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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:17:49 UTC
[33/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/rest-2-3.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-3.t2flow
deleted file mode 100755
index f16f340..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-3.t2flow
+++ /dev/null
@@ -1,94 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="e63fe2cd-a6f3-46e2-9d5a-06e7b2fbb0d5" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>default</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>GET</httpMethod>
- <urlSignature>http://www.uniprot.org/uniprot/{id}.xml</urlSignature>
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>id</string>
- <java-class>java.lang.String</java-class>
- </entry>
- </activityInputs>
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>put</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>PUT</httpMethod>
- <urlSignature>http://www.uniprot.org/{db}/{id}.xml</urlSignature>
- <acceptsHeaderValue>audio/mp4</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>true</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>true</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders>
- <list>
- <string>X-Fish</string>
- <string>Soup</string>
- </list>
- <list>
- <string>X-Taverna</string>
- <string>Very funny</string>
- </list>
- </otherHTTPHeaders>
- <activityInputs>
- <entry>
- <string>id</string>
- <java-class>java.lang.String</java-class>
- </entry>
- <entry>
- <string>db</string>
- <java-class>java.lang.String</java-class>
- </entry>
- </activityInputs>
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>post</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
- <httpMethod>POST</httpMethod>
- <urlSignature>http://www.uniprot.org/uniprot/{id}.xml</urlSignature>
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>
- <contentTypeForUpdates>application/zip</contentTypeForUpdates>
- <outgoingDataFormat>Binary</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>id</string>
- <java-class>java.lang.String</java-class>
- </entry>
- </activityInputs>
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>e63fe2cd-a6f3-46e2-9d5a-06e7b2fbb0d5</identification>
- </annotationBean>
- <date>2011-08-30 16:15:25.25 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/rshell-2-3.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/rshell-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/rshell-2-3.t2flow
deleted file mode 100755
index aad989d..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rshell-2-3.t2flow
+++ /dev/null
@@ -1,183 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="5d233528-119e-4f39-be13-0cd8e6f8b280" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Rshell</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rshell.RshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>str</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>str2</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>logVec</name>
- <depth>1</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>regxp</name>
- <depth>1</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>rexpr</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>str</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>logicVector</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>numVector</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>intVector</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>strVector</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>png</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>txt</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>log</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>num</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>int</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <rVersion>false</rVersion>
- <script>rshell
-script</script>
- <connectionSettings>
- <host>localhost</host>
- <port>6311</port>
- <keepSessionAlive>false</keepSessionAlive>
- <newRVersion>false</newRVersion>
- </connectionSettings>
- <inputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>str</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>str2</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>logVec</name>
- <symanticType>BOOL_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>regxp</name>
- <symanticType>R_EXP</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </inputSymanticTypes>
- <outputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>rexpr</name>
- <symanticType>R_EXP</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>str</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>logicVector</name>
- <symanticType>BOOL_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>numVector</name>
- <symanticType>DOUBLE_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>intVector</name>
- <symanticType>INTEGER_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>strVector</name>
- <symanticType>STRING_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>png</name>
- <symanticType>PNG_FILE</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>txt</name>
- <symanticType>TEXT_FILE</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>log</name>
- <symanticType>BOOL</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>num</name>
- <symanticType>DOUBLE</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>int</name>
- <symanticType>INTEGER</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </outputSymanticTypes>
-</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>5d233528-119e-4f39-be13-0cd8e6f8b280</identification>
- </annotationBean>
- <date>2011-08-18 16:54:54.497 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3-xsd.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3-xsd.t2flow
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index c76cd05..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3-xsd.t2flow
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@@ -1,199 +0,0 @@
-<workflow xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://taverna.sf.net/2008/xml/t2flow ../../main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2flow-extended.xsd "
- xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0">
- <dataflow id="cdeba2f0-1c33-4a10-9806-7cc713bb91c6" role="top">
- <name>Workflow1</name>
- <inputPorts />
- <outputPorts />
- <processors>
- <processor>
- <name>Rshell</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>rshell-activity</artifact>
- <version>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.rshell.RshellActivity</class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in1</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in2</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in3</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out2</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out3</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <rVersion>false</rVersion>
- <script />
- <connectionSettings>
- <host>localhost</host>
- <port>6311</port>
- <keepSessionAlive>false</keepSessionAlive>
- <newRVersion>false</newRVersion>
- </connectionSettings>
- <inputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in1</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in2</name>
- <symanticType>DOUBLE</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in3</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </inputSymanticTypes>
- <outputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out1</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out2</name>
- <symanticType>BOOL_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out3</name>
- <symanticType>STRING_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </outputSymanticTypes>
- </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>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.3</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>1.3</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>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- </processors>
- <conditions />
- <datalinks />
- <annotations>
- <annotation_chain_2_2 encoding="xstream">
- <net.sf.taverna.t2.annotation.AnnotationChainImpl
- xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean
- class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>cdeba2f0-1c33-4a10-9806-7cc713bb91c6
- </identification>
- </annotationBean>
- <date>2011-08-18 17:04:20.369 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain_2_2>
- </annotations>
- </dataflow>
-</workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3.t2flow
deleted file mode 100755
index 6a0d2c9..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rshell-simple-2-3.t2flow
+++ /dev/null
@@ -1,94 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="cdeba2f0-1c33-4a10-9806-7cc713bb91c6" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Rshell</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rshell.RshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in1</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in2</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in3</name>
- <depth>0</depth>
- <allowsLiteralValues>false</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out2</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out3</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <rVersion>false</rVersion>
- <script>too
-simple</script>
- <connectionSettings>
- <host>localhost</host>
- <port>6311</port>
- <keepSessionAlive>false</keepSessionAlive>
- <newRVersion>false</newRVersion>
- </connectionSettings>
- <inputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in1</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in2</name>
- <symanticType>DOUBLE</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>in3</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </inputSymanticTypes>
- <outputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out1</name>
- <symanticType>STRING</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out2</name>
- <symanticType>BOOL_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out3</name>
- <symanticType>STRING_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </outputSymanticTypes>
-</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>cdeba2f0-1c33-4a10-9806-7cc713bb91c6</identification>
- </annotationBean>
- <date>2011-08-18 17:04:20.369 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow
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--- a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow
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-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0SNAPSHOT"><dataflow id="2d726ace-4635-4bd1-89d5-703a50c96c1a" role="top"><name>Example_component</name><inputPorts><port><name>suffix</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>result</name><annotations /></port></outputPorts><processors><processor><name>Create_Lots_Of_Strings</name><inputPorts /><outputPorts><port><name>strings</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap><map from="strings" to="strings" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>strings</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>List strings = new ArrayList();
-for (int i = 0; i < 40; i++) {
- strings.add("String" + i);
-}
-</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Sometimes_Fails</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><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>import java.util.Random;
-
-Random r = new Random();
-
-if ((r.nextInt() % 4) == 0) {
- throw new RuntimeException("Fails every four runs!");
-}
-
-out = in;</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.TestSometimesFails</localworkerName>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><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>Concatenate_two_strings</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xst
ream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>output = string1 + string2;</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><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="string2" depth="0" /><port name="string1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Sometimes_Fails</processor><port>in</port></sink><source type="processor"><processor>Create_Lots_Of_Strings</processor><port>strings</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="dataflow"><port>suffix</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source
type="processor"><processor>Sometimes_Fails</processor><port>out</port></source></datalink><datalink><sink type="dataflow"><port>result</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
- <mimeType>text/rdf+n3</mimeType>
- <content><>
- <http://purl.org/dc/terms/abstract>
- "A not very interesting component"^^<http://www.w3.org/2001/XMLSchema#string> ;
- <http://purl.org/dc/terms/accessRights>
- <http://creativecommons.org/licenses/by-sa/3.0/> ;
- <http://purl.org/dc/terms/alternative>
- "A very interesting component"^^<http://www.w3.org/2001/XMLSchema#string> ;
- <http://purl.org/dc/terms/audience>
- <http://purl.org/dc/terms/Agent> ;
- <http://purl.org/dc/terms/title>
- "Alan's annotated title"^^<http://www.w3.org/2001/XMLSchema#string> .
