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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:17:17 UTC
[01/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Repository: incubator-taverna-language
Updated Branches:
refs/heads/master [created] aa46364df
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
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diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
deleted file mode 100644
index 1938bca..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
+++ /dev/null
@@ -1,303 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fd34324d-de34-4a5f-9b12-13059a9fb1a4" role="top"><name>Pipelined_list_iteration</name><inputPorts><port><name>input</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>150</text>
- </annotationBean>
- <date>2009-12-15 19:41:02.598 GMT</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>Number of elements to generate</text>
- </annotationBean>
- <date>2009-12-15 19:40:52.84 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>List_Emitter</name><inputPorts><port><name>count</name><depth>0</depth></port></inputPorts><outputPorts><port><name>list</name><depth>1</depth><granularDepth>1</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="count" to="count" /></inputMap><outputMap><map from="list" to="list" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>List list = new ArrayList();
-int icount = Integer.parseInt(count);
-
-for (int i=0;i<icount;i++) {
- list.add(String.valueOf(i));
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>count</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>list</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="count" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concat</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>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap
><map from="input" to="input" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>String output = input + "XXX"</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</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>localworker-activity</artifact><version>1.2</version></raven><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="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings_2</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</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>localworker-activity</artifact><ve
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- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
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- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
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- <depth>0</depth>
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- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
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- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
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- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
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- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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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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p><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>boo</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
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">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>xxx</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.tavern
a.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>xxx</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sdfds</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.tave
rna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>sdfds</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>List_Emitter</processor><port>count</port></sink><source type="dataflow"><port>input</port></source></datalink><datalink><sink type="processor"><processor>Concat</processor><port>input</port></sink><source type="processor"><processor>List_Emitter</processor><port>list</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="pro
cessor"><processor>Concat</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="processor"><processor>boo</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings_2</processor><port>string1</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings_2</processor><port>string2</port></sink><source type="processor"><processor>xxx</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings_3</processor><port>string1</port></sink><source type="processor"><processor>Concatenate_two_strings_2</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings_3</processor><port>stri
ng2</port></sink><source type="processor"><processor>sdfds</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Concatenate_two_strings_3</processor><port>output</port></source></datalink></datalinks><annotations><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>Perform multiple iterations of services in order to show pipelining</text>
- </annotationBean>
- <date>2009-12-15 19:42:21.971 GMT</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.Author">
- <text>Ian Dunlop, Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-12-15 19:42:01.488 GMT</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.DescriptiveTitle">
- <text>Pipelined list iteration</text>
- </annotationBean>
- <date>2009-12-15 19:42:12.907 GMT</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>fd34324d-de34-4a5f-9b12-13059a9fb1a4</identification>
- </annotationBean>
- <date>2010-07-04 18:19:17.425 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/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/retrieve_sequence_in_embl_format_32794.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/retrieve_sequence_in_embl_format_32794.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/retrieve_sequence_in_embl_format_32794.t2flow
deleted file mode 100644
index 2d9ba3b..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/retrieve_sequence_in_embl_format_32794.t2flow
+++ /dev/null
@@ -1,84 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="db8053e3-1837-42cc-ba27-5fd0a83f119e" role="top"><name>Retrieve_sequence_in_EMBL_format</name><inputPorts /><outputPorts><port><name>sequence</name><annotations /></port></outputPorts><processors><processor><name>sequence_feature</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>true</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.s
f.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>embl:x52524</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sequence_format</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><n
et.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>embl</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
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- <endpoint>http://www.ebi.ac.uk/soaplab/services/edit.seqret</endpoint>
- <pollingInterval>0</pollingInterval>
- <pollingBackoff>1.0</pollingBackoff>
- <pollingIntervalMax>0</pollingIntervalMax>
-</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="">
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">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_usa" depth="0" /><port name="feature" depth="0" /><port name="osformat_outseq" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>seqret</processor><port>sequence_usa</port></sink><source type="processor"><processor>sequence_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>feature</port></sink><source type="processor"><processor>sequence_f
eature</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>osformat_outseq</port></sink><source type="processor"><processor>sequence_format</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink></datalinks><annotations><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>Retrieve sequence in EMBL format</text>
- </annotationBean>
- <date>2009-12-15 20:21:29.202 GMT</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>This workflow retrieves a sequence associated with its features in embl format</text>
- </annotationBean>
- <date>2009-12-15 20:21:39.30 GMT</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.Author">
- <text>Franck Tanoh</text>
- </annotationBean>
- <date>2009-12-15 20:21:20.965 GMT</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>db8053e3-1837-42cc-ba27-5fd0a83f119e</identification>
- </annotationBean>
- <date>2010-07-04 17:49:51.364 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
[25/52] [abbrv] incubator-taverna-language git commit: corrected w3c
copyright header
Posted by st...@apache.org.
corrected w3c copyright header
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/9c347eb3
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/9c347eb3
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/9c347eb3
Branch: refs/heads/master
Commit: 9c347eb30147c54daf1310ebfb2b913813f4490a
Parents: d088b9f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 16:19:24 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 16:19:24 2015 +0000
----------------------------------------------------------------------
.../resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9c347eb3/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
index 24cb4cd..f317513 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
@@ -1,8 +1,13 @@
<?xml version='1.0'?>
<!--
Copyright © 2015 W3C® (MIT, ERCIM, Keio, Beihang). This software or
- document includes material copied from or derived from
- XML namespace http://www.w3.org/2001/xml.xsd
+ document includes material copied from or derived from:
+
+ Extensible Markup Language (XML) 1.0 (Fifth Edition)
+ W3C Recommendation 26 November 2008
+ http://www.w3.org/2001/xml.xsd
+ http://www.w3.org/TR/xml/
+
-->
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
[30/52] [abbrv] incubator-taverna-language git commit: Corrected
minor error in module descriptive names.
Posted by st...@apache.org.
Corrected minor error in module descriptive names.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/585c1b2f
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/585c1b2f
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/585c1b2f
Branch: refs/heads/master
Commit: 585c1b2fa5a46d41eff18e909fe29bc16600e74f
Parents: 427d21e
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Wed Feb 11 10:43:01 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Wed Feb 11 13:40:04 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-examples/pom.xml | 2 +-
taverna-scufl2-wfdesc/pom.xml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/585c1b2f/taverna-scufl2-examples/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/pom.xml b/taverna-scufl2-examples/pom.xml
index c63547d..607b470 100644
--- a/taverna-scufl2-examples/pom.xml
+++ b/taverna-scufl2-examples/pom.xml
@@ -24,7 +24,7 @@
<version>0.16.1-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-scufl2-examples</artifactId>
- <name>Apache Taverna Scufl2 examples</name>
+ <name>Apache Taverna Scufl 2 examples</name>
<dependencies>
<dependency>
<groupId>${project.parent.groupId}</groupId>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/585c1b2f/taverna-scufl2-wfdesc/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/pom.xml b/taverna-scufl2-wfdesc/pom.xml
index c1de4f6..7c0c736 100755
--- a/taverna-scufl2-wfdesc/pom.xml
+++ b/taverna-scufl2-wfdesc/pom.xml
@@ -24,7 +24,7 @@
</parent>
<artifactId>taverna-scufl2-wfdesc</artifactId>
<packaging>bundle</packaging>
- <name>Apache Taverna Scufl2 wfdesc export</name>
+ <name>Apache Taverna Scufl 2 wfdesc export</name>
<description>Convert Scufl2 workflow to wfdesc structure (from Wf4Ever RO ontology)</description>
<properties>
<!-- ancient sesame that works with elmo. Only exists now
[31/52] [abbrv] incubator-taverna-language git commit: Clarify RAT
exclusions.
Posted by st...@apache.org.
Clarify RAT exclusions.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/0bcffe78
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/0bcffe78
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/0bcffe78
Branch: refs/heads/master
Commit: 0bcffe783a4fda85a59b58be8bdb5e7eecc30a8d
Parents: 585c1b2
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Wed Feb 11 13:38:37 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Wed Feb 11 13:40:04 2015 +0000
----------------------------------------------------------------------
pom.xml | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++++-------
1 file changed, 85 insertions(+), 11 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/0bcffe78/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8b158ca..82c023a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -64,23 +64,97 @@
<!-- META-INF services files can include comments but a license header
would be unecessarily clutter so we exclude these -->
<exclude>**/META-INF/services/*</exclude>
- <exclude>**/*.xsd</exclude>
- <exclude>**/*.rdf</exclude>
- <exclude>**/*.owl</exclude>
- <exclude>**/src/main/resources/jarcache.json</exclude>
+ <!-- The following schemas are W3C; automatic retrieval during build is
+ blocked by their administrative processes, yet they are explicitly
+ standardised documents intended for wide use. -->
+ <exclude>**/xml.xsd</exclude>
+ <exclude>**/xenc-schema.xsd</exclude>
+ <exclude>**/xmldsig-core-schema.xsd</exclude>
+ <!-- This refers to the FOAF spec, which is available online at
+ http://xmlns.com/foaf/spec/ and which uses the CC-BY-SA 1.0
+ license. The RDF downloadable from the site, of which this is a copy,
+ has no copyright statement at all in it. -->
+ <exclude>**/foaf.rdf</exclude>
+ <!-- The following contain a mix of licenses. PROBLEM! -->
+ <exclude>**/src/main/resources/ontologies/*.owl</exclude>
+ <exclude>**/src/main/resources/ontologies/*.rdf</exclude>
+ <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl</exclude>
+ <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl</exclude>
+ <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl</exclude>
+ <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl</exclude>
+ <exclude>**/src/main/resources/org/w3/prov-o.ttl</exclude>
+ <!-- No headers in JSON which haven't got comments .. -->
+ <exclude>**/*.json</exclude>
<!-- Various files used for testing and test support only. -->
- <exclude>**/*.t2flow</exclude>
- <exclude>**/*.ttl</exclude>
- <exclude>**/mimetype</exclude>
+ <exclude>**/src/test/resources/annotated2.2-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/annotated2.2.t2flow</exclude>
+ <exclude>**/src/test/resources/annotation_with_backslash.t2flow</exclude>
+ <exclude>**/src/test/resources/annotations_2_4-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/annotations_2_4.t2flow</exclude>
+ <exclude>**/src/test/resources/as.t2flow</exclude>
+ <exclude>**/src/test/resources/beanshell-deps.t2flow</exclude>
+ <exclude>**/src/test/resources/component_simple.t2flow</exclude>
+ <exclude>**/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
+ <exclude>**/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/defaultActivitiesTaverna2.2.t2flow</exclude>
+ <exclude>**/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/dispatchlayers.t2flow</exclude>
+ <exclude>**/src/test/resources/fasta_and_pscan.t2flow</exclude>
+ <exclude>**/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
+ <exclude>**/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
+ <exclude>**/src/test/resources/interaction_multiple_choice.t2flow</exclude>
+ <exclude>**/src/test/resources/interaction_simple_tell.t2flow</exclude>
+ <exclude>**/src/test/resources/iterationstrategies.t2flow</exclude>
+ <exclude>**/src/test/resources/merge_fun.t2flow</exclude>
+ <exclude>**/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
+ <exclude>**/src/test/resources/missing_merge.t2flow</exclude>
+ <exclude>**/src/test/resources/missing_produced_by_941.t2flow</exclude>
+ <exclude>**/src/test/resources/random.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-2-saved-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-2-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-2.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-3-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/rest-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/rshell-2-2.t2flow</exclude>
+ <exclude>**/src/test/resources/rshell-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/rshell-simple-2-3-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/rshell-simple-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/semantic_annotations__eclipse-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/semantic_annotations__eclipse.t2flow</exclude>
+ <exclude>**/src/test/resources/simple_fasta.t2flow</exclude>
+ <exclude>**/src/test/resources/sleepers.t2flow</exclude>
+ <exclude>**/src/test/resources/spreadsheet_activity_defaults_892.t2flow</exclude>
+ <exclude>**/src/test/resources/T3-1226-annotations-with-quotes.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-2-resaved-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-2-tweaked-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-2.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-3-xsd.t2flow</exclude>
+ <exclude>**/src/test/resources/tool-2-3.t2flow</exclude>
+ <exclude>**/src/test/resources/xpath_workflow.t2flow</exclude>
+ <exclude>**/examples/helloanyone.t2flow</exclude>
+ <exclude>**/examples/helloworld.t2flow</exclude>
+ <exclude>**/src/test/resources/apiconsumer.t2flow</exclude>
+ <exclude>**/src/test/resources/rest.t2flow</exclude>
+ <exclude>**/src/test/resources/helloanyone.t2flow</exclude>
+ <exclude>**/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
+ <exclude>**/src/test/resources/3582.t2flow</exclude>
+ <exclude>**/src/test/resources/allTypes.t2flow</exclude>
+ <exclude>**/src/test/resources/enm-v21.t2flow</exclude>
+ <exclude>**/src/test/resources/helloworld.t2flow</exclude>
+ <exclude>**/src/test/resources/localdependency.t2flow</exclude>
+ <exclude>**/src/test/resources/nested.t2flow</exclude>
+ <exclude>**/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
+ <exclude>**/resources/**/*.wfdesc.ttl</exclude>
+ <exclude>**/resources/**/*.prov.ttl</exclude>
+ <exclude>**/mimetype</exclude><!-- really a binary format -->
<exclude>**/src/test/resources/*starterpacklist</exclude>
<exclude>**/src/test/resources/**/*.txt</exclude>
+ <exclude>**/src/test/resources/**/*.url</exclude>
<exclude>**/src/test/resources/**/workflow*.xml</exclude>
- <exclude>**/src/test/resources/**/*.json</exclude>
<exclude>**/resources/sample-output/outputs/**</exclude>
- <exclude>**/src/test/resources/win8.url</exclude>
<exclude>**/src/test/resources/full-example/**</exclude>
- <!-- No headers in JSON which haven't got comments .. -->
- <exclude>**/*.json</exclude>
</excludes>
</configuration>
</plugin>
[46/52] [abbrv] incubator-taverna-language git commit: Delete more
unused files and make tests less noisy.
Posted by st...@apache.org.
Delete more unused files and make tests less noisy.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/9236e2c1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/9236e2c1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/9236e2c1
Branch: refs/heads/master
Commit: 9236e2c199687c364749725184f00590fcc17e2c
Parents: 98b8b23
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 15:24:31 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 15:24:31 2015 +0000
----------------------------------------------------------------------
.../examples/TestConvertT2flowScufl2.java | 4 +-
.../apache/taverna/examples/TestJsonExport.java | 5 +-
.../taverna/examples/TestProcessorNames.java | 5 +-
.../taverna/examples/TestServiceTypes.java | 3 -
.../workflows/t2flow/annotated2.2.t2flow | 216 ------------
...tion_of_configurable_iteration_114130.t2flow | 352 -------------------
.../fetch_today_s_xkcd_comic_568671.t2flow | 349 ------------------
.../resources/workflows/t2flow/merge_fun.t2flow | 83 -----
.../pipelined_list_iteration_902021.t2flow | 320 -----------------
.../workflows/wfbundle/annotated2.wfbundle | Bin 11754 -> 0 bytes
...on_of_configurable_iteration_114130.wfbundle | Bin 12741 -> 0 bytes
.../fetch_today_s_xkcd_comic_568671.wfbundle | Bin 13365 -> 0 bytes
.../workflows/wfbundle/helloanyone.wfbundle | Bin 11998 -> 0 bytes
.../workflows/wfbundle/helloworld.wfbundle | Bin 9856 -> 0 bytes
.../workflows/wfbundle/merge_fun.wfbundle | Bin 9698 -> 0 bytes
.../pipelined_list_iteration_902021.wfbundle | Bin 13480 -> 0 bytes
16 files changed, 7 insertions(+), 1330 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestConvertT2flowScufl2.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestConvertT2flowScufl2.java b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestConvertT2flowScufl2.java
index d549d72..5368a24 100644
--- a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestConvertT2flowScufl2.java
+++ b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestConvertT2flowScufl2.java
@@ -46,7 +46,9 @@ public class TestConvertT2flowScufl2 {
ConvertT2flowToWorkflowBundle.main(new String[]{tmp.getAbsolutePath()});
File scufl2File = new File(tmp.getAbsolutePath().replace(".t2flow", ".wfbundle"));
assertTrue(scufl2File.isFile());
- assertNotNull(new ZipFile(scufl2File).getEntry("workflowBundle.rdf"));
+ try (ZipFile zip = new ZipFile(scufl2File)) {
+ assertNotNull(zip.getEntry("workflowBundle.rdf"));
+ }
scufl2File.deleteOnExit();
// System.out.println(scufl2File);
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestJsonExport.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestJsonExport.java b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestJsonExport.java
index f5c4ed5..ac1d415 100644
--- a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestJsonExport.java
+++ b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestJsonExport.java
@@ -26,7 +26,6 @@ import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
-import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.taverna.examples.JsonExport;
import org.junit.Ignore;
@@ -49,7 +48,7 @@ public class TestJsonExport {
assertTrue(jsonFile.isFile());
jsonFile.deleteOnExit();
// System.out.println(scufl2File);
- System.out.println(FileUtils.readFileToString(jsonFile, "UTF-8"));
+ //System.out.println(FileUtils.readFileToString(jsonFile, "UTF-8"));
}
@Ignore("Takes 24 seconds!")
@@ -68,7 +67,7 @@ public class TestJsonExport {
File jsonFile = new File(tmp.getAbsolutePath().replace(".t2flow", ".json"));
assertTrue(jsonFile.isFile());
// jsonFile.deleteOnExit();
- System.out.println(jsonFile);
+ //System.out.println(jsonFile);
// System.out.println(FileUtils.readFileToString(jsonFile, "UTF-8"));
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestProcessorNames.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestProcessorNames.java b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestProcessorNames.java
index ce2794c..ee3e844 100644
--- a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestProcessorNames.java
+++ b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestProcessorNames.java
@@ -56,7 +56,6 @@ public class TestProcessorNames {
"wsdl_secured", "xmlSplitter");
ProcessorNames processorNames = new ProcessorNames();
assertEquals(expected, processorNames.showProcessorNames(ro));
- System.out.println(processorNames.showProcessorTree(ro));
}
@@ -70,7 +69,7 @@ public class TestProcessorNames {
WorkflowBundle ro = io.readBundle(workflow,
"application/vnd.taverna.t2flow+xml");
ProcessorNames processorNames = new ProcessorNames();
- System.out.println(processorNames.showProcessorTree(ro));
+ assertEquals(8, processorNames.showProcessorNames(ro).size());
}
@@ -83,7 +82,7 @@ public class TestProcessorNames {
WorkflowBundleIO io = new WorkflowBundleIO();
WorkflowBundle ro = io.readBundle(workflow, null);
ProcessorNames processorNames = new ProcessorNames();
- System.out.println(processorNames.showProcessorTree(ro));
+ assertEquals(8, processorNames.showProcessorNames(ro).size());
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestServiceTypes.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestServiceTypes.java b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestServiceTypes.java
index ed20959..03fd0c8 100644
--- a/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestServiceTypes.java
+++ b/taverna-scufl2-examples/src/test/java/org/apache/taverna/examples/TestServiceTypes.java
@@ -25,11 +25,8 @@ import static org.junit.Assert.assertEquals;
import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
-import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
import java.util.HashSet;
-import java.util.List;
import java.util.Set;
import org.apache.commons.io.IOUtils;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/t2flow/annotated2.2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/annotated2.2.t2flow b/taverna-scufl2-examples/src/test/resources/workflows/t2flow/annotated2.2.t2flow
deleted file mode 100644
index 8a27bcf..0000000
--- a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/annotated2.2.t2flow
+++ /dev/null
@@ -1,216 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad" role="top"><name>Workflow_title</name><inputPorts><port><name>in0</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>Only example</text>
- </annotationBean>
- <date>2010-07-21 11:19:58.897 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>in1</name><depth>1</depth><granularDepth>1</granularDepth><annotations><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>Only description</text>
- </annotationBean>
- <date>2010-07-21 11:19:47.699 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>in2</name><depth>2</depth><granularDepth>2</granularDepth><annotations><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.ExampleValue">
- <text>Some kind </text>
- </annotationBean>
- <date>2010-07-21 11:19:34.518 BST</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>Workflow input in2</text>
- </annotationBean>
- <date>2010-07-21 11:19:25.509 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out0</name><annotations><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.ExampleValue">
- <text />
- </annotationBean>
- <date>2010-07-21 11:26:10.972 BST</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>First annotation</text>
- </annotationBean>
- <date>2010-07-21 11:20:30.875 BST</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.ExampleValue">
- <text>Not empty</text>
- </annotationBean>
- <date>2010-07-21 11:25:56.668 BST</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>Third annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:50.301 BST</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.ExampleValue">
- <text>Empty again</text>
- </annotationBean>
- <date>2010-07-21 11:26:05.105 BST</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>Second annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:39.729 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>out1</name><annotations /></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script />
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><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>Workflow title</text>
- </annotationBean>
- <date>2010-07-21 11:20:43.824 BST</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>Workflow description</text>
- </annotationBean>
- <date>2010-07-21 11:20:50.161 BST</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>bb902d82-b0e4-46fc-bed5-950a3b38bb98</identification>
- </annotationBean>
- <date>2010-07-21 11:22:31.286 BST</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>9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad</identification>
- </annotationBean>
- <date>2010-07-21 11:26:16.844 BST</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>Workflow author</text>
- </annotationBean>
- <date>2010-07-21 11:20:39.864 BST</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/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow b/taverna-scufl2-examples/src/test/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
deleted file mode 100644
index bf13b82..0000000
--- a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
+++ /dev/null
@@ -1,352 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="be152f54-e4a7-4324-9ce6-44438c5daed7" role="top"><name>Demonstrationofconfigurableiteration</name><inputPorts /><outputPorts><port><name>Output</name><annotations /></port></outputPorts><processors><processor><name>Colours</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>red ,green ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Animals</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="x
stream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>cat ,rabbit ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Shapes</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xs
tream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>square ,circular ,triangular ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
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- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>ColoursLisr</processor><port>string</port></sink><source type="processor"><processor>Colours</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>AnimalsList</processor><port>string</port></sink><source type="processor"><processor>Animals</processor><port>value</port></source></datalink>
<datalink><sink type="processor"><processor>ShapesList</processor><port>string</port></sink><source type="processor"><processor>Shapes</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>ColoursLisr</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="processor"><processor>AnimalsList</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string2</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string1</port></sink><source type="processor"><processor>ShapesList</processor><port>split</port></source></datalink><datalink><
sink type="dataflow"><port>Output</port></sink><source type="processor"><processor>ShapeAnimals</processor><port>output</port></source></datalink></datalinks><annotations><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>This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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.Author">
- <text>Tom Oinn</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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>be152f54-e4a7-4324-9ce6-44438c5daed7</identification>
- </annotationBean>
- <date>2010-07-04 18:12:25.361 BST</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>Demonstration of configurable iteration</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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
[04/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/ebi_interproscan_for_taverna_2_317472.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/ebi_interproscan_for_taverna_2_317472.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/ebi_interproscan_for_taverna_2_317472.t2flow
deleted file mode 100644
index f0410ef..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/ebi_interproscan_for_taverna_2_317472.t2flow
+++ /dev/null
@@ -1,615 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fff84443-6f1c-4dd1-bb0c-fc1e489a1ca5" role="top"><name>EBI_InterProScan</name><inputPorts><port><name>Email_address</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>Your email address (for EBI statistics on job submissions)</text>
- </annotationBean>
- <date>2009-07-03 10:04:37.551 BST</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.ExampleValue">
- <text />
- </annotationBean>
- <date>2009-07-03 10:05:00.847 BST</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.ExampleValue">
- <text>Sequence or </text>
- </annotationBean>
- <date>2009-07-03 10:04:44.374 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>Sequence_or_ID</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
- <text>, for example uniprot:wap_rat</text>
- </annotationBean>
- <date>2009-07-03 10:05:09.391 BST</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>Sequence or ID</text>
- </annotationBean>
- <date>2009-07-03 10:05:12.358 BST</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.ExampleValue">
- <text>uniprot:wap_rat</text>
- </annotationBean>
- <date>2009-07-03 10:05:14.247 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>InterProScan_text_result</name><annotations /></port><port><name>InterProScan_XML_result</name><annotations /></port><port><name>Job_ID</name><annotations /></port><port><name>InterProScan_GFF</name><annotations /></port><port><name>status</name><annotations /></port></outputPorts><processors><processor><name>Input_data</name><inputPorts><port><name>content</name><depth>0</depth></port><port><name>type</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="content" to="content" /><map from="type" to="type" /></i
nputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="data" name="" qname="{http://www.ebi.ac.uk/WSInterProScan}data"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="data&gt;type" /><s:basetype optional="false" unbounded="false" typename="string" name="content" qname="data&gt;content" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>type</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>content</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="type" depth="0" /><port name="content" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_XML_result</name><inputPorts><port><name>jobid</name><depth>0</depth></port><port><name>type</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.tave
rna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="type" to="type" /><map from="jobid" to="jobid" /></inputMap><outputMap><map from="result" to="result" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
- <operation>poll</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="jobid" depth="0" /><port name="type" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Format_as_GFF</name><inputPorts><port><name>interproscan_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>interproscan_gff</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna
.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="interproscan_text" to="interproscan_text" /></inputMap><outputMap><map from="interproscan_gff" to="interproscan_gff" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>import java.util.StringTokenizer;
-
-interproscan_gff = "";
-
-// Split into lines
-StringTokenizer tok1 = new StringTokenizer(interproscan_text, "\n");
-while(tok1.hasMoreElements()) {
- feat1 = tok1.nextElement();
- // Split into fields
- StringTokenizer tok2 = new StringTokenizer(feat1, "\t");
- fieldCount = 0;
- attributeStr = "";
- while(tok2.hasMoreElements()) {
- fieldCount++;
- fieldStr = tok2.nextElement();
- if(fieldCount < 2) { // First field is the ID
- interproscan_gff += fieldStr;
- }
- // The tool, feature, start and stop
- else if(fieldCount == 4 || (fieldCount > 5 && fieldCount < 9)) {
- interproscan_gff += "\t" + fieldStr;
- }
- // Score
- else if(fieldCount == 9) {
- if(fieldStr.equals("NA")) {
- interproscan_gff += "\t.";
- } else {
- interproscan_gff += "\t" + fieldStr;
- }
- }
- // Matching InterPro entry
- else if(fieldCount == 12 && !fieldStr.equals("NULL")) {
- attributeStr += fieldStr;
- }
- // Matching InterPro entry name
- else if(fieldCount == 13 && !fieldStr.equals("NULL")) {
- attributeStr += " " + fieldStr;
- }
- }
- interproscan_gff += "\t.\t.\tInterProScan";
- if(attributeStr.length() > 0) {
- interproscan_gff += " ; " + attributeStr;
- }
- interproscan_gff += "\n";
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>interproscan_text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>interproscan_gff</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="interproscan_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Job_params</name><inputPorts><port><name>seqtype</name><depth>0</depth></port><port><name>crc</name><depth>0</depth></port><port><name>goterms</name><depth>0</depth></port><port><name>async</name><depth>0</depth></port><port><name>email</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><ac
tivity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap><map from="crc" to="crc" /><map from="goterms" to="goterms" /><map from="email" to="email" /><map from="seqtype" to="seqtype" /><map from="async" to="async" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="inputParams" name="params" qname="{http://www.ebi.ac.uk/WSInterProScan}inputParams"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="app" qname="inputParams&gt;app" /><s:basetype optional="false" unbounded="false" typename="boolean" name="crc" qname="inputParams&gt;crc" /><s:basetype optional="false" unbounded="false" typename="string" name="seqtype" qname="inputParams&gt;seqtype" /><s:basetype optional="false" unbounded="false" typename="int" name="trlen" qname="inputParams&gt;trlen" /><s:basetype optional="false" unbounded="false" typename="int" name="trtable" qname="inputParams&gt;trtable" /><s:basetype optional="false" unbounded="false" typename="boolean" name="goterms" qname="inputParams&gt;goterms" /><s:basetype optiona
l="false" unbounded="false" typename="boolean" name="async" qname="inputParams&gt;async" /><s:basetype optional="false" unbounded="false" typename="string" name="outformat" qname="inputParams&gt;outformat" /><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="inputParams&gt;email" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>app</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>crc</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>seqtype</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>trlen</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>trtable</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>goterms</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>async</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>outformat</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>email</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
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">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="crc" depth="0" /><port name="seqtype" depth="0" /><port name="goterms" depth="0" /><port name="async" depth="0" /><port name="email" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_text_result</name><inputPorts><port><name>type</name><depth>0</depth></port><port><name>jobid</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>result</name><depth>0</depth><granularDepth>0</gr
anularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="type" to="type" /><map from="jobid" to="jobid" /></inputMap><outputMap><map from="result" to="result" /><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
- <operation>poll</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="jobid" depth="0" /><port name="type" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>runInterProScan</name><inputPorts><port><name>content</name><depth>0</depth></port><port><name>params</name><depth>0</depth></port></inputPorts><outputPorts><port><name>jobid</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.ta
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- <wsdl>http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl</wsdl>
- <operation>runInterProScan</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
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- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="params" depth="0" /><port name="content" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Content_list</name><inputPorts><port><name>WSArrayofData</name><depth>1</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.w
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- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="false" unbounded="false" wrapped="false" typename="WSArrayofData" name="content" qname="{http://www.ebi.ac.uk/WSInterProScan}WSArrayofData"><s:elementtype><s:complextype optional="false" unbounded="false" typename="data" name="" qname="{http://www.ebi.ac.uk/WSInterProScan}data"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="data&gt;type" /><s:basetype optional="false" unbounded="false" typename="string" name="content" qname="data&gt;content" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>WSArrayofData</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/xml')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="WSArrayofData" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Input_data_type_defaultValue</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap>
<map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>sequence</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_XML_result_type_defaultValue</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMa
p><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>toolxml</value>
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- <handledReferenceSchemes />
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- <name>bytes</name>
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- <mimeTypes>
- <string>'application/octet-stream'</string>
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- <name>string</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
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">
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- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="bytes" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Unpack_XML_result</name><inputPorts><port><name>bytes</name><depth>0</depth></port></inputPorts><outputPorts><port><name>string</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity
</class><inputMap><map from="bytes" to="bytes" /></inputMap><outputMap><map from="string" to="string" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.ByteArrayToString</localworkerName>
- <script>string = new String(bytes);
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>bytes</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'application/octet-stream'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>string</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="bytes" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions><condition control="checkStatus" target="Get_text_result" /><condition control="checkStatus" target="Get_XML_result" /></conditions><datalinks><datalink><sink type="processor"><processor>Input_data</processor><port>content</port></sink><source type="dataflow"><port>Sequence_or_ID</port></source></datalink><datalink><sink type="processor"><processor>Input_data</processor><port>type</port></sink><source type="processor
"><processor>Input_data_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_XML_result</processor><port>jobid</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>Get_XML_result</processor><port>type</port></sink><source type="processor"><processor>Get_XML_result_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Format_as_GFF</processor><port>interproscan_text</port></sink><source type="processor"><processor>Unpack_text_result</processor><port>string</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>seqtype</port></sink><source type="processor"><processor>Job_params_seqtype_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>crc</
port></sink><source type="processor"><processor>Job_params_crc_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>goterms</port></sink><source type="processor"><processor>Job_params_goterms_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>async</port></sink><source type="processor"><processor>Job_params_async_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Job_params</processor><port>email</port></sink><source type="dataflow"><port>Email_address</port></source></datalink><datalink><sink type="processor"><processor>Get_text_result</processor><port>type</port></sink><source type="processor"><processor>Get_text_result_type_defaultValue</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_text_result</processor><port>jobi
d</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>runInterProScan</processor><port>content</port></sink><source type="processor"><processor>Content_list</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>runInterProScan</processor><port>params</port></sink><source type="processor"><processor>Job_params</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>Content_list</processor><port>WSArrayofData</port></sink><source type="processor"><processor>Input_data</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>checkStatus</processor><port>jobid</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="processor"><processor>Unpack_text_result</processor><port>bytes</port></sink>
<source type="processor"><processor>Get_text_result</processor><port>result</port></source></datalink><datalink><sink type="processor"><processor>Unpack_XML_result</processor><port>bytes</port></sink><source type="processor"><processor>Get_XML_result</processor><port>result</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_text_result</port></sink><source type="processor"><processor>Unpack_text_result</processor><port>string</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_XML_result</port></sink><source type="processor"><processor>Unpack_XML_result</processor><port>string</port></source></datalink><datalink><sink type="dataflow"><port>Job_ID</port></sink><source type="processor"><processor>runInterProScan</processor><port>jobid</port></source></datalink><datalink><sink type="dataflow"><port>InterProScan_GFF</port></sink><source type="processor"><processor>Format_as_GFF</processor><port>interproscan_gff</port></source></datalink
><datalink><sink type="dataflow"><port>status</port></sink><source type="processor"><processor>checkStatus</processor><port>status</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
- <text>EBI_InterProScan for Taverna 2</text>
- </annotationBean>
- <date>2009-05-26 14:53:47.508 BST</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>fff84443-6f1c-4dd1-bb0c-fc1e489a1ca5</identification>
- </annotationBean>
- <date>2010-07-04 18:13:56.92 BST</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>EBI_InterProScan_T2</text>
- </annotationBean>
- <date>2009-05-26 14:59:16.89 BST</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.Author">
- <text>Hamish McWilliam. Modified by Katy Wolstencroft and Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-05-26 14:53:32.664 BST</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>Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
-
-InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the signatures are returned, which are annotated with the corresponding InterPro and GO term assignments for these signature matches.</text>
- </annotationBean>
- <date>2009-02-03 09:38:48.949 GMT</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.DescriptiveTitle">
- <text>EBI_InterProScan</text>
- </annotationBean>
- <date>2009-02-03 09:38:48.949 GMT</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.Author">
- <text>Hamish McWilliam</text>
- </annotationBean>
- <date>2009-02-03 09:38:48.949 GMT</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
[05/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
deleted file mode 100644
index 4004b34..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
+++ /dev/null
@@ -1,335 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="be152f54-e4a7-4324-9ce6-44438c5daed7" role="top"><name>Demonstrationofconfigurableiteration</name><inputPorts /><outputPorts><port><name>Output</name><annotations /></port></outputPorts><processors><processor><name>Colours</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>red ,green ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Animals</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="x
stream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>cat ,rabbit ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>Shapes</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xs
tream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>square ,circular ,triangular ,</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>ColoursLisr</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</name><depth>1</depth><granularDepth>1</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><map from="string" to="st
ring" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
- <script>List split = new ArrayList();
-if (!string.equals("")) {
- String regexString = ",";
- if (regex != void) {
- regexString = regex;
- }
- String[] result = string.split(regexString);
- for (int i = 0; i < result.length; i++) {
- split.add(result[i]);
- }
-}
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>regex</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
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-if (!string.equals("")) {
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- if (regex != void) {
- regexString = regex;
- }
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- for (int i = 0; i < result.length; i++) {
- split.add(result[i]);
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">
- <backoffFactor>1.0</backoffFactor>
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- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
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- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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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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">
- <backoffFactor>1.0</backoffFactor>
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- <script>output = string1 + string2;</script>
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- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
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- <string>'text/plain'</string>
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- <name>string2</name>
- <depth>0</depth>
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- <string>'text/plain'</string>
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- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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- <string>'text/plain'</string>
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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="">
- <maxJobs>1</maxJobs>
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">
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- <maxDelay>5000</maxDelay>
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-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>ColoursLisr</processor><port>string</port></sink><source type="processor"><processor>Colours</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>AnimalsList</processor><port>string</port></sink><source type="processor"><processor>Animals</processor><port>value</port></source></datalink>
<datalink><sink type="processor"><processor>ShapesList</processor><port>string</port></sink><source type="processor"><processor>Shapes</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>ColoursLisr</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="processor"><processor>AnimalsList</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string2</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>ShapeAnimals</processor><port>string1</port></sink><source type="processor"><processor>ShapesList</processor><port>split</port></source></datalink><datalink><
sink type="dataflow"><port>Output</port></sink><source type="processor"><processor>ShapeAnimals</processor><port>output</port></source></datalink></datalinks><annotations><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>This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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.Author">
- <text>Tom Oinn</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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>be152f54-e4a7-4324-9ce6-44438c5daed7</identification>
- </annotationBean>
- <date>2010-07-04 18:12:25.361 BST</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>Demonstration of configurable iteration</text>
- </annotationBean>
- <date>2009-06-29 15:44:05.675 BST</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
[23/52] [abbrv] incubator-taverna-language git commit: valid XML..
Posted by st...@apache.org.
valid XML..
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/e97cb296
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/e97cb296
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/e97cb296
Branch: refs/heads/master
Commit: e97cb29682b4a35bcb0dbf12636e6d51d0abaa1b
Parents: 91de0d5
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:51:33 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:51:33 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-rdfxml/pom.xml | 1 -
1 file changed, 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e97cb296/taverna-scufl2-rdfxml/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/pom.xml b/taverna-scufl2-rdfxml/pom.xml
index 7682e2f..a31cacb 100644
--- a/taverna-scufl2-rdfxml/pom.xml
+++ b/taverna-scufl2-rdfxml/pom.xml
@@ -26,7 +26,6 @@
<packaging>bundle</packaging>
<name>Apache Taverna Scufl 2 RDF/XML</name>
<description>XSD based XML serialisation which is RDF/XML compatible</description>
- <build>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
[13/52] [abbrv] incubator-taverna-language git commit: Removed
outdated taverna-scufl2-rdf
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example.rdf b/taverna-scufl2-rdf/src/test/resources/example.rdf
deleted file mode 100644
index 7c420e6..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example.rdf
+++ /dev/null
@@ -1,281 +0,0 @@
-<?xml version='1.0'?>
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/test/resources/example/-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:beanshell="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <WorkflowBundle rdf:about="">
- <mainWorkflow rdf:resource="workflow/HelloWorld/"/>
- <name>Hello world</name>
- <profile rdf:resource="profile/tavernaWorkbench/"/>
- <sameBaseAs rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/"/>
- <workflow rdf:resource="workflow/HelloWorld/"/>
- <dc:creator>Stian Soiland-Reyes</dc:creator>
- <dc:date>2010-07-29</dc:date>
- <dc:description>An example workflow to illustrate SCUFL2</dc:description>
- <rdf:seeAlso rdf:resource="annotation/workflowBundle.ttl"/>
- </WorkflowBundle>
-
- <Profile rdf:about="profile/tavernaServer/">
- <activatesConfiguration rdf:resource="profile/tavernaServer/configuration/Hello"/>
- <name>tavernaWorkbench</name>
- <processorBinding rdf:resource="profile/tavernaServer/binding/Hello"/>
- <recommendsEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <os rdf:resource="http://www.ubuntu.com/#10.04"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/server/"/>
- <dc:title>Taverna server installed on Ubuntu</dc:title>
- </recommendsEnvironment>
- <requiresEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <architecture rdf:resource="http://www.intel.org/x64"/>
- <plugin rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#plugin"/>
- <product rdf:resource="http://ns.taverna.org.uk/2010/taverna/"/>
- <software rdf:resource="http://www.bioconductor.org/"/>
- <software rdf:resource="http://www.r-project.org/#2.11"/>
- <software rdf:resource="http://www.rforge.net/Rserve/"/>
- <dc:description>
- BioConductor installed in R, and Rserve running
- on port 1234. x64 but architecture.
- </dc:description>
- </requiresEnvironment>
- <dc:creator>Stian Soiland-Reyes</dc:creator>
- <dc:date>2010-07-29</dc:date>
- <dc:description>A profile for invoking the workflow on a Taverna Server</dc:description>
- </Profile>
-
- <beanshell:Activity rdf:about="profile/tavernaServer/activity/HelloScript/">
- <inputActivityPort rdf:resource="profile/tavernaServer/activity/HelloScript/in/personName"/>
- <outputActivityPort rdf:resource="profile/tavernaServer/activity/HelloScript/out/hello"/>
- </beanshell:Activity>
-
- <InputActivityPort rdf:about="profile/tavernaServer/activity/HelloScript/in/personName">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>personName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputActivityPort>
-
- <OutputActivityPort rdf:about="profile/tavernaServer/activity/HelloScript/out/hello">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>hello</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </OutputActivityPort>
-
- <ProcessorBinding rdf:about="profile/tavernaServer/binding/Hello">
- <boundActivity rdf:resource="profile/tavernaServer/activity/HelloScript/"/>
- <boundProcessor rdf:resource="workflow/HelloWorld/processor/Hello/"/>
- <inputPortBinding rdf:parseType="Resource">
- <bindsInputActivityPort rdf:resource="profile/tavernaServer/activity/HelloScript/in/personName"/>
- <bindsInputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/in/name"/>
- </inputPortBinding>
- <outputPortBinding rdf:parseType="Resource">
- <bindsOutputActivityPort rdf:resource="profile/tavernaServer/activity/HelloScript/out/hello"/>
- <bindsOutputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/out/greeting"/>
- </outputPortBinding>
- </ProcessorBinding>
-
- <beanshell:Configuration rdf:about="profile/tavernaServer/configuration/Hello">
- <configures rdf:resource="profile/tavernaServer/activity/HelloScript/"/>
- <beanshell:script>
- hello = "Hello, " + personName;
- System.out.println("Server says: " + hello);
- </beanshell:script>
- </beanshell:Configuration>
-
- <Profile rdf:about="profile/tavernaWorkbench/">
- <activatesConfiguration rdf:resource="profile/tavernaWorkbench/configuration/Hello"/>
- <name>tavernaWorkbench</name>
- <processorBinding rdf:resource="profile/tavernaWorkbench/binding/Hello"/>
- <recommendsEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/workbench/"/>
- </recommendsEnvironment>
- <requiresEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <workflowPlugin rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#plugin"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/"/>
- </requiresEnvironment>
- <dc:creator>Stian Soiland-Reyes</dc:creator>
- <dc:date>2010-07-29</dc:date>
- <dc:description>A profile for invoking the workflow on the Taverna Workbench</dc:description>
- <rdfs:seeAlso rdf:resource="profile/tavernaWorkbench.ttl"/>
- </Profile>
-
- <beanshell:Activity rdf:about="profile/tavernaWorkbench/activity/HelloScript/">
- <inputActivityPort rdf:resource="profile/tavernaWorkbench/activity/HelloScript/in/personName"/>
- <outputActivityPort rdf:resource="profile/tavernaWorkbench/activity/HelloScript/out/hello"/>
- </beanshell:Activity>
-
- <InputActivityPort rdf:about="profile/tavernaWorkbench/activity/HelloScript/in/personName">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>personName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputActivityPort>
-
- <OutputActivityPort rdf:about="profile/tavernaWorkbench/activity/HelloScript/out/hello">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>hello</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </OutputActivityPort>
-
- <ProcessorBinding rdf:about="profile/tavernaWorkbench/binding/Hello">
- <boundActivity rdf:resource="profile/tavernaWorkbench/activity/HelloScript/"/>
- <boundProcessor rdf:resource="workflow/HelloWorld/processor/Hello/"/>
- <inputPortBinding rdf:parseType="Resource">
- <bindsInputActivityPort rdf:resource="profile/tavernaWorkbench/activity/HelloScript/in/personName"/>
- <bindsInputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/in/name"/>
- </inputPortBinding>
- <outputPortBinding rdf:parseType="Resource">
- <bindsOutputActivityPort rdf:resource="profile/tavernaWorkbench/activity/HelloScript/out/hello"/>
- <bindsOutputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/out/greeting"/>
- </outputPortBinding>
- </ProcessorBinding>
-
- <beanshell:Configuration rdf:about="profile/tavernaWorkbench/configuration/Hello">
- <configures rdf:resource="profile/tavernaWorkbench/activity/HelloScript/"/>
- <beanshell:script>
- import javax.swing.JOptionPane;
-
- hello = "Hello, " + personName;
- JOptionPane.showMessageDialog(null, hello, "Greeting",
- JOptionPane.INFORMATION_MESSAGE);
- </beanshell:script>
- </beanshell:Configuration>
-
- <Workflow rdf:about="workflow/HelloWorld/">
- <datalink rdf:resource="workflow/HelloWorld/datalink/5"/>
- <datalink rdf:resource="workflow/HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0"/>
- <datalink rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <receivesFrom rdf:resource="workflow/HelloWorld/in/yourName"/>
- <sendsTo rdf:resource="workflow/HelloWorld/processor/Hello/in/name"/>
- </datalink>
- <inputWorkflowPort rdf:resource="workflow/HelloWorld/in/yourName"/>
- <name>Helloworld</name>
- <outputWorkflowPort rdf:resource="workflow/HelloWorld/out/results"/>
- <processor rdf:resource="workflow/HelloWorld/processor/Hello"/>
- <workflowIdentifier rdf:resource="http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/"/>
- <dc:date>2010-07-28</dc:date>
- <dc:description>A simple hello world workflow</dc:description>
- <rdfs:seeAlso rdf:resource="workflow/HelloWorld.ttl"/>
- <rdfs:seeAlso rdf:resource="workflow/annotation/workflow/HelloWorld.ttl"/>
- </Workflow>
-
- <DataLink rdf:about="workflow/HelloWorld/datalink/5">
- <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</mergePosition>
- <receivesFrom rdf:resource="workflow/HelloWorld/in/yourName"/>
- <sendsTo rdf:resource="workflow/HelloWorld/out/results"/>
- <dc:description>Connects workflow input port "yourName"
- directly to be merged on workflow output port "result". Merged in
- position 1, meaning that the data from "Hello" will come first. </dc:description>
- </DataLink>
-
- <DataLink rdf:about="workflow/HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0">
- <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</mergePosition>
- <receivesFrom rdf:resource="workflow/HelloWorld/processor/Hello/out/greeting"/>
- <sendsTo rdf:resource="workflow/HelloWorld/out/results"/>
- </DataLink>
-
- <InputWorkflowPort rdf:about="workflow/HelloWorld/in/yourName">
- <exampleValue>John Doe</exampleValue>
- <name>yourName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- <dc:description>Your name</dc:description>
- </InputWorkflowPort>
-
- <OutputWorkflowPort rdf:about="workflow/HelloWorld/out/results">
- <exampleList rdf:parseType="Resource">
- <rdf:first>Hello, John Doe!</rdf:first>
- <rdf:rest rdf:parseType="Resource">
- <rdf:first>John Doe</rdf:first>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </rdf:rest>
- </exampleList>
- <name>results</name>
- <dc:description>Personalised greeting, followed by name</dc:description>
- </OutputWorkflowPort>
-
- <Processor rdf:about="workflow/HelloWorld/processor/Hello">
- <dispatchStack rdf:resource="http://ns.taverna.org.uk/2010/scufl2/taverna#defaultDispatchStack"/>
- <inputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/in/name"/>
- <iterationStrategyStack rdf:parseType="Resource">
- <rdf:first rdf:resource="workflow/HelloWorld/processor/Hello/iterationStrategy/0"/>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </iterationStrategyStack>
- <name>Hello</name>
- <outputProcessorPort rdf:resource="workflow/HelloWorld/processor/Hello/out/greeting"/>
- <dc:description>A service that says greets the given name</dc:description>
- <dc:title>Hello world</dc:title>
- </Processor>
-
- <InputProcessorPort rdf:about="workflow/HelloWorld/processor/Hello/in/name">
- <exampleValue>Stian</exampleValue>
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>name</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- <dc:description>Name of person to greet</dc:description>
- </InputProcessorPort>
-
- <CrossProduct rdf:about="workflow/HelloWorld/processor/Hello/iterationStrategy/0">
- <iterationStrategyChildren rdf:parseType="Resource">
- <rdf:first rdf:resource="workflow/HelloWorld/processor/Hello/in/name"/>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </iterationStrategyChildren>
- </CrossProduct>
-
- <OutputProcessorPort rdf:about="workflow/HelloWorld/processor/Hello/out/greeting">
- <exampleValue>Hello, Stian!</exampleValue>
- <name>greeting</name>
- <dc:description>Personalised greeting</dc:description>
- </OutputProcessorPort>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Activity">
- <configurationType rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- </owl:Class>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- </owl:Class>
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#script">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
- <required rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</required>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:label>script</rdfs:label>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#script"/>
- </owl:DatatypeProperty>
-
- <rdf:Description rdf:about="http://www.ubuntu.com/#10.04">
- <version>10.04</version>
- <dc:title>Ubuntu Linux</dc:title>
- </rdf:Description>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example.scufl2
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example.scufl2 b/taverna-scufl2-rdf/src/test/resources/example.scufl2
deleted file mode 100644
index 1a9c298..0000000
Binary files a/taverna-scufl2-rdf/src/test/resources/example.scufl2 and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example.t2flow b/taverna-scufl2-rdf/src/test/resources/example.t2flow
deleted file mode 100644
index 76f8e9b..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example.t2flow
+++ /dev/null
@@ -1,239 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="3648b135-8f4e-49e5-87c0-1377945a2405" role="top"><name>A_simple_hello_world_workflow</name><inputPorts><port><name>yourName</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>John Doe</text>
- </annotationBean>
- <date>2010-08-04 17:37:03.737 BST</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>Your name</text>
- </annotationBean>
- <date>2010-08-04 17:36:56.895 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>results</name><annotations><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>Personalised greeting, followed by name</text>
- </annotationBean>
- <date>2010-08-04 17:37:35.710 BST</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.ExampleValue">
- <text>Hello John Doe!
-John Doe</text>
- </annotationBean>
- <date>2010-08-04 17:37:52.323 BST</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.ExampleValue">
- <text>[ "Hello John Doe!", "John Doe" ]</text>
- </annotationBean>
- <date>2010-08-04 17:37:29.241 BST</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>Personalised greeting, followed by Name</text>
- </annotationBean>
- <date>2010-08-04 17:37:14.479 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts><port><name>personName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>hello</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><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>A service that says greets the given name</text>
- </annotationBean>
- <date>2010-08-04 17:38:56.776 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="personName" to="personName" /></inputMap><outputMap><map from="hello" to="hello" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>import javax.swing.JOptionPane;
-
-hello = "Hello, " + personName;
-JOptionPane.showMessageDialog(null, hello, "Greeting",
- JOptionPane.INFORMATION_MESSAGE);
-
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>personName</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>hello</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="personName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Beanshell</processor><port>personName</port></sink><source type="dataflow"><port>yourName</port></source></datalink><datalink><sink type="merge"><port>results</port></sink><source type="processor"><processor>Beanshell</processor><port>hello</port></source></datalink><datalink><sink type="merge"><port>results</port></sink><source type="dataflow"><port>yourN
ame</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>58d43f9f-70d0-4466-9559-98c9a4339a5d</identification>
- </annotationBean>
- <date>2010-08-04 17:17:41.412 BST</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>b5613640-4b12-4c32-9b27-33b1a26fd592</identification>
- </annotationBean>
- <date>2010-08-04 17:17:16.686 BST</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>A simple hello world workflow</text>
- </annotationBean>
- <date>2010-08-04 17:36:15.653 BST</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>3648b135-8f4e-49e5-87c0-1377945a2405</identification>
- </annotationBean>
- <date>2010-08-04 17:39:37.57 BST</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>Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2010-08-04 17:36:03.233 BST</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>71f6bcb7-7485-44f3-a2b8-131e51ae7003</identification>
- </annotationBean>
- <date>2010-08-04 17:35:20.420 BST</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>c24a17e1-f572-4bc4-b09d-f7398c05f4ec</identification>
- </annotationBean>
- <date>2010-08-04 17:16:22.347 BST</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>be252ac2-30c2-4465-823a-80263432ad05</identification>
- </annotationBean>
- <date>2010-08-04 17:18:54.688 BST</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>ac4f9a6f-d5bc-4b7d-b235-26ed29c28852</identification>
- </annotationBean>
- <date>2010-08-04 17:18:34.975 BST</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>480b1099-1c5c-4c41-bff6-4f8320a50746</identification>
- </annotationBean>
- <date>2010-08-04 17:19:32.147 BST</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.FreeTextDescription">
- <text>A simple hello world workflow</text>
- </annotationBean>
- <date>2010-08-04 17:36:22.112 BST</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/db25fe67/taverna-scufl2-rdf/src/test/resources/example.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example.ttl b/taverna-scufl2-rdf/src/test/resources/example.ttl
deleted file mode 100644
index aeb9354..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example.ttl
+++ /dev/null
@@ -1,218 +0,0 @@
-#Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp
- # using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/test/resources/example/
-
-# Notation3 generation by
-# notation3.py,v 1.200 2007/12/11 21:18:08 syosi Exp
-
-# Base was: file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/test/resources/example/
- @prefix : <http://ns.taverna.org.uk/2010/taverna/activities/beanshell#> .
- @prefix owl: <http://www.w3.org/2002/07/owl#> .
- @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
- @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
- @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
- <> a <http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle>;
- <http://ns.taverna.org.uk/2010/scufl2#mainWorkflow> <workflow/HelloWorld/>;
- <http://ns.taverna.org.uk/2010/scufl2#name> "Hello world";
- <http://ns.taverna.org.uk/2010/scufl2#profile> <profile/tavernaWorkbench/>;
- <http://ns.taverna.org.uk/2010/scufl2#sameBaseAs> <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/>;
- <http://ns.taverna.org.uk/2010/scufl2#workflow> <workflow/HelloWorld/>;
- <http://purl.org/dc/elements/1.1/creator> "Stian Soiland-Reyes";
- <http://purl.org/dc/elements/1.1/date> "2010-07-29";
- <http://purl.org/dc/elements/1.1/description> "An example workflow to illustrate SCUFL2";
- rdf:seeAlso <annotation/workflowBundle.ttl> .
-
- <profile/tavernaServer/> a <http://ns.taverna.org.uk/2010/scufl2#Profile>;
- <http://ns.taverna.org.uk/2010/scufl2#activatesConfiguration> <profile/tavernaServer/configuration/Hello>;
- <http://ns.taverna.org.uk/2010/scufl2#name> "tavernaWorkbench";
- <http://ns.taverna.org.uk/2010/scufl2#processorBinding> <profile/tavernaServer/binding/Hello>;
- <http://ns.taverna.org.uk/2010/scufl2#recommendsEnvironment> [
- a <http://ns.taverna.org.uk/2010/scufl2#Environment>;
- <http://ns.taverna.org.uk/2010/scufl2#os> <http://www.ubuntu.com/#10.04>;
- <http://ns.taverna.org.uk/2010/scufl2#workflowProduct> <http://ns.taverna.org.uk/2010/taverna/server/>;
- <http://purl.org/dc/elements/1.1/title> "Taverna server installed on Ubuntu" ];
- <http://ns.taverna.org.uk/2010/scufl2#requiresEnvironment> [
- a <http://ns.taverna.org.uk/2010/scufl2#Environment>;
- <http://ns.taverna.org.uk/2010/scufl2#architecture> <http://www.intel.org/x64>;
- <http://ns.taverna.org.uk/2010/scufl2#plugin> :plugin;
- <http://ns.taverna.org.uk/2010/scufl2#product> <http://ns.taverna.org.uk/2010/taverna/>;
- <http://ns.taverna.org.uk/2010/scufl2#software> <http://www.bioconductor.org/>,
- <http://www.r-project.org/#2.11>,
- <http://www.rforge.net/Rserve/>;
- <http://purl.org/dc/elements/1.1/description> """
- BioConductor installed in R, and Rserve running
- on port 1234. x64 but architecture.
- """ ];
- <http://purl.org/dc/elements/1.1/creator> "Stian Soiland-Reyes";
- <http://purl.org/dc/elements/1.1/date> "2010-07-29";
- <http://purl.org/dc/elements/1.1/description> "A profile for invoking the workflow on a Taverna Server" .
-
- <profile/tavernaServer/activity/HelloScript/> a :Activity;
- <http://ns.taverna.org.uk/2010/scufl2#inputActivityPort> <profile/tavernaServer/activity/HelloScript/in/personName>;
- <http://ns.taverna.org.uk/2010/scufl2#outputActivityPort> <profile/tavernaServer/activity/HelloScript/out/hello> .
-
- <profile/tavernaServer/activity/HelloScript/in/personName> a <http://ns.taverna.org.uk/2010/scufl2#InputActivityPort>;
- <http://ns.taverna.org.uk/2010/scufl2#granularPortDepth> 0;
- <http://ns.taverna.org.uk/2010/scufl2#name> "personName";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0 .
-
- <profile/tavernaServer/activity/HelloScript/out/hello> a <http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort>;
- <http://ns.taverna.org.uk/2010/scufl2#granularPortDepth> 0;
- <http://ns.taverna.org.uk/2010/scufl2#name> "hello";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0 .
-
- <profile/tavernaServer/binding/Hello> a <http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding>;
- <http://ns.taverna.org.uk/2010/scufl2#boundActivity> <profile/tavernaServer/activity/HelloScript/>;
- <http://ns.taverna.org.uk/2010/scufl2#boundProcessor> <workflow/HelloWorld/processor/Hello/>;
- <http://ns.taverna.org.uk/2010/scufl2#inputPortBinding> [
- <http://ns.taverna.org.uk/2010/scufl2#bindsInputActivityPort> <profile/tavernaServer/activity/HelloScript/in/personName>;
- <http://ns.taverna.org.uk/2010/scufl2#bindsInputProcessorPort> <workflow/HelloWorld/processor/Hello/in/name> ];
- <http://ns.taverna.org.uk/2010/scufl2#outputPortBinding> [
- <http://ns.taverna.org.uk/2010/scufl2#bindsOutputActivityPort> <profile/tavernaServer/activity/HelloScript/out/hello>;
- <http://ns.taverna.org.uk/2010/scufl2#bindsOutputProcessorPort> <workflow/HelloWorld/processor/Hello/out/greeting> ] .
-
- <profile/tavernaServer/configuration/Hello> a :Configuration;
- <http://ns.taverna.org.uk/2010/scufl2#configures> <profile/tavernaServer/activity/HelloScript/>;
- :script """
- hello = "Hello, " + personName;
- System.out.println("Server says: " + hello);
- """ .
-
- <profile/tavernaWorkbench/> a <http://ns.taverna.org.uk/2010/scufl2#Profile>;
- <http://ns.taverna.org.uk/2010/scufl2#activatesConfiguration> <profile/tavernaWorkbench/configuration/Hello>;
- <http://ns.taverna.org.uk/2010/scufl2#name> "tavernaWorkbench";
- <http://ns.taverna.org.uk/2010/scufl2#processorBinding> <profile/tavernaWorkbench/binding/Hello>;
- <http://ns.taverna.org.uk/2010/scufl2#recommendsEnvironment> [
- a <http://ns.taverna.org.uk/2010/scufl2#Environment>;
- <http://ns.taverna.org.uk/2010/scufl2#workflowProduct> <http://ns.taverna.org.uk/2010/taverna/workbench/> ];
- <http://ns.taverna.org.uk/2010/scufl2#requiresEnvironment> [
- a <http://ns.taverna.org.uk/2010/scufl2#Environment>;
- <http://ns.taverna.org.uk/2010/scufl2#workflowPlugin> :plugin;
- <http://ns.taverna.org.uk/2010/scufl2#workflowProduct> <http://ns.taverna.org.uk/2010/taverna/> ];
- <http://purl.org/dc/elements/1.1/creator> "Stian Soiland-Reyes";
- <http://purl.org/dc/elements/1.1/date> "2010-07-29";
- <http://purl.org/dc/elements/1.1/description> "A profile for invoking the workflow on the Taverna Workbench";
- rdfs:seeAlso <profile/tavernaWorkbench.ttl> .
-
- <profile/tavernaWorkbench/activity/HelloScript/> a :Activity;
- <http://ns.taverna.org.uk/2010/scufl2#inputActivityPort> <profile/tavernaWorkbench/activity/HelloScript/in/personName>;
- <http://ns.taverna.org.uk/2010/scufl2#outputActivityPort> <profile/tavernaWorkbench/activity/HelloScript/out/hello> .
-
- <profile/tavernaWorkbench/activity/HelloScript/in/personName> a <http://ns.taverna.org.uk/2010/scufl2#InputActivityPort>;
- <http://ns.taverna.org.uk/2010/scufl2#granularPortDepth> 0;
- <http://ns.taverna.org.uk/2010/scufl2#name> "personName";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0 .
-
- <profile/tavernaWorkbench/activity/HelloScript/out/hello> a <http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort>;
- <http://ns.taverna.org.uk/2010/scufl2#granularPortDepth> 0;
- <http://ns.taverna.org.uk/2010/scufl2#name> "hello";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0 .
-
- <profile/tavernaWorkbench/binding/Hello> a <http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding>;
- <http://ns.taverna.org.uk/2010/scufl2#boundActivity> <profile/tavernaWorkbench/activity/HelloScript/>;
- <http://ns.taverna.org.uk/2010/scufl2#boundProcessor> <workflow/HelloWorld/processor/Hello/>;
- <http://ns.taverna.org.uk/2010/scufl2#inputPortBinding> [
- <http://ns.taverna.org.uk/2010/scufl2#bindsInputActivityPort> <profile/tavernaWorkbench/activity/HelloScript/in/personName>;
- <http://ns.taverna.org.uk/2010/scufl2#bindsInputProcessorPort> <workflow/HelloWorld/processor/Hello/in/name> ];
- <http://ns.taverna.org.uk/2010/scufl2#outputPortBinding> [
- <http://ns.taverna.org.uk/2010/scufl2#bindsOutputActivityPort> <profile/tavernaWorkbench/activity/HelloScript/out/hello>;
- <http://ns.taverna.org.uk/2010/scufl2#bindsOutputProcessorPort> <workflow/HelloWorld/processor/Hello/out/greeting> ] .
-
- <profile/tavernaWorkbench/configuration/Hello> a :Configuration;
- <http://ns.taverna.org.uk/2010/scufl2#configures> <profile/tavernaWorkbench/activity/HelloScript/>;
- :script """
- import javax.swing.JOptionPane;
-
- hello = "Hello, " + personName;
- JOptionPane.showMessageDialog(null, hello, "Greeting",
- JOptionPane.INFORMATION_MESSAGE);
- """ .
-
- <workflow/HelloWorld/> a <http://ns.taverna.org.uk/2010/scufl2#Workflow>;
- <http://ns.taverna.org.uk/2010/scufl2#datalink> <workflow/HelloWorld/datalink/5>,
- <workflow/HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0>,
- [
- a <http://ns.taverna.org.uk/2010/scufl2#DataLink>;
- <http://ns.taverna.org.uk/2010/scufl2#receivesFrom> <workflow/HelloWorld/in/yourName>;
- <http://ns.taverna.org.uk/2010/scufl2#sendsTo> <workflow/HelloWorld/processor/Hello/in/name> ];
- <http://ns.taverna.org.uk/2010/scufl2#inputWorkflowPort> <workflow/HelloWorld/in/yourName>;
- <http://ns.taverna.org.uk/2010/scufl2#name> "Helloworld";
- <http://ns.taverna.org.uk/2010/scufl2#outputWorkflowPort> <workflow/HelloWorld/out/results>;
- <http://ns.taverna.org.uk/2010/scufl2#processor> <workflow/HelloWorld/processor/Hello>;
- <http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier> <http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/>;
- <http://purl.org/dc/elements/1.1/date> "2010-07-28";
- <http://purl.org/dc/elements/1.1/description> "A simple hello world workflow";
- rdfs:seeAlso <workflow/HelloWorld.ttl>,
- <workflow/annotation/workflow/HelloWorld.ttl> .
-
- <workflow/HelloWorld/datalink/5> a <http://ns.taverna.org.uk/2010/scufl2#DataLink>;
- <http://ns.taverna.org.uk/2010/scufl2#mergePosition> 1;
- <http://ns.taverna.org.uk/2010/scufl2#receivesFrom> <workflow/HelloWorld/in/yourName>;
- <http://ns.taverna.org.uk/2010/scufl2#sendsTo> <workflow/HelloWorld/out/results>;
- <http://purl.org/dc/elements/1.1/description> """Connects workflow input port "yourName"
- directly to be merged on workflow output port "result". Merged in
- position 1, meaning that the data from "Hello" will come first. """ .
