On Tue, May 5, 2009 at 09:44, Stian Soiland-Reyes
<[email protected]> wrote:
> On Mon, May 4, 2009 at 19:40, Wei Tan <[email protected]> wrote:
>> Would you update us about the progress regarding this bug?
>
> Hi, I've noted this as
> http://www.mygrid.org.uk/dev/issues/browse/T2-531 and I'm
> investigating it now.
See new comments:
Resolved by changing LiteralBodyBuilder.java:111 to:
if (NS_XSI.equals(node.getNamespaceURI()) && TYPE.equals(node.getLocalName())) {
The old version did node.getNamespaceURI().equals() - which would give
an NPE if no namespace is set.
However, the attached workflow now gives:
ERROR 2009-05-05 15:24:30,819
(net.sf.taverna.t2.activities.wsdl.WSDLActivity:301) - Error invoking
WSDL service performAnalysis
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
faultSubcode:
faultString: java.lang.NullPointerException
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:java.lang.NullPointerException
at
org.genepattern.io.DefaultDatasetCreator.data(DefaultDatasetCreator.java:41)
at org.genepattern.io.gct.GctParser.readData(GctParser.java:107)
at org.genepattern.io.gct.GctParser.parse(GctParser.java:77)
at org.genepattern.io.IOUtil.read(IOUtil.java:845)
at org.genepattern.io.IOUtil.readDataset(IOUtil.java:503)
at org.genepattern.io.IOUtil.readDataset(IOUtil.java:484)
at
org.genepattern.cabig.util.StatmlConverter.readGctFile(StatmlConverter.java:110)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.PreprocessDatasetSTATMLServiceImpl.parseResultFile(PreprocessDatasetSTATMLServiceImpl.java:164)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.PreprocessDatasetSTATMLServiceImpl.performAnalysis(PreprocessDatasetSTATMLServiceImpl.java:98)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.globus.PreprocessDatasetSTATMLServiceProviderImpl.performAnalysis(PreprocessDatasetSTATMLServiceProviderImpl.java:31)
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:585)
at
org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:384)
at
org.globus.axis.providers.RPCProvider.invokeMethodSub(RPCProvider.java:107)
at
org.globus.axis.providers.RPCProvider.invokeMethod(RPCProvider.java:90)
at
org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:281)
at
org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:319)
at
org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at
org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:450)
at org.apache.axis.server.AxisServer.invoke(AxisServer.java:285)
at
org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:697)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
at
org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:327)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:237)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:157)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:214)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:198)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:152)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:118)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:102)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:929)
at
org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:160)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:799)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:705)
at
org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:577)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:683)
at java.lang.Thread.run(Thread.java:595)
{http://xml.apache.org/axis/}hostname:node255
This seems like a server-side error (from org.genepattern) from the
performAnalysis method in the processor called "preProcessTestData".
[ Show » ]
Stian Soiland-Reyes added a comment - 2009-05-05 16:05 Resolved by
changing LiteralBodyBuilder.java:111 to:
if (NS_XSI.equals(node.getNamespaceURI()) && TYPE.equals(node.getLocalName())) {
The old version did node.getNamespaceURI().equals() - which would give
an NPE if no namespace is set. However, the attached workflow now
gives:
ERROR 2009-05-05 15:24:30,819
(net.sf.taverna.t2.activities.wsdl.WSDLActivity:301) - Error invoking
WSDL service performAnalysis
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
faultSubcode:
faultString: java.lang.NullPointerException
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:java.lang.NullPointerException
at
org.genepattern.io.DefaultDatasetCreator.data(DefaultDatasetCreator.java:41)
at org.genepattern.io.gct.GctParser.readData(GctParser.java:107)
at org.genepattern.io.gct.GctParser.parse(GctParser.java:77)
at org.genepattern.io.IOUtil.read(IOUtil.java:845)
at org.genepattern.io.IOUtil.readDataset(IOUtil.java:503)
at org.genepattern.io.IOUtil.readDataset(IOUtil.java:484)
at
org.genepattern.cabig.util.StatmlConverter.readGctFile(StatmlConverter.java:110)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.PreprocessDatasetSTATMLServiceImpl.parseResultFile(PreprocessDatasetSTATMLServiceImpl.java:164)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.PreprocessDatasetSTATMLServiceImpl.performAnalysis(PreprocessDatasetSTATMLServiceImpl.java:98)
at
org.genepattern.cagrid.service.preprocessdataset.statml.service.globus.PreprocessDatasetSTATMLServiceProviderImpl.performAnalysis(PreprocessDatasetSTATMLServiceProviderImpl.java:31)
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:585)
at
org.apache.axis.providers.java.RPCProvider.invokeMethod(RPCProvider.java:384)
at
org.globus.axis.providers.RPCProvider.invokeMethodSub(RPCProvider.java:107)
at
org.globus.axis.providers.RPCProvider.invokeMethod(RPCProvider.java:90)
at
org.apache.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:281)
at
org.apache.axis.providers.java.JavaProvider.invoke(JavaProvider.java:319)
at
org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at
org.apache.axis.handlers.soap.SOAPService.invoke(SOAPService.java:450)
at org.apache.axis.server.AxisServer.invoke(AxisServer.java:285)
at
org.apache.axis.transport.http.AxisServlet.doPost(AxisServlet.java:697)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
at
org.apache.axis.transport.http.AxisServletBase.service(AxisServletBase.java:327)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:237)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:157)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:214)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:198)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:152)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:118)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:102)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at
org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104)
at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:929)
at
org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:160)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:799)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:705)
at
org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:577)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:683)
at java.lang.Thread.run(Thread.java:595)
{http://xml.apache.org/axis/}hostname:node255
This seems like a server-side error (from org.genepattern) from the
performAnalysis method in the processor called "preProcessTestData".
The fix should make it into the next nightly build.
Your workflow took quite a bit of time to run.. :-)
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
taverna-hackers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/taverna-hackers
Developers Guide: http://www.mygrid.org.uk/usermanual1.7/dev_guide.html
FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq
