taverna workkflow

gistfile1.txt

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-core-2.5.0"><dataflow id="752f564d-f407-4495-a48e-f6e866787edc" role="top"><name>Workflow1</name><inputPorts><port><name>ID</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>pscanOut</name><annotations /></port></outputPorts><processors><processor><name>Get_Protein_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.5</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
  <inputs>
    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <name>id</name>
      <depth>0</depth>
      <mimeTypes>
        <string>'text/plain'</string>
      </mimeTypes>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
  </inputs>
  <outputs>
    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <name>outputText</name>
      <depth>0</depth>
      <mimeTypes>
        <string>'text/plain'</string>
      </mimeTypes>
      <granularDepth>0</granularDepth>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
  <classLoaderSharing>workflow</classLoaderSharing>
  <localDependencies />
  <artifactDependencies />
  <script>if ((id == void) || (id == null) || id.equals("")) {
	throw new RunTimeException("port id must have a non-empty value");
}

URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=protein&amp;retmode=text&amp;id=" + id);

BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
StringWriter writer = new StringWriter();

char[] buffer = new char[1024];
    while (true) {
        int r = reader.read(buffer);
        if (r &lt;= 0) {
            break;
        }
        writer.write(buffer, 0, r);
    }
reader.close();
outputText = writer.toString();
</script>
  <dependencies />
  <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker</localworkerName>
</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>1.5</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>1.5</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>1.5</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>1.5</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>1.5</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Protein_FASTA</processor><port>id</port></sink><source type="dataflow"><port>ID</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>752f564d-f407-4495-a48e-f6e866787edc</identification>
      </annotationBean>
      <date>2016-03-14 13:21:04.777 UTC</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>d7cb855c-cc9f-4b69-9251-92105b81ce79</identification>
      </annotationBean>
      <date>2016-03-14 06:17:44.301 UTC</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>