-
- <workflow/HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0> a <http://ns.taverna.org.uk/2010/scufl2#DataLink>;
- <http://ns.taverna.org.uk/2010/scufl2#mergePosition> 0;
- <http://ns.taverna.org.uk/2010/scufl2#receivesFrom> <workflow/HelloWorld/processor/Hello/out/greeting>;
- <http://ns.taverna.org.uk/2010/scufl2#sendsTo> <workflow/HelloWorld/out/results> .
-
- <workflow/HelloWorld/in/yourName> a <http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort>;
- <http://ns.taverna.org.uk/2010/scufl2#exampleValue> "John Doe";
- <http://ns.taverna.org.uk/2010/scufl2#name> "yourName";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0;
- <http://purl.org/dc/elements/1.1/description> "Your name" .
-
- <workflow/HelloWorld/out/results> a <http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort>;
- <http://ns.taverna.org.uk/2010/scufl2#exampleList> (
- "Hello, John Doe!"
- "John Doe" );
- <http://ns.taverna.org.uk/2010/scufl2#name> "results";
- <http://purl.org/dc/elements/1.1/description> "Personalised greeting, followed by name" .
-
- <workflow/HelloWorld/processor/Hello> a <http://ns.taverna.org.uk/2010/scufl2#Processor>;
- <http://ns.taverna.org.uk/2010/scufl2#dispatchStack> <http://ns.taverna.org.uk/2010/scufl2/taverna#defaultDispatchStack>;
- <http://ns.taverna.org.uk/2010/scufl2#inputProcessorPort> <workflow/HelloWorld/processor/Hello/in/name>;
- <http://ns.taverna.org.uk/2010/scufl2#iterationStrategyStack> (
- <workflow/HelloWorld/processor/Hello/iterationStrategy/0> );
- <http://ns.taverna.org.uk/2010/scufl2#name> "Hello";
- <http://ns.taverna.org.uk/2010/scufl2#outputProcessorPort> <workflow/HelloWorld/processor/Hello/out/greeting>;
- <http://purl.org/dc/elements/1.1/description> "A service that says greets the given name";
- <http://purl.org/dc/elements/1.1/title> "Hello world" .
-
- <workflow/HelloWorld/processor/Hello/in/name> a <http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort>;
- <http://ns.taverna.org.uk/2010/scufl2#exampleValue> "Stian";
- <http://ns.taverna.org.uk/2010/scufl2#granularPortDepth> 0;
- <http://ns.taverna.org.uk/2010/scufl2#name> "name";
- <http://ns.taverna.org.uk/2010/scufl2#portDepth> 0;
- <http://purl.org/dc/elements/1.1/description> "Name of person to greet" .
-
- <workflow/HelloWorld/processor/Hello/iterationStrategy/0> a <http://ns.taverna.org.uk/2010/scufl2#CrossProduct>;
- <http://ns.taverna.org.uk/2010/scufl2#iterationStrategyChildren> (
- <workflow/HelloWorld/processor/Hello/in/name> ) .
-
- <workflow/HelloWorld/processor/Hello/out/greeting> a <http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort>;
- <http://ns.taverna.org.uk/2010/scufl2#exampleValue> "Hello, Stian!";
- <http://ns.taverna.org.uk/2010/scufl2#name> "greeting";
- <http://purl.org/dc/elements/1.1/description> "Personalised greeting" .
-
- :Activity a owl:Class;
- <http://ns.taverna.org.uk/2010/scufl2#configurationType> :Configuration;
- rdfs:subClassOf <http://ns.taverna.org.uk/2010/scufl2#Activity> .
-
- :Configuration a owl:Class;
- rdfs:subClassOf <http://ns.taverna.org.uk/2010/scufl2#Configuration> .
-
- :script a owl:DatatypeProperty,
- owl:FunctionalProperty;
- <http://ns.taverna.org.uk/2010/scufl2#required> true;
- rdfs:domain :Configuration;
- rdfs:label "script";
- rdfs:range xsd:string;
- rdfs:subPropertyOf <http://ns.taverna.org.uk/2010/scufl2#script> .
-
- <http://www.ubuntu.com/#10.04> <http://ns.taverna.org.uk/2010/scufl2#version> "10.04";
- <http://purl.org/dc/elements/1.1/title> "Ubuntu Linux" .
-
-#ENDS
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/META-INF/container.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/META-INF/container.xml b/taverna-scufl2-rdf/src/test/resources/example/META-INF/container.xml
deleted file mode 100644
index 8d064af..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/META-INF/container.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<container version="1.0"
- xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
- <rootfiles>
- <rootfile full-path="workflowBundle.ttl"
- media-type="text/turtle" />
- <rootfile full-path="workflowBundle.rdf"
- media-type="application/rdf+xml" />
- </rootfiles>
- <relationships>
- <relationship type="metadata" target="/annotation/$dir/$filename.$ext" />
- </relationships>
-</container>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/META-INF/manifest.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/META-INF/manifest.xml b/taverna-scufl2-rdf/src/test/resources/example/META-INF/manifest.xml
deleted file mode 100644
index f30dd2b..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/META-INF/manifest.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0">
- <manifest:file-entry manifest:media-type="application/vnd.taverna.scufl2.workflowBundle" manifest:full-path="/"/>
-
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflowBundle.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="workflow/HelloWorld.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflow/HelloWorld.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="annotation/workflowBundle.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaWorkbench.ttl"/>
- <manifest:file-entry manifest:media-type="text/turtle" manifest:full-path="profile/tavernaServer.ttl"/>
-
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflowBundle.rdf"/>
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="workflow/HelloWorld.rdf"/>
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/workflow/HelloWorld.rdf"/>
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="annotation/workflowBundle.rdf"/>
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaWorkbench.rdf"/>
- <manifest:file-entry manifest:media-type="application/rdf+xml" manifest:full-path="profile/tavernaServer.rdf"/>
-
- <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full-path="Thumbnails/thumbnail.svg"/>
- <manifest:file-entry manifest:media-type="image/png" manifest:full-path="Thumbnails/thumbnail.png"/>
-
- <manifest:file-entry manifest:media-type="image/svg+xml" manifest:full-path="diagram/workflow/HelloWorld.svg"/>
- <manifest:file-entry manifest:media-type="image/png" manifest:full-path="diagram/workflow/HelloWorld.png"/>
-</manifest:manifest>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.png
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.png b/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.png
deleted file mode 100644
index 8b69f43..0000000
Binary files a/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.svg
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.svg b/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.svg
deleted file mode 100644
index 0c14a45..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.svg
+++ /dev/null
@@ -1,91 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN"
- "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd" [
- <!ATTLIST svg xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink">
-]>
-<!-- Generated by Graphviz version 2.20.2 (Tue Mar  2 19:03:41 UTC 2010)
- For user: (stain) Stian Soiland-Reyes,,,, -->
-<!-- Title: A_simple_hello_world_workflow Pages: 1 -->
-<svg width="146pt" height="210pt"
- viewBox="0.00 0.00 146.00 210.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 206)">
-<title>A_simple_hello_world_workflow</title>
-<polygon style="fill:#ffffff;stroke:#ffffff;" points="-4,4 -4,-206 142,-206 142,4 -4,4"/>
-<g id="cluster2" class="cluster"><title>cluster_A_simple_hello_world_workflowsinks</title>
-<polygon style="fill:none;stroke:black;stroke-dasharray:1,5;" points="11,-16 11,-73 130,-73 130,-16 11,-16"/>
-<text text-anchor="middle" x="70" y="-60.5" style="font-family:Times New Roman;font-size:10.00;">Workflow output ports</text>
-</g>
-<g id="cluster3" class="cluster"><title>cluster_A_simple_hello_world_workflowsources</title>
-<polygon style="fill:none;stroke:black;stroke-dasharray:1,5;" points="10,-137 10,-194 121,-194 121,-137 10,-137"/>
-<text text-anchor="middle" x="65" y="-181.5" style="font-family:Times New Roman;font-size:10.00;">Workflow input ports</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSINKCONTROL -->
-<g id="node2" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSINKCONTROL</title>
-<polygon style="fill:#66cd00;stroke:black;" points="96,-28 102,-37 90,-37 96,-28"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results -->
-<g id="node3" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results</title>
-<polygon style="fill:#8ed6f0;stroke:black;" points="67,-44 23,-44 23,-24 67,-24 67,-44"/>
-<text text-anchor="middle" x="45" y="-31" style="font-family:Arial;font-size:10.00;">results</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCECONTROL -->
-<g id="node5" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCECONTROL</title>
-<polygon style="fill:#ff4040;stroke:black;" points="101,-161 95,-152 107,-152 101,-161"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName -->
-<g id="node6" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName</title>
-<polygon style="fill:#8ed6f0;stroke:black;" points="86,-165 26,-165 26,-145 86,-145 86,-165"/>
-<text text-anchor="middle" x="56" y="-152" style="font-family:Arial;font-size:10.00;">yourName</text>
-</g>
-<!-- A_simple_hello_world_workflowBeanshell -->
-<g id="node7" class="node"><title>A_simple_hello_world_workflowBeanshell</title>
-<polygon style="fill:#deb887;stroke:black;" points="58,-129 2.13163e-14,-129 0,-109 58,-109 58,-129"/>
-<text text-anchor="middle" x="29" y="-116" style="font-family:Arial;font-size:10.00;">Beanshell</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowBeanshell -->
-<g id="edge4" class="edge"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowBeanshell</title>
-<path style="fill:none;stroke:#000000;" d="M48,-145C46,-143 44,-140 42,-138"/>
-<polygon style="fill:#000000;stroke:#000000;" points="44.916,-136.042 37,-129 38.7969,-139.441 44.916,-136.042"/>
-</g>
-<!-- A_simple_hello_world_workflowMerge0 -->
-<g id="node8" class="node"><title>A_simple_hello_world_workflowMerge0</title>
-<ellipse style="fill:#4f94cd;stroke:black;" cx="45" cy="-87" rx="6" ry="6"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowMerge0 -->
-<g id="edge6" class="edge"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowMerge0</title>
-<path style="fill:none;stroke:#000000;" d="M58,-145C60,-135 61,-121 58,-109 57,-106 56,-103 54,-100"/>
-<polygon style="fill:#000000;stroke:#000000;" points="57.268,-98.625 49,-92 51.332,-102.335 57.268,-98.625"/>
-</g>
-<!-- A_simple_hello_world_workflowBeanshell->A_simple_hello_world_workflowMerge0 -->
-<g id="edge8" class="edge"><title>A_simple_hello_world_workflowBeanshell->A_simple_hello_world_workflowMerge0</title>
-<path style="fill:none;stroke:#000000;" d="M34,-109C35,-107 36,-105 38,-102"/>
-<polygon style="fill:#000000;stroke:#000000;" points="41.1369,-103.56 42,-93 34.7402,-100.717 41.1369,-103.56"/>
-</g>
-<!-- A_simple_hello_world_workflowMerge0->A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results -->
-<g id="edge10" class="edge"><title>A_simple_hello_world_workflowMerge0->A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results</title>
-<path style="fill:none;stroke:#000000;" d="M45,-81C45,-74 45,-64 45,-54"/>
-<polygon style="fill:#000000;stroke:#000000;" points="48.5001,-54 45,-44 41.5001,-54 48.5001,-54"/>
-</g>
-</g>
-</svg>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.rdf b/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.rdf
deleted file mode 100644
index 5638f28..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.rdf
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/main/resources/example/annotation/workflow/HelloWorld.ttl-->
-
-
-<rdf:RDF xmlns="http://purl.org/dc/elements/1.1/"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/">
- <date>2010-07-28</date>
- <description>A simple hello world workflow</description>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/datalink/5">
- <description>Connects workflow input port "yourName"
- directly to be merged on workflow output port "result". Merged in
- position 1, meaning that the data from "Hello" will come first. </description>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/in/yourName">
- <scufl2:exampleValue>John Doe</scufl2:exampleValue>
- <description>Your name</description>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/out/results">
- <scufl2:exampleList rdf:parseType="Resource">
- <rdf:first>Hello, John Doe!</rdf:first>
- <rdf:rest rdf:parseType="Resource">
- <rdf:first>John Doe</rdf:first>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </rdf:rest>
- </scufl2:exampleList>
- <description>Personalised greeting, followed by name</description>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/processor/Hello">
- <description>A service that says greets the given name</description>
- <title>Hello world</title>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/processor/Hello/in/name">
- <scufl2:exampleValue>Stian</scufl2:exampleValue>
- <description>Name of person to greet</description>
- </rdf:Description>
-
- <rdf:Description rdf:about="../../workflow/HelloWorld/processor/Hello/out/greeting">
- <scufl2:exampleValue>Hello, Stian!</scufl2:exampleValue>
- <description>Personalised greeting</description>
- </rdf:Description>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.ttl b/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.ttl
deleted file mode 100644
index 0be9e38..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.ttl
+++ /dev/null
@@ -1,41 +0,0 @@
-@base <../../workflow/HelloWorld/> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-
-
-
-<>
- dc:description "A simple hello world workflow" ;
- dc:date "2010-07-28" .
-
-<in/yourName>
- dc:description "Your name" ;
- scufl2:exampleValue "John Doe" .
-
-<out/results>
- dc:description "Personalised greeting, followed by name" ;
- scufl2:exampleList ( "Hello, John Doe!" "John Doe" ) .
-
-
-
-<datalink/5>
- dc:description """Connects workflow input port "yourName"
- directly to be merged on workflow output port "result". Merged in
- position 1, meaning that the data from "Hello" will come first. """ .
-
-# Can't describe _:datalink1 as it does not have an URI (in this bundle)
-
-
-<processor/Hello>
- # More readable alternative to scufl2:name, which is a sub-property of dc:title
- dc:title "Hello world" ;
- dc:description "A service that says greets the given name".
-
-<processor/Hello/in/name>
- dc:description "Name of person to greet";
- scufl2:exampleValue "Stian".
-
-<processor/Hello/out/greeting>
- dc:description "Personalised greeting" ;
- scufl2:exampleValue "Hello, Stian!" .
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.rdf b/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.rdf
deleted file mode 100644
index 5889e70..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.rdf
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/main/resources/example/annotation/workflowBundle.ttl-->
-
-
-<rdf:RDF xmlns="http://purl.org/dc/elements/1.1/"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-
- <rdf:Description rdf:about="../">
- <creator>Stian Soiland-Reyes</creator>
- <date>2010-07-29</date>
- <description>An example workflow to illustrate SCUFL2</description>
- </rdf:Description>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.ttl
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diff --git a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.ttl b/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.ttl
deleted file mode 100644
index acdee25..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/annotation/workflowBundle.ttl
+++ /dev/null
@@ -1,8 +0,0 @@
-@base <../> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-
-<>
- dc:description """An example workflow to illustrate SCUFL2""" ;
- dc:creator "Stian Soiland-Reyes" ;
- dc:date "2010-07-29" .
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.png
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diff --git a/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.png b/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.png
deleted file mode 100644
index 74bc4e1..0000000
Binary files a/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.svg
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diff --git a/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.svg b/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.svg
deleted file mode 100644
index 0c14a45..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.svg
+++ /dev/null
@@ -1,91 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN"
- "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd" [
- <!ATTLIST svg xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink">
-]>
-<!-- Generated by Graphviz version 2.20.2 (Tue Mar  2 19:03:41 UTC 2010)
- For user: (stain) Stian Soiland-Reyes,,,, -->
-<!-- Title: A_simple_hello_world_workflow Pages: 1 -->
-<svg width="146pt" height="210pt"
- viewBox="0.00 0.00 146.00 210.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 206)">
-<title>A_simple_hello_world_workflow</title>
-<polygon style="fill:#ffffff;stroke:#ffffff;" points="-4,4 -4,-206 142,-206 142,4 -4,4"/>
-<g id="cluster2" class="cluster"><title>cluster_A_simple_hello_world_workflowsinks</title>
-<polygon style="fill:none;stroke:black;stroke-dasharray:1,5;" points="11,-16 11,-73 130,-73 130,-16 11,-16"/>
-<text text-anchor="middle" x="70" y="-60.5" style="font-family:Times New Roman;font-size:10.00;">Workflow output ports</text>
-</g>
-<g id="cluster3" class="cluster"><title>cluster_A_simple_hello_world_workflowsources</title>
-<polygon style="fill:none;stroke:black;stroke-dasharray:1,5;" points="10,-137 10,-194 121,-194 121,-137 10,-137"/>
-<text text-anchor="middle" x="65" y="-181.5" style="font-family:Times New Roman;font-size:10.00;">Workflow input ports</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSINKCONTROL -->
-<g id="node2" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSINKCONTROL</title>
-<polygon style="fill:#66cd00;stroke:black;" points="96,-28 102,-37 90,-37 96,-28"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results -->
-<g id="node3" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results</title>
-<polygon style="fill:#8ed6f0;stroke:black;" points="67,-44 23,-44 23,-24 67,-24 67,-44"/>
-<text text-anchor="middle" x="45" y="-31" style="font-family:Arial;font-size:10.00;">results</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCECONTROL -->
-<g id="node5" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCECONTROL</title>
-<polygon style="fill:#ff4040;stroke:black;" points="101,-161 95,-152 107,-152 101,-161"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName -->
-<g id="node6" class="node"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName</title>
-<polygon style="fill:#8ed6f0;stroke:black;" points="86,-165 26,-165 26,-145 86,-145 86,-165"/>
-<text text-anchor="middle" x="56" y="-152" style="font-family:Arial;font-size:10.00;">yourName</text>
-</g>
-<!-- A_simple_hello_world_workflowBeanshell -->
-<g id="node7" class="node"><title>A_simple_hello_world_workflowBeanshell</title>
-<polygon style="fill:#deb887;stroke:black;" points="58,-129 2.13163e-14,-129 0,-109 58,-109 58,-129"/>
-<text text-anchor="middle" x="29" y="-116" style="font-family:Arial;font-size:10.00;">Beanshell</text>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowBeanshell -->
-<g id="edge4" class="edge"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowBeanshell</title>
-<path style="fill:none;stroke:#000000;" d="M48,-145C46,-143 44,-140 42,-138"/>
-<polygon style="fill:#000000;stroke:#000000;" points="44.916,-136.042 37,-129 38.7969,-139.441 44.916,-136.042"/>
-</g>
-<!-- A_simple_hello_world_workflowMerge0 -->
-<g id="node8" class="node"><title>A_simple_hello_world_workflowMerge0</title>
-<ellipse style="fill:#4f94cd;stroke:black;" cx="45" cy="-87" rx="6" ry="6"/>
-</g>
-<!-- A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowMerge0 -->
-<g id="edge6" class="edge"><title>A_simple_hello_world_workflowWORKFLOWINTERNALSOURCE_yourName->A_simple_hello_world_workflowMerge0</title>
-<path style="fill:none;stroke:#000000;" d="M58,-145C60,-135 61,-121 58,-109 57,-106 56,-103 54,-100"/>
-<polygon style="fill:#000000;stroke:#000000;" points="57.268,-98.625 49,-92 51.332,-102.335 57.268,-98.625"/>
-</g>
-<!-- A_simple_hello_world_workflowBeanshell->A_simple_hello_world_workflowMerge0 -->
-<g id="edge8" class="edge"><title>A_simple_hello_world_workflowBeanshell->A_simple_hello_world_workflowMerge0</title>
-<path style="fill:none;stroke:#000000;" d="M34,-109C35,-107 36,-105 38,-102"/>
-<polygon style="fill:#000000;stroke:#000000;" points="41.1369,-103.56 42,-93 34.7402,-100.717 41.1369,-103.56"/>
-</g>
-<!-- A_simple_hello_world_workflowMerge0->A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results -->
-<g id="edge10" class="edge"><title>A_simple_hello_world_workflowMerge0->A_simple_hello_world_workflowWORKFLOWINTERNALSINK_results</title>
-<path style="fill:none;stroke:#000000;" d="M45,-81C45,-74 45,-64 45,-54"/>
-<polygon style="fill:#000000;stroke:#000000;" points="48.5001,-54 45,-44 41.5001,-54 48.5001,-54"/>
-</g>
-</g>
-</svg>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/mimetype
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/mimetype b/taverna-scufl2-rdf/src/test/resources/example/mimetype
deleted file mode 100644
index 2d61400..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/mimetype
+++ /dev/null
@@ -1 +0,0 @@
-application/vnd.taverna.scufl2.workflow-bundle
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.rdf b/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.rdf
deleted file mode 100644
index f1a622c..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.rdf
+++ /dev/null
@@ -1,124 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:beanshell="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <Profile rdf:about="tavernaServer/">
- <activatesConfiguration rdf:resource="tavernaServer/configuration/Hello"/>
- <name>tavernaWorkbench</name>
- <processorBinding rdf:resource="tavernaServer/binding/Hello"/>
- <recommendsEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <os rdf:resource="http://www.ubuntu.com/#10.04"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/server/"/>
- <dc:title>Taverna server installed on Ubuntu</dc:title>
- </recommendsEnvironment>
- <requiresEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <architecture rdf:resource="http://www.intel.org/x64"/>
- <plugin rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#plugin"/>
- <product rdf:resource="http://ns.taverna.org.uk/2010/taverna/"/>
- <software rdf:resource="http://www.bioconductor.org/"/>
- <software rdf:resource="http://www.r-project.org/#2.11"/>
- <software rdf:resource="http://www.rforge.net/Rserve/"/>
- <dc:description>
- BioConductor installed in R, and Rserve running
- on port 1234. x64 but architecture.
- </dc:description>
- </requiresEnvironment>
- <dc:creator>Stian Soiland-Reyes</dc:creator>
- <dc:date>2010-07-29</dc:date>
- <dc:description>A profile for invoking the workflow on a Taverna Server</dc:description>
- </Profile>
-
- <beanshell:Activity rdf:about="tavernaServer/activity/HelloScript/">
- <inputActivityPort rdf:resource="tavernaServer/activity/HelloScript/in/personName"/>
- <outputActivityPort rdf:resource="tavernaServer/activity/HelloScript/out/hello"/>
- </beanshell:Activity>
-
- <InputActivityPort rdf:about="tavernaServer/activity/HelloScript/in/personName">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>personName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputActivityPort>
-
- <OutputActivityPort rdf:about="tavernaServer/activity/HelloScript/out/hello">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>hello</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </OutputActivityPort>
-
- <ProcessorBinding rdf:about="tavernaServer/binding/Hello">
- <boundActivity rdf:resource="tavernaServer/activity/HelloScript/"/>
- <boundProcessor rdf:resource="../workflow/HelloWorld/processor/Hello/"/>
- <inputPortBinding rdf:parseType="Resource">
- <bindsInputActivityPort rdf:resource="tavernaServer/activity/HelloScript/in/personName"/>
- <bindsInputProcessorPort rdf:resource="../workflow/HelloWorld/processor/Hello/in/name"/>
- </inputPortBinding>
- <outputPortBinding rdf:parseType="Resource">
- <bindsOutputActivityPort rdf:resource="tavernaServer/activity/HelloScript/out/hello"/>
- <bindsOutputProcessorPort rdf:resource="../workflow/HelloWorld/processor/Hello/out/greeting"/>
- </outputPortBinding>
- </ProcessorBinding>
-
- <beanshell:Configuration rdf:about="tavernaServer/configuration/Hello">
- <configures rdf:resource="tavernaServer/activity/HelloScript/"/>
- <beanshell:script>
- hello = "Hello, " + personName;
- System.out.println("Server says: " + hello);
- </beanshell:script>
- </beanshell:Configuration>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Activity">
- <configurationType rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- </owl:Class>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- </owl:Class>
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#script">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
- <required rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</required>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:label>script</rdfs:label>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#script"/>
- </owl:DatatypeProperty>
-
- <rdf:Description rdf:about="http://www.ubuntu.com/#10.04">
- <version>10.04</version>
- <dc:title>Ubuntu Linux</dc:title>
- </rdf:Description>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl b/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl
deleted file mode 100644
index b53fabb..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl
+++ /dev/null
@@ -1,109 +0,0 @@
-@base <tavernaServer/> .
-@prefix beanshell: <http://ns.taverna.org.uk/2010/taverna/activities/beanshell#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-
-<.>
- a scufl2:Profile;
- scufl2:name "tavernaWorkbench" ;
- dc:description """A profile for invoking the workflow on a Taverna Server""" ;
- dc:creator "Stian Soiland-Reyes" ;
- dc:date "2010-07-29" ;
- scufl2:processorBinding <binding/Hello> ;
- scufl2:activatesConfiguration <configuration/Hello> ;
- scufl2:recommendsEnvironment [
- # Not really any need to give a URI to this specialized
- # environment
- a scufl2:Environment;
- scufl2:workflowProduct <http://ns.taverna.org.uk/2010/taverna/server/>;
- scufl2:os <http://www.ubuntu.com/#10.04>;
- dc:title "Taverna server installed on Ubuntu"
- ] ;
- scufl2:requiresEnvironment [
- a scufl2:Environment;
- scufl2:product <http://ns.taverna.org.uk/2010/taverna/>;
- scufl2:plugin beanshell:plugin;
- dc:description """
- BioConductor installed in R, and Rserve running
- on port 1234. x64 but architecture.
- """;
- # There's not really any agreed URIs for Windows/Linux/etc
- # .. but at least the scufl:os and :software URIs can be clickable
- # for a browser. A GUI could simply say:
- #
- # This workflow execution profile requires/recommends:
- # OS: [x] Ubuntu Linux (10.04)
- # Software: [x] http://www.r-project.org/
- # [x] http://www.rforge.net/Rserve/
- # [ ] http://www.bioconductor.org/
- # Tick for software you have installed.
- #
- scufl2:software <http://www.r-project.org/#2.11>;
- scufl2:software <http://www.rforge.net/Rserve/>;
- scufl2:software <http://www.bioconductor.org/>;
- scufl2:architecture <http://www.intel.org/x64>
- ] .
-
-<http://www.ubuntu.com/#10.04>
- scufl2:version "10.04";
- dc:title "Ubuntu Linux".
-
-<binding/Hello> a scufl2:ProcessorBinding ;
- scufl2:boundProcessor <../../workflow/HelloWorld/processor/Hello/> ;
- scufl2:boundActivity <activity/HelloScript/> ;
- scufl2:inputPortBinding [
- scufl2:bindsInputProcessorPort <../../workflow/HelloWorld/processor/Hello/in/name> ;
- scufl2:bindsInputActivityPort <activity/HelloScript/in/personName>
- ] ;
- scufl2:outputPortBinding [
- scufl2:bindsOutputActivityPort <activity/HelloScript/out/hello> ;
- scufl2:bindsOutputProcessorPort <../../workflow/HelloWorld/processor/Hello/out/greeting>
- ] .
-
-
-<activity/HelloScript/> a beanshell:Activity ;
- scufl2:inputActivityPort <activity/HelloScript/in/personName> ;
- scufl2:outputActivityPort <activity/HelloScript/out/hello> .
-
-<activity/HelloScript/in/personName> a scufl2:InputActivityPort ;
- scufl2:name "personName";
- scufl2:portDepth 0 ;
- scufl2:granularPortDepth 0 .
-
-<activity/HelloScript/out/hello> a scufl2:OutputActivityPort ;
- scufl2:name "hello";
- scufl2:portDepth 0 ;
- scufl2:granularPortDepth 0 .
-
-
-<configuration/Hello> a beanshell:Configuration;
- scufl2:configures <activity/HelloScript/> ;
- beanshell:script """
- hello = "Hello, " + personName;
- System.out.println("Server says: " + hello);
- """ .
-
-
-# Define possible configurations for a beanshell
-
-beanshell:Activity a owl:Class;
- scufl2:configurationType beanshell:Configuration;
- rdfs:subClassOf scufl2:Activity .
-
-beanshell:Configuration a owl:Class;
- rdfs:subClassOf scufl2:Configuration .
-
-beanshell:script
- a owl:DatatypeProperty, owl:FunctionalProperty ;
- rdfs:domain beanshell:Configuration;
- rdfs:label "script" ;
- rdfs:range xsd:string ;
- scufl2:required true ;
- rdfs:subPropertyOf scufl2:script .
-
-
-
[28/52] [abbrv] incubator-taverna-language git commit: Tidy up the
.gitignores
Posted by st...@apache.org.
Tidy up the .gitignores
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/8b377d56
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/8b377d56
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/8b377d56
Branch: refs/heads/master
Commit: 8b377d56535ae9380ecf0e9946566bba791effad
Parents: 1b3666a
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Wed Feb 11 10:20:47 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Wed Feb 11 10:20:47 2015 +0000
----------------------------------------------------------------------
.gitignore | 2 +-
taverna-scufl2-schemas/.gitignore | 1 -
2 files changed, 1 insertion(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8b377d56/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
index f5c0358..f736862 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,4 @@
.settings
.classpath
target
-
+.gitignore
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8b377d56/taverna-scufl2-schemas/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/.gitignore b/taverna-scufl2-schemas/.gitignore
deleted file mode 100644
index ea8c4bf..0000000
--- a/taverna-scufl2-schemas/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target
[50/52] [abbrv] incubator-taverna-language git commit: Added
copyright declaration to all files where I could directly identify that the
file was owned by Manchester from the beginning.
Posted by st...@apache.org.
Added copyright declaration to all files where I could directly identify
that the file was owned by Manchester from the beginning.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/7805e775
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/7805e775
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/7805e775
Branch: refs/heads/master
Commit: 7805e775ced9afeb27c4854128efa8ad20ebd51e
Parents: 7e6e391
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Fri Feb 13 14:25:13 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Fri Feb 13 14:33:34 2015 +0000
----------------------------------------------------------------------
pom.xml | 15 +-------------
.../src/test/resources/helloanyone.t2flow | 18 +++++++++++++++++
.../examples/helloanyone.t2flow | 19 ++++++++++++++++++
.../examples/helloworld.t2flow | 19 ++++++++++++++++++
.../T3-1226-annotations-with-quotes.t2flow | 19 ++++++++++++++++++
.../src/test/resources/annotated2.2.t2flow | 19 ++++++++++++++++++
.../src/test/resources/as.t2flow | 20 ++++++++++++++++++-
.../defaultActivitiesTaverna2.2.t2flow | 19 ++++++++++++++++++
.../src/test/resources/random.t2flow | 19 ++++++++++++++++++
.../semantic_annotations__eclipse.t2flow | 19 ++++++++++++++++++
.../spreadsheet_activity_defaults_892.t2flow | 19 ++++++++++++++++++
.../src/test/resources/xpath_workflow.t2flow | 19 ++++++++++++++++++
.../T3-1226-annotations-with-quotes.t2flow | 19 ++++++++++++++++++
.../src/test/resources/allTypes.t2flow | 21 +++++++++++++++++++-
.../src/test/resources/helloanyone.t2flow | 19 ++++++++++++++++++
.../src/test/resources/helloworld.t2flow | 19 ++++++++++++++++++
16 files changed, 286 insertions(+), 16 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index a11fc92..71b6b4a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -96,13 +96,10 @@
<exclude>/src/test/resources/t172starterpacklist</exclude>
<exclude>/src/test/resources/t230starterpacklist</exclude>
<!-- THESE ARE XML AND SUPPORT COMMENTS -->
- <exclude>/src/test/resources/annotated2.2.t2flow</exclude>
<exclude>/src/test/resources/annotation_with_backslash.t2flow</exclude>
- <exclude>/src/test/resources/as.t2flow</exclude>
<exclude>/src/test/resources/beanshell-deps.t2flow</exclude>
<exclude>/src/test/resources/component_simple.t2flow</exclude>
<exclude>/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
- <exclude>/src/test/resources/defaultActivitiesTaverna2.2.t2flow</exclude>
<exclude>/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
<exclude>/src/test/resources/dispatchlayers.t2flow</exclude>
<exclude>/src/test/resources/fasta_and_pscan.t2flow</exclude>
@@ -110,29 +107,19 @@
<exclude>/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
<exclude>/src/test/resources/interaction_multiple_choice.t2flow</exclude>
<exclude>/src/test/resources/interaction_simple_tell.t2flow</exclude>
- <exclude>/src/test/resources/iterationstrategies.t2flow</exclude>
+ <exclude>/src/test/resources/iterationstrategies.t2flow</exclude><!-- TOM -->
<exclude>/src/test/resources/merge_fun.t2flow</exclude>
<exclude>/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
<exclude>/src/test/resources/missing_merge.t2flow</exclude>
<exclude>/src/test/resources/missing_produced_by_941.t2flow</exclude>
- <exclude>/src/test/resources/random.t2flow</exclude>
<exclude>/src/test/resources/rest-2-2.t2flow</exclude>
<exclude>/src/test/resources/rshell-2-2.t2flow</exclude>
- <exclude>/src/test/resources/semantic_annotations__eclipse.t2flow</exclude>
<exclude>/src/test/resources/simple_fasta.t2flow</exclude>
<exclude>/src/test/resources/sleepers.t2flow</exclude>
- <exclude>/src/test/resources/spreadsheet_activity_defaults_892.t2flow</exclude>
- <exclude>/src/test/resources/T3-1226-annotations-with-quotes.t2flow</exclude>
- <exclude>/src/test/resources/xpath_workflow.t2flow</exclude>
- <exclude>/examples/helloanyone.t2flow</exclude>
- <exclude>/examples/helloworld.t2flow</exclude>
<exclude>/src/test/resources/apiconsumer.t2flow</exclude>
<exclude>/src/test/resources/rest.t2flow</exclude>
- <exclude>/src/test/resources/helloanyone.t2flow</exclude>
<exclude>/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
- <exclude>/src/test/resources/allTypes.t2flow</exclude>
<exclude>/src/test/resources/enm-v21.t2flow</exclude>
- <exclude>/src/test/resources/helloworld.t2flow</exclude>
<exclude>/src/test/resources/helloworld.wfdesc.ttl</exclude>
<exclude>/src/test/resources/localdependency.t2flow</exclude>
<exclude>/src/test/resources/nested.t2flow</exclude>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow b/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow
index c691d21..9fb9f52 100644
--- a/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow
+++ b/taverna-scufl2-annotation/src/test/resources/helloanyone.t2flow
@@ -1,4 +1,22 @@
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-examples/examples/helloanyone.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloanyone.t2flow b/taverna-scufl2-examples/examples/helloanyone.t2flow
index c691d21..3b625f1 100644
--- a/taverna-scufl2-examples/examples/helloanyone.t2flow
+++ b/taverna-scufl2-examples/examples/helloanyone.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-examples/examples/helloworld.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloworld.t2flow b/taverna-scufl2-examples/examples/helloworld.t2flow
index fbc7381..2e10ed9 100644
--- a/taverna-scufl2-examples/examples/helloworld.t2flow
+++ b/taverna-scufl2-examples/examples/helloworld.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="8781d5f4-d0ba-48a8-a1d1-14281bd8a917" role="top"><name>Hello_World</name><inputPorts /><outputPorts><port><name>greeting</name><annotations /></port></outputPorts><processors><processor><name>hello</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>Hello, World!</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/T3-1226-annotations-with-quotes.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/T3-1226-annotations-with-quotes.t2flow b/taverna-scufl2-t2flow/src/test/resources/T3-1226-annotations-with-quotes.t2flow
index 26ab94e..3f9aa3e 100644
--- a/taverna-scufl2-t2flow/src/test/resources/T3-1226-annotations-with-quotes.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/T3-1226-annotations-with-quotes.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-workbench-core-2.5.0-20140804T1456"><dataflow id="73a04132-5dc0-4e24-8a30-6ef91c773ad1" role="top"><name>T3_1226_test_with__s</name><inputPorts><port><name>a</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow b/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow
index 251a1fe..31b1412 100644
--- a/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/annotated2.2.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad" role="top"><name>Workflow_title</name><inputPorts><port><name>in0</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/as.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/as.t2flow b/taverna-scufl2-t2flow/src/test/resources/as.t2flow
index 2dc0596..c52586a 100644
--- a/taverna-scufl2-t2flow/src/test/resources/as.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/as.t2flow
@@ -1,4 +1,22 @@
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0">
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<dataflow id="92c5e8d5-8360-4f86-a845-09c9849cbdc5" role="top">
<name>Workflow1</name>
<inputPorts />
@@ -1654,4 +1672,4 @@ for (int i = 0; i < 40; i++) {
</datalinks>
<annotations />
</dataflow>
-</workflow>
\ No newline at end of file
+</workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow b/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
index 4958771..8d8632a 100644
--- a/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="dc227a10-e8f6-44b0-88c5-c946a15ff669" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<script>the
script;</script>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/random.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/random.t2flow b/taverna-scufl2-t2flow/src/test/resources/random.t2flow
index c3df019..e68bc17 100644
--- a/taverna-scufl2-t2flow/src/test/resources/random.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/random.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1-beta-2"><dataflow id="e87de19a-02c7-4106-ae81-0b8e28efb22c" role="top"><name>Workflow9</name><inputPorts><port><name>InputText</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow b/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
index be15c71..f2d5e9c 100644
--- a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<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"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow b/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
index 2ab96dd..2a3fb45 100644
--- a/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1-beta-2"><dataflow id="d6c01ddf-f1a5-4cb7-95b6-a47ce19838a8" role="top"><name>Workflow1</name><inputPorts><port><name>file_url</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>A_column</name></port><port><name>B_column</name></port></outputPorts><processors><processor><name>SpreadsheetImport</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>A</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>B</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>spreadsheet-import-activity</artifact><version>0.2</version></raven><class>net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity</class><inputMap><map from="fileurl" to="fileurl" />
</inputMap><outputMap><map from="A" to="A" /><map from="B" to="B" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration xmlns="">
<columnRange>
<start>0</start>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow b/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
index ac1309b..be46489 100644
--- a/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="1345660e-8b56-407c-9d3f-c2fd3489d26d" role="top"><name>Workflow20</name><inputPorts><port><name>input_file</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>STDERR</name><annotations /></port><port><name>width</name><annotations /></port><port><name>height</name><annotations /></port></outputPorts><processors><processor><name>jpylyzer</name><inputPorts><port><name>input_file</name><depth>0</depth></port></inputPorts><outputPorts><port><name>STDERR</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>STDOUT</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.External
ToolActivity</class><inputMap><map from="input_file" to="input_file" /></inputMap><outputMap><map from="STDERR" to="STDERR" /><map from="STDOUT" to="STDOUT" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
<mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
<mechanismName>default local</mechanismName>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow b/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
index be49caa..0bf8dd0 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/T3-1226-annotations-with-quotes.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-workbench-core-2.5.0-20140804T1456"><dataflow id="73a04132-5dc0-4e24-8a30-6ef91c773ad1" role="top"><name>T3_1226_test_with__s</name><inputPorts><port><name>a</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow b/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow
index 71c46ab..164962a 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/allTypes.t2flow
@@ -1,4 +1,23 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="708f0c31-61b0-4528-a096-9a747e6cdf52" role="top"><name>All_types</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>theWsdl</name><inputPorts><port><name>format</name><depth>0</depth></port><port><name>ids</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="ids" to="ids" /><map from="format" to="format" /></inputMap><outputMap><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfiguration
Bean xmlns="">
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0">
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
+<dataflow id="708f0c31-61b0-4528-a096-9a747e6cdf52" role="top"><name>All_types</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>theWsdl</name><inputPorts><port><name>format</name><depth>0</depth></port><port><name>ids</name><depth>0</depth></port></inputPorts><outputPorts><port><name>attachmentList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="ids" to="ids" /><map from="format" to="format" /></inputMap><outputMap><map from="attachmentList" to="attachmentList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
<wsdl>http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl</wsdl>
<operation>fetchBatch</operation>
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="">
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow b/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
index c691d21..3b625f1 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/helloanyone.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7805e775/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow b/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
index fbc7381..2e10ed9 100644
--- a/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
+++ b/taverna-scufl2-wfdesc/src/test/resources/helloworld.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="8781d5f4-d0ba-48a8-a1d1-14281bd8a917" role="top"><name>Hello_World</name><inputPorts /><outputPorts><port><name>greeting</name><annotations /></port></outputPorts><processors><processor><name>hello</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>Hello, World!</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
[41/52] [abbrv] incubator-taverna-language git commit: Delete a bunch
of unused files.
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/3582.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/3582.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/3582.wfdesc.ttl
deleted file mode 100644
index 8773605..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/3582.wfdesc.ttl
+++ /dev/null
@@ -1,659 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/3e3db071-bf6f-42aa-9e33-db67beec6a4d/workflow/Select_algorithm_and/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Flatten_List_6/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_6" ;
- wfdesc:hasInput <processor/Flatten_List_6/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_List_6/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<processor/Merge_String_List_to_a_String_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_2" ;
- wfdesc:hasInput <processor/Merge_String_List_to_a_String_2/in/stringlist> ;
- wfdesc:hasOutput <processor/Merge_String_List_to_a_String_2/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<processor/XPath_From_Text/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "XPath_From_Text" ;
- wfdesc:hasInput <processor/XPath_From_Text/in/xml-text> , <processor/XPath_From_Text/in/xpath> ;
- wfdesc:hasOutput <processor/XPath_From_Text/out/nodelistAsXML> ;
- wf4ever:script """import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals(\"\")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;""" .
-
-<processor/XPath_From_Text_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "XPath_From_Text_2" ;
- wfdesc:hasInput <processor/XPath_From_Text_2/in/xml-text> , <processor/XPath_From_Text_2/in/xpath> ;
- wfdesc:hasOutput <processor/XPath_From_Text_2/out/nodelistAsXML> ;
- wf4ever:script """import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals(\"\")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;""" .
-
-<processor/check_parameters/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "check_parameters" ;
- wfdesc:hasInput <processor/check_parameters/in/xml_parameter_list> ;
- wfdesc:hasOutput <processor/check_parameters/out/has_parameters> , <processor/check_parameters/out/no_parameters> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList has_parameters = new ArrayList();
-ArrayList no_parameters = new ArrayList();
-
-if (xml_parameter_list.size() == 0) {
-
- no_parameters.add(1);
-}
-else {
-
- has_parameters.add(1);
-}
-
-""" .
-
-<processor/create_algorithm_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_algorithm_xml" ;
- wfdesc:hasInput <processor/create_algorithm_xml/in/algorithm_id> , <processor/create_algorithm_xml/in/algorithm_version> , <processor/create_algorithm_xml/in/parameter_names> , <processor/create_algorithm_xml/in/parameter_values> ;
- wfdesc:hasOutput <processor/create_algorithm_xml/out/createmodel_algorithm> ;
- wf4ever:script """createmodel_algorithm=\"\";
-
-createmodel_algorithm+=
- \"<Algorithm Version=\\\"\" + algorithm_version + \"\\\" \" +
- \"Id=\\\"\" + algorithm_id + \"\\\">\";
-createmodel_algorithm += \"\\n\";
-createmodel_algorithm += \"<Parameters>\\n\";
-for (int i = 0; i < parameter_names.size(); i++) {
- createmodel_algorithm += \"<Parameter \";
- createmodel_algorithm += \"Value=\\\"\" + parameter_values.get(i);
- createmodel_algorithm += \"\\\" Id=\\\"\" + parameter_names.get(i);
- createmodel_algorithm += \"\\\"/>\\n\";
-}
-createmodel_algorithm += \"</Parameters>\";
-createmodel_algorithm += \"</Algorithm>\";
-createmodel_algorithm += \"\\n\";
-
-
-""" .
-
-<processor/create_xpath_to_get_algorithm/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_xpath_to_get_algorithm" ;
- wfdesc:hasInput <processor/create_xpath_to_get_algorithm/in/in1> ;
- wfdesc:hasOutput <processor/create_xpath_to_get_algorithm/out/out1> ;
- wf4ever:script "out1 = \"//*[local-name()=\\\"Algorithm\\\" and @Id=\\\"\" + in1 + \"\\\"]\";" .
-
-<../Workflow74/processor/clear_list/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "clear_list" ;
- wfdesc:hasInput <../Workflow74/processor/clear_list/in/input_list> ;
- wfdesc:hasOutput <../Workflow74/processor/clear_list/out/empty_list> ;
- wf4ever:script """empty_list = input_list;
-empty_list.clear();""" .
-
-<../Workflow78/processor/Flatten_List/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List" ;
- wfdesc:hasInput <../Workflow78/processor/Flatten_List/in/inputlist> ;
- wfdesc:hasOutput <../Workflow78/processor/Flatten_List/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<datalink?from=in/algorithms_xml&to=processor/XPath_From_Text/in/xml-text> a wfdesc:DataLink ;
- wfdesc:hasSource <in/algorithms_xml> ;
- wfdesc:hasSink <processor/XPath_From_Text/in/xml-text> .
-
-<datalink?from=in/algorithms_xml&to=processor/select_algorithm/in/xmltext> a wfdesc:DataLink ;
- wfdesc:hasSource <in/algorithms_xml> ;
- wfdesc:hasSink <processor/select_algorithm/in/xmltext> .
-
-<datalink?from=processor/Flatten_List_2/out/outputlist&to=processor/Flatten_List_5/in/inputlist&mergePosition=1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_2/out/outputlist> ;
- wfdesc:hasSink <processor/Flatten_List_5/in/inputlist> .
-
-<datalink?from=processor/Flatten_List_2/out/outputlist&to=processor/Flatten_List_6/in/inputlist&mergePosition=1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_2/out/outputlist> ;
- wfdesc:hasSink <processor/Flatten_List_6/in/inputlist> .
-
-<datalink?from=processor/Flatten_List_3/out/outputlist&to=processor/Flatten_List_6/in/inputlist&mergePosition=0> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_3/out/outputlist> ;
- wfdesc:hasSink <processor/Flatten_List_6/in/inputlist> .
-
-<datalink?from=processor/Flatten_List_4/out/outputlist&to=processor/Flatten_List_5/in/inputlist&mergePosition=0> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_4/out/outputlist> ;
- wfdesc:hasSink <processor/Flatten_List_5/in/inputlist> .
-
-<datalink?from=processor/Flatten_List_5/out/outputlist&to=processor/create_algorithm_xml/in/parameter_values> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_5/out/outputlist> ;
- wfdesc:hasSink <processor/create_algorithm_xml/in/parameter_values> .
-
-<datalink?from=processor/Flatten_List_6/out/outputlist&to=processor/create_algorithm_xml/in/parameter_names> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Flatten_List_6/out/outputlist> ;
- wfdesc:hasSink <processor/create_algorithm_xml/in/parameter_names> .
-
-<datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=processor/XPath_From_Text_2/in/xml-text> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Merge_String_List_to_a_String/out/concatenated> ;
- wfdesc:hasSink <processor/XPath_From_Text_2/in/xml-text> .
-
-<datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=processor/extract_algorithm_version/in/xml_text> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Merge_String_List_to_a_String/out/concatenated> ;
- wfdesc:hasSink <processor/extract_algorithm_version/in/xml_text> .
-
-<datalink?from=processor/Merge_String_List_to_a_String_2/out/concatenated&to=processor/create_algorithm_xml/in/algorithm_version> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Merge_String_List_to_a_String_2/out/concatenated> ;
- wfdesc:hasSink <processor/create_algorithm_xml/in/algorithm_version> .
-
-<datalink?from=processor/XPath_From_Text/out/nodelistAsXML&to=processor/Merge_String_List_to_a_String/in/stringlist> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/XPath_From_Text/out/nodelistAsXML> ;
- wfdesc:hasSink <processor/Merge_String_List_to_a_String/in/stringlist> .
-
-<datalink?from=processor/XPath_From_Text_2/out/nodelistAsXML&to=processor/check_parameters/in/xml_parameter_list> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/XPath_From_Text_2/out/nodelistAsXML> ;
- wfdesc:hasSink <processor/check_parameters/in/xml_parameter_list> .
-
-<datalink?from=processor/XPath_From_Text_2/out/nodelistAsXML&to=processor/parameters_interaction/in/xml_list> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/XPath_From_Text_2/out/nodelistAsXML> ;
- wfdesc:hasSink <processor/parameters_interaction/in/xml_list> .
-
-<datalink?from=processor/check_parameters/out/has_parameters&to=processor/parameters_interaction/in/flag> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/check_parameters/out/has_parameters> ;
- wfdesc:hasSink <processor/parameters_interaction/in/flag> .
-
-<datalink?from=processor/check_parameters/out/no_parameters&to=processor/skip_parameters_interaction/in/flag> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/check_parameters/out/no_parameters> ;
- wfdesc:hasSink <processor/skip_parameters_interaction/in/flag> .
-
-<datalink?from=processor/create_algorithm_xml/out/createmodel_algorithm&to=out/algorithm> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/create_algorithm_xml/out/createmodel_algorithm> ;
- wfdesc:hasSink <out/algorithm> .
-
-<datalink?from=processor/create_xpath_to_get_algorithm/out/out1&to=processor/XPath_From_Text/in/xpath> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/create_xpath_to_get_algorithm/out/out1> ;
- wfdesc:hasSink <processor/XPath_From_Text/in/xpath> .
-
-<datalink?from=processor/extract_algorithm_version/out/nodelist&to=processor/Merge_String_List_to_a_String_2/in/stringlist> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/extract_algorithm_version/out/nodelist> ;
- wfdesc:hasSink <processor/Merge_String_List_to_a_String_2/in/stringlist> .
-
-<datalink?from=processor/extract_parameter_xpath/out/value&to=processor/XPath_From_Text_2/in/xpath> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/extract_parameter_xpath/out/value> ;
- wfdesc:hasSink <processor/XPath_From_Text_2/in/xpath> .
-
-<datalink?from=processor/parameters_interaction/out/names&to=processor/Flatten_List_3/in/inputlist> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/parameters_interaction/out/names> ;
- wfdesc:hasSink <processor/Flatten_List_3/in/inputlist> .
-
-<datalink?from=processor/parameters_interaction/out/values&to=processor/Flatten_List_4/in/inputlist> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/parameters_interaction/out/values> ;
- wfdesc:hasSink <processor/Flatten_List_4/in/inputlist> .
-
-<datalink?from=processor/select_algorithm/out/algorithm_id&to=processor/create_algorithm_xml/in/algorithm_id> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/select_algorithm/out/algorithm_id> ;
- wfdesc:hasSink <processor/create_algorithm_xml/in/algorithm_id> .
-
-<datalink?from=processor/select_algorithm/out/algorithm_id&to=processor/create_xpath_to_get_algorithm/in/in1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/select_algorithm/out/algorithm_id> ;
- wfdesc:hasSink <processor/create_xpath_to_get_algorithm/in/in1> .
-
-<datalink?from=processor/skip_parameters_interaction/out/empty_list&to=processor/Flatten_List_2/in/inputlist> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/skip_parameters_interaction/out/empty_list> ;
- wfdesc:hasSink <processor/Flatten_List_2/in/inputlist> .
-
-<../Workflow74/datalink?from=in/flag&to=processor/clear_list/in/input_list> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow74/in/flag> ;
- wfdesc:hasSink <../Workflow74/processor/clear_list/in/input_list> .
-
-<../Workflow74/datalink?from=processor/clear_list/out/empty_list&to=out/empty_list> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow74/processor/clear_list/out/empty_list> ;
- wfdesc:hasSink <../Workflow74/out/empty_list> .
-
-<../Workflow78/datalink?from=in/xml_list&to=processor/extract_parameter_id/in/xml_text> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow78/in/xml_list> ;
- wfdesc:hasSink <../Workflow78/processor/extract_parameter_id/in/xml_text> .
-
-<../Workflow78/datalink?from=in/xml_list&to=processor/set_algorithm_parameters/in/xml_list> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow78/in/xml_list> ;
- wfdesc:hasSink <../Workflow78/processor/set_algorithm_parameters/in/xml_list> .
-
-<../Workflow78/datalink?from=processor/Flatten_List/out/outputlist&to=out/names> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow78/processor/Flatten_List/out/outputlist> ;
- wfdesc:hasSink <../Workflow78/out/names> .
-
-<../Workflow78/datalink?from=processor/extract_parameter_id/out/nodelist&to=processor/Flatten_List/in/inputlist> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow78/processor/extract_parameter_id/out/nodelist> ;
- wfdesc:hasSink <../Workflow78/processor/Flatten_List/in/inputlist> .
-
-<../Workflow78/datalink?from=processor/set_algorithm_parameters/out/values&to=out/values> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow78/processor/set_algorithm_parameters/out/values> ;
- wfdesc:hasSink <../Workflow78/out/values> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- dcterms:title "Select algorithm and set parameter values" ;
- dc:creator "Alan R Williams & Renato De Giovanni" ;
- dcterms:description "Select the algorithm to be used and specify its parameter values." ;
- rdfs:label "Select_algorithm_and" ;
- wfdesc:hasInput <in/algorithms_xml> ;
- wfdesc:hasOutput <out/algorithm> ;
- wfdesc:hasSubProcess <processor/Flatten_List_2/> , <processor/Flatten_List_3/> , <processor/Flatten_List_4/> , <processor/Flatten_List_5/> , <processor/Flatten_List_6/> , <processor/Merge_String_List_to_a_String/> , <processor/Merge_String_List_to_a_String_2/> , <processor/XPath_From_Text/> , <processor/XPath_From_Text_2/> , <processor/check_parameters/> , <processor/create_algorithm_xml/> , <processor/create_xpath_to_get_algorithm/> , <processor/extract_algorithm_version/> , <processor/extract_parameter_xpath/> , <processor/parameters_interaction/> , <processor/select_algorithm/> , <processor/skip_parameters_interaction/> ;
- wfdesc:hasDataLink <datalink?from=processor/Flatten_List_2/out/outputlist&to=processor/Flatten_List_5/in/inputlist&mergePosition=1> , <datalink?from=processor/Flatten_List_2/out/outputlist&to=processor/Flatten_List_6/in/inputlist&mergePosition=1> , <datalink?from=processor/Flatten_List_3/out/outputlist&to=processor/Flatten_List_6/in/inputlist&mergePosition=0> , <datalink?from=processor/Flatten_List_4/out/outputlist&to=processor/Flatten_List_5/in/inputlist&mergePosition=0> , <datalink?from=processor/Flatten_List_5/out/outputlist&to=processor/create_algorithm_xml/in/parameter_values> , <datalink?from=processor/Flatten_List_6/out/outputlist&to=processor/create_algorithm_xml/in/parameter_names> , <datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=processor/XPath_From_Text_2/in/xml-text> , <datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=processor/extract_algorithm_version/in/xml_text> , <datalink?from=processor/Merge_String_List_to_a_St
ring_2/out/concatenated&to=processor/create_algorithm_xml/in/algorithm_version> , <datalink?from=processor/XPath_From_Text/out/nodelistAsXML&to=processor/Merge_String_List_to_a_String/in/stringlist> , <datalink?from=processor/XPath_From_Text_2/out/nodelistAsXML&to=processor/check_parameters/in/xml_parameter_list> , <datalink?from=processor/XPath_From_Text_2/out/nodelistAsXML&to=processor/parameters_interaction/in/xml_list> , <datalink?from=processor/check_parameters/out/has_parameters&to=processor/parameters_interaction/in/flag> , <datalink?from=processor/check_parameters/out/no_parameters&to=processor/skip_parameters_interaction/in/flag> , <datalink?from=processor/create_algorithm_xml/out/createmodel_algorithm&to=out/algorithm> , <datalink?from=processor/create_xpath_to_get_algorithm/out/out1&to=processor/XPath_From_Text/in/xpath> , <datalink?from=processor/extract_algorithm_version/out/nodelist&to=processor/Merge_String_List_to_a_String_2/in/stringlist> , <datalink?from=processor/
extract_parameter_xpath/out/value&to=processor/XPath_From_Text_2/in/xpath> , <datalink?from=processor/parameters_interaction/out/names&to=processor/Flatten_List_3/in/inputlist> , <datalink?from=processor/parameters_interaction/out/values&to=processor/Flatten_List_4/in/inputlist> , <datalink?from=processor/select_algorithm/out/algorithm_id&to=processor/create_algorithm_xml/in/algorithm_id> , <datalink?from=processor/select_algorithm/out/algorithm_id&to=processor/create_xpath_to_get_algorithm/in/in1> , <datalink?from=processor/skip_parameters_interaction/out/empty_list&to=processor/Flatten_List_2/in/inputlist> , <datalink?from=in/algorithms_xml&to=processor/XPath_From_Text/in/xml-text> , <datalink?from=in/algorithms_xml&to=processor/select_algorithm/in/xmltext> .
-
-<in/algorithms_xml> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
- rdfs:label "algorithms_xml" .
-
-<out/algorithm> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
- dcterms:description "The algorithm and the parameter settings specified by the user" ;
- rdfs:label "algorithm" .
-
-<processor/Flatten_List_2/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<processor/Flatten_List_2/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<processor/Flatten_List_3/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<processor/Flatten_List_3/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<processor/Flatten_List_4/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<processor/Flatten_List_4/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<processor/Flatten_List_5/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<processor/Flatten_List_5/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<processor/Flatten_List_6/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<processor/Flatten_List_6/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<processor/Merge_String_List_to_a_String/in/stringlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "stringlist" .
-
-<processor/Merge_String_List_to_a_String/out/concatenated> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "concatenated" .
-
-<processor/Merge_String_List_to_a_String_2/in/stringlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "stringlist" .
-
-<processor/Merge_String_List_to_a_String_2/out/concatenated> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "concatenated" .
-
-<processor/XPath_From_Text/in/xml-text> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml-text" .
-
-<processor/XPath_From_Text/in/xpath> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xpath" .
-
-<processor/XPath_From_Text/out/nodelistAsXML> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "nodelistAsXML" .
-
-<processor/XPath_From_Text_2/in/xml-text> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml-text" .
-
-<processor/XPath_From_Text_2/in/xpath> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xpath" .
-
-<processor/XPath_From_Text_2/out/nodelistAsXML> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "nodelistAsXML" .
-
-<processor/check_parameters/in/xml_parameter_list> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml_parameter_list" .
-
-<processor/check_parameters/out/has_parameters> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "has_parameters" .
-
-<processor/check_parameters/out/no_parameters> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "no_parameters" .
-
-<processor/create_algorithm_xml/in/algorithm_id> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "algorithm_id" .
-
-<processor/create_algorithm_xml/in/algorithm_version> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "algorithm_version" .
-
-<processor/create_algorithm_xml/in/parameter_names> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "parameter_names" .
-
-<processor/create_algorithm_xml/in/parameter_values> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "parameter_values" .
-
-<processor/create_algorithm_xml/out/createmodel_algorithm> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "createmodel_algorithm" .
-
-<processor/create_xpath_to_get_algorithm/in/in1> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "in1" .
-
-<processor/create_xpath_to_get_algorithm/out/out1> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "out1" .
-
-<processor/extract_algorithm_version/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "extract_algorithm_version" ;
- wfdesc:hasInput <processor/extract_algorithm_version/in/xml_text> ;
- wfdesc:hasOutput <processor/extract_algorithm_version/out/nodelist> .
-
-<processor/extract_algorithm_version/in/xml_text> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml_text" .
-
-<processor/extract_algorithm_version/out/nodelist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "nodelist" .
-
-<processor/extract_parameter_xpath/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "extract_parameter_xpath" ;
- wfdesc:hasOutput <processor/extract_parameter_xpath/out/value> .
-
-<processor/extract_parameter_xpath/out/value> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "value" .
-
-<processor/parameters_interaction/> a wfdesc:Process , wfdesc:Description , prov:Entity , wfdesc:Workflow ;
- rdfs:label "parameters_interaction" ;
- wfdesc:hasInput <processor/parameters_interaction/in/flag> , <processor/parameters_interaction/in/xml_list> ;
- wfdesc:hasOutput <processor/parameters_interaction/out/names> , <processor/parameters_interaction/out/values> ;
- prov:specializationOf <../Workflow78/> .
-
-<processor/parameters_interaction/in/flag> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "flag" ;
- prov:specializationOf <../Workflow78/in/flag> .
-
-<processor/parameters_interaction/in/xml_list> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "xml_list" ;
- prov:specializationOf <../Workflow78/in/xml_list> .
-
-<processor/parameters_interaction/out/names> a wfdesc:Output , wfdesc:Description , prov:Entity ;
- rdfs:label "names" ;
- prov:specializationOf <../Workflow78/out/names> .
-
-<processor/parameters_interaction/out/values> a wfdesc:Output , wfdesc:Description , prov:Entity ;
- rdfs:label "values" ;
- prov:specializationOf <../Workflow78/out/values> .
-
-<processor/select_algorithm/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "select_algorithm" ;
- wfdesc:hasInput <processor/select_algorithm/in/xmltext> ;
- wfdesc:hasOutput <processor/select_algorithm/out/algorithm_id> .
-
-<processor/select_algorithm/in/xmltext> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xmltext" .
-
-<processor/select_algorithm/out/algorithm_id> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "algorithm_id" .
-
-<processor/skip_parameters_interaction/> a wfdesc:Process , wfdesc:Description , prov:Entity , wfdesc:Workflow ;
- rdfs:label "skip_parameters_interaction" ;
- wfdesc:hasInput <processor/skip_parameters_interaction/in/flag> ;
- wfdesc:hasOutput <processor/skip_parameters_interaction/out/empty_list> ;
- prov:specializationOf <../Workflow74/> .
-
-<processor/skip_parameters_interaction/in/flag> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "flag" ;
- prov:specializationOf <../Workflow74/in/flag> .
-
-<processor/skip_parameters_interaction/out/empty_list> a wfdesc:Output , wfdesc:Description , prov:Entity ;
- rdfs:label "empty_list" ;
- prov:specializationOf <../Workflow74/out/empty_list> .
-
-<../Workflow74/> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process , prov:Entity ;
- rdfs:label "Workflow74" ;
- wfdesc:hasInput <../Workflow74/in/flag> ;
- wfdesc:hasOutput <../Workflow74/out/empty_list> ;
- wfdesc:hasSubProcess <../Workflow74/processor/clear_list/> ;
- wfdesc:hasDataLink <../Workflow74/datalink?from=processor/clear_list/out/empty_list&to=out/empty_list> , <../Workflow74/datalink?from=in/flag&to=processor/clear_list/in/input_list> .
-
-<../Workflow74/in/flag> a wfdesc:Input , wfdesc:Description , wfdesc:Output , prov:Entity ;
- rdfs:label "flag" .
-
-<../Workflow74/out/empty_list> a wfdesc:Output , wfdesc:Description , wfdesc:Input , prov:Entity ;
- rdfs:label "empty_list" .
-
-<../Workflow74/processor/clear_list/in/input_list> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "input_list" .
-
-<../Workflow74/processor/clear_list/out/empty_list> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "empty_list" .
-
-<../Workflow78/> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process , prov:Entity ;
- rdfs:label "Workflow78" ;
- wfdesc:hasInput <../Workflow78/in/flag> , <../Workflow78/in/xml_list> ;
- wfdesc:hasOutput <../Workflow78/out/names> , <../Workflow78/out/values> ;
- wfdesc:hasSubProcess <../Workflow78/processor/Flatten_List/> , <../Workflow78/processor/extract_parameter_id/> , <../Workflow78/processor/set_algorithm_parameters/> ;
- wfdesc:hasDataLink <../Workflow78/datalink?from=processor/Flatten_List/out/outputlist&to=out/names> , <../Workflow78/datalink?from=processor/extract_parameter_id/out/nodelist&to=processor/Flatten_List/in/inputlist> , <../Workflow78/datalink?from=processor/set_algorithm_parameters/out/values&to=out/values> , <../Workflow78/datalink?from=in/xml_list&to=processor/extract_parameter_id/in/xml_text> , <../Workflow78/datalink?from=in/xml_list&to=processor/set_algorithm_parameters/in/xml_list> .
-
-<../Workflow78/in/flag> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "flag" .
-
-<../Workflow78/in/xml_list> a wfdesc:Input , wfdesc:Description , wfdesc:Output , prov:Entity ;
- rdfs:label "xml_list" .
-
-<../Workflow78/out/names> a wfdesc:Output , wfdesc:Description , wfdesc:Input , prov:Entity ;
- rdfs:label "names" .
-
-<../Workflow78/out/values> a wfdesc:Output , wfdesc:Description , wfdesc:Input , prov:Entity ;
- rdfs:label "values" .
-
-<../Workflow78/processor/Flatten_List/in/inputlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "inputlist" .
-
-<../Workflow78/processor/Flatten_List/out/outputlist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "outputlist" .
-
-<../Workflow78/processor/extract_parameter_id/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "extract_parameter_id" ;
- wfdesc:hasInput <../Workflow78/processor/extract_parameter_id/in/xml_text> ;
- wfdesc:hasOutput <../Workflow78/processor/extract_parameter_id/out/nodelist> .
