG/1/gridExtensions">
   <soapenv:Header/>
   <soapenv:Body>
      <prep:PerformAnalysisRequest>
         <prep:bioAssay>
            <!--1 or more repetitions:-->
            <gov:BioAssay>
               <gov:name>0</gov:name>
               <gov:identifier></gov:identifier>
            </gov:BioAssay>
         </prep:bioAssay>
         <prep:preprocessDatasetParameterSet>
            <grid:PreprocessDatasetParameterSet>
               <ceiling>2.1f</ceiling>
               <columnThreshold>3.14159E0</columnThreshold>
               <filterFlag>false</filterFlag>
               <logBaseTwo>true</logBaseTwo>
               <maxSigmaBinning>1</maxSigmaBinning>
               <minChange>3f</minChange>
               <minDelta>100f</minDelta>
               <numberOfColumnsAboveThreshold>1</numberOfColumnsAboveThreshold>
               <numExclude>0</numExclude>
               <preprocessingFlag>discretize</preprocessingFlag>
               <probabilityThreshold>1f</probabilityThreshold>
               <threshold>20f</threshold>
            </grid:PreprocessDatasetParameterSet>
         </prep:preprocessDatasetParameterSet>
      </prep:PerformAnalysisRequest>
   </soapenv:Body>
</soapenv:Envelope>

which produces the same error as you report: <faultstring>org.xml.sax.SAXException: Unable to create JavaBean of type gov.nih.nci.mageom.domain.bioassay.BioAssay.  Missing default constructor?  Error was: java.lang.InstantiationException.</faultstring>

So it may be a problem with the service. Have you tried any other clients?
Or is this service a WSRF type of service? The WSDL URL suggests it might be.

regards,
Stuart.

On 24 Jan 2008, at 05:48, Wei Tan wrote:

Hi,
 
   I'm using Taverna to invoke a WSDL service which takes input like:
 
<SOAP-ENV:Envelope xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:m0="gme://caArray.caBIG/1.1/gov.nih.nci.mageom.domain.BioAssay" xmlns:m1="gme://GenePattern.caBIG/1/gridExtensions">
 <SOAP-ENV:Body>
  <m:PerformAnalysisRequest xmlns:m="http://mage.preprocessdataset.service.cagrid.genepattern.org/PreprocessDatasetMAGEService">
    <m:bioAssay>
  <ns3:BioAssay xmlns:ns3="gme://caArray.caBIG/1.1/gov.nih.nci.mageom.domain.BioAssay" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ns3:DerivedBioAssay">
   <ns3:name>0</ns3:name>
   <ns3:identifier xsi:nil="true"/>
   <ns3:derivedBioAssayData>
    <ns3:name xsi:nil="true"/>
    <ns3:identifier xsi:nil="true"/>
    <ns3:designElementDimension xsi:type="ns3:ReporterDimension">
     <ns3:name xsi:nil="true"/>
     <ns3:identifier xsi:nil="true"/>
     <ns3:reporters>
      <ns3:name>0_at</ns3:name>
      <ns3:identifier xsi:nil="true"/>
     </ns3:reporters>
    </ns3:designElementDimension>
    <ns3:bioDataValues xsi:type="ns3:BioDataCube">
     <ns3:cube>18950.0\</ns3:cube>
     <ns3:order xsi:nil="true"/>
    </ns3:bioDataValues>
    <ns3:quantitationTypeDimension>
     <ns3:name xsi:nil="true"/>
     <ns3:identifier>QT:1</ns3:identifier>
     <ns3:identifier2 xsi:nil="true"/>
     <ns3:name2 xsi:nil="true"/>
    </ns3:quantitationTypeDimension>
   </ns3:derivedBioAssayData>
  </ns3:BioAssay>
 </m:bioAssay>
 <m:preprocessDatasetParameterSet>
  <m1:PreprocessDatasetParameterSet xmlns:m1="gme://GenePattern.caBIG/1/gridExtensions">
   <ceiling>2.1f</ceiling>
   <columnThreshold>3.14159E0</columnThreshold>
   <filterFlag>false</filterFlag>
   <logBaseTwo>true</logBaseTwo>
   <maxSigmaBinning>1</maxSigmaBinning>
   <minChange>3f</minChange>
   <minDelta>100f</minDelta>
   <numberOfColumnsAboveThreshold>1</numberOfColumnsAboveThreshold>
   <numExclude>0</numExclude>
   <preprocessingFlag>discretize</preprocessingFlag>
   <probabilityThreshold>1f</probabilityThreshold>
   <threshold>20f</threshold>
  </m1:PreprocessDatasetParameterSet>
 </m:preprocessDatasetParameterSet>
  </m:PerformAnalysisRequest>
 </SOAP-ENV:Body>
</SOAP-ENV:Envelope>
 
    The service works correctly if I use other tools to send the soap message directly.
    When I use Taverna to invoke it, an error occurs like:
  <soapenv:Fault>
   <faultcode>soapenv:Server.userException</faultcode>
   <faultstring>org.xml.sax.SAXException: Unable to create JavaBean of type gov.nih.nci.mageom.domain.bioassay.BioAssay.  Missing default constructor?  Error was: java.lang.InstantiationException.</faultstring>
   <detail>
    <ns1:stackTrace xmlns:ns1="http://xml.apache.org/axis/">org.xml.sax.SAXException: Unable to create JavaBean of type gov.nih.nci.mageom.domain.bioassay.BioAssay.  Missing default constructor?  Error was: java.lang.InstantiationException.
 at org.apache.axis.encoding.ser.BeanDeserializer.startElement(BeanDeserializer.java:124)
 
   
   I monitored the http port to find that when Taverna sends out the SOAP request, the xsi:type attributes are simply taken out so that the target service will report an error.
 
  Can anyone help to solove this issue? Thanks in advance!
  The workflow containing this service is attached.
 
 
Wei
 

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