Hi all,
Progressing from my previous emails about the XSD setup, I've downloaded the
wsdl and xsd, made the small changes to the xsd to get it to work (modified
the name of filter/dataset/attribute) and then tried to connect with a
really basic Java client. I'm getting the error shown at the bottom of the
email. It seems that it cannot connect to the service. The wsdl and xsd are
completely standard so I don't need to attach them here, but I am connecting
via cxf with the attached test class, which is what fails at line 33 when
you read the error messsage below.
Can anyone help me with why this isn't connecting? Btw, if I switch the URLs
in the wsdl and xsd to be my local biomart installation, I get the exact
same error.
thanks very much! :)
log4j:WARN No appenders could be found for logger
(org.apache.cxf.bus.spring.BusApplicationContext).
log4j:WARN Please initialize the log4j system properly.
09-Jan-2009 11:21:30
org.apache.cxf.service.factory.ReflectionServiceFactoryBean
buildServiceFromWSDL
INFO: Creating Service {
http://www.biomart.org:80/MartServiceSoap}BioMartSoapService from WSDL:
file:/media/share/unsynched/IdeaProjects/saint/trunk/src/main/resources/biomart.wsdl
09-Jan-2009 11:21:31 org.apache.cxf.phase.PhaseInterceptorChain doIntercept
INFO: Interceptor has thrown exception, unwinding now
org.apache.cxf.interceptor.Fault: Response was of unexpected text/html
ContentType. Incoming portion of HTML stream: <!DOCTYPE HTML PUBLIC
"-//W3C//DTD HTML 4.01 Transitional//EN" "
http://www.w3.org/TR/html4/loose.dtd";>
<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;
charset=iso-8859-1">
<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
<STYLE
type="text/css"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
</HEAD><BODY>
<H1>ERROR</H1>
<H2>The requested URL could not be retrieved</H2>
<HR noshade size="1px">
<P>
While trying to retrieve the URL:
<A HREF="http://www.biomart.org/biomart/martsoap";>
http://www.biomart.org/biomart/martsoap</A>
<P>
The following error was encountered:
<UL>
<LI>
<STRONG>
Unsupported Request Method and Protocol
</STRONG>
</UL>
<P>
Squid does not support all request methods for all access protocols.
For example, you can not POST a Gopher request.
<P>Your cache administrator is <A HREF="mailto:root";>root</A>.
<BR clear="all">
<HR noshade size="1px">
<ADDRESS>
Generated Fri, 09 Jan 2009 11:21:31 GMT by radius2.ncl.ac.uk(squid/2.6.STABLE6)
</ADDRESS>
</BODY></HTML>
at
org.apache.cxf.interceptor.StaxInInterceptor.handleMessage(StaxInInterceptor.java:73)
at
org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:221)
at org.apache.cxf.endpoint.ClientImpl.onMessage(ClientImpl.java:429)
at
org.apache.cxf.transport.http.HTTPConduit$WrappedOutputStream.handleResponse(HTTPConduit.java:1988)
at
org.apache.cxf.transport.http.HTTPConduit$WrappedOutputStream.close(HTTPConduit.java:1824)
at
org.apache.cxf.transport.AbstractConduit.close(AbstractConduit.java:66)
at org.apache.cxf.transport.http.HTTPConduit.close(HTTPConduit.java:583)
at
org.apache.cxf.interceptor.MessageSenderInterceptor$MessageSenderEndingInterceptor.handleMessage(MessageSenderInterceptor.java:62)
at
org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:221)
at org.apache.cxf.endpoint.ClientImpl.invoke(ClientImpl.java:276)
at org.apache.cxf.endpoint.ClientImpl.invoke(ClientImpl.java:222)
at org.apache.cxf.frontend.ClientProxy.invokeSync(ClientProxy.java:73)
at
org.apache.cxf.jaxws.JaxWsClientProxy.invoke(JaxWsClientProxy.java:177)
at $Proxy31.getRegistry(Unknown Source)
at
uk.ac.cisban.saint.server.TestSaintBiomartSoapClient.checkMartExistence(TestSaintBiomartSoapClient.java:33)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
org.junit.internal.runners.TestMethodRunner.executeMethodBody(TestMethodRunner.java:99)
at
org.junit.internal.runners.TestMethodRunner.runUnprotected(TestMethodRunner.java:81)
at
org.junit.internal.runners.BeforeAndAfterRunner.runProtected(BeforeAndAfterRunner.java:34)
at
org.junit.internal.runners.TestMethodRunner.runMethod(TestMethodRunner.java:75)
at
org.junit.internal.runners.TestMethodRunner.run(TestMethodRunner.java:45)
at
org.junit.internal.runners.TestClassMethodsRunner.invokeTestMethod(TestClassMethodsRunner.java:71)
at