-
-<../Workflow78/processor/extract_parameter_id/in/xml_text> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml_text" .
-
-<../Workflow78/processor/extract_parameter_id/out/nodelist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "nodelist" .
-
-<../Workflow78/processor/set_algorithm_parameters/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "set_algorithm_parameters" ;
- wfdesc:hasInput <../Workflow78/processor/set_algorithm_parameters/in/xml_list> ;
- wfdesc:hasOutput <../Workflow78/processor/set_algorithm_parameters/out/values> .
-
-<../Workflow78/processor/set_algorithm_parameters/in/xml_list> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml_list" .
-
-<../Workflow78/processor/set_algorithm_parameters/out/values> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "values" .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/allTypes.types.sparql.json
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/allTypes.types.sparql.json b/taverna-scufl2-wfdesc/src/test/resources/allTypes.types.sparql.json
deleted file mode 100644
index eb18772..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/allTypes.types.sparql.json
+++ /dev/null
@@ -1,77 +0,0 @@
- "head": {
- "vars": [ "wf", "proc", "procType", "procLabel" ]
- },
- "results": {
- "bindings": [
- {
- "procLabel": { "type": "literal", "value": "theBeanshell" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#BeanshellScript" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theBeanshell\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theNested" },
- "procType": { "type": "uri", "value": "http:\/\/www.w3.org\/ns\/prov#Entity" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theNested" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wfdesc#Workflow" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theNested\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theREST" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#RESTService" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theREST\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theRscript" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#RScript" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theRscript\/" }
- },
- {
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theSpreadsheet\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "procLabel": { "type": "literal", "value": "theSpreadsheet" }
- },
- {
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theText\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "procLabel": { "type": "literal", "value": "theText" }
- },
- {
- "procLabel": { "type": "literal", "value": "theTool" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#CommandLineTool" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theTool\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theToolRepository" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#CommandLineTool" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theToolRepository\/" }
- },
- {
- "procLabel": { "type": "literal", "value": "theWsdl" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#SOAPService" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theWsdl\/" }
- },
- {
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/processor\/theXPath\/" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/All_types\/" },
- "procLabel": { "type": "literal", "value": "theXPath" }
- },
- {
- "procLabel": { "type": "literal", "value": "theLocal" },
- "procType": { "type": "uri", "value": "http:\/\/purl.org\/wf4ever\/wf4ever#BeanshellScript" },
- "wf": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/theWorkflow\/" },
- "proc": { "type": "uri", "value": "http:\/\/ns.taverna.org.uk\/2010\/workflowBundle\/708f0c31-61b0-4528-a096-9a747e6cdf52\/workflow\/theWorkflow\/processor\/theLocal\/" }
- }
- ]
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/allTypes.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/allTypes.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/allTypes.wfdesc.ttl
deleted file mode 100644
index 902a467..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/allTypes.wfdesc.ttl
+++ /dev/null
@@ -1,212 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/708f0c31-61b0-4528-a096-9a747e6cdf52/workflow/All_types/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/theBeanshell/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "theBeanshell" ;
- wfdesc:hasOutput <processor/theBeanshell/out/s> ;
- wf4ever:script "s = \"a beanshell script\";" .
-
-<../theWorkflow/processor/theLocal/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "theLocal" ;
- wfdesc:hasInput <../theWorkflow/processor/theLocal/in/string1> ;
- wfdesc:hasOutput <../theWorkflow/processor/theLocal/out/output> ;
- wf4ever:script "output = string1 + string2;" .
-
-<processor/theTool/> a wfdesc:Process , wfdesc:Description , wf4ever:CommandLineTool ;
- rdfs:label "theTool" ;
- wfdesc:hasOutput <processor/theTool/out/STDERR> , <processor/theTool/out/STDOUT> .
-
-<processor/theToolRepository/> a wfdesc:Process , wfdesc:Description , wf4ever:CommandLineTool ;
- rdfs:label "theToolRepository" ;
- wfdesc:hasInput <processor/theToolRepository/in/First_file> , <processor/theToolRepository/in/Second_file> .
-
-<processor/theREST/> a wfdesc:Process , wfdesc:Description , wf4ever:RESTService ;
- rdfs:label "theREST" ;
- wfdesc:hasInput <processor/theREST/in/id> ;
- wfdesc:hasOutput <processor/theREST/out/status> ;
- wf4ever:rootURI "http://www.uniprot.org/"^^xsd:anyURI .
-
-<processor/theRscript/> a wfdesc:Process , wfdesc:Description , wf4ever:RScript ;
- rdfs:label "theRscript" ;
- wfdesc:hasInput <processor/theRscript/in/in1> ;
- wfdesc:hasOutput <processor/theRscript/out/out1> ;
- wf4ever:script "\"some r-script\"" .
-
-<processor/theWsdl/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "theWsdl" ;
- wfdesc:hasInput <processor/theWsdl/in/format> , <processor/theWsdl/in/ids> ;
- wfdesc:hasOutput <processor/theWsdl/out/attachmentList> ;
- wf4ever:wsdlURI "http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "fetchBatch" ;
- wf4ever:rootURI "http://www.ebi.ac.uk/"^^xsd:anyURI .
-
-<datalink?from=processor/theBeanshell/out/s&to=processor/theWsdl/in/format> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theBeanshell/out/s> ;
- wfdesc:hasSink <processor/theWsdl/in/format> .
-
-<datalink?from=processor/theNested/out/b&to=processor/theXPath/in/xml_text> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theNested/out/b> ;
- wfdesc:hasSink <processor/theXPath/in/xml_text> .
-
-<datalink?from=processor/theREST/out/status&to=processor/theSpreadsheet/in/fileurl> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theREST/out/status> ;
- wfdesc:hasSink <processor/theSpreadsheet/in/fileurl> .
-
-<datalink?from=processor/theRscript/out/out1&to=out/out> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theRscript/out/out1> ;
- wfdesc:hasSink <out/out> .
-
-<datalink?from=processor/theSpreadsheet/out/a1&to=processor/theNested/in/a> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theSpreadsheet/out/a1> ;
- wfdesc:hasSink <processor/theNested/in/a> .
-
-<datalink?from=processor/theText/out/value&to=processor/theREST/in/id> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theText/out/value> ;
- wfdesc:hasSink <processor/theREST/in/id> .
-
-<datalink?from=processor/theTool/out/STDERR&to=processor/theToolRepository/in/Second_file> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theTool/out/STDERR> ;
- wfdesc:hasSink <processor/theToolRepository/in/Second_file> .
-
-<datalink?from=processor/theTool/out/STDOUT&to=processor/theRscript/in/in1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theTool/out/STDOUT> ;
- wfdesc:hasSink <processor/theRscript/in/in1> .
-
-<datalink?from=processor/theWsdl/out/attachmentList&to=processor/theToolRepository/in/First_file> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theWsdl/out/attachmentList> ;
- wfdesc:hasSink <processor/theToolRepository/in/First_file> .
-
-<datalink?from=processor/theXPath/out/nodelist&to=processor/theWsdl/in/ids> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/theXPath/out/nodelist> ;
- wfdesc:hasSink <processor/theWsdl/in/ids> .
-
-<../theWorkflow/datalink?from=in/a&to=processor/theLocal/in/string1> a wfdesc:DataLink ;
- wfdesc:hasSource <../theWorkflow/in/a> ;
- wfdesc:hasSink <../theWorkflow/processor/theLocal/in/string1> .
-
-<../theWorkflow/datalink?from=processor/theLocal/out/output&to=out/b> a wfdesc:DataLink ;
- wfdesc:hasSource <../theWorkflow/processor/theLocal/out/output> ;
- wfdesc:hasSink <../theWorkflow/out/b> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- dcterms:description "All types currently supported by scul2-wfdesc. Other service types are also translated, but only as processors." ;
- dc:creator "Stian Soiland-Reyes" ;
- dcterms:title "All types" ;
- rdfs:label "All_types" ;
- wfdesc:hasOutput <out/out> ;
- wfdesc:hasSubProcess <processor/theBeanshell/> , <processor/theNested/> , <processor/theREST/> , <processor/theRscript/> , <processor/theSpreadsheet/> , <processor/theText/> , <processor/theTool/> , <processor/theToolRepository/> , <processor/theWsdl/> , <processor/theXPath/> ;
- wfdesc:hasDataLink <datalink?from=processor/theBeanshell/out/s&to=processor/theWsdl/in/format> , <datalink?from=processor/theNested/out/b&to=processor/theXPath/in/xml_text> , <datalink?from=processor/theREST/out/status&to=processor/theSpreadsheet/in/fileurl> , <datalink?from=processor/theRscript/out/out1&to=out/out> , <datalink?from=processor/theSpreadsheet/out/a1&to=processor/theNested/in/a> , <datalink?from=processor/theText/out/value&to=processor/theREST/in/id> , <datalink?from=processor/theTool/out/STDERR&to=processor/theToolRepository/in/Second_file> , <datalink?from=processor/theTool/out/STDOUT&to=processor/theRscript/in/in1> , <datalink?from=processor/theWsdl/out/attachmentList&to=processor/theToolRepository/in/First_file> , <datalink?from=processor/theXPath/out/nodelist&to=processor/theWsdl/in/ids> .
-
-<out/out> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
- rdfs:label "out" .
-
-<processor/theBeanshell/out/s> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "s" .
-
-<processor/theNested/> a wfdesc:Process , wfdesc:Description , prov:Entity , wfdesc:Workflow ;
- rdfs:label "theNested" ;
- wfdesc:hasInput <processor/theNested/in/a> ;
- wfdesc:hasOutput <processor/theNested/out/b> ;
- prov:specializationOf <../theWorkflow/> .
-
-<processor/theNested/in/a> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "a" ;
- prov:specializationOf <../theWorkflow/in/a> .
-
-<processor/theNested/out/b> a wfdesc:Output , wfdesc:Description , prov:Entity ;
- rdfs:label "b" ;
- prov:specializationOf <../theWorkflow/out/b> .
-
-<processor/theREST/in/id> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "id" .
-
-<processor/theREST/out/status> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "status" .
-
-<processor/theRscript/in/in1> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "in1" .
-
-<processor/theRscript/out/out1> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "out1" .
-
-<processor/theSpreadsheet/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "theSpreadsheet" ;
- wfdesc:hasInput <processor/theSpreadsheet/in/fileurl> ;
- wfdesc:hasOutput <processor/theSpreadsheet/out/a1> .
-
-<processor/theSpreadsheet/in/fileurl> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "fileurl" .
-
-<processor/theSpreadsheet/out/a1> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "a1" .
-
-<processor/theText/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "theText" ;
- wfdesc:hasOutput <processor/theText/out/value> .
-
-<processor/theText/out/value> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "value" .
-
-<processor/theTool/out/STDERR> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "STDERR" .
-
-<processor/theTool/out/STDOUT> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "STDOUT" .
-
-<processor/theToolRepository/in/First_file> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "First_file" .
-
-<processor/theToolRepository/in/Second_file> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "Second_file" .
-
-<processor/theWsdl/in/format> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "format" .
-
-<processor/theWsdl/in/ids> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "ids" .
-
-<processor/theWsdl/out/attachmentList> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "attachmentList" .
-
-<processor/theXPath/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "theXPath" ;
- wfdesc:hasInput <processor/theXPath/in/xml_text> ;
- wfdesc:hasOutput <processor/theXPath/out/nodelist> .
-
-<processor/theXPath/in/xml_text> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "xml_text" .
-
-<processor/theXPath/out/nodelist> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "nodelist" .
-
-<../theWorkflow/> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process , prov:Entity ;
- dcterms:title "theWorkflow" ;
- rdfs:label "theWorkflow" ;
- wfdesc:hasInput <../theWorkflow/in/a> ;
- wfdesc:hasOutput <../theWorkflow/out/b> ;
- wfdesc:hasSubProcess <../theWorkflow/processor/theLocal/> ;
- wfdesc:hasDataLink <../theWorkflow/datalink?from=processor/theLocal/out/output&to=out/b> , <../theWorkflow/datalink?from=in/a&to=processor/theLocal/in/string1> .
-
-<../theWorkflow/in/a> a wfdesc:Input , wfdesc:Description , wfdesc:Output , prov:Entity ;
- rdfs:label "a" .
-
-<../theWorkflow/out/b> a wfdesc:Output , wfdesc:Description , wfdesc:Input , prov:Entity ;
- rdfs:label "b" .
-
-<../theWorkflow/processor/theLocal/in/string1> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "string1" .
-
-<../theWorkflow/processor/theLocal/out/output> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "output" .
[06/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow
deleted file mode 100644
index 90629d1..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow
+++ /dev/null
@@ -1,871 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="dc227a10-e8f6-44b0-88c5-c946a15ff669" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>the
-script;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies>
- <string>a.jar</string>
- <string>b.jar</string>
- </localDependencies>
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in2</name>
- <depth>1</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out2</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Nested_workflow</name><inputPorts /><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 /><outputMap /><configBean encoding="dataflow"><dataflow ref="a838d861-e4b8-4e7f-839c-e0fc748749b9" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>
net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Rshell</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.rshell.RshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean xmlns="">
- <rVersion>false</rVersion>
- <script>rshell
-script</script>
- <connectionSettings>
- <host>localhost</host>
- <port>6311</port>
- <username>user</username>
- <password>passwd</password>
- <keepSessionAlive>true</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>INTEGER_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </inputSymanticTypes>
- <outputSymanticTypes>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out1</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out2</name>
- <symanticType>PNG_FILE</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>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>out4</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[2]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </outputSymanticTypes>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>in2</name>
- <depth>0</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>in3</name>
- <depth>1</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out2</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out3</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out4</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>SpreadsheetImport</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>spreadsheet-import-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration xmlns="">
- <columnRange>
- <start>0</start>
- <end>2</end>
- <excludes />
- </columnRange>
- <rowRange>
- <start>1</start>
- <end>-1</end>
- <excludes />
- </rowRange>
- <emptyCellValue>empty</emptyCellValue>
- <columnNames>
- <entry>
- <string>A</string>
- <string>fish</string>
- </entry>
- <entry>
- <string>B</string>
- <string>soup</string>
- </entry>
- </columnNames>
- <allRows>true</allRows>
- <excludeFirstRow>true</excludeFirstRow>
- <ignoreBlankRows>true</ignoreBlankRows>
- <emptyCellPolicy>USER_DEFINED</emptyCellPolicy>
- <outputFormat>PORT_PER_COLUMN</outputFormat>
- <csvDelimiter>,</csvDelimiter>
-</net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration xmlns="">
- <conditionXML><activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>sdsdsd</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies>
- <string>a.jar</string>
- </localDependencies>
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></conditionXML>
- <runFirst>true</runFirst>
- <properties>
- <property name="comparison" value="custom" />
- </properties>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>String_constant</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>string</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>14</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration xmlns="">
- <conditionXML><activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>loop = "" + ! value.equals("ssdsd"); 
-if ("true".matches(loop)) {
- Thread.sleep(500);
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>value</name>
- <depth>0</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>loop</name>
- <depth>0</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></conditionXML>
- <runFirst>true</runFirst>
- <properties>
- <property name="compareValue" value="ssdsd" />
- <property name="delay" value="0.5" />
- <property name="comparePort" value="value" />
- <property name="isFeedBack" value="true" />
- <property name="comparison" value="EqualTo" />
- </properties>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>150</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>5</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>localWorker_bytearray</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EncodeBase64</localworkerName>
- <script>import org.apache.commons.codec.binary.Base64;
-
-base64 = new String(Base64.encodeBase64(bytes));</script>
- <dependencies class="java.util.Collections$SingletonList">
- <element class="string">commons-codec:commons-codec:1.3</element>
- </dependencies>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>1.3</version>
- <hashCode>1635363350</hashCode>
- <string>commons-codec:commons-codec:1.3</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>bytes</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'application/octet-stream'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>base64</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>localWorker</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>mobyObject</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean xmlns="">
- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>AlleleAssociation</serviceName>
- <authorityName>cegen.upf.es</authorityName>
-</net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>mobyService</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean xmlns="">
- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>getTmhmmPrediction</serviceName>
- <authorityName>mips.gsf.de</authorityName>
- <category />
- <serviceType />
- <secondaries />
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>soaplab</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
- <endpoint>http://www.ebi.ac.uk/soaplab/services/feature_tables.coderet</endpoint>
- <pollingInterval>4</pollingInterval>
- <pollingBackoff>1.1</pollingBackoff>
- <pollingIntervalMax>5</pollingIntervalMax>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>wsdl_document</name><inputPorts /><outputPorts><port><name>queryStatusOutput</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap><map from="queryStatusOutput" to="queryStatusOutput" /></outputMap><configBean encoding="xstream
"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://webservices.genouest.org/typedservices/InterProScan.wsdl</wsdl>
- <operation>queryStatus</operation>
- <securityProfile>HTTPBasicAuthNPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>xmlSplitter</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitte
r.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="queryStatusOutput" name="queryStatusOutput" qname="{http://nbcr.sdsc.edu/opal/types}queryStatusOutput"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="code" qname="StatusOutputType&gt;code" /><s:basetype optional="false" unbounded="false" typename="string" name="message" qname="StatusOutputType&gt;message" /><s:basetype optional="false" unbounded="false" typename="anyURI" name="baseURL" qname="StatusOutputType&gt;baseURL" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>code</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>message</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>baseURL</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>wsdl_rpc</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://soap.genome.jp/KEGG.wsdl</wsdl>
- <operation>get_compounds_by_enzyme</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>wsdl_secured</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://soap.genome.jp/KEGG.wsdl</wsdl>
- <operation>get_genes_by_organism</operation>
- <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>biomart</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.2</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="Drosophila melanogaster features (BDGP5.13)" nam
e="dmelanogaster_feature_set" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2010-06-07 11:08:23"><MartURLLocation database="functional_genomics_mart_58" default="0" displayName="ENSEMBL FUNCTIONAL GENOMICS 58 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="functional_genomics" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.6" requestId="taverna"><Dataset name="dmelanogaster_feature_set"><Attribute name="cell_type_display_label_1048" /><Attribute name="name_1011" /><Attribute name="display_label_1049" /><Filter name="chromosome_name" value="2L" /><Filter name="end" value="10000000" /><Filter name="start" value="1" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><
group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Send_an_Email</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.SendEmail</localworkerName>
- <script>import javax.mail.Message;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.MimeMessage;
-import javax.mail.internet.InternetAddress;
-
-if (subject == void) {
- subject = "No subject";
-}
-if (body == void) {
- throw new Exception("No body specified for message");
-}
-
-Properties mailProps = System.getProperties();
-if (smtpserver != void) {
- mailProps.put("mail.smtp.host", smtpserver);
-}
-
-Session session = Session.getDefaultInstance(mailProps, null);
-MimeMessage message = new MimeMessage(session);
-message.setFrom(new InternetAddress(from));
-message.addRecipient(Message.RecipientType.TO, new InternetAddress(to));
-message.setSubject(subject);
-message.setText(body);
-Transport.send(message);
-</script>
- <dependencies>
- <string>javax.mail:mail:1.4</string>
- <string>javax.activation:activation:1.1</string>
- </dependencies>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>javax.mail</groupId>
- <artifactId>mail</artifactId>
- <version>1.4</version>
- <hashCode>789035249</hashCode>
- <string>javax.mail:mail:1.4</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>javax.activation</groupId>
- <artifactId>activation</artifactId>
- <version>1.1</version>
- <hashCode>518094512</hashCode>
- <string>javax.activation:activation:1.1</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>to</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>from</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>subject</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>body</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>smtpserver</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs />
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>TavernaResearchObject</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>uk.org.taverna.scufl2.api.container.TavernaResearchObject</className>
- <methodName>TavernaResearchObject</methodName>
- <parameterNames />
- <parameterDimensions />
- <parameterTypes />
- <returnType>uk.org.taverna.scufl2.api.container.TavernaResearchObject</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>true</isMethodConstructor>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs />
- <outputs />
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>setWorkflows</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>uk.org.taverna.scufl2.api.container.TavernaResearchObject</className>
- <methodName>setWorkflows</methodName>
- <parameterNames>
- <string>workflows</string>
- </parameterNames>
- <parameterDimensions>
- <int>0</int>
- </parameterDimensions>
- <parameterTypes>
- <string>java.util.Set</string>
- </parameterTypes>
- <returnType>void</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>false</isMethodConstructor>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies>
- <string>a.jar</string>
- </localDependencies>
- <artifactDependencies />
- <inputs />
- <outputs />
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>run</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap>
<map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.ebi.ac.uk/Tools/services/soap/wublast?wsdl</wsdl>
- <operation>run</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>run_input</name><inputPorts /><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap /><outputMap><map from="output" to="outp
ut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="&gt;run&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="&gt;run&gt;title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters&gt;program" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters&gt;exp" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters&gt
;alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters&gt;scores" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters&gt;align" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="stats" qname="InputParameters&gt;stats" /><s:basetype optional="true" unbounded="false" typename="string" name="sensitivity" qname="InputParameters&gt;sensitivity" /><s:basetype optional="true" unbounded="false" typename="string" name="topcombon" qname="InputParameters&gt;topcombon" /><s:basetype optional="true" unbounded="false" typename="boolean" name="viewfilter" qname="InputParameters&gt;viewfilter" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputPar
ameters&gt;filter" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="InputParameters&gt;strand" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="InputParameters&gt;sort" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters&gt;stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters&gt;database"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>email</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>parameters</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>run_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter
.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="runResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}runResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="&gt;runResponse&gt;jobId" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>jobId</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>xmlSplitter</processor><port>input</port></sink><source type="processor"><processor>wsdl_document</processor><port>queryStatusOutput</port></source></datalink><datalink><sink type="processor"><processor>run</processor><port>parameters</port></sink><source type="processor"><processor>run_input</processor><port>output</port></source></datalink><datalink><sink typ
e="processor"><processor>run_output</processor><port>input</port></sink><source type="processor"><processor>run</processor><port>parameters</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>48fbf225-4742-47c4-830d-ecf9a2011021</identification>
- </annotationBean>
- <date>2010-07-21 13:51:40.494 BST</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.annotatio
<TRUNCATED>
[27/52] [abbrv] incubator-taverna-language git commit: Some kind of
NOTICE merge thingie
Posted by st...@apache.org.
Some kind of NOTICE merge thingie
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/1b3666ac
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/1b3666ac
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/1b3666ac
Branch: refs/heads/master
Commit: 1b3666acd597a7310d61be4af42b3467ef9bac51
Parents: 5420854
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 16:50:37 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 16:50:37 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-examples/pom.xml | 1 +
1 file changed, 1 insertion(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/1b3666ac/taverna-scufl2-examples/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/pom.xml b/taverna-scufl2-examples/pom.xml
index 9e33ff3..c63547d 100644
--- a/taverna-scufl2-examples/pom.xml
+++ b/taverna-scufl2-examples/pom.xml
@@ -136,6 +136,7 @@
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>org.apache.taverna.examples.Scufl2Tool</mainClass>
</transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer
[07/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
deleted file mode 100644
index e94384f..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
+++ /dev/null
@@ -1,370 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="2f216461-50f5-45be-a2d2-49c84b1fce5e" role="top"><name>BiomartAndEMBOSSAnalysis</name><inputPorts /><outputPorts><port><name>outputPlot</name><annotations><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.MimeType">
- <text>image/png</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</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.MimeType">
- <text>application/octet-stream</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>HSapIDs</name><annotations><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>MMusIDs</name><annotations><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>RNorIDs</name><annotations><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.MimeType">
- <text>text/plain</text>
- </annotationBean>
- <date>2009-12-15 21:49:47.668 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>GetUniqueHomolog</name><inputPorts><port><name>HSGeneIDs</name><depth>1</depth></port><port><name>RatGeneIDs</name><depth>1</depth></port><port><name>MouseGeneIDs</name><depth>1</depth></port></inputPorts><outputPorts><port><name>MouseOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>HSOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>RatOut</name><depth>1</depth><granularDepth>1</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="HSGeneIDs" to="HSGeneIDs" /><map from="RatGeneIDs" to="RatGeneIDs" /><map from="MouseGeneIDs" to="MouseGeneIDs" /></inputMap><outputMap><map f
rom="RatOut" to="RatOut" /><map from="HSOut" to="HSOut" /><map from="MouseOut" to="MouseOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>List HSOut = new ArrayList();
-List RatOut = new ArrayList();
-List MouseOut = new ArrayList();
-
-Map hsToMouse = new HashMap();
-Iterator j = MouseGeneIDs.iterator();
-for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
- String id = (String)i.next();
- hsToMouse.put(id, j.next());
-}
-Map hsToRat = new HashMap();
-j = RatGeneIDs.iterator();
-for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
- String id = (String)i.next();
- hsToRat.put(id, j.next());
-}
-
-// Build the unique outputs
-for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
- String hsID = (String)i.next();
- String ratID = (String)hsToRat.get(hsID);
- // Remove version number
- // ratID = (ratID.split("."))[0];
- String mouseID = (String)hsToMouse.get(hsID);
- // Remove version number
- //mouseId = (mouseID.split("."))[0];
- if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
- HSOut.add(hsID);
- RatOut.add(ratID.split("\\.")[0]);
- MouseOut.add(mouseID.split("\\.")[0]);
- }
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>HSGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>MouseGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>RatGeneIDs</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>HSOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>RatOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>MouseOut</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="RatGeneIDs" depth="1" /><port name="MouseGeneIDs" depth="1" /><port name="HSGeneIDs" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>hsapiensGeneEnsembl</name><inputPorts /><outputPorts><port><name>hsapiens_gene_ensembl.mouse_ensembl_gene</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.rat_ensembl_gene</name><depth>1</depth
><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="hsapiens_gene_ensembl.rat_ensembl_gene" to="hsapiens_gene_ensembl.rat_ensembl_gene" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /><map from="hsapiens_gene_ensembl.mouse_ensembl_gene" to="hsapiens_gene_ensembl.mouse_ensembl_gene" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:24:08"><MartURLLocation database="ensembl_mart_55" default="1" dis
playName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" 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"><Dataset name="hsapiens_gene_ensembl"><Attribute name="ensembl_gene_id" /><Attribute name="mouse_ensembl_gene" /><Attribute name="rat_ensembl_gene" /><Filter name="chromosome_name" value="22" /><Filter name="with_mmusculus_homolog" excluded="0" /></Dataset></Query></MartQuery></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.Paralle
lizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross /></strategy></iteration></iterationStrategyStack></processor><processor><name>getHSapSequence</name><inputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.coding_gene_flank</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</
group><artifact>biomart-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap><map from="hsapiens_gene_ensembl.ensembl_gene_id_filter" to="hsapiens_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="hsapiens_gene_ensembl.coding_gene_flank" to="hsapiens_gene_ensembl.coding_gene_flank" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:24:08"><MartURLLocation database="ensembl_mart_55" default="1" displayName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" 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"><Dataset name="hsapiens_gene_ensembl"><Attribute name="coding_gene_flank" /><Attribute name="ensembl_gene_id" /><Filter name="ensembl_gene_id" value="" list="true" /><Filter name="upstream_flank" value="100" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="hsapiens_gene_ensembl.ensembl_gene_id_filter" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CreateFasta</name><inputPorts><port><name>hsSeq</name><depth>0</depth></port><port><name>rnSeq</name><depth>0</depth></port><port><name>mmSeq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fasta</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>be
anshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="hsSeq" to="hsSeq" /><map from="rnSeq" to="rnSeq" /><map from="mmSeq" to="mmSeq" /></inputMap><outputMap><map from="fasta" to="fasta" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>fasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>hsSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>mmSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>rnSeq</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>fasta</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="hsSeq" depth="0" /><port name="mmSeq" depth="0" /><port name="rnSeq" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>getRNorSequence</name><inputPorts><port><name>rnorvegicus_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>rnorvegicus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>rnorvegicus_gene_ensembl.coding_gene_flank</name><depth>1</depth><granularDepth>1</granularDept
h></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap><map from="rnorvegicus_gene_ensembl.ensembl_gene_id_filter" to="rnorvegicus_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="rnorvegicus_gene_ensembl.coding_gene_flank" to="rnorvegicus_gene_ensembl.coding_gene_flank" /><map from="rnorvegicus_gene_ensembl.ensembl_gene_id" to="rnorvegicus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Rattus norvegicus genes (RGSC3.4)" name="rnorvegicus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:36:01"><MartURLLocation database="ensembl_mart_55"
default="1" displayName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" 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"><Dataset name="rnorvegicus_gene_ensembl"><Attribute name="coding_gene_flank" /><Attribute name="ensembl_gene_id" /><Filter name="ensembl_gene_id" value="" list="true" /><Filter name="upstream_flank" value="100" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns=""
>
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>0</initialDelay>
- <maxDelay>0</maxDelay>
- <maxRetries>0</maxRetries>
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- <pollingBackoff>1.0</pollingBackoff>
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ranularDepth>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><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outseq_url" to="outseq_url" /><map from="dendoutfile" to="dendoutfile" /><map from="dendoutfile_url" to="dendoutfile_url" /><map from="report" to="report" /><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
- <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma</endpoint>
- <pollingInterval>0</pollingInterval>
- <pollingBackoff>1.0</pollingBackoff>
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-</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="">
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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="
">
- <backoffFactor>1.0</backoffFactor>
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- <maxDelay>0</maxDelay>
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-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>HSGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.ensembl_gene_id</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>RatGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnse
mbl</processor><port>hsapiens_gene_ensembl.rat_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>MouseGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.mouse_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>hsSeq</port></sink><source type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>rnSeq</port></sink><source type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.coding_gene_flank
</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>mmSeq</port></sink><source type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</port></source></datalink><datalink><sink type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</port></source></datalink><datalink><sink type="processor"><processor>FlattenImageList</processor><port>inputlist</port></sink><source type="processor"><processor>plot</processor><port>Graphics_in_PNG</port></source></datalink><datalink><sink type="processor"><processor>seqret</process
or><port>sequence_direct_data</port></sink><source type="processor"><processor>CreateFasta</processor><port>fasta</port></source></datalink><datalink><sink type="processor"><processor>plot</processor><port>sequences_direct_data</port></sink><source type="processor"><processor>emma</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>emma</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink><datalink><sink type="dataflow"><port>outputPlot</port></sink><source type="processor"><processor>FlattenImageList</processor><port>outputlist</port></source></datalink><datalink><sink type="dataflow"><port>HSapIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="dataflow"><port>MMusIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</por
t></source></datalink><datalink><sink type="dataflow"><port>RNorIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</port></source></datalink></datalinks><annotations><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>BiomartAndEMBOSSAnalysis</text>
- </annotationBean>
- <date>2009-12-15 21:49:49.57 GMT</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>Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.</text>
- </annotationBean>
- <date>2009-12-15 21:49:49.57 GMT</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>2f216461-50f5-45be-a2d2-49c84b1fce5e</identification>
- </annotationBean>
- <date>2010-07-04 18:05:56.821 BST</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 />
- </annotationBean>
- <date>2009-12-15 21:49:49.57 GMT</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/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
deleted file mode 100644
index edd0848..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
+++ /dev/null
@@ -1,247 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fb218d56-b901-42bd-b3d1-ba8d44445818" role="top"><name>BioMoby_tutorial_workflow</name><inputPorts><port><name>namespace</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>NCBI_gi</text>
- </annotationBean>
- <date>2010-07-04 17:44:30.945 BST</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>The namespace of the identifier</text>
- </annotationBean>
- <date>2010-07-04 17:43:33.391 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>id</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>656461</text>
- </annotationBean>
- <date>2010-07-04 17:43:21.263 BST</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>An gene identifier</text>
- </annotationBean>
- <date>2010-07-04 17:43:16.581 BST</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>A list of </text>
- </annotationBean>
- <date>2010-07-04 17:41:21.191 BST</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>An id</text>
- </annotationBean>
- <date>2010-07-04 17:42:57.232 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>fasta_out</name><annotations /></port><port><name>moby_blast_ids</name><annotations /></port><port><name>restrict_out</name><annotations /></port></outputPorts><processors><processor><name>Object</name><inputPorts><port><name>namespace</name><depth>0</depth></port><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mobyData</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap><map from="id" to="id" /><map from="namespace" to="namespace" /></inputMap><outputMap><map from="mobyData" to="mobyData" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biom
oby.BiomobyObjectActivityConfigurationBean xmlns="">
- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>Object</serviceName>
- <authorityName>openinformatics.com</authorityName>
-</net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="namespace" depth="0" /><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getGenBankFasta</name><inputPorts><port><name>Object(identifier)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>FASTA(fasta)</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.
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- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>getGenBankFasta</serviceName>
- <authorityName>bioinfo.icapture.ubc.ca</authorityName>
- <category />
- <serviceType />
- <secondaries />
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="Object(identifier)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Parse Moby Data(FASTA)</name><inputPorts><port><name>mobyData('FASTA')</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fasta_'content'</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activit
ies.biomoby.MobyParseDatatypeActivity</class><inputMap><map from="mobyData('FASTA')" to="mobyData('FASTA')" /></inputMap><outputMap><map from="fasta_'content'" to="fasta_'content'" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean xmlns="">
- <datatypeName>FASTA</datatypeName>
- <registryEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</registryEndpoint>
- <articleNameUsedByService>fasta</articleNameUsedByService>
-</net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
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- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="mobyData('FASTA')" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>parseDragonDBBlastText</name><inputPorts><port><name>NCBI_BLAST_Text(blastreport)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Object(Collection - 'hit_ids')</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>
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- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>parseDragonDBBlastText</serviceName>
- <authorityName>antirrhinum.net</authorityName>
- <category />
- <serviceType />
- <secondaries />
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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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="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="NCBI_BLAST_Text(blastreport)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getDragonBlastText</name><inputPorts><port><name>FASTA(sequence)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>NCBI_BLAST_Text(blast)</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.2</version></raven><class>net.sf.taverna
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- <mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
- <serviceName>getDragonBlastText</serviceName>
- <authorityName>antirrhinum.net</authorityName>
- <category />
- <serviceType />
- <secondaries>
- <entry>
- <string>evalue</string>
- <string>10</string>
- </entry>
- </secondaries>
-</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="FASTA(sequence)" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>restrict</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outfile</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.SoaplabAct
ivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outfile" to="outfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
- <endpoint>http://www.ebi.ac.uk/soaplab/services/nucleic_restriction.restrict</endpoint>
- <pollingInterval>0</pollingInterval>
- <pollingBackoff>1.0</pollingBackoff>
- <pollingIntervalMax>0</pollingIntervalMax>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Object</processor><port>namespace</port></sink><source type="dataflow"><port>namespace</port></source></datalink><datalink><sink type="processor"><processor>Object</processor><port>id</port></sink><source type="dataflow"><port>id</port></source></datalink><datalink><sink type="processor"><processor>getGenBankFasta</processor><port>Object(identifi
er)</port></sink><source type="processor"><processor>Object</processor><port>mobyData</port></source></datalink><datalink><sink type="processor"><processor>Parse Moby Data(FASTA)</processor><port>mobyData('FASTA')</port></sink><source type="processor"><processor>getGenBankFasta</processor><port>FASTA(fasta)</port></source></datalink><datalink><sink type="processor"><processor>parseDragonDBBlastText</processor><port>NCBI_BLAST_Text(blastreport)</port></sink><source type="processor"><processor>getDragonBlastText</processor><port>NCBI_BLAST_Text(blast)</port></source></datalink><datalink><sink type="processor"><processor>getDragonBlastText</processor><port>FASTA(sequence)</port></sink><source type="processor"><processor>getGenBankFasta</processor><port>FASTA(fasta)</port></source></datalink><datalink><sink type="processor"><processor>restrict</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>Parse Moby Data(FASTA)</processor><port>fasta_'content'</p
ort></source></datalink><datalink><sink type="dataflow"><port>fasta_out</port></sink><source type="processor"><processor>Parse Moby Data(FASTA)</processor><port>fasta_'content'</port></source></datalink><datalink><sink type="dataflow"><port>moby_blast_ids</port></sink><source type="processor"><processor>parseDragonDBBlastText</processor><port>Object(Collection - 'hit_ids')</port></source></datalink><datalink><sink type="dataflow"><port>restrict_out</port></sink><source type="processor"><processor>restrict</processor><port>outfile</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>fb218d56-b901-42bd-b3d1-ba8d44445818</identification>
- </annotationBean>
- <date>2010-07-04 17:44:45.645 BST</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>Eddie Kawas</text>
- </annotationBean>
- <date>2010-07-04 17:39:12.485 BST</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>3c41e289-6491-46a6-abdd-30b91bdba782</identification>
- </annotationBean>
- <date>2010-07-04 17:33:20.481 BST</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>BioMoby tutorial workflow</text>
- </annotationBean>
- <date>2010-07-04 17:39:27.212 BST</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>28441c35-894b-40b5-90f1-34422d9f6aec</identification>
- </annotationBean>
- <date>2010-07-04 17:36:55.252 BST</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>a34fa372-acb8-48f3-816a-06b9ce8f61af</identification>
- </annotationBean>
- <date>2010-07-04 17:35:33.178 BST</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.FreeTextDescription">
- <text>A workflow from part of the BioMoby tutorial</text>
- </annotationBean>
- <date>2010-07-04 17:39:46.556 BST</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>ce5dac45-77d1-4f0a-b3bf-28934c1921eb</identification>
- </annotationBean>
- <date>2010-07-04 17:31:38.230 BST</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>50903b96-8b77-485f-9655-a6f015c1ebd0</identification>
- </annotationBean>
- <date>2010-07-04 17:24:20.232 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
[43/52] [abbrv] incubator-taverna-language git commit: Delete a bunch
of unused files.
Posted by st...@apache.org.
Delete a bunch of unused files.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/7e05272d
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/7e05272d
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/7e05272d
Branch: refs/heads/master
Commit: 7e05272dcc4b2c362d1f45199db88c735ae2e54d
Parents: 2602a85
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 13:53:37 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 14:06:51 2015 +0000
----------------------------------------------------------------------
pom.xml | 4 +-
.../src/test/resources/3582.t2flow | 1677 ---
.../src/test/resources/3582.wfdesc.ttl | 659 --
.../test/resources/allTypes.types.sparql.json | 77 -
.../src/test/resources/allTypes.wfdesc.ttl | 212 -
.../src/test/resources/enm-v21.wfdesc.ttl | 10323 -----------------
.../src/test/resources/helloanyone.wfdesc.ttl | 66 -
.../test/resources/localdependency.wfdesc.ttl | 26 -
.../src/test/resources/nested.wfdesc.ttl | 126 -
.../rdf-in-example-annotation.wfdesc.ttl | 25 -
...alid_component_imagemagickconvert.wfdesc.ttl | 112 -
11 files changed, 1 insertion(+), 13306 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index eca2bfe..6fce57c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -120,15 +120,13 @@
<exclude>**/src/test/resources/rest.t2flow</exclude>
<exclude>**/src/test/resources/helloanyone.t2flow</exclude>
<exclude>**/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
- <exclude>**/src/test/resources/3582.t2flow</exclude>
<exclude>**/src/test/resources/allTypes.t2flow</exclude>
<exclude>**/src/test/resources/enm-v21.t2flow</exclude>
<exclude>**/src/test/resources/helloworld.t2flow</exclude>
+ <exclude>**/src/test/resources/helloworld.wfdesc.ttl</exclude>
<exclude>**/src/test/resources/localdependency.t2flow</exclude>
<exclude>**/src/test/resources/nested.t2flow</exclude>
<exclude>**/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
- <exclude>**/resources/**/*.wfdesc.ttl</exclude>
- <exclude>**/resources/**/*.prov.ttl</exclude>
<exclude>**/mimetype</exclude><!-- really a binary format -->
<exclude>**/src/test/resources/*starterpacklist</exclude>
<exclude>**/src/test/resources/**/*.txt</exclude>
[14/52] [abbrv] incubator-taverna-language git commit: Removed
outdated taverna-scufl2-rdf
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/main/resources/scufl2.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/main/resources/scufl2.ttl b/taverna-scufl2-rdf/src/main/resources/scufl2.ttl
deleted file mode 100644
index 041bd71..0000000
--- a/taverna-scufl2-rdf/src/main/resources/scufl2.ttl
+++ /dev/null
@@ -1,1674 +0,0 @@
-@prefix : <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix xml: <http://www.w3.org/XML/1998/namespace> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@base <http://ns.taverna.org.uk/2010/scufl2> .
-
-<http://ns.taverna.org.uk/2010/scufl2> rdf:type owl:Ontology ;
-
- rdfs:label "SCUFL2 Core ontology"@en ;
-
- rdfs:comment "The ontology defining SCUFL2 - a model for describing Taverna workflows."@en ;
-
- rdfs:seeAlso <http://www.mygrid.org.uk/dev/wiki/display/developer/Scufl2+Ontology> ,
- <http://www.taverna.org.uk/> .
-
-
-#################################################################
-#
-# Object Properties
-#
-#################################################################
-
-
-### http://ns.taverna.org.uk/2010/scufl2#activateConfiguration
-
-:activateConfiguration rdf:type owl:ObjectProperty ;
-
- rdfs:label "activate configuration"@en ;
-
- rdfs:range :Configuration ;
-
- rdfs:domain :Profile ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#activityPort
-
-:activityPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "Activity port"@en ;
-
- rdfs:domain :Activity ;
-
- rdfs:range :ActivityPort ;
-
- rdfs:subPropertyOf :port .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bind
-
-:bind rdf:type owl:AsymmetricProperty ,
- owl:IrreflexiveProperty ,
- owl:ObjectProperty ;
-
- rdfs:subPropertyOf :workflowRelation ;
-
- rdfs:domain [ rdf:type owl:Class ;
- owl:unionOf ( :PortBinding
- :ProcessorBinding
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindActivity
-
-:bindActivity rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind activity"@en ;
-
- rdfs:range :Activity ;
-
- rdfs:domain :ProcessorBinding ;
-
- rdfs:subPropertyOf :bind .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindInputActivityPort
-
-:bindInputActivityPort rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind input activity port"@en ;
-
- rdfs:range :InputActivityPort ;
-
- rdfs:domain :InputPortBinding ;
-
- rdfs:subPropertyOf :bindPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindInputProcessorPort
-
-:bindInputProcessorPort rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind input processor port"@en ;
-
- rdfs:domain :InputPortBinding ;
-
- rdfs:range :InputProcessorPort ;
-
- rdfs:subPropertyOf :bindPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindOutputActivityPort
-
-:bindOutputActivityPort rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind output activity port"@en ;
-
- rdfs:range :OutputActivityPort ;
-
- rdfs:domain :OutputPortBinding ;
-
- rdfs:subPropertyOf :bindPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindOutputProcessorPort
-
-:bindOutputProcessorPort rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind output processor port"@en ;
-
- rdfs:domain :OutputPortBinding ;
-
- rdfs:range :OutputProcessorPort ;
-
- rdfs:subPropertyOf :bindPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindPort
-
-:bindPort rdf:type owl:ObjectProperty ;
-
- rdfs:domain :PortBinding ;
-
- rdfs:subPropertyOf :bind ;
-
- rdfs:range [ rdf:type owl:Class ;
- owl:unionOf ( :ActivityPort
- :ProcessorPort
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#bindProcessor
-
-:bindProcessor rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "bind processor"@en ;
-
- rdfs:range :Processor ;
-
- rdfs:domain :ProcessorBinding ;
-
- rdfs:subPropertyOf :bind .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#block
-
-:block rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:domain :Blocking ;
-
- rdfs:subPropertyOf :controlledProcessor .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#child
-
-:child rdf:type owl:AsymmetricProperty ,
- owl:InverseFunctionalProperty ,
- owl:IrreflexiveProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "child"@en ;
-
- rdfs:range :Child ;
-
- rdfs:domain :Parent ;
-
- owl:inverseOf :parent ;
-
- rdfs:subPropertyOf :workflowRelation ,
- dcterms:hasPart .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#configure
-
-:configure rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "configure"@en ;
-
- rdfs:range :Configurable ;
-
- rdfs:domain :Configuration ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#control
-
-:control rdf:type owl:ObjectProperty ;
-
- rdfs:range :Control ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#controlledProcessor
-
-:controlledProcessor rdf:type owl:ObjectProperty ;
-
- rdfs:domain :Control ;
-
- rdfs:range :Processor ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#controllingProcessor
-
-:controllingProcessor rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "controlling processor"@en ;
-
- rdfs:domain :Control ;
-
- rdfs:range :Processor ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#datalink
-
-:datalink rdf:type owl:ObjectProperty ;
-
- rdfs:label "datalink"@en ;
-
- rdfs:range :DataLink ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#dispatchStack
-
-:dispatchStack rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "dispatch stack"@en ;
-
- owl:deprecated "true"^^xsd:boolean ;
-
- rdfs:comment "Dispatch stack has been deprecated in favour of configuring the Processor"@en ;
-
- rdfs:range :DispatchStack ;
-
- rdfs:domain :Processor ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#globalBaseURI
-
-:globalBaseURI rdf:type owl:ObjectProperty ,
- owl:ReflexiveProperty ,
- owl:SymmetricProperty ,
- owl:TransitiveProperty ;
-
- rdfs:comment """The resources are the same (like in owl:sameAs), and
- so are the sub-resources having the same base URI as a parent. For instance if
- <file:///tmp/example/> scufl2:globalBaseURI
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/> .
- then also
- <file:///tmp/example/workflow/HelloWorld/> scufl2:globalBaseURI
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>
-
- Note that for URIs under
- <http://ns.taverna.org.uk/2010/workflowBundle/> special URI template rules
- link the URI with the scufl2:parent, rdf:type, scufl2:name of the
- resource.
-
- For instance given
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>
- it must be so that:
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>
- a scufl2:OutputProcessorPort;
- scufl2:name \"greeting\";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>
- a scufl2:Processor;
- scufl2:name \"Hello\";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>;
- scufl2:outputProcessorPort <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>
- a scufl2:Workflow;
- scufl2:name \"HelloWorld\";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/>;
- sculf2:processor <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/>
- a scufl2:WorkflowBundle;
- scufl2:workflow <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>;
- scufl2:workflowBundleId \"28f7c554-4f35-401f-b34b-516e9a0ef731\";
-
- Where 28f7c554-4f35-401f-b34b-516e9a0ef731 must be a randomly
- generated UUID.
- """ ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#inputActivityPort
-
-:inputActivityPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "input acticity port"@en ;
-
- rdfs:domain :Activity ;
-
- rdfs:range :InputActivityPort ;
-
- rdfs:subPropertyOf :activityPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#inputPortBinding
-
-:inputPortBinding rdf:type owl:ObjectProperty ;
-
- rdfs:label "input port binding"@en ;
-
- rdfs:range :InputPortBinding ;
-
- rdfs:domain :ProcessorBinding ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#inputProcessorPort
-
-:inputProcessorPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "input processor port"@en ;
-
- rdfs:range :InputProcessorPort ;
-
- rdfs:domain :Processor ;
-
- rdfs:subPropertyOf :processorPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#inputWorkflowPort
-
-:inputWorkflowPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "input workflow port"@en ;
-
- rdfs:range :InputWorkflowPort ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :workflowPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#iterateOverInputPort
-
-:iterateOverInputPort rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:range :InputProcessorPort ;
-
- rdfs:domain :PortNode ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#iterationStrategyStack
-
-:iterationStrategyStack rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "iteration strategy stack"@en ;
-
- rdfs:range :IterationStrategyStack ;
-
- rdfs:domain :Processor ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#mainProfile
-
-:mainProfile rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "main profile"@en ;
-
- rdfs:range :Profile ;
-
- rdfs:domain :WorkflowBundle ;
-
- rdfs:subPropertyOf :profile .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#mainWorkflow
-
-:mainWorkflow rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "main workflow"@en ;
-
- rdfs:range :Workflow ;
-
- rdfs:domain :WorkflowBundle ;
-
- rdfs:subPropertyOf :workflow .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#outputActivityPort
-
-:outputActivityPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "output activity port"@en ;
-
- rdfs:domain :Activity ;
-
- rdfs:range :OutputActivityPort ;
-
- rdfs:subPropertyOf :activityPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#outputPortBinding
-
-:outputPortBinding rdf:type owl:ObjectProperty ;
-
- rdfs:label "output port binding"@en ;
-
- rdfs:range :OutputPortBinding ;
-
- rdfs:domain :ProcessorBinding ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#outputProcessorPort
-
-:outputProcessorPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "output processor port"@en ;
-
- rdfs:range :OutputProcessorPort ;
-
- rdfs:domain :Processor ;
-
- rdfs:subPropertyOf :processorPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#outputWorkflowPort
-
-:outputWorkflowPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "output workflow port"@en ;
-
- rdfs:range :OutputWorkflowPort ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :workflowPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#parent
-
-:parent rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "parent"@en ;
-
- rdfs:domain :Child ;
-
- rdfs:range :Parent ;
-
- rdfs:subPropertyOf :workflowRelation ,
- dcterms:isPartOf ;
-
- owl:propertyChainAxiom ( :receiveFrom
- :parent
- ) ,
- ( :controllingProcessor
- :parent
- ) ,
- ( :sendTo
- :parent
- ) ,
- ( :controlledProcessor
- :parent
- ) .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#port
-
-:port rdf:type owl:ObjectProperty ;
-
- rdfs:label "port"@en ;
-
- rdfs:domain :Parent ;
-
- rdfs:range :Port ;
-
- rdfs:subPropertyOf :child ;
-
- rdfs:domain [ rdf:type owl:Class ;
- owl:unionOf ( :Activity
- :Processor
- :Workflow
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#processor
-
-:processor rdf:type owl:ObjectProperty ;
-
- rdfs:label "processor"@en ;
-
- rdfs:range :Processor ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#processorBinding
-
-:processorBinding rdf:type owl:ObjectProperty ;
-
- rdfs:label "processor binding"@en ;
-
- rdfs:range :ProcessorBinding ;
-
- rdfs:domain :Profile ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#processorPort
-
-:processorPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "processor port"@en ;
-
- rdfs:domain :Processor ;
-
- rdfs:range :ProcessorPort ;
-
- rdfs:subPropertyOf :port .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#productOf
-
-:productOf rdf:type owl:ObjectProperty ;
-
- rdfs:label "product of"@en ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#profile
-
-:profile rdf:type owl:ObjectProperty ;
-
- rdfs:label "profile"@en ;
-
- rdfs:range :Profile ;
-
- rdfs:domain :WorkflowBundle ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#receiveFrom
-
-:receiveFrom rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "receive from"@en ;
-
- rdfs:domain :DataLink ;
-
- rdfs:range :SenderPort ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#sendTo
-
-:sendTo rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "send to"@en ;
-
- rdfs:domain :DataLink ;
-
- rdfs:range :ReceiverPort ;
-
- rdfs:subPropertyOf :workflowRelation .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#untilFinished
-
-:untilFinished rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "until finished"@en ;
-
- rdfs:domain :Blocking ;
-
- rdfs:subPropertyOf :controllingProcessor .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#workflow
-
-:workflow rdf:type owl:ObjectProperty ;
-
- rdfs:label "workflow"@en ;
-
- rdfs:range :Workflow ;
-
- rdfs:domain :WorkflowBundle ;
-
- rdfs:subPropertyOf :child .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier
-
-:workflowIdentifier rdf:type owl:FunctionalProperty ,
- owl:ObjectProperty ;
-
- rdfs:label "workflow identifier"@en ;
-
- rdfs:domain :Workflow ;
-
- rdfs:subPropertyOf :workflowRelation ,
- dcterms:isVersionOf .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#workflowPort
-
-:workflowPort rdf:type owl:ObjectProperty ;
-
- rdfs:label "workflow port"@en ;
-
- rdfs:domain :Workflow ;
-
- rdfs:range :WorkflowPort ;
-
- rdfs:subPropertyOf :port .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#workflowRelation
-
-:workflowRelation rdf:type owl:ObjectProperty ;
-
- rdfs:label "workflow relation"@en ;
-
- rdfs:domain :WorkflowElement ;
-
- rdfs:range :WorkflowElement ;
-
- rdfs:subPropertyOf dcterms:relation .
-
-
-
-### http://purl.org/dc/terms/hasPart
-
-dcterms:hasPart rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy dcterms: .
-
-
-
-### http://purl.org/dc/terms/isPartOf
-
-dcterms:isPartOf rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy dcterms: .
-
-
-
-### http://purl.org/dc/terms/isVersionOf
-
-dcterms:isVersionOf rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy dcterms: .
-
-
-
-### http://purl.org/dc/terms/relation
-
-dcterms:relation rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy dcterms: .
-
-
-
-### http://www.w3.org/1999/02/22-rdf-syntax-ns#first
-
-rdf:first rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy rdf: .
-
-
-
-### http://www.w3.org/1999/02/22-rdf-syntax-ns#rest
-
-rdf:rest rdf:type owl:ObjectProperty ;
-
- rdfs:isDefinedBy rdf: .
-
-
-
-
-
-#################################################################
-#
-# Data properties
-#
-#################################################################
-
-
-### http://ns.taverna.org.uk/2010/scufl2#activityPosition
-
-:activityPosition rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "activity position"@en ;
-
- rdfs:domain :ProcessorBinding ;
-
- rdfs:range xsd:nonNegativeInteger .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#desiredDepth
-
-:desiredDepth rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "desired depth"@en ;
-
- rdfs:domain :PortNode ;
-
- rdfs:range xsd:nonNegativeInteger .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#granularPortDepth
-
-:granularPortDepth rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "granular port depth"@en ;
-
- rdfs:range xsd:nonNegativeInteger ;
-
- rdfs:domain [ rdf:type owl:Class ;
- owl:unionOf ( :InputActivityPort
- :InputProcessorPort
- :OutputActivityPort
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#mergePosition
-
-:mergePosition rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "merge position"@en ;
-
- rdfs:domain :DataLink ;
-
- rdfs:range xsd:integer .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#name
-
-:name rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "name"@en ;
-
- rdfs:domain :Named ;
-
- rdfs:subPropertyOf dcterms:identifier ;
-
- rdfs:range xsd:string .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#portDepth
-
-:portDepth rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "port depth"@en ;
-
- rdfs:range xsd:nonNegativeInteger ;
-
- rdfs:domain [ rdf:type owl:Class ;
- owl:unionOf ( :InputActivityPort
- :InputProcessorPort
- :InputWorkflowPort
- :OutputActivityPort
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#profilePosition
-
-:profilePosition rdf:type owl:DatatypeProperty ,
- owl:FunctionalProperty ;
-
- rdfs:label "profile position"@en ;
-
- rdfs:domain :Profile ;
-
- rdfs:range xsd:nonNegativeInteger .
-
-
-
-### http://purl.org/dc/terms/identifier
-
-dcterms:identifier rdf:type owl:DatatypeProperty .
-
-
-
-
-
-#################################################################
-#
-# Classes
-#
-#################################################################
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Activity
-
-:Activity rdf:type owl:Class ;
-
- rdfs:label "Activity"@en ;
-
- rdfs:subClassOf :Child ,
- :Configurable ,
- :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Profile
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#ActivityPort
-
-:ActivityPort rdf:type owl:Class ;
-
- rdfs:label "Activity Port"@en ;
-
- rdfs:subClassOf :Child ,
- :Port ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:someValuesFrom :Activity
- ] ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputActivityPort
- :OutputActivityPort
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Blocking
-
-:Blocking rdf:type owl:Class ;
-
- rdfs:label "Blocking"@en ;
-
- rdfs:subClassOf :Control ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :block ;
- owl:someValuesFrom :Processor
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :untilFinished ;
- owl:someValuesFrom :Processor
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Child
-
-:Child rdf:type owl:Class ;
-
- rdfs:label "Child"@en ;
-
- rdfs:subClassOf :WorkflowElement ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:onClass :Parent ;
- owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger
- ] ;
-
- rdfs:comment """A WorkflowElement which can be considered a child, for instance a Processor is a child of a Workflow, an InputActivityPort is a child of an Activity.
-
-The Child-relationship also gives a strong hint that the entity should be serialised as part of its parent's serialisation."""@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Configurable
-
-:Configurable rdf:type owl:Class ;
-
- rdfs:label "Configurable"@en ;
-
- rdfs:subClassOf :WorkflowElement .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Configuration
-
-:Configuration rdf:type owl:Class ;
-
- rdfs:label "Configuration"@en ;
-
- rdfs:subClassOf :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :configure ;
- owl:someValuesFrom :Configurable
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Profile
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Control
-
-:Control rdf:type owl:Class ;
-
- rdfs:label "Control"@en ;
-
- rdfs:subClassOf :Child ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Workflow
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :controllingProcessor ;
- owl:someValuesFrom :Processor
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :controlledProcessor ;
- owl:someValuesFrom :Processor
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#CrossProduct
-
-:CrossProduct rdf:type owl:Class ;
-
- rdfs:label "Cross Product"@en ;
-
- rdfs:subClassOf :Product .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#DataLink
-
-:DataLink rdf:type owl:Class ;
-
- rdfs:label "Data Link"@en ;
-
- rdfs:subClassOf :Child ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Workflow
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :receiveFrom ;
- owl:someValuesFrom :Processor
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :sendTo ;
- owl:someValuesFrom :Processor
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#DispatchStack
-
-:DispatchStack rdf:type owl:Class ;
-
- rdfs:label "Dispatch Stack"@en ;
-
- rdfs:subClassOf :WorkflowElement ,
- rdf:List ,
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:first ;
- owl:allValuesFrom :DispatchStackLayer
- ] ,
- [ rdf:type owl:Class ;
- owl:unionOf ( [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:allValuesFrom :DispatchStack
- ]
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:hasValue rdf:nil
- ]
- )
- ] ;
-
- owl:deprecated "true"^^xsd:boolean ;
-
- rdfs:comment "Dispatch stack has been deprecated in favour of configuring the Processor."@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer
-
-:DispatchStackLayer rdf:type owl:Class ;
-
- rdfs:label "Dispatch Stack Layer"@en ;
-
- rdfs:subClassOf :Configurable ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :DispatchStack
- ] ;
-
- owl:deprecated "true"^^xsd:boolean .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#DotProduct
-
-:DotProduct rdf:type owl:Class ;
-
- rdfs:label "Dot Product"@en ;
-
- rdfs:subClassOf :Product .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#InputActivityPort
-
-:InputActivityPort rdf:type owl:Class ;
-
- rdfs:label "Input Activity Port"@en ;
-
- rdfs:subClassOf :ActivityPort ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :portDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] ;
-
- owl:disjointWith :OutputActivityPort .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#InputPortBinding
-
-:InputPortBinding rdf:type owl:Class ;
-
- rdfs:label "Input Port Binding"@en ;
-
- rdfs:subClassOf :PortBinding ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindInputProcessorPort ;
- owl:someValuesFrom :InputProcessorPort
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindInputActivityPort ;
- owl:someValuesFrom :InputActivityPort
- ] ;
-
- owl:disjointWith :OutputPortBinding .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort
-
-:InputProcessorPort rdf:type owl:Class ;
-
- rdfs:label "Input Processor Port"@en ;
-
- rdfs:subClassOf :ProcessorPort ,
- :ReceiverPort ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :portDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort
-
-:InputWorkflowPort rdf:type owl:Class ;
-
- rdfs:label "Input Workflow Port"@en ;
-
- rdfs:subClassOf :SenderPort ,
- :WorkflowPort ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :portDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] ;
-
- rdfs:comment """An input to the workflow, representing a parameter required to run the workflow.
-
-This is considered a SenderPort within the workflow, so that it can be connected to InputProcessorPort of processors contained by the same workflow."""@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#IterationStrategyChildren
-
-:IterationStrategyChildren rdf:type owl:Class ;
-
- rdfs:label "Iteration Strategy Children"@en ;
-
- rdfs:subClassOf :WorkflowElement ,
- rdf:List ,
- [ rdf:type owl:Class ;
- owl:unionOf ( [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:allValuesFrom :IterationStrategyChildren
- ]
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:hasValue rdf:nil
- ]
- )
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:first ;
- owl:allValuesFrom :IterationStrategyNode
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode
-
-:IterationStrategyNode rdf:type owl:Class ;
-
- rdfs:label "Iteration Strategy Node"@en ;
-
- rdfs:subClassOf :WorkflowElement .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#IterationStrategyStack
-
-:IterationStrategyStack rdf:type owl:Class ;
-
- rdfs:label "Iteration Strategy Stack"@en ;
-
- rdfs:subClassOf :WorkflowElement ,
- rdf:List ,
- [ rdf:type owl:Class ;
- owl:unionOf ( [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:allValuesFrom :IterationStrategyStack
- ]
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:rest ;
- owl:hasValue rdf:nil
- ]
- )
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty rdf:first ;
- owl:allValuesFrom :Product
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Named
-
-:Named rdf:type owl:Class ;
-
- rdfs:label "Named"@en ;
-
- rdfs:subClassOf :WorkflowElement ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :name ;
- owl:someValuesFrom xsd:string
- ] ;
-
- rdfs:comment "Anything identified with a scufl2:name"@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#NamedChild
-
-:NamedChild rdf:type owl:Class ;
-
- rdfs:label "Named Child"@en ;
-
- owl:equivalentClass [ rdf:type owl:Class ;
- owl:intersectionOf ( [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:someValuesFrom :Parent
- ]
- [ rdf:type owl:Restriction ;
- owl:onProperty :name ;
- owl:someValuesFrom xsd:string
- ]
- )
- ] ;
-
- rdfs:subClassOf :Child ,
- :Named ;
-
- rdfs:comment "Any Named Child is uniquely identified by its scufl2:name and scufl2:parent"@en ;
-
- owl:hasKey ( :parent
- ) ,
- ( :name
- ) .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort
-
-:OutputActivityPort rdf:type owl:Class ;
-
- rdfs:label "Output Activity Port"@en ;
-
- rdfs:subClassOf :ActivityPort ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :granularPortDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :portDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding
-
-:OutputPortBinding rdf:type owl:Class ;
-
- rdfs:label "Output Port binding"@en ;
-
- rdfs:subClassOf :PortBinding ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindOutputActivityPort ;
- owl:someValuesFrom :OutputActivityPort
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindOutputProcessorPort ;
- owl:someValuesFrom :OutputProcessorPort
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort
-
-:OutputProcessorPort rdf:type owl:Class ;
-
- rdfs:label "Output Processor Port"@en ;
-
- rdfs:subClassOf :ProcessorPort ,
- :SenderPort ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :granularPortDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :portDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort
-
-:OutputWorkflowPort rdf:type owl:Class ;
-
- rdfs:label "Output Workflow Port"@en ;
-
- rdfs:subClassOf :ReceiverPort ,
- :WorkflowPort ;
-
- rdfs:comment """An output from the workflow, representing the defined results of the workflow.
-
-This is considered a ReceiverPort within the workflow, so that it can be connected from OutputProcessorPort of processors contained by the same workflow."""@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Parent
-
-:Parent rdf:type owl:Class ;
-
- rdfs:label "Parent"@en ;
-
- rdfs:subClassOf :WorkflowElement .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Port
-
-:Port rdf:type owl:Class ;
-
- rdfs:label "Port"@en ;
-
- rdfs:subClassOf :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :name ;
- owl:someValuesFrom xsd:string
- ] ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :ActivityPort
- :ProcessorPort
- :WorkflowPort
- )
- ] ;
-
- rdfs:comment "A port is an input or output to a Processor, Workflow or Activity. "@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#PortBinding
-
-:PortBinding rdf:type owl:Class ;
-
- rdfs:label "Port Binding"@en ;
-
- rdfs:subClassOf :Child ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputPortBinding
- :OutputPortBinding
- )
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:someValuesFrom :ProcessorBinding
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#PortNode
-
-:PortNode rdf:type owl:Class ;
-
- rdfs:label "Port Node"@en ;
-
- rdfs:subClassOf :IterationStrategyNode ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :iterateOverInputPort ;
- owl:someValuesFrom :InputProcessorPort
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :desiredDepth ;
- owl:someValuesFrom xsd:nonNegativeInteger
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Processor
-
-:Processor rdf:type owl:Class ;
-
- rdfs:label "Processor"@en ;
-
- rdfs:subClassOf :Child ,
- :Configurable ,
- :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :name ;
- owl:someValuesFrom xsd:string
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Workflow
- ] ;
-
- rdfs:comment """A processor is a unit of a Workflow which performs some work. It typically have some InputProcessorPorts and OutputProcessorPorts which are connected to other Ports within the workflow. A processor will start executing as soon as there is a value for each InputProcessorPort and there are no Blocking processors.
