Re: [Taverna-users] Taverna2 weird output while processing list: bug?

Thu, 12 Mar 2009 06:20:34 -0700 

Hello
I get a similar output even with the beanshell processors. Workflow attached. 
The inputs are list with depth one.

Regards
Ketan

Paul Fisher wrote:

Hi,
Just from looking at your diagram, it seems that you have multiple outputs going into the same inputs of each processor. E.g. Image_crop has 2 outputs that look as if they are going into the same input. This may be causing your problem, especially if you have some iteration strategy on each processor/service. I could be wrong though. After all, I'm only looking at your workflow with no ports showing. 

Paul.

Ketan wrote:

Hello
I am trying to run a workflow that accepts a list of depth 1 as input.
The workflow runs into some java exception for a missing library.
But on the interface I get a weird output in the form of a list of too much depth. 

Screenshot attached.

Regards
Ketan.

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------------------------------------------------------------------------------
Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
easily build your RIAs with Flex Builder, the Eclipse(TM)based development
software that enables intelligent coding and step-through debugging.
Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
_______________________________________________
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Documentation: http://www.mygrid.org.uk/usermanual1.7/
FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"><dataflow 
id="5aa4c36c-0f26-4fa4-b58f-fcb55ec0d0a9" 
role="top"><name>dataflow0</name><inputPorts><port><name>Patient_Data</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Config</name><depth>1</depth><granularDepth>1</granularDepth></port></inputPorts><outputPorts><port><name>Results</name></port></outputPorts><processors><processor><name>Image_Crop</name><inputPorts><port><name>DataIn</name><depth>0</depth></port><port><name>ConfigIn</name><depth>0</depth></port></inputPorts><outputPorts><port><name>DataOut</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>ConfigOut</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
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/></inputMap><outputMap><map from="DataOut" to="DataOut" /><map 
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print(configIn);</script>
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  <outputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <granularDepth>0</granularDepth>
      <name>DataOut</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <granularDepth>0</granularDepth>
      <name>ConfigOut</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
 xmlns="">
  <maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
 xmlns="">
  <backoffFactor>1.0</backoffFactor>
  <initialDelay>1000</initialDelay>
  <maxDelay>5000</maxDelay>
  <maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
 name="ConfigIn" depth="0" /><port name="DataIn" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Motion_Estimation</name><inputPorts><port><name>DataFromGC</name><depth>0</depth></port><port><name>ConfigFromGC</name><depth>0</depth></port><port><name>ConfigFromBD</name><depth>0</depth></port><port><name>DataFromBD</name><depth>0</depth></port></inputPorts><outputPorts><port><name>DataOut</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
 from="ConfigFromBD" to="ConfigFromBD" /><map from="DataFromGC" to="DataFromGC" 
/><map from="ConfigFromGC" to="ConfigFromGC" /><map from="DataFromBD" 
to="DataFromBD" /></inputMap><outputMap><map from="DataOut" to="DataOut" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
 xmlns="">
  <script />
  <dependencies />
  <classLoaderSharing>workflow</classLoaderSharing>
  <localDependencies />
  <artifactDependencies />
  <inputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
      <name>DataFromGC</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
      <name>DataFromBD</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
      <name>ConfigFromGC</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
      <name>ConfigFromBD</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
  </inputs>
  <outputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <granularDepth>0</granularDepth>
      <name>DataOut</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
 xmlns="">
  <maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
 xmlns="">
  <backoffFactor>1.0</backoffFactor>
  <initialDelay>1000</initialDelay>
  <maxDelay>5000</maxDelay>
  <maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
 name="DataFromGC" depth="0" /><port name="ConfigFromGC" depth="0" /><port 
name="ConfigFromBD" depth="0" /><port name="DataFromBD" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
 /><datalinks><datalink><sink 
type="processor"><processor>Image_Crop</processor><port>DataIn</port></sink><source
 type="dataflow"><port>Patient_Data</port></source></datalink><datalink><sink 
type="processor"><processor>Image_Crop</processor><port>ConfigIn</port></sink><source
 type="dataflow"><port>Config</port></source></datalink><datalink><sink 
type="processor"><processor>Interpolation</processor><port>DataIn</port></sink><source
 
type="processor"><processor>Image_Crop</processor><port>DataOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Interpolation</processor><port>ConfigIn</port></sink><source
 
type="processor"><processor>Image_Crop</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>DataIn</port></sink><source
 
type="processor"><processor>Interpolation</processor><port>DataOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>ConfigIn</port></sink><source
 
type="processor"><processor>Interpolation</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Gradient_Computing</processor><port>ConfigIn</port></sink><source
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Gradient_Computing</processor><port>DataIn</port></sink><source
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>DataOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Border_Detection</processor><port>ConfigIn</port></sink><source
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Border_Detection</processor><port>DataIn</port></sink><source
 
type="processor"><processor>Image_Pyramid_Decomposition</processor><port>DataOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Motion_Estimation</processor><port>DataFromGC</port></sink><source
 
type="processor"><processor>Gradient_Computing</processor><port>DataOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Motion_Estimation</processor><port>ConfigFromGC</port></sink><source
 
type="processor"><processor>Gradient_Computing</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Motion_Estimation</processor><port>ConfigFromBD</port></sink><source
 
type="processor"><processor>Border_Detection</processor><port>ConfigOut</port></source></datalink><datalink><sink
 
type="processor"><processor>Motion_Estimation</processor><port>DataFromBD</port></sink><source
 
type="processor"><processor>Border_Detection</processor><port>DataOut</port></source></datalink><datalink><sink
 type="dataflow"><port>Results</port></sink><source 
type="processor"><processor>Motion_Estimation</processor><port>DataOut</port></source></datalink></datalinks><annotations
 /></dataflow></workflow>
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