| <?xml version="1.0"?> |
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| * Licensed to the Apache Software Foundation (ASF) under one |
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| * http://www.apache.org/licenses/LICENSE-2.0 |
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| --> |
| <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="a5b440ec-9bc1-4dc6-98b1-6c41fa17a21a" role="top"><name>Workflow1</name><inputPorts><port><name>ID</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns=""> |
| <annotationAssertions> |
| <net.sf.taverna.t2.annotation.AnnotationAssertionImpl> |
| <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue"> |
| <text>P15409</text> |
| </annotationBean> |
| <date>2013-07-25 10:20:45.653 UTC</date> |
| <creators /> |
| <curationEventList /> |
| </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> |
| </annotationAssertions> |
| </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>sequence</name><annotations /></port><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><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>1.4</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=""> |
| <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&db=protein&retmode=text&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 <= 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>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>pscan</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outfile</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outfile" to="outfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns=""> |
| <endpoint>http://wsembnet.vital-it.ch/soaplab2/services/protein_motifs.pscan</endpoint> |
| <pollingInterval>0</pollingInterval> |
| <pollingBackoff>1.0</pollingBackoff> |
| <pollingIntervalMax>0</pollingIntervalMax> |
| </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="sequence_direct_data" 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><datalink><sink type="processor"><processor>pscan</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>pscanOut</port></sink><source type="processor"><processor>pscan</processor><port>outfile</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>ce96163a-d930-4e1a-b000-a35b847ef7b4</identification> |
| </annotationBean> |
| <date>2013-07-25 10:20:51.37 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>a5b440ec-9bc1-4dc6-98b1-6c41fa17a21a</identification> |
| </annotationBean> |
| <date>2013-07-25 10:24:17.837 UTC</date> |
| <creators /> |
| <curationEventList /> |
| </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> |
| </annotationAssertions> |
| </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow> |
