taverna-t2flow 0.2.0 → 0.3.0
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- data/CHANGES.rdoc +16 -0
- data/README.rdoc +30 -21
- data/Rakefile +54 -0
- data/lib/t2flow/model.rb +7 -0
- data/lib/t2flow/parser.rb +7 -2
- data/taverna-t2flow.gemspec +76 -0
- data/test/fixtures/1000.t2flow +244 -0
- data/test/fixtures/1001.t2flow +321 -0
- data/test/fixtures/1002.t2flow +474 -0
- data/test/fixtures/1003.t2flow +292 -0
- data/test/fixtures/1004.t2flow +73 -0
- data/test/fixtures/996.t2flow +193 -0
- data/test/fixtures/997.t2flow +359 -0
- data/test/fixtures/998.t2flow +324 -0
- data/test/fixtures/999.t2flow +604 -0
- data/test/fixtures/basic.t2flow +94 -0
- data/test/fixtures/coordinated.t2flow +63 -0
- data/test/fixtures/linked.t2flow +88 -0
- data/test/fixtures/nested.t2flow +270 -0
- data/test/fixtures/processors.t2flow +174 -0
- data/test/run_tests.rb +7 -0
- data/test/test_bogus_workflows.rb +80 -0
- data/test/test_helper.rb +50 -0
- data/test/test_starter_pack_workflows.rb +132 -0
- metadata +121 -69
- data/ChangeLog.rdoc +0 -7
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="fff84443-6f1c-4dd1-bb0c-fc1e489a1ca5" role="top"><name>EBI_InterProScan</name><inputPorts><port><name>Email_address</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationAssertions>
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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<text />
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</annotationBean>
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<date>2009-07-03 10:05:00.847 BST</date>
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<creators />
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<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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<text>Your email address (for EBI statistics on job submissions)</text>
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</annotationBean>
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<date>2009-07-03 10:04:37.551 BST</date>
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<creators />
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<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationAssertions>
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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<text>Sequence or </text>
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</annotationBean>
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<date>2009-07-03 10:04:44.374 BST</date>
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<creators />
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>Sequence_or_ID</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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<text>, for example uniprot:wap_rat</text>
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</annotationBean>
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<date>2009-07-03 10:05:09.391 BST</date>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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<text>uniprot:wap_rat</text>
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<date>2009-07-03 10:05:14.247 BST</date>
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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<text>Sequence or ID</text>
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</annotationBean>
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<date>2009-07-03 10:05:12.358 BST</date>
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<creators />
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<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>InterProScan_text_result</name><annotations /></port><port><name>InterProScan_XML_result</name><annotations /></port><port><name>Job_ID</name><annotations /></port><port><name>InterProScan_GFF</name><annotations /></port><port><name>status</name><annotations /></port></outputPorts><processors><processor><name>Input_data</name><inputPorts><port><name>content</name><depth>0</depth></port><port><name>type</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>wsdl-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="content" to="content" /><map from="type" to="type" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
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<wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="data" name="" qname="{http://www.ebi.ac.uk/WSInterProScan}data"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="data&gt;type" /><s:basetype optional="false" unbounded="false" typename="string" name="content" qname="data&gt;content" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>type</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>content</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>0</granularDepth>
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<name>output</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/xml'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></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="">
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<maxJobs>1</maxJobs>
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</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="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>0</initialDelay>
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
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</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="type" depth="0" /><port name="content" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_XML_result</name><inputPorts><port><name>jobid</name><depth>0</depth></port><port><name>type</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port><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>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="type" to="type" /><map from="jobid" to="jobid" /></inputMap><outputMap><map from="result" to="result" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
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<wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
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<operation>poll</operation>
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</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></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="">
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<maxJobs>1</maxJobs>
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</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="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>0</initialDelay>
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
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</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="jobid" depth="0" /><port name="type" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Format_as_GFF</name><inputPorts><port><name>interproscan_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>interproscan_gff</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>1.0</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="interproscan_text" to="interproscan_text" /></inputMap><outputMap><map from="interproscan_gff" to="interproscan_gff" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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<script>import java.util.StringTokenizer;
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interproscan_gff = "";
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// Split into lines
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StringTokenizer tok1 = new StringTokenizer(interproscan_text, "\n");
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while(tok1.hasMoreElements()) {
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feat1 = tok1.nextElement();
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// Split into fields
