taverna-t2flow 0.2.0 → 0.3.0

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Files changed (26) hide show
  1. data/CHANGES.rdoc +16 -0
  2. data/README.rdoc +30 -21
  3. data/Rakefile +54 -0
  4. data/lib/t2flow/model.rb +7 -0
  5. data/lib/t2flow/parser.rb +7 -2
  6. data/taverna-t2flow.gemspec +76 -0
  7. data/test/fixtures/1000.t2flow +244 -0
  8. data/test/fixtures/1001.t2flow +321 -0
  9. data/test/fixtures/1002.t2flow +474 -0
  10. data/test/fixtures/1003.t2flow +292 -0
  11. data/test/fixtures/1004.t2flow +73 -0
  12. data/test/fixtures/996.t2flow +193 -0
  13. data/test/fixtures/997.t2flow +359 -0
  14. data/test/fixtures/998.t2flow +324 -0
  15. data/test/fixtures/999.t2flow +604 -0
  16. data/test/fixtures/basic.t2flow +94 -0
  17. data/test/fixtures/coordinated.t2flow +63 -0
  18. data/test/fixtures/linked.t2flow +88 -0
  19. data/test/fixtures/nested.t2flow +270 -0
  20. data/test/fixtures/processors.t2flow +174 -0
  21. data/test/run_tests.rb +7 -0
  22. data/test/test_bogus_workflows.rb +80 -0
  23. data/test/test_helper.rb +50 -0
  24. data/test/test_starter_pack_workflows.rb +132 -0
  25. metadata +121 -69
  26. data/ChangeLog.rdoc +0 -7
data/test/fixtures/nested.t2flow ADDED
@@ -0,0 +1,270 @@
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+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="a035bf55-c8b9-44f7-8af1-6ae296bd0c72" role="top"><name>nested</name><inputPorts><port><name>in0</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.MimeType">
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+ <text>text/plain</text>
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.179 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><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.FreeTextDescription">
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+ <text />
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.179 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>out0</name><annotations /></port><port><name>out1</name><annotations /></port></outputPorts><processors><processor><name>beanshell</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>1.2</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;</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>in</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>out</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.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>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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+ <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>1.2</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="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Decode_base64_to_byte</name><inputPorts /><outputPorts><port><name>bytes</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>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="bytes" to="bytes" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
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+ <script>import org.apache.commons.codec.binary.Base64;
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+
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+ bytes = Base64.decodeBase64(base64.getBytes());
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+ </script>
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+ <dependencies class="java.util.Collections$SingletonList">
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+ <element class="string">commons-codec:commons-codec:1.3</element>
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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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+ <net.sf.taverna.raven.repository.BasicArtifact>
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+ <groupId>commons-codec</groupId>
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+ <artifactId>commons-codec</artifactId>
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+ <version>1.3</version>
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+ <hashCode>1635363350</hashCode>
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+ </net.sf.taverna.raven.repository.BasicArtifact>
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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>base64</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>bytes</name>
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+ <depth>0</depth>