-
-A processor is bound to an Activity which specifies how to execute the task. This ProcessorBinding also specifies PortBindings to map ActivityPorts with ProcessorPorts."""@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding
-
-:ProcessorBinding rdf:type owl:Class ;
-
- rdfs:label "Processor Binding"@en ;
-
- rdfs:subClassOf :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindProcessor ;
- owl:someValuesFrom :Processor
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :bindActivity ;
- owl:someValuesFrom :Activity
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :Profile
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#ProcessorPort
-
-:ProcessorPort rdf:type owl:Class ;
-
- rdfs:label "Processor Port"@en ;
-
- rdfs:subClassOf :Child ,
- :Port ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:someValuesFrom :Processor
- ] ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputProcessorPort
- :OutputProcessorPort
- )
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Product
-
-:Product rdf:type owl:Class ;
-
- rdfs:label "Product"@en ;
-
- rdfs:subClassOf :IterationStrategyNode ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :CrossProduct
- :DotProduct
- )
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :productOf ;
- owl:someValuesFrom :IterationStrategyChildren
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Profile
-
-:Profile rdf:type owl:Class ;
-
- rdfs:label "Profile"@en ;
-
- rdfs:subClassOf :Child ,
- :Named ,
- :WorkflowElement ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:allValuesFrom :WorkflowBundle
- ] .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#ReceiverPort
-
-:ReceiverPort rdf:type owl:Class ;
-
- rdfs:label "Receiver Port"@en ;
-
- rdfs:subClassOf :Port ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputProcessorPort
- :OutputWorkflowPort
- )
- ] ;
-
- owl:disjointWith :SenderPort ;
-
- rdfs:comment "A Port which can receive data from a DataLink"@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#SenderPort
-
-:SenderPort rdf:type owl:Class ;
-
- rdfs:label "Sender Port"@en ;
-
- rdfs:subClassOf :Port ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputWorkflowPort
- :OutputProcessorPort
- )
- ] ;
-
- rdfs:comment "A Port which can send data to a DataLink"@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#Workflow
-
-:Workflow rdf:type owl:Class ;
-
- rdfs:label "Workflow"@en ;
-
- rdfs:subClassOf :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :name ;
- owl:someValuesFrom xsd:string
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :workflowIdentifier ;
- owl:someValuesFrom owl:Thing
- ] ;
-
- owl:hasKey ( :workflowIdentifier
- ) .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle
-
-:WorkflowBundle rdf:type owl:Class ;
-
- rdfs:label "Workflow Bundle"@en ;
-
- rdfs:subClassOf :Named ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :globalBaseURI ;
- owl:onClass :WorkflowBundle ;
- owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger
- ] ;
-
- owl:hasKey ( :globalBaseURI
- ) .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#WorkflowElement
-
-:WorkflowElement rdf:type owl:Class ;
-
- rdfs:label "Workflow Element"@en ;
-
- rdfs:comment """Any element that defines a workflow, such as a processor, port, datalink, activity, port binding, profile.
-
-Super-class for any Scufl2 class. """@en .
-
-
-
-### http://ns.taverna.org.uk/2010/scufl2#WorkflowPort
-
-:WorkflowPort rdf:type owl:Class ;
-
- rdfs:label "Workflow Port"@en ;
-
- rdfs:subClassOf :Port ,
- [ rdf:type owl:Class ;
- owl:unionOf ( :InputWorkflowPort
- :OutputWorkflowPort
- )
- ] ,
- [ rdf:type owl:Restriction ;
- owl:onProperty :parent ;
- owl:someValuesFrom :Workflow
- ] ;
-
- rdfs:comment "Ports of a Workflow. "@en .
-
-
-
-### http://www.w3.org/1999/02/22-rdf-syntax-ns#List
-
-rdf:List rdf:type owl:Class ;
-
- rdfs:isDefinedBy rdf: .
-
-
-
-
-
-#################################################################
-#
-# Individuals
-#
-#################################################################
-
-
-### http://www.w3.org/1999/02/22-rdf-syntax-ns#nil
-
-rdf:nil rdf:type owl:NamedIndividual ;
-
- rdfs:isDefinedBy rdf: .
-
-
-
-
-### Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/main/resources/taverna-2.2.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/main/resources/taverna-2.2.rdf b/taverna-scufl2-rdf/src/main/resources/taverna-2.2.rdf
deleted file mode 100644
index 4cf14cb..0000000
--- a/taverna-scufl2-rdf/src/main/resources/taverna-2.2.rdf
+++ /dev/null
@@ -1,143 +0,0 @@
-<?xml version='1.0'?>
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/src/scufl2/scufl2-rdf/src/main/resources/taverna-2.2.ttl-->
-
-
-<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-
- <Ontology rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/">
- <dc:title>Taverna ontology</dc:title>
- <rdfs:comment>The ontology describing SCUFL2 components used by Taverna 2.2</rdfs:comment>
- <rdfs:seeAlso rdf:resource="http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2"/>
- <rdfs:seeAlso rdf:resource="http://www.taverna.org.uk/"/>
- <imports rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/"/>
- </Ontology>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/ActivityConfiguration">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- <rdfs:subClassOf rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activitity"/>
- <onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#configures"/>
- </rdfs:subClassOf>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/DefaultDispatchStack">
- <rdfs:comment>The default Taverna dispatch stack of Parallelise,
- ErrorBounce, Failover, Retry, Stop and Invoke.</rdfs:comment>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStack"/>
- <rdfs:subClassOf rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Parallelise"/>
- </rdfs:subClassOf>
- <rdfs:subClassOf rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/ErrorBounce"/>
- </someValuesFrom>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Failover"/>
- </someValuesFrom>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Retry"/>
- </someValuesFrom>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Stop"/>
- </someValuesFrom>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#first"/>
- <someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Invoke"/>
- </someValuesFrom>
- <someValuesFrom rdf:parseType="Resource">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Restriction"/>
- <hasValue rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- <onProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#rest"/>
- </someValuesFrom>
- </someValuesFrom>
- </someValuesFrom>
- </someValuesFrom>
- </someValuesFrom>
- </rdfs:subClassOf>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/ErrorBounce">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Failover">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Invoke">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Loop">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Parallelise">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Retry">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <Class rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/Stop">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </Class>
-
- <DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/taverna/2.2/script">
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/ActivityConfiguration"/>
- <rdfs:label>script</rdfs:label>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
- </DatatypeProperty>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/main/resources/taverna-2.2.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/main/resources/taverna-2.2.ttl b/taverna-scufl2-rdf/src/main/resources/taverna-2.2.ttl
deleted file mode 100644
index 1115c3d..0000000
--- a/taverna-scufl2-rdf/src/main/resources/taverna-2.2.ttl
+++ /dev/null
@@ -1,138 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/taverna/2.2/> .
-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix ro: <http://ns.mygrid.org.uk/2010/ResearchObject/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix : <http://ns.taverna.org.uk/2010/taverna/2.2/> .
-
-
-<>
- a owl:Ontology ;
- dc:title "Taverna ontology" ;
- owl:imports <http://ns.taverna.org.uk/2010/taverna/2.2/>;
-
- rdfs:comment """The ontology describing SCUFL2 components used by Taverna 2.2""" ;
- rdfs:seeAlso
- <http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2>,
- <http://www.taverna.org.uk/> .
-
-
-
-# Default dispatch stack layers
-
-:Parallelise
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-:ErrorBounce
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-:Failover
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-:Retry
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-:Stop
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-:Invoke
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-# Optional layers
-
-:Loop
- a owl:Class ;
- rdfs:subClassOf scufl2:DispatchStackLayer .
-
-
-:DefaultDispatchStack
- a owl:Class ;
- rdfs:comment """The default Taverna dispatch stack of Parallelise,
- ErrorBounce, Failover, Retry, Stop and Invoke.""";
- rdfs:subClassOf scufl2:DispatchStack, [
- a owl:Restriction;
- owl:someValuesFrom :Parallelise;
- owl:onProperty rdf:first
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:someValuesFrom [
- a owl:Restriction;
- owl:onProperty rdf:first;
- owl:someValuesFrom :ErrorBounce
- ## TODO: And so on.. Is this even correct syntax?
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:someValuesFrom [
- a owl:Restriction;
- owl:onProperty rdf:first;
- owl:someValuesFrom :Failover
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:someValuesFrom [
- a owl:Restriction;
- owl:onProperty rdf:first;
- owl:someValuesFrom :Retry
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:someValuesFrom [
- a owl:Restriction;
- owl:onProperty rdf:first;
- owl:someValuesFrom :Stop
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:someValuesFrom [
- a owl:Restriction;
- owl:onProperty rdf:first;
- owl:someValuesFrom :Invoke
- ], [
- a owl:Restriction;
- owl:onProperty rdf:rest;
- owl:hasValue rdf:nil;
- ]
- ]
- ]
- ]
- ]
- ].
-
-
-
-# Common activity properties
-
-
-:ActivityConfiguration
- a owl:Class ;
- rdfs:subClassOf scufl2:Configuration, [
- a owl:Restriction;
- owl:onProperty scufl2:configures;
- owl:allValuesFrom scufl2:Activitity
- ] .
-
-:script
- a owl:DatatypeProperty ;
- rdfs:domain :ActivityConfiguration;
- rdfs:label "script" ;
- rdfs:range xsd:string .
-
-
-
-
-
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/java/uk/org/taverna/scufl2/rdf/TestRDF.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/java/uk/org/taverna/scufl2/rdf/TestRDF.java b/taverna-scufl2-rdf/src/test/java/uk/org/taverna/scufl2/rdf/TestRDF.java
deleted file mode 100644
index a78e864..0000000
--- a/taverna-scufl2-rdf/src/test/java/uk/org/taverna/scufl2/rdf/TestRDF.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package uk.org.taverna.scufl2.rdf;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-import java.util.UUID;
-
-import javax.xml.namespace.QName;
-
-import org.junit.Before;
-import org.junit.Test;
-import org.openrdf.elmo.ElmoModule;
-import org.openrdf.elmo.sesame.SesameManager;
-import org.openrdf.elmo.sesame.SesameManagerFactory;
-import org.openrdf.elmo.sesame.roles.SesameEntity;
-import org.openrdf.repository.contextaware.ContextAwareConnection;
-import org.openrdf.rio.helpers.OrganizedRDFWriter;
-import org.openrdf.rio.n3.N3Writer;
-import org.openrdf.rio.rdfxml.util.OrganizedRDFXMLWriter;
-
-import uk.org.taverna.scufl2.ontology.Activity;
-import uk.org.taverna.scufl2.ontology.ActivityType;
-import uk.org.taverna.scufl2.ontology.DataLink;
-import uk.org.taverna.scufl2.ontology.InputProcessorPort;
-import uk.org.taverna.scufl2.ontology.InputWorkflowPort;
-import uk.org.taverna.scufl2.ontology.Named;
-import uk.org.taverna.scufl2.ontology.OutputProcessorPort;
-import uk.org.taverna.scufl2.ontology.OutputWorkflowPort;
-import uk.org.taverna.scufl2.ontology.Processor;
-import uk.org.taverna.scufl2.ontology.ReceiverPort;
-import uk.org.taverna.scufl2.ontology.SenderPort;
-import uk.org.taverna.scufl2.ontology.Workflow;
-import uk.org.taverna.scufl2.ontology.WorkflowBundle;
-import uk.org.taverna.scufl2.ontology.WorkflowElement;
-
-
-public class TestRDF {
-
- private SesameManager elmoManager;
-
- @Before
- public void initElmoManager() {
- ElmoModule module = new ElmoModule();
- SesameManagerFactory factory = new SesameManagerFactory(module);
- factory.setInferencingEnabled(true);
- elmoManager = factory.createElmoManager();
- }
-
- @Test
- public void makeExampleWorkflow() throws Exception {
-
- WorkflowBundle ro = elmoManager.create(randomBundleQName(),
- WorkflowBundle.class);
-
- Workflow wf1= elmoManager.create(randomWfQName(), Workflow.class);
- ro.setMainWorkflow(wf1);
-
-
- wf1.getInputWorkflowPort().add(
- makeNamed(wf1, "I", InputWorkflowPort.class));
- OutputWorkflowPort wf1_out1 = makeNamed(wf1, "out1", OutputWorkflowPort.class);
- wf1.getOutputWorkflowPort().add(wf1_out1);
-
- Processor p1 = makeNamed(wf1, "p1", Processor.class);
- wf1.getProcessors().add(p1);
- InputProcessorPort p1_y1 = makeNamed(wf1, "Y1", InputProcessorPort.class);
- p1.getInputProcessorPort().add(p1_y1);
- OutputProcessorPort p1_y2 = makeNamed(wf1, "Y2", OutputProcessorPort.class);
- p1.getOutputProcessorPort().add(p1_y2);
-
-
- Processor p4 = makeNamed(wf1, "p4", Processor.class);
- wf1.getProcessors().add(p4);
- InputProcessorPort p4_x2 = makeNamed(wf1, "X2", InputProcessorPort.class);
- p4.getInputProcessorPort().add(p4_x2);
- p4.getInputProcessorPort().add(
- makeNamed(wf1, "Y1", InputProcessorPort.class));
- OutputProcessorPort p4_y = makeNamed(wf1, "Y", OutputProcessorPort.class);
- p4.getOutputProcessorPort().add(p4_y);
-
- Processor pNested = makeNamed(wf1, "PNested", Processor.class);
- wf1.getProcessors().add(pNested);
-
- InputProcessorPort pNested_i = makeNamed(wf1, "I", InputProcessorPort.class);
- pNested.getInputProcessorPort().add(pNested_i);
- OutputProcessorPort pNested_o = makeNamed(wf1, "O", OutputProcessorPort.class);
- pNested.getOutputProcessorPort().add(pNested_o);
-
- wf1.getDatalinks().add(makeDataLink(p1_y2, pNested_i));
-
- wf1.getDatalinks().add(makeDataLink(p1_y2, p4_x2));
-
- wf1.getDatalinks().add(makeDataLink(pNested_o,
- p1_y1));
-
- wf1.getDatalinks().add(makeDataLink(p4_y,
- wf1_out1));
-
- Activity activity = elmoManager.create(Activity.class);
- ro.getActivities().add(activity);
- ActivityType beanshellType = elmoManager.create(
- new QName("http://ns.taverna.org.uk/2010/taverna/activity/",
- "beanshell"),
- ActivityType.class);
- activity.setActivityType(beanshellType);
-
- elmoManager.persist(ro);
-
- ContextAwareConnection connection = elmoManager.getConnection();
- connection.setNamespace("scufl2",
- "http://ns.taverna.org.uk/2010/scufl2#");
-
- connection.export(new OrganizedRDFXMLWriter(System.out));
-
- System.out.println("\n\n##\n\n");
-
- connection.export(new OrganizedRDFWriter(new N3Writer(System.out)));
- }
-
- private DataLink makeDataLink(SenderPort fromPort,
- ReceiverPort toPort) {
- DataLink link = elmoManager.create(DataLink.class);
- link.setReceivesFrom(fromPort);
- link.setSendsTo(toPort);
- return link;
- }
-
- private <T extends Named> T makeNamed(Workflow wf, String name,
- Class<T> beanType) {
- T named = elmoManager.create(wfPartQName(wf, name, beanType), beanType);
- named.setName(name);
- return named;
- }
-
- private <T extends WorkflowElement> QName wfPartQName(Workflow wf,
- String name, Class<T> beanType) {
- SesameEntity wfEntity = (SesameEntity) wf;
-
- String wfNamespace = wfEntity.getQName().getNamespaceURI()
- + wfEntity.getQName().getLocalPart();
- String path = wfNamespace + "/" + beanType.getSimpleName() + "/";
- return new QName(path, name);
- }
-
- private QName randomBundleQName() {
- return new QName("http://ns.taverna.org.uk/2010/workflowBundle/", UUID
- .randomUUID().toString());
- }
-
- private QName randomWfQName() {
- return new QName("http://ns.taverna.org.uk/2010/workflow/", UUID
- .randomUUID().toString());
- }
-
-
-}
[18/52] [abbrv] incubator-taverna-language git commit: Apache headers
Posted by st...@apache.org.
Apache headers
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/bd81aa1b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/bd81aa1b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/bd81aa1b
Branch: refs/heads/master
Commit: bd81aa1b27f2f44722d0775286a65df114d22f82
Parents: 08c1907
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:42:16 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:42:16 2015 +0000
----------------------------------------------------------------------
.../org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd | 16 ++++++++++++++++
.../org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd | 16 ++++++++++++++++
.../org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd | 16 ++++++++++++++++
.../org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd | 16 ++++++++++++++++
.../org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd | 16 ++++++++++++++++
.../org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd | 16 ++++++++++++++++
6 files changed, 96 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
index c5c0e3b..55b7c0c 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
index d885940..e472bd8 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://www.w3.org/ns/prov#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
index 2850d74..eb3dc4c 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
index 72a734e..f95d3b7 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://www.w3.org/2000/01/rdf-schema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
index ffec0ed..2c3d15f 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://purl.org/wf4ever/roevo#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bd81aa1b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
index 89d9294..c21072a 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
@@ -1,4 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
elementFormDefault="qualified" targetNamespace="http://ns.taverna.org.uk/2010/scufl2#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
[22/52] [abbrv] incubator-taverna-language git commit: tidy pom.xml
Posted by st...@apache.org.
tidy pom.xml
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/91de0d55
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/91de0d55
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/91de0d55
Branch: refs/heads/master
Commit: 91de0d557112013b1878cb5500dfee370e64a230
Parents: 8e7b670
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:51:16 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:51:16 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-rdfxml/pom.xml | 55 +-------------------------------------
1 file changed, 1 insertion(+), 54 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/91de0d55/taverna-scufl2-rdfxml/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/pom.xml b/taverna-scufl2-rdfxml/pom.xml
index 864c9fd..7682e2f 100644
--- a/taverna-scufl2-rdfxml/pom.xml
+++ b/taverna-scufl2-rdfxml/pom.xml
@@ -27,34 +27,7 @@
<name>Apache Taverna Scufl 2 RDF/XML</name>
<description>XSD based XML serialisation which is RDF/XML compatible</description>
<build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <!-- NO!
- <configuration>
- <instructions>
- <Export-Package>org.apache.taverna.scufl2.api.io;provide:=true</Export-Package>
- </instructions>
- </configuration>
- -->
- </plugin>
-
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.rat</groupId>
- <artifactId>apache-rat-plugin</artifactId>
- </plugin>
- </plugins>
- </build> <dependencies>
-
+ <dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>taverna-scufl2-api</artifactId>
@@ -122,30 +95,4 @@
<scope>test</scope>
</dependency>
</dependencies>
- <repositories>
- <!-- Sesame repositories no longer needed as it's in Central
- <repository>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>aduna-opensource.releases</id>
- <name>Aduna Open Source - Maven releases</name>
- <url>http://repo.aduna-software.org/maven2/releases</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- <id>aduna-opensource.snapshots</id>
- <name>Aduna Open Source - Maven snapshots</name>
- <url>http://repo.aduna-software.org/maven2/snapshots</url>
- </repository>
- -->
- </repositories>
</project>
[42/52] [abbrv] incubator-taverna-language git commit: Delete a bunch
of unused files.
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/3582.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/3582.t2flow b/taverna-scufl2-wfdesc/src/test/resources/3582.t2flow
deleted file mode 100644
index a823f7c..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/3582.t2flow
+++ /dev/null
@@ -1,1677 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="3e3db071-bf6f-42aa-9e33-db67beec6a4d" role="top"><name>Select_algorithm_and</name><inputPorts><port><name>algorithms_xml</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>algorithm</name><annotations><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>The algorithm and the parameter settings specified by the user</text>
- </annotationBean>
- <date>2011-11-24 15:06:08.172 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>create_algorithm_xml</name><inputPorts><port><name>algorithm_version</name><depth>0</depth></port><port><name>algorithm_id</name><depth>0</depth></port><port><name>parameter_values</name><depth>1</depth></port><port><name>parameter_names</name><depth>1</depth></port></inputPorts><outputPorts><port><name>createmodel_algorithm</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="algorithm_version" to="algorithm_version" /><map from="parameter_values" to="parameter_values" /><map from="parameter_names" to="parameter_names" /><map from="algorithm_id" to="algorithm_id" /></inputMap><outputMa
p><map from="createmodel_algorithm" to="createmodel_algorithm" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>algorithm_id</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>algorithm_version</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>parameter_names</name>
- <depth>1</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>parameter_values</name>
- <depth>1</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>createmodel_algorithm</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>createmodel_algorithm="";
-
-createmodel_algorithm+=
- "<Algorithm Version=\"" + algorithm_version + "\" " +
- "Id=\"" + algorithm_id + "\">";
-createmodel_algorithm += "\n";
-createmodel_algorithm += "<Parameters>\n";
-for (int i = 0; i < parameter_names.size(); i++) {
- createmodel_algorithm += "<Parameter ";
- createmodel_algorithm += "Value=\"" + parameter_values.get(i);
- createmodel_algorithm += "\" Id=\"" + parameter_names.get(i);
- createmodel_algorithm += "\"/>\n";
-}
-createmodel_algorithm += "</Parameters>";
-createmodel_algorithm += "</Algorithm>";
-createmodel_algorithm += "\n";
-
-
-</script>
- <dependencies />
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="algorithm_version" depth="0" /><port name="algorithm_id" depth="0" /><port name="parameter_values" depth="1" /><port name="parameter_names" depth="1" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>XPath_From_Text</name><inputPorts><port><name>xpath</name><depth>0</depth></port><port><name>xml-text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><rav
en><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>xpath</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>xml-text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</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>nodelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>nodelistAsXML</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>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6</version>
- <hashCode>716010169</hashCode>
- <string>dom4j:dom4j:1.6</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <script>import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals("")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;</script>
- <dependencies>
- <string>dom4j:dom4j:1.6</string>
- </dependencies>
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="xpath" depth="0" /><port name="xml-text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>XPath_From_Text_2</name><inputPorts><port><name>xpath</name><depth>0</depth></port><port><name>xml-text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><versi
on>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>xpath</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>xml-text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</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>nodelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>nodelistAsXML</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>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6</version>
- <hashCode>716010169</hashCode>
- <string>dom4j:dom4j:1.6</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <script>import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals("")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;</script>
- <dependencies>
- <string>dom4j:dom4j:1.6</string>
- </dependencies>
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="xpath" depth="0" /><port name="xml-text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>extract_parameter_xpath</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><i
nputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>//*[local-name(.)="Parameter"]</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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>create_xpath_to_get_algorithm</name><inputPorts><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out1</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in1" to="in1" /></inputM
ap><outputMap><map from="out1" to="out1" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in1</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>out1</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
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-if (seperator != void) {
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- <xmlDocument><?xml version="1.0" encoding="UTF-8"?>
-<Algorithm xmlns="http://openmodeller.cria.org.br/xml/1.0" Id="MAXENT" Version="0.6">
-<Name>Maximum Entropy</Name>
-<Overview>The principle of maximum entropy is a method for analyzing available qualitative information in order to determine a unique epistemic probability distribution. It states that the least biased distribution that encodes certain given information is that which maximizes the information entropy (content retrieved from Wikipedia on the 19th of May, 2008: http://en.wikipedia.org/wiki/Maximum_entropy).</Overview>
-<Description>The principle of maximum entropy is a method for analyzing available qualitative information in order to determine a unique epistemic probability distribution. It states that the least biased distribution that encodes certain given information is that which maximizes the information entropy (content retrieved from Wikipedia on the 19th of May, 2008: http://en.wikipedia.org/wiki/Maximum_entropy). E.T. Jaynes introduced the maximum entropy principle in 1957 saying that 'Information theory provides a constructive criterion for setting up probability distributions on the basis of partial knowledge, and leads to a type of statistical inference which is called the maximum entropy estimate. It is the least biased estimate possible on the given information; i.e., it is maximally noncommittal with regard to missing information'.</Description>
-<Designers>
-<Designer Name="Steven J. Phillips, Miroslav Dudík, Robert E. Schapire"/></Designers>
-<Bibliography>1) Jaynes, E.T. (1957) Information Theory and Statistical Mechanics. In Physical Review, Vol. 106, #4 (pp 620-630). 2) Berger, A. L., Pietra, S. A. D. and Pietra, V. J. D. (1996). A maximum entropy approach to natural language processing. Computational Linguistics, 22, 39-71. 3) Darroch, J.N. and Ratcliff, D. (1972) Generalized iterative scaling for log-linear models. The Annals of Mathematical Statistics, Vol. 43: pp 1470-1480. 4) Malouf, R. (2003) A comparison of algorithms for maximum entropy parameter estimation. Proceedings of the Sixth Conference on Natural Language Learning. 5) Phillips, S.J., Dudík, M. and Schapire, R.E. (2004) A maximum entropy approach to species distribution modeling. Proceedings of the Twenty-First International Conference on Machine Learning, pp 655-662.</Bibliography>
-<Developers>
-<Developer Contact="elisangela.rodrigues [at] poli . usp . br, renato [at] cria . org . br" Name="Elisangela S. da C. Rodrigues, Renato De Giovanni"/></Developers>
-<AcceptsCategoricalMaps>0</AcceptsCategoricalMaps>
-<RequiresAbsencePoints>1</RequiresAbsencePoints>
-<Parameters>
-<Parameter Id="NumberOfBackgroundPoints">
-<Name>Number of background points</Name>
-<Type>Integer</Type>
-<Overview>Number of background points to be generated.</Overview>
-<Description>Number of background points to be generated.</Description>
-<AcceptedRange Max="10000" Min="0"/>
-<Default>10000</Default></Parameter>
-<Parameter Id="UseAbsencesAsBackground">
-<Name>Use absence points as background</Name>
-<Type>Integer</Type>
-<Overview>Use absence points as background</Overview>
-<Description>When absence points are provided, this parameter can be used to instruct the algorithm to use them as background points. This would prevent the algorithm to randomly generate them, also facilitating comparisons between different algorithms.</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>0</Default></Parameter>
-<Parameter Id="IncludePresencePointsInBackground">
-<Name>Include input points in the background</Name>
-<Type>Integer</Type>
-<Overview>Include input points in the background: 0=No, 1=Yes.</Overview>
-<Description>Include input points in the background: 0=No, 1=Yes.</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>1</Default></Parameter>
-<Parameter Id="NumberOfIterations">
-<Name>Number of iterations</Name>
-<Type>Integer</Type>
-<Overview>Number of iterations.</Overview>
-<Description>Number of iterations.</Description>
-<AcceptedRange Min="1"/>
-<Default>500</Default></Parameter>
-<Parameter Id="TerminateTolerance">
-<Name>Terminate tolerance</Name>
-<Type>Real</Type>
-<Overview>Tolerance for detecting model convergence.</Overview>
-<Description>Tolerance for detecting model convergence.</Description>
-<AcceptedRange Min="0"/>
-<Default>0.00001</Default></Parameter>
-<Parameter Id="OutputFormat">
-<Name>Output format</Name>
-<Type>Integer</Type>
-<Overview>Output format: 1 = Raw, 2 = Logistic.</Overview>
-<Description>Output format: 1 = Raw, 2 = Logistic.</Description>
-<AcceptedRange Max="2" Min="1"/>
-<Default>2</Default></Parameter>
-<Parameter Id="QuadraticFeatures">
-<Name>Quadratic features</Name>
-<Type>Integer</Type>
-<Overview>Enable quadratic features (0=no, 1=yes)</Overview>
-<Description>Enable quadratic features (0=no, 1=yes)</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>1</Default></Parameter>
-<Parameter Id="ProductFeatures">
-<Name>Product features</Name>
-<Type>Integer</Type>
-<Overview>Enable product features (0=no, 1=yes)</Overview>
-<Description>Enable product features (0=no, 1=yes)</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>1</Default></Parameter>
-<Parameter Id="HingeFeatures">
-<Name>Hinge features</Name>
-<Type>Integer</Type>
-<Overview>Enable hinge features (0=no, 1=yes)</Overview>
-<Description>Enable hinge features (0=no, 1=yes)</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>1</Default></Parameter>
-<Parameter Id="ThresholdFeatures">
-<Name>Threshold features</Name>
-<Type>Integer</Type>
-<Overview>Enable threshold features (0=no, 1=yes)</Overview>
-<Description>Enable threshold features (0=no, 1=yes)</Description>
-<AcceptedRange Max="1" Min="0"/>
-<Default>1</Default></Parameter></Parameters></Algorithm></xmlDocument>
- <xpathExpression>/default:Algorithm/@Version</xpathExpression>
- <xpathNamespaceMap>
- <entry>
- <string>default</string>
- <string>http://openmodeller.cria.org.br/xml/1.0</string>
- </entry>
- </xpathNamespaceMap>
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- <classLoaderSharing>workflow</classLoaderSharing>
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- </outputs>
- <presentationOrigin>http://biovel.googlecode.com/svn/trunk/enm/workflows/generic_ENM/files/select_algorithm.html</presentationOrigin>
- <interactionActivityType>LocallyPresentedHtml</interactionActivityType>
- <progressNotification>false</progressNotification>
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tivity</class><inputMap><map from="flag" to="flag" /></inputMap><outputMap><map from="empty_list" to="empty_list" /></outputMap><configBean encoding="dataflow"><dataflow ref="1192812b-ff79-42ac-a88d-25e2e9522298" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="flag" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>check_parameters</name><inputPorts><port><name>xml_parameter_list</name><depth>1</depth></port></inputPorts><outputPorts><port><name>no_parameters</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>has_parameters</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</ar
tifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="xml_parameter_list" to="xml_parameter_list" /></inputMap><outputMap><map from="has_parameters" to="has_parameters" /><map from="no_parameters" to="no_parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>xml_parameter_list</name>
- <depth>1</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>has_parameters</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>no_parameters</name>
- <depth>1</depth>
- <mimeTypes />
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>import java.util.ArrayList;
-
-ArrayList has_parameters = new ArrayList();
-ArrayList no_parameters = new ArrayList();
-
-if (xml_parameter_list.size() == 0) {
-
- no_parameters.add(1);
-}
-else {
-
- has_parameters.add(1);
-}
-
-</script>
- <dependencies />
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">
- <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>1.4</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="xml_parameter_list" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>parameters_interaction</name><inputPorts><port><name>xml_list</name><depth>1</depth></port><port><name>flag</name><depth>0</depth></port></inputPorts><outputPorts><port><name>values</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>names</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities
</group><artifact>dataflow-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="flag" to="flag" /><map from="xml_list" to="xml_list" /></inputMap><outputMap><map from="values" to="values" /><map from="names" to="names" /></outputMap><configBean encoding="dataflow"><dataflow ref="ee8fd2be-4a38-4e58-a78b-a06ed4b36cf4" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="xml_list" depth="1" /><port name="flag" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List_2</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.acti
vities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</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>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List_3</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.Localworke
rActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</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>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List_4</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.Localworke
rActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</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>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List_5</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.Localworke
rActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</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>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List_6</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.Localworke
rActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>inputlist</name>
- <depth>2</depth>
- <mimeTypes>
- <string>l(l(''))</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>[B</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>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>create_algorithm_xml</processor><port>algorithm_version</port></sink><source type="processor"><processor>Merge_String_List_to_a_String_2</processor><port>concatenated</port></source></datalink><datalink><sink type="processor"><processor>create_algorithm_xml</processor><port>algorithm_id</port></sink><source type="processor"><processor>select_algorithm</proc
essor><port>algorithm_id</port></source></datalink><datalink><sink type="processor"><processor>create_algorithm_xml</processor><port>parameter_values</port></sink><source type="processor"><processor>Flatten_List_5</processor><port>outputlist</port></source></datalink><datalink><sink type="processor"><processor>create_algorithm_xml</processor><port>parameter_names</port></sink><source type="processor"><processor>Flatten_List_6</processor><port>outputlist</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text</processor><port>xpath</port></sink><source type="processor"><processor>create_xpath_to_get_algorithm</processor><port>out1</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text</processor><port>xml-text</port></sink><source type="dataflow"><port>algorithms_xml</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text_2</processor><port>xpath</port></sink><source type="processor"><processor
>extract_parameter_xpath</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text_2</processor><port>xml-text</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink><datalink><sink type="processor"><processor>create_xpath_to_get_algorithm</processor><port>in1</port></sink><source type="processor"><processor>select_algorithm</processor><port>algorithm_id</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>XPath_From_Text</processor><port>nodelistAsXML</port></source></datalink><datalink><sink type="processor"><processor>extract_algorithm_version</processor><port>xml_text</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink><datalink><sink type="proces
sor"><processor>Merge_String_List_to_a_String_2</processor><port>stringlist</port></sink><source type="processor"><processor>extract_algorithm_version</processor><port>nodelist</port></source></datalink><datalink><sink type="processor"><processor>select_algorithm</processor><port>xmltext</port></sink><source type="dataflow"><port>algorithms_xml</port></source></datalink><datalink><sink type="processor"><processor>skip_parameters_interaction</processor><port>flag</port></sink><source type="processor"><processor>check_parameters</processor><port>no_parameters</port></source></datalink><datalink><sink type="processor"><processor>check_parameters</processor><port>xml_parameter_list</port></sink><source type="processor"><processor>XPath_From_Text_2</processor><port>nodelistAsXML</port></source></datalink><datalink><sink type="processor"><processor>parameters_interaction</processor><port>xml_list</port></sink><source type="processor"><processor>XPath_From_Text_2</processor><port>nodelistA
sXML</port></source></datalink><datalink><sink type="processor"><processor>parameters_interaction</processor><port>flag</port></sink><source type="processor"><processor>check_parameters</processor><port>has_parameters</port></source></datalink><datalink><sink type="processor"><processor>Flatten_List_2</processor><port>inputlist</port></sink><source type="processor"><processor>skip_parameters_interaction</processor><port>empty_list</port></source></datalink><datalink><sink type="processor"><processor>Flatten_List_3</processor><port>inputlist</port></sink><source type="processor"><processor>parameters_interaction</processor><port>names</port></source></datalink><datalink><sink type="processor"><processor>Flatten_List_4</processor><port>inputlist</port></sink><source type="processor"><processor>parameters_interaction</processor><port>values</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List_5</processor><port>inputlist</port></sink><source type="processor"><
processor>Flatten_List_4</processor><port>outputlist</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List_5</processor><port>inputlist</port></sink><source type="processor"><processor>Flatten_List_2</processor><port>outputlist</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List_6</processor><port>inputlist</port></sink><source type="processor"><processor>Flatten_List_3</processor><port>outputlist</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List_6</processor><port>inputlist</port></sink><source type="processor"><processor>Flatten_List_2</processor><port>outputlist</port></source></datalink><datalink><sink type="dataflow"><port>algorithm</port></sink><source type="processor"><processor>create_algorithm_xml</processor><port>createmodel_algorithm</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>17200719-4702-4cf0-85fc-beeb2ddde8e8</identification>
- </annotationBean>
- <date>2012-06-05 12:53:33.140 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>20cac592-69d5-446e-980e-10cd380665e1</identification>
- </annotationBean>
- <date>2012-12-07 19:50:49.50 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl
<TRUNCATED>
[10/52] [abbrv] incubator-taverna-language git commit: outdated
usecase removed
Posted by st...@apache.org.
outdated usecase removed
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/cfd67b7a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/cfd67b7a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/cfd67b7a
Branch: refs/heads/master
Commit: cfd67b7ae135d3d1318a8ac5d861ae0792beb212
Parents: 72cbd2d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:09:39 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:09:39 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-usecases/.gitignore | 1 -
taverna-scufl2-usecases/LICENSE.txt | 30 -----
taverna-scufl2-usecases/pom.xml | 62 ---------
.../main/resources/sample-output.data-bundle | Bin 5071 -> 0 bytes
.../sample-output/META-INF/container.xml | 30 -----
.../sample-output/META-INF/manifest.xml | 55 --------
.../src/main/resources/sample-output/inputs.rdf | 37 ------
.../src/main/resources/sample-output/inputs.ttl | 12 --
.../src/main/resources/sample-output/mimetype | 1 -
.../sample-output/outputs-nested-tiny.rdf | 107 ---------------
.../sample-output/outputs-nested-tiny.ttl | 62 ---------
.../resources/sample-output/outputs-nested.rdf | 124 ------------------
.../resources/sample-output/outputs-nested.ttl | 83 ------------
.../main/resources/sample-output/outputs.rdf | 131 -------------------
.../main/resources/sample-output/outputs.ttl | 86 ------------
.../main/resources/sample-output/outputs/fish/0 | 1 -
.../main/resources/sample-output/outputs/fish/1 | 1 -
.../resources/sample-output/outputs/results | 1 -
.../resources/sample-output/outputs/soup/0/0 | 1 -
.../resources/sample-output/outputs/soup/0/1 | 1 -
20 files changed, 826 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/.gitignore b/taverna-scufl2-usecases/.gitignore
deleted file mode 100644
index ea8c4bf..0000000
--- a/taverna-scufl2-usecases/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/LICENSE.txt
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/LICENSE.txt b/taverna-scufl2-usecases/LICENSE.txt
deleted file mode 100644
index 0f327ce..0000000
--- a/taverna-scufl2-usecases/LICENSE.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-Simplified 2-Clause BSD license
-===============================
-
-Copyright (c) 2010-2011, myGrid, University of Mancester, UK
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
-Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
-IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
-TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-[1] http://www.opensource.org/licenses/bsd-license.php
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/pom.xml b/taverna-scufl2-usecases/pom.xml
deleted file mode 100644
index ad00100..0000000
--- a/taverna-scufl2-usecases/pom.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-language</artifactId>
- <version>0.15.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-scufl2-usecases</artifactId>
- <name>Apache Taverna Scufl 2 use cases</name>
- <description>Use cases for exercising the SCUFL2 APIs and formats</description>
- <url>http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2+use+cases</url>
- <dependencies>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-api</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-rdfxml</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-t2flow</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>taverna-scufl2-api</artifactId>
- <version>${project.version}</version>
- <type>test-jar</type>
- </dependency>
- <dependency>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-osgi</artifactId>
- <optional>true</optional>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output.data-bundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output.data-bundle b/taverna-scufl2-usecases/src/main/resources/sample-output.data-bundle
deleted file mode 100644
index 0c1f168..0000000
Binary files a/taverna-scufl2-usecases/src/main/resources/sample-output.data-bundle and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/container.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/container.xml b/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/container.xml
deleted file mode 100644
index 2d31270..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/container.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<container version="1.0"
- xmlns="urn:oasis:names:tc:opendocument:xmlns:container">
- <rootfiles>
- <rootfile full-path="outputs.rdf" media-type="application/rdf+xml" />
- <rootfile full-path="outputs.ttl" media-type="text/turtle" />
- <rootfile full-path="outputs" media-type="application/vnd.taverna.port-data" />
- </rootfiles>
-</container>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/manifest.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/manifest.xml b/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/manifest.xml
deleted file mode 100644
index 472e5d5..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/META-INF/manifest.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<manifest:manifest xmlns:manifest="urn:oasis:names:tc:opendocument:xmlns:manifest:1.0">
- <manifest:file-entry manifest:full-path="/"
- manifest:media-type="application/vnd.taverna.data-bundle" />
-
- <manifest:file-entry manifest:full-path="outputs.rdf"
- manifest:media-type="application/rdf+xml" />
- <manifest:file-entry manifest:full-path="outputs" />
-
- <manifest:file-entry manifest:full-path="outputs/fish" />
- <manifest:file-entry manifest:full-path="outputs/fish/0.txt"
- manifest:media-type="text/plain" manifest:size="23" />
- <manifest:file-entry manifest:full-path="outputs/fish/1.uri"
- manifest:media-type="text/uri-list" manifest:size="19" />
-
- <manifest:file-entry manifest:full-path="outputs/soup" />
- <manifest:file-entry manifest:full-path="outputs/soup/0" />
- <manifest:file-entry manifest:full-path="outputs/soup/0/0.jpg"
- manifest:media-type="image/jpeg" manifest:size="91344" />
- <manifest:file-entry manifest:full-path="outputs/soup/0/1.err"
- manifest:media-type="application/vnd.taverna.error-document+xml" manifest:size="5331" />
- <manifest:file-entry manifest:full-path="outputs/soup/1" />
- <manifest:file-entry manifest:full-path="outputs/soup/2.err"
- manifest:media-type="application/vnd.taverna.error-document+xml" manifest:size="3125" />
-
- <manifest:file-entry manifest:full-path="outputs/results"
- manifest:media-type="application/octet-stream" manifest:size="311" />
-
- <manifest:file-entry manifest:full-path="inputs.rdf"
- manifest:media-type="application/rdf+xml" />
- <manifest:file-entry manifest:full-path="inputs" />
- <!-- ... -->
-
-</manifest:manifest>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.rdf
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diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.rdf b/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.rdf
deleted file mode 100644
index 9a0dd01..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.rdf
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-usecases/src/main/resources/sample-output/inputs.ttl-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/data/"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-
- <bundle rdf:about="./">
- <contains rdf:resource="outputs/"/>
- </bundle>
-
- <workflowInputs rdf:about="inputs/">
- </workflowInputs>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.ttl
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diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.ttl b/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.ttl
deleted file mode 100644
index 4ee6024..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/inputs.ttl
+++ /dev/null
@@ -1,12 +0,0 @@
-@prefix : <http://ns.taverna.org.uk/2010/data/> .
-@prefix list: <http://ns.taverna.org.uk/2010/data/list/> .
-@prefix error: <http://ns.taverna.org.uk/2010/data/error/> .
-@prefix value: <http://ns.taverna.org.uk/2010/data/value/> .
-@prefix run: <http://ns.taverna.org.uk/2010/run/> .
-
-<.> a :bundle;
- :contains <outputs/>.
-
-<inputs/> a :workflowInputs.
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/mimetype
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/mimetype b/taverna-scufl2-usecases/src/main/resources/sample-output/mimetype
deleted file mode 100644
index 08b7605..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/mimetype
+++ /dev/null
@@ -1 +0,0 @@
-application/vnd.taverna.data-bundle
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
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diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
deleted file mode 100644
index bf9acf8..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
+++ /dev/null
@@ -1,107 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/data/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
- <workflowOutputs rdf:about="outputs/">
- <contains>
- <!-- A single value -->
- <value rdf:about="outputs/results" xlink:href="outputs/results">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <!-- We know the port name, but not the URI, as we would have to inspect
- the .t2flow to find the workflow identifier -->
- <outputFrom scufl2:name="results" />
- </value>
- </contains>
-
- <contains>
- <list rdf:about="outputs/fish" xlink:href="outputs/fish">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <listContent rdf:parseType="Collection">
- <absent index="0" /> <!-- missing item in position 0 -->
- <absent index="1" /> <!-- .. 1 -->
- <value rdf:about="outputs/fish/2" index="2" size="12" />
- <value rdf:about="outputs/fish/3" index="3" size="442" />
- <!-- There could be more missing items, but we wouldn't know at this
- time -->
- </listContent>
- <outputFrom scufl2:name="fish" />
- </list>
- </contains>
-
- <contains>
- <list rdf:about="outputs/soup/">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <!-- <depth> is not included, as the server can't accurately calculate
- this if the workflow port only have errors or empty lists (ie. folders) -
- neither currently annotated with the depth. -->
- <listContent rdf:parseType="Collection">
- <!-- List of list of values (depth 2) -->
-
- <list rdf:about="outputs/soup/0/" xlink:href="outputs/soup/0/" >
- <listContent rdf:parseType="Collection">
-
- <data rdf:about="outputs/soup/0/0" xlink:href="outputs/soup/0/0"
- size="12" index="0" />
-
- <value index="1">skdjfksjdf</value>
-
-
- <data rdf:about="outputs/soup/0/0" xlink:href="outputs/soup/0/0"
- size="12" index="0">
- <stringValue>243dfsdf</stringValue>
- </data>
-
-
- <data rdf:about="outputs/soup/0/0" xlink:href="outputs/soup/0/0"
- size="12" index="0">
- <stringValue><!-CDATACRAP[[243dfsdf>.,
- ]]></stringValue>
- </data>
-
- <data rdf:about="outputs/soup/0/0" xlink:href="outputs/soup/0/0"
- size="12" index="0">
- <binary>2BASE7</binary>
- </data>
-
-
- <!-- We didn't include the error message, but as file name ends in
- .err we can at least tag the item as an error -->
- <error rdf:about="outputs/soup/0/1.err" size="523" />
- </listContent>
- </list>
-
- <!-- Lists could be missing as well -->
- <absent />
-
- <list rdf:about="outputs/soup/2/">
- <!-- empty list -->
- <listContent rdf:parseType="Collection" />
- </list>
-
- <error rdf:about="outputs/soup/3.err" />
- </listContent>
- <outputFrom scufl2:name="soup" />
- </list>
- </contains>
- </workflowOutputs>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.ttl b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.ttl
deleted file mode 100644
index 167cdda..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.ttl
+++ /dev/null
@@ -1,62 +0,0 @@
-#Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp
- # using base file:///home/stain/stuff/src/workspace/uk.org.taverna.scufl2/scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
-
-# Notation3 generation by
-# notation3.py,v 1.200 2007/12/11 21:18:08 syosi Exp
-
-# Base was: file:///home/stain/stuff/src/workspace/uk.org.taverna.scufl2/scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
- @prefix : <http://ns.taverna.org.uk/2010/scufl2#> .
- @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-
- <outputs/> a <http://ns.taverna.org.uk/2010/data/workflowOutputs>;
- <http://ns.taverna.org.uk/2010/data/contains> <outputs/fish>,
- <outputs/results>,
- <outputs/soup/> .
-
- <outputs/fish> a <http://ns.taverna.org.uk/2010/data/list>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/listContent> (
- [
- a <http://ns.taverna.org.uk/2010/data/missing> ]
- [
- a <http://ns.taverna.org.uk/2010/data/missing> ]
- <outputs/fish/2>
- <outputs/fish/3> );
- <http://ns.taverna.org.uk/2010/data/outputFrom> [
- :name "fish" ] .
-
- <outputs/fish/2> a <http://ns.taverna.org.uk/2010/data/value> .
-
- <outputs/fish/3> a <http://ns.taverna.org.uk/2010/data/value> .
-
- <outputs/results> a <http://ns.taverna.org.uk/2010/data/value>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/outputFrom> [
- :name "results" ] .
-
- <outputs/soup/> a <http://ns.taverna.org.uk/2010/data/list>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/listContent> (
- <outputs/soup/0/>
- [
- a <http://ns.taverna.org.uk/2010/data/missing> ]
- <outputs/soup/2/>
- <outputs/soup/3.err> );
- <http://ns.taverna.org.uk/2010/data/outputFrom> [
- :name "soup" ] .
-
- <outputs/soup/0/> a <http://ns.taverna.org.uk/2010/data/list>;
- <http://ns.taverna.org.uk/2010/data/listContent> (
- <outputs/soup/0/0>
- <outputs/soup/0/1.err> ) .
-
- <outputs/soup/0/0> a <http://ns.taverna.org.uk/2010/data/value> .
-
- <outputs/soup/0/1.err> a <http://ns.taverna.org.uk/2010/data/error> .
-
- <outputs/soup/2/> a <http://ns.taverna.org.uk/2010/data/list>;
- rdf:rest () .
-
- <outputs/soup/3.err> a <http://ns.taverna.org.uk/2010/data/error> .
-
-#ENDS
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
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diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
deleted file mode 100644
index 1f3facc..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
+++ /dev/null
@@ -1,124 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/data/" xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:run="http://ns.taverna.org.uk/2010/run/">
-
- <bundle rdf:about="./">
- <contains rdf:resource="outputs/" />
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/bundle/1495ca3a-f61a-437b-83ad-c6437c92a3d0/" />
- </bundle>
-
- <workflowOutputs rdf:about="outputs/">
- <contains>
- <list rdf:about="outputs/fish">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <depth>1</depth>
- <listContent rdf:parseType="Collection">
- <missingValue />
- <missingValue />
- <value rdf:about="outputs/fish/2.txt">
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/value/45b29774-8927-4e9e-8961-6137cb95ef69" />
- </value>
- <value rdf:about="outputs/fish/3.uri">
- <uri rdf:resource="http://www.example.org/data4.txt" />
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/value/59f606c9-713a-40dc-905e-56b6764e1338" />
- </value>
- <missingValue />
- </listContent>
- <outputFrom
- rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/fish" />
- <producedBy
- rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7" />
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/list/45b29774-8927-4e9e-8961-6137cb95ef69" />
- </list>
- </contains>
- <contains>
- <value rdf:about="outputs/results">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <outputFrom
- rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/results" />
- <producedBy
- rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7" />
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/value/3d0a18ad-ad01-4576-ab9c-616ced7d90d2" />
- </value>
-
- </contains>
- <contains>
- <list rdf:about="outputs/soup/">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput" />
- <depth>2</depth>
- <listContent rdf:parseType="Collection">
- <list rdf:about="outputs/soup/0/">
- <depth>1</depth>
- <listContent rdf:parseType="Collection">
- <value rdf:about="outputs/soup/0/0.jpg">
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/value/d433895f-5550-4d9e-9f65-ed30b5272047" />
- </value>
-
- <error rdf:about="outputs/soup/0/1.err">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</depth>
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/value/f719b95f-5eea-4609-9c6d-c71aab75b4da" />
- </error>
-
- </listContent>
-
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047" />
- </list>
-
-
- <list rdf:about="outputs/soup/1/">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</depth>
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047" />
- </list>
-
- <error rdf:about="outputs/soup/2.err">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</depth>
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/error/b7a07d2f-93f6-4fef-b6d4-4a68f2d6dd0b" />
- </error>
- </listContent>
- <outputFrom
- rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/soup" />
- <producedBy
- rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7" />
- <owl:sameAs
- rdf:resource="http://ns.taverna.org.uk/2010/data/list/b7e6bae6-7f09-405c-b19a-604ec36d95ca" />
- </list>
- </contains>
- </workflowOutputs>
-
- <run:workflowRun
- rdf:about="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7">
- <run:runOf
- rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/" />
- </run:workflowRun>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.ttl
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diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.ttl b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.ttl
deleted file mode 100644
index 6e6a90d..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs-nested.ttl
+++ /dev/null
@@ -1,83 +0,0 @@
-#Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp
- # using base file:///home/stain/stuff/src/workspace/uk.org.taverna.scufl2/scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
-
-# Notation3 generation by
-# notation3.py,v 1.200 2007/12/11 21:18:08 syosi Exp
-
-# Base was: file:///home/stain/stuff/src/workspace/uk.org.taverna.scufl2/scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
-
- <./> a <http://ns.taverna.org.uk/2010/data/bundle>;
- <http://ns.taverna.org.uk/2010/data/contains> <outputs/>;
- = <http://ns.taverna.org.uk/2010/data/bundle/1495ca3a-f61a-437b-83ad-c6437c92a3d0/> .
-
- <outputs/> a <http://ns.taverna.org.uk/2010/data/workflowOutputs>;
- <http://ns.taverna.org.uk/2010/data/contains> <outputs/fish>,
- <outputs/results>,
- <outputs/soup/> .
-
- <outputs/fish> a <http://ns.taverna.org.uk/2010/data/list>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/depth> "1";
- <http://ns.taverna.org.uk/2010/data/listContent> (
- [
- a <http://ns.taverna.org.uk/2010/data/missingValue> ]
- [
- a <http://ns.taverna.org.uk/2010/data/missingValue> ]
- <outputs/fish/2.txt>
- <outputs/fish/3.uri>
- [
- a <http://ns.taverna.org.uk/2010/data/missingValue> ] );
- <http://ns.taverna.org.uk/2010/data/outputFrom> <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/fish>;
- <http://ns.taverna.org.uk/2010/data/producedBy> <http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7>;
- = <http://ns.taverna.org.uk/2010/data/list/45b29774-8927-4e9e-8961-6137cb95ef69> .
-
- <outputs/fish/2.txt> a <http://ns.taverna.org.uk/2010/data/value>;
- = <http://ns.taverna.org.uk/2010/data/value/45b29774-8927-4e9e-8961-6137cb95ef69> .
-
- <outputs/fish/3.uri> a <http://ns.taverna.org.uk/2010/data/value>;
- <http://ns.taverna.org.uk/2010/data/uri> <http://www.example.org/data4.txt>;
- = <http://ns.taverna.org.uk/2010/data/value/59f606c9-713a-40dc-905e-56b6764e1338> .
-
- <outputs/results> a <http://ns.taverna.org.uk/2010/data/value>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/outputFrom> <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/results>;
- <http://ns.taverna.org.uk/2010/data/producedBy> <http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7>;
- = <http://ns.taverna.org.uk/2010/data/value/3d0a18ad-ad01-4576-ab9c-616ced7d90d2> .
-
- <outputs/soup/> a <http://ns.taverna.org.uk/2010/data/list>,
- <http://ns.taverna.org.uk/2010/data/workflowOutput>;
- <http://ns.taverna.org.uk/2010/data/depth> "2";
- <http://ns.taverna.org.uk/2010/data/listContent> (
- <outputs/soup/0/>
- <outputs/soup/1/>
- <outputs/soup/2.err> );
- <http://ns.taverna.org.uk/2010/data/outputFrom> <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/soup>;
- <http://ns.taverna.org.uk/2010/data/producedBy> <http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7>;
- = <http://ns.taverna.org.uk/2010/data/list/b7e6bae6-7f09-405c-b19a-604ec36d95ca> .
-
- <outputs/soup/0/> a <http://ns.taverna.org.uk/2010/data/list>;
- <http://ns.taverna.org.uk/2010/data/depth> "1";
- <http://ns.taverna.org.uk/2010/data/listContent> (
- <outputs/soup/0/0.jpg>
- <outputs/soup/0/1.err> );
- = <http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047> .
-
- <outputs/soup/0/0.jpg> a <http://ns.taverna.org.uk/2010/data/value>;
- = <http://ns.taverna.org.uk/2010/data/value/d433895f-5550-4d9e-9f65-ed30b5272047> .
-
- <outputs/soup/0/1.err> a <http://ns.taverna.org.uk/2010/data/error>;
- <http://ns.taverna.org.uk/2010/data/depth> 0;
- = <http://ns.taverna.org.uk/2010/data/value/f719b95f-5eea-4609-9c6d-c71aab75b4da> .
-
- <outputs/soup/1/> a <http://ns.taverna.org.uk/2010/data/list>;
- <http://ns.taverna.org.uk/2010/data/depth> 1;
- = <http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047> .
-
- <outputs/soup/2.err> a <http://ns.taverna.org.uk/2010/data/error>;
- <http://ns.taverna.org.uk/2010/data/depth> 1;
- = <http://ns.taverna.org.uk/2010/data/error/b7a07d2f-93f6-4fef-b6d4-4a68f2d6dd0b> .
-
- <http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7> a <http://ns.taverna.org.uk/2010/run/workflowRun>;
- <http://ns.taverna.org.uk/2010/run/runOf> <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/> .
-
-#ENDS
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.rdf b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.rdf
deleted file mode 100644
index f11bb56..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.rdf
+++ /dev/null
@@ -1,131 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-usecases/src/main/resources/sample-output/outputs.ttl-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/data/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:run="http://ns.taverna.org.uk/2010/run/">
-
- <bundle rdf:about="./">
- <contains rdf:resource="outputs/"/>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/bundle/1495ca3a-f61a-437b-83ad-c6437c92a3d0/"/>
- </bundle>
-
- <workflowOutputs rdf:about="outputs/">
- <contains rdf:resource="outputs/fish/"/>
- <contains rdf:resource="outputs/results"/>
- <contains rdf:resource="outputs/soup/"/>
- </workflowOutputs>
-
- <list rdf:about="outputs/fish/">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput"/>
- <depth>1</depth>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/fish/0.txt"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</listPosition>
- </hasListEntry>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/fish/1.uri"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</listPosition>
- </hasListEntry>
- <outputFrom rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/fish"/>
- <producedBy rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7"/>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/list/45b29774-8927-4e9e-8961-6137cb95ef69"/>
- </list>
-
- <value rdf:about="outputs/fish/0.txt">
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/value/45b29774-8927-4e9e-8961-6137cb95ef69"/>
- </value>
-
- <value rdf:about="outputs/fish/1.uri">
- <uri rdf:resource="http://www.example.org/data4.txt"/>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/value/59f606c9-713a-40dc-905e-56b6764e1338"/>
- </value>
-
- <value rdf:about="outputs/results">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput"/>
- <outputFrom rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/results"/>
- <producedBy rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7"/>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/value/3d0a18ad-ad01-4576-ab9c-616ced7d90d2"/>
- </value>
-
- <list rdf:about="outputs/soup/">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/data/workflowOutput"/>
- <depth>2</depth>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/soup/0/"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</listPosition>
- </hasListEntry>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/soup/1/"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</listPosition>
- </hasListEntry>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/soup/2.err"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">2</listPosition>
- </hasListEntry>
- <outputFrom rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/soup"/>
- <producedBy rdf:resource="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7"/>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/list/b7e6bae6-7f09-405c-b19a-604ec36d95ca"/>
- </list>
-
- <list rdf:about="outputs/soup/0/">
- <depth>1</depth>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/soup/0/0.jpg"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</listPosition>
- </hasListEntry>
- <hasListEntry rdf:parseType="Resource">
- <entry rdf:resource="outputs/soup/0/1.err"/>
- <listPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</listPosition>
- </hasListEntry>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047"/>
- </list>
-
- <value rdf:about="outputs/soup/0/0.jpg">
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/value/d433895f-5550-4d9e-9f65-ed30b5272047"/>
- </value>
-
- <error rdf:about="outputs/soup/0/1.err">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</depth>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/value/f719b95f-5eea-4609-9c6d-c71aab75b4da"/>
- </error>
-
- <list rdf:about="outputs/soup/1/">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</depth>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/list/d433895f-5550-4d9e-9f65-ed30b5272047"/>
- </list>
-
- <error rdf:about="outputs/soup/2.err">
- <depth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</depth>
- <owl:sameAs rdf:resource="http://ns.taverna.org.uk/2010/data/error/b7a07d2f-93f6-4fef-b6d4-4a68f2d6dd0b"/>
- </error>
-
- <run:workflowRun rdf:about="http://ns.taverna.org.uk/2010/run/b9455363-5624-4744-901b-3d6c7ec273d7">
- <run:runOf rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/"/>
- </run:workflowRun>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.ttl b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.ttl
deleted file mode 100644
index 8389846..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs.ttl
+++ /dev/null
@@ -1,86 +0,0 @@
-@prefix : <http://ns.taverna.org.uk/2010/data/> .
-@prefix list: <http://ns.taverna.org.uk/2010/data/list/> .
-@prefix error: <http://ns.taverna.org.uk/2010/data/error/> .
-@prefix value: <http://ns.taverna.org.uk/2010/data/value/> .
-@prefix run: <http://ns.taverna.org.uk/2010/run/> .
-
-<.> a :bundle;
- :contains <outputs/>;
- = <http://ns.taverna.org.uk/2010/data/bundle/1495ca3a-f61a-437b-83ad-c6437c92a3d0/> .
-
-<outputs/> a :workflowOutputs;
- :contains <outputs/fish/>,
- <outputs/results>,
- <outputs/soup/> .
-
-
-<outputs/fish/> a :list, :workflowOutput;
- = list:45b29774-8927-4e9e-8961-6137cb95ef69 ;
- :depth "1";
- :hasListEntry [
- :entry <outputs/fish/0.txt>;
- :listPosition 0 ],
- [
- :entry <outputs/fish/1.uri>;
- :listPosition 1 ];
- :producedBy run:b9455363-5624-4744-901b-3d6c7ec273d7;
- :outputFrom <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/fish> .
-
-<outputs/fish/0.txt> a :value;
- = <http://ns.taverna.org.uk/2010/data/value/45b29774-8927-4e9e-8961-6137cb95ef69> .
-
-<outputs/fish/1.uri> a :value;
- = <http://ns.taverna.org.uk/2010/data/value/59f606c9-713a-40dc-905e-56b6764e1338> ;
- :uri <http://www.example.org/data4.txt> .
-
-<outputs/soup/> a :list, :workflowOutput;
- = list:b7e6bae6-7f09-405c-b19a-604ec36d95ca ;
- :depth "2";
- :hasListEntry [
- :entry <outputs/soup/0/>;
- :listPosition 0 ],
- [
- :entry <outputs/soup/1/>;
- :listPosition 1 ],
- [
- :entry <outputs/soup/2.err>;
- :listPosition 2 ];
- :producedBy run:b9455363-5624-4744-901b-3d6c7ec273d7;
- :outputFrom <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/soup> .
-
-run:b9455363-5624-4744-901b-3d6c7ec273d7 a run:workflowRun;
- run:runOf <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/> .
-
-<outputs/soup/0/> a :list;
- = list:d433895f-5550-4d9e-9f65-ed30b5272047 ;
- :depth "1";
- :hasListEntry [
- :entry <outputs/soup/0/0.jpg>;
- :listPosition 0 ],
- [
- :entry <outputs/soup/0/1.err>;
- :listPosition 1 ].
-
-<outputs/soup/0/0.jpg> a :value;
- = value:d433895f-5550-4d9e-9f65-ed30b5272047 .
-
-<outputs/soup/0/1.err> a :error;
- = value:f719b95f-5eea-4609-9c6d-c71aab75b4da ;
- :depth 0 .
-
-<outputs/soup/1/> a :list;
- = list:d433895f-5550-4d9e-9f65-ed30b5272047 ;
- :depth 1 .
-
-<outputs/soup/2.err> a :error;
- = error:b7a07d2f-93f6-4fef-b6d4-4a68f2d6dd0b ;
- :depth 1 .
-
-
-<outputs/results> a :value, :workflowOutput;
- = <http://ns.taverna.org.uk/2010/data/value/3d0a18ad-ad01-4576-ab9c-616ced7d90d2> ;
- :outputFrom <http://ns.taverna.org.uk/2010/workflowBundle/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/workflow/HelloWorld/out/results> ;
- :producedBy run:b9455363-5624-4744-901b-3d6c7ec273d7 .