org.junit.internal.runners.TestClassMethodsRunner.run(TestClassMethodsRunner.java:35)
at
org.junit.internal.runners.TestClassRunner$1.runUnprotected(TestClassRunner.java:42)
at
org.junit.internal.runners.BeforeAndAfterRunner.runProtected(BeforeAndAfterRunner.java:34)
at
org.junit.internal.runners.TestClassRunner.run(TestClassRunner.java:52)
at com.intellij.rt.junit4.Junit4ClassSuite.run(Junit4ClassSuite.java:99)
at junit.textui.TestRunner.doRun(TestRunner.java:115)
at
com.intellij.rt.execution.junit.IdeaTestRunner.doRun(IdeaTestRunner.java:94)
at junit.textui.TestRunner.doRun(TestRunner.java:108)
at
com.intellij.rt.execution.junit.IdeaTestRunner.startRunnerWithArgs(IdeaTestRunner.java:22)
at
com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:118)
at
com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:40)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:90)
javax.xml.ws.soap.SOAPFaultException: Response was of unexpected text/html
ContentType. Incoming portion of HTML stream: <!DOCTYPE HTML PUBLIC
"-//W3C//DTD HTML 4.01 Transitional//EN" "
http://www.w3.org/TR/html4/loose.dtd";>
<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;
charset=iso-8859-1">
<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
<STYLE
type="text/css"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
</HEAD><BODY>
<H1>ERROR</H1>
<H2>The requested URL could not be retrieved</H2>
<HR noshade size="1px">
<P>
While trying to retrieve the URL:
<A HREF="http://www.biomart.org/biomart/martsoap";>
http://www.biomart.org/biomart/martsoap</A>
<P>
The following error was encountered:
<UL>
<LI>
<STRONG>
Unsupported Request Method and Protocol
</STRONG>
</UL>
<P>
Squid does not support all request methods for all access protocols.
For example, you can not POST a Gopher request.
<P>Your cache administrator is <A HREF="mailto:root";>root</A>.
<BR clear="all">
<HR noshade size="1px">
<ADDRESS>
Generated Fri, 09 Jan 2009 11:21:31 GMT by radius2.ncl.ac.uk(squid/2.6.STABLE6)
</ADDRESS>
</BODY></HTML>
at
org.apache.cxf.jaxws.JaxWsClientProxy.invoke(JaxWsClientProxy.java:218)
at $Proxy31.getRegistry(Unknown Source)
at
uk.ac.cisban.saint.server.TestSaintBiomartSoapClient.checkMartExistence(TestSaintBiomartSoapClient.java:33)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at
org.junit.internal.runners.TestMethodRunner.executeMethodBody(TestMethodRunner.java:99)
at
org.junit.internal.runners.TestMethodRunner.runUnprotected(TestMethodRunner.java:81)
at
org.junit.internal.runners.BeforeAndAfterRunner.runProtected(BeforeAndAfterRunner.java:34)
at
org.junit.internal.runners.TestMethodRunner.runMethod(TestMethodRunner.java:75)
at
org.junit.internal.runners.TestMethodRunner.run(TestMethodRunner.java:45)
at
org.junit.internal.runners.TestClassMethodsRunner.invokeTestMethod(TestClassMethodsRunner.java:71)
at
org.junit.internal.runners.TestClassMethodsRunner.run(TestClassMethodsRunner.java:35)
at
org.junit.internal.runners.TestClassRunner$1.runUnprotected(TestClassRunner.java:42)
at
org.junit.internal.runners.BeforeAndAfterRunner.runProtected(BeforeAndAfterRunner.java:34)
at
org.junit.internal.runners.TestClassRunner.run(TestClassRunner.java:52)
at com.intellij.rt.junit4.Junit4ClassSuite.run(Junit4ClassSuite.java:99)
at
com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:40)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:90)
Caused by: org.apache.cxf.interceptor.Fault: Response was of unexpected
text/html ContentType. Incoming portion of HTML stream: <!DOCTYPE HTML
PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "
http://www.w3.org/TR/html4/loose.dtd";>
<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;
charset=iso-8859-1">
<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
<STYLE
type="text/css"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
</HEAD><BODY>
<H1>ERROR</H1>
<H2>The requested URL could not be retrieved</H2>
<HR noshade size="1px">
<P>
While trying to retrieve the URL:
<A HREF="http://www.biomart.org/biomart/martsoap";>
http://www.biomart.org/biomart/martsoap</A>
<P>
The following error was encountered:
<UL>
<LI>
<STRONG>
Unsupported Request Method and Protocol
</STRONG>
</UL>
<P>
Squid does not support all request methods for all access protocols.