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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.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>1.2</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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+ <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>1.2</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>Nested_Workflow</name><inputPorts><port><name>input</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>dataflow-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="dataflow"><dataflow ref="1f62dff0-5348-43a3-9818-0b589031630b" /></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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+ <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>1.2</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="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions><condition control="Nested_Workflow" target="Decode_base64_to_byte" /></conditions><datalinks><datalink><sink type="processor"><processor>beanshell</processor><port>in</port></sink><source type="dataflow"><port>in0</port></source></datalink><datalink><sink type="processor"><processor>Nested_Workflow</processor><port>input</port></sink><source type="processor"><processor>beanshell</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>out0</port></sink><source type="processor"><processor>Nested_Workflow</processor><port>output</port></source></datalink></datalinks><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.Author">
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+ <text />
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.519 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><annotation_chain_2_2 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.IdentificationAssertion">
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+ <identification>a035bf55-c8b9-44f7-8af1-6ae296bd0c72</identification>
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+ </annotationBean>
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+ <date>2010-07-27 14:08:55.812 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_2_2><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.FreeTextDescription">
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+ <text />
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.519 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><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.DescriptiveTitle">
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+ <text>nested</text>
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.519 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></dataflow><dataflow id="1f62dff0-5348-43a3-9818-0b589031630b" role="nested"><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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+ <annotationAssertions>
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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 />
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.394 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><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.MimeType">
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+ <text>text/plain</text>
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+ </annotationBean>
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+ <date>2009-10-02 12:44:52.394 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>output</name><annotations /></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>1.2</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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+ <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>in</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>out</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.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>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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+ <maxRetries>0</maxRetries>
214
+ </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="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>diffseq</name><inputPorts /><outputPorts><port><name>aoutfeat_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>boutfeat</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outfile_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>boutfeat_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>aoutfeat</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outfile</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>1.2</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap /><outputMap><map from="boutfeat" to="boutfeat" /><map from="boutfeat_url" to="boutfeat_url" /><map from="aoutfeat_url" to="aoutfeat_url" /><map from="report" to="report" /><map from="aoutfeat" to="aoutfeat" /><map from="outfile" to="outfile" /><map from="outfile_url" to="outfile_url" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
215
+ <endpoint>http://www.ebi.ac.uk/soaplab/services/alignment_differences.diffseq</endpoint>
216
+ <pollingInterval>0</pollingInterval>
217
+ <pollingBackoff>1.0</pollingBackoff>
218
+ <pollingIntervalMax>0</pollingIntervalMax>
219
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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="">
220
+ <maxJobs>1</maxJobs>
221
+ </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="">
222
+ <backoffFactor>1.0</backoffFactor>
223
+ <initialDelay>0</initialDelay>
224
