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-beta-2"><dataflow id="83b6cdb4-b5dd-4c87-9044-7319252758b3" role="top"><name>basic</name><inputPorts><port><name>input</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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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.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>output</name></port></outputPorts><processors><processor><name>Beanshell_scripting_host</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</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>0.8</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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<script>int x = 5 * in;
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int y = 3 * in;</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies>
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<string>ojdbc14.jar</string>
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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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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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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.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>0.8</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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</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>0.8</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>0.8</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>0.8</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>0.8</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="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Beanshell_scripting_host</processor><port>in</port></sink><source type="dataflow"><port>input</port></source></datalink><datalink><sink type="dataflow"><port>output</port></sink><source type="processor"><processor>Beanshell_scripting_host</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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<date>2009-10-02 12:44:14.685 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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</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.DescriptiveTitle">
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<text>basic</text>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="addec2b4-8e1c-4dbe-a1bd-fb75cad028c0" role="top"><name>coordinated</name><inputPorts /><outputPorts /><processors><processor><name>String_Constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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<value>edit me!</value>
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</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></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="">
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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>1.2</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="">
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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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</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 /></strategy></iteration></iterationStrategyStack></processor><processor><name>String_Constant1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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<value>edit me!</value>
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</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></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="">
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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>1.2</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="">
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<backoffFactor>1.0</backoffFactor>
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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>1.2</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 /></strategy></iteration></iterationStrategyStack></processor></processors><conditions><condition control="String_Constant" target="String_Constant1" /></conditions><datalinks /><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<date>2009-10-02 12:44:37.376 BST</date>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
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<identification>addec2b4-8e1c-4dbe-a1bd-fb75cad028c0</identification>
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<date>2010-07-27 13:51:11.937 BST</date>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<date>2009-10-02 12:44:37.376 BST</date>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1-beta-2"><dataflow id="6866f560-5419-419c-b2d2-1ad00f44329d" role="top"><name>linked</name><inputPorts /><outputPorts /><processors><processor><name>BIVGetNeighbours</name><inputPorts /><outputPorts><port><name>BIVInteraction</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>0.8</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap><map from="BIVInteraction" to="BIVInteraction" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
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2
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+
<wsdl>http://soap.bind.ca/wsdl/bind.wsdl</wsdl>
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3
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+
<operation>BIVGetNeighbours</operation>
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4
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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>0.8</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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5
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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>0.8</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>0.8</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>0.8</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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7
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+
<backoffFactor>1.0</backoffFactor>
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8
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+
<initialDelay>0</initialDelay>
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9
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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>0.8</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>search_drugs_by_name</name><inputPorts><port><name>name</name><depth>0</depth></port></inputPorts><outputPorts><port><name>return</name><depth>1</depth><granularDepth>1</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>0.8</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="name" to="name" /></inputMap><outputMap><map from="return" to="return" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
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+
<wsdl>http://soap.genome.jp/KEGG.wsdl</wsdl>
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<operation>search_drugs_by_name</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>0.8</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>0.8</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>0.8</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>0.8</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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17
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+
<backoffFactor>1.0</backoffFactor>
|
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18
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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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21
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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>0.8</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="name" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>run_eSummary_MS</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="attachmentList" to="attachmentList" /><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
