<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="a0059959-9a35-4366-b5c7-af22146bfaaf" role="top"><name>Workflow37</name><inputPorts><port><name>AGI_identifier</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>result</name><annotations /></port></outputPorts><processors><processor><name>GabiPDCheckMaterialByAGI</name><inputPorts><port><name>Object(Identifier)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>BasicClone(Collection - 'Material' As Simples)</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyActivity</class><inputMap><map from="Object(Identifier)" to="Object(Identifier)" /></inputMap><outputMap><map from="BasicClone(Collection - 'Material' As Simples)" to="BasicClone(Collection - 'Material' As Simples)" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean xmlns=""> <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint> <serviceName>GabiPDCheckMaterialByAGI</serviceName> <authorityName>www.gabipd.org</authorityName> <category /> <serviceType /> <secondaries /> </net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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>1.2</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>1.2</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>1.2</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>1.2</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="Object(Identifier)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Object</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mobyData</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="mobyData" to="mobyData" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean xmlns=""> <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint> <serviceName>Object</serviceName> <authorityName>openinformatics.com</authorityName> </net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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>1.2</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>1.2</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>1.2</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>1.2</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>Parse Moby Data(BasicClone)</name><inputPorts><port><name>mobyData('BasicClone')</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Material_'Identifier'</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Material_'Kind'</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Material_'AccessPageUrl'</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Material_'Sequence'_'Length'</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Material_'Sequence'_'SequenceString'</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity</class><inputMap><map from="mobyData('BasicClone')" to="mobyData('BasicClone')" /></inputMap><outputMap><map from="Material_'Sequence'_'SequenceString'" to="Material_'Sequence'_'SequenceString'" /><map from="Material_'Identifier'" to="Material_'Identifier'" /><map from="Material_'Kind'" to="Material_'Kind'" /><map from="Material_'Sequence'_'Length'" to="Material_'Sequence'_'Length'" /><map from="Material_'AccessPageUrl'" to="Material_'AccessPageUrl'" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean xmlns=""> <datatypeName>BasicClone</datatypeName> <registryEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</registryEndpoint> <articleNameUsedByService>Material</articleNameUsedByService> </net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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>1.2</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>1.2</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>1.2</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>1.2</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="mobyData('BasicClone')" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>concatenate_results</name><inputPorts><port><name>matIDList</name><depth>2</depth></port><port><name>matKindList</name><depth>2</depth></port><port><name>matURLList</name><depth>2</depth></port><port><name>seqLengthList</name><depth>2</depth></port><port><name>seqStringList</name><depth>2</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>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="matKindList" to="matKindList" /><map from="seqLengthList" to="seqLengthList" /><map from="seqStringList" to="seqStringList" /><map from="matIDList" to="matIDList" /><map from="matURLList" to="matURLList" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns=""> <script>output = ""; for (int i = 0; i < matIDList.size(); ++i) { output += (i+1) + ". Clone\n"; if (matIDList.get(i) != null && matIDList.get(i).size() > 0) { output += "\tIdentifier : " + matIDList.get(i).get(0) + "\n"; } else { output += "\tIdentifier : \n"; } if (matKindList.get(i) != null && matKindList.get(i).size() > 0) { output += "\tKind : " + matKindList.get(i).get(0) + "\n"; } else { output += "\tKind : \n"; } if (matURLList.get(i) != null && matURLList.get(i).size() > 0) { output += "\tAccessPageURL : " + matURLList.get(i).get(0) + "\n"; } else { output += "\tAccessPageURL : \n"; } if (seqLengthList.get(i) != null && seqLengthList.get(i).size() > 0) { output += "\tsequenceLength: " + seqLengthList.get(i).get(0) + "\n"; } else { output += "\tsequenceLength: \n"; } if (seqStringList.get(i) != null && seqStringList.get(i).size() > 0) { output += "\tsequenceString: " + seqStringList.get(i).get(0) + "\n"; } else { output += "\tsequenceString: \n"; } } </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>matURLList</name> <depth>2</depth> <mimeTypes> <string>text/plain</string> </mimeTypes> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <handledReferenceSchemes /> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> <name>matIDList</name> <depth>2</depth> <mimeTypes> <string>text/plain</string> </mimeTypes> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <handledReferenceSchemes /> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> <name>matKindList</name> <depth>2</depth> <mimeTypes> <string>text/plain</string> </mimeTypes> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <handledReferenceSchemes /> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> <name>seqStringList</name> <depth>2</depth> <mimeTypes> <string>text/plain</string> </mimeTypes> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <handledReferenceSchemes /> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> <name>seqLengthList</name> <depth>2</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>output</name> <depth>0</depth> <mimeTypes /> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> </outputs> </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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>1.2</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>1.2</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>1.2</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>1.2</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="matIDList" depth="2" /><port name="matKindList" depth="2" /><port name="matURLList" depth="2" /><port name="seqLengthList" depth="2" /><port name="seqStringList" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GabiPDCheckMaterialByAGI</processor><port>Object(Identifier)</port></sink><source type="processor"><processor>Object</processor><port>mobyData</port></source></datalink><datalink><sink type="processor"><processor>Object</processor><port>id</port></sink><source type="dataflow"><port>AGI_identifier</port></source></datalink><datalink><sink type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>mobyData('BasicClone')</port></sink><source type="processor"><processor>GabiPDCheckMaterialByAGI</processor><port>BasicClone(Collection - 'Material' As Simples)</port></source></datalink><datalink><sink type="processor"><processor>concatenate_results</processor><port>matIDList</port></sink><source type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>Material_'Identifier'</port></source></datalink><datalink><sink type="processor"><processor>concatenate_results</processor><port>matKindList</port></sink><source type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>Material_'Kind'</port></source></datalink><datalink><sink type="processor"><processor>concatenate_results</processor><port>matURLList</port></sink><source type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>Material_'AccessPageUrl'</port></source></datalink><datalink><sink type="processor"><processor>concatenate_results</processor><port>seqLengthList</port></sink><source type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>Material_'Sequence'_'Length'</port></source></datalink><datalink><sink type="processor"><processor>concatenate_results</processor><port>seqStringList</port></sink><source type="processor"><processor>Parse Moby Data(BasicClone)</processor><port>Material_'Sequence'_'SequenceString'</port></source></datalink><datalink><sink type="dataflow"><port>result</port></sink><source type="processor"><processor>concatenate_results</processor><port>output</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>a0059959-9a35-4366-b5c7-af22146bfaaf</identification> </annotationBean> <date>2010-07-23 11:46:19.165 CEST</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>