For example, you can not POST a Gopher request.
<P>Your cache administrator is <A HREF="mailto:root";>root</A>.
<BR clear="all">
<HR noshade size="1px">
<ADDRESS>
Generated Fri, 09 Jan 2009 11:21:31 GMT by radius2.ncl.ac.uk(squid/2.6.STABLE6)
</ADDRESS>
</BODY></HTML>
at
org.apache.cxf.interceptor.StaxInInterceptor.handleMessage(StaxInInterceptor.java:73)
at
org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:221)
at org.apache.cxf.endpoint.ClientImpl.onMessage(ClientImpl.java:429)
at
org.apache.cxf.transport.http.HTTPConduit$WrappedOutputStream.handleResponse(HTTPConduit.java:1988)
at
org.apache.cxf.transport.http.HTTPConduit$WrappedOutputStream.close(HTTPConduit.java:1824)
at
org.apache.cxf.transport.AbstractConduit.close(AbstractConduit.java:66)
at org.apache.cxf.transport.http.HTTPConduit.close(HTTPConduit.java:583)
at
org.apache.cxf.interceptor.MessageSenderInterceptor$MessageSenderEndingInterceptor.handleMessage(MessageSenderInterceptor.java:62)
at
org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:221)
at org.apache.cxf.endpoint.ClientImpl.invoke(ClientImpl.java:276)
at org.apache.cxf.endpoint.ClientImpl.invoke(ClientImpl.java:222)
at org.apache.cxf.frontend.ClientProxy.invokeSync(ClientProxy.java:73)
at
org.apache.cxf.jaxws.JaxWsClientProxy.invoke(JaxWsClientProxy.java:177)
... 28 more
Process finished with exit code 255
--
Thanks,
Allyson :)
Allyson Lister
Research Associate
Centre for Integrated Systems Biology for Ageing and Nutrition
Newcastle University
http://www.cisban.ac.uk
School of Computing Science
Newcastle University
Newcastle upon Tyne, NE1 7RU
package uk.ac.cisban.saint.server;
import org.junit.Before;
import org.junit.Test;
import org.biomart._80.martservicesoap.MartServiceSoap;
import org.biomart._80.martservicesoap.BioMartSoapService;
import org.biomart._80.martservicesoap.Mart;
import org.biomart._80.martservicesoap.BioMartException_Exception;
import java.util.List;
import java.util.ArrayList;
/**
* Performs a variety of tests to ensure that the connection the BioMart is working correctly.
*/
public class TestSaintBiomartSoapClient {
MartServiceSoap martServiceSoap;
@Before
public void setUp() {
BioMartSoapService bioMartSoapService = new BioMartSoapService();
martServiceSoap = bioMartSoapService.getBioMartSoapPort();
}
@Test
public void checkMartExistence() {
List<Mart> localQueryResults;
try {
localQueryResults = martServiceSoap.getRegistry( );
} catch ( BioMartException_Exception e ) {
e.printStackTrace();
localQueryResults = new ArrayList<Mart>();
}
for ( Mart localQueryResult : localQueryResults ) {
System.out.println(localQueryResult.getName());
}
assert(!localQueryResults.isEmpty());
}
}