|
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22
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<wsdl>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl</wsdl>
|
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|
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<operation>run_eSummary_MS</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>0.8</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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25
|
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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>0.8</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>0.8</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>0.8</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="">
|
|
27
|
+
<backoffFactor>1.0</backoffFactor>
|
|
28
|
+
<initialDelay>0</initialDelay>
|
|
29
|
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<maxDelay>0</maxDelay>
|
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30
|
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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>0.8</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="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>fdrawtree</name><inputPorts><port><name>bscale</name><depth>0</depth></port></inputPorts><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>plotfile</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>plotfile_url</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="bscale" to="bscale" /></inputMap><outputMap><map from="plotfile_url" to="plotfile_url" /><map from="report" to="report" /><map from="plotfile" to="plotfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
|
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32
|
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<endpoint>http://www.ebi.ac.uk/soaplab/services/phylogeny_tree_drawing.fdrawtree</endpoint>
|
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33
|
+
<pollingInterval>0</pollingInterval>
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34
|
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<pollingBackoff>1.0</pollingBackoff>
|
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35
|
+
<pollingIntervalMax>0</pollingIntervalMax>
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36
|
+
</net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>0.8</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>0.8</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>0.8</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>0.8</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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39
|
+
<backoffFactor>1.0</backoffFactor>
|
|
40
|
+
<initialDelay>0</initialDelay>
|
|
41
|
+
<maxDelay>0</maxDelay>
|
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42
|
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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>0.8</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="bscale" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>diffseq</name><inputPorts><port><name>offormat_boutfeat</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outfile</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>aoutfeat</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>boutfeat</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>aoutfeat_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>boutfeat_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outfile_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="offormat_boutfeat" to="offormat_boutfeat" /></inputMap><outputMap><map from="aoutfeat" to="aoutfeat" /><map from="aoutfeat_url" to="aoutfeat_url" /><map from="report" to="report" /><map from="outfile_url" to="outfile_url" /><map from="outfile" to="outfile" /><map from="boutfeat_url" to="boutfeat_url" /><map from="boutfeat" to="boutfeat" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
|
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44
|
+
<endpoint>http://www.ebi.ac.uk/soaplab/services/alignment_differences.diffseq</endpoint>
|
|
45
|
+
<pollingInterval>0</pollingInterval>
|
|
46
|
+
<pollingBackoff>1.0</pollingBackoff>
|
|
47
|
+
<pollingIntervalMax>0</pollingIntervalMax>
|
|
48
|
+
</net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>0.8</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="">
|
|
49
|
+
<maxJobs>1</maxJobs>
|
|
50
|
+
</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>0.8</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>0.8</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>0.8</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="">
|
|
51
|
+
<backoffFactor>1.0</backoffFactor>
|
|
52
|
+
<initialDelay>0</initialDelay>
|
|
53
|
+
<maxDelay>0</maxDelay>
|
|
54
|
+
<maxRetries>0</maxRetries>
|
|
55
|
+
</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>0.8</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="offormat_boutfeat" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>search_drugs_by_name</processor><port>name</port></sink><source type="processor"><processor>run_eSummary_MS</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>run_eSummary_MS</processor><port>parameters</port></sink><source type="processor"><processor>BIVGetNeighbours</processor><port>BIVInteraction</port></source></datalink><datalink><sink type="processor"><processor>fdrawtree</processor><port>bscale</port></sink><source type="processor"><processor>diffseq</processor><port>boutfeat</port></source></datalink><datalink><sink type="processor"><processor>diffseq</processor><port>offormat_boutfeat</port></sink><source type="processor"><processor>run_eSummary_MS</processor><port>attachmentList</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
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56
|
+
<annotationAssertions>
|
|
57
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
58
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
|
|
59
|
+
<text>linked</text>
|
|
60
|
+
</annotationBean>
|
|
61
|
+
<date>2009-10-02 12:45:19.476 BST</date>
|
|
62
|
+
<creators />
|
|
63
|
+
<curationEventList />
|
|
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|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
65
|
+
</annotationAssertions>
|
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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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67
|
+
<annotationAssertions>
|
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68
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
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69
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
|
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70
|
+
<text />
|
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|
+
</annotationBean>
|
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|
+
<date>2009-10-02 12:45:19.476 BST</date>
|
|
73
|
+
<creators />
|
|
74
|
+
<curationEventList />
|
|
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|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
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|
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</annotationAssertions>
|
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|
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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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78
|
+
<annotationAssertions>
|
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79
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
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|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
|
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81
|
+
<text />
|
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|
+
</annotationBean>
|
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|
+
<date>2009-10-02 12:45:19.476 BST</date>
|
|
84
|
+
<creators />
|
|
85
|
+
<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></dataflow></workflow>
|