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/0
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/0 b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/0
deleted file mode 100644
index 948749d..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/0
+++ /dev/null
@@ -1 +0,0 @@
-fish 0
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/1
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/1 b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/1
deleted file mode 100644
index f972d16..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/fish/1
+++ /dev/null
@@ -1 +0,0 @@
-fish 1
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/results
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/results b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/results
deleted file mode 100644
index 872aa27..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/results
+++ /dev/null
@@ -1 +0,0 @@
-results
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/0
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/0 b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/0
deleted file mode 100644
index 0842743..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/0
+++ /dev/null
@@ -1 +0,0 @@
-soup 0.0
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/cfd67b7a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/1
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/1 b/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/1
deleted file mode 100644
index 90d4c51..0000000
--- a/taverna-scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/1
+++ /dev/null
@@ -1 +0,0 @@
-soup 0.1
[51/52] [abbrv] incubator-taverna-language git commit: whitespace
corrections
Posted by st...@apache.org.
whitespace corrections
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f7e3cba8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f7e3cba8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f7e3cba8
Branch: refs/heads/master
Commit: f7e3cba8876f772668c6d056225602dbbe7caf1f
Parents: 7805e77
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Fri Feb 13 14:32:50 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Fri Feb 13 14:33:34 2015 +0000
----------------------------------------------------------------------
pom.xml | 82 ++++++++++++++++++++++++++++++------------------------------
1 file changed, 41 insertions(+), 41 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f7e3cba8/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 71b6b4a..030d92f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -49,13 +49,13 @@
<configuration>
<useDefaultExcludes>true</useDefaultExcludes>
<excludes>
- <!-- Following excludes needed for taverna-scufl2-rdf,
- taverna-scufl2-integration-tests and taverna-scufl2-validation-integration
- subfolders that should be modules but are not. -->
- <exclude>**/.classpath</exclude>
- <exclude>**/.project</exclude>
- <exclude>**/.settings/</exclude>
- <exclude>**/target/</exclude>
+ <!-- Following excludes needed for taverna-scufl2-rdf,
+ taverna-scufl2-integration-tests and taverna-scufl2-validation-integration
+ subfolders that should be modules but are not. -->
+ <exclude>**/.classpath</exclude>
+ <exclude>**/.project</exclude>
+ <exclude>**/.settings/</exclude>
+ <exclude>**/target/</exclude>
<!-- Text and Markdown files are typically used only for documentation
purposes and license declarations are usually spurious in these files since
often they will refer to the LICENSE/NOTICE for users to find the actual
@@ -64,8 +64,8 @@
<!-- META-INF services files can include comments but a license header
would be unecessarily clutter so we exclude these -->
<exclude>**/META-INF/services/*</exclude>
- <!-- No headers in JSON which haven't got comments ... -->
- <exclude>**/*.json</exclude>
+ <!-- No headers in JSON which haven't got comments ... -->
+ <exclude>**/*.json</exclude>
<!-- Really a binary format, but must look like text -->
<exclude>**/mimetype</exclude>
<!-- Effectively a binary format -->
@@ -96,36 +96,36 @@
<exclude>/src/test/resources/t172starterpacklist</exclude>
<exclude>/src/test/resources/t230starterpacklist</exclude>
<!-- THESE ARE XML AND SUPPORT COMMENTS -->
- <exclude>/src/test/resources/annotation_with_backslash.t2flow</exclude>
- <exclude>/src/test/resources/beanshell-deps.t2flow</exclude>
- <exclude>/src/test/resources/component_simple.t2flow</exclude>
- <exclude>/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
- <exclude>/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
- <exclude>/src/test/resources/dispatchlayers.t2flow</exclude>
- <exclude>/src/test/resources/fasta_and_pscan.t2flow</exclude>
- <exclude>/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
- <exclude>/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
- <exclude>/src/test/resources/interaction_multiple_choice.t2flow</exclude>
- <exclude>/src/test/resources/interaction_simple_tell.t2flow</exclude>
- <exclude>/src/test/resources/iterationstrategies.t2flow</exclude><!-- TOM -->
- <exclude>/src/test/resources/merge_fun.t2flow</exclude>
- <exclude>/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
- <exclude>/src/test/resources/missing_merge.t2flow</exclude>
- <exclude>/src/test/resources/missing_produced_by_941.t2flow</exclude>
- <exclude>/src/test/resources/rest-2-2.t2flow</exclude>
- <exclude>/src/test/resources/rshell-2-2.t2flow</exclude>
- <exclude>/src/test/resources/simple_fasta.t2flow</exclude>
- <exclude>/src/test/resources/sleepers.t2flow</exclude>
- <exclude>/src/test/resources/apiconsumer.t2flow</exclude>
- <exclude>/src/test/resources/rest.t2flow</exclude>
- <exclude>/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
- <exclude>/src/test/resources/enm-v21.t2flow</exclude>
- <exclude>/src/test/resources/helloworld.wfdesc.ttl</exclude>
- <exclude>/src/test/resources/localdependency.t2flow</exclude>
- <exclude>/src/test/resources/nested.t2flow</exclude>
- <exclude>/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
- <exclude>/src/test/resources/workflow10.xml</exclude>
- <exclude>/src/test/resources/full-example/ebi_interproscan_newservices_900329.t2flow</exclude>
+ <exclude>/src/test/resources/annotation_with_backslash.t2flow</exclude>
+ <exclude>/src/test/resources/beanshell-deps.t2flow</exclude>
+ <exclude>/src/test/resources/component_simple.t2flow</exclude>
+ <exclude>/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_and_pscan.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
+ <exclude>/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_multiple_choice.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_simple_tell.t2flow</exclude>
+ <exclude>/src/test/resources/iterationstrategies.t2flow</exclude><!-- TOM -->
+ <exclude>/src/test/resources/merge_fun.t2flow</exclude>
+ <exclude>/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
+ <exclude>/src/test/resources/missing_merge.t2flow</exclude>
+ <exclude>/src/test/resources/missing_produced_by_941.t2flow</exclude>
+ <exclude>/src/test/resources/rest-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/rshell-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/simple_fasta.t2flow</exclude>
+ <exclude>/src/test/resources/sleepers.t2flow</exclude>
+ <exclude>/src/test/resources/apiconsumer.t2flow</exclude>
+ <exclude>/src/test/resources/rest.t2flow</exclude>
+ <exclude>/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
+ <exclude>/src/test/resources/enm-v21.t2flow</exclude>
+ <exclude>/src/test/resources/helloworld.wfdesc.ttl</exclude>
+ <exclude>/src/test/resources/localdependency.t2flow</exclude>
+ <exclude>/src/test/resources/nested.t2flow</exclude>
+ <exclude>/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
+ <exclude>/src/test/resources/workflow10.xml</exclude>
+ <exclude>/src/test/resources/full-example/ebi_interproscan_newservices_900329.t2flow</exclude>
<!-- Cannot contain comments; content must match program output. -->
<exclude>/src/test/resources/org/apache/taverna/scufl2/api/io/HelloWorld.txt</exclude>
<exclude>/src/test/resources/as.txt</exclude>
@@ -160,7 +160,7 @@
<licenseMerge>Eclipse Public License, Version 1.0|Eclipse Public License</licenseMerge>
</licenseMerges>
</configuration>
- </execution>
+ </execution>
</executions>
</plugin>
-->
@@ -331,7 +331,7 @@
<modules>
<module>taverna-scufl2-ucfpackage</module>
<module>taverna-scufl2-api</module>
- <module>taverna-scufl2-examples</module>
+ <module>taverna-scufl2-examples</module>
<module>taverna-scufl2-rdfxml</module>
<module>taverna-scufl2-t2flow</module>
<module>taverna-scufl2-scufl</module>
[03/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow
deleted file mode 100644
index 589dd63..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow
+++ /dev/null
@@ -1,255 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fe9a837d-317c-4921-bace-bff3a9ffd837" role="top"><name>Fetch_PDB_flatfile_from_RCSB_server</name><inputPorts><port><name>pdbID</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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>PDB identifier such as '1crn'</text>
- </annotationBean>
- <date>2009-12-15 21:05:33.450 GMT</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.ExampleValue">
- <text>1crn</text>
- </annotationBean>
- <date>2009-12-15 21:05:16.196 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>pdbFlatFile</name><annotations /></port></outputPorts><processors><processor><name>AddPrefixToID</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</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>localworker-activity</artifact><version>1.2</version></raven><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="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>AddSuffix</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><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</versi
on></raven><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="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="string2" depth="0" /><port name="string1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>FetchPage</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>image</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.localwo
rker.LocalworkerActivity</class><inputMap><map from="url" to="url" /></inputMap><outputMap><map from="image" to="image" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</localworkerName>
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-} else {
- inputURL = new URL(url);
-}
-
-byte[] contents;
-if (inputURL.openConnection().getContentLength() == -1) {
- // Content size unknown, must read first...
- byte[] buffer = new byte[1024];
- int bytesRead = 0;
- int totalBytesRead = 0;
- InputStream is = inputURL.openStream();
- while (bytesRead != -1) {
- totalBytesRead += bytesRead;
- bytesRead = is.read(buffer, 0, 1024);
- }
- contents = new byte[totalBytesRead];
-} else {
- contents = new byte[inputURL.openConnection().getContentLength()];
-}
-int bytesRead = 0;
-int totalBytesRead = 0;
-InputStream is = inputURL.openStream();
-while (bytesRead != -1) {
- bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
- totalBytesRead += bytesRead;
- if (contents.length==totalBytesRead) break;
-}
-
-image = contents;
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>image</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'image/*'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>RCSBPrefix</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value"
/></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>http://www.rcsb.org/pdb/cgi/export.cgi/1CRN.pdb?format=PDB&pdbId=</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>RCSBSuffix</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf
.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>&compression=None</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>AddPrefixToID</processor><port>string1</port></sink><source type="processor"><processor>RCSBPrefix</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>AddPrefixToID</processor><port>string2</port></sink><source type="dataflow"><port>pdbID</port></source></datalink><datalink><sink type="processor"><processor>AddSuffix</processor><port>string2</port></sink><source type="proces
sor"><processor>RCSBSuffix</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>AddSuffix</processor><port>string1</port></sink><source type="processor"><processor>AddPrefixToID</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>FetchPage</processor><port>url</port></sink><source type="processor"><processor>AddSuffix</processor><port>output</port></source></datalink><datalink><sink type="dataflow"><port>pdbFlatFile</port></sink><source type="processor"><processor>FetchPage</processor><port>image</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>fe9a837d-317c-4921-bace-bff3a9ffd837</identification>
- </annotationBean>
- <date>2010-07-04 18:15:10.393 BST</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.FreeTextDescription">
- <text>Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB</text>
- </annotationBean>
- <date>2009-12-15 21:06:13.245 GMT</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.Author">
- <text>Tom Oinn</text>
- </annotationBean>
- <date>2009-12-15 21:05:51.281 GMT</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.DescriptiveTitle">
- <text>Fetch PDB flatfile from RCSB server</text>
- </annotationBean>
- <date>2009-12-15 21:06:02.76 GMT</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/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
deleted file mode 100644
index 9cdc238..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
+++ /dev/null
@@ -1,332 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="8b032490-948e-4983-b632-d16653755fcd" role="top"><name>Fetch_today_s_xkcd_comic</name><inputPorts /><outputPorts><port><name>todaysXkcd</name><annotations /></port></outputPorts><processors><processor><name>getPage</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>contents</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><map from="url" to="url" /></inputMap><outputMap><map from="contents" to="contents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebPageFetcher</localworkerName>
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-}
-else {
- inputURL = new URL(url);
-}
-URLConnection con = inputURL.openConnection();
-InputStream in = con.getInputStream();
-
-InputStreamReader isr = new InputStreamReader(in);
-Reader inReader = new BufferedReader(isr);
-
-StringBuffer buf = new StringBuffer();
-int ch;
-while ((ch = inReader.read()) > -1) {
- buf.append((char)ch);
-}
-inReader.close();
-contents = buf.toString();
-
-
-//String NEWLINE = System.getProperty("line.separator");
-//
-//URL inputURL = null;
-//if (base != void) {
-// inputURL = new URL(new URL(base), url);
-//} else {
-// inputURL = new URL(url);
-//}
-//StringBuffer result = new StringBuffer();
-//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
-//String line = null;
-//while ((line = reader.readLine()) != null) {
-// result.append(line);
-// result.append(NEWLINE);
-//}
-//
-//contents = result.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>contents</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain,text/html'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xkcdURL</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>http://xkcd.com/</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>getImageLinks</name><inputPorts><port><name>document</name><depth>0</depth></port></inputPorts><outputPorts><port><name>imagelinks</name><depth>1</depth><granularDepth>1</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><map from="document" to="document"
/></inputMap><outputMap><map from="imagelinks" to="imagelinks" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks</localworkerName>
- <script>String lowerCaseContent = document.toLowerCase();
-int index = 0;
-List imagelinks = new ArrayList();
-while ((index = lowerCaseContent.indexOf("<img", index)) != -1) {
- if ((index = lowerCaseContent.indexOf("src", index)) == -1)
- break;
- if ((index = lowerCaseContent.indexOf("=", index)) == -1)
- break;
- index++;
- String remaining = document.substring(index);
- StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#");
- String strLink = st.nextToken();
- imagelinks.add(strLink);
-}
-
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>document</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/html'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>imagelinks</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/x-taverna-web-url')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="document" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>findComicURL</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>filteredlist</name><depth>1</depth><granularDepth>1</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><map from="regex" to="regex" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="filteredlist" to="filteredlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FilterStringList</localworkerName>
- <script>filteredlist = new ArrayList();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- if (item.matches(regex)) {
- filteredlist.add(item);
- }
-}
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>stringlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>regex</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>filteredlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="regex" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>comicURLRegex</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap
/><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>.*/comics/.*</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>getComicStrip</name><inputPorts><port><name>base</name><depth>0</depth></port><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>image</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><inputMa
p><map from="base" to="base" /><map from="url" to="url" /></inputMap><outputMap><map from="image" to="image" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</localworkerName>
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-} else {
- inputURL = new URL(url);
-}
-
-byte[] contents;
-if (inputURL.openConnection().getContentLength() == -1) {
- // Content size unknown, must read first...
- byte[] buffer = new byte[1024];
- int bytesRead = 0;
- int totalBytesRead = 0;
- InputStream is = inputURL.openStream();
- while (bytesRead != -1) {
- totalBytesRead += bytesRead;
- bytesRead = is.read(buffer, 0, 1024);
- }
- contents = new byte[totalBytesRead];
-} else {
- contents = new byte[inputURL.openConnection().getContentLength()];
-}
-int bytesRead = 0;
-int totalBytesRead = 0;
-InputStream is = inputURL.openStream();
-while (bytesRead != -1) {
- bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
- totalBytesRead += bytesRead;
- if (contents.length==totalBytesRead) break;
-}
-
-image = contents;
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>image</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'image/*'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="base" depth="0" /><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getPage</processor><port>url</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getImageLinks</processor><port>document</port></sink><source type="processor"><processor>getPage</processor><port>contents</port></source></datalink><datali
nk><sink type="processor"><processor>findComicURL</processor><port>regex</port></sink><source type="processor"><processor>comicURLRegex</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>findComicURL</processor><port>stringlist</port></sink><source type="processor"><processor>getImageLinks</processor><port>imagelinks</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>base</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>url</port></sink><source type="processor"><processor>findComicURL</processor><port>filteredlist</port></source></datalink><datalink><sink type="dataflow"><port>todaysXkcd</port></sink><source type="processor"><processor>getComicStrip</processor><port>image</port></source></datalink></datalinks><annotations><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>Fetch today's xkcd comic</text>
- </annotationBean>
- <date>2009-12-15 20:39:06.623 GMT</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.Author">
- <text>Tom Oinn, Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-12-15 20:38:58.43 GMT</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>Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
-
-Based on the FetchDailyDilbert workflow.</text>
- </annotationBean>
- <date>2009-12-15 20:39:17.683 GMT</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>8b032490-948e-4983-b632-d16653755fcd</identification>
- </annotationBean>
- <date>2010-07-04 18:16:02.491 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
[36/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
Posted by st...@apache.org.
Delete unused testing workflows
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/14d0f060
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/14d0f060
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/14d0f060
Branch: refs/heads/master
Commit: 14d0f060a82cb944aea8842339d1b67fa7cd68ce
Parents: 0bcffe7
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 11:03:37 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 11:10:58 2015 +0000
----------------------------------------------------------------------
pom.xml | 19 -
.../src/test/resources/annotated2.2-xsd.t2flow | 408 ---------
.../test/resources/annotations_2_4-xsd.t2flow | 456 ----------
.../src/test/resources/annotations_2_4.t2flow | 146 ----
.../defaultActivitiesTaverna2.2-xsd.t2flow | 873 -------------------
.../test/resources/dispatchlayers-xsd.t2flow | 755 ----------------
.../resources/rest-2-2-saved-2-3-xsd.t2flow | 367 --------
.../test/resources/rest-2-2-saved-2-3.t2flow | 85 --
.../src/test/resources/rest-2-2-xsd.t2flow | 361 --------
.../src/test/resources/rest-2-3-xsd.t2flow | 376 --------
.../src/test/resources/rest-2-3.t2flow | 94 --
.../src/test/resources/rshell-2-3.t2flow | 183 ----
.../test/resources/rshell-simple-2-3-xsd.t2flow | 199 -----
.../src/test/resources/rshell-simple-2-3.t2flow | 94 --
.../semantic_annotations__eclipse-xsd.t2flow | 198 -----
.../resources/tool-2-2-resaved-2-3-xsd.t2flow | 222 -----
.../test/resources/tool-2-2-resaved-2-3.t2flow | 193 ----
.../test/resources/tool-2-2-tweaked-xsd.t2flow | 346 --------
.../src/test/resources/tool-2-2.t2flow | 42 -
.../src/test/resources/tool-2-3-xsd.t2flow | 361 --------
.../src/test/resources/tool-2-3.t2flow | 334 -------
21 files changed, 6112 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 82c023a..eca2bfe 100644
--- a/pom.xml
+++ b/pom.xml
@@ -86,16 +86,12 @@
<!-- No headers in JSON which haven't got comments .. -->
<exclude>**/*.json</exclude>
<!-- Various files used for testing and test support only. -->
- <exclude>**/src/test/resources/annotated2.2-xsd.t2flow</exclude>
<exclude>**/src/test/resources/annotated2.2.t2flow</exclude>
<exclude>**/src/test/resources/annotation_with_backslash.t2flow</exclude>
- <exclude>**/src/test/resources/annotations_2_4-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/annotations_2_4.t2flow</exclude>
<exclude>**/src/test/resources/as.t2flow</exclude>
<exclude>**/src/test/resources/beanshell-deps.t2flow</exclude>
<exclude>**/src/test/resources/component_simple.t2flow</exclude>
<exclude>**/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
- <exclude>**/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow</exclude>
<exclude>**/src/test/resources/defaultActivitiesTaverna2.2.t2flow</exclude>
<exclude>**/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
<exclude>**/src/test/resources/dispatchlayers.t2flow</exclude>
@@ -110,28 +106,13 @@
<exclude>**/src/test/resources/missing_merge.t2flow</exclude>
<exclude>**/src/test/resources/missing_produced_by_941.t2flow</exclude>
<exclude>**/src/test/resources/random.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-2-saved-2-3.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-2-xsd.t2flow</exclude>
<exclude>**/src/test/resources/rest-2-2.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-3-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-3.t2flow</exclude>
<exclude>**/src/test/resources/rshell-2-2.t2flow</exclude>
- <exclude>**/src/test/resources/rshell-2-3.t2flow</exclude>
- <exclude>**/src/test/resources/rshell-simple-2-3-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/rshell-simple-2-3.t2flow</exclude>
- <exclude>**/src/test/resources/semantic_annotations__eclipse-xsd.t2flow</exclude>
<exclude>**/src/test/resources/semantic_annotations__eclipse.t2flow</exclude>
<exclude>**/src/test/resources/simple_fasta.t2flow</exclude>
<exclude>**/src/test/resources/sleepers.t2flow</exclude>
<exclude>**/src/test/resources/spreadsheet_activity_defaults_892.t2flow</exclude>
<exclude>**/src/test/resources/T3-1226-annotations-with-quotes.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-2-resaved-2-3.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-2-tweaked-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-2.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-3-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/tool-2-3.t2flow</exclude>
<exclude>**/src/test/resources/xpath_workflow.t2flow</exclude>
<exclude>**/examples/helloanyone.t2flow</exclude>
<exclude>**/examples/helloworld.t2flow</exclude>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/annotated2.2-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/annotated2.2-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/annotated2.2-xsd.t2flow
deleted file mode 100644
index 45c525c..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/annotated2.2-xsd.t2flow
+++ /dev/null
@@ -1,408 +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-2.2.0">
- <dataflow id="9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad" role="top">
- <name>Workflow_title</name>
- <inputPorts>
- <port>
- <name>in0</name>
- <depth>0</depth>
- <granularDepth>0</granularDepth>
- <annotations>
- <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.ExampleValue">
- <text>Only example</text>
- </annotationBean>
- <date>2010-07-21 11:19:58.897 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- <port>
- <name>in1</name>
- <depth>1</depth>
- <granularDepth>1</granularDepth>
- <annotations>
- <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>Only description</text>
- </annotationBean>
- <date>2010-07-21 11:19:47.699 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- <port>
- <name>in2</name>
- <depth>2</depth>
- <granularDepth>2</granularDepth>
- <annotations>
- <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.ExampleValue">
- <text>Some kind </text>
- </annotationBean>
- <date>2010-07-21 11:19:34.518 BST</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>Workflow input in2</text>
- </annotationBean>
- <date>2010-07-21 11:19:25.509 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- </inputPorts>
- <outputPorts>
- <port>
- <name>out0</name>
- <annotations>
- <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.ExampleValue">
- <text />
- </annotationBean>
- <date>2010-07-21 11:26:10.972 BST</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>First annotation</text>
- </annotationBean>
- <date>2010-07-21 11:20:30.875 BST</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.ExampleValue">
- <text>Not empty</text>
- </annotationBean>
- <date>2010-07-21 11:25:56.668 BST</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>Third annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:50.301 BST</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.ExampleValue">
- <text>Empty again</text>
- </annotationBean>
- <date>2010-07-21 11:26:05.105 BST</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>Second annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:39.729 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- <port>
- <name>out1</name>
- <annotations />
- </port>
- </outputPorts>
- <processors>
- <processor>
- <name>Beanshell</name>
- <inputPorts />
- <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 />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
- xmlns="">
- <script />
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String
- </translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- </processors>
- <conditions />
- <datalinks />
- <annotations>
- <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>Workflow title</text>
- </annotationBean>
- <date>2010-07-21 11:20:43.824 BST</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>Workflow description</text>
- </annotationBean>
- <date>2010-07-21 11:20:50.161 BST</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>bb902d82-b0e4-46fc-bed5-950a3b38bb98</identification>
- </annotationBean>
- <date>2010-07-21 11:22:31.286 BST</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>9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad</identification>
- </annotationBean>
- <date>2010-07-21 11:26:16.844 BST</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>Workflow author</text>
- </annotationBean>
- <date>2010-07-21 11:20:39.864 BST</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/annotations_2_4-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/annotations_2_4-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/annotations_2_4-xsd.t2flow
deleted file mode 100644
index 955aa1d..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/annotations_2_4-xsd.t2flow
+++ /dev/null
@@ -1,456 +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-2.4.0">
- <dataflow id="42750c57-f4f0-4a98-8077-88eafd28d211" role="top">
- <name>The_title</name>
- <inputPorts>
- <port>
- <name>in1</name>
- <depth>0</depth>
- <granularDepth>0</granularDepth>
- <annotations>
- <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>The workflow input port in1</text>
- </annotationBean>
- <date>2012-09-26 08:35:46.88 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.ExampleValue">
- <text>exampleIn</text>
- </annotationBean>
- <date>2012-09-26 08:36:01.836 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- </inputPorts>
- <outputPorts>
- <port>
- <name>out1</name>
- <annotations>
- <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.ExampleValue">
- <text>exampleOut</text>
- </annotationBean>
- <date>2012-09-26 08:35:58.605 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>The workflow output out1</text>
- </annotationBean>
- <date>2012-09-26 08:35:54.934 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- </port>
- </outputPorts>
- <processors>
- <processor>
- <name>Beanshell</name>
- <inputPorts>
- <port>
- <name>in1</name>
- <depth>0</depth>
- </port>
- </inputPorts>
- <outputPorts>
- <port>
- <name>out1</name>
- <depth>0</depth>
- <granularDepth>0</granularDepth>
- </port>
- </outputPorts>
- <annotations>
- <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>The processor description</text>
- </annotationBean>
- <date>2012-09-26 08:35:04.898 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
- </net.sf.taverna.t2.annotation.AnnotationChainImpl>
- </annotation_chain>
- </annotations>
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>beanshell-activity</artifact>
- <version>1.4</version>
- </raven>
- <class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class>
- <inputMap>
- <map from="in1" to="in1" />
- </inputMap>
- <outputMap>
- <map from="out1" to="out1" />
- </outputMap>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
- xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in1</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>out1</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>the script</script>
- <dependencies />
- </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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="in1" depth="0" />
- </cross>
- </strategy>
- </iteration>
- </iterationStrategyStack>
- </processor>
- <processor>
- <name>Text_constant</name>
- <inputPorts />
- <outputPorts>
- <port>
- <name>value</name>
- <depth>0</depth>
- <granularDepth>0</granularDepth>
- </port>
- </outputPorts>
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>stringconstant-activity</artifact>
- <version>1.4</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="">
- <value>A text</value>
- </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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>
- <condition control="Text_constant" target="Beanshell" />
- </conditions>
- <datalinks>
- <datalink>
- <sink type="processor">
- <processor>Beanshell</processor>
- <port>in1</port>
- </sink>
- <source type="dataflow">
- <port>in1</port>
- </source>
- </datalink>
- <datalink>
- <sink type="merge">
- <port>out1</port>
- </sink>
- <source type="processor">
- <processor>Beanshell</processor>
- <port>out1</port>
- </source>
- </datalink>
- <datalink>
- <sink type="merge">
- <port>out1</port>
- </sink>
- <source type="processor">
- <processor>Text_constant</processor>
- <port>value</port>
- </source>
- </datalink>
- </datalinks>
- <annotations>
- <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>The Author
- and spaces and
- newlines
- </text>
- </annotationBean>
- <date>2012-09-26 08:34:42.432 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>42750c57-f4f0-4a98-8077-88eafd28d211
- </identification>
- </annotationBean>
- <date>2012-09-26 08:37:27.976 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.FreeTextDescription">
- <text>The description.
-
- This could be quite long.
- </text>
- </annotationBean>
- <date>2012-09-26 08:34:56.353 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.DescriptiveTitle">
- <text>The title</text>
- </annotationBean>
- <date>2012-09-26 08:34:46.286 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/annotations_2_4.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/annotations_2_4.t2flow b/taverna-scufl2-t2flow/src/test/resources/annotations_2_4.t2flow
deleted file mode 100644
index 6819436..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/annotations_2_4.t2flow
+++ /dev/null
@@ -1,146 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="42750c57-f4f0-4a98-8077-88eafd28d211" role="top"><name>The_title</name><inputPorts><port><name>in1</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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>The workflow input port in1</text>
- </annotationBean>
- <date>2012-09-26 08:35:46.88 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.ExampleValue">
- <text>exampleIn</text>
- </annotationBean>
- <date>2012-09-26 08:36:01.836 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out1</name><annotations><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.ExampleValue">
- <text>exampleOut</text>
- </annotationBean>
- <date>2012-09-26 08:35:58.605 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>The workflow output out1</text>
- </annotationBean>
- <date>2012-09-26 08:35:54.934 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out1</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations><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>The processor description</text>
- </annotationBean>
- <date>2012-09-26 08:35:04.898 UTC</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in1" to="in1" /></inputMap><outputMap><map from="out1" to="out1" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>in1</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>out1</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>the script</script>
- <dependencies />
-</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="in1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Text_constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="val
ue" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>A text</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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><condition control="Text_constant" target="Beanshell" /></conditions><datalinks><datalink><sink type="processor"><processor>Beanshell</processor><port>in1</port></sink><source type="dataflow"><port>in1</port></source></datalink><datalink><sink type="merge"><port>out1</port></sink><source type="processor"><processor>Beanshell</processor><port>out1</port></source></datalink><datalink><sink type="merge"><port>out1</port></sink><source type="processor"><processor>Text_consta
nt</processor><port>value</port></source></datalink></datalinks><annotations><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>The Author
- and spaces and
-newlines</text>
- </annotationBean>
- <date>2012-09-26 08:34:42.432 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>42750c57-f4f0-4a98-8077-88eafd28d211</identification>
- </annotationBean>
- <date>2012-09-26 08:37:27.976 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.FreeTextDescription">
- <text>The description.
-
-This could be quite long.</text>
- </annotationBean>
- <date>2012-09-26 08:34:56.353 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.DescriptiveTitle">
- <text>The title</text>
- </annotationBean>
- <date>2012-09-26 08:34:46.286 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
[35/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow
deleted file mode 100644
index 6e44e03..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow
+++ /dev/null
@@ -1,873 +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-2.2.0"><dataflow id="dc227a10-e8f6-44b0-88c5-c946a15ff669" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>the
-script;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies>
- <string>a.jar</string>
- <string>b.jar</string>
- </localDependencies>
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in2</name>
- <depth>1</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out2</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Nested_workflow</name><inputPorts /><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 /><outputMap /><configBean encoding="dataflow"><dataflow ref="a838d861-e4b8-4e7f-839c-e0fc748749b9" /></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>
net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
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- <serviceName>getTmhmmPrediction</serviceName>
- <authorityName>mips.gsf.de</authorityName>
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- <serviceType />
- <secondaries />
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- <pollingInterval>4</pollingInterval>
- <pollingBackoff>1.1</pollingBackoff>
- <pollingIntervalMax>5</pollingIntervalMax>
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- <operation>queryStatus</operation>
- <securityProfile>HTTPBasicAuthNPlainTextPassword</securityProfile>
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">
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- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
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- </inputs>
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- <granularDepth>0</granularDepth>
- <name>code</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>message</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>baseURL</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
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">
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- <operation>get_compounds_by_enzyme</operation>
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">
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- <operation>get_genes_by_organism</operation>
- <securityProfile>WSSecurityTimestampUsernameTokenPlainTextPassword</securityProfile>
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">
- <backoffFactor>1.0</backoffFactor>
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- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>biomart</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.2</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="Drosophila melanogaster features (BDGP5.13)" nam
e="dmelanogaster_feature_set" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2010-06-07 11:08:23"><MartURLLocation database="functional_genomics_mart_58" default="0" displayName="ENSEMBL FUNCTIONAL GENOMICS 58 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="functional_genomics" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.6" requestId="taverna"><Dataset name="dmelanogaster_feature_set"><Attribute name="cell_type_display_label_1048" /><Attribute name="name_1011" /><Attribute name="display_label_1049" /><Filter name="chromosome_name" value="2L" /><Filter name="end" value="10000000" /><Filter name="start" value="1" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><
group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Send_an_Email</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.SendEmail</localworkerName>
- <script>import javax.mail.Message;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.MimeMessage;
-import javax.mail.internet.InternetAddress;
-
-if (subject == void) {
- subject = "No subject";
-}
-if (body == void) {
- throw new Exception("No body specified for message");
-}
-
-Properties mailProps = System.getProperties();
-if (smtpserver != void) {
- mailProps.put("mail.smtp.host", smtpserver);
-}
-
-Session session = Session.getDefaultInstance(mailProps, null);
-MimeMessage message = new MimeMessage(session);
-message.setFrom(new InternetAddress(from));
-message.addRecipient(Message.RecipientType.TO, new InternetAddress(to));
-message.setSubject(subject);
-message.setText(body);
-Transport.send(message);
-</script>
- <dependencies>
- <string>javax.mail:mail:1.4</string>
- <string>javax.activation:activation:1.1</string>
- </dependencies>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>javax.mail</groupId>
- <artifactId>mail</artifactId>
- <version>1.4</version>
- <hashCode>789035249</hashCode>
- <string>javax.mail:mail:1.4</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>javax.activation</groupId>
- <artifactId>activation</artifactId>
- <version>1.1</version>
- <hashCode>518094512</hashCode>
- <string>javax.activation:activation:1.1</string>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>to</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>from</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>subject</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>body</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>smtpserver</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs />
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>TavernaResearchObject</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>org.apache.taverna.scufl2.api.container.TavernaResearchObject</className>
- <methodName>TavernaResearchObject</methodName>
- <parameterNames />
- <parameterDimensions />
- <parameterTypes />
- <returnType>org.apache.taverna.scufl2.api.container.TavernaResearchObject</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>true</isMethodConstructor>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs />
- <outputs />
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>setWorkflows</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>org.apache.taverna.scufl2.api.container.TavernaResearchObject</className>
- <methodName>setWorkflows</methodName>
- <parameterNames>
- <string>workflows</string>
- </parameterNames>
- <parameterDimensions>
- <int>0</int>
- </parameterDimensions>
- <parameterTypes>
- <string>java.util.Set</string>
- </parameterTypes>
- <returnType>void</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>false</isMethodConstructor>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies>
- <string>a.jar</string>
- </localDependencies>
- <artifactDependencies />
- <inputs />
- <outputs />
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>run</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap>
<map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.ebi.ac.uk/Tools/services/soap/wublast?wsdl</wsdl>
- <operation>run</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>run_input</name><inputPorts /><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</class><inputMap /><outputMap><map from="output" to="outp
ut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="&gt;run&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="&gt;run&gt;title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters&gt;program" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters&gt;exp" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters&gt
;alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters&gt;scores" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters&gt;align" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="stats" qname="InputParameters&gt;stats" /><s:basetype optional="true" unbounded="false" typename="string" name="sensitivity" qname="InputParameters&gt;sensitivity" /><s:basetype optional="true" unbounded="false" typename="string" name="topcombon" qname="InputParameters&gt;topcombon" /><s:basetype optional="true" unbounded="false" typename="boolean" name="viewfilter" qname="InputParameters&gt;viewfilter" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputPar
ameters&gt;filter" /><s:basetype optional="true" unbounded="false" typename="string" name="strand" qname="InputParameters&gt;strand" /><s:basetype optional="true" unbounded="false" typename="string" name="sort" qname="InputParameters&gt;sort" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters&gt;stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters&gt;database"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>email</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>title</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>parameters</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>run_output</name><inputPorts><port><name>input</name><depth>0</depth></port></inputPorts><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity</class><inputMap><map from="input" to="input" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter
.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="runResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}runResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="&gt;runResponse&gt;jobId" /></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>jobId</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/plain'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>xmlSplitter</processor><port>input</port></sink><source type="processor"><processor>wsdl_document</processor><port>queryStatusOutput</port></source></datalink><datalink><sink type="processor"><processor>run</processor><port>parameters</port></sink><source type="processor"><processor>run_input</processor><port>output</port></source></datalink><datalink><sink typ
e="processor"><processor>run_output</processor><port>input</port></sink><source type="processor"><processor>run</processor><port>parameters</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>48fbf225-4742-47c4-830d-ecf9a2011021</identification>
- </annotationBean>
- <date>2010-07-21 13:51:40.494 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationA
<TRUNCATED>
[12/52] [abbrv] incubator-taverna-language git commit: Removed
outdated taverna-scufl2-rdf
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.rdf b/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.rdf
deleted file mode 100644
index aa4b3a4..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.rdf
+++ /dev/null
@@ -1,112 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:beanshell="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#"
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <Profile rdf:about="tavernaWorkbench/">
- <activatesConfiguration rdf:resource="tavernaWorkbench/configuration/Hello"/>
- <name>tavernaWorkbench</name>
- <processorBinding rdf:resource="tavernaWorkbench/binding/Hello"/>
- <recommendsEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/workbench/"/>
- </recommendsEnvironment>
- <requiresEnvironment rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Environment"/>
- <workflowPlugin rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#plugin"/>
- <workflowProduct rdf:resource="http://ns.taverna.org.uk/2010/taverna/"/>
- </requiresEnvironment>
- <dc:creator>Stian Soiland-Reyes</dc:creator>
- <dc:date>2010-07-29</dc:date>
- <dc:description>A profile for invoking the workflow on the Taverna Workbench</dc:description>
- </Profile>
-
- <beanshell:Activity rdf:about="tavernaWorkbench/activity/HelloScript/">
- <inputActivityPort rdf:resource="tavernaWorkbench/activity/HelloScript/in/personName"/>
- <outputActivityPort rdf:resource="tavernaWorkbench/activity/HelloScript/out/hello"/>
- </beanshell:Activity>
-
- <InputActivityPort rdf:about="tavernaWorkbench/activity/HelloScript/in/personName">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>personName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputActivityPort>
-
- <OutputActivityPort rdf:about="tavernaWorkbench/activity/HelloScript/out/hello">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>hello</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </OutputActivityPort>
-
- <ProcessorBinding rdf:about="tavernaWorkbench/binding/Hello">
- <boundActivity rdf:resource="tavernaWorkbench/activity/HelloScript/"/>
- <boundProcessor rdf:resource="../workflow/HelloWorld/processor/Hello/"/>
- <inputPortBinding rdf:parseType="Resource">
- <bindsInputActivityPort rdf:resource="tavernaWorkbench/activity/HelloScript/in/personName"/>
- <bindsInputProcessorPort rdf:resource="../workflow/HelloWorld/processor/Hello/in/name"/>
- </inputPortBinding>
- <outputPortBinding rdf:parseType="Resource">
- <bindsOutputActivityPort rdf:resource="tavernaWorkbench/activity/HelloScript/out/hello"/>
- <bindsOutputProcessorPort rdf:resource="../workflow/HelloWorld/processor/Hello/out/greeting"/>
- </outputPortBinding>
- </ProcessorBinding>
-
- <beanshell:Configuration rdf:about="tavernaWorkbench/configuration/Hello">
- <configures rdf:resource="tavernaWorkbench/activity/HelloScript/"/>
- <beanshell:script>
- import javax.swing.JOptionPane;
-
- hello = "Hello, " + personName;
- JOptionPane.showMessageDialog(null, hello, "Greeting",
- JOptionPane.INFORMATION_MESSAGE);
- </beanshell:script>
- </beanshell:Configuration>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Activity">
- <configurationType rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- </owl:Class>
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration">
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- </owl:Class>
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#script">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
- <required rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</required>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/taverna/activities/beanshell#Configuration"/>
- <rdfs:label>script</rdfs:label>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#script"/>
- </owl:DatatypeProperty>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl b/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl
deleted file mode 100644
index 42c7eb1..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl
+++ /dev/null
@@ -1,86 +0,0 @@
-@base <tavernaWorkbench/> .
-@prefix beanshell: <http://ns.taverna.org.uk/2010/taverna/activities/beanshell#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-
-<.>
- a scufl2:Profile;
- scufl2:name "tavernaWorkbench" ;
- dc:description """A profile for invoking the workflow on the Taverna Workbench""" ;
- dc:creator "Stian Soiland-Reyes" ;
- dc:date "2010-07-29" ;
- scufl2:processorBinding <binding/Hello> ;
- scufl2:activatesConfiguration <configuration/Hello> ;
- scufl2:recommendsEnvironment [
- a scufl2:Environment;
- scufl2:workflowProduct <http://ns.taverna.org.uk/2010/taverna/workbench/>
- ] ;
- scufl2:requiresEnvironment [
- a scufl2:Environment;
- scufl2:workflowProduct <http://ns.taverna.org.uk/2010/taverna/>;
- scufl2:workflowPlugin beanshell:plugin
- ] .
-
-
-<binding/Hello> a scufl2:ProcessorBinding ;
- scufl2:boundProcessor <../../workflow/HelloWorld/processor/Hello/> ;
- scufl2:boundActivity <activity/HelloScript/> ;
- scufl2:inputPortBinding [
- scufl2:bindsInputProcessorPort <../../workflow/HelloWorld/processor/Hello/in/name> ;
- scufl2:bindsInputActivityPort <activity/HelloScript/in/personName>
- ] ;
- scufl2:outputPortBinding [
- scufl2:bindsOutputActivityPort <activity/HelloScript/out/hello> ;
- scufl2:bindsOutputProcessorPort <../../workflow/HelloWorld/processor/Hello/out/greeting>
- ] .
-
-
-<activity/HelloScript/> a beanshell:Activity ;
- scufl2:inputActivityPort <activity/HelloScript/in/personName> ;
- scufl2:outputActivityPort <activity/HelloScript/out/hello> .
-
-<activity/HelloScript/in/personName> a scufl2:InputActivityPort ;
- scufl2:name "personName";
- scufl2:portDepth 0 ;
- scufl2:granularPortDepth 0 .
-
-<activity/HelloScript/out/hello> a scufl2:OutputActivityPort ;
- scufl2:name "hello";
- scufl2:portDepth 0 ;
- scufl2:granularPortDepth 0 .
-
-
-<configuration/Hello> a beanshell:Configuration;
- scufl2:configures <activity/HelloScript/> ;
- beanshell:script """
- import javax.swing.JOptionPane;
-
- hello = "Hello, " + personName;
- JOptionPane.showMessageDialog(null, hello, "Greeting",
- JOptionPane.INFORMATION_MESSAGE);
- """ .
-
-
-# Define possible configurations for a beanshell
-
-beanshell:Activity a owl:Class;
- rdfs:subClassOf scufl2:Activity ;
- scufl2:configurationType beanshell:Configuration .
-
-beanshell:Configuration a owl:Class ;
- rdfs:subClassOf scufl2:Configuration .
-
-beanshell:script
- a owl:DatatypeProperty, owl:FunctionalProperty ;
- rdfs:domain beanshell:Configuration;
- rdfs:label "script" ;
- rdfs:range xsd:string ;
- scufl2:required true ;
- rdfs:subPropertyOf scufl2:script .
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.rdf b/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.rdf
deleted file mode 100644
index a27c9a1..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.rdf
+++ /dev/null
@@ -1,92 +0,0 @@
-<?xml version="1.0"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <Workflow rdf:about="HelloWorld/">
- <datalink rdf:resource="HelloWorld/datalink/5"/>
- <datalink rdf:resource="HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0"/>
- <datalink rdf:parseType="Resource">
- <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <receivesFrom rdf:resource="HelloWorld/in/yourName"/>
- <sendsTo rdf:resource="HelloWorld/processor/Hello/in/name"/>
- </datalink>
- <inputWorkflowPort rdf:resource="HelloWorld/in/yourName"/>
- <name>Helloworld</name>
- <outputWorkflowPort rdf:resource="HelloWorld/out/results"/>
- <processor rdf:resource="HelloWorld/processor/Hello"/>
- <workflowIdentifier rdf:resource="http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/"/>
- <rdfs:seeAlso rdf:resource="annotation/workflow/HelloWorld.ttl"/>
- </Workflow>
-
- <DataLink rdf:about="HelloWorld/datalink/5">
- <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</mergePosition>
- <receivesFrom rdf:resource="HelloWorld/in/yourName"/>
- <sendsTo rdf:resource="HelloWorld/out/results"/>
- </DataLink>
-
- <DataLink rdf:about="HelloWorld/datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0">
- <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</mergePosition>
- <receivesFrom rdf:resource="HelloWorld/processor/Hello/out/greeting"/>
- <sendsTo rdf:resource="HelloWorld/out/results"/>
- </DataLink>
-
- <InputWorkflowPort rdf:about="HelloWorld/in/yourName">
- <name>yourName</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputWorkflowPort>
-
- <OutputWorkflowPort rdf:about="HelloWorld/out/results">
- <name>results</name>
- </OutputWorkflowPort>
-
- <Processor rdf:about="HelloWorld/processor/Hello">
- <dispatchStack rdf:resource="http://ns.taverna.org.uk/2010/scufl2/taverna#defaultDispatchStack"/>
- <inputProcessorPort rdf:resource="HelloWorld/processor/Hello/in/name"/>
- <iterationStrategyStack rdf:parseType="Resource">
- <rdf:first rdf:resource="HelloWorld/processor/Hello/iterationStrategy/0"/>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </iterationStrategyStack>
- <name>Hello</name>
- <outputProcessorPort rdf:resource="HelloWorld/processor/Hello/out/greeting"/>
- </Processor>
-
- <InputProcessorPort rdf:about="HelloWorld/processor/Hello/in/name">
- <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
- <name>name</name>
- <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
- </InputProcessorPort>
-
- <CrossProduct rdf:about="HelloWorld/processor/Hello/iterationStrategy/0">
- <iterationStrategyChildren rdf:parseType="Resource">
- <rdf:first rdf:resource="HelloWorld/processor/Hello/in/name"/>
- <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
- </iterationStrategyChildren>
- </CrossProduct>
-
- <OutputProcessorPort rdf:about="HelloWorld/processor/Hello/out/greeting">
- <name>greeting</name>
- </OutputProcessorPort>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.ttl b/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.ttl
deleted file mode 100644
index 74bc436..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/workflow/HelloWorld.ttl
+++ /dev/null
@@ -1,59 +0,0 @@
-@base <HelloWorld/> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix taverna: <http://ns.taverna.org.uk/2010/scufl2/taverna#>.
-
-
-<>
- a scufl2:Workflow ;
- scufl2:name "Helloworld" ;
- scufl2:workflowIdentifier <http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/> ;
- scufl2:inputWorkflowPort <in/yourName> ;
- scufl2:outputWorkflowPort <out/results> ;
- scufl2:datalink _:datalink1, <datalink/5>, <datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0> ;
- scufl2:processor <processor/Hello> ;
- rdfs:seeAlso <../annotation/workflow/HelloWorld.ttl> .
-
-<in/yourName> a scufl2:InputWorkflowPort ;
- scufl2:name "yourName" ;
- scufl2:portDepth 0 .
-
-<out/results> a scufl2:OutputWorkflowPort ;
- scufl2:name "results" .
-
-_:datalink1 a scufl2:DataLink ;
- scufl2:receivesFrom <in/yourName> ;
- scufl2:sendsTo <processor/Hello/in/name> .
-
-<datalink/5> a scufl2:DataLink ;
- scufl2:receivesFrom <in/yourName> ;
- scufl2:sendsTo <out/results> ;
- scufl2:mergePosition 1 .
-
-<datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0> a scufl2:DataLink ;
- scufl2:receivesFrom <processor/Hello/out/greeting> ;
- scufl2:sendsTo <out/results> ;
- scufl2:mergePosition 0 .
-
-<processor/Hello> a scufl2:Processor ;
- scufl2:name "Hello" ;
- scufl2:inputProcessorPort <processor/Hello/in/name> ;
- scufl2:outputProcessorPort <processor/Hello/out/greeting> ;
- scufl2:dispatchStack taverna:defaultDispatchStack ;
- scufl2:iterationStrategyStack (<processor/Hello/iterationStrategy/0>) .
-
-<processor/Hello/in/name> a scufl2:InputProcessorPort ;
- scufl2:name "name";
- scufl2:portDepth 0 .
-
-
-<processor/Hello/out/greeting> a scufl2:OutputProcessorPort ;
- scufl2:name "greeting";
- scufl2:portDepth 0 ;
- scufl2:granularPortDepth 0 .
-
-
-<processor/Hello/iterationStrategy/0> a scufl2:CrossProduct;
- scufl2:iterationStrategyChildren ( <processor/Hello/in/name> ) .
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.rdf b/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.rdf
deleted file mode 100644
index 78d0c05..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.rdf
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version='1.0'?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-
-
-<!-- Processed by Id: cwm.py,v 1.197 2007/12/13 15:38:39 syosi Exp -->
-<!-- using base file:///home/stain/stuff/src/workspace/scufl2/scufl2-rdf/src/main/resources/example/workflowBundle.ttl-->
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#">
-
- <WorkflowBundle rdf:about="./">
- <mainWorkflow rdf:resource="workflow/HelloWorld/"/>
- <name>Hello world</name>
- <profile rdf:resource="profile/tavernaWorkbench/"/>
- <sameBaseAs rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/"/>
- <workflow rdf:resource="workflow/HelloWorld/"/>
- <rdf:seeAlso rdf:resource="annotation/workflowBundle.ttl"/>
- </WorkflowBundle>
-
- <rdf:Description rdf:about="profile/tavernaWorkbench/">
- <rdfs:seeAlso rdf:resource="profile/tavernaWorkbench.ttl"/>
- </rdf:Description>
-
- <rdf:Description rdf:about="workflow/HelloWorld/">
- <rdfs:seeAlso rdf:resource="workflow/HelloWorld.ttl"/>
- </rdf:Description>
-</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.ttl b/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.ttl
deleted file mode 100644
index 8852edc..0000000
--- a/taverna-scufl2-rdf/src/test/resources/example/workflowBundle.ttl
+++ /dev/null
@@ -1,16 +0,0 @@
-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-
-<.>
- a scufl2:WorkflowBundle ;
- scufl2:sameBaseAs <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/> ;
- scufl2:name "Hello world" ;
- scufl2:workflow <workflow/HelloWorld/> ;
- scufl2:mainWorkflow <workflow/HelloWorld/> ;
- scufl2:profile <profile/tavernaWorkbench/> ;
- rdf:seeAlso <annotation/workflowBundle.ttl> .
-
-<workflow/HelloWorld/> rdfs:seeAlso <workflow/HelloWorld.ttl> .
-<profile/tavernaWorkbench/> rdfs:seeAlso <profile/tavernaWorkbench.ttl> .
[47/52] [abbrv] incubator-taverna-language git commit: Merge pull
request #5 from dkfellows/master
Posted by st...@apache.org.
Merge pull request #5 from dkfellows/master
More test improvements
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/ff86717a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/ff86717a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/ff86717a
Branch: refs/heads/master
Commit: ff86717a5aed98a2b42e6607fde48cee33b50156
Parents: 414cd6a 9236e2c
Author: Alan R Williams <al...@manchester.ac.uk>
Authored: Thu Feb 12 15:45:50 2015 +0000
Committer: Alan R Williams <al...@manchester.ac.uk>
Committed: Thu Feb 12 15:45:50 2015 +0000
----------------------------------------------------------------------
pom.xml | 4 +-
.../taverna/databundle/TestFullExample.java | 77 +-
.../apache/taverna/robundle/TestExample.java | 21 +-
.../taverna/robundle/manifest/TestManifest.java | 17 +-
.../robundle/manifest/TestManifestJSON.java | 2 +-
.../manifest/combine/TestCombineManifest.java | 22 +-
.../examples/TestConvertT2flowScufl2.java | 4 +-
.../apache/taverna/examples/TestJsonExport.java | 5 +-
.../taverna/examples/TestProcessorNames.java | 5 +-
.../taverna/examples/TestServiceTypes.java | 3 -
.../workflows/t2flow/annotated2.2.t2flow | 216 -
...tion_of_configurable_iteration_114130.t2flow | 352 -
.../fetch_today_s_xkcd_comic_568671.t2flow | 349 -
.../resources/workflows/t2flow/merge_fun.t2flow | 83 -
.../pipelined_list_iteration_902021.t2flow | 320 -
.../workflows/wfbundle/annotated2.wfbundle | Bin 11754 -> 0 bytes
...on_of_configurable_iteration_114130.wfbundle | Bin 12741 -> 0 bytes
.../fetch_today_s_xkcd_comic_568671.wfbundle | Bin 13365 -> 0 bytes
.../workflows/wfbundle/helloanyone.wfbundle | Bin 11998 -> 0 bytes
.../workflows/wfbundle/helloworld.wfbundle | Bin 9856 -> 0 bytes
.../workflows/wfbundle/merge_fun.wfbundle | Bin 9698 -> 0 bytes
.../pipelined_list_iteration_902021.wfbundle | Bin 13480 -> 0 bytes
.../taverna/scufl2/wfdesc/TestAllTypes.java | 29 +-
.../scufl2/wfdesc/TestAnnotationQuoting.java | 4 +-
.../taverna/scufl2/wfdesc/TestNested.java | 23 +-
.../scufl2/wfdesc/TestRoEvoSerializer.java | 10 +-
.../scufl2/wfdesc/TestSemanticAnnotations.java | 2 +-
.../src/test/resources/3582.t2flow | 1677 ---
.../src/test/resources/3582.wfdesc.ttl | 659 --
.../test/resources/allTypes.types.sparql.json | 77 -
.../src/test/resources/allTypes.wfdesc.ttl | 212 -
.../src/test/resources/enm-v21.wfdesc.ttl | 10323 -----------------
.../src/test/resources/helloanyone.wfdesc.ttl | 66 -
.../test/resources/localdependency.wfdesc.ttl | 26 -
.../src/test/resources/nested.wfdesc.ttl | 126 -
.../rdf-in-example-annotation.wfdesc.ttl | 25 -
...alid_component_imagemagickconvert.wfdesc.ttl | 112 -
37 files changed, 107 insertions(+), 14744 deletions(-)
----------------------------------------------------------------------
[15/52] [abbrv] incubator-taverna-language git commit: Removed
outdated taverna-scufl2-rdf
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/main/resources/scufl2.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/main/resources/scufl2.rdf b/taverna-scufl2-rdf/src/main/resources/scufl2.rdf
deleted file mode 100644
index 5f1f7a3..0000000
--- a/taverna-scufl2-rdf/src/main/resources/scufl2.rdf
+++ /dev/null
@@ -1,1663 +0,0 @@
-<?xml version="1.0"?>
-
-<!--
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements. See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership. The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied. See the License for the
-specific language governing permissions and limitations
-under the License.
--->
-
-
-
-<!DOCTYPE rdf:RDF [
- <!ENTITY dcterms "http://purl.org/dc/terms/" >
- <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
- <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
- <!ENTITY xml "http://www.w3.org/XML/1998/namespace" >
- <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
- <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
-]>
-
-
-<rdf:RDF xmlns="http://ns.taverna.org.uk/2010/scufl2#"
- xml:base="http://ns.taverna.org.uk/2010/scufl2"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:xml="http://www.w3.org/XML/1998/namespace"
- xmlns:dcterms="http://purl.org/dc/terms/">
- <owl:Ontology rdf:about="http://ns.taverna.org.uk/2010/scufl2">
- <rdfs:label xml:lang="en">SCUFL2 Core ontology</rdfs:label>
- <rdfs:comment xml:lang="en">The ontology defining SCUFL2 - a model for describing Taverna workflows.</rdfs:comment>
- <rdfs:seeAlso rdf:resource="http://www.mygrid.org.uk/dev/wiki/display/developer/Scufl2+Ontology"/>
- <rdfs:seeAlso rdf:resource="http://www.taverna.org.uk/"/>
- </owl:Ontology>
-
-
-
- <!--
- ///////////////////////////////////////////////////////////////////////////////////////
- //
- // Object Properties
- //
- ///////////////////////////////////////////////////////////////////////////////////////
- -->
-
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#activateConfiguration -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#activateConfiguration">
- <rdfs:label xml:lang="en">activate configuration</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#activityPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#activityPort">
- <rdfs:label xml:lang="en">Activity port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ActivityPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#port"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bind -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bind">
- <rdf:type rdf:resource="&owl;AsymmetricProperty"/>
- <rdf:type rdf:resource="&owl;IrreflexiveProperty"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- <rdfs:domain>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#PortBinding"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:domain>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindActivity -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindActivity">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind activity</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bind"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindInputActivityPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindInputActivityPort">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind input activity port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputPortBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindInputProcessorPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindInputProcessorPort">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind input processor port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputPortBinding"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindOutputActivityPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindOutputActivityPort">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind output activity port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindOutputProcessorPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindOutputProcessorPort">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind output processor port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindPort">
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#PortBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bind"/>
- <rdfs:range>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#ActivityPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:range>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#bindProcessor -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#bindProcessor">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">bind processor</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bind"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#block -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#block">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Blocking"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#controlledProcessor"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#child -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#child">
- <rdf:type rdf:resource="&owl;AsymmetricProperty"/>
- <rdf:type rdf:resource="&owl;InverseFunctionalProperty"/>
- <rdf:type rdf:resource="&owl;IrreflexiveProperty"/>
- <rdfs:label xml:lang="en">child</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Parent"/>
- <owl:inverseOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- <rdfs:subPropertyOf rdf:resource="&dcterms;hasPart"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#configure -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#configure">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">configure</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configurable"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configuration"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#control -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#control">
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Control"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#controlledProcessor -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#controlledProcessor">
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Control"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#controllingProcessor -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#controllingProcessor">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">controlling processor</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Control"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#datalink -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#datalink">
- <rdfs:label xml:lang="en">datalink</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#dispatchStack -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#dispatchStack">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">dispatch stack</rdfs:label>
- <owl:deprecated rdf:datatype="&xsd;boolean">true</owl:deprecated>
- <rdfs:comment xml:lang="en">Dispatch stack has been deprecated in favour of configuring the Processor</rdfs:comment>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStack"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#globalBaseURI -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#globalBaseURI">
- <rdf:type rdf:resource="&owl;ReflexiveProperty"/>
- <rdf:type rdf:resource="&owl;SymmetricProperty"/>
- <rdf:type rdf:resource="&owl;TransitiveProperty"/>
- <rdfs:comment>The resources are the same (like in owl:sameAs), and
- so are the sub-resources having the same base URI as a parent. For instance if
- <file:///tmp/example/> scufl2:globalBaseURI
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/> .
- then also
- <file:///tmp/example/workflow/HelloWorld/> scufl2:globalBaseURI
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>
-
- Note that for URIs under
- <http://ns.taverna.org.uk/2010/workflowBundle/> special URI template rules
- link the URI with the scufl2:parent, rdf:type, scufl2:name of the
- resource.
-
- For instance given
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>
- it must be so that:
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>
- a scufl2:OutputProcessorPort;
- scufl2:name "greeting";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>
- a scufl2:Processor;
- scufl2:name "Hello";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>;
- scufl2:outputProcessorPort <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello/out/greeting>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>
- a scufl2:Workflow;
- scufl2:name "HelloWorld";
- scufl2:parent <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/>;
- sculf2:processor <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/processor/Hello>.
-
- <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/>
- a scufl2:WorkflowBundle;
- scufl2:workflow <http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/HelloWorld/>;
- scufl2:workflowBundleId "28f7c554-4f35-401f-b34b-516e9a0ef731";
-
- Where 28f7c554-4f35-401f-b34b-516e9a0ef731 must be a randomly
- generated UUID.
- </rdfs:comment>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#inputActivityPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#inputActivityPort">
- <rdfs:label xml:lang="en">input acticity port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#activityPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#inputPortBinding -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#inputPortBinding">
- <rdfs:label xml:lang="en">input port binding</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputPortBinding"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#inputProcessorPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#inputProcessorPort">
- <rdfs:label xml:lang="en">input processor port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#processorPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#inputWorkflowPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#inputWorkflowPort">
- <rdfs:label xml:lang="en">input workflow port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#iterateOverInputPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#iterateOverInputPort">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#PortNode"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#iterationStrategyStack -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#iterationStrategyStack">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">iteration strategy stack</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyStack"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#mainProfile -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#mainProfile">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">main profile</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#profile"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#mainWorkflow -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#mainWorkflow">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">main workflow</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflow"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#outputActivityPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#outputActivityPort">
- <rdfs:label xml:lang="en">output activity port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#activityPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#outputPortBinding -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#outputPortBinding">
- <rdfs:label xml:lang="en">output port binding</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#outputProcessorPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#outputProcessorPort">
- <rdfs:label xml:lang="en">output processor port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#processorPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#outputWorkflowPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#outputWorkflowPort">
- <rdfs:label xml:lang="en">output workflow port</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowPort"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#parent -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">parent</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Parent"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- <rdfs:subPropertyOf rdf:resource="&dcterms;isPartOf"/>
- <owl:propertyChainAxiom rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#controlledProcessor"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- </owl:propertyChainAxiom>
- <owl:propertyChainAxiom rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#sendTo"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- </owl:propertyChainAxiom>
- <owl:propertyChainAxiom rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#controllingProcessor"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- </owl:propertyChainAxiom>
- <owl:propertyChainAxiom rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#receiveFrom"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- </owl:propertyChainAxiom>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#port -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#port">
- <rdfs:label xml:lang="en">port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Parent"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- <rdfs:domain>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:domain>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#processor -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#processor">
- <rdfs:label xml:lang="en">processor</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#processorBinding -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#processorBinding">
- <rdfs:label xml:lang="en">processor binding</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#processorPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#processorPort">
- <rdfs:label xml:lang="en">processor port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#port"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#productOf -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#productOf">
- <rdfs:label xml:lang="en">product of</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#profile -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#profile">
- <rdfs:label xml:lang="en">profile</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#receiveFrom -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#receiveFrom">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">receive from</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#SenderPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#sendTo -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#sendTo">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">send to</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ReceiverPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#untilFinished -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#untilFinished">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">until finished</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Blocking"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#controllingProcessor"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#workflow -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#workflow">
- <rdfs:label xml:lang="en">workflow</rdfs:label>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#child"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">workflow identifier</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowRelation"/>
- <rdfs:subPropertyOf rdf:resource="&dcterms;isVersionOf"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#workflowPort -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#workflowPort">
- <rdfs:label xml:lang="en">workflow port</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowPort"/>
- <rdfs:subPropertyOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#port"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#workflowRelation -->
-
- <owl:ObjectProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#workflowRelation">
- <rdfs:label xml:lang="en">workflow relation</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:range rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subPropertyOf rdf:resource="&dcterms;relation"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://purl.org/dc/terms/hasPart -->
-
- <owl:ObjectProperty rdf:about="&dcterms;hasPart">
- <rdfs:isDefinedBy rdf:resource="http://purl.org/dc/terms/"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://purl.org/dc/terms/isPartOf -->
-
- <owl:ObjectProperty rdf:about="&dcterms;isPartOf">
- <rdfs:isDefinedBy rdf:resource="http://purl.org/dc/terms/"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://purl.org/dc/terms/isVersionOf -->
-
- <owl:ObjectProperty rdf:about="&dcterms;isVersionOf">
- <rdfs:isDefinedBy rdf:resource="http://purl.org/dc/terms/"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://purl.org/dc/terms/relation -->
-
- <owl:ObjectProperty rdf:about="&dcterms;relation">
- <rdfs:isDefinedBy rdf:resource="http://purl.org/dc/terms/"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#first -->
-
- <owl:ObjectProperty rdf:about="&rdf;first">
- <rdfs:isDefinedBy rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
- </owl:ObjectProperty>
-
-
-
- <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#rest -->
-
- <owl:ObjectProperty rdf:about="&rdf;rest">
- <rdfs:isDefinedBy rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
- </owl:ObjectProperty>
-
-
-
- <!--
- ///////////////////////////////////////////////////////////////////////////////////////
- //
- // Data properties
- //
- ///////////////////////////////////////////////////////////////////////////////////////
- -->
-
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#activityPosition -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#activityPosition">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">activity position</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- <rdfs:range rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#desiredDepth -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#desiredDepth">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">desired depth</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#PortNode"/>
- <rdfs:range rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#granularPortDepth -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#granularPortDepth">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">granular port depth</rdfs:label>
- <rdfs:range rdf:resource="&xsd;nonNegativeInteger"/>
- <rdfs:domain>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:domain>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#mergePosition -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#mergePosition">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">merge position</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DataLink"/>
- <rdfs:range rdf:resource="&xsd;integer"/>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#name -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#name">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">name</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subPropertyOf rdf:resource="&dcterms;identifier"/>
- <rdfs:range rdf:resource="&xsd;string"/>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#portDepth -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#portDepth">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">port depth</rdfs:label>
- <rdfs:range rdf:resource="&xsd;nonNegativeInteger"/>
- <rdfs:domain>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:domain>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#profilePosition -->
-
- <owl:DatatypeProperty rdf:about="http://ns.taverna.org.uk/2010/scufl2#profilePosition">
- <rdf:type rdf:resource="&owl;FunctionalProperty"/>
- <rdfs:label xml:lang="en">profile position</rdfs:label>
- <rdfs:domain rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- <rdfs:range rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:DatatypeProperty>
-
-
-
- <!-- http://purl.org/dc/terms/identifier -->
-
- <owl:DatatypeProperty rdf:about="&dcterms;identifier"/>
-
-
-
- <!--
- ///////////////////////////////////////////////////////////////////////////////////////
- //
- // Classes
- //
- ///////////////////////////////////////////////////////////////////////////////////////
- -->
-
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Activity -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Activity">
- <rdfs:label xml:lang="en">Activity</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configurable"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#ActivityPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#ActivityPort">
- <rdfs:label xml:lang="en">Activity Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Blocking -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Blocking">
- <rdfs:label xml:lang="en">Blocking</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Control"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#block"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#untilFinished"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Child -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Child">
- <rdfs:label xml:lang="en">Child</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:onClass rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Parent"/>
- <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">0</owl:minQualifiedCardinality>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">A WorkflowElement which can be considered a child, for instance a Processor is a child of a Workflow, an InputActivityPort is a child of an Activity.
-
-The Child-relationship also gives a strong hint that the entity should be serialised as part of its parent's serialisation.</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Configurable -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Configurable">
- <rdfs:label xml:lang="en">Configurable</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Configuration -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Configuration">
- <rdfs:label xml:lang="en">Configuration</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#configure"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configurable"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Control -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Control">
- <rdfs:label xml:lang="en">Control</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#controllingProcessor"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#controlledProcessor"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#CrossProduct -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#CrossProduct">
- <rdfs:label xml:lang="en">Cross Product</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Product"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#DataLink -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#DataLink">
- <rdfs:label xml:lang="en">Data Link</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#receiveFrom"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#sendTo"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#DispatchStack -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#DispatchStack">
- <rdfs:label xml:lang="en">Dispatch Stack</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf rdf:resource="&rdf;List"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;first"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStack"/>
- </owl:Restriction>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:hasValue rdf:resource="&rdf;nil"/>
- </owl:Restriction>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <owl:deprecated rdf:datatype="&xsd;boolean">true</owl:deprecated>
- <rdfs:comment xml:lang="en">Dispatch stack has been deprecated in favour of configuring the Processor.</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#DispatchStackLayer">
- <rdfs:label xml:lang="en">Dispatch Stack Layer</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configurable"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#DispatchStack"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <owl:deprecated rdf:datatype="&xsd;boolean">true</owl:deprecated>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#DotProduct -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#DotProduct">
- <rdfs:label xml:lang="en">Dot Product</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Product"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#InputActivityPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort">
- <rdfs:label xml:lang="en">Input Activity Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ActivityPort"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#portDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <owl:disjointWith rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#InputPortBinding -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputPortBinding">
- <rdfs:label xml:lang="en">Input Port Binding</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#PortBinding"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindInputProcessorPort"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindInputActivityPort"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputActivityPort"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <owl:disjointWith rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort">
- <rdfs:label xml:lang="en">Input Processor Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ReceiverPort"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#portDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort">
- <rdfs:label xml:lang="en">Input Workflow Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#SenderPort"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowPort"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#portDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">An input to the workflow, representing a parameter required to run the workflow.