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StringTokenizer tok2 = new StringTokenizer(feat1, "\t");
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fieldCount = 0;
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attributeStr = "";
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while(tok2.hasMoreElements()) {
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fieldCount++;
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fieldStr = tok2.nextElement();
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if(fieldCount < 2) { // First field is the ID
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interproscan_gff += fieldStr;
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}
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// The tool, feature, start and stop
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else if(fieldCount == 4 || (fieldCount > 5 && fieldCount < 9)) {
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interproscan_gff += "\t" + fieldStr;
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}
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// Score
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else if(fieldCount == 9) {
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if(fieldStr.equals("NA")) {
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interproscan_gff += "\t.";
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} else {
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interproscan_gff += "\t" + fieldStr;
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}
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}
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// Matching InterPro entry
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else if(fieldCount == 12 && !fieldStr.equals("NULL")) {
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attributeStr += fieldStr;
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}
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// Matching InterPro entry name
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else if(fieldCount == 13 && !fieldStr.equals("NULL")) {
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attributeStr += " " + fieldStr;
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}
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}
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interproscan_gff += "\t.\t.\tInterProScan";
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if(attributeStr.length() > 0) {
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interproscan_gff += " ; " + attributeStr;
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}
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interproscan_gff += "\n";
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}</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>interproscan_text</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>0</granularDepth>
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<name>interproscan_gff</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain'</string>
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</outputs>
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
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</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="interproscan_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Job_params</name><inputPorts><port><name>seqtype</name><depth>0</depth></port><port><name>crc</name><depth>0</depth></port><port><name>goterms</name><depth>0</depth></port><port><name>async</name><depth>0</depth></port><port><name>email</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>wsdl-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="crc" to="crc" /><map from="goterms" to="goterms" /><map from="email" to="email" /><map from="seqtype" to="seqtype" /><map from="async" to="async" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
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<wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="inputParams" name="params" qname="{http://www.ebi.ac.uk/WSInterProScan}inputParams"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="app" qname="inputParams&gt;app" /><s:basetype optional="false" unbounded="false" typename="boolean" name="crc" qname="inputParams&gt;crc" /><s:basetype optional="false" unbounded="false" typename="string" name="seqtype" qname="inputParams&gt;seqtype" /><s:basetype optional="false" unbounded="false" typename="int" name="trlen" qname="inputParams&gt;trlen" /><s:basetype optional="false" unbounded="false" typename="int" name="trtable" qname="inputParams&gt;trtable" /><s:basetype optional="false" unbounded="false" typename="boolean" name="goterms" qname="inputParams&gt;goterms" /><s:basetype optional="false" unbounded="false" typename="boolean" name="async" qname="inputParams&gt;async" /><s:basetype optional="false" unbounded="false" typename="string" name="outformat" qname="inputParams&gt;outformat" /><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="inputParams&gt;email" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>app</name>
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<string>'text/plain'</string>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>crc</name>
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<depth>0</depth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>seqtype</name>
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<depth>0</depth>
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<mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>trlen</name>
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<depth>0</depth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>trtable</name>
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<depth>0</depth>
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<mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>goterms</name>
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<depth>0</depth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>async</name>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>outformat</name>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>email</name>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>0</granularDepth>
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<name>output</name>
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<depth>0</depth>
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<string>'text/xml'</string>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></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="">
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<maxJobs>1</maxJobs>
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</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="">
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<backoffFactor>1.0</backoffFactor>
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|
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<initialDelay>0</initialDelay>
|
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<maxDelay>0</maxDelay>
|
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<maxRetries>0</maxRetries>
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</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="crc" depth="0" /><port name="seqtype" depth="0" /><port name="goterms" depth="0" /><port name="async" depth="0" /><port name="email" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_text_result</name><inputPorts><port><name>type</name><depth>0</depth></port><port><name>jobid</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port><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>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="type" to="type" /><map from="jobid" to="jobid" /></inputMap><outputMap><map from="result" to="result" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