-</content>
- </annotationBean>
- <date>2013-03-13 15:22:30.556 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
- <text>Example component</text>
- </annotationBean>
- <date>2013-03-13 15:19:26.250 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>Example component for Stian</text>
- </annotationBean>
- <date>2013-03-13 15:19:35.27 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>2d726ace-4635-4bd1-89d5-703a50c96c1a</identification>
- </annotationBean>
- <date>2013-03-13 15:22:59.520 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>1eefd4e6-f1e2-45f3-b085-10a372d4afca</identification>
- </annotationBean>
- <date>2013-03-13 15:18:53.766 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
- <text>Alan R Williams</text>
- </annotationBean>
- <date>2013-03-13 15:19:22.146 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow
deleted file mode 100755
index e6776c4..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow
+++ /dev/null
@@ -1,222 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://taverna.sf.net/2008/xml/t2flow ../../main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2flow-extended.xsd"
- xsi:noNamespaceSchemaLocation="../../main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/externaltoolactivity.xsd"
- version="1" producedBy="taverna-2.3.0">
- <dataflow id="84dc0b70-e086-487d-94de-ab56d85fbde5" role="top">
- <name>Workflow2</name>
- <inputPorts />
- <outputPorts />
- <processors>
- <processor>
- <name>cat</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>external-tool-activity</artifact>
- <version>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity
- </class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean
- xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation />
-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>cat</externaltoolid>
- <useCaseDescription>
- <usecaseid>cat</usecaseid>
- <group>Testing</group>
- <description>concatenation of two streams</description>
- <command>cat file1.txt file2.txt</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>Second_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file2.txt</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>First_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file1.txt</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs />
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean>
-<annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>bourne_shell_script</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation />
-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>bourne_shell_script</externaltoolid>
- <useCaseDescription>
- <usecaseid>bourne_shell_script</usecaseid>
- <group />
- <description>execute shell script</description>
- <command>/bin/sh input</command>
- <test__local>test -x /bin/sh</test__local>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>shell_script</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>input</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs />
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>cmbuild</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation />
-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>cmbuild</externaltoolid>
- <useCaseDescription>
- <usecaseid>cmbuild</usecaseid>
- <group>Alignment:Infernal</group>
- <description>Preparation of model for RNA structure with Infernal</description>
- <command>cmbuild cmfile alignment</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs>
- <de.uni__luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint>
- <id>APPS/BIO/INFERNAL-0.8.1</id>
- <name>APPS/BIO/INFERNAL</name>
- <version>0.8.1</version>
- <relation>>=</relation>
- </de.uni__luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint>
- </REs>
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>RNA_sequence_alignment</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>alignment</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs>
- <entry>
- <string>Infernal_s_representation_of_RNA_structure</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>cmfile</path>
- <binary>false</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- </outputs>
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>84dc0b70-e086-487d-94de-ab56d85fbde5</identification>
- </annotationBean>
- <date>2011-08-23 09:35:20.489 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3.t2flow
deleted file mode 100755
index b6f6b16..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3.t2flow
+++ /dev/null
@@ -1,193 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="84dc0b70-e086-487d-94de-ab56d85fbde5" role="top"><name>Workflow2</name><inputPorts /><outputPorts /><processors><processor><name>cat</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation />
-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>cat</externaltoolid>
- <useCaseDescription>
- <usecaseid>cat</usecaseid>
- <group>Testing</group>
- <description>concatenation of two streams</description>
- <command>cat file1.txt file2.txt</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>Second_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file2.txt</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>First_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file1.txt</tag>
- <file>true</file>
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- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
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- <list>false</list>
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- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs />
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</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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- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>bourne_shell_script</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
- <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
- <mechanismName>default local</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation />
-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>bourne_shell_script</externaltoolid>
- <useCaseDescription>
- <usecaseid>bourne_shell_script</usecaseid>
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- <description>execute shell script</description>
- <command>/bin/sh input</command>
- <test__local>test -x /bin/sh</test__local>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>shell_script</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>input</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>false</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs />
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</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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- <initialDelay>1000</initialDelay>
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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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>cmbuild</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
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-</mechanismXML>
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <externaltoolid>cmbuild</externaltoolid>
- <useCaseDescription>
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- <group>Alignment:Infernal</group>
- <description>Preparation of model for RNA structure with Infernal</description>
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- <id>APPS/BIO/INFERNAL-0.8.1</id>
- <name>APPS/BIO/INFERNAL</name>
- <version>0.8.1</version>
- <relation>>=</relation>
- </de.uni__luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint>
- </REs>
- <queue__preferred />
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- <inputs>
- <entry>
- <string>RNA_sequence_alignment</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>alignment</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
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- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- </inputs>
- <outputs>
- <entry>
- <string>Infernal_s_representation_of_RNA_structure</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>cmfile</path>
- <binary>false</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- </outputs>
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes />
- </useCaseDescription>
- <edited>false</edited>
-</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>84dc0b70-e086-487d-94de-ab56d85fbde5</identification>
- </annotationBean>
- <date>2011-08-23 09:35:20.489 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file