[Taverna-users] soaplab emboss services

Achille Zappa Mon, 03 Aug 2009 08:23:43 -0700

> Hello everybody,
I was trying the new 6.1 version of soaplab2 Emboss services in taverna
1.7, especially the fproml service with bootstrap (fseqboot) like the
attach, do you know if is that correct!, and the result is some kind of
error like :
<<
[Text: Task failed due to problem invoking soaplab service<br>  
SoaplabTask.execute(..) : line 201 &lt;SoaplabTask.java&gt;<br>  
ProcessorTask.runAndGenerateTemplates(..) : line 585
&lt;ProcessorTask.java&gt;<br>  
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
&lt;ProcessorTask.java&gt;<br>
ProcessorTask.invokeOnce(..) : line 443 &lt;
ProcessorTask.java&gt;<br>
ProcessorTask.invokeWithoutIteration(..) : line 652
&lt;ProcessorTask.java&gt;<br>
ProcessorTask.invoke(..) : line 356 &lt;
ProcessorTask.java&gt;<br>
ProcessorTask.handleRun(..) : line 282 &lt;
ProcessorTask.java&gt;<br>
NewState$1.run(..) : line 67 &lt;NewState.java&gt;<br><br>; nested
exception is:
        java.net.SocketException: Connection reset<br>   AxisFault.makeFault(..)
: line 101 &lt;AxisFault.java&gt;<br>   HTTPSender.invoke(..) : line 154
&lt;HTTPSender.java&gt;<br>   InvocationStrategy.visit(..) : line 32
&lt;InvocationStrategy.java&gt;<br>
SimpleChain.doVisiting(..) : line 118 &lt;
SimpleChain.java&gt;<br>
SimpleChain.invoke(..) : line 83 &lt;
SimpleChain.java&gt;<br>
AxisClient.invoke(..) : line 165 &lt;
AxisClient.java&gt;<br>
Call.invokeEngine(..) : line 2784 &lt;
Call.java&gt;<br>
Call.invoke(..) : line 2767 &lt;
Call.java&gt;<br>
Call.invoke(..) : line 2443 &lt;
Call.java&gt;<br>
Call.invoke(..) : line 2366 &lt;Call.java&gt;<br>   Call.invoke(..) : line
1812 &lt;Call.java&gt;<br>
SoaplabTask.execute(..) : line 120 &lt;
SoaplabTask.java&gt;<br>
ProcessorTask.runAndGenerateTemplates(..) : line 585
&lt;ProcessorTask.java&gt;<br>  
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
&lt;ProcessorTask.java&gt;<br>
ProcessorTask.invokeOnce(..) : line 443 &lt;
ProcessorTask.java&gt;<br>
ProcessorTask.invokeWithoutIteration(..) : line 652
&lt;ProcessorTask.java&gt;<br>
ProcessorTask.invoke(..) : line 356 &lt;
ProcessorTask.java&gt;<br>
ProcessorTask.handleRun(..) : line 282 &lt;
ProcessorTask.java&gt;<br>
NewState$1.run(..) : line 67 &lt;NewState.java&gt;<br><br>
Connection reset<br>   SocketInputStream.read(..) : line 168 &lt;
SocketInputStream.java&gt;<br>
BufferedInputStream.fill(..) : line 218 &lt;BufferedInputStream.java&gt;<br>
BufferedInputStream.read(..) : line 237 &lt;BufferedInputStream.java&gt;<br>
HTTPSender.readHeadersFromSocket(..) : line 583 &lt;HTTPSender.java&gt;<br>
HTTPSender.invoke(..) : line 143 &lt;
HTTPSender.java&gt;<br>
InvocationStrategy.visit(..) : line 32 &lt;InvocationStrategy.java&gt;<br>
SimpleChain.doVisiting(..) : line 118 &lt;
SimpleChain.java&gt;<br>
SimpleChain.invoke(..) : line 83 &lt;
SimpleChain.java&gt;<br>
AxisClient.invoke(..) : line 165 &lt;
AxisClient.java&gt;<br>
Call.invokeEngine(..) : line 2784 &lt;Call.java&gt;<br>   Call.invoke(..)
: line 2767 &lt;Call.java&gt;<br>   Call.invoke(..) : line 2443
&lt;Call.java&gt;<br>
Call.invoke(..) : line 2366 &lt;Call.java&gt;<br>   Call.invoke(..) : line
1812 &lt;Call.java&gt;<br>
SoaplabTask.execute(..) : line 120 &lt;SoaplabTask.java&gt;<br>  
ProcessorTask.runAndGenerateTemplates(..) : line 585
&lt;ProcessorTask.java&gt;<br>  
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeOnce(..) : line 443
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeWithoutIteration(..)
: line 652 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.invoke(..) :
line 356 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.handleRun(..) :
line 282 &lt;ProcessorTask.java&gt;<br>   NewState$1.run(..) : line 67
&lt;NewState.java&gt;<br>]
>>
or this one
<<
[Text: Task failed due to problem invoking soaplab service<br>  
SoaplabTask.execute(..) : line 201 &lt;SoaplabTask.java&gt;<br>  
ProcessorTask.runAndGenerateTemplates(..) : line 585
&lt;ProcessorTask.java&gt;<br>  
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeOnce(..) : line 443
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeWithoutIteration(..)
: line 652 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.invoke(..) :
line 356 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.handleRun(..) :
line 282 &lt;ProcessorTask.java&gt;<br>   NewState$1.run(..) : line 67
&lt;NewState.java&gt;<br><br>java.net.SocketTimeoutException: Read timed
out<br>   SOAPFaultBuilder.createFault(..) : line 222
&lt;SOAPFaultBuilder.java&gt;<br>   SOAPFaultBuilder.endElement(..) : line
129 &lt;SOAPFaultBuilder.java&gt;<br>  
DeserializationContext.endElement(..) : line 1087
&lt;DeserializationContext.java&gt;<br>   AbstractSAXParser.endElement(..)
: line -1 &lt;Unknown filename&gt;<br>  
XMLNSDocumentScannerImpl.scanEndElement(..) : line -1 &lt;Unknown
filename&gt;<br>  
XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(..) :
line -1 &lt;Unknown filename&gt;<br>  
XMLDocumentFragmentScannerImpl.scanDocument(..) : line -1 &lt;Unknown
filename&gt;<br>   XML11Configuration.parse(..) : line -1 &lt;Unknown
filename&gt;<br>   XML11Configuration.parse(..) : line -1 &lt;Unknown
filename&gt;<br>   XMLParser.parse(..) : line -1 &lt;Unknown
filename&gt;<br>   AbstractSAXParser.parse(..) : line -1 &lt;Unknown
filename&gt;<br>   SAXParser.parse(..) : line 395
&lt;SAXParser.java&gt;<br>   DeserializationContext.parse(..) : line 227
&lt;DeserializationContext.java&gt;<br>   SOAPPart.getAsSOAPEnvelope(..) :
line 696 &lt;SOAPPart.java&gt;<br>   Message.getSOAPEnvelope(..) : line
435 &lt;Message.java&gt;<br>   MustUnderstandChecker.invoke(..) : line 62
&lt;MustUnderstandChecker.java&gt;<br>   AxisClient.invoke(..) : line 206
&lt;AxisClient.java&gt;<br>   Call.invokeEngine(..) : line 2784
&lt;Call.java&gt;<br>   Call.invoke(..) : line 2767 &lt;Call.java&gt;<br> 
 Call.invoke(..) : line 2443 &lt;Call.java&gt;<br>   Call.invoke(..) :
line 2366 &lt;Call.java&gt;<br>   Call.invoke(..) : line 1812
&lt;Call.java&gt;<br>   SoaplabTask.execute(..) : line 92
&lt;SoaplabTask.java&gt;<br>   ProcessorTask.runAndGenerateTemplates(..) :
line 585 &lt;ProcessorTask.java&gt;<br>  
ProcessorTask.doInvocationWithRetryLogic(..) : line 524
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeOnce(..) : line 443
&lt;ProcessorTask.java&gt;<br>   ProcessorTask.invokeWithoutIteration(..)
: line 652 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.invoke(..) :
line 356 &lt;ProcessorTask.java&gt;<br>   ProcessorTask.handleRun(..) :
line 282 &lt;ProcessorTask.java&gt;<br>   NewState$1.run(..) : line 67
&lt;NewState.java&gt;<br>]
>>


