Re: [Taverna-hackers] SADI activity plugin for Taverna

David Withers Wed, 28 Apr 2010 10:39:53 -0700

On 28/04/2010 09:53, Alan Williams wrote:
> David Withers wrote:
>> On 28/04/2010 09:20, Alan Williams wrote:
>>> David Withers wrote:
>>>> Thanks Alex. Which version of java are you using?
>>> I can see it if I run Taverna in Java 1.6.  Did you compile the plugin 
>>> with Java 1.6?
>>
>> No but it's dependencies have been compiled with 1.6
> 
> David, can you send me an example workflow using the services?  I'm 
> probably doing something stupid but I just get back empty lists.


I've attached a very simple workflow.

David.
-- 
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
+44 (0)161 275 0683

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-2.1.0"><dataflow id="21b088ff-c23e-43e2-8505-00f24d18542d" 
role="top"><name>Workflow9</name><inputPorts 
/><outputPorts><port><name>getGOTerm_hasTermName</name><annotations 
/></port></outputPorts><processors><processor><name>getGOTerm</name><inputPorts><port><name>GO_Record</name><depth>1</depth></port></inputPorts><outputPorts><port><name>hasTermName
 
(Literal)</name><depth>2</depth><granularDepth>2</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>sadi-activity</artifact><version>0.2.0-SNAPSHOT</version></raven><class>net.sf.taverna.t2.activities.sadi.SADIActivity</class><inputMap><map
 from="GO_Record" to="GO_Record" /></inputMap><outputMap><map from="hasTermName 
(Literal)" to="hasTermName (Literal)" /></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.sadi.SADIActivityConfigurationBean
 xmlns="">
  <sparqlEndpoint>http://biordf.net/sparql</sparqlEndpoint>
  <graphName>http://sadiframework.org/registry/</graphName>
  <serviceURI>http://sadiframework.org/services/getGOTerm</serviceURI>
  <inputRestrictionPaths>
    <list>
      <string>GO_Record</string>
    </list>
  </inputRestrictionPaths>
  <outputRestrictionPaths>
    <list>
      <string>getGOTerm_Output</string>
      <string>hasTermName (Literal)</string>
    </list>
  </outputRestrictionPaths>
  <attributes />
</net.sf.taverna.t2.activities.sadi.SADIActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</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>1.0</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>1.0</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>1.0</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>1.0</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="GO_Record" depth="1" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>create_list</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map
 from="string" to="string" /></inputMap><outputMap><map from="split" to="split" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean
 xmlns="">
  
<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
  <script>List split = new ArrayList();
if (!string.equals("")) {
        String regexString = ",";
        if (regex != void) {
                regexString = regex;
        }
        String[] result = string.split(regexString);
        for (int i = 0; i &lt; result.length; i++) {
                split.add(result[i]);
        }
}
</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>string</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>regex</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>1</granularDepth>
      <name>split</name>
      <depth>1</depth>
      <mimeTypes>
        <string>l('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>1.0</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>1.0</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>1.0</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>1.0</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>1.0</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="string" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>string_value</name><inputPorts
 
/><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap
 /><outputMap><map from="value" to="value" /></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean
 xmlns="">
  <value>0005515,0005525</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</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>1.0</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>1.0</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>1.0</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>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy
 /></iteration></iterationStrategyStack></processor></processors><conditions 
/><datalinks><datalink><sink 
type="processor"><processor>getGOTerm</processor><port>GO_Record</port></sink><source
 
type="processor"><processor>create_list</processor><port>split</port></source></datalink><datalink><sink
 
type="processor"><processor>create_list</processor><port>string</port></sink><source
 
type="processor"><processor>string_value</processor><port>value</port></source></datalink><datalink><sink
 type="dataflow"><port>getGOTerm_hasTermName</port></sink><source 
type="processor"><processor>getGOTerm</processor><port>hasTermName 
(Literal)</port></source></datalink></datalinks><annotations 
/></dataflow></workflow>

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Re: [Taverna-hackers] SADI activity plugin for Taverna

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