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|
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<wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
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|
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<operation>poll</operation>
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|
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</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></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="">
|
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<maxJobs>1</maxJobs>
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</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="">
|
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|
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<backoffFactor>1.0</backoffFactor>
|
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|
+
<initialDelay>0</initialDelay>
|
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|
+
<maxDelay>0</maxDelay>
|
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|
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<maxRetries>0</maxRetries>
|
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|
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</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="jobid" depth="0" /><port name="type" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>runInterProScan</name><inputPorts><port><name>content</name><depth>0</depth></port><port><name>params</name><depth>0</depth></port></inputPorts><outputPorts><port><name>jobid</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="content" to="content" /><map from="params" to="params" /></inputMap><outputMap><map from="attachmentList" to="attachmentList" /><map from="jobid" to="jobid" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
|
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|
+
<wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
|
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|
+
<operation>runInterProScan</operation>
|
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|
+
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></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="">
|
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|
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<maxJobs>1</maxJobs>
|
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|
+
</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="">
|
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|
+
<backoffFactor>1.0</backoffFactor>
|
|
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|
+
<initialDelay>0</initialDelay>
|
|
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|
+
<maxDelay>0</maxDelay>
|
|
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|
+
<maxRetries>0</maxRetries>
|
|
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|
+
</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="params" depth="0" /><port name="content" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Content_list</name><inputPorts><port><name>WSArrayofData</name><depth>1</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>wsdl-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="WSArrayofData" to="WSArrayofData" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
|
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|
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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341
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342
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343
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344
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345
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346
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347
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<mimeTypes>
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348
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<string>'text/xml'</string>
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349
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350
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351
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352
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353
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354
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355
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359
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360
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361
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362
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363
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364
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365
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368
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|
369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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380
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381
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382
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383
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384
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385
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386
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|
387
|
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388
|
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389
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390
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391
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396
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398
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400
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401
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405
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407
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|
414
|
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415
|
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416
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417
|
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</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 /></strategy></iteration></iterationStrategyStack></processor><processor><name>checkStatus</name><inputPorts><port><name>jobid</name><depth>0</depth></port></inputPorts><outputPorts><port><name>status</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>1.0</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="jobid" to="jobid" /></inputMap><outputMap><map from="status" to="status" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
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<wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
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<operation>checkStatus</operation>
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</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></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="">
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<maxJobs>1</maxJobs>
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</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.Loop</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration xmlns="">
|
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428
|
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<conditionXML><activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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<script>loop = "" + status.equals("RUNNING");</script>