Any ideas!

thanks
regards
Achille

<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0">
  <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:9e93930f-ed90-4443-99db-6843e6ed9328" author="" title="M_proml_boot" />
  <s:processor name="fconsense">
    <s:description>Majority-rule and strict consensus tree</s:description>
    <s:soaplabwsdl interval="3000" backoff="1.0" maxinterval="6000">http://www.ebi.ac.uk/soaplab/services/phylogeny_consensus.fconsense</s:soaplabwsdl>
  </s:processor>
  <s:processor name="fseqboot">
    <s:description>Bootstrapped sequences algorithm</s:description>
    <s:defaults>
      <s:default name="sprotein_sequence">Yes</s:default>
      <s:default name="seqtype">p</s:default>
    </s:defaults>
    <s:soaplabwsdl interval="3000" backoff="1.0" maxinterval="6000">http://www.ebi.ac.uk/soaplab/services/phylogeny_molecular_sequence.fseqboot</s:soaplabwsdl>
  </s:processor>
  <s:processor name="fproml">
    <s:description>Protein phylogeny by maximum likelihood</s:description>
    <s:defaults>
      <s:default name="sprotein_sequence">Yes</s:default>
    </s:defaults>
    <s:soaplabwsdl interval="3000" backoff="1.0" maxinterval="6000">http://www.ebi.ac.uk/soaplab/services/phylogeny_molecular_sequence.fproml</s:soaplabwsdl>
  </s:processor>
  <s:link source="i" sink="fseqboot:sequence_direct_data" />
  <s:link source="fconsense:outfile" sink="o" />
  <s:link source="fconsense:outtreefile" sink="o2" />
  <s:link source="fproml:outfile" sink="a" />
  <s:link source="fproml:outtreefile" sink="fconsense:intreefile_direct_data" />
  <s:link source="fseqboot:outfile" sink="fproml:sequence_direct_data" />
  <s:source name="i" />
  <s:sink name="o" />
  <s:sink name="a" />
  <s:sink name="o2" />
</s:scufl>

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july

_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/

[Taverna-users] soaplab emboss services

Reply via email to