SatelliteG-language: getFasta2gcskew.t2flow

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1"><dataflow id="8c24ae0c-5db9-4cdc-8aa8-15e10cefd334" role="top"><name>dataflow0</name><inputPorts><port><name>id</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>window</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>cumulative</name><depth>0</depth><granularDepth>0</granularDepth></port></inputPorts><outputPorts><port><name>image_gcskew</name></port><port><name>outseq</name></port><port><name>param</name></port></outputPorts><processors><processor><name>Get_Nucleotide_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>0.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
  <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=nucleotide&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);
    }
outputText = writer.toString();
</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>id</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>outputText</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</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>
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  <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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gcskew</name><inputPorts><port><name>in0</name><depth>0</depth></port><port><name>params</name><depth>0</depth></port></inputPorts><outputPorts><port><name>result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="in0" to="in0" /><map from="params" to="params" /></inputMap><outputMap><map from="result" to="result" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
  <wsdl>http://www.g-language.org/g-language.wsdl</wsdl>
  <operation>gcskew</operation>
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></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="in0" depth="0" /><port name="params" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Image_From_URL</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>image</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>0.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="url" to="url" /></inputMap><outputMap><map from="image" to="image" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
  <script>URL inputURL = null;
if (base != void) {
        inputURL = new URL(new URL(base), url);
} else {
        inputURL = new URL(url);
}

byte[] contents;
if (inputURL.openConnection().getContentLength() == -1) {
        // Content size unknown, must read first...
        byte[] buffer = new byte[1024];
        int bytesRead = 0;
        int totalBytesRead = 0;
        InputStream is = inputURL.openStream();
        while (bytesRead != -1) {
                totalBytesRead += bytesRead;
                bytesRead = is.read(buffer, 0, 1024);
        }
        contents = new byte[totalBytesRead];
} else {
        contents = new byte[inputURL.openConnection().getContentLength()];
}
int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
while (bytesRead != -1) {
        bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
        totalBytesRead += bytesRead;
        if (contents.length==totalBytesRead) break;
}

image = contents;
</script>
  <dependencies />
  <classLoaderSharing>workflow</classLoaderSharing>
  <localDependencies />
  <artifactDependencies />
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    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
      <name>url</name>
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        <string>'text/x-taverna-web-url'</string>
      </mimeTypes>
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    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <handledReferenceSchemes />
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      <name>base</name>
      <depth>0</depth>
      <mimeTypes>
        <string>'text/x-taverna-web-url'</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>image</name>
      <depth>0</depth>
      <mimeTypes>
        <string>'image/*'</string>
      </mimeTypes>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
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  <maxJobs>1</maxJobs>
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  <wrappedTypeXML>&lt;s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"&gt;&lt;s:complextype optional="false" unbounded="false" typename="gcskewInputParams" name="params" qname="{http://www.g-language.org/GLANG}gcskewInputParams"&gt;&lt;s:elements&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="window" qname="gcskewInputParams&amp;gt;window" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="string" name="filename" qname="gcskewInputParams&amp;gt;filename" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="at" qname="gcskewInputParams&amp;gt;at" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="purine" qname="gcskewInputParams&amp;gt;purine" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="string" name="output" qname="gcskewInputParams&amp;gt;output" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="cumulative" qname="gcskewInputParams&amp;gt;cumulative" /&gt;&lt;s:basetype optional="false" unbounded="false" typename="int" name="keto" qname="gcskewInputParams&amp;gt;keto" /&gt;&lt;/s:elements&gt;&lt;/s:complextype&gt;&lt;/s:extensions&gt;</wrappedTypeXML>
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      </mimeTypes>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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      </mimeTypes>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
  </inputs>
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    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <granularDepth>0</granularDepth>
      <name>output</name>
      <depth>0</depth>
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      </mimeTypes>
    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
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  <maxJobs>1</maxJobs>
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</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="window" depth="0" /><port name="cumulative" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Nucleotide_FASTA</processor><port>id</port></sink><source type="dataflow"><port>id</port></source></datalink><datalink><sink type="processor"><processor>gcskew</processor><port>in0</port></sink><source type="processor"><processor>Get_Nucleotide_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="processor"><processor>gcskew</processor><port>params</port></sink><source type="processor"><processor>gcskew_params</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Get_Image_From_URL</processor><port>url</port></sink><source type="processor"><processor>gcskew</processor><port>result</port></source></datalink><datalink><sink type="processor"><processor>gcskew_params</processor><port>window</port></sink><source type="dataflow"><port>window</port></source></datalink><datalink><sink type="processor"><processor>gcskew_params</processor><port>cumulative</port></sink><source type="dataflow"><port>cumulative</port></source></datalink><datalink><sink type="dataflow"><port>image_gcskew</port></sink><source type="processor"><processor>Get_Image_From_URL</processor><port>image</port></source></datalink><datalink><sink type="dataflow"><port>outseq</port></sink><source type="processor"><processor>Get_Nucleotide_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>param</port></sink><source type="processor"><processor>gcskew</processor><port>result</port></source></datalink></datalinks><annotations /></dataflow></workflow>