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|
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<dependencies />
|
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431
|
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<classLoaderSharing>workflow</classLoaderSharing>
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432
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<localDependencies />
|
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433
|
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<artifactDependencies />
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<inputs>
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435
|
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>status</name>
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<depth>0</depth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
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+
<granularDepth>0</granularDepth>
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<name>loop</name>
|
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|
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<depth>0</depth>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
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|
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</outputs>
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+
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></conditionXML>
|
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|
+
<runFirst>true</runFirst>
|
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|
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<properties>
|
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|
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<property name="compareValue" value="RUNNING" />
|
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|
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<property name="comparePort" value="status" />
|
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|
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<property name="isFeedBack" value="false" />
|
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|
+
<property name="comparison" value="custom" />
|
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|
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</properties>
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration></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="">
|
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458
|
+
<backoffFactor>1.0</backoffFactor>
|
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|
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<initialDelay>1000</initialDelay>
|
|
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|
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<maxDelay>5000</maxDelay>
|
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|
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<maxRetries>0</maxRetries>
|
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|
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</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="jobid" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Unpack_text_result</name><inputPorts><port><name>bytes</name><depth>0</depth></port></inputPorts><outputPorts><port><name>string</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="bytes" to="bytes" /></inputMap><outputMap><map from="string" to="string" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
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463
|
+
<localworkerName>org.embl.ebi.escience.scuflworkers.java.ByteArrayToString</localworkerName>
|
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|
+
<script>string = new String(bytes);
|
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|
+
</script>
|
|
466
|
+
<dependencies />
|
|
467
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
|
468
|
+
<localDependencies />
|
|
469
|
+
<artifactDependencies />
|
|
470
|
+
<inputs>
|
|
471
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
472
|
+
<handledReferenceSchemes />
|
|
473
|
+
<translatedElementType>[B</translatedElementType>
|
|
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|
+
<allowsLiteralValues>true</allowsLiteralValues>
|
|
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|
+
<name>bytes</name>
|
|
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|
+
<depth>0</depth>
|
|
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|
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<mimeTypes>
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|
+
<string>'application/octet-stream'</string>
|
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|
+
</mimeTypes>
|
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
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|
+
</inputs>
|
|
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|
+
<outputs>
|
|
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|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
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|
+
<granularDepth>0</granularDepth>
|
|
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|
+
<name>string</name>
|
|
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|
+
<depth>0</depth>
|
|
487
|
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<mimeTypes>
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|
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|
+
<string>'text/plain'</string>
|
|
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|
+
</mimeTypes>
|
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
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|
+
</outputs>
|
|
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|
+
</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="">
|
|
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|
+
<maxJobs>1</maxJobs>
|
|
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|
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</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="">
|
|
495
|
+
<backoffFactor>1.0</backoffFactor>
|
|
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|
+
<initialDelay>1000</initialDelay>
|
|
497
|
+
<maxDelay>5000</maxDelay>
|
|
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|
+
<maxRetries>0</maxRetries>
|
|
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|
+
</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="bytes" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Unpack_XML_result</name><inputPorts><port><name>bytes</name><depth>0</depth></port></inputPorts><outputPorts><port><name>string</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="bytes" to="bytes" /></inputMap><outputMap><map from="string" to="string" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
|
500
|
+
<localworkerName>org.embl.ebi.escience.scuflworkers.java.ByteArrayToString</localworkerName>
|
|
501
|
+
<script>string = new String(bytes);
|
|
502
|
+
</script>
|
|
503
|
+
<dependencies />
|
|
504
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
|
505
|
+
<localDependencies />
|
|
506
|
+
<artifactDependencies />
|
|
507
|
+
<inputs>
|
|
508
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
509
|
+
<handledReferenceSchemes />
|
|
510
|
+
<translatedElementType>[B</translatedElementType>
|
|
511
|
+
<allowsLiteralValues>true</allowsLiteralValues>
|
|
512
|
+
<name>bytes</name>
|
|
513
|
+
<depth>0</depth>
|
|
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|
+
<mimeTypes>
|
|
515
|
+
<string>'application/octet-stream'</string>
|
|
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|
+
</mimeTypes>
|
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
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|
+
</inputs>
|
|
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|