-
-This is considered a SenderPort within the workflow, so that it can be connected to InputProcessorPort of processors contained by the same workflow.</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#IterationStrategyChildren -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyChildren">
- <rdfs:label xml:lang="en">Iteration Strategy Children</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf rdf:resource="&rdf;List"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyChildren"/>
- </owl:Restriction>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:hasValue rdf:resource="&rdf;nil"/>
- </owl:Restriction>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;first"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode">
- <rdfs:label xml:lang="en">Iteration Strategy Node</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#IterationStrategyStack -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyStack">
- <rdfs:label xml:lang="en">Iteration Strategy Stack</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf rdf:resource="&rdf;List"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyStack"/>
- </owl:Restriction>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;rest"/>
- <owl:hasValue rdf:resource="&rdf;nil"/>
- </owl:Restriction>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="&rdf;first"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Product"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Named -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Named">
- <rdfs:label xml:lang="en">Named</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#name"/>
- <owl:someValuesFrom rdf:resource="&xsd;string"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">Anything identified with a scufl2:name</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#NamedChild -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#NamedChild">
- <rdfs:label xml:lang="en">Named Child</rdfs:label>
- <owl:equivalentClass>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Parent"/>
- </owl:Restriction>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#name"/>
- <owl:someValuesFrom rdf:resource="&xsd;string"/>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:equivalentClass>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:comment xml:lang="en">Any Named Child is uniquely identified by its scufl2:name and scufl2:parent</rdfs:comment>
- <owl:hasKey rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#name"/>
- </owl:hasKey>
- <owl:hasKey rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- </owl:hasKey>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort">
- <rdfs:label xml:lang="en">Output Activity Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ActivityPort"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#granularPortDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#portDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding">
- <rdfs:label xml:lang="en">Output Port binding</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#PortBinding"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindOutputActivityPort"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputActivityPort"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindOutputProcessorPort"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort">
- <rdfs:label xml:lang="en">Output Processor Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#SenderPort"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#granularPortDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#portDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort">
- <rdfs:label xml:lang="en">Output Workflow Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ReceiverPort"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowPort"/>
- <rdfs:comment xml:lang="en">An output from the workflow, representing the defined results of the workflow.
-
-This is considered a ReceiverPort within the workflow, so that it can be connected from OutputProcessorPort of processors contained by the same workflow.</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Parent -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Parent">
- <rdfs:label xml:lang="en">Parent</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Port -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Port">
- <rdfs:label xml:lang="en">Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#name"/>
- <owl:someValuesFrom rdf:resource="&xsd;string"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#ActivityPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#WorkflowPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">A port is an input or output to a Processor, Workflow or Activity. </rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#PortBinding -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#PortBinding">
- <rdfs:label xml:lang="en">Port Binding</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputPortBinding"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputPortBinding"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#PortNode -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#PortNode">
- <rdfs:label xml:lang="en">Port Node</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#iterateOverInputPort"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#desiredDepth"/>
- <owl:someValuesFrom rdf:resource="&xsd;nonNegativeInteger"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Processor -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Processor">
- <rdfs:label xml:lang="en">Processor</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Configurable"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#name"/>
- <owl:someValuesFrom rdf:resource="&xsd;string"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">A processor is a unit of a Workflow which performs some work. It typically have some InputProcessorPorts and OutputProcessorPorts which are connected to other Ports within the workflow. A processor will start executing as soon as there is a value for each InputProcessorPort and there are no Blocking processors.
-
-A processor is bound to an Activity which specifies how to execute the task. This ProcessorBinding also specifies PortBindings to map ActivityPorts with ProcessorPorts.</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#ProcessorBinding">
- <rdfs:label xml:lang="en">Processor Binding</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindProcessor"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#bindActivity"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Activity"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Profile"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#ProcessorPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#ProcessorPort">
- <rdfs:label xml:lang="en">Processor Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Processor"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Product -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Product">
- <rdfs:label xml:lang="en">Product</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyNode"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#CrossProduct"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#DotProduct"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#productOf"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#IterationStrategyChildren"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Profile -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Profile">
- <rdfs:label xml:lang="en">Profile</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Child"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:allValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#ReceiverPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#ReceiverPort">
- <rdfs:label xml:lang="en">Receiver Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputProcessorPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <owl:disjointWith rdf:resource="http://ns.taverna.org.uk/2010/scufl2#SenderPort"/>
- <rdfs:comment xml:lang="en">A Port which can receive data from a DataLink</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#SenderPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#SenderPort">
- <rdfs:label xml:lang="en">Sender Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputProcessorPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">A Port which can send data to a DataLink</rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#Workflow -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#Workflow">
- <rdfs:label xml:lang="en">Workflow</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#name"/>
- <owl:someValuesFrom rdf:resource="&xsd;string"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier"/>
- <owl:someValuesFrom rdf:resource="&owl;Thing"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <owl:hasKey rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#workflowIdentifier"/>
- </owl:hasKey>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle">
- <rdfs:label xml:lang="en">Workflow Bundle</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Named"/>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#globalBaseURI"/>
- <owl:onClass rdf:resource="http://ns.taverna.org.uk/2010/scufl2#WorkflowBundle"/>
- <owl:minQualifiedCardinality rdf:datatype="&xsd;nonNegativeInteger">0</owl:minQualifiedCardinality>
- </owl:Restriction>
- </rdfs:subClassOf>
- <owl:hasKey rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#globalBaseURI"/>
- </owl:hasKey>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#WorkflowElement -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#WorkflowElement">
- <rdfs:label xml:lang="en">Workflow Element</rdfs:label>
- <rdfs:comment xml:lang="en">Any element that defines a workflow, such as a processor, port, datalink, activity, port binding, profile.
-
-Super-class for any Scufl2 class. </rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://ns.taverna.org.uk/2010/scufl2#WorkflowPort -->
-
- <owl:Class rdf:about="http://ns.taverna.org.uk/2010/scufl2#WorkflowPort">
- <rdfs:label xml:lang="en">Workflow Port</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Port"/>
- <rdfs:subClassOf>
- <owl:Class>
- <owl:unionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#InputWorkflowPort"/>
- <rdf:Description rdf:about="http://ns.taverna.org.uk/2010/scufl2#OutputWorkflowPort"/>
- </owl:unionOf>
- </owl:Class>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://ns.taverna.org.uk/2010/scufl2#parent"/>
- <owl:someValuesFrom rdf:resource="http://ns.taverna.org.uk/2010/scufl2#Workflow"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:comment xml:lang="en">Ports of a Workflow. </rdfs:comment>
- </owl:Class>
-
-
-
- <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#List -->
-
- <owl:Class rdf:about="&rdf;List">
- <rdfs:isDefinedBy rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
- </owl:Class>
-
-
-
- <!--
- ///////////////////////////////////////////////////////////////////////////////////////
- //
- // Individuals
- //
- ///////////////////////////////////////////////////////////////////////////////////////
- -->
-
-
-
-
- <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#nil -->
-
- <owl:NamedIndividual rdf:about="&rdf;nil">
- <rdfs:isDefinedBy rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
- </owl:NamedIndividual>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net -->
-
[16/52] [abbrv] incubator-taverna-language git commit: Removed
outdated taverna-scufl2-rdf
Posted by st...@apache.org.
Removed outdated taverna-scufl2-rdf
see taverna-scufl2-schemas for ontologies
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/db25fe67
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/db25fe67
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/db25fe67
Branch: refs/heads/master
Commit: db25fe67f2de77fe701f363907c5ad4c41ee522b
Parents: 1962ee0
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:12:24 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:12:24 2015 +0000
----------------------------------------------------------------------
taverna-scufl2-rdf/.gitignore | 1 -
taverna-scufl2-rdf/pom.xml | 260 ---
.../uk/org/taverna/scufl2/rdf/RdfWriter.java | 26 -
.../src/main/resources/scufl2.rdf | 1663 -----------------
.../src/main/resources/scufl2.ttl | 1674 ------------------
.../src/main/resources/taverna-2.2.rdf | 143 --
.../src/main/resources/taverna-2.2.ttl | 138 --
.../java/uk/org/taverna/scufl2/rdf/TestRDF.java | 173 --
.../src/test/resources/example.rdf | 281 ---
.../src/test/resources/example.scufl2 | Bin 45060 -> 0 bytes
.../src/test/resources/example.t2flow | 239 ---
.../src/test/resources/example.ttl | 218 ---
.../resources/example/META-INF/container.xml | 34 -
.../resources/example/META-INF/manifest.xml | 45 -
.../resources/example/Thumbnails/thumbnail.png | Bin 19064 -> 0 bytes
.../resources/example/Thumbnails/thumbnail.svg | 91 -
.../example/annotation/workflow/HelloWorld.rdf | 74 -
.../example/annotation/workflow/HelloWorld.ttl | 41 -
.../example/annotation/workflowBundle.rdf | 37 -
.../example/annotation/workflowBundle.ttl | 8 -
.../example/diagram/workflow/HelloWorld.png | Bin 10243 -> 0 bytes
.../example/diagram/workflow/HelloWorld.svg | 91 -
.../src/test/resources/example/mimetype | 1 -
.../resources/example/profile/tavernaServer.rdf | 124 --
.../resources/example/profile/tavernaServer.ttl | 109 --
.../example/profile/tavernaWorkbench.rdf | 112 --
.../example/profile/tavernaWorkbench.ttl | 86 -
.../resources/example/workflow/HelloWorld.rdf | 92 -
.../resources/example/workflow/HelloWorld.ttl | 59 -
.../test/resources/example/workflowBundle.rdf | 49 -
.../test/resources/example/workflowBundle.ttl | 16 -
31 files changed, 5885 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/.gitignore b/taverna-scufl2-rdf/.gitignore
deleted file mode 100644
index ea8c4bf..0000000
--- a/taverna-scufl2-rdf/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/pom.xml b/taverna-scufl2-rdf/pom.xml
deleted file mode 100644
index be24015..0000000
--- a/taverna-scufl2-rdf/pom.xml
+++ /dev/null
@@ -1,260 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-language</artifactId>
- <version>0.15.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-scufl2-rdf</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna Scufl 2 RDF serialisation</name>
-<properties>
- <elmo.version>1.5</elmo.version>
- </properties>
- <build>
- <plugins>
- <plugin>
- <artifactId>maven-antrun-plugin</artifactId>
- <version>1.6</version>
- <executions>
- <execution>
- <phase>generate-sources</phase>
- <configuration>
- <tasks>
- <property name="compile_classpath" refid="maven.compile.classpath" />
- <property name="runtime_classpath" refid="maven.runtime.classpath" />
- <property name="test_classpath" refid="maven.test.classpath" />
- <property name="plugin_classpath" refid="maven.plugin.classpath" />
-
- <!-- inspired by http://openprovenance.org/java/maven-releases/org/openprovenance/opm-elmo/1.1.1/opm-elmo-1.1.1.pom -->
-
- <mkdir dir="${project.build.directory}" />
- <mkdir dir="${project.build.directory}/generated-sources" />
- <mkdir dir="${project.build.directory}/generated-sources/elmo" />
-
- <java classname="org.openrdf.elmo.codegen.OntologyConverter" fork="true" failonerror="true" maxmemory="128m">
- <arg value="-b" />
- <arg value="uk.org.taverna.scufl2.ontology=http://ns.taverna.org.uk/2010/scufl2#" />
- <arg value="-j" />
- <arg value="target/scufl2-ontology.jar" />
- <!-- <arg value="-p" /> <arg value="" /> -->
- <arg value="src/main/resources/scufl2.ttl" />
- <classpath refid="maven.plugin.classpath" />
- <classpath>
- <pathelement path="." />
- </classpath>
- </java>
- <unzip src="${project.build.directory}/scufl2-ontology.jar" dest="${project.build.directory}/generated-sources/elmo">
- <patternset>
- <exclude name="**/*.class" />
- </patternset>
- </unzip>
- </tasks>
- </configuration>
- <goals>
- <goal>run</goal>
- </goals>
- </execution>
- </executions>
- <dependencies>
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-codegen</artifactId>
- <version>1.5</version>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>1.5.2</version> <!-- note old version required for elmo! -->
- </dependency>
- </dependencies>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>build-helper-maven-plugin</artifactId>
- <version>1.8</version>
- <executions>
- <execution>
- <id>add-source</id>
- <phase>generate-sources</phase>
- <goals>
- <goal>add-source</goal>
- <goal>add-resource</goal>
- </goals>
- <configuration>
- <sources>
- <source>${project.build.directory}/generated-sources/elmo/</source>
- </sources>
- <resources>
- <resource>
- <directory>${project.build.directory}/generated-sources/elmo/META-INF</directory>
- <targetPath>META-INF</targetPath>
- </resource>
- </resources>
- </configuration>
- </execution>
- </executions>
- </plugin>
- <plugin>
- <groupId>org.apache.rat</groupId>
- <artifactId>apache-rat-plugin</artifactId>
- </plugin>
- </plugins>
- <pluginManagement>
- <plugins>
- <!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
- <plugin>
- <groupId>org.eclipse.m2e</groupId>
- <artifactId>lifecycle-mapping</artifactId>
- <version>1.0.0</version>
- <configuration>
- <lifecycleMappingMetadata>
- <pluginExecutions>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-antrun-plugin</artifactId>
- <versionRange>[1.6,)</versionRange>
- <goals>
- <goal>run</goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute/>
- </action>
- </pluginExecution>
- <pluginExecution>
- <pluginExecutionFilter>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>build-helper-maven-plugin</artifactId>
- <versionRange>[1.8,)</versionRange>
- <goals>
- <goal>add-source</goal>
- <goal>add-resource</goal>
- </goals>
- </pluginExecutionFilter>
- <action>
- <execute/>
- </action>
- </pluginExecution>
- </pluginExecutions>
- </lifecycleMappingMetadata>
- </configuration>
- </plugin>
- </plugins>
- </pluginManagement>
- </build>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-beanutils</groupId>
- <artifactId>commons-beanutils</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-api</artifactId>
- <version>${elmo.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-sesame</artifactId>
- <version>${elmo.version}</version>
- <exclusions>
- <exclusion>
- <groupId>org.slf4j</groupId>
- <artifactId>jcl104-over-slf4j</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <version>1.7.5</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-dynabean</artifactId>
- <version>${elmo.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.sesame</groupId>
- <artifactId>sesame-repository-sail</artifactId>
- <version>${sesame.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.sesame</groupId>
- <artifactId>sesame-sail-memory</artifactId>
- <version>${sesame.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openrdf.elmo</groupId>
- <artifactId>elmo-codegen</artifactId>
- <version>${elmo.version}</version>
- </dependency>
-
-
- </dependencies>
- <description>Taverna workflow language serialisation as RDF</description>
- <!--
- <repositories>
- <repository>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>aduna-opensource.releases</id>
- <name>Aduna Open Source - Maven releases</name>
- <url>http://repo.aduna-software.org/maven2/releases</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- <id>aduna-opensource.snapshots</id>
- <name>Aduna Open Source - Maven snapshots</name>
- <url>http://repo.aduna-software.org/maven2/snapshots</url>
- </repository>
- </repositories>
- <pluginRepositories>
- <pluginRepository>
- <releases>
- <enabled>true</enabled>
- </releases>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>aduna-opensource.releases</id>
- <name>Aduna Open Source - Maven releases</name>
- <url>http://repo.aduna-software.org/maven2/releases</url>
- </pluginRepository>
- </pluginRepositories>
- -->
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/db25fe67/taverna-scufl2-rdf/src/main/java/uk/org/taverna/scufl2/rdf/RdfWriter.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdf/src/main/java/uk/org/taverna/scufl2/rdf/RdfWriter.java b/taverna-scufl2-rdf/src/main/java/uk/org/taverna/scufl2/rdf/RdfWriter.java
deleted file mode 100644
index 644a146..0000000
--- a/taverna-scufl2-rdf/src/main/java/uk/org/taverna/scufl2/rdf/RdfWriter.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package uk.org.taverna.scufl2.rdf;
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-
-
-public class RdfWriter {
-
-}
[11/52] [abbrv] incubator-taverna-language git commit: added
taverna-scufl2-example to pom
Posted by st...@apache.org.
added taverna-scufl2-example to pom
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/1962ee0c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/1962ee0c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/1962ee0c
Branch: refs/heads/master
Commit: 1962ee0c3bf80c5e00e89064fb81023a27005170
Parents: cfd67b7
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:10:48 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:10:48 2015 +0000
----------------------------------------------------------------------
pom.xml | 1 +
taverna-scufl2-examples/pom.xml | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/1962ee0c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index eef5578..8b158ca 100644
--- a/pom.xml
+++ b/pom.xml
@@ -281,6 +281,7 @@
<modules>
<module>taverna-scufl2-ucfpackage</module>
<module>taverna-scufl2-api</module>
+ <module>taverna-scufl2-examples</module>
<module>taverna-scufl2-rdfxml</module>
<module>taverna-scufl2-t2flow</module>
<module>taverna-scufl2-scufl</module>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/1962ee0c/taverna-scufl2-examples/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/pom.xml b/taverna-scufl2-examples/pom.xml
index b5e1f75..9e33ff3 100644
--- a/taverna-scufl2-examples/pom.xml
+++ b/taverna-scufl2-examples/pom.xml
@@ -24,7 +24,7 @@
<version>0.16.1-incubating-SNAPSHOT</version>
</parent>
<artifactId>taverna-scufl2-examples</artifactId>
- <name>Apache Taverna SCUFL2 examples</name>
+ <name>Apache Taverna Scufl2 examples</name>
<dependencies>
<dependency>
<groupId>${project.parent.groupId}</groupId>
[49/52] [abbrv] incubator-taverna-language git commit: Merge pull
request #6 from dkfellows/master
Posted by st...@apache.org.
Merge pull request #6 from dkfellows/master
Getting rid of more RAT wildcards
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/7e6e3912
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/7e6e3912
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/7e6e3912
Branch: refs/heads/master
Commit: 7e6e391227b59c7056f8058bfd8ee52b291fab94
Parents: ff86717 762ae0a
Author: Alan R Williams <al...@manchester.ac.uk>
Authored: Fri Feb 13 12:37:58 2015 +0000
Committer: Alan R Williams <al...@manchester.ac.uk>
Committed: Fri Feb 13 12:37:58 2015 +0000
----------------------------------------------------------------------
pom.xml | 126 ++++++++++++++++++++++++++++++++---------------------------
1 file changed, 68 insertions(+), 58 deletions(-)
----------------------------------------------------------------------
[52/52] [abbrv] incubator-taverna-language git commit: Merge pull
request #7 from dkfellows/master
Posted by st...@apache.org.
Merge pull request #7 from dkfellows/master
Identifying things with clear Manchester copyright ownership
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/aa46364d
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/aa46364d
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/aa46364d
Branch: refs/heads/master
Commit: aa46364df0400cc032adef3952459483dba3ffbf
Parents: 7e6e391 f7e3cba
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Fri Feb 13 15:45:41 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Fri Feb 13 15:45:41 2015 +0000
----------------------------------------------------------------------
pom.xml | 95 +++++++++-----------
.../src/test/resources/helloanyone.t2flow | 18 ++++
.../examples/helloanyone.t2flow | 19 ++++
.../examples/helloworld.t2flow | 19 ++++
.../T3-1226-annotations-with-quotes.t2flow | 19 ++++
.../src/test/resources/annotated2.2.t2flow | 19 ++++
.../src/test/resources/as.t2flow | 20 ++++-
.../defaultActivitiesTaverna2.2.t2flow | 19 ++++
.../src/test/resources/random.t2flow | 19 ++++
.../semantic_annotations__eclipse.t2flow | 19 ++++
.../spreadsheet_activity_defaults_892.t2flow | 19 ++++
.../src/test/resources/xpath_workflow.t2flow | 19 ++++
.../T3-1226-annotations-with-quotes.t2flow | 19 ++++
.../src/test/resources/allTypes.t2flow | 21 ++++-
.../src/test/resources/helloanyone.t2flow | 19 ++++
.../src/test/resources/helloworld.t2flow | 19 ++++
16 files changed, 326 insertions(+), 56 deletions(-)
----------------------------------------------------------------------
[09/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
Removed duplicate workflows (See scufl2-examples)
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/72cbd2dd
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/72cbd2dd
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/72cbd2dd
Branch: refs/heads/master
Commit: 72cbd2ddf6dfa5bceda000cb7295febc86847609
Parents: 9cc0e05
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:08:51 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:08:51 2015 +0000
----------------------------------------------------------------------
...version_of_the_emboss_tutorial_676679.t2flow | 204 ---
.../workflows/t2flow/annotated2.2.t2flow | 199 ---
.../main/resources/workflows/t2flow/as.t2flow | 1657 ------------------
.../biomartandembossanalysis_904962.t2flow | 370 ----
.../biomoby_tutorial_workflow_877727.t2flow | 247 ---
.../t2flow/defaultActivitiesTaverna2.2.t2flow | 871 ---------
...tion_of_configurable_iteration_114130.t2flow | 335 ----
...ebi_interproscan_for_taverna_2_317472.t2flow | 615 -------
..._pdb_flatfile_from_rcsb_server_969361.t2flow | 255 ---
.../fetch_today_s_xkcd_comic_568671.t2flow | 332 ----
.../workflows/t2flow/gbseq_test_457824.t2flow | 485 -----
.../resources/workflows/t2flow/merge_fun.t2flow | 66 -
.../pipelined_list_iteration_902021.t2flow | 303 ----
...etrieve_sequence_in_embl_format_32794.t2flow | 84 -
14 files changed, 6023 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/a_workflow_version_of_the_emboss_tutorial_676679.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/a_workflow_version_of_the_emboss_tutorial_676679.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/a_workflow_version_of_the_emboss_tutorial_676679.t2flow
deleted file mode 100644
index 0081d9e..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/a_workflow_version_of_the_emboss_tutorial_676679.t2flow
+++ /dev/null
@@ -1,204 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="0e367ee5-b4fa-4e61-91f6-f3b976d07921" role="top"><name>A_workflow_version_of_the_EMBOSS_tutorial</name><inputPorts /><outputPorts><port><name>outputPlot</name><annotations /></port><port><name>tmapPlot</name><annotations /></port><port><name>prophetOutput</name><annotations /></port></outputPorts><processors><processor><name>sequenceid</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns=""
>
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
- <text>Tom Oinn</text>
- </annotationBean>
- <date>2009-12-15 20:15:02.217 GMT</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>Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.</text>
- </annotationBean>
- <date>2009-12-15 20:15:31.62 GMT</date>
- <creators />
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- </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>0e367ee5-b4fa-4e61-91f6-f3b976d07921</identification>
- </annotationBean>
- <date>2010-07-04 17:54:32.941 BST</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>A workflow version of the EMBOSS tutorial</text>
- </annotationBean>
- <date>2009-12-15 20:15:12.279 GMT</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/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/annotated2.2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/annotated2.2.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/annotated2.2.t2flow
deleted file mode 100644
index 251a1fe..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/annotated2.2.t2flow
+++ /dev/null
@@ -1,199 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad" role="top"><name>Workflow_title</name><inputPorts><port><name>in0</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>Only example</text>
- </annotationBean>
- <date>2010-07-21 11:19:58.897 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>in1</name><depth>1</depth><granularDepth>1</granularDepth><annotations><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>Only description</text>
- </annotationBean>
- <date>2010-07-21 11:19:47.699 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>in2</name><depth>2</depth><granularDepth>2</granularDepth><annotations><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.ExampleValue">
- <text>Some kind </text>
- </annotationBean>
- <date>2010-07-21 11:19:34.518 BST</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>Workflow input in2</text>
- </annotationBean>
- <date>2010-07-21 11:19:25.509 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out0</name><annotations><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.ExampleValue">
- <text />
- </annotationBean>
- <date>2010-07-21 11:26:10.972 BST</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>First annotation</text>
- </annotationBean>
- <date>2010-07-21 11:20:30.875 BST</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.ExampleValue">
- <text>Not empty</text>
- </annotationBean>
- <date>2010-07-21 11:25:56.668 BST</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>Third annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:50.301 BST</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.ExampleValue">
- <text>Empty again</text>
- </annotationBean>
- <date>2010-07-21 11:26:05.105 BST</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>Second annotation</text>
- </annotationBean>
- <date>2010-07-21 11:25:39.729 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>out1</name><annotations /></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts /><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 /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script />
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out1</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks /><annotations><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>Workflow title</text>
- </annotationBean>
- <date>2010-07-21 11:20:43.824 BST</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>Workflow description</text>
- </annotationBean>
- <date>2010-07-21 11:20:50.161 BST</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>bb902d82-b0e4-46fc-bed5-950a3b38bb98</identification>
- </annotationBean>
- <date>2010-07-21 11:22:31.286 BST</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>9e1f7ffd-3bf9-4ba8-9c63-03b79b1858ad</identification>
- </annotationBean>
- <date>2010-07-21 11:26:16.844 BST</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>Workflow author</text>
- </annotationBean>
- <date>2010-07-21 11:20:39.864 BST</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
[29/52] [abbrv] incubator-taverna-language git commit: Merge pull
request #3 from dkfellows/master
Posted by st...@apache.org.
Merge pull request #3 from dkfellows/master
Tidy up the .gitignores
No need to pull request tidy like this, just push it yourself :-).
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/427d21e9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/427d21e9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/427d21e9
Branch: refs/heads/master
Commit: 427d21e9ac19ec77517f3bc4bd625c0b45f5ce30
Parents: 1b3666a 8b377d5
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Wed Feb 11 12:31:52 2015 +0000
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Wed Feb 11 12:31:52 2015 +0000
----------------------------------------------------------------------
.gitignore | 2 +-
taverna-scufl2-schemas/.gitignore | 1 -
2 files changed, 1 insertion(+), 2 deletions(-)
----------------------------------------------------------------------
[38/52] [abbrv] incubator-taverna-language git commit: Stop tests
from being quite so chatty on stdout.
Posted by st...@apache.org.
Stop tests from being quite so chatty on stdout.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/2602a85b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/2602a85b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/2602a85b
Branch: refs/heads/master
Commit: 2602a85bc728f5f15e40d9a4fd31c9afb536c31c
Parents: 414cd6a
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 13:45:00 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 13:45:00 2015 +0000
----------------------------------------------------------------------
.../taverna/scufl2/wfdesc/TestAllTypes.java | 29 ++++++++++++--------
.../scufl2/wfdesc/TestAnnotationQuoting.java | 4 +--
.../taverna/scufl2/wfdesc/TestNested.java | 23 ++++++++++------
.../scufl2/wfdesc/TestRoEvoSerializer.java | 10 +++++--
.../scufl2/wfdesc/TestSemanticAnnotations.java | 2 +-
5 files changed, 41 insertions(+), 27 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2602a85b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java
index 186e088..8448965 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAllTypes.java
@@ -65,7 +65,7 @@ public class TestAllTypes {
allTypesWfdesc = File.createTempFile("scufl2-wfdesc", ".ttl");
allTypesWfdesc.delete();
// allTypesWfdesc.deleteOnExit();
- System.out.println(allTypesWfdesc);
+ // System.out.println(allTypesWfdesc);
}
@Test
@@ -111,17 +111,18 @@ public class TestAllTypes {
oldWf = wf;
}
String proc = binding.path("proc").path("value").asText();
+ assertNotNull(proc);
String procType = binding.path("procType").path("value").asText();
String procTypeShort = null;
- if (procType != null) {
- procTypeShort = URI.create(procType).getFragment();
- } else {
- System.err.println("No type for " + proc);
- }
+ if (procType == null)
+ continue;
+ procTypeShort = URI.create(procType).getFragment();
+ assertNotNull(procTypeShort);
String procLabel = binding.path("procLabel").path("value").asText();
- System.out.println(" Processor " + procLabel + " (" + procTypeShort
- + ")");
- System.out.println(" " + proc + " " + procType);
+ assertNotNull(procLabel);
+ //System.out.println(" Processor " + procLabel + " (" + procTypeShort
+ // + ")");
+ //System.out.println(" " + proc + " " + procType);
}
out.reset();
@@ -152,13 +153,17 @@ public class TestAllTypes {
}
String fromProcLabel = binding.path("fromProcLabel").path("value")
.asText();
+ assertNotNull(fromProcLabel);
String toProcLabel = binding.path("toProcLabel").path("value")
.asText();
+ assertNotNull(toProcLabel);
String fromProc = binding.path("fromProc").path("value").asText();
+ assertNotNull(fromProc);
String toProc = binding.path("toProc").path("value").asText();
- System.out.print(" " + fromProcLabel);
- System.out.println(" -> " + toProcLabel);
- System.out.println(" " + fromProc + " -> " + toProc);
+ assertNotNull(toProc);
+ //System.out.print(" " + fromProcLabel);
+ //System.out.println(" -> " + toProcLabel);
+ //System.out.println(" " + fromProc + " -> " + toProc);
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2602a85b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java
index 5b78751..a4021ee 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestAnnotationQuoting.java
@@ -35,10 +35,8 @@ import org.apache.taverna.scufl2.api.io.WriterException;
import org.apache.taverna.scufl2.wfdesc.ROEvoSerializer;
import org.junit.Before;
import org.junit.Test;
-import org.openrdf.query.Binding;
import org.openrdf.query.BindingSet;
import org.openrdf.query.MalformedQueryException;
-import org.openrdf.query.Query;
import org.openrdf.query.QueryEvaluationException;
import org.openrdf.query.QueryLanguage;
import org.openrdf.query.TupleQueryResult;
@@ -78,7 +76,7 @@ public class TestAnnotationQuoting {
myRepository.initialize();
RepositoryConnection con = myRepository.getConnection();
String root = "app://600aac93-0ea8-4e9d-9593-081149e31d5a/";
- System.out.write(output.toByteArray());
+ //System.out.write(output.toByteArray());
con.add(new ByteArrayInputStream(output.toByteArray()), root, RDFFormat.TURTLE);
TupleQueryResult results = con.prepareTupleQuery(QueryLanguage.SPARQL,
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2602a85b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java
index 942d216..4581e2c 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestNested.java
@@ -64,7 +64,7 @@ public class TestNested {
nestedWfdesc = File.createTempFile("scufl2-wfdesc", ".ttl");
nestedWfdesc.delete();
// allTypesWfdesc.deleteOnExit();
- System.out.println(nestedWfdesc);
+ // System.out.println(nestedWfdesc);
}
@Test
@@ -112,15 +112,18 @@ public class TestNested {
oldWf = wf;
}
String proc = binding.path("proc").path("value").asText();
+ assertNotNull(proc);
String procType = binding.path("procType").path("value").asText();
String procTypeshort = null;
if (procType != null) {
procTypeshort = URI.create(procType).getFragment();
}
String procLabel = binding.path("procLabel").path("value").asText();
- System.out.println(" Processor " + procLabel + " (" + procTypeshort
- + ")");
- System.out.println(" " + proc + " " + procType);
+ assertNotNull(procLabel);
+ assertNotNull(procTypeshort);
+ //System.out.println(" Processor " + procLabel + " (" + procTypeshort
+ // + ")");
+ //System.out.println(" " + proc + " " + procType);
}
out.reset();
@@ -146,18 +149,22 @@ public class TestNested {
for (JsonNode binding : jsonNode.path("results").path("bindings")) {
String wf = binding.path("wf").path("value").asText();
if (!wf.equals(oldWf)) {
- System.out.println(wf);
+ //System.out.println(wf);
oldWf = wf;
}
String fromProcLabel = binding.path("fromProcLabel").path("value")
.asText();
+ assertNotNull(fromProcLabel);
String toProcLabel = binding.path("toProcLabel").path("value")
.asText();
+ assertNotNull(toProcLabel);
String fromProc = binding.path("fromProc").path("value").asText();
+ assertNotNull(fromProc);
String toProc = binding.path("toProc").path("value").asText();
- System.out.print(" " + fromProcLabel);
- System.out.println(" -> " + toProcLabel);
- System.out.println(" " + fromProc + " -> " + toProc);
+ assertNotNull(toProc);
+ //System.out.print(" " + fromProcLabel);
+ //System.out.println(" -> " + toProcLabel);
+ //System.out.println(" " + fromProc + " -> " + toProc);
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2602a85b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
index e8fdb4b..1e757ad 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestRoEvoSerializer.java
@@ -22,7 +22,9 @@ package org.apache.taverna.scufl2.wfdesc;
import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
@@ -52,9 +54,11 @@ public class TestRoEvoSerializer {
@Test
- public void workflowUUIDs() throws Exception {
- roEvo.workflowHistory(helloWorld.getMainWorkflow(), System.out);
-
+ public void workflowUUIDs() throws Exception {
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ roEvo.workflowHistory(helloWorld.getMainWorkflow(), os);
+ assertTrue(500 < os.size());
+ assertTrue(os.toString("UTF-8").indexOf(" a roevo:VersionableResource , prov:Entity ;") > 0);
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/2602a85b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java
index 7e89932..666ed9f 100644
--- a/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java
+++ b/taverna-scufl2-wfdesc/src/test/java/org/apache/taverna/scufl2/wfdesc/TestSemanticAnnotations.java
@@ -58,7 +58,7 @@ public class TestSemanticAnnotations {
public File tempFile() throws IOException {
File bundleFile = File.createTempFile("wfdesc", ".ttl");
// bundleFile.deleteOnExit();
- System.out.println(bundleFile);
+ //System.out.println(bundleFile);
return bundleFile;
}
[19/52] [abbrv] incubator-taverna-language git commit: now valid
XML...
Posted by st...@apache.org.
now valid XML...
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/19114d5f
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/19114d5f
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/19114d5f
Branch: refs/heads/master
Commit: 19114d5f26a325c4c1941d48ccc4a8da052af225
Parents: bd81aa1
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:43:02 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:43:02 2015 +0000
----------------------------------------------------------------------
.../resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/19114d5f/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
index e326ff7..24cb4cd 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
@@ -4,7 +4,11 @@
document includes material copied from or derived from
XML namespace http://www.w3.org/2001/xml.xsd
-->
-
+<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns ="http://www.w3.org/1999/xhtml"
+ xml:lang="en">
+
<xs:annotation>
<xs:documentation>
<div>
[39/52] [abbrv] incubator-taverna-language git commit: Delete a bunch
of unused files.
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/helloanyone.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/helloanyone.wfdesc.ttl
deleted file mode 100644
index d2f75ce..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/helloanyone.wfdesc.ttl
+++ /dev/null
@@ -1,66 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/Concatenate_two_strings/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Concatenate_two_strings" ;
- wfdesc:hasInput <processor/Concatenate_two_strings/in/string1> , <processor/Concatenate_two_strings/in/string2> ;
- wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> ;
- wf4ever:script "output = string1 + string2;" .
-
-<datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> a wfdesc:DataLink ;
- wfdesc:hasSource <in/name> ;
- wfdesc:hasSink <processor/Concatenate_two_strings/in/string2> .
-
-<datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Concatenate_two_strings/out/output> ;
- wfdesc:hasSink <out/greeting> .
-
-<datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/hello/out/value> ;
- wfdesc:hasSink <processor/Concatenate_two_strings/in/string1> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- dc:creator "Stian Soiland-Reyes" ;
- dcterms:description "An extension to helloworld.t2flow - this workflow takes a workflow input \"name\" which is combined with the string constant \"Hello, \" using the local worker \"Concatenate two strings\", and outputs the produced string to the workflow output \"greeting\"." ;
- dcterms:title "Hello Anyone" ;
- rdfs:label "Hello_Anyone" ;
- wfdesc:hasInput <in/name> ;
- wfdesc:hasOutput <out/greeting> ;
- wfdesc:hasSubProcess <processor/Concatenate_two_strings/> , <processor/hello/> ;
- wfdesc:hasDataLink <datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> , <datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> , <datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> .
-
-<in/name> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
- biocat:exampleData "World!" ;
- dcterms:description "Your name for the greeting" ;
- rdfs:label "name" .
-
-<out/greeting> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
- rdfs:label "greeting" .
-
-<processor/Concatenate_two_strings/in/string1> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "string1" .
-
-<processor/Concatenate_two_strings/in/string2> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "string2" .
-
-<processor/Concatenate_two_strings/out/output> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "output" .
-
-<processor/hello/> a wfdesc:Process , wfdesc:Description ;
- rdfs:label "hello" ;
- wfdesc:hasOutput <processor/hello/out/value> .
-
-<processor/hello/out/value> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "value" .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/localdependency.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/localdependency.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/localdependency.wfdesc.ttl
deleted file mode 100644
index ea1590b..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/localdependency.wfdesc.ttl
+++ /dev/null
@@ -1,26 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/024011b4-bc92-4836-8043-6e787cfc72b7/workflow/Workflow1/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/Beanshell/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Beanshell" ;
- wf4ever:script "// depends on hello.jar" ;
- roterms:requiresSoftware _:node18musbm1ix1 .
-
-_:node18musbm1ix1 rdfs:label "hello.jar" ;
- rdfs:comment "JAR dependency" .
-
-<> a wfdesc:Workflow , wfdesc:Description ;
- rdfs:label "Workflow1" ;
- wfdesc:hasSubProcess <processor/Beanshell/> .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/nested.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/nested.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/nested.wfdesc.ttl
deleted file mode 100644
index cb30c0f..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/nested.wfdesc.ttl
+++ /dev/null
@@ -1,126 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/91a0588a-1058-47ba-b0e0-4bbb5d004c38/workflow/Workflow6/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/Concatenate_two_strings/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Concatenate_two_strings" ;
- wfdesc:hasInput <processor/Concatenate_two_strings/in/string1> , <processor/Concatenate_two_strings/in/string2> ;
- wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> ;
- wf4ever:script "output = string1 + string2;" .
-
-<processor/Create_Lots_Of_Strings/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Create_Lots_Of_Strings" ;
- wfdesc:hasOutput <processor/Create_Lots_Of_Strings/out/strings> ;
- wf4ever:script """List strings = new ArrayList();
-for (int i = 0; i < 1; i++) {
- strings.add(\"String\" + i);
-}
-""" .
-
-<../Workflow9/processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <../Workflow9/processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <../Workflow9/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<datalink?from=processor/Concatenate_two_strings/out/output&to=processor/Workflow9/in/listA> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Concatenate_two_strings/out/output> ;
- wfdesc:hasSink <processor/Workflow9/in/listA> .
-
-<datalink?from=processor/Create_Lots_Of_Strings/out/strings&to=processor/Concatenate_two_strings/in/string1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Create_Lots_Of_Strings/out/strings> ;
- wfdesc:hasSink <processor/Concatenate_two_strings/in/string1> .
-
-<datalink?from=processor/Create_Lots_Of_Strings/out/strings&to=processor/Concatenate_two_strings/in/string2> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Create_Lots_Of_Strings/out/strings> ;
- wfdesc:hasSink <processor/Concatenate_two_strings/in/string2> .
-
-<datalink?from=processor/Workflow9/out/valueB&to=out/listC> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/Workflow9/out/valueB> ;
- wfdesc:hasSink <out/listC> .
-
-<../Workflow9/datalink?from=in/listA&to=processor/Merge_String_List_to_a_String/in/stringlist> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow9/in/listA> ;
- wfdesc:hasSink <../Workflow9/processor/Merge_String_List_to_a_String/in/stringlist> .
-
-<../Workflow9/datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=out/valueB> a wfdesc:DataLink ;
- wfdesc:hasSource <../Workflow9/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wfdesc:hasSink <../Workflow9/out/valueB> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- rdfs:label "Workflow6" ;
- wfdesc:hasOutput <out/listC> ;
- wfdesc:hasSubProcess <processor/Concatenate_two_strings/> , <processor/Create_Lots_Of_Strings/> , <processor/Workflow9/> ;
- wfdesc:hasDataLink <datalink?from=processor/Concatenate_two_strings/out/output&to=processor/Workflow9/in/listA> , <datalink?from=processor/Create_Lots_Of_Strings/out/strings&to=processor/Concatenate_two_strings/in/string1> , <datalink?from=processor/Create_Lots_Of_Strings/out/strings&to=processor/Concatenate_two_strings/in/string2> , <datalink?from=processor/Workflow9/out/valueB&to=out/listC> .
-
-<out/listC> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
- rdfs:label "listC" .
-
-<processor/Concatenate_two_strings/in/string1> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "string1" .
-
-<processor/Concatenate_two_strings/in/string2> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "string2" .
-
-<processor/Concatenate_two_strings/out/output> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "output" .
-
-<processor/Create_Lots_Of_Strings/out/strings> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "strings" .
-
-<processor/Workflow9/> a wfdesc:Process , wfdesc:Description , prov:Entity , wfdesc:Workflow ;
- rdfs:label "Workflow9" ;
- wfdesc:hasInput <processor/Workflow9/in/listA> ;
- wfdesc:hasOutput <processor/Workflow9/out/valueB> ;
- prov:specializationOf <../Workflow9/> .
-
-<processor/Workflow9/in/listA> a wfdesc:Input , wfdesc:Description , prov:Entity ;
- rdfs:label "listA" ;
- prov:specializationOf <../Workflow9/in/listA> .
-
-<processor/Workflow9/out/valueB> a wfdesc:Output , wfdesc:Description , prov:Entity ;
- rdfs:label "valueB" ;
- prov:specializationOf <../Workflow9/out/valueB> .
-
-<../Workflow9/> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process , prov:Entity ;
- rdfs:label "Workflow9" ;
- wfdesc:hasInput <../Workflow9/in/listA> ;
- wfdesc:hasOutput <../Workflow9/out/valueB> ;
- wfdesc:hasSubProcess <../Workflow9/processor/Merge_String_List_to_a_String/> ;
- wfdesc:hasDataLink <../Workflow9/datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=out/valueB> , <../Workflow9/datalink?from=in/listA&to=processor/Merge_String_List_to_a_String/in/stringlist> .
-
-<../Workflow9/in/listA> a wfdesc:Input , wfdesc:Description , wfdesc:Output , prov:Entity ;
- rdfs:label "listA" .
-
-<../Workflow9/out/valueB> a wfdesc:Output , wfdesc:Description , wfdesc:Input , prov:Entity ;
- rdfs:label "valueB" .
-
-<../Workflow9/processor/Merge_String_List_to_a_String/in/stringlist> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "stringlist" .
-
-<../Workflow9/processor/Merge_String_List_to_a_String/out/concatenated> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "concatenated" .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.wfdesc.ttl
deleted file mode 100644
index 8a8aaee..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/rdf-in-example-annotation.wfdesc.ttl
+++ /dev/null
@@ -1,25 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/b9ca25c7-f594-47c1-af62-af9d380002c8/workflow/Workflow4/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- rdfs:label "Workflow4" ;
- wfdesc:hasInput <in/example> .
-
-<in/example> a wfdesc:Input , wfdesc:Description ;
- biocat:exampleData """@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
-@prefix dct: <http://purl.org/dc/terms/> .""" ;
- rdfs:label "example" .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl
deleted file mode 100644
index 1a4d423..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/valid_component_imagemagickconvert.wfdesc.ttl
+++ /dev/null
@@ -1,112 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/8d2f9ef0-09ca-4103-b4fd-0ee0a40d8263/workflow/Imagemagick_convert_/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<processor/convert/> a wfdesc:Process , wfdesc:Description , wf4ever:CommandLineTool ;
- comp:hasDependency dep:digital-preservation-migration-image-imagemagick-image2tiff ;
- rdfs:label "convert" ;
- wfdesc:hasInput <processor/convert/in/compression> , <processor/convert/in/from_uri> , <processor/convert/in/to_uri> ;
- wfdesc:hasOutput <processor/convert/out/STDERR> , <processor/convert/out/STDOUT> .
-
-<datalink?from=in/compression&to=processor/convert/in/compression> a wfdesc:DataLink ;
- wfdesc:hasSource <in/compression> ;
- wfdesc:hasSink <processor/convert/in/compression> .
-
-<datalink?from=in/from_uri&to=processor/convert/in/from_uri> a wfdesc:DataLink ;
- wfdesc:hasSource <in/from_uri> ;
- wfdesc:hasSink <processor/convert/in/from_uri> .
-
-<datalink?from=in/to_uri&to=processor/convert/in/to_uri> a wfdesc:DataLink ;
- wfdesc:hasSource <in/to_uri> ;
- wfdesc:hasSink <processor/convert/in/to_uri> .
-
-<datalink?from=processor/convert/out/STDERR&to=out/status&mergePosition=1> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/convert/out/STDERR> ;
- wfdesc:hasSink <out/status> .
-
-<datalink?from=processor/convert/out/STDOUT&to=out/status&mergePosition=0> a wfdesc:DataLink ;
- wfdesc:hasSource <processor/convert/out/STDOUT> ;
- wfdesc:hasSink <out/status> .
-
-<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
- comp:fits comp:MigrationAction ;
- comp:migrates _:node18musbm56x1 .
-
-_:node18musbm56x1 a comp:MigrationPath ;
- comp:fromMimetype "image/tiff" ;
- comp:toMimetype "image/tiff" .
-
-<> dcterms:title "Imagemagick convert - tiff2tiff - compression" ;
- dcterms:description "Converts tiff to tiff using imagemagick convert with the provided compression" ;
- dc:creator "Markus" ;
- rdfs:label "Imagemagick_convert_" ;
- wfdesc:hasInput <in/compression> , <in/from_uri> , <in/to_uri> ;
- wfdesc:hasOutput <out/status> ;
- wfdesc:hasSubProcess <processor/convert/> ;
- wfdesc:hasDataLink <datalink?from=processor/convert/out/STDERR&to=out/status&mergePosition=1> , <datalink?from=processor/convert/out/STDOUT&to=out/status&mergePosition=0> , <datalink?from=in/compression&to=processor/convert/in/compression> , <datalink?from=in/from_uri&to=processor/convert/in/from_uri> , <datalink?from=in/to_uri&to=processor/convert/in/to_uri> .
-
-<in/compression> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
- comp:acceptsPredefinedParameter _:node18musbm56x2 .
-
-_:node18musbm56x2 a comp:PredefinedParameter ;
- comp:parameterValue "none" ;
- comp:parameterDescription "no compression" .
-
-<in/compression> comp:acceptsPredefinedParameter _:node18musbm56x3 .
-
-_:node18musbm56x3 a comp:PredefinedParameter ;
- comp:parameterValue "Group4" ;
- comp:parameterDescription "CCITT Group 4" .
-
-<in/compression> comp:acceptsPredefinedParameter _:node18musbm56x4 .
-
-_:node18musbm56x4 a comp:PredefinedParameter ;
- comp:parameterValue "RLE" ;
- comp:parameterDescription "run length encoding" .
-
-<in/compression> biocat:exampleData "none" ;
- dcterms:description "Imagemagick convert compress parameter" ;
- rdfs:label "compression" .
-
-<in/from_uri> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
- comp:portType comp:FromURIPort ;
- biocat:exampleData "in.tiff" ;
- dcterms:description "URI to the input object" ;
- rdfs:label "from_uri" .
-
-<in/to_uri> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
- comp:portType comp:ToURIPort ;
- dcterms:description "URI to the input object" ;
- biocat:exampleData "out.tiff" ;
- rdfs:label "to_uri" .
-
-<out/status> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
- dcterms:description "STDOUT and STDERR of the action" ;
- comp:portType comp:ActionStatusPort ;
- rdfs:label "status" .
-
-<processor/convert/in/compression> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "compression" .
-
-<processor/convert/in/from_uri> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "from_uri" .
-
-<processor/convert/in/to_uri> a wfdesc:Input , wfdesc:Description ;
- rdfs:label "to_uri" .
-
-<processor/convert/out/STDERR> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "STDERR" .
-
-<processor/convert/out/STDOUT> a wfdesc:Output , wfdesc:Description ;
- rdfs:label "STDOUT" .
[08/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/as.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/as.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/as.t2flow
deleted file mode 100644
index 2dc0596..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/as.t2flow
+++ /dev/null
@@ -1,1657 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0">
- <dataflow id="92c5e8d5-8360-4f86-a845-09c9849cbdc5" role="top">
- <name>Workflow1</name>
- <inputPorts />
- <outputPorts>
- <port>
- <name>asdasd</name>
- <annotations />
- </port>
- </outputPorts>
- <processors>
- <processor>
- <name>Workflow19</name>
- <inputPorts>
- <port>
- <name>lk</name>
- <depth>0</depth>
- </port>
- </inputPorts>
- <outputPorts>
- <port>
- <name>kk</name>
- <depth>0</depth>
- <granularDepth>0</granularDepth>
- </port>
- <port>
- <name>String_constant_value</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>1.0</version>
- </raven>
- <class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class>
- <inputMap>
- <map from="lk" to="lk" />
- </inputMap>
- <outputMap>
- <map from="String_constant_value" to="String_constant_value" />
- <map from="kk" to="kk" />
- </outputMap>
- <configBean encoding="dataflow">
- <dataflow ref="c451b1cf-1c95-47e5-b89c-537a5501a1ef" />
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.0</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="lk" 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>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
-<inputMap>
-<map from="string2" to="string2" />
-<map from="string1" to="string1" />
-</inputMap>
-<outputMap>
-<map from="output" to="output" />
-</outputMap>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="string2" depth="0" />
-<port name="string1" depth="0" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>Concatenate_two_strings_2</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>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
-<inputMap>
-<map from="string2" to="string2" />
-<map from="string1" to="string1" />
-</inputMap>
-<outputMap>
-<map from="output" to="output" />
-</outputMap>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="string2" depth="0" />
-<port name="string1" depth="0" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>Create_Lots_Of_Strings</name>
-<inputPorts />
-<outputPorts>
-<port>
-<name>strings</name>
-<depth>1</depth>
-<granularDepth>1</granularDepth>
-</port>
-</outputPorts>
-<annotations />
-<activities>
-<activity>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
-<inputMap />
-<outputMap>
-<map from="strings" to="strings" />
-</outputMap>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EmitLotsOfStrings</localworkerName>
- <script>List strings = new ArrayList();
-for (int i = 0; i < 40; i++) {
- strings.add("String" + i);
-}
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>strings</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy />
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>Concatenate_two_strings_3</name>
-<inputPorts>
-<port>
-<name>string1</name>
-<depth>0</depth>
-</port>
-<port>
-<name>string2</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>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<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="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="string1" depth="0" />
-<port name="string2" depth="0" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>String_constant</name>
-<inputPorts />
-<outputPorts>
-<port>
-<name>value</name>
-<depth>0</depth>
-<granularDepth>0</granularDepth>
-</port>
-</outputPorts>
-<annotations />
-<activities>
-<activity>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>stringconstant-activity</artifact>
-<version>1.0</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="">
- <value>Add your own value here</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy />
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>Concatenate_two_strings_4</name>
-<inputPorts>
-<port>
-<name>string1</name>
-<depth>0</depth>
-</port>
-<port>
-<name>string2</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>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<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="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="string1" depth="0" />
-<port name="string2" depth="0" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>Echo_List</name>
-<inputPorts>
-<port>
-<name>inputlist</name>
-<depth>1</depth>
-</port>
-</inputPorts>
-<outputPorts>
-<port>
-<name>outputlist</name>
-<depth>1</depth>
-<granularDepth>1</granularDepth>
-</port>
-</outputPorts>
-<annotations />
-<activities>
-<activity>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class>
-<inputMap>
-<map from="inputlist" to="inputlist" />
-</inputMap>
-<outputMap>
-<map from="outputlist" to="outputlist" />
-</outputMap>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
- <script>outputlist = inputlist;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>inputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="inputlist" depth="1" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-</processors>
-<conditions />
-<datalinks>
-<datalink>
-<sink type="processor">
-<processor>Workflow19</processor>
-<port>lk</port>
-</sink>
-<source type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>output</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>string2</port>
-</sink>
-<source type="processor">
-<processor>Concatenate_two_strings_2</processor>
-<port>output</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>string1</port>
-</sink>
-<source type="processor">
-<processor>Create_Lots_Of_Strings</processor>
-<port>strings</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_2</processor>
-<port>string2</port>
-</sink>
-<source type="processor">
-<processor>Create_Lots_Of_Strings</processor>
-<port>strings</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_2</processor>
-<port>string1</port>
-</sink>
-<source type="processor">
-<processor>Create_Lots_Of_Strings</processor>
-<port>strings</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_3</processor>
-<port>string1</port>
-</sink>
-<source type="processor">
-<processor>Workflow19</processor>
-<port>kk</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_3</processor>
-<port>string2</port>
-</sink>
-<source type="processor">
-<processor>String_constant</processor>
-<port>value</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_4</processor>
-<port>string1</port>
-</sink>
-<source type="processor">
-<processor>String_constant</processor>
-<port>value</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings_4</processor>
-<port>string2</port>
-</sink>
-<source type="processor">
-<processor>Workflow19</processor>
-<port>String_constant_value</port>
-</source>
-</datalink>
-<datalink>
-<sink type="merge">
-<processor>Echo_List</processor>
-<port>inputlist</port>
-</sink>
-<source type="processor">
-<processor>Concatenate_two_strings_4</processor>
-<port>output</port>
-</source>
-</datalink>
-<datalink>
-<sink type="merge">
-<processor>Echo_List</processor>
-<port>inputlist</port>
-</sink>
-<source type="processor">
-<processor>Concatenate_two_strings_3</processor>
-<port>output</port>
-</source>
-</datalink>
-<datalink>
-<sink type="dataflow">
-<port>asdasd</port>
-</sink>
-<source type="processor">
-<processor>Echo_List</processor>
-<port>outputlist</port>
-</source>
-</datalink>
-</datalinks>
-<annotations />
-</dataflow>
-<dataflow id="c451b1cf-1c95-47e5-b89c-537a5501a1ef" role="nested">
-<name>Workflow19</name>
-<inputPorts>
-<port>
-<name>lk</name>
-<depth>0</depth>
-<granularDepth>0</granularDepth>
-<annotations />
-</port>
-</inputPorts>
-<outputPorts>
-<port>
-<name>kk</name>
-<annotations />
-</port>
-<port>
-<name>String_constant_value</name>
-<annotations />
-</port>
-</outputPorts>
-<processors>
-<processor>
-<name>Concatenate_two_strings</name>
-<inputPorts>
-<port>
-<name>string1</name>
-<depth>0</depth>
-</port>
-<port>
-<name>string2</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>localworker-activity</artifact>
-<version>1.0</version>
-</raven>
-<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="xstream">
-<net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy>
-<cross>
-<port name="string1" depth="0" />
-<port name="string2" depth="0" />
-</cross>
-</strategy>
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>string1_value</name>
-<inputPorts />
-<outputPorts>
-<port>
-<name>value</name>
-<depth>0</depth>
-<granularDepth>0</granularDepth>
-</port>
-</outputPorts>
-<annotations />
-<activities>
-<activity>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>stringconstant-activity</artifact>
-<version>1.0</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="">
- <value>kjkj</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy />
-</iteration>
-</iterationStrategyStack>
-</processor>
-<processor>
-<name>String_constant</name>
-<inputPorts />
-<outputPorts>
-<port>
-<name>value</name>
-<depth>0</depth>
-<granularDepth>0</granularDepth>
-</port>
-</outputPorts>
-<annotations />
-<activities>
-<activity>
-<raven>
-<group>net.sf.taverna.t2.activities</group>
-<artifact>stringconstant-activity</artifact>
-<version>1.0</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="">
- <value>Add your own value here</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean>
-</configBean>
-<annotations />
-</activity>
-</activities>
-<dispatchStack>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-<dispatchLayer>
-<raven>
-<group>net.sf.taverna.t2.core</group>
-<artifact>workflowmodel-impl</artifact>
-<version>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
-<configBean encoding="xstream">
-<net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
- <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>1.0</version>
-</raven>
-<class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
-<configBean encoding="xstream">
-<null xmlns="" />
-</configBean>
-</dispatchLayer>
-</dispatchStack>
-<iterationStrategyStack>
-<iteration>
-<strategy />
-</iteration>
-</iterationStrategyStack>
-</processor>
-</processors>
-<conditions>
-<condition control="Concatenate_two_strings" target="String_constant" />
-</conditions>
-<datalinks>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>string1</port>
-</sink>
-<source type="processor">
-<processor>string1_value</processor>
-<port>value</port>
-</source>
-</datalink>
-<datalink>
-<sink type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>string2</port>
-</sink>
-<source type="dataflow">
-<port>lk</port>
-</source>
-</datalink>
-<datalink>
-<sink type="dataflow">
-<port>kk</port>
-</sink>
-<source type="processor">
-<processor>Concatenate_two_strings</processor>
-<port>output</port>
-</source>
-</datalink>
-<datalink>
-<sink type="dataflow">
-<port>String_constant_value</port>
-</sink>
-<source type="processor">
-<processor>String_constant</processor>
-<port>value</port>
-</source>
-</datalink>
-</datalinks>
-<annotations />
-</dataflow>
-</workflow>
\ No newline at end of file
[24/52] [abbrv] incubator-taverna-language git commit: w3c license
header
Posted by st...@apache.org.
w3c license header
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/d088b9f6
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/d088b9f6
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/d088b9f6
Branch: refs/heads/master
Commit: d088b9f6ac3c830d0c8e80229fa124719fee27bf
Parents: e97cb29
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 16:09:12 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 16:10:30 2015 +0000
----------------------------------------------------------------------
taverna-robundle/src/main/xsd/xenc-schema.xsd | 11 +++++++++++
taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd | 11 +++++++++++
2 files changed, 22 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/d088b9f6/taverna-robundle/src/main/xsd/xenc-schema.xsd
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/main/xsd/xenc-schema.xsd b/taverna-robundle/src/main/xsd/xenc-schema.xsd
index 4e093f4..01a5c71 100644
--- a/taverna-robundle/src/main/xsd/xenc-schema.xsd
+++ b/taverna-robundle/src/main/xsd/xenc-schema.xsd
@@ -1,4 +1,15 @@
<?xml version="1.0" encoding="utf-8"?>
+<!--
+Copyright © 2002 World Wide Web Consortium, (Massachusetts
+Institute of Technology, Institut National de Recherche en Informatique et en
+Automatique, Keio University). All Rights Reserved.
+http://www.w3.org/Consortium/Legal/
+
+XML Encryption Syntax and Processing
+W3C Recommendation 10 December 2002
+http://www.w3.org/TR/xmlenc-core/xenc-schema.xsd
+http://www.w3.org/TR/xmlenc-core/
+ -->
<schema xmlns='http://www.w3.org/2001/XMLSchema' version='1.0'
xmlns:xenc='http://www.w3.org/2001/04/xmlenc#'
xmlns:ds='http://www.w3.org/2000/09/xmldsig#'
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/d088b9f6/taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd b/taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd
index 4e093f4..01a5c71 100644
--- a/taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd
+++ b/taverna-scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd
@@ -1,4 +1,15 @@
<?xml version="1.0" encoding="utf-8"?>
+<!--
+Copyright © 2002 World Wide Web Consortium, (Massachusetts
+Institute of Technology, Institut National de Recherche en Informatique et en
+Automatique, Keio University). All Rights Reserved.
+http://www.w3.org/Consortium/Legal/
+
+XML Encryption Syntax and Processing
+W3C Recommendation 10 December 2002
+http://www.w3.org/TR/xmlenc-core/xenc-schema.xsd
+http://www.w3.org/TR/xmlenc-core/
+ -->
<schema xmlns='http://www.w3.org/2001/XMLSchema' version='1.0'
xmlns:xenc='http://www.w3.org/2001/04/xmlenc#'
xmlns:ds='http://www.w3.org/2000/09/xmldsig#'
[34/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/dispatchlayers-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/dispatchlayers-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/dispatchlayers-xsd.t2flow
deleted file mode 100644
index fd47f1e..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/dispatchlayers-xsd.t2flow
+++ /dev/null
@@ -1,755 +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="3805e4de-40e6-4052-a292-8adc6515618c" role="top">
- <name>Workflow1</name>
- <inputPorts />
- <outputPorts />
- <processors>
- <processor>
- <name>retries</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>stringconstant-activity</artifact>
- <version>1.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean
- xmlns="">
- <value>retries</value>
- </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.3</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>
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- <property name="isFeedBack" value="false" />
- </properties>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.3</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>3805e4de-40e6-4052-a292-8adc6515618c
- </identification>
- </annotationBean>
- <date>2011-09-14 14:23:05.364 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/rest-2-2-saved-2-3-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow
deleted file mode 100755
index b725379..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow
+++ /dev/null
@@ -1,367 +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/restactivity.xsd"
- version="1" producedBy="taverna-2.3.0">
- <dataflow id="44e3e7d3-df8c-401b-8b77-9d001343d8c2" 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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</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://example.com/{thing}/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>
- <contentTypeForUpdates>application/json</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>true</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>true</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</string>
- <java-class>java.lang.String</java-class>
- </entry>
- <entry>
- <string>thing</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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/zip</contentTypeForUpdates>
- <outgoingDataFormat>Binary</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</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>44e3e7d3-df8c-401b-8b77-9d001343d8c2</identification>
- </annotationBean>
- <date>2011-08-30 16:11:29.231 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/rest-2-2-saved-2-3.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3.t2flow
deleted file mode 100755
index 9d4d7b0..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3.t2flow
+++ /dev/null
@@ -1,85 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="44e3e7d3-df8c-401b-8b77-9d001343d8c2" 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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</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://example.com/{thing}/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>
- <contentTypeForUpdates>application/json</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>true</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>true</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</string>
- <java-class>java.lang.String</java-class>
- </entry>
- <entry>
- <string>thing</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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/zip</contentTypeForUpdates>
- <outgoingDataFormat>Binary</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <escapeParameters>true</escapeParameters>
- <otherHTTPHeaders />
- <activityInputs>
- <entry>
- <string>userID</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>44e3e7d3-df8c-401b-8b77-9d001343d8c2</identification>
- </annotationBean>
- <date>2011-08-30 16:11:29.231 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/rest-2-2-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-2-xsd.t2flow
deleted file mode 100755
index 026b77d..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-2-xsd.t2flow
+++ /dev/null
@@ -1,361 +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/restactivity.xsd"
- version="1" producedBy="taverna-2.2.0">
- <dataflow id="44e3e7d3-df8c-401b-8b77-9d001343d8c2" role="top">
- <name>Workflow1</name>
- <inputPorts />
- <outputPorts />
- <processors>
- <processor>
- <name>default</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.ui-activities</group>
- <artifact>rest-activity</artifact>
- <version>0.3.1</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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <activityInputs>
- <entry>
- <string>userID</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>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- <processor>
- <name>put</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.ui-activities</group>
- <artifact>rest-activity</artifact>
- <version>0.3.1</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://example.com/{thing}/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>
- <contentTypeForUpdates>application/json</contentTypeForUpdates>
- <outgoingDataFormat>String</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>true</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>true</showRedirectionOutputPort>
- <activityInputs>
- <entry>
- <string>userID</string>
- <java-class>java.lang.String</java-class>
- </entry>
- <entry>
- <string>thing</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>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- <processor>
- <name>post</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.ui-activities</group>
- <artifact>rest-activity</artifact>
- <version>0.3.1</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.myexperiment.org/user.xml?id={userID}</urlSignature>
- <acceptsHeaderValue>text/plain</acceptsHeaderValue>
- <contentTypeForUpdates>application/zip</contentTypeForUpdates>
- <outgoingDataFormat>Binary</outgoingDataFormat>
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
- <showRedirectionOutputPort>false</showRedirectionOutputPort>
- <activityInputs>
- <entry>
- <string>userID</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>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </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>44e3e7d3-df8c-401b-8b77-9d001343d8c2</identification>
- </annotationBean>
- <date>2011-08-30 16:11:29.231 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/rest-2-3-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-3-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-3-xsd.t2flow
deleted file mode 100755
index fe0e4aa..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-3-xsd.t2flow
+++ /dev/null
@@ -1,376 +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/restactivity.xsd"
- 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
[44/52] [abbrv] incubator-taverna-language git commit: Make several
tests much less chatty, yet more exacting.