+ <maxDelay>0</maxDelay>
225
+ <maxRetries>0</maxRetries>
226
+ </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 /><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_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
227
+ <annotationAssertions>
228
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
229
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
230
+ <identification>1f62dff0-5348-43a3-9818-0b589031630b</identification>
231
+ </annotationBean>
232
+ <date>2010-07-27 14:08:55.886 BST</date>
233
+ <creators />
234
+ <curationEventList />
235
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
236
+ </annotationAssertions>
237
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
238
+ <annotationAssertions>
239
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
240
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
241
+ <text />
242
+ </annotationBean>
243
+ <date>2009-10-02 12:44:52.517 BST</date>
244
+ <creators />
245
+ <curationEventList />
246
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
247
+ </annotationAssertions>
248
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
249
+ <annotationAssertions>
250
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
251
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
252
+ <text>basic</text>
253
+ </annotationBean>
254
+ <date>2009-10-02 12:44:52.517 BST</date>
255
+ <creators />
256
+ <curationEventList />
257
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
258
+ </annotationAssertions>
259
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
260
+ <annotationAssertions>
261
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
262
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
263
+ <text />
264
+ </annotationBean>
265
+ <date>2009-10-02 12:44:52.517 BST</date>
266
+ <creators />
267
+ <curationEventList />
268
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
269
+ </annotationAssertions>
270
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
data/test/fixtures/processors.t2flow ADDED
@@ -0,0 +1,174 @@
1
+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1-beta-2"><dataflow id="d89e9c09-c482-4ba4-9881-34a3194cfdbe" role="top"><name>processors</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>0.8</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="">
2
+ <value>edit me!</value>
3
+ </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>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="">
4
+ <maxJobs>1</maxJobs>
5
+ </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="">
6
+ <backoffFactor>1.0</backoffFactor>
7
+ <initialDelay>0</initialDelay>
8
+ <maxDelay>0</maxDelay>
9
+ <maxRetries>0</maxRetries>
10
+ </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>Beanshell_scripting_host</name><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 /><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
11
+ <script>int x = 10;
12
+ int y = x * 3;</script>
13
+ <dependencies />
14
+ <classLoaderSharing>workflow</classLoaderSharing>
15
+ <localDependencies />
16
+ <artifactDependencies />
17
+ <inputs>
18
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
19
+ <handledReferenceSchemes />
20
+ <translatedElementType>java.lang.String</translatedElementType>
21
+ <allowsLiteralValues>true</allowsLiteralValues>
22
+ <name>in</name>
23
+ <depth>0</depth>
24
+ <mimeTypes>
25
+ <string>'text/plain'</string>
26
+ </mimeTypes>
27
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
28
+ </inputs>
29
+ <outputs>
30
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
31
+ <granularDepth>0</granularDepth>
32
+ <name>out</name>
33
+ <depth>0</depth>
34
+ <mimeTypes>
35
+ <string>'text/plain'</string>
36
+ </mimeTypes>
37
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
38
+ </outputs>
39
+ </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="">
40
+ <maxJobs>1</maxJobs>
41
+ </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="">
42
+ <backoffFactor>1.0</backoffFactor>
43
+ <initialDelay>0</initialDelay>
44
+ <maxDelay>0</maxDelay>
45
+ <maxRetries>0</maxRetries>
46
+ </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>hsapiens_gene_vega</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap /><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_vega" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-09-11 10:04:37"><MartURLLocation database="vega_mart_56" default="0" displayName="VEGA 36 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="vega" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna" /></MartQuery></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="">
47
+ <maxJobs>1</maxJobs>
48
+ </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="">
49
+ <backoffFactor>1.0</backoffFactor>
50
+ <initialDelay>0</initialDelay>
51
+ <maxDelay>0</maxDelay>
52
+ <maxRetries>0</maxRetries>
53