+
<outputs>
|
|
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|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
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|
+
<granularDepth>0</granularDepth>
|
|
522
|
+
<name>string</name>
|
|
523
|
+
<depth>0</depth>
|
|
524
|
+
<mimeTypes>
|
|
525
|
+
<string>'text/plain'</string>
|
|
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|
+
</mimeTypes>
|
|
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|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
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|
+
</outputs>
|
|
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|
+
</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="">
|
|
530
|
+
<maxJobs>1</maxJobs>
|
|
531
|
+
</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="">
|
|
532
|
+
<backoffFactor>1.0</backoffFactor>
|
|
533
|
+
<initialDelay>1000</initialDelay>
|
|
534
|
+
<maxDelay>5000</maxDelay>
|
|
535
|
+
<maxRetries>0</maxRetries>
|
|
536
|
+
</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="bytes" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions><condition control="checkStatus" target="Get_XML_result" /><condition control="checkStatus" target="Get_text_result" /></conditions><datalinks><datalink><sink type="processor"><processor>Input_data</processor><port>content</port></sink><source type="dataflow"><port>Sequence_or_ID</port></source></datalink><datalink><sink type="processor"><processor>Input_data</processor><port>type</port></sink><source type="processor"><processor>Input_data_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_XML_result</processor><port>jobid</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>Get_XML_result</processor><port>type</port></sink><source type="processor"><processor>Get_XML_result_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Format_as_GFF</processor><port>interproscan_text</port></sink><source type="processor"><processor>Unpack_text_result</processor><port>string</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>seqtype</port></sink><source type="processor"><processor>Job_params_seqtype_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>crc</port></sink><source type="processor"><processor>Job_params_crc_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>goterms</port></sink><source type="processor"><processor>Job_params_goterms_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>async</port></sink><source type="processor"><processor>Job_params_async_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>email</port></sink><source type="dataflow"><port>Email_address</port></source></datalink><datalink><sink type="processor"><processor>Get_text_result</processor><port>type</port></sink><source type="processor"><processor>Get_text_result_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_text_result</processor><port>jobid</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>runInterProScan</processor><port>content</port></sink><source type="processor"><processor>Content_list</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>runInterProScan</processor><port>params</port></sink><source type="processor"><processor>Job_params</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Content_list</processor><port>WSArrayofData</port></sink><source type="processor"><processor>Input_data</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>checkStatus</processor><port>jobid</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>Unpack_text_result</processor><port>bytes</port></sink><source type="processor"><processor>Get_text_result</processor><port>result</port></source></datalink><datalink><sink type="processor"><processor>Unpack_XML_result</processor><port>bytes</port></sink><source type="processor"><processor>Get_XML_result</processor><port>result</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_text_result</port></sink><source type="processor"><processor>Unpack_text_result</processor><port>string</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_XML_result</port></sink><source type="processor"><processor>Unpack_XML_result</processor><port>string</port></source></datalink><datalink><sink type="dataflow"><port>Job_ID</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_GFF</port></sink><source type="processor"><processor>Format_as_GFF</processor><port>interproscan_gff</port></source></datalink><datalink><sink type="dataflow"><port>status</port></sink><source type="processor"><processor>checkStatus</processor><port>status</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
537
|
+
<annotationAssertions>
|
|
538
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
539
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
|
|
540
|
+
<text>Hamish McWilliam</text>
|
|
541
|
+
</annotationBean>
|
|
542
|
+
<date>2009-02-03 09:38:48.949 GMT</date>
|
|
543
|
+
<creators />
|
|
544
|
+
<curationEventList />
|
|
545
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
546
|
+
</annotationAssertions>
|
|
547
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
548
|
+
<annotationAssertions>
|
|
549
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
550
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
|
|
551
|
+
<text>Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
|
|
552
|
+
|
|
553
|
+
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the signatures are returned, which are annotated with the corresponding InterPro and GO term assignments for these signature matches.</text>
|
|
554
|
+
</annotationBean>
|
|
555
|
+
<date>2009-02-03 09:38:48.949 GMT</date>
|
|
556
|
+
<creators />
|
|
557
|
+
<curationEventList />
|
|
558
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
559
|
+
</annotationAssertions>
|
|
560
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
561
|
+
<annotationAssertions>
|
|
562
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
563
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
|
|
564
|
+
<text>EBI_InterProScan_T2</text>
|
|
565
|
+
</annotationBean>
|
|
566
|
+
<date>2009-05-26 14:59:16.89 BST</date>
|
|
567
|
+
<creators />
|
|
568
|
+
<curationEventList />
|
|
569
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
570
|
+
</annotationAssertions>
|
|
571
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
572
|
+
<annotationAssertions>
|
|
573
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
574
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
|
|
575
|
+
<text>EBI_InterProScan</text>
|
|
576
|
+
</annotationBean>
|
|
577
|
+
<date>2009-02-03 09:38:48.949 GMT</date>
|
|
578
|
+
<creators />
|
|
579
|
+
<curationEventList />
|
|
580
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
581
|
+
</annotationAssertions>
|
|
582
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
583
|
+
<annotationAssertions>
|
|
584
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
585
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
|
|
586
|
+
<text>EBI_InterProScan for Taverna 2</text>
|
|
587
|
+
</annotationBean>
|
|
588
|
+
<date>2009-05-26 14:53:47.508 BST</date>
|
|
589
|
+
<creators />
|
|
590
|
+
<curationEventList />
|
|
591
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
592
|
+
</annotationAssertions>
|
|
593
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
594
|
+
<annotationAssertions>
|
|
595
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
596
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
|
|
597
|
+
<text>Hamish McWilliam. Modified by Katy Wolstencroft and Stian Soiland-Reyes</text>
|
|
598
|
+
</annotationBean>
|
|
599
|
+
<date>2009-05-26 14:53:32.664 BST</date>
|
|
600
|
+
<creators />
|
|
601
|
+
<curationEventList />
|
|
602
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
603
|
+
</annotationAssertions>
|
|
604
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
|