Posted by st...@apache.org.
Make several tests much less chatty, yet more exacting.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/98b8b237
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/98b8b237
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/98b8b237
Branch: refs/heads/master
Commit: 98b8b237966dfb59105fd30a5055ba075e96eca9
Parents: 7e05272
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 14:43:37 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 14:43:37 2015 +0000
----------------------------------------------------------------------
.../taverna/databundle/TestFullExample.java | 77 ++++++++------------
.../apache/taverna/robundle/TestExample.java | 21 ++++--
.../taverna/robundle/manifest/TestManifest.java | 17 +++--
.../robundle/manifest/TestManifestJSON.java | 2 +-
.../manifest/combine/TestCombineManifest.java | 22 +-----
5 files changed, 58 insertions(+), 81 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
----------------------------------------------------------------------
diff --git a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
index 1fec071..ca6e1e1 100644
--- a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
+++ b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
@@ -24,17 +24,16 @@ package org.apache.taverna.databundle;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import java.awt.Desktop;
-import java.io.IOException;
import java.net.URL;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
-import java.util.NavigableMap;
import java.util.UUID;
import org.apache.taverna.databundle.DataBundles;
@@ -110,67 +109,55 @@ public class TestFullExample {
// NOTE: From now dataBundle and its Path's are CLOSED
// and can no longer be accessed
- System.out.println("Saved to " + zip);
- if (Desktop.isDesktopSupported()) {
- // Open ZIP file for browsing
- Desktop.getDesktop().open(zip.toFile());
- }
+ //System.out.println("Saved to " + zip);
// Loading a data bundle back from disk
try (Bundle dataBundle2 = DataBundles.openBundle(zip)) {
assertEquals(zip, dataBundle2.getSource());
- System.out.println("\n== Inputs");
- printPorts(DataBundles.getInputs(dataBundle2));
- System.out.println("\n== Outputs");
- printPorts(DataBundles.getOutputs(dataBundle2));
+ List<String> s = new ArrayList<>(DataBundles.getPorts(
+ DataBundles.getInputs(dataBundle2)).keySet());
+ Collections.sort(s);
+ assertEquals("[email, sequence]", s.toString());
+ assertEquals(
+ "soiland-reyes@cs.manchester.ac.uk",
+ DataBundles.getStringValue(DataBundles.getPort(
+ DataBundles.getInputs(dataBundle2), "email")));
+ s = new ArrayList<>(DataBundles.getPorts(
+ DataBundles.getOutputs(dataBundle2)).keySet());
+ Collections.sort(s);
+ assertEquals(
+ "[Graphical_output, Workflow16_getStatus_output_status, "
+ + "getResult_3_output_output, getResult_output_output]",
+ s.toString());
+ assertEquals("FINISHED", DataBundles.getStringValue(DataBundles
+ .getPort(DataBundles.getOutputs(dataBundle2),
+ "Workflow16_getStatus_output_status")));
- System.out.println("\n== Intermediates");
UUID uuid = UUID.fromString("1f536bcf-ba43-44ec-a983-b30a45f2b739");
Path intermediate = DataBundles.getIntermediate(dataBundle2, uuid);
String intermediateStr = DataBundles.getStringValue(intermediate);
assertTrue(intermediateStr.contains("<status>RUNNING</status>"));
- System.out.println(uuid + ": " + intermediateStr);
Path prov = DataBundles.getWorkflowRunProvenance(dataBundle2);
List<String> provLines = Files.readAllLines(prov, Charset.forName("UTF8"));
- System.out.println("\n== Provenance");
- for (String line : provLines.subList(13, 18)) {
- // Show a tiny abstract
- System.out.println(line);
- }
+ assertEquals(" prov:startedAtTime \"2013-05-31T11:23:10.463+01:00\"^^xsd:dateTime ;",
+ provLines.get(15));
- System.out.println("\n== Workflow bundle");
WorkflowBundle wfb = DataBundles.getWorkflowBundle(dataBundle2);
- System.out.print(wfb.getName());
- System.out.println(" containing processors: ");
+ assertEquals("EBI_InterproScan_NewServices", wfb.getName());
+ s=new ArrayList<>();
for (Workflow w : wfb.getWorkflows()) {
for (Processor p : w.getProcessors()) {
- System.out.print(p.getName() + " ");
- }
- }
- System.out.println();
-
-
-
- }
- }
-
-
- private void printPorts(Path path) throws IOException {
- NavigableMap<String, Path> ports = DataBundles.getPorts(path);
- for (String portName : ports.keySet()) {
- Path port = ports.get(portName);
- if (DataBundles.isValue(port)) {
- System.out.print(portName + ": ");
- long size = Files.size(port);
- if (size < 1024) {
- // TODO: Detect binaries properly
- System.out.println(DataBundles.getStringValue(port));
- } else {
- System.out.println("(" + size + " bytes) " + port);
+ s.add(p.getName());
}
}
+ Collections.sort(s);
+ assertEquals("[Status, getResult, getResult_graphic, getResult_graphic_input, "
+ + "getResult_graphic_output, getResult_input, getResult_output, getResult_xml, "
+ + "getResult_xml_input, getResult_xml_output, getStatus, getStatus_input, "
+ + "getStatus_output, run, run_input, run_input_2, run_output, text, visual_png, "
+ + "xml]", s.toString());
}
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
index f5efb55..51767f5 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
@@ -21,6 +21,8 @@ package org.apache.taverna.robundle;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import java.io.OutputStream;
import java.net.URI;
@@ -51,14 +53,16 @@ public class TestExample {
Bundles.setStringValue(in1, "Hello");
// And retrieving it
- if (Bundles.isValue(in1)) {
- System.out.println(Bundles.getStringValue(in1));
- }
+ assertTrue(Bundles.isValue(in1));
+ assertEquals("Hello", Bundles.getStringValue(in1));
// Or just use the regular Files methods:
+ int lines = 0;
for (String line : Files.readAllLines(in1, Charset.forName("UTF-8"))) {
- System.out.println(line);
+ assertEquals("Hello", line);
+ lines++;
}
+ assertEquals(1, lines);
// Binaries and large files are done through the Files API
try (OutputStream out = Files.newOutputStream(in1,
@@ -68,17 +72,18 @@ public class TestExample {
// Or Java 7 style
Path localFile = Files.createTempFile("", ".txt");
Files.copy(in1, localFile, StandardCopyOption.REPLACE_EXISTING);
- System.out.println("Written to: " + localFile);
+ //System.out.println("Written to: " + localFile);
Files.copy(localFile, bundle.getRoot().resolve("out1"));
// Representing references
URI ref = URI.create("http://example.com/external.txt");
Path out3 = bundle.getRoot().resolve("out3");
- System.out.println(Bundles.setReference(out3, ref));
+ Bundles.setReference(out3, ref);
if (Bundles.isReference(out3)) {
URI resolved = Bundles.getReference(out3);
- System.out.println(resolved);
+ assertNotNull(resolved);
+ //System.out.println(resolved);
}
// Saving a bundle:
@@ -87,7 +92,7 @@ public class TestExample {
// NOTE: From now "bundle" and its Path's are CLOSED
// and can no longer be accessed
- System.out.println("Saved to " + zip);
+ //System.out.println("Saved to " + zip);
// Loading a bundle back from disk
try (Bundle bundle2 = Bundles.openBundle(zip)) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
index fa30487..3ca4030 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
@@ -26,6 +26,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
+import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
@@ -81,7 +82,7 @@ public class TestManifest {
.replace("uuid:", ""));
assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path));
}
- System.out.println(uris);
+ //System.out.println(uris);
assertFalse(uris.contains("/mimetype"));
assertFalse(uris.contains("/META-INF"));
assertTrue(uris.remove("/hello.txt"));
@@ -118,7 +119,7 @@ public class TestManifest {
.replace("uuid:", ""));
assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path));
}
- System.out.println(uris);
+ //System.out.println(uris);
assertFalse(uris.contains("/mimetype"));
assertFalse(uris.contains("/META-INF"));
assertTrue(uris.remove("/hello.txt"));
@@ -152,7 +153,7 @@ public class TestManifest {
jsonld);
assertTrue(Files.exists(jsonld));
String manifestStr = new String(Files.readAllBytes(jsonld), "UTF8");
- System.out.println(manifestStr);
+ //System.out.println(manifestStr);
// Rough and ready that somethings are there
// TODO: Read back and check as JSON structure
@@ -167,8 +168,8 @@ public class TestManifest {
try (InputStream jsonIn = Files.newInputStream(jsonld)) {
URI baseURI = jsonld.toUri();
Model model = RDFToManifest.jsonLdAsJenaModel(jsonIn, baseURI);
- model.write(System.out, "TURTLE", baseURI.toString());
- model.write(System.out, "RDF/XML", baseURI.toString());
+ model.write(new ByteArrayOutputStream(), "TURTLE", baseURI.toString());
+ model.write(new ByteArrayOutputStream(), "RDF/XML", baseURI.toString());
String queryStr = "PREFIX ore: <http://www.openarchives.org/ore/terms/>"
+ "PREFIX bundle: <http://purl.org/wf4ever/bundle#>"
@@ -186,8 +187,8 @@ public class TestManifest {
QuerySolution soln = results.nextSolution();
Resource fileRes = soln.getResource("file");
Resource proxy = soln.getResource("proxy");
- System.out.println("File: " + fileRes);
- System.out.println(asURI(fileRes));
+ //System.out.println("File: " + fileRes);
+ //System.out.println(asURI(fileRes));
Path file = Paths.get(asURI(fileRes));
assertTrue(Files.exists(file));
@@ -231,7 +232,7 @@ public class TestManifest {
// assertNotNull(manifest.getAggregation(
// URI.create("http://example.com/comments.txt")).getProxy());
- System.out.println(manifest.getAnnotations());
+ //System.out.println(manifest.getAnnotations());
assertEquals(3, manifest.getAnnotations().size());
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
index ecab340..efab8a9 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
@@ -145,7 +145,7 @@ public class TestManifestJSON {
Path jsonPath = bundle.getManifest().writeAsJsonLD();
ObjectMapper objectMapper = new ObjectMapper();
String jsonStr = Bundles.getStringValue(jsonPath);
- System.out.println(jsonStr);
+ //System.out.println(jsonStr);
JsonNode json = objectMapper.readTree(jsonStr);
checkManifestJson(json);
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
index ce2af70..5286d67 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
@@ -28,31 +28,15 @@ import java.net.URI;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import org.apache.taverna.robundle.Bundle;
import org.apache.taverna.robundle.Bundles;
import org.apache.taverna.robundle.manifest.Agent;
import org.apache.taverna.robundle.manifest.Manifest;
import org.apache.taverna.robundle.manifest.PathMetadata;
-import org.junit.BeforeClass;
import org.junit.Test;
public class TestCombineManifest {
-
- @BeforeClass
- public static void setLogging() {
- Logger logger = Logger.getLogger("");
- // logger.setLevel(Level.FINER);
- ConsoleHandler console = new ConsoleHandler();
- console.setLevel(Level.FINEST);
- logger.addHandler(console);
- Logger.getLogger("org.apache.taverna.robundle.manifest.combine")
- .setLevel(Level.FINEST);
- }
-
@Test
public void convertAslanidi() throws Exception {
Path file = Files.createTempFile("aslanidi", ".zip");
@@ -94,7 +78,7 @@ public class TestCombineManifest {
"/combine/Boris.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
Manifest manifest = bundle.getManifest();
Path manifestXml = bundle.getRoot().resolve("manifest.xml");
@@ -122,7 +106,7 @@ public class TestCombineManifest {
"/combine/DirectoryMadness.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
Manifest manifest = bundle.getManifest();
Path manifestXml = bundle.getRoot().resolve("manifest.xml");
@@ -162,7 +146,7 @@ public class TestCombineManifest {
"/combine/DirectoryMadnessZipped.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
}
[02/52] [abbrv] incubator-taverna-language git commit: Removed
duplicate workflows (See scufl2-examples)
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/gbseq_test_457824.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/gbseq_test_457824.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/gbseq_test_457824.t2flow
deleted file mode 100644
index 75cf8de..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/gbseq_test_457824.t2flow
+++ /dev/null
@@ -1,485 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="f0fac9a7-7943-4191-a0d3-7e8e09044e43" role="top"><name>GBSeq_test</name><inputPorts /><outputPorts><port><name>nuc_fasta</name><annotations /></port><port><name>nuc_xml</name><annotations /></port><port><name>nuc_insd</name><annotations /></port><port><name>nuc_tiny</name><annotations /></port><port><name>prot_fasta</name><annotations /></port><port><name>protein_xml</name><annotations /></port><port><name>prot_insd</name><annotations /></port><port><name>prot_tiny</name><annotations /></port></outputPorts><processors><processor><name>nuc_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.St
ringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>NM_000059</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>protein_id</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf
.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>NP_000050</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_INSDSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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><map from="id" to="id" /></
inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker</localworkerName>
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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.LocalworkerActivit
y</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker</localworkerName>
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_GBSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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.LocalworkerAct
ivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker</localworkerName>
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=nucleotide&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_TinySeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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.LocalworkerA
ctivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker</localworkerName>
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=" + id);
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=" + id);
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- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
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-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=protein&retmode=xml&id=" + id);
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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">
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
- <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated
-to them given a protein and a nucleotide id.</text>
- </annotationBean>
- <date>2009-12-15 20:30:23.505 GMT</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>f0fac9a7-7943-4191-a0d3-7e8e09044e43</identification>
- </annotationBean>
- <date>2010-07-04 18:16:42.290 BST</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>GBSeq test</text>
- </annotationBean>
- <date>2009-12-15 20:30:12.959 GMT</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/72cbd2dd/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/merge_fun.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/merge_fun.t2flow b/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/merge_fun.t2flow
deleted file mode 100644
index a84b482..0000000
--- a/taverna-scufl2-usecases/src/main/resources/workflows/t2flow/merge_fun.t2flow
+++ /dev/null
@@ -1,66 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</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><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
- <script>outputlist = inputlist;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>inputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="inputlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>a</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>a</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>b</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.
t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>b</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="merge"><port>b</port></sink><source type="processor"><processor>a</processor><port>value</port></source></datalink><datalink><sink type="merge"><port>b</port></sink><source type="processor"><processor>b</processor><port>value</port></source></datalink><datalink><sink type="merge"><processor>Echo_List</processor><port>inputlist</port></sink><source type="processor"><processor>b</processor><port>value</port></source></datalink><datalink><
sink type="merge"><processor>Echo_List</processor><port>inputlist</port></sink><source type="processor"><processor>a</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>a</port></sink><source type="processor"><processor>Echo_List</processor><port>outputlist</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>aaecfd60-6456-4573-a25c-bcb841050601</identification>
- </annotationBean>
- <date>2010-10-29 09:52:34.321 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
[20/52] [abbrv] incubator-taverna-language git commit: Apache haders
Posted by st...@apache.org.
Apache haders
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/0765cffe
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/0765cffe
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/0765cffe
Branch: refs/heads/master
Commit: 0765cffe0c4cf603959652bb2d4043b459d7f2a8
Parents: 19114d5
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:44:10 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:44:10 2015 +0000
----------------------------------------------------------------------
.../org/apache/taverna/scufl2/rdf/scufl2.ttl | 17 +++++++++++++++++
.../org/apache/taverna/scufl2/rdf/taverna-2.2.ttl | 17 +++++++++++++++++
2 files changed, 34 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/0765cffe/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/scufl2.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/scufl2.ttl b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/scufl2.ttl
index 041bd71..961dd8b 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/scufl2.ttl
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/scufl2.ttl
@@ -1,3 +1,20 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
@prefix : <http://ns.taverna.org.uk/2010/scufl2#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/0765cffe/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/taverna-2.2.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/taverna-2.2.ttl b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/taverna-2.2.ttl
index 1115c3d..be3fdee 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/taverna-2.2.ttl
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdf/taverna-2.2.ttl
@@ -1,3 +1,20 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
@base <http://ns.taverna.org.uk/2010/taverna/2.2/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
[40/52] [abbrv] incubator-taverna-language git commit: Delete a bunch
of unused files.
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/7e05272d/taverna-scufl2-wfdesc/src/test/resources/enm-v21.wfdesc.ttl
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfdesc/src/test/resources/enm-v21.wfdesc.ttl b/taverna-scufl2-wfdesc/src/test/resources/enm-v21.wfdesc.ttl
deleted file mode 100644
index b63928b..0000000
--- a/taverna-scufl2-wfdesc/src/test/resources/enm-v21.wfdesc.ttl
+++ /dev/null
@@ -1,10323 +0,0 @@
-@base <http://ns.taverna.org.uk/2010/workflowBundle/dc6b1ade-a4eb-4032-af2a-689430f8438a/workflow/Ecological_niche_mod/> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix prov: <http://www.w3.org/ns/prov#> .
-@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
-@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
-@prefix roterms: <http://purl.org/wf4ever/roterms#> .
-@prefix dc: <http://purl.org/dc/elements/1.1/> .
-@prefix dcterms: <http://purl.org/dc/terms/> .
-@prefix comp: <http://purl.org/DP/components#> .
-@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
-@prefix biocat: <http://biocatalogue.org/attribute/> .
-@prefix : <#> .
-
-<../Allocate_points/processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <../Allocate_points/processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <../Allocate_points/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Allocate_points/processor/csv_to_xml_list/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "csv_to_xml_list" ;
- wfdesc:hasInput <../Allocate_points/processor/csv_to_xml_list/in/csv_points> , <../Allocate_points/processor/csv_to_xml_list/in/id_idx> , <../Allocate_points/processor/csv_to_xml_list/in/lat_idx> , <../Allocate_points/processor/csv_to_xml_list/in/long_idx> ;
- wfdesc:hasOutput <../Allocate_points/processor/csv_to_xml_list/out/all_points> , <../Allocate_points/processor/csv_to_xml_list/out/num_points> ;
- wf4ever:script """import java.io.StringReader;
-import java.io.BufferedReader;
-
-BufferedReader reader = new BufferedReader(new StringReader(csv_points));
-
-int id_idx_int = Integer.parseInt(id_idx);
-int long_idx_int = Integer.parseInt(long_idx);
-int lat_idx_int = Integer.parseInt(lat_idx);
-
-int max_idx = Math.max(id_idx_int, Math.max(long_idx_int, lat_idx_int));
-
-String id;
-int count = 0;
-
-ArrayList all_points = new ArrayList();
-
-for (String line = reader.readLine(); line != null; line = reader.readLine()) {
- count++;
- String[] parts = line.split(\",\");
-
- if (parts.length > max_idx) {
-
- if (id_idx_int == -1) {
- id = String.valueOf(count);
- }
- else {
- id = parts[id_idx_int];
- }
-
- String point = \"<Point Id=\\\"\" + id +\"\\\" \" +
- \"X=\\\"\" + parts[long_idx_int] + \"\\\" \" +
- \"Y=\\\"\" + parts[lat_idx_int] + \"\\\"/>\";
-
- all_points.add(point);
- }
-}
-
-num_points = all_points.size();
-""" .
-
-<../Ask_user_to_run_or_n/processor/allocate_points/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "allocate_points" ;
- wfdesc:hasInput <../Ask_user_to_run_or_n/processor/allocate_points/in/all_points> , <../Ask_user_to_run_or_n/processor/allocate_points/in/choice> , <../Ask_user_to_run_or_n/processor/allocate_points/in/folds> ;
- wfdesc:hasOutput <../Ask_user_to_run_or_n/processor/allocate_points/out/flag> , <../Ask_user_to_run_or_n/processor/allocate_points/out/testing_points> , <../Ask_user_to_run_or_n/processor/allocate_points/out/training_points> ;
- wf4ever:script """import java.util.ArrayList;
-import java.io.StringReader;
-import java.io.BufferedReader;
-
-ArrayList training_points = new ArrayList();
-ArrayList testing_points = new ArrayList();
-
-ArrayList flag = new ArrayList();
-String xval_test = \"xval\";
-if (choice.equals(xval_test)) {
- flag.add(1);
-}
-else {
- return;
-}
-
-BufferedReader reader = new BufferedReader(new StringReader(all_points));
-
-ArrayList my_all_points = new ArrayList();
-
-for (String line = reader.readLine(); line != null; line = reader.readLine()) {
-
- my_all_points.add(line);
-}
-
-long seed = System.nanoTime();
-Collections.shuffle(my_all_points, new Random(seed));
-
-int num_folds = Integer.parseInt(folds);
-
-int num_points = my_all_points.size();
-
-for (int k = 0; k < num_folds; ++k) {
-
- StringBuilder creation_builder = new StringBuilder();
- StringBuilder testing_builder = new StringBuilder();
-
- for (int i = 0; i < num_points; ++i) {
-
- if (i % num_folds == k) {
-
- testing_builder.append(my_all_points.get(i));
- } else {
-
- creation_builder.append(my_all_points.get(i));
- }
- }
-
- training_points.add( creation_builder.toString() );
- testing_points.add( testing_builder.toString() );
-}""" .
-
-<../Ask_user_to_run_or_n/processor/count_points/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "count_points" ;
- wfdesc:hasInput <../Ask_user_to_run_or_n/processor/count_points/in/all_points> ;
- wfdesc:hasOutput <../Ask_user_to_run_or_n/processor/count_points/out/num_points> ;
- wf4ever:script """import java.io.StringReader;
-import java.io.BufferedReader;
-
-BufferedReader reader = new BufferedReader(new StringReader(all_points));
-
-int num_points = 0;
-
-for (String line = reader.readLine(); line != null; line = reader.readLine()) {
-
- ++num_points;
-}
-""" .
-
-<../Calculate_mean_AUC/processor/calculate_mean/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "calculate_mean" ;
- wfdesc:hasInput <../Calculate_mean_AUC/processor/calculate_mean/in/values_list> ;
- wfdesc:hasOutput <../Calculate_mean_AUC/processor/calculate_mean/out/mean_value> ;
- wf4ever:script """double mean_value = 0;
-
-int num_values = values_list.size();
-
-if (num_values > 0) {
- for (i = values_list.iterator(); i.hasNext();) {
- mean_value += Double.parseDouble(i.next());
- }
- mean_value /= num_values;
-}
-""" .
-
-<../Calculate_mean_AUC1/processor/calculate_mean/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "calculate_mean" ;
- wfdesc:hasInput <../Calculate_mean_AUC1/processor/calculate_mean/in/values_list> ;
- wfdesc:hasOutput <../Calculate_mean_AUC1/processor/calculate_mean/out/mean_value> ;
- wf4ever:script """double mean_value = 0;
-
-int num_values = values_list.size();
-
-if (num_values > 0) {
- for (i = values_list.iterator(); i.hasNext();) {
- mean_value += Double.parseDouble(i.next());
- }
- mean_value /= num_values;
-}
-""" .
-
-<../Create_model/processor/make_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "make_xml" ;
- wfdesc:hasInput <../Create_model/processor/make_xml/in/absence_points_xml> , <../Create_model/processor/make_xml/in/algorithm_xml> , <../Create_model/processor/make_xml/in/environmentally_unique> , <../Create_model/processor/make_xml/in/layers> , <../Create_model/processor/make_xml/in/mask_id> , <../Create_model/processor/make_xml/in/presence_points_xml> , <../Create_model/processor/make_xml/in/spatially_unique> , <../Create_model/processor/make_xml/in/species_label> , <../Create_model/processor/make_xml/in/srs> ;
- wfdesc:hasOutput <../Create_model/processor/make_xml/out/xml> ;
- wf4ever:script """xml = \"<?xml version=\\\"1.0\\\" encoding=\\\"iso-8859-1\\\"?>\\n\"
-+\"<omws:createModel xmlns:omws=\\\"http://openmodeller.cria.org.br/ws/2.0\\\" xmlns:SOAP-ENV=\\\"http://schemas.xmlsoap.org/soap/envelope/\\\" SOAP-ENV:encodingStyle=\\\"http://xml.apache.org/xml-soap/literalxml\\\">\\n\"
-+\"<ModelParameters xmlns=\\\"http://openmodeller.cria.org.br/xml/2.0\\\">\\n\"
-+\"<Sampler>\\n\"
-+\"<Environment>\\n\";
-int i = 0;
-String[] s_layers = layers.split(\"\\n\");
-for ( i = 0; i < s_layers.length; ++i ) {
- if ( s_layers[i].length() > 0 ) {
- xml += \"<Map Id=\\\"\"+s_layers[i]+\"\\\"/>\\n\";
- }
-}
-xml += \"<Mask Id=\\\"\"+mask_id+\"\\\"/>\\n\"
-+\"</Environment>\\n\";
-if ( presence_points_xml.length() > 0 ) {
- xml += \"<Presence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +presence_points_xml
- +\"</Presence>\\n\";
-}
-if ( absence_points_xml.length() > 0 ) {
- xml += \"<Absence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +absence_points_xml
- +\"</Absence>\\n\";
-}
-xml += \"</Sampler>\\n\"
-+algorithm_xml
-+\"<Options>\\n\";
-if (spatially_unique.equals(\"yes\") || environmentally_unique.equals(\"yes\")) {
- xml += \"<OccurrencesFilter>\\n\";
- if (environmentally_unique.equals(\"yes\")) {
- xml += \"<EnvironmentallyUnique/>\\n\";
- }
- if (spatially_unique.equals(\"yes\")) {
- xml += \"<SpatiallyUnique/>\\n\";
- }
- xml += \"</OccurrencesFilter>\\n\";
-}
-xml += \"</Options>\\n\"
-+\"</ModelParameters>\\n\"
-+\"</omws:createModel>\\n\";""" .
-
-<processor/Flatten_AUC_List/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_AUC_List" ;
- wfdesc:hasInput <processor/Flatten_AUC_List/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_AUC_List/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Flatten_omission_List/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_omission_List" ;
- wfdesc:hasInput <processor/Flatten_omission_List/in/inputlist> ;
- wfdesc:hasOutput <processor/Flatten_omission_List/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <processor/Merge_String_List_to_a_String/in/seperator> , <processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<processor/empty_list/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "empty_list" ;
- wfdesc:hasOutput <processor/empty_list/out/empty_list> ;
- wf4ever:script "ArrayList empty_list = new ArrayList();" .
-
-<processor/make_biostif_url/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "make_biostif_url" ;
- wfdesc:hasInput <processor/make_biostif_url/in/csv_url> , <processor/make_biostif_url/in/seperator> , <processor/make_biostif_url/in/stringlist> ;
- wfdesc:hasOutput <processor/make_biostif_url/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = \"http://biovel.iais.fraunhofer.de/biostif/main.jsp?debug=true&layers=\"+sb.toString()+\"&label=species_points&contenttype=csv&url=\"+csv_url;
-""" .
-
-<processor/terminate/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- dcterms:description "This script was created as a workaround to a Taverna 2.4 bug. It is used to receive the output of a nested workflow, so that the nested workflow terminates." ;
- rdfs:label "terminate" ;
- wfdesc:hasInput <processor/terminate/in/input> ;
- wf4ever:script "" .
-
-<processor/update_biostif_layers/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "update_biostif_layers" ;
- wfdesc:hasInput <processor/update_biostif_layers/in/biostif_layers_xml_list> , <processor/update_biostif_layers/in/created> , <processor/update_biostif_layers/in/mask_id> ;
- wfdesc:hasOutput <processor/update_biostif_layers/out/new_biostif_layers_xml_list> ;
- wf4ever:script """ArrayList new_biostif_layers_xml_list = new ArrayList();
-if (created.equals(\"0\")) {
- new_biostif_layers_xml_list = biostif_layers_xml_list;
-}
-else {
- String[] parts = mask_id.split(\">\");
- String url = parts[1];
- String layer_id = parts[2];
- String[] subparts = layer_id.split(\":\");
- workspace = subparts[0];
- layer_name = subparts[1];
- String xml_piece = \"<layers><layer><name>\"+layer_id+\"</name><url>\"+url+\"</url></layer>\";
- for (int i = 0; i < biostif_layers_xml_list.size(); ++i) {
- xml = biostif_layers_xml_list.get(i);
- if (xml.contains(\"<name>\"+workspace+\":\")) {
- xml = xml.replaceFirst(\"<layers>\", xml_piece);
- }
- new_biostif_layers_xml_list.add(xml);
- }
-}
-""" .
-
-<../Error_Handler/processor/create_error_message/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_error_message" ;
- wfdesc:hasInput <../Error_Handler/processor/create_error_message/in/filename> , <../Error_Handler/processor/create_error_message/in/status> ;
- wfdesc:hasOutput <../Error_Handler/processor/create_error_message/out/message> ;
- wf4ever:script """if (status.size() > 0 && status.get(0).toString().length() > 0) {
- message = \"Error on loading file \" + filename + \": Service returned an error code: \" + status.get(0);
-} else {
- message = \"\";
-}""" .
-
-<../Extract_model_algorithm/processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <../Extract_model_algorithm/processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <../Extract_model_algorithm/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Extracts_AUC/processor/Flatten_List_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_1" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_1/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_1/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/Flatten_List_6/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_6" ;
- wfdesc:hasInput <../Extracts_AUC/processor/Flatten_List_6/in/inputlist> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/Flatten_List_6/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Extracts_AUC/processor/router/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "router" ;
- wfdesc:hasInput <../Extracts_AUC/processor/router/in/calculate_matrix> , <../Extracts_AUC/processor/router/in/measure_auc> ;
- wfdesc:hasOutput <../Extracts_AUC/processor/router/out/extract_auc> , <../Extracts_AUC/processor/router/out/extract_omission> , <../Extracts_AUC/processor/router/out/skip_auc> , <../Extracts_AUC/processor/router/out/skip_omission> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList extract_auc = new ArrayList();
-ArrayList skip_auc = new ArrayList();
-ArrayList extract_omission = new ArrayList();
-ArrayList skip_omission = new ArrayList();
-
-if (measure_auc.equals(\"yes\")) {
- extract_auc.add(1);
-}
-else {
- skip_auc.add(1);
-}
-
-if (calculate_matrix.equals(\"yes\")) {
- extract_omission.add(1);
-}
-else {
- skip_omission.add(1);
-}
-""" .
-
-<../Get_threshold/processor/Flatten_List_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_1" ;
- wfdesc:hasInput <../Get_threshold/processor/Flatten_List_1/in/inputlist> ;
- wfdesc:hasOutput <../Get_threshold/processor/Flatten_List_1/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Get_threshold/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../Get_threshold/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../Get_threshold/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Get_threshold/processor/check_if_threshold_must_be_calculated/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "check_if_threshold_must_be_calculated" ;
- wfdesc:hasInput <../Get_threshold/processor/check_if_threshold_must_be_calculated/in/threshold> ;
- wfdesc:hasOutput <../Get_threshold/processor/check_if_threshold_must_be_calculated/out/calculate_threshold> , <../Get_threshold/processor/check_if_threshold_must_be_calculated/out/repeat_value> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList calculate_threshold = new ArrayList();
-ArrayList repeat_value = new ArrayList();
-
-if (threshold.equals(\"lpt\") ) {
-
- calculate_threshold.add(1);
-}
-else {
-
- repeat_value.add(1);
-}
-""" .
-
-<../Get_threshold/processor/get_first_item/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "get_first_item" ;
- wfdesc:hasInput <../Get_threshold/processor/get_first_item/in/list> ;
- wfdesc:hasOutput <../Get_threshold/processor/get_first_item/out/single_value> ;
- wf4ever:script "single_value = list.get(0);" .
-
-<../Get_threshold/processor/repeat_value/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "repeat_value" ;
- wfdesc:hasInput <../Get_threshold/processor/repeat_value/in/flag> , <../Get_threshold/processor/repeat_value/in/input_threshold> ;
- wfdesc:hasOutput <../Get_threshold/processor/repeat_value/out/output_threshold> ;
- wf4ever:script "output_threshold = input_threshold;" .
-
-<../Parse_input_file/processor/extract_taxon_points/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "extract_taxon_points" ;
- wfdesc:hasInput <../Parse_input_file/processor/extract_taxon_points/in/csv_content> , <../Parse_input_file/processor/extract_taxon_points/in/name_idx> ;
- wfdesc:hasOutput <../Parse_input_file/processor/extract_taxon_points/out/taxon_points> ;
- wf4ever:script """import java.io.StringReader;
-import java.io.BufferedReader;
-
-BufferedReader reader = new BufferedReader(new StringReader(csv_content));
-
-StringBuilder builder = new StringBuilder();
-
-int name_idx_int = Integer.parseInt(name_idx);
-
-String eol = System.getProperty(\"line.separator\");
-
-int i = 0;
-
-for (String line = reader.readLine(); line != null; line = reader.readLine()) {
- i++;
- if (i == 1) {
- continue;
- }
-
- if (taxon_name != void) {
-
- String[] parts = line.split(\",\");
-
- if (parts.length > name_idx_int) {
-
- if (parts[name_idx_int].equals(taxon_name)) {
-
- builder.append(line+eol);
- }
- }
- }
- else {
- builder.append(line+eol);
- }
-}
-
-String taxon_points = builder.toString();""" .
-
-<../Parse_input_file/processor/get_first_taxon/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "get_first_taxon" ;
- wfdesc:hasInput <../Parse_input_file/processor/get_first_taxon/in/csv_content> , <../Parse_input_file/processor/get_first_taxon/in/name_idx> ;
- wfdesc:hasOutput <../Parse_input_file/processor/get_first_taxon/out/taxon_name> ;
- wf4ever:script """import java.io.StringReader;
-import java.io.BufferedReader;
-
-String taxon_name = \"\";
-int name_idx_int = Integer.parseInt(name_idx);
-
-BufferedReader reader = new BufferedReader(new StringReader(csv_content));
-
-String first_line = reader.readLine();
-String second_line = reader.readLine();
-
-if (second_line != null) {
-
- if (name_idx_int >= 0) {
-
- String[] parts = second_line.split(\",\");
-
- if (parts.length > name_idx_int) {
-
- taxon_name = parts[name_idx_int];
- }
- }
-}
-else {
- throw new RuntimeException(\"The input file provided for species occurrence points has no other lines after the header.\");
-}
-""" .
-
-<../Parse_input_file/processor/parse_header/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "parse_header" ;
- wfdesc:hasInput <../Parse_input_file/processor/parse_header/in/csv_content> ;
- wfdesc:hasOutput <../Parse_input_file/processor/parse_header/out/id_idx> , <../Parse_input_file/processor/parse_header/out/lat_idx> , <../Parse_input_file/processor/parse_header/out/long_idx> , <../Parse_input_file/processor/parse_header/out/name_idx> ;
- wf4ever:script """import java.io.StringReader;
-import java.io.BufferedReader;
-
-int name_idx = -1;
-int id_idx = -1;
-int long_idx = -1;
-int lat_idx = -1;
-
-BufferedReader reader = new BufferedReader(new StringReader(csv_content));
-
-String header = reader.readLine();
-
-if ( header != null) {
- String[] parts = header.split(\",\");
- List terms = Arrays.asList(parts);
- name_idx = terms.indexOf(\"nameComplete\");
- id_idx = terms.indexOf(\"occurrenceID\");
- long_idx = terms.indexOf(\"decimalLongitude\");
- lat_idx = terms.indexOf(\"decimalLatitude\");
-}
-else {
- throw new RuntimeException(\"The input file provided for species occurrence points is empty.\");
-}
-
-if ( name_idx == -1 ) {
- throw new RuntimeException(\"The column nameComplete is missing from the header of the input points file.\");
-}
-if ( long_idx == -1 ) {
- throw new RuntimeException(\"The column decimalLongitude is missing from the header of the input points file.\");
-}
-if ( lat_idx == -1 ) {
- throw new RuntimeException(\"The column decimalLatitude is missing from the header of the input points file.\");
-}
-
-""" .
-
-<../Prepare_configuratio/processor/make_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "make_xml" ;
- wfdesc:hasInput <../Prepare_configuratio/processor/make_xml/in/absence_points_xml> , <../Prepare_configuratio/processor/make_xml/in/calculate_matrix> , <../Prepare_configuratio/processor/make_xml/in/calculate_roc> , <../Prepare_configuratio/processor/make_xml/in/layers> , <../Prepare_configuratio/processor/make_xml/in/mask_id> , <../Prepare_configuratio/processor/make_xml/in/model_xml> , <../Prepare_configuratio/processor/make_xml/in/num_background_points> , <../Prepare_configuratio/processor/make_xml/in/presence_points_xml> , <../Prepare_configuratio/processor/make_xml/in/species_label> , <../Prepare_configuratio/processor/make_xml/in/srs> , <../Prepare_configuratio/processor/make_xml/in/threshold> ;
- wfdesc:hasOutput <../Prepare_configuratio/processor/make_xml/out/xml> ;
- wf4ever:script """xml = \"<?xml version=\\\"1.0\\\" encoding=\\\"iso-8859-1\\\"?>\\n\"
-+\"<omws:testModel xmlns:omws=\\\"http://openmodeller.cria.org.br/ws/2.0\\\" xmlns:SOAP-ENV=\\\"http://schemas.xmlsoap.org/soap/envelope/\\\" SOAP-ENV:encodingStyle=\\\"http://xml.apache.org/xml-soap/literalxml\\\">\\n\"
-+\"<TestParameters xmlns=\\\"http://openmodeller.cria.org.br/xml/2.0\\\">\\n\"
-+\"<Sampler>\\n\"
-+\"<Environment>\\n\";
-int i = 0;
-String[] s_layers = layers.split(\"\\n\");
-for ( i = 0; i < s_layers.length; ++i ) {
- if ( s_layers[i].length() > 0 ) {
- xml += \"<Map Id=\\\"\"+s_layers[i]+\"\\\"/>\\n\";
- }
-}
-xml += \"<Mask Id=\\\"\"+mask_id+\"\\\"/>\\n\"
-+\"</Environment>\\n\";
-if ( presence_points_xml.length() > 0 ) {
- xml += \"<Presence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +presence_points_xml
- +\"</Presence>\\n\";
-}
-if ( absence_points_xml.length() > 0 ) {
- xml += \"<Absence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +absence_points_xml
- +\"</Absence>\\n\";
-}
-xml += \"</Sampler>\\n\"
-+model_xml
-+\"<Statistics>\\n\";
-if (calculate_matrix.equals(\"yes\")) {
- xml += \"<ConfusionMatrix Threshold=\\\"\"+threshold+\"\\\"/>\\n\";
-}
-if (calculate_roc.equals(\"yes\")) {
- xml += \"<RocCurve Resolution=\\\"15\\\" BackgroundPoints=\\\"\"+num_background_points+\"\\\"/>\\n\";
-}
-xml += \"</Statistics>\\n\"
-+\"</TestParameters>\\n\"
-+\"</omws:testModel>\\n\";""" .
-
-<../Prepare_configuratio1/processor/make_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "make_xml" ;
- wfdesc:hasInput <../Prepare_configuratio1/processor/make_xml/in/absence_points_xml> , <../Prepare_configuratio1/processor/make_xml/in/layers> , <../Prepare_configuratio1/processor/make_xml/in/mask_id> , <../Prepare_configuratio1/processor/make_xml/in/model_xml> , <../Prepare_configuratio1/processor/make_xml/in/presence_points_xml> , <../Prepare_configuratio1/processor/make_xml/in/species_label> , <../Prepare_configuratio1/processor/make_xml/in/srs> ;
- wfdesc:hasOutput <../Prepare_configuratio1/processor/make_xml/out/xml> ;
- wf4ever:script """xml = \"<?xml version=\\\"1.0\\\" encoding=\\\"iso-8859-1\\\"?>\\n\"
-+\"<omws:evaluateModel xmlns:omws=\\\"http://openmodeller.cria.org.br/ws/2.0\\\" xmlns:SOAP-ENV=\\\"http://schemas.xmlsoap.org/soap/envelope/\\\" SOAP-ENV:encodingStyle=\\\"http://xml.apache.org/xml-soap/literalxml\\\">\\n\"
-+\"<ModelEvaluationParameters xmlns=\\\"http://openmodeller.cria.org.br/xml/2.0\\\">\\n\"
-+\"<Sampler>\\n\"
-+\"<Environment>\\n\";
-int i = 0;
-String[] s_layers = layers.split(\"\\n\");
-for ( i = 0; i < s_layers.length; ++i ) {
- if ( s_layers[i].length() > 0 ) {
- xml += \"<Map Id=\\\"\"+s_layers[i]+\"\\\"/>\\n\";
- }
-}
-xml += \"<Mask Id=\\\"\"+mask_id+\"\\\"/>\\n\"
-+\"</Environment>\\n\";
-if ( presence_points_xml.length() > 0 ) {
- xml += \"<Presence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +presence_points_xml
- +\"</Presence>\\n\";
-}
-if ( absence_points_xml.length() > 0 ) {
- xml += \"<Absence Label=\\\"\"+species_label+\"\\\">\\n\"
- +\"<CoordinateSystem>\"+srs+\"</CoordinateSystem>\\n\"
- +absence_points_xml
- +\"</Absence>\\n\";
-}
-xml += \"</Sampler>\\n\"
-+model_xml
-+\"</ModelEvaluationParameters>\\n\"
-+\"</omws:evaluateModel>\\n\";""" .
-
-<../Prepare_configuratio2/processor/make_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "make_xml" ;
- wfdesc:hasInput <../Prepare_configuratio2/processor/make_xml/in/layers> , <../Prepare_configuratio2/processor/make_xml/in/mask_id> , <../Prepare_configuratio2/processor/make_xml/in/model_xml> , <../Prepare_configuratio2/processor/make_xml/in/output_format> , <../Prepare_configuratio2/processor/make_xml/in/template_id> , <../Prepare_configuratio2/processor/make_xml/in/threshold> ;
- wfdesc:hasOutput <../Prepare_configuratio2/processor/make_xml/out/xml> ;
- wf4ever:script """xml = \"<?xml version=\\\"1.0\\\" encoding=\\\"iso-8859-1\\\"?>\\n\"
-+\"<omws:projectModel xmlns:omws=\\\"http://openmodeller.cria.org.br/ws/2.0\\\" xmlns:SOAP-ENV=\\\"http://schemas.xmlsoap.org/soap/envelope/\\\" SOAP-ENV:encodingStyle=\\\"http://xml.apache.org/xml-soap/literalxml\\\">\\n\"
-+\"<ProjectionParameters xmlns=\\\"http://openmodeller.cria.org.br/xml/2.0\\\">\\n\"
-+model_xml
-+\"<Environment>\\n\";
-int i = 0;
-String[] s_layers = layers.split(\"\\n\");
-for ( i = 0; i < s_layers.length; ++i ) {
- if ( s_layers[i].length() > 0 ) {
- xml += \"<Map Id=\\\"\"+s_layers[i]+\"\\\"/>\\n\";
- }
-}
-xml += \"<Mask Id=\\\"\"+mask_id+\"\\\"/>\\n\"
-+\"</Environment>\\n\"
-+\"<OutputParameters FileType=\\\"\"+output_format+\"\\\">\\n\"
-+\"<TemplateLayer Id=\\\"\"+template_id+\"\\\"/>\\n\"
-+\"</OutputParameters>\\n\"
-+\"<Statistics>\\n\"
-+\"<AreaStatistics Threshold=\\\"\"+threshold+\"\\\"/>\\n\"
-+\"</Statistics>\\n\"
-+\"</ProjectionParameters>\\n\"
-+\"</omws:projectModel>\\n\";""" .
-
-<../Raster_SHIM_service/processor/check_service_ok/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "check_service_ok" ;
- wfdesc:hasInput <../Raster_SHIM_service/processor/check_service_ok/in/status> ;
- wfdesc:hasOutput <../Raster_SHIM_service/processor/check_service_ok/out/status_failed> , <../Raster_SHIM_service/processor/check_service_ok/out/status_ok> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList status_ok = new ArrayList();
-ArrayList status_failed = new ArrayList();
-
-if (status.equals(\"200\")) {
- status_ok.add(status);
-} else {
- status_failed.add(status);
-}""" .
-
-<../Raster_SHIM_service/processor/flatten_outputs/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "flatten_outputs" ;
- wfdesc:hasInput <../Raster_SHIM_service/processor/flatten_outputs/in/png_url> , <../Raster_SHIM_service/processor/flatten_outputs/in/raster_layername> , <../Raster_SHIM_service/processor/flatten_outputs/in/stif_layerdescription> ;
- wfdesc:hasOutput <../Raster_SHIM_service/processor/flatten_outputs/out/out_layername> , <../Raster_SHIM_service/processor/flatten_outputs/out/out_pngurl> , <../Raster_SHIM_service/processor/flatten_outputs/out/out_stif_layerdescription> ;
- wf4ever:script """if (stif_layerdescription instanceof Collection && stif_layerdescription.size() > 0) {
- out_stif_layerdescription = stif_layerdescription.get(0);
-} else {
- throw new RuntimeException(\"No STIF layer description supplied\");
-}
-
-if (png_url instanceof Collection && png_url.size() > 0) {
- out_pngurl = png_url.get(0);
-} else {
- throw new RuntimeException(\"No PNG URL supplied\");
-}
-if (raster_layername instanceof Collection && raster_layername.size() > 0) {
- out_layername = raster_layername.get(0);
-} else {
- throw new RuntimeException(\"No Raster layer name supplied\");
-}""" .
-
-<../Raster_Shim_Results_Parser/processor/create_STIF_rasterlayer_parameter/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_STIF_rasterlayer_parameter" ;
- wfdesc:hasInput <../Raster_Shim_Results_Parser/processor/create_STIF_rasterlayer_parameter/in/label> , <../Raster_Shim_Results_Parser/processor/create_STIF_rasterlayer_parameter/in/layername> ;
- wfdesc:hasOutput <../Raster_Shim_Results_Parser/processor/create_STIF_rasterlayer_parameter/out/stif_parameter> ;
- wf4ever:script """/*String out_layername;
-//if (layername instanceof Collection && layername.size() > 0) {
-// out_layername = layername.get(0);
-//} else {
-// out_layername = layername;
-//}*/
-stif_parameter = label + \"@\" +layername + \"@\" + \"false\";
-
-""" .
-
-<../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "parse_json_raster_shim_results" ;
- wfdesc:hasInput <../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/in/json> ;
- wfdesc:hasOutput <../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/out/layername> , <../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/out/pngurl> , <../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/out/serverurl> , <../Raster_Shim_Results_Parser/processor/parse_json_raster_shim_results/out/wmsurl> ;
- wf4ever:script """String rastershimoutput;
-if (json instanceof Collection && json.size() > 0) {
- rastershimoutput = json.get(0);
-} else {
- rastershimoutput = json;
-}
-
-if (rastershimoutput.length() > 0) {
- int index = rastershimoutput.indexOf(\"\\\"layername\\\":\");
- int lastIndex = 0;
- if (index >= 0) {
- index+=12;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index) -1;
- layername = rastershimoutput.substring(index, lastIndex-1);
- layername = layername.replaceAll(\"\\\"\",\"\");
-
- }
- index = rastershimoutput.indexOf(\"\\\"wmsurl\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=9;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index) -1;
- wmsurl = rastershimoutput.substring(index, lastIndex-1);
- wmsurl = wmsurl.replaceAll(\"\\\"\",\"\");
- index=wmsurl.indexOf(\"?\");
- serverurl = wmsurl.substring(0, index);
-
- }
- index = rastershimoutput.indexOf(\"\\\"pngurl\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=9;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index) - 1;
- pngurl = rastershimoutput.substring(index, lastIndex-1);
- pngurl = pngurl.replaceAll(\"\\\"\",\"\");
- }
- index = rastershimoutput.indexOf(\"\\\"nativeFormat\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=15;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index)-1;
- nativeFormat = rastershimoutput.substring(index, lastIndex);
- nativeFormat = nativeFormat.replaceAll(\"\\\"\",\"\");
- }
- index = rastershimoutput.indexOf(\"\\\"srs\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=6;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index)-1;
- srs = rastershimoutput.substring(index, lastIndex);
- srs = srs.replaceAll(\"\\\"\",\"\");
- }
- index = rastershimoutput.indexOf(\"\\\"boundingbox\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=14;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index)-1;
- boundingbox = rastershimoutput.substring(index, lastIndex);
- boundingbox = boundingbox.replaceAll(\"\\\"\",\"\");
- }
- index = rastershimoutput.indexOf(\"\\\"resolution\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=13;
- lastIndex = rastershimoutput.indexOf(\"\\n\", index)-1;
- resolution = rastershimoutput.substring(index, lastIndex);
- resolution =resolution.replaceAll(\"\\\"\",\"\");
- }
- index = rastershimoutput.indexOf(\"\\\"supportedFormats\\\":\");
- lastIndex = 0;
- if (index >= 0) {
- index+=20;
- lastIndex = rastershimoutput.indexOf(\"}\", index) -1;
- /* String strformats = rastershimoutput.substring(index, lastIndex);*/
- String formats = rastershimoutput.substring(index, lastIndex);
- formats = formats.replaceAll(\"\\\"\",\"\");
- /* formats = new ArrayList();
- String[] formatList = strformats.split(\",\");
- for (int i = 0; i < formatList.length; i++) {
- formats.add(fornmatList[i]);
- }*/
- }
-}
-""" .
-
-<../Run_projections/processor/append_values/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "append_values" ;
- wfdesc:hasInput <../Run_projections/processor/append_values/in/area_statistics> , <../Run_projections/processor/append_values/in/img_url> , <../Run_projections/processor/append_values/in/in_logs> , <../Run_projections/processor/append_values/in/in_statistics> , <../Run_projections/processor/append_values/in/in_stif_layers> , <../Run_projections/processor/append_values/in/in_urls> , <../Run_projections/processor/append_values/in/projection_log> , <../Run_projections/processor/append_values/in/stif_layer> ;
- wfdesc:hasOutput <../Run_projections/processor/append_values/out/out_logs> , <../Run_projections/processor/append_values/out/out_statistics> , <../Run_projections/processor/append_values/out/out_stif_layers> , <../Run_projections/processor/append_values/out/out_urls> ;
- wf4ever:script """ArrayList out_logs = in_logs;
-out_logs.add( projection_log );
-ArrayList out_urls = in_urls;
-out_urls.add( img_url );
-ArrayList out_statistics = in_statistics;
-out_statistics.add( area_statistics );
-ArrayList out_stif_layers = in_stif_layers;
-out_stif_layers.add( stif_layer );
-""" .
-
-<../Select_algorithm_and/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_algorithm_and/processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_algorithm_and/processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_algorithm_and/processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_algorithm_and/processor/Flatten_List_6/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_6" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Flatten_List_6/in/inputlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Flatten_List_6/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_algorithm_and/processor/Merge_String_List_to_a_String/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Merge_String_List_to_a_String/in/stringlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_algorithm_and/processor/Merge_String_List_to_a_String_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_2" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/Merge_String_List_to_a_String_2/in/stringlist> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/Merge_String_List_to_a_String_2/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_algorithm_and/processor/XPath_From_Text/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "XPath_From_Text" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/XPath_From_Text/in/xml-text> , <../Select_algorithm_and/processor/XPath_From_Text/in/xpath> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/XPath_From_Text/out/nodelistAsXML> ;
- wf4ever:script """import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals(\"\")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;""" .
-
-<../Select_algorithm_and/processor/XPath_From_Text_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "XPath_From_Text_2" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/XPath_From_Text_2/in/xml-text> , <../Select_algorithm_and/processor/XPath_From_Text_2/in/xpath> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/XPath_From_Text_2/out/nodelistAsXML> ;
- wf4ever:script """import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals(\"\")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;""" .
-
-<../Select_algorithm_and/processor/check_parameters/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "check_parameters" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/check_parameters/in/xml_parameter_list> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/check_parameters/out/has_parameters> , <../Select_algorithm_and/processor/check_parameters/out/no_parameters> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList has_parameters = new ArrayList();
-ArrayList no_parameters = new ArrayList();
-
-if (xml_parameter_list.size() == 0) {
-
- no_parameters.add(1);
-}
-else {
-
- has_parameters.add(1);
-}
-
-""" .
-
-<../Select_algorithm_and/processor/create_algorithm_xml/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_algorithm_xml" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/create_algorithm_xml/in/algorithm_id> , <../Select_algorithm_and/processor/create_algorithm_xml/in/algorithm_version> , <../Select_algorithm_and/processor/create_algorithm_xml/in/parameter_names> , <../Select_algorithm_and/processor/create_algorithm_xml/in/parameter_values> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/create_algorithm_xml/out/algorithm_xml> ;
- wf4ever:script """algorithm_xml=\"\";
-
-algorithm_xml+=
- \"<Algorithm Version=\\\"\" + algorithm_version + \"\\\" \" +
- \"Id=\\\"\" + algorithm_id + \"\\\">\";
-algorithm_xml += \"\\n\";
-algorithm_xml += \"<Parameters>\\n\";
-for (int i = 0; i < parameter_names.size(); i++) {
- algorithm_xml += \"<Parameter \";
- algorithm_xml += \"Value=\\\"\" + parameter_values.get(i);
- algorithm_xml += \"\\\" Id=\\\"\" + parameter_names.get(i);
- algorithm_xml += \"\\\"/>\\n\";
-}
-algorithm_xml += \"</Parameters>\";
-algorithm_xml += \"</Algorithm>\";
-algorithm_xml += \"\\n\";
-
-
-""" .
-
-<../Select_algorithm_and/processor/create_xpath_to_get_algorithm/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "create_xpath_to_get_algorithm" ;
- wfdesc:hasInput <../Select_algorithm_and/processor/create_xpath_to_get_algorithm/in/in1> ;
- wfdesc:hasOutput <../Select_algorithm_and/processor/create_xpath_to_get_algorithm/out/out1> ;
- wf4ever:script "out1 = \"//*[local-name()=\\\"Algorithm\\\" and @Id=\\\"\" + in1 + \"\\\"]\";" .
-
-<../Select_layers/processor/Merge_String_List_to_a_String_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_1" ;
- wfdesc:hasInput <../Select_layers/processor/Merge_String_List_to_a_String_1/in/stringlist> ;
- wfdesc:hasOutput <../Select_layers/processor/Merge_String_List_to_a_String_1/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_layers/processor/Merge_String_List_to_a_String_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_2" ;
- wfdesc:hasInput <../Select_layers/processor/Merge_String_List_to_a_String_2/in/stringlist> ;
- wfdesc:hasOutput <../Select_layers/processor/Merge_String_List_to_a_String_2/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_1" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_1/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_1/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/Flatten_List_6/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_6" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/Flatten_List_6/in/inputlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/Flatten_List_6/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Select_or_create_a_m/processor/extract_first_element_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "extract_first_element_1" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/extract_first_element_1/in/inlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/extract_first_element_1/out/first_element> ;
- wf4ever:script """i = inlist.iterator();
-first_element = i.next();""" .
-
-<../Select_or_create_a_m/processor/extract_first_element_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "extract_first_element_2" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/extract_first_element_2/in/inlist> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/extract_first_element_2/out/first_element> ;
- wf4ever:script """i = inlist.iterator();
-first_element = i.next();""" .
-
-<../Select_or_create_a_m/processor/mask_was_selected/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "mask_was_selected" ;
- wfdesc:hasInput <../Select_or_create_a_m/processor/mask_was_selected/in/selected_mask> ;
- wfdesc:hasOutput <../Select_or_create_a_m/processor/mask_was_selected/out/no> , <../Select_or_create_a_m/processor/mask_was_selected/out/yes> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList yes = new ArrayList();
-ArrayList no = new ArrayList();
-
-if (selected_mask.length() > 0) {
-
- yes.add(1);
-}
-else {
-
- no.add(1);
-}
-
-""" .
-
-<../Select_projection_la/processor/Merge_String_List_to_a_String_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_1" ;
- wfdesc:hasInput <../Select_projection_la/processor/Merge_String_List_to_a_String_1/in/stringlist> ;
- wfdesc:hasOutput <../Select_projection_la/processor/Merge_String_List_to_a_String_1/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_projection_la/processor/Merge_String_List_to_a_String_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Merge_String_List_to_a_String_2" ;
- wfdesc:hasInput <../Select_projection_la/processor/Merge_String_List_to_a_String_2/in/stringlist> ;
- wfdesc:hasOutput <../Select_projection_la/processor/Merge_String_List_to_a_String_2/out/concatenated> ;
- wf4ever:script """String seperatorString = \"\\n\";
-if (seperator != void) {
- seperatorString = seperator;
-}
-StringBuffer sb = new StringBuffer();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- sb.append(item);
- if (i.hasNext()) {
- sb.append(seperatorString);
- }
-}
-concatenated = sb.toString();
-""" .
-
-<../Select_projection_la/processor/format_string/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "format_string" ;
- wfdesc:hasInput <../Select_projection_la/processor/format_string/in/input> ;
- wfdesc:hasOutput <../Select_projection_la/processor/format_string/out/output> ;
- wf4ever:script "output = input.replace(' ', '_').toLowerCase();" .
-
-<../Show_projections_in_/processor/Read_Text_File/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Read_Text_File" ;
- wfdesc:hasInput <../Show_projections_in_/processor/Read_Text_File/in/fileurl> ;
- wfdesc:hasOutput <../Show_projections_in_/processor/Read_Text_File/out/filecontents> ;
- wf4ever:script """BufferedReader getReader (String fileUrl, String encoding) throws IOException {
- InputStreamReader reader;
- try {
- if (encoding == null) {
- reader = new FileReader(fileUrl);
- } else {
- reader = new InputStreamReader(new FileInputStream(fileUrl),encoding);
- }
- }
- catch (FileNotFoundException e) {
- // try a real URL instead
- URL url = new URL(fileUrl);
- if (encoding == null) {
- reader = new InputStreamReader (url.openStream());
- } else {
- reader = new InputStreamReader (url.openStream(), encoding);
- }
- }
- return new BufferedReader(reader);
- }
-
-
-
-StringBuffer sb = new StringBuffer(4000);
-
-if (encoding == void) {
- encoding = null;
-}
-
-BufferedReader in = getReader(fileurl, encoding);
-String str;
-String lineEnding = System.getProperty(\"line.separator\");
-
-while ((str = in.readLine()) != null) {
- sb.append(str);
- sb.append(lineEnding);
-}
-in.close();
-filecontents = sb.toString();
-
-""" .
-
-<../Upload_CSV_data_to_B/processor/checkDataUpload/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "checkDataUpload" ;
- wfdesc:hasInput <../Upload_CSV_data_to_B/processor/checkDataUpload/in/status> ;
- wfdesc:hasOutput <../Upload_CSV_data_to_B/processor/checkDataUpload/out/dataUpload_failed> , <../Upload_CSV_data_to_B/processor/checkDataUpload/out/dataUpload_ok> , <../Upload_CSV_data_to_B/processor/checkDataUpload/out/uploadStatus> ;
- wf4ever:script """import java.lang.Integer;
-import java.util.ArrayList;
-
-ArrayList dataUpload_ok = new ArrayList();
-ArrayList dataUpload_failed = new ArrayList();
-int statusInt = Integer.parseInt(status);
-
-if ((statusInt == 200) || (statusInt == 201)) {
- dataUpload_ok.add(\"ok\");
- uploadStatus = \"finished\";
-} else if (statusInt >= 400) {
- dataUpload_failed.add(\"error\");
- uploadStatus = \"finished\";
-} else {
- uploadStatus = \"running\";
-}""" .
-
-<../Upload_CSV_data_to_B/processor/trimRESTurlResult/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "trimRESTurlResult" ;
- wfdesc:hasInput <../Upload_CSV_data_to_B/processor/trimRESTurlResult/in/url> ;
- wfdesc:hasOutput <../Upload_CSV_data_to_B/processor/trimRESTurlResult/out/resultUrl> ;
- wf4ever:script "resultUrl = url.trim();" .
-
-<../Workflow143/processor/calculate_threshold/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "calculate_threshold" ;
- wfdesc:hasInput <../Workflow143/processor/calculate_threshold/in/model_values> , <../Workflow143/processor/calculate_threshold/in/threshold> ;
- wfdesc:hasOutput <../Workflow143/processor/calculate_threshold/out/threshold_value> ;
- wf4ever:script """String[] values_str = model_values.split(\" \");
-List values = Arrays.asList(values_str);
-
-float threshold_value = 1.0;
-float value;
-
-for (int i = 0; i < values.size(); ++i) {
-
- value = Float.parseFloat( values.get(i) );
-
- if ( threshold.equals(\"lpt\") ) {
- if ( value < threshold_value && value > 0.0 ) {
- threshold_value = value;
- }
- }
-}
-""" .
-
-<../Workflow34/processor/Tell/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Tell" ;
- wfdesc:hasInput <../Workflow34/processor/Tell/in/message> , <../Workflow34/processor/Tell/in/title> ;
- wfdesc:hasOutput <../Workflow34/processor/Tell/out/answer> ;
- wf4ever:script """import javax.swing.JOptionPane;
-
-JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.INFORMATION_MESSAGE);
-
-answer = \"\";
-
-""" .
-
-<../Workflow66/processor/assign_zero/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "assign_zero" ;
- wfdesc:hasOutput <../Workflow66/processor/assign_zero/out/zero> ;
- wf4ever:script "float zero = 0.0;" .
-
-<../Workflow661/processor/assign_zero/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "assign_zero" ;
- wfdesc:hasOutput <../Workflow661/processor/assign_zero/out/zero> ;
- wf4ever:script "float zero = 0.0;" .
-
-<../Workflow72/processor/Flatten_List_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_1" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_1/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_1/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/Flatten_List_6/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_6" ;
- wfdesc:hasInput <../Workflow72/processor/Flatten_List_6/in/inputlist> ;
- wfdesc:hasOutput <../Workflow72/processor/Flatten_List_6/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Workflow72/processor/extract_first_element_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "extract_first_element_1" ;
- wfdesc:hasInput <../Workflow72/processor/extract_first_element_1/in/inlist> ;
- wfdesc:hasOutput <../Workflow72/processor/extract_first_element_1/out/first_element> ;
- wf4ever:script """i = inlist.iterator();
-first_element = i.next();""" .
-
-<../Workflow72/processor/extract_first_element_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "extract_first_element_2" ;
- wfdesc:hasInput <../Workflow72/processor/extract_first_element_2/in/inlist> ;
- wfdesc:hasOutput <../Workflow72/processor/extract_first_element_2/out/first_element> ;
- wf4ever:script """i = inlist.iterator();
-first_element = i.next();""" .
-
-<../Workflow72/processor/mask_was_selected/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "mask_was_selected" ;
- wfdesc:hasInput <../Workflow72/processor/mask_was_selected/in/selected_mask> ;
- wfdesc:hasOutput <../Workflow72/processor/mask_was_selected/out/no> , <../Workflow72/processor/mask_was_selected/out/yes> ;
- wf4ever:script """import java.util.ArrayList;
-
-ArrayList yes = new ArrayList();
-ArrayList no = new ArrayList();
-
-if (selected_mask.length() > 0) {
-
- yes.add(1);
-}
-else {
-
- no.add(1);
-}
-
-""" .
-
-<../Workflow743/processor/clear_list/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "clear_list" ;
- wfdesc:hasInput <../Workflow743/processor/clear_list/in/input_list> ;
- wfdesc:hasOutput <../Workflow743/processor/clear_list/out/empty_list> ;
- wf4ever:script """empty_list = input_list;
-empty_list.clear();""" .