+ </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>RShell</name><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>rshell-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.rshell.RshellActivity</class><inputMap /><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean xmlns="">
54
+ <rVersion>false</rVersion>
55
+ <script>// something here</script>
56
+ <connectionSettings>
57
+ <host>localhost</host>
58
+ <port>6311</port>
59
+ <username>username</username>
60
+ <password>password</password>
61
+ <keepSessionAlive>false</keepSessionAlive>
62
+ <newRVersion>false</newRVersion>
63
+ </connectionSettings>
64
+ <inputSymanticTypes>
65
+ <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
66
+ <name>in</name>
67
+ <symanticType>REXP</symanticType>
68
+ </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
69
+ </inputSymanticTypes>
70
+ <outputSymanticTypes>
71
+ <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
72
+ <name>out</name>
73
+ <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean/symanticType" />
74
+ </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
75
+ </outputSymanticTypes>
76
+ <inputs>
77
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
78
+ <handledReferenceSchemes />
79
+ <translatedElementType>[B</translatedElementType>
80
+ <allowsLiteralValues>true</allowsLiteralValues>
81
+ <name>in</name>
82
+ <depth>0</depth>
83
+ <mimeTypes>
84
+ <string>'application/x-java-serialized-object'</string>
85
+ </mimeTypes>
86
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
87
+ </inputs>
88
+ <outputs>
89
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
90
+ <granularDepth>0</granularDepth>
91
+ <name>out</name>
92
+ <depth>0</depth>
93
+ <mimeTypes>
94
+ <string>'application/x-java-serialized-object'</string>
95
+ </mimeTypes>
96
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
97
+ </outputs>
98
+ </net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean></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="">
99
+ <maxJobs>1</maxJobs>
100
+ </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="">
101
+ <backoffFactor>1.0</backoffFactor>
102
+ <initialDelay>0</initialDelay>
103
+ <maxDelay>0</maxDelay>
104
+ <maxRetries>0</maxRetries>
105
+ </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>getNucSeq</name><inputPorts /><outputPorts><port><name>result</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="result" to="result" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
106
+ <wsdl>http://www.ebi.ac.uk/xembl/XEMBL.wsdl</wsdl>
107
+ <operation>getNucSeq</operation>
108
+ </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="">
109
+ <maxJobs>1</maxJobs>
110
+ </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="">
111
+ <backoffFactor>1.0</backoffFactor>
112
+ <initialDelay>0</initialDelay>
113
+ <maxDelay>0</maxDelay>
114
+ <maxRetries>0</maxRetries>
115
+ </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>showalign</name><inputPorts /><outputPorts><port><name>outfile</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outfile_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 /><outputMap><map from="report" to="report" /><map from="outfile_url" to="outfile_url" /><map from="outfile" to="outfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
116
+ <endpoint>http://www.ebi.ac.uk/soaplab/services/display.showalign</endpoint>
117
+ <pollingInterval>0</pollingInterval>
118
+ <pollingBackoff>1.0</pollingBackoff>
119
+ <pollingIntervalMax>0</pollingIntervalMax>
120
+ </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="">
121
+ <maxJobs>1</maxJobs>
122
+ </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="">
123
+ <backoffFactor>1.0</backoffFactor>
124
+ <initialDelay>0</initialDelay>
125
+ <maxDelay>0</maxDelay>
126
+ <maxRetries>0</maxRetries>
127
+ </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>ObjectUnion</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean xmlns="">
128
+ <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
129
+ <serviceName>ObjectUnion</serviceName>
130
+ <authorityName>icapture.mrl.ubc.ca</authorityName>
131
+ <category />
132
+ <serviceType />
133
+ <secondaries />
134
+ </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>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="">
135
+ <maxJobs>1</maxJobs>
136
+ </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="">
137
+ <backoffFactor>1.0</backoffFactor>
138
+ <initialDelay>0</initialDelay>
139
+ <maxDelay>0</maxDelay>
140
+ <maxRetries>0</maxRetries>
141
+ </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></processors><conditions /><datalinks /><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
142
+ <annotationAssertions>
143
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
144
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
145
+ <text />
146
+ </annotationBean>
147
+ <date>2009-10-02 12:44:56.623 BST</date>
148
+ <creators />
149
+ <curationEventList />
150
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
151
+ </annotationAssertions>
152
