Re: [Taverna-hackers] Dot product for implicit iterator?

Thu, 08 Apr 2010 08:12:41 -0700 

Paul Gordon wrote:

Hi all,


Hello,


When I try to use a dot product on input ports that are of depth 0, the 
workflow does not validate.  Is there any kung foo I can use to get this 
to work?  I am trying to do the following


    x
    | \
    y |
    |  /
    z


Where all ports have depth 0, but when it goes to processor z, I want 
each iteration of x's output to only be matched up with its 
corresponding output from processor y.  So a cross product (which does 
validate) is not an option.


Is x being called multiple times?


Thanks for any help you can provide, I'm stumped on this one!



I'm attaching a workflow that does what you describe (assuming you are 
feeding a list into x) and it works OK.



Paul


Alan

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-2.1.2"><dataflow id="8c4ba7a4-3d5c-45a4-8b6e-31a8a84b3364" 
role="top"><name>Workflow21</name><inputPorts><port><name>input</name><depth>1</depth><granularDepth>1</granularDepth><annotations
 /></port></inputPorts><outputPorts><port><name>result</name><annotations 
/></port></outputPorts><processors><processor><name>addFred</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out0</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>1.1</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
 from="in0" to="in0" /></inputMap><outputMap><map from="out0" to="out0" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
 xmlns="">
  <script>out0 = in0 + " fred";</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>in0</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>out0</name>
      <depth>0</depth>
      <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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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="in0" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>addBob</name><inputPorts><port><name>in0</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out0</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>1.1</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
 from="in0" to="in0" /></inputMap><outputMap><map from="out0" to="out0" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
 xmlns="">
  <script>out0 = in0 + " bob";</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>in0</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>out0</name>
      <depth>0</depth>
      <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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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="in0" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.1</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map
 from="string1" to="string1" /><map from="string2" to="string2" 
/></inputMap><outputMap><map from="output" to="output" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean
 xmlns="">
  
<localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
  <script>output = string1 + string2;</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>string1</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>string2</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>output</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.localworker.LocalworkerActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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.core</group><artifact>workflowmodel-impl</artifact><version>1.1</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port
 name="string2" depth="0" /><port name="string1" depth="0" 
/></dot></strategy></iteration></iterationStrategyStack></processor></processors><conditions
 /><datalinks><datalink><sink 
type="processor"><processor>addFred</processor><port>in0</port></sink><source 
type="dataflow"><port>input</port></source></datalink><datalink><sink 
type="processor"><processor>addBob</processor><port>in0</port></sink><source 
type="processor"><processor>addFred</processor><port>out0</port></source></datalink><datalink><sink
 
type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source
 
type="processor"><processor>addFred</processor><port>out0</port></source></datalink><datalink><sink
 
type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source
 
type="processor"><processor>addBob</processor><port>out0</port></source></datalink><datalink><sink
 type="dataflow"><port>result</port></sink><source 
type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations
 /></dataflow></workflow>
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