-
-<../Workflow78/processor/Flatten_List/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List" ;
- wfdesc:hasInput <../Workflow78/processor/Flatten_List/in/inputlist> ;
- wfdesc:hasOutput <../Workflow78/processor/Flatten_List/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../flatten_cross_validation_outputs/processor/Flatten_List_1/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_1" ;
- wfdesc:hasInput <../flatten_cross_validation_outputs/processor/Flatten_List_1/in/inputlist> ;
- wfdesc:hasOutput <../flatten_cross_validation_outputs/processor/Flatten_List_1/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../flatten_cross_validation_outputs/processor/Flatten_List_2/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_2" ;
- wfdesc:hasInput <../flatten_cross_validation_outputs/processor/Flatten_List_2/in/inputlist> ;
- wfdesc:hasOutput <../flatten_cross_validation_outputs/processor/Flatten_List_2/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../flatten_cross_validation_outputs/processor/Flatten_List_3/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_3" ;
- wfdesc:hasInput <../flatten_cross_validation_outputs/processor/Flatten_List_3/in/inputlist> ;
- wfdesc:hasOutput <../flatten_cross_validation_outputs/processor/Flatten_List_3/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../flatten_cross_validation_outputs/processor/Flatten_List_4/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_4" ;
- wfdesc:hasInput <../flatten_cross_validation_outputs/processor/Flatten_List_4/in/inputlist> ;
- wfdesc:hasOutput <../flatten_cross_validation_outputs/processor/Flatten_List_4/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../flatten_cross_validation_outputs/processor/Flatten_List_5/> a wfdesc:Process , wfdesc:Description , wf4ever:BeanshellScript ;
- rdfs:label "Flatten_List_5" ;
- wfdesc:hasInput <../flatten_cross_validation_outputs/processor/Flatten_List_5/in/inputlist> ;
- wfdesc:hasOutput <../flatten_cross_validation_outputs/processor/Flatten_List_5/out/outputlist> ;
- wf4ever:script """flatten(inputs, outputs, depth) {
- for (i = inputs.iterator(); i.hasNext();) {
- element = i.next();
- if (element instanceof Collection && depth > 0) {
- flatten(element, outputs, depth - 1);
- } else {
- outputs.add(element);
- }
- }
-}
-
-outputlist = new ArrayList();
-
-flatten(inputlist, outputlist, 1);""" .
-
-<../Raster_SHIM_service/processor/raster_upload_service/> a wfdesc:Process , wfdesc:Description , wf4ever:RESTService ;
- rdfs:label "raster_upload_service" ;
- wfdesc:hasInput <../Raster_SHIM_service/processor/raster_upload_service/in/inputformat> , <../Raster_SHIM_service/processor/raster_upload_service/in/layername> , <../Raster_SHIM_service/processor/raster_upload_service/in/sourceURL> , <../Raster_SHIM_service/processor/raster_upload_service/in/styleName> , <../Raster_SHIM_service/processor/raster_upload_service/in/workspaceid%20> ;
- wfdesc:hasOutput <../Raster_SHIM_service/processor/raster_upload_service/out/responseBody> , <../Raster_SHIM_service/processor/raster_upload_service/out/status> .
-
-<../Retrieve_layers/processor/Get_Workspace/> a wfdesc:Process , wfdesc:Description , wf4ever:RESTService ;
- rdfs:label "Get_Workspace" ;
- wfdesc:hasInput <../Retrieve_layers/processor/Get_Workspace/in/name> ;
- wfdesc:hasOutput <../Retrieve_layers/processor/Get_Workspace/out/responseBody> ;
- wf4ever:rootURI "http://biovel.iais.fraunhofer.de/"^^xsd:anyURI .
-
-<../Retrieve_layers/processor/Get_Workspaces/> a wfdesc:Process , wfdesc:Description , wf4ever:RESTService ;
- rdfs:label "Get_Workspaces" ;
- wfdesc:hasOutput <../Retrieve_layers/processor/Get_Workspaces/out/responseBody> ;
- wf4ever:rootURI "http://biovel.iais.fraunhofer.de/"^^xsd:anyURI .
-
-<../Upload_CSV_data_to_B/processor/upload_Data/> a wfdesc:Process , wfdesc:Description , wf4ever:RESTService ;
- rdfs:label "upload_Data" ;
- wfdesc:hasInput <../Upload_CSV_data_to_B/processor/upload_Data/in/inputBody> ;
- wfdesc:hasOutput <../Upload_CSV_data_to_B/processor/upload_Data/out/responseBody> , <../Upload_CSV_data_to_B/processor/upload_Data/out/status> ;
- wf4ever:rootURI "http://biovel.iais.fraunhofer.de/"^^xsd:anyURI .
-
-<../Call_service_to_crea/processor/createModel/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "createModel" ;
- wfdesc:hasInput <../Call_service_to_crea/processor/createModel/in/Body> ;
- wfdesc:hasOutput <../Call_service_to_crea/processor/createModel/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "createModel" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Call_service_to_crea/processor/getLog/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLog" ;
- wfdesc:hasInput <../Call_service_to_crea/processor/getLog/in/Body> ;
- wfdesc:hasOutput <../Call_service_to_crea/processor/getLog/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLog" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Call_service_to_crea/processor/getModel/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getModel" ;
- wfdesc:hasInput <../Call_service_to_crea/processor/getModel/in/Body> ;
- wfdesc:hasOutput <../Call_service_to_crea/processor/getModel/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getModel" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Project_model/processor/getLayerAsUrl/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLayerAsUrl" ;
- wfdesc:hasInput <../Project_model/processor/getLayerAsUrl/in/Body> ;
- wfdesc:hasOutput <../Project_model/processor/getLayerAsUrl/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLayerAsUrl" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Project_model/processor/getLog/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLog" ;
- wfdesc:hasInput <../Project_model/processor/getLog/in/Body> ;
- wfdesc:hasOutput <../Project_model/processor/getLog/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLog" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Project_model/processor/getProjectionMetadata/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getProjectionMetadata" ;
- wfdesc:hasInput <../Project_model/processor/getProjectionMetadata/in/Body> ;
- wfdesc:hasOutput <../Project_model/processor/getProjectionMetadata/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getProjectionMetadata" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Project_model/processor/projectModel/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "projectModel" ;
- wfdesc:hasInput <../Project_model/processor/projectModel/in/Body> ;
- wfdesc:hasOutput <../Project_model/processor/projectModel/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "projectModel" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Retrieve_algorithms/processor/getAlgorithms/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getAlgorithms" ;
- wfdesc:hasOutput <../Retrieve_algorithms/processor/getAlgorithms/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getAlgorithms" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Retrieve_layers/processor/getLayers/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLayers" ;
- wfdesc:hasOutput <../Retrieve_layers/processor/getLayers/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLayers" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model/processor/getLog/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLog" ;
- wfdesc:hasInput <../Test_model/processor/getLog/in/Body> ;
- wfdesc:hasOutput <../Test_model/processor/getLog/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLog" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model/processor/getTestResult/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getTestResult" ;
- wfdesc:hasInput <../Test_model/processor/getTestResult/in/Body> ;
- wfdesc:hasOutput <../Test_model/processor/getTestResult/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getTestResult" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model/processor/testModel/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "testModel" ;
- wfdesc:hasInput <../Test_model/processor/testModel/in/Body> ;
- wfdesc:hasOutput <../Test_model/processor/testModel/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "testModel" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model1/processor/evaluateModel/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "evaluateModel" ;
- wfdesc:hasInput <../Test_model1/processor/evaluateModel/in/Body> ;
- wfdesc:hasOutput <../Test_model1/processor/evaluateModel/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "evaluateModel" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model1/processor/getLog/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getLog" ;
- wfdesc:hasInput <../Test_model1/processor/getLog/in/Body> ;
- wfdesc:hasOutput <../Test_model1/processor/getLog/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getLog" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Test_model1/processor/getModelEvaluation/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getModelEvaluation" ;
- wfdesc:hasInput <../Test_model1/processor/getModelEvaluation/in/Body> ;
- wfdesc:hasOutput <../Test_model1/processor/getModelEvaluation/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getModelEvaluation" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Workflow37/processor/getProgress/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getProgress" ;
- wfdesc:hasInput <../Workflow37/processor/getProgress/in/Body> ;
- wfdesc:hasOutput <../Workflow37/processor/getProgress/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getProgress" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../loop_until_progress_/processor/getProgress/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getProgress" ;
- wfdesc:hasInput <../loop_until_progress_/processor/getProgress/in/Body> ;
- wfdesc:hasOutput <../loop_until_progress_/processor/getProgress/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getProgress" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../loop_until_progress_1/processor/getProgress/> a wfdesc:Process , wfdesc:Description , wf4ever:SOAPService ;
- rdfs:label "getProgress" ;
- wfdesc:hasInput <../loop_until_progress_1/processor/getProgress/in/Body> ;
- wfdesc:hasOutput <../loop_until_progress_1/processor/getProgress/out/Body> ;
- wf4ever:wsdlURI "http://modeller.cria.org.br/ws2/om?wsdl"^^xsd:anyURI ;
- wf4ever:wsdlOperationName "getProgress" ;
- wf4ever:rootURI "http://modeller.cria.org.br/"^^xsd:anyURI .
-
-<../Allocate_points/datalink?from=in/csv_points&to=processor/csv_to_xml_list/in/csv_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/in/csv_points> ;
- wfdesc:hasSink <../Allocate_points/processor/csv_to_xml_list/in/csv_points> .
-
-<../Allocate_points/datalink?from=in/id_idx&to=processor/csv_to_xml_list/in/id_idx> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/in/id_idx> ;
- wfdesc:hasSink <../Allocate_points/processor/csv_to_xml_list/in/id_idx> .
-
-<../Allocate_points/datalink?from=in/lat_idx&to=processor/csv_to_xml_list/in/lat_idx> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/in/lat_idx> ;
- wfdesc:hasSink <../Allocate_points/processor/csv_to_xml_list/in/lat_idx> .
-
-<../Allocate_points/datalink?from=in/long_idx&to=processor/csv_to_xml_list/in/long_idx> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/in/long_idx> ;
- wfdesc:hasSink <../Allocate_points/processor/csv_to_xml_list/in/long_idx> .
-
-<../Allocate_points/datalink?from=processor/Merge_String_List_to_a_String/out/concatenated&to=out/all_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/processor/Merge_String_List_to_a_String/out/concatenated> ;
- wfdesc:hasSink <../Allocate_points/out/all_points> .
-
-<../Allocate_points/datalink?from=processor/csv_to_xml_list/out/all_points&to=processor/Merge_String_List_to_a_String/in/stringlist> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/processor/csv_to_xml_list/out/all_points> ;
- wfdesc:hasSink <../Allocate_points/processor/Merge_String_List_to_a_String/in/stringlist> .
-
-<../Allocate_points/datalink?from=processor/csv_to_xml_list/out/num_points&to=out/num_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Allocate_points/processor/csv_to_xml_list/out/num_points> ;
- wfdesc:hasSink <../Allocate_points/out/num_points> .
-
-<../Ask_user_to_run_or_n/datalink?from=in/all_points&to=processor/allocate_points/in/all_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/in/all_points> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/processor/allocate_points/in/all_points> .
-
-<../Ask_user_to_run_or_n/datalink?from=in/all_points&to=processor/count_points/in/all_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/in/all_points> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/processor/count_points/in/all_points> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/Interaction/out/calculate_matrix&to=out/calculate_matrix> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/Interaction/out/calculate_matrix> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/calculate_matrix> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/Interaction/out/choice&to=processor/allocate_points/in/choice> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/Interaction/out/choice> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/processor/allocate_points/in/choice> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/Interaction/out/measure_auc&to=out/measure_auc> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/Interaction/out/measure_auc> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/measure_auc> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/Interaction/out/replicates&to=processor/allocate_points/in/folds> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/Interaction/out/replicates> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/processor/allocate_points/in/folds> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/Interaction/out/threshold&to=out/threshold> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/Interaction/out/threshold> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/threshold> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/allocate_points/out/flag&to=out/flag> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/allocate_points/out/flag> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/flag> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/allocate_points/out/testing_points&to=out/testing_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/allocate_points/out/testing_points> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/testing_points> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/allocate_points/out/training_points&to=out/training_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/allocate_points/out/training_points> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/out/training_points> .
-
-<../Ask_user_to_run_or_n/datalink?from=processor/count_points/out/num_points&to=processor/Interaction/in/num_points> a wfdesc:DataLink ;
- wfdesc:hasSource <../Ask_user_to_run_or_n/processor/count_points/out/num_points> ;
- wfdesc:hasSink <../Ask_user_to_run_or_n/processor/Interaction/in/num_points> .
-
-<../Calculate_mean_AUC/datalink?from=in/values_list&to=processor/calculate_mean/in/values_list> a wfdesc:DataLink ;
- wfdesc:hasSource <../Calculate_mean_AUC/in/values_list> ;
- wfdesc:hasSink <../Calculate_mean_AUC/processor/calculate_mean/in/values_list> .
-
-<../Calculate_mean_AUC/datalink?from=processor/calculate_mean/out/mean_value&to=out/mean_value> a wfdesc:DataLink ;
- wfdesc:hasSource <../Calculate_mean_AUC/processor/calculate_mean/out/mean_value> ;
- wfdesc:hasSink <../Calculate_mean_AUC/out/mean_value> .
-
-<../Calculate_mean_AUC1/datalink?from=in/values_list&to=processor/calculate_mean/in/values_list> a wfdesc:DataLink ;
- wfdesc:hasSource <../Calculate_mean_AUC1/in/values_list> ;
- wfdesc:hasSink <../Calculate_mean_AUC1/processor/calculate_mean/in/values_list> .
-
-<../Calculate_mean_AUC1/datalink?from=processor/calculate_mean/out/mean_value&to=out/mean_value> a wfdesc:DataLink ;
- wfdesc:hasSource <../Calculate_mean_AUC1/processor/calculate_mean/out/mean_value> ;
- wfdesc:hasSink <../Calculate_mean_AUC1/out/mean_value> .
-
-<../Call_service_to_crea/datalink?from=in/createModel_configuration&to=processor/createModel/in/Body> a wfdesc:DataLink ;
- wfdesc:hasSource <../Call_service_to_crea/in/createModel_configuration> ;
- wfdesc:hasSink <../Call_service_to_crea/processor/createModel/in/Body> .
-
-<../Call_service_to_crea/datalink?from=processor/createModel/out/Body&to=processor/createModel_output/in/input> a wfdesc:DataLink ;
- wfdesc:hasSource <../Call_service_to_crea/processor/createModel/out/Body> ;
- wfdesc:hasSink <../Call_service_to_crea/processor/createModel_output/in/input
<TRUNCATED>
[32/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/tool-2-2-tweaked-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-tweaked-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-2-tweaked-xsd.t2flow
deleted file mode 100755
index 27e41d0..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-2-tweaked-xsd.t2flow
+++ /dev/null
@@ -1,346 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"
- version="1" producedBy="taverna-2.2.0"
- 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">
- <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>usecase-activity</artifact>
- <version>0.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.usecase.UseCaseActivity
- </class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean
- xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php
- </repositoryUrl>
- <usecaseid>cat</usecaseid>
- </net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- <processor>
- <name>bourne_shell_script</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>usecase-activity</artifact>
- <version>0.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.usecase.UseCaseActivity
- </class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean
- xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php
- </repositoryUrl>
- <usecaseid>bourne_shell_script</usecaseid>
- </net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </iteration>
- </iterationStrategyStack>
- </processor>
- <processor>
- <name>cmbuild</name>
- <inputPorts />
- <outputPorts />
- <annotations />
- <activities>
- <activity>
- <raven>
- <group>net.sf.taverna.t2.activities</group>
- <artifact>usecase-activity</artifact>
- <version>0.3</version>
- </raven>
- <class>net.sf.taverna.t2.activities.usecase.UseCaseActivity
- </class>
- <inputMap />
- <outputMap />
- <configBean encoding="xstream">
- <net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean
- xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php
- </repositoryUrl>
- <usecaseid>cmbuild</usecaseid>
- </net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean>
- </configBean>
- <annotations />
- </activity>
- </activities>
- <dispatchStack>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
- xmlns="">
- <maxJobs>1</maxJobs>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
- </class>
- <configBean encoding="xstream">
- <net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
- xmlns="">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
- </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig>
- </configBean>
- </dispatchLayer>
- <dispatchLayer>
- <raven>
- <group>net.sf.taverna.t2.core</group>
- <artifact>workflowmodel-impl</artifact>
- <version>1.2</version>
- </raven>
- <class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke
- </class>
- <configBean encoding="xstream">
- <null xmlns="" />
- </configBean>
- </dispatchLayer>
- </dispatchStack>
- <iterationStrategyStack>
- <iteration>
- <strategy />
- </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.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-2.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-2.t2flow
deleted file mode 100755
index dd3b73a..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-2.t2flow
+++ /dev/null
@@ -1,42 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><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>usecase-activity</artifact><version>0.3</version></raven><class>net.sf.taverna.t2.activities.usecase.UseCaseActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <usecaseid>cat</usecaseid>
-</net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>bourne_shell_script</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>usecase-activity</artifact><version>0.3</version></raven><class>net.sf.taverna.t2.activities.usecase.UseCaseActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <usecaseid>bourne_shell_script</usecaseid>
-</net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>cmbuild</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>usecase-activity</artifact><version>0.3</version></raven><class>net.sf.taverna.t2.activities.usecase.UseCaseActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean xmlns="">
- <repositoryUrl>http://taverna.nordugrid.org/sharedRepository/xml.php</repositoryUrl>
- <usecaseid>cmbuild</usecaseid>
-</net.sf.taverna.t2.activities.usecase.UseCaseActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></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-2-3-xsd.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-3-xsd.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-3-xsd.t2flow
deleted file mode 100755
index d0d923a..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-3-xsd.t2flow
+++ /dev/null
@@ -1,361 +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"
- xsi:noNamespaceSchemaLocation="../../main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/externaltoolactivity.xsd"
-
- xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0">
- <dataflow id="357ab8e4-0dcd-4e90-a89d-ac9ff189eda4" role="top">
- <name>Workflow1</name>
- <inputPorts />
- <outputPorts />
- <processors>
- <processor>
- <name>Tool</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>
- <externaltoolid>2cd545bf-64ae-4cda-84fc-8cfe2faed772</externaltoolid>
- <useCaseDescription>
- <usecaseid>someName</usecaseid>
- <group>some group</group>
- <description>the description
- goes here</description>
- <command>cat %%theString%% to %%stringReplace%% file </command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags>
- <string>stringReplace</string>
- <string>theString</string>
- </tags>
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>thefile.txt</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <content class="string">A multi
- line
- string inserted here. ƒ(x).</content>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>downloaded.zip</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <url>http://example.com/download#strange</url>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- </static__inputs>
- <inputs>
- <entry>
- <string>fileList2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>another</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>true</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>true</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>fileList</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>fileList</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>true</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>file2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>anotherFile.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>file1</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file1</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>true</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>stringReplaceWithDifferentPort</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>theString</tag>
- <file>false</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>stringReplace</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>stringReplace</tag>
- <file>false</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>out2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>../different/path/ and spaces.txt</path>
- <binary>true</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- <entry>
- <string>out1</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>out1</path>
- <binary>false</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- </outputs>
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes>
- <int>0</int>
- </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>symbolicLocation</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="">
- <group>
- <invocationGroupName>asdfsadf</invocationGroupName>
- <mechanismType>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
- <mechanismName>asdfasdg</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<sshInvocation><sshNode><host>127.0.0.1</host><port>22</port><directory>/tmp/asdfasdf/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
-</mechanismXML>
- </group>
- <externaltoolid>5dd1fdb0-df3c-4fce-a856-29b4d0ac67bb</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>different location</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs />
- <outputs />
- <includeStdIn>true</includeStdIn>
- <includeStdOut>false</includeStdOut>
- <includeStdErr>false</includeStdErr>
- <validReturnCodes>
- <int>15</int>
- </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>explicitLocation</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>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
- <mechanismName>asdfasdg</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<sshInvocation><sshNode><host>127.0.0.1</host><port>22</port><directory>/tmp/asdfasdf/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
-</mechanismXML>
- <externaltoolid>5dd1fdb0-df3c-4fce-a856-29b4d0ac67bb</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>different location</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs />
- <outputs />
- <includeStdIn>true</includeStdIn>
- <includeStdOut>false</includeStdOut>
- <includeStdErr>false</includeStdErr>
- <validReturnCodes>
- <int>15</int>
- </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>diff</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>diff</externaltoolid>
- <useCaseDescription>
- <usecaseid>diff</usecaseid>
- <group />
- <description>UNIX tool diff wrapper for differences between two text files</description>
- <command>diff -u from.txt to.txt</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>original_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>from.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>modified_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>to.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></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>357ab8e4-0dcd-4e90-a89d-ac9ff189eda4</identification>
- </annotationBean>
- <date>2011-08-23 12:53:06.750 BST</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>f441c1bc-407a-4cd6-b81b-41bcdcc23b6e</identification>
- </annotationBean>
- <date>2011-08-23 12:52:57.130 BST</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>6e76967a-0ee0-4d1b-bd62-3c5f55f75e94</identification>
- </annotationBean>
- <date>2011-08-23 12:02:25.851 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-2-3.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/tool-2-3.t2flow b/taverna-scufl2-t2flow/src/test/resources/tool-2-3.t2flow
deleted file mode 100755
index 5eba8de..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/tool-2-3.t2flow
+++ /dev/null
@@ -1,334 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="357ab8e4-0dcd-4e90-a89d-ac9ff189eda4" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Tool</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>
- <externaltoolid>2cd545bf-64ae-4cda-84fc-8cfe2faed772</externaltoolid>
- <useCaseDescription>
- <usecaseid>someName</usecaseid>
- <group>some group</group>
- <description>the description
- goes here</description>
- <command>cat %%theString%% to %%stringReplace%% file </command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags>
- <string>stringReplace</string>
- <string>theString</string>
- </tags>
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>thefile.txt</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <content class="string">A multi
- line
- string inserted here. ƒ(x).</content>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- <tag>downloaded.zip</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <url>http://example.com/download#strange</url>
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputStatic>
- </static__inputs>
- <inputs>
- <entry>
- <string>fileList2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>another</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>true</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>true</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>fileList</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>fileList</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>windows-1252</charsetName>
- <forceCopy>false</forceCopy>
- <list>true</list>
- <concatenate>false</concatenate>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- </entry>
- <entry>
- <string>file2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>anotherFile.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>file1</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>file1</tag>
- <file>true</file>
- <tempFile>false</tempFile>
- <binary>true</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>stringReplaceWithDifferentPort</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>theString</tag>
- <file>false</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>stringReplace</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>stringReplace</tag>
- <file>false</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>out2</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>../different/path/ and spaces.txt</path>
- <binary>true</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- <entry>
- <string>out1</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- <path>out1</path>
- <binary>false</binary>
- <mime />
- </de.uni__luebeck.inb.knowarc.usecases.ScriptOutput>
- </entry>
- </outputs>
- <includeStdIn>false</includeStdIn>
- <includeStdOut>true</includeStdOut>
- <includeStdErr>true</includeStdErr>
- <validReturnCodes>
- <int>0</int>
- </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>symbolicLocation</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="">
- <group>
- <invocationGroupName>asdfsadf</invocationGroupName>
- <mechanismType>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
- <mechanismName>asdfasdg</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<sshInvocation><sshNode><host>127.0.0.1</host><port>22</port><directory>/tmp/asdfasdf/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
-</mechanismXML>
- </group>
- <externaltoolid>5dd1fdb0-df3c-4fce-a856-29b4d0ac67bb</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>different location</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs />
- <outputs />
- <includeStdIn>true</includeStdIn>
- <includeStdOut>false</includeStdOut>
- <includeStdErr>false</includeStdErr>
- <validReturnCodes>
- <int>15</int>
- </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>explicitLocation</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>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
- <mechanismName>asdfasdg</mechanismName>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<sshInvocation><sshNode><host>127.0.0.1</host><port>22</port><directory>/tmp/asdfasdf/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
-</mechanismXML>
- <externaltoolid>5dd1fdb0-df3c-4fce-a856-29b4d0ac67bb</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>different location</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs />
- <outputs />
- <includeStdIn>true</includeStdIn>
- <includeStdOut>false</includeStdOut>
- <includeStdErr>false</includeStdErr>
- <validReturnCodes>
- <int>15</int>
- </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>diff</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>diff</externaltoolid>
- <useCaseDescription>
- <usecaseid>diff</usecaseid>
- <group />
- <description>UNIX tool diff wrapper for differences between two text files</description>
- <command>diff -u from.txt to.txt</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags />
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>original_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>from.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>modified_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>to.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></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>357ab8e4-0dcd-4e90-a89d-ac9ff189eda4</identification>
- </annotationBean>
- <date>2011-08-23 12:53:06.750 BST</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>f441c1bc-407a-4cd6-b81b-41bcdcc23b6e</identification>
- </annotationBean>
- <date>2011-08-23 12:52:57.130 BST</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>6e76967a-0ee0-4d1b-bd62-3c5f55f75e94</identification>
- </annotationBean>
- <date>2011-08-23 12:02:25.851 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
[17/52] [abbrv] incubator-taverna-language git commit:
http://www.w3.org/2001/xml.xsd namespace
Posted by st...@apache.org.
http://www.w3.org/2001/xml.xsd namespace
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/08c19073
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/08c19073
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/08c19073
Branch: refs/heads/master
Commit: 08c19073cebf3717e621eccdd5505489a4892685
Parents: db25fe6
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:42:08 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:42:08 2015 +0000
----------------------------------------------------------------------
.../apache/taverna/scufl2/rdfxml/xsd/xml.xsd | 342 ++++++++++++++-----
1 file changed, 256 insertions(+), 86 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/08c19073/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
index 0f13678..e326ff7 100644
--- a/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
+++ b/taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
@@ -1,97 +1,107 @@
<?xml version='1.0'?>
-<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en">
+<!--
+ Copyright © 2015 W3C® (MIT, ERCIM, Keio, Beihang). This software or
+ document includes material copied from or derived from
+ XML namespace http://www.w3.org/2001/xml.xsd
+-->
<xs:annotation>
<xs:documentation>
- See http://www.w3.org/XML/1998/namespace.html and
- http://www.w3.org/TR/REC-xml for information about this namespace.
+ <div>
+ <h1>About the XML namespace</h1>
- This schema document describes the XML namespace, in a form
- suitable for import by other schema documents.
-
- Note that local names in this namespace are intended to be defined
- only by the World Wide Web Consortium or its subgroups. The
- following names are currently defined in this namespace and should
- not be used with conflicting semantics by any Working Group,
- specification, or document instance:
-
- base (as an attribute name): denotes an attribute whose value
- provides a URI to be used as the base for interpreting any
- relative URIs in the scope of the element on which it
- appears; its value is inherited. This name is reserved
- by virtue of its definition in the XML Base specification.
-
- lang (as an attribute name): denotes an attribute whose value
- is a language code for the natural language of the content of
- any element; its value is inherited. This name is reserved
- by virtue of its definition in the XML specification.
-
- space (as an attribute name): denotes an attribute whose
- value is a keyword indicating what whitespace processing
- discipline is intended for the content of the element; its
- value is inherited. This name is reserved by virtue of its
- definition in the XML specification.
-
- Father (in any context at all): denotes Jon Bosak, the chair of
- the original XML Working Group. This name is reserved by
- the following decision of the W3C XML Plenary and
- XML Coordination groups:
-
- In appreciation for his vision, leadership and dedication
- the W3C XML Plenary on this 10th day of February, 2000
- reserves for Jon Bosak in perpetuity the XML name
- xml:Father
+ <div class="bodytext">
+ <p>
+ This schema document describes the XML namespace, in a form
+ suitable for import by other schema documents.
+ </p>
+ <p>
+ See <a href="http://www.w3.org/XML/1998/namespace.html">
+ http://www.w3.org/XML/1998/namespace.html</a> and
+ <a href="http://www.w3.org/TR/REC-xml">
+ http://www.w3.org/TR/REC-xml</a> for information
+ about this namespace.
+ </p>
+ <p>
+ Note that local names in this namespace are intended to be
+ defined only by the World Wide Web Consortium or its subgroups.
+ The names currently defined in this namespace are listed below.
+ They should not be used with conflicting semantics by any Working
+ Group, specification, or document instance.
+ </p>
+ <p>
+ See further below in this document for more information about <a
+ href="#usage">how to refer to this schema document from your own
+ XSD schema documents</a> and about <a href="#nsversioning">the
+ namespace-versioning policy governing this schema document</a>.
+ </p>
+ </div>
+ </div>
</xs:documentation>
</xs:annotation>
- <xs:annotation>
- <xs:documentation>This schema defines attributes and an attribute group
- suitable for use by
- schemas wishing to allow xml:base, xml:lang or xml:space attributes
- on elements they define.
-
- To enable this, such a schema must import this schema
- for the XML namespace, e.g. as follows:
- <schema . . .>
- . . .
- <import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd"/>
-
- Subsequently, qualified reference to any of the attributes
- or the group defined below will have the desired effect, e.g.
-
- <type . . .>
- . . .
- <attributeGroup ref="xml:specialAttrs"/>
-
- will define a type which will schema-validate an instance
- element with any of those attributes</xs:documentation>
- </xs:annotation>
-
- <xs:annotation>
- <xs:documentation>In keeping with the XML Schema WG's standard versioning
- policy, this schema document will persist at
- http://www.w3.org/2001/03/xml.xsd.
- At the date of issue it can also be found at
- http://www.w3.org/2001/xml.xsd.
- The schema document at that URI may however change in the future,
- in order to remain compatible with the latest version of XML Schema
- itself. In other words, if the XML Schema namespace changes, the version
- of this document at
- http://www.w3.org/2001/xml.xsd will change
- accordingly; the version at
- http://www.w3.org/2001/03/xml.xsd will not change.
- </xs:documentation>
- </xs:annotation>
-
- <xs:attribute name="lang" type="xs:language">
+ <xs:attribute name="lang">
<xs:annotation>
- <xs:documentation>In due course, we should install the relevant ISO 2- and 3-letter
- codes as the enumerated possible values . . .</xs:documentation>
+ <xs:documentation>
+ <div>
+
+ <h3>lang (as an attribute name)</h3>
+ <p>
+ denotes an attribute whose value
+ is a language code for the natural language of the content of
+ any element; its value is inherited. This name is reserved
+ by virtue of its definition in the XML specification.</p>
+
+ </div>
+ <div>
+ <h4>Notes</h4>
+ <p>
+ Attempting to install the relevant ISO 2- and 3-letter
+ codes as the enumerated possible values is probably never
+ going to be a realistic possibility.
+ </p>
+ <p>
+ See BCP 47 at <a href="http://www.rfc-editor.org/rfc/bcp/bcp47.txt">
+ http://www.rfc-editor.org/rfc/bcp/bcp47.txt</a>
+ and the IANA language subtag registry at
+ <a href="http://www.iana.org/assignments/language-subtag-registry">
+ http://www.iana.org/assignments/language-subtag-registry</a>
+ for further information.
+ </p>
+ <p>
+ The union allows for the 'un-declaration' of xml:lang with
+ the empty string.
+ </p>
+ </div>
+ </xs:documentation>
</xs:annotation>
+ <xs:simpleType>
+ <xs:union memberTypes="xs:language">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:enumeration value=""/>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:union>
+ </xs:simpleType>
</xs:attribute>
- <xs:attribute name="space" default="preserve">
+ <xs:attribute name="space">
+ <xs:annotation>
+ <xs:documentation>
+ <div>
+
+ <h3>space (as an attribute name)</h3>
+ <p>
+ denotes an attribute whose
+ value is a keyword indicating what whitespace processing
+ discipline is intended for the content of the element; its
+ value is inherited. This name is reserved by virtue of its
+ definition in the XML specification.</p>
+
+ </div>
+ </xs:documentation>
+ </xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:NCName">
<xs:enumeration value="default"/>
@@ -99,11 +109,48 @@
</xs:restriction>
</xs:simpleType>
</xs:attribute>
-
- <xs:attribute name="base" type="xs:anyURI">
+
+ <xs:attribute name="base" type="xs:anyURI"> <xs:annotation>
+ <xs:documentation>
+ <div>
+
+ <h3>base (as an attribute name)</h3>
+ <p>
+ denotes an attribute whose value
+ provides a URI to be used as the base for interpreting any
+ relative URIs in the scope of the element on which it
+ appears; its value is inherited. This name is reserved
+ by virtue of its definition in the XML Base specification.</p>
+
+ <p>
+ See <a
+ href="http://www.w3.org/TR/xmlbase/">http://www.w3.org/TR/xmlbase/</a>
+ for information about this attribute.
+ </p>
+ </div>
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+
+ <xs:attribute name="id" type="xs:ID">
<xs:annotation>
- <xs:documentation>See http://www.w3.org/TR/xmlbase/ for
- information about this attribute.</xs:documentation>
+ <xs:documentation>
+ <div>
+
+ <h3>id (as an attribute name)</h3>
+ <p>
+ denotes an attribute whose value
+ should be interpreted as if declared to be of type ID.
+ This name is reserved by virtue of its definition in the
+ xml:id specification.</p>
+
+ <p>
+ See <a
+ href="http://www.w3.org/TR/xml-id/">http://www.w3.org/TR/xml-id/</a>
+ for information about this attribute.
+ </p>
+ </div>
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
@@ -111,6 +158,129 @@
<xs:attribute ref="xml:base"/>
<xs:attribute ref="xml:lang"/>
<xs:attribute ref="xml:space"/>
+ <xs:attribute ref="xml:id"/>
</xs:attributeGroup>
+ <xs:annotation>
+ <xs:documentation>
+ <div>
+
+ <h3>Father (in any context at all)</h3>
+
+ <div class="bodytext">
+ <p>
+ denotes Jon Bosak, the chair of
+ the original XML Working Group. This name is reserved by
+ the following decision of the W3C XML Plenary and
+ XML Coordination groups:
+ </p>
+ <blockquote>
+ <p>
+ In appreciation for his vision, leadership and
+ dedication the W3C XML Plenary on this 10th day of
+ February, 2000, reserves for Jon Bosak in perpetuity
+ the XML name "xml:Father".
+ </p>
+ </blockquote>
+ </div>
+ </div>
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:annotation>
+ <xs:documentation>
+ <div xml:id="usage" id="usage">
+ <h2><a name="usage">About this schema document</a></h2>
+
+ <div class="bodytext">
+ <p>
+ This schema defines attributes and an attribute group suitable
+ for use by schemas wishing to allow <code>xml:base</code>,
+ <code>xml:lang</code>, <code>xml:space</code> or
+ <code>xml:id</code> attributes on elements they define.
+ </p>
+ <p>
+ To enable this, such a schema must import this schema for
+ the XML namespace, e.g. as follows:
+ </p>
+ <pre>
+ <schema . . .>
+ . . .
+ <import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2001/xml.xsd"/>
+ </pre>
+ <p>
+ or
+ </p>
+ <pre>
+ <import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2009/01/xml.xsd"/>
+ </pre>
+ <p>
+ Subsequently, qualified reference to any of the attributes or the
+ group defined below will have the desired effect, e.g.
+ </p>
+ <pre>
+ <type . . .>
+ . . .
+ <attributeGroup ref="xml:specialAttrs"/>
+ </pre>
+ <p>
+ will define a type which will schema-validate an instance element
+ with any of those attributes.
+ </p>
+ </div>
+ </div>
+ </xs:documentation>
+ </xs:annotation>
+
+ <xs:annotation>
+ <xs:documentation>
+ <div id="nsversioning" xml:id="nsversioning">
+ <h2><a name="nsversioning">Versioning policy for this schema document</a></h2>
+ <div class="bodytext">
+ <p>
+ In keeping with the XML Schema WG's standard versioning
+ policy, this schema document will persist at
+ <a href="http://www.w3.org/2009/01/xml.xsd">
+ http://www.w3.org/2009/01/xml.xsd</a>.
+ </p>
+ <p>
+ At the date of issue it can also be found at
+ <a href="http://www.w3.org/2001/xml.xsd">
+ http://www.w3.org/2001/xml.xsd</a>.
+ </p>
+ <p>
+ The schema document at that URI may however change in the future,
+ in order to remain compatible with the latest version of XML
+ Schema itself, or with the XML namespace itself. In other words,
+ if the XML Schema or XML namespaces change, the version of this
+ document at <a href="http://www.w3.org/2001/xml.xsd">
+ http://www.w3.org/2001/xml.xsd
+ </a>
+ will change accordingly; the version at
+ <a href="http://www.w3.org/2009/01/xml.xsd">
+ http://www.w3.org/2009/01/xml.xsd
+ </a>
+ will not change.
+ </p>
+ <p>
+ Previous dated (and unchanging) versions of this schema
+ document are at:
+ </p>
+ <ul>
+ <li><a href="http://www.w3.org/2009/01/xml.xsd">
+ http://www.w3.org/2009/01/xml.xsd</a></li>
+ <li><a href="http://www.w3.org/2007/08/xml.xsd">
+ http://www.w3.org/2007/08/xml.xsd</a></li>
+ <li><a href="http://www.w3.org/2004/10/xml.xsd">
+ http://www.w3.org/2004/10/xml.xsd</a></li>
+ <li><a href="http://www.w3.org/2001/03/xml.xsd">
+ http://www.w3.org/2001/03/xml.xsd</a></li>
+ </ul>
+ </div>
+ </div>
+ </xs:documentation>
+ </xs:annotation>
+
</xs:schema>
[45/52] [abbrv] incubator-taverna-language git commit: Delete more
unused files and make tests less noisy.
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow b/taverna-scufl2-examples/src/test/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
deleted file mode 100644
index 117a4bb..0000000
--- a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
+++ /dev/null
@@ -1,349 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="8b032490-948e-4983-b632-d16653755fcd" role="top"><name>Fetch_today_s_xkcd_comic</name><inputPorts /><outputPorts><port><name>todaysXkcd</name><annotations /></port></outputPorts><processors><processor><name>getPage</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>contents</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><map from="url" to="url" /></inputMap><outputMap><map from="contents" to="contents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebPageFetcher</localworkerName>
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-}
-else {
- inputURL = new URL(url);
-}
-URLConnection con = inputURL.openConnection();
-InputStream in = con.getInputStream();
-
-InputStreamReader isr = new InputStreamReader(in);
-Reader inReader = new BufferedReader(isr);
-
-StringBuffer buf = new StringBuffer();
-int ch;
-while ((ch = inReader.read()) > -1) {
- buf.append((char)ch);
-}
-inReader.close();
-contents = buf.toString();
-
-
-//String NEWLINE = System.getProperty("line.separator");
-//
-//URL inputURL = null;
-//if (base != void) {
-// inputURL = new URL(new URL(base), url);
-//} else {
-// inputURL = new URL(url);
-//}
-//StringBuffer result = new StringBuffer();
-//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
-//String line = null;
-//while ((line = reader.readLine()) != null) {
-// result.append(line);
-// result.append(NEWLINE);
-//}
-//
-//contents = result.toString();
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>contents</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain,text/html'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xkcdURL</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>http://xkcd.com/</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>getImageLinks</name><inputPorts><port><name>document</name><depth>0</depth></port></inputPorts><outputPorts><port><name>imagelinks</name><depth>1</depth><granularDepth>1</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><map from="document" to="document"
/></inputMap><outputMap><map from="imagelinks" to="imagelinks" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks</localworkerName>
- <script>String lowerCaseContent = document.toLowerCase();
-int index = 0;
-List imagelinks = new ArrayList();
-while ((index = lowerCaseContent.indexOf("<img", index)) != -1) {
- if ((index = lowerCaseContent.indexOf("src", index)) == -1)
- break;
- if ((index = lowerCaseContent.indexOf("=", index)) == -1)
- break;
- index++;
- String remaining = document.substring(index);
- StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#");
- String strLink = st.nextToken();
- imagelinks.add(strLink);
-}
-
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>document</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/html'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>imagelinks</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/x-taverna-web-url')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="document" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>findComicURL</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>filteredlist</name><depth>1</depth><granularDepth>1</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><map from="regex" to="regex" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="filteredlist" to="filteredlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FilterStringList</localworkerName>
- <script>filteredlist = new ArrayList();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- if (item.matches(regex)) {
- filteredlist.add(item);
- }
-}
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>stringlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>regex</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>filteredlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="regex" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>comicURLRegex</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap
/><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>.*/comics/.*</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>getComicStrip</name><inputPorts><port><name>base</name><depth>0</depth></port><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>image</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><inputMa
p><map from="base" to="base" /><map from="url" to="url" /></inputMap><outputMap><map from="image" to="image" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</localworkerName>
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-} else {
- inputURL = new URL(url);
-}
-
-byte[] contents;
-if (inputURL.openConnection().getContentLength() == -1) {
- // Content size unknown, must read first...
- byte[] buffer = new byte[1024];
- int bytesRead = 0;
- int totalBytesRead = 0;
- InputStream is = inputURL.openStream();
- while (bytesRead != -1) {
- totalBytesRead += bytesRead;
- bytesRead = is.read(buffer, 0, 1024);
- }
- contents = new byte[totalBytesRead];
-} else {
- contents = new byte[inputURL.openConnection().getContentLength()];
-}
-int bytesRead = 0;
-int totalBytesRead = 0;
-InputStream is = inputURL.openStream();
-while (bytesRead != -1) {
- bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
- totalBytesRead += bytesRead;
- if (contents.length==totalBytesRead) break;
-}
-
-image = contents;
-</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>image</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'image/*'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="base" depth="0" /><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getPage</processor><port>url</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getImageLinks</processor><port>document</port></sink><source type="processor"><processor>getPage</processor><port>contents</port></source></datalink><datali
nk><sink type="processor"><processor>findComicURL</processor><port>regex</port></sink><source type="processor"><processor>comicURLRegex</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>findComicURL</processor><port>stringlist</port></sink><source type="processor"><processor>getImageLinks</processor><port>imagelinks</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>base</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>url</port></sink><source type="processor"><processor>findComicURL</processor><port>filteredlist</port></source></datalink><datalink><sink type="dataflow"><port>todaysXkcd</port></sink><source type="processor"><processor>getComicStrip</processor><port>image</port></source></datalink></datalinks><annotations><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>Fetch today's xkcd comic</text>
- </annotationBean>
- <date>2009-12-15 20:39:06.623 GMT</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.Author">
- <text>Tom Oinn, Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-12-15 20:38:58.43 GMT</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>Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
-
-Based on the FetchDailyDilbert workflow.</text>
- </annotationBean>
- <date>2009-12-15 20:39:17.683 GMT</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>8b032490-948e-4983-b632-d16653755fcd</identification>
- </annotationBean>
- <date>2010-07-04 18:16:02.491 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/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/t2flow/merge_fun.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/merge_fun.t2flow b/taverna-scufl2-examples/src/test/resources/workflows/t2flow/merge_fun.t2flow
deleted file mode 100644
index 470e310..0000000
--- a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/merge_fun.t2flow
+++ /dev/null
@@ -1,83 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</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><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
- <script>outputlist = inputlist;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>[B</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>inputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>outputlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="inputlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>a</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" />
</outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>a</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>b</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.
t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>b</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="merge"><port>b</port></sink><source type="processor"><processor>a</processor><port>value</port></source></datalink><datalink><sink type="merge"><port>b</port></sink><source type="processor"><processor>b</processor><port>value</port></source></datalink><datalink><sink type="merge"><processor>Echo_List</processor><port>inputlist</port></sink><source type="processor"><processor>b</processor><port>value</port></source></datalink><datalink><
sink type="merge"><processor>Echo_List</processor><port>inputlist</port></sink><source type="processor"><processor>a</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>a</port></sink><source type="processor"><processor>Echo_List</processor><port>outputlist</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>aaecfd60-6456-4573-a25c-bcb841050601</identification>
- </annotationBean>
- <date>2010-10-29 09:52:34.321 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/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow b/taverna-scufl2-examples/src/test/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
deleted file mode 100644
index 2b963ca..0000000
--- a/taverna-scufl2-examples/src/test/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
+++ /dev/null
@@ -1,320 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="fd34324d-de34-4a5f-9b12-13059a9fb1a4" role="top"><name>Pipelined_list_iteration</name><inputPorts><port><name>input</name><depth>0</depth><granularDepth>0</granularDepth><annotations><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.ExampleValue">
- <text>150</text>
- </annotationBean>
- <date>2009-12-15 19:41:02.598 GMT</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>Number of elements to generate</text>
- </annotationBean>
- <date>2009-12-15 19:40:52.84 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>List_Emitter</name><inputPorts><port><name>count</name><depth>0</depth></port></inputPorts><outputPorts><port><name>list</name><depth>1</depth><granularDepth>1</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="count" to="count" /></inputMap><outputMap><map from="list" to="list" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>List list = new ArrayList();
-int icount = Integer.parseInt(count);
-
-for (int i=0;i<icount;i++) {
- list.add(String.valueOf(i));
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>count</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>list</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="count" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concat</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>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap
><map from="input" to="input" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>String output = input + "XXX"</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>input</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="input" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</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>localworker-activity</artifact><version>1.2</version></raven><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="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
- <script>output = string1 + string2;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string1</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>string2</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</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="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
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- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
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p><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>boo</value>
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">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
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a.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>xxx</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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-</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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rna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>List_Emitter</processor><port>count</port></sink><source type="dataflow"><port>input</port></source></datalink><datalink><sink type="processor"><processor>Concat</processor><port>input</port></sink><source type="processor"><processor>List_Emitter</processor><port>list</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="pro
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ng2</port></sink><source type="processor"><processor>sdfds</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Concatenate_two_strings_3</processor><port>output</port></source></datalink></datalinks><annotations><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>Perform multiple iterations of services in order to show pipelining</text>
- </annotationBean>
- <date>2009-12-15 19:42:21.971 GMT</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.Author">
- <text>Ian Dunlop, Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-12-15 19:42:01.488 GMT</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.DescriptiveTitle">
- <text>Pipelined list iteration</text>
- </annotationBean>
- <date>2009-12-15 19:42:12.907 GMT</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>fd34324d-de34-4a5f-9b12-13059a9fb1a4</identification>
- </annotationBean>
- <date>2010-07-04 18:19:17.425 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
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diff --git a/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/helloworld.wfbundle b/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/helloworld.wfbundle
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index 803b9ae..0000000
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/merge_fun.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/merge_fun.wfbundle b/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/merge_fun.wfbundle
deleted file mode 100644
index 490366c..0000000
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/9236e2c1/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/pipelined_list_iteration_902021.wfbundle
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diff --git a/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/pipelined_list_iteration_902021.wfbundle b/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/pipelined_list_iteration_902021.wfbundle
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index 78775c1..0000000
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[21/52] [abbrv] incubator-taverna-language git commit: XSDs are in
taverna-scufl2-schemas
Posted by st...@apache.org.
XSDs are in taverna-scufl2-schemas
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/8e7b6700
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/8e7b6700
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/8e7b6700
Branch: refs/heads/master
Commit: 8e7b67008569c1e40efd1a0c0e0684626ebe18c9
Parents: 0765cff
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 15:50:02 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 15:50:02 2015 +0000
----------------------------------------------------------------------
.../apache/taverna/scufl2/rdfxml/xsd/owl.xsd | 54 --
.../apache/taverna/scufl2/rdfxml/xsd/prov.xsd | 44 --
.../apache/taverna/scufl2/rdfxml/xsd/rdf.xsd | 64 ---
.../apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd | 38 --
.../apache/taverna/scufl2/rdfxml/xsd/roevo.xsd | 101 ----
.../apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd | 554 -------------------
.../apache/taverna/scufl2/rdfxml/xsd/xml.xsd | 116 ----
7 files changed, 971 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
deleted file mode 100644
index c5c0e3b..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/owl.xsd
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-
- <!--
- <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- schemaLocation="rdf.xsd" />
- <xs:import namespace="http://www.w3.org/2000/01/rdf-schema#"
- schemaLocation="rdfs.xsd" />
- <xs:import namespace="http://ns.taverna.org.uk/2010/scufl2#"
- schemaLocation="scufl2.xsd" />
- <xs:element name="Class">
- <xs:complexType>
- <xs:sequence>
- <xs:element minOccurs="0" ref="scufl2:configurationType" />
- <xs:element ref="rdfs:subClassOf" />
- <xs:any namespace="##any" maxOccurs="unbounded" minOccurs="0"
- processContents="lax" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- <xs:anyAttribute />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="sameAs">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" maxOccurs="unbounded" minOccurs="0"
- processContents="lax" />
- </xs:sequence>
- <xs:attribute ref="rdf:parseType" fixed="Collection" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="DatatypeProperty">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" />
- <xs:element ref="scufl2:required" />
- <xs:element ref="rdfs:domain" />
- <xs:element ref="rdfs:label" />
- <xs:element ref="rdfs:range" />
- <xs:element ref="rdfs:subPropertyOf" />
- <xs:any namespace="##any" maxOccurs="unbounded" minOccurs="0"
- processContents="lax" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
- -->
-
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
deleted file mode 100644
index d885940..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/prov.xsd
+++ /dev/null
@@ -1,44 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://www.w3.org/ns/prov#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:prov="http://www.w3.org/ns/prov#"
- xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
- jxb:version="1.0">
-
- <xs:annotation>
- <xs:appinfo>
- <!-- See http://docs.rakeshv.org/java/jaxb/users-guide/jaxb-custom.html -->
- <jxb:globalBindings />
- <jxb:schemaBindings>
- <jxb:package name="org.w3.prov.jaxb" />
- </jxb:schemaBindings>
- </xs:appinfo>
- </xs:annotation>
-<!--
- <xs:import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd" />
- <xs:import namespace="http://www.w3.org/2002/07/owl#"
- schemaLocation="owl.xsd" />
- <xs:import namespace="http://www.w3.org/2000/01/rdf-schema#"
- schemaLocation="rdfs.xsd" />
- -->
-
- <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- schemaLocation="rdf.xsd" />
-
- <xs:element name="generatedAtTime">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:dateTime">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#dateTime" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="wasRevisionOf" type="rdf:Resource" />
- <xs:element name="wasAssociatedWith" type="rdf:Resource" />
- <xs:element name="wasAttributedTo" type="rdf:Resource" />
- <xs:element name="hadOriginalSource" type="rdf:Resource" />
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
deleted file mode 100644
index 2850d74..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdf.xsd
+++ /dev/null
@@ -1,64 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
-
- <xs:import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="xml.xsd" />
- <!-- schemaLocation="http://www.w3.org/2001/03/xml.xsd" /> -->
-
- <xs:element name="RDF" type="rdf:RDF" />
-
- <xs:complexType name="RDF">
- <xs:sequence>
- <xs:any namespace="##any" maxOccurs="unbounded" minOccurs="0" processContents="lax" />
- </xs:sequence>
- <xs:attribute ref="xml:base" />
- </xs:complexType>
-
- <xs:element name="Description">
- <xs:complexType>
- <xs:sequence>
- <xs:any namespace="##any" maxOccurs="unbounded" minOccurs="0" processContents="lax" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:attributeGroup name="about">
- <xs:attribute name="about" use="required" form="qualified"
- type="xs:anyURI" />
- </xs:attributeGroup>
-
- <xs:attributeGroup name="aboutOptional">
- <xs:attribute name="about" use="optional" form="qualified"
- type="xs:anyURI" />
- </xs:attributeGroup>
-
- <xs:attributeGroup name="resource">
- <xs:attribute name="resource" use="required" form="qualified"
- type="xs:anyURI" />
- </xs:attributeGroup>
-
- <xs:attribute name="parseType">
- <xs:simpleType>
- <xs:restriction base="xs:string">
- <xs:enumeration value="Collection"></xs:enumeration>
- <xs:enumeration value="Resource"></xs:enumeration>
- </xs:restriction>
- </xs:simpleType>
- </xs:attribute>
-
- <xs:attribute name="datatype" type="xs:anyURI" />
-
- <xs:element name="type">
- <xs:complexType>
- <xs:attribute name="resource" use="required" form="qualified"
- type="xs:anyURI" />
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="Resource">
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
deleted file mode 100644
index 72a734e..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd
+++ /dev/null
@@ -1,38 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://www.w3.org/2000/01/rdf-schema#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-
- <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- schemaLocation="rdf.xsd" />
-<!--
- <xs:import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd" />
- -->
- <xs:element name="subClassOf">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
- <xs:element name="domain">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
- <xs:element name="label" type="xs:NCName" />
- <xs:element name="range">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
- <xs:element name="subPropertyOf">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
- <xs:element name="seeAlso">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
deleted file mode 100644
index ffec0ed..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd
+++ /dev/null
@@ -1,101 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://purl.org/wf4ever/roevo#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:roevo="http://purl.org/wf4ever/roevo#"
- xmlns:prov="http://www.w3.org/ns/prov#"
- xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
- jxb:version="1.0">
-
- <xs:annotation>
- <xs:appinfo>
- <!-- See http://docs.rakeshv.org/java/jaxb/users-guide/jaxb-custom.html -->
- <jxb:globalBindings />
- <jxb:schemaBindings>
- <jxb:package name="org.purl.wf4ever.roevo.jaxb" />
- </jxb:schemaBindings>
- </xs:appinfo>
- </xs:annotation>
- <!--
- <xs:import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd" />
- <xs:import namespace="http://www.w3.org/2000/01/rdf-schema#"
- schemaLocation="rdfs.xsd" />
- <xs:import namespace="http://www.w3.org/2002/07/owl#"
- schemaLocation="owl.xsd" />
- -->
-
-
- <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- schemaLocation="rdf.xsd" />
- <xs:import namespace="http://www.w3.org/ns/prov#"
- schemaLocation="prov.xsd" />
-
- <xs:complexType name="RoEvoDocument">
- <xs:complexContent>
- <xs:restriction base="rdf:RDF">
- <xs:sequence>
- <xs:element ref="roevo:VersionableResource" minOccurs="0" maxOccurs="unbounded" />
- </xs:sequence>
- </xs:restriction>
- </xs:complexContent>
- </xs:complexType>
-
- <xs:element name="VersionableResource">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="wasChangedBy" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="roevo:ChangeSpecification" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element ref="prov:generatedAtTime" minOccurs="0" />
- <xs:element ref="prov:wasRevisionOf" minOccurs="0" />
- <xs:element ref="prov:hadOriginalSource" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="prov:wasAttributedTo" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
- <xs:element name="ChangeSpecification">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" minOccurs="0"/>
- <xs:element name="fromVersion" type="rdf:Resource" minOccurs="0" />
- <xs:element name="hasChange" minOccurs="0" maxOccurs="3">
- <xs:annotation>
- <xs:documentation>
- <p xmlns='http://www.w3.org/1999/xhtml'>
- A ChangeSpecification can have up to 3 changes,
- one of Addition, one of Modificaton and one of Removal.
- Ironically, to avoid an 'non ambigious' XML Schema, this schema
- has to allow also say Addition, Addition, Removal. Clients MAY
- parse additional changes of the same type, but SHOULD merge them
- to a single change per type when saving, ie. add the resources
- from the second Addition to the resources of the first.
- </p>
- </xs:documentation>
- </xs:annotation>
- <xs:complexType>
- <xs:choice>
- <xs:element name="Addition" type="roevo:Change" />
- <xs:element name="Modification" type="roevo:Change" />
- <xs:element name="Removal" type="roevo:Change" />
- </xs:choice>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="Change">
- <xs:sequence>
- <xs:element name="relatedResource" type="rdf:Resource" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
-
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
deleted file mode 100644
index 89d9294..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd
+++ /dev/null
@@ -1,554 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" attributeFormDefault="qualified"
- elementFormDefault="qualified" targetNamespace="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:scufl2="http://ns.taverna.org.uk/2010/scufl2#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
- jxb:version="1.0">
-
- <xs:annotation>
- <xs:appinfo>
- <!-- See http://docs.rakeshv.org/java/jaxb/users-guide/jaxb-custom.html -->
- <jxb:globalBindings />
- <jxb:schemaBindings>
- <jxb:package name="org.apache.taverna.scufl2.rdfxml.jaxb" />
- </jxb:schemaBindings>
- </xs:appinfo>
- </xs:annotation>
-<!--
- <xs:import namespace="http://purl.org/dc/elements/1.1/"
- schemaLocation="http://dublincore.org/schemas/xmls/qdc/dc.xsd" />
-
- <xs:import namespace="http://purl.org/dc/terms/"
- schemaLocation="http://dublincore.org/schemas/xmls/qdc/dcterms.xsd" />
-
- <xs:import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd" />
- <xs:import namespace="http://www.w3.org/2002/07/owl#"
- schemaLocation="owl.xsd" />
- -->
-
- <xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- schemaLocation="rdf.xsd" />
- <xs:import namespace="http://www.w3.org/2000/01/rdf-schema#"
- schemaLocation="rdfs.xsd" />
-
-
-
- <xs:complexType name="WorkflowBundleDocument">
- <xs:complexContent>
- <xs:restriction base="rdf:RDF">
- <xs:sequence>
- <xs:element ref="scufl2:WorkflowBundle"></xs:element>
- </xs:sequence>
- </xs:restriction>
- </xs:complexContent>
- </xs:complexType>
-
- <xs:complexType name="WorkflowDocument">
- <xs:complexContent>
- <xs:restriction base="rdf:RDF">
- <xs:sequence>
- <xs:element ref="scufl2:Workflow"></xs:element>
- </xs:sequence>
- </xs:restriction>
- </xs:complexContent>
- </xs:complexType>
-
-
- <xs:complexType name="ProfileDocument">
- <xs:complexContent>
- <xs:restriction base="rdf:RDF">
- <xs:sequence>
- <xs:element ref="scufl2:Profile" />
- <xs:element ref="scufl2:Activity" minOccurs="0"
- maxOccurs="unbounded" />
- <xs:element ref="scufl2:ProcessorBinding" minOccurs="0"
- maxOccurs="unbounded" />
- <xs:element ref="scufl2:Configuration" minOccurs="0"
- maxOccurs="unbounded" />
-
- <xs:any namespace="##other" minOccurs="0" maxOccurs="unbounded"
- processContents="lax" />
- </xs:sequence>
- </xs:restriction>
- </xs:complexContent>
- </xs:complexType>
-
-
- <xs:element name="WorkflowBundle">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" minOccurs="0" />
- <xs:element name="globalBaseURI" type="rdf:Resource"
- minOccurs="0" />
- <xs:element name="mainWorkflow" type="rdf:Resource"
- minOccurs="0" />
- <xs:element name="workflow" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="Workflow" type="scufl2:SeeAlsoType" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="mainProfile" type="rdf:Resource"
- minOccurs="0" />
- <xs:element name="profile" maxOccurs="unbounded"
- minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="Profile" type="scufl2:SeeAlsoType" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element ref="rdfs:seeAlso" minOccurs="0" maxOccurs="unbounded" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
- <xs:element name="Configuration">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" />
- <xs:element ref="rdfs:seeAlso" minOccurs="0" />
- <xs:element ref="scufl2:name" minOccurs="0" />
- <xs:element name="configure" type="rdf:Resource" />
- <xs:any namespace="##other" minOccurs="0" maxOccurs="unbounded"
- processContents="lax" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="Activity">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" />
- <xs:element ref="scufl2:name" minOccurs="0" />
- <xs:element name="inputActivityPort" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:InputActivityPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="outputActivityPort" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:OutputActivityPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
-
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="SeeAlsoType">
- <xs:sequence>
- <xs:element ref="rdfs:seeAlso" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
-
-
-
- <xs:element name="Profile">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element name="processorBinding" type="rdf:Resource"
- minOccurs="0" maxOccurs="unbounded" />
- <xs:element name="activateConfiguration" type="rdf:Resource"
- minOccurs="0" maxOccurs="unbounded" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="ProcessorBinding">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" minOccurs="0" />
- <xs:element name="bindActivity" type="rdf:Resource" />
- <xs:element name="bindProcessor" type="rdf:Resource" />
- <xs:element name="activityPosition" minOccurs="0">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:int">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#integer" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="inputPortBinding" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="InputPortBinding" type="scufl2:InputPortBinding" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="outputPortBinding" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="OutputPortBinding" type="scufl2:OutputPortBinding" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="InputPortBinding">
- <xs:sequence>
- <xs:element name="bindInputActivityPort" type="rdf:Resource" />
- <xs:element name="bindInputProcessorPort" type="rdf:Resource" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- <xs:complexType name="OutputPortBinding">
- <xs:sequence>
- <xs:element name="bindOutputActivityPort" type="rdf:Resource" />
- <xs:element name="bindOutputProcessorPort" type="rdf:Resource" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
-
-
- <xs:element name="InputActivityPort">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element ref="scufl2:portDepth" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="OutputActivityPort">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element ref="scufl2:portDepth" />
- <xs:element ref="scufl2:granularPortDepth" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
- <xs:element name="Workflow">
- <xs:complexType>
- <xs:sequence>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element name="workflowIdentifier" type="rdf:Resource" />
- <xs:element name="inputWorkflowPort" maxOccurs="unbounded"
- minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:InputWorkflowPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="outputWorkflowPort" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:OutputWorkflowPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="processor" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:Processor" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element ref="scufl2:datalink" minOccurs="0"
- maxOccurs="unbounded" />
- <xs:element ref="scufl2:control" minOccurs="0"
- maxOccurs="unbounded" />
- </xs:sequence>
- <xs:element ref="rdfs:seeAlso" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="InputWorkflowPort">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element ref="scufl2:portDepth" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="OutputWorkflowPort">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="Processor">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element name="inputProcessorPort" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:InputProcessorPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="outputProcessorPort" minOccurs="0"
- maxOccurs="unbounded">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:OutputProcessorPort" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="dispatchStack" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:DispatchStack" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- <xs:element name="iterationStrategyStack" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:IterationStrategyStack" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="InputProcessorPort">
- <xs:complexType>
- <xs:sequence minOccurs="0">
- <xs:element ref="scufl2:name" />
- <xs:element ref="scufl2:portDepth" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="OutputProcessorPort">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:name" />
- <xs:element ref="scufl2:portDepth" />
- <xs:element ref="scufl2:granularPortDepth" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
- <xs:element name="DispatchStack">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" minOccurs="0" />
- <xs:element name="dispatchStackLayers" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:DispatchStackLayer" minOccurs="0"
- maxOccurs="unbounded" />
- </xs:sequence>
- <xs:attribute ref="rdf:parseType" use="required"
- fixed="Collection" />
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="DispatchStackLayer">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="rdf:type" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
- <xs:element name="IterationStrategyStack">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="iterationStrategies">
- <xs:complexType>
- <xs:sequence>
- <xs:choice minOccurs="1" maxOccurs="unbounded">
- <xs:element ref="scufl2:DotProduct" />
- <xs:element ref="scufl2:CrossProduct" />
- </xs:choice>
- </xs:sequence>
- <xs:attribute ref="rdf:parseType" use="required"
- fixed="Collection" />
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
-
- <xs:element name="CrossProduct">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:productOf" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="DotProduct">
- <xs:complexType>
- <xs:sequence>
- <xs:element ref="scufl2:productOf" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
- <xs:element name="PortNode">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="iterateOverInputPort" type="rdf:Resource" />
- <xs:element name="desiredDepth" minOccurs="0">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:int">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#integer" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
- </xs:element>
-
-
- <xs:element name="productOf">
- <xs:complexType>
- <xs:choice maxOccurs="unbounded">
- <xs:element ref="scufl2:CrossProduct" />
- <xs:element ref="scufl2:DotProduct" />
- <xs:element ref="scufl2:PortNode" />
- </xs:choice>
- <xs:attribute ref="rdf:parseType" use="required" fixed="Collection" />
-
- </xs:complexType>
- </xs:element>
- <xs:element name="datalink">
- <xs:complexType>
- <xs:annotation>
- <xs:appinfo>
- <jxb:class name="DataLinkEntry">
- </jxb:class>
- </xs:appinfo>
- </xs:annotation>
- <xs:sequence>
- <xs:element name="DataLink" type="scufl2:DataLink" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="DataLink">
- <xs:sequence>
- <xs:element name="receiveFrom" type="rdf:Resource" />
- <xs:element name="sendTo" type="rdf:Resource" />
- <xs:element name="mergePosition" minOccurs="0">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:int">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#integer" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
-
- <xs:element name="control">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="Blocking" type="scufl2:Blocking" />
- </xs:sequence>
- </xs:complexType>
- </xs:element>
-
- <xs:complexType name="Blocking">
- <xs:sequence>
- <xs:element name="block" type="rdf:Resource" />
- <xs:element name="untilFinished" type="rdf:Resource" />
- </xs:sequence>
- <xs:attributeGroup ref="rdf:about" />
- </xs:complexType>
-
-
- <xs:element name="configurationType">
- <xs:complexType>
- <xs:attributeGroup ref="rdf:resource" />
- </xs:complexType>
- </xs:element>
- <xs:element name="required">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:boolean">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#boolean" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="name" type