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
153
+ <annotationAssertions>
154
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
155
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
156
+ <text>processors</text>
157
+ </annotationBean>
158
+ <date>2009-10-02 12:44:56.623 BST</date>
159
+ <creators />
160
+ <curationEventList />
161
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
162
+ </annotationAssertions>
163
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
164
+ <annotationAssertions>
165
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
166
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
167
+ <text />
168
+ </annotationBean>
169
+ <date>2009-10-02 12:44:56.623 BST</date>
170
+ <creators />
171
+ <curationEventList />
172
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
173
+ </annotationAssertions>
174
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
data/test/run_tests.rb ADDED
@@ -0,0 +1,7 @@
1
+ require 'rubygems'
2
+ require 'test/unit'
3
+
4
+ require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
5
+
6
+ require File.expand_path(File.join(__FILE__, "..", "test_bogus_workflows.rb"))
7
+ require File.expand_path(File.join(__FILE__, "..", "test_starter_pack_workflows.rb"))
data/test/test_bogus_workflows.rb ADDED
@@ -0,0 +1,80 @@
1
+ require 'rubygems'
2
+ require 'test/unit'
3
+
4
+ require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
5
+ require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
6
+
7
+ require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
8
+
9
+ class BogusWorkflowTest < Test::Unit::TestCase
10
+
11
+ include TestHelper
12
+
13
+ def setup
14
+ path = File.expand_path(File.join(__FILE__, "..", "fixtures", "basic.t2flow"))
15
+ @bogus_basic_wf = T2Flow::Parser.new.parse(File.new(path))
16
+
17
+ path = File.expand_path(File.join(__FILE__, "..", "fixtures", "coordinated.t2flow"))
18
+ @bogus_coordinated_wf = T2Flow::Parser.new.parse(File.new(path))
19
+
20
+ path = File.expand_path(File.join(__FILE__, "..", "fixtures", "linked.t2flow"))
21
+ @bogus_linked_wf = T2Flow::Parser.new.parse(File.new(path))
22
+
23
+ path = File.expand_path(File.join(__FILE__, "..", "fixtures", "nested.t2flow"))
24
+ @bogus_nested_wf = T2Flow::Parser.new.parse(File.new(path))
25
+
26
+ path = File.expand_path(File.join(__FILE__, "..", "fixtures", "processors.t2flow"))
27
+ @bogus_processors_wf = T2Flow::Parser.new.parse(File.new(path))
28
+ end
29
+
30
+ def test_bogus_basic_wf
31
+ generic_model_test(@bogus_basic_wf)
32
+
33
+ assert_count(@bogus_basic_wf.processors, 1, "@bogus_basic_wf.processors")
34
+ assert_count(@bogus_basic_wf.sources, 1, "@bogus_basic_wf.sources")
35
+ assert_count(@bogus_basic_wf.sinks, 1, "@bogus_basic_wf.sinks")
36
+ assert_count(@bogus_basic_wf.datalinks, 2, "@bogus_basic_wf.datalinks")
37
+ assert_count(@bogus_basic_wf.coordinations, 0, "@bogus_basic_wf.coordinations")
38
+ end
39
+
40
+ def test_bogus_coordinated_wf
41
+ generic_model_test(@bogus_coordinated_wf)
42
+
43
+ assert_count(@bogus_coordinated_wf.processors, 2, "@bogus_coordinated_wf.processors")
44
+ assert_count(@bogus_coordinated_wf.sources, 0, "@bogus_coordinated_wf.sources")
45
+ assert_count(@bogus_coordinated_wf.sinks, 0, "@bogus_coordinated_wf.sinks")
46
+ assert_count(@bogus_coordinated_wf.datalinks, 0, "@bogus_coordinated_wf.datalinks")
47
+ assert_count(@bogus_coordinated_wf.coordinations, 1, "@bogus_coordinated_wf.coordinations")
48
+ end
49
+
50
+ def test_bogus_linked_wf
51
+ generic_model_test(@bogus_linked_wf)
52
+
53
+ assert_count(@bogus_linked_wf.processors, 5, "@bogus_linked_wf.processors")
54
+ assert_count(@bogus_linked_wf.sources, 0, "@bogus_linked_wf.sources")
55
+ assert_count(@bogus_linked_wf.sinks, 0, "@bogus_linked_wf.sinks")
56
+ assert_count(@bogus_linked_wf.datalinks, 4, "@bogus_linked_wf.datalinks")
57
+ assert_count(@bogus_linked_wf.coordinations, 0, "@bogus_linked_wf.coordinations")
58
+ end
59
+
60
+ def test_bogus_nested_wf
61
+ generic_model_test(@bogus_nested_wf)
62
+
63
+ assert_count(@bogus_nested_wf.processors, 3, "@bogus_nested_wf.processors")
64
+ assert_count(@bogus_nested_wf.sources, 1, "@bogus_nested_wf.sources")
65
+ assert_count(@bogus_nested_wf.sinks, 2, "@bogus_nested_wf.sinks")
66
+ assert_count(@bogus_nested_wf.datalinks, 3, "@bogus_nested_wf.datalinks")
67
+ assert_count(@bogus_nested_wf.coordinations, 1, "@bogus_nested_wf.coordinations")
68
+ end
69
+
70
+ def test_bogus_processors_wf
71
+ generic_model_test(@bogus_processors_wf)
72
+
73
+ assert_count(@bogus_processors_wf.processors, 7, "@bogus_processors_wf.processors")
74
+ assert_count(@bogus_processors_wf.sources, 0, "@bogus_processors_wf.sources")
75
+ assert_count(@bogus_processors_wf.sinks, 0, "@bogus_processors_wf.sinks")
76
+ assert_count(@bogus_processors_wf.datalinks, 0, "@bogus_processors_wf.datalinks")
77
+ assert_count(@bogus_processors_wf.coordinations, 0, "@bogus_processors_wf.coordinations")
78
+ end
79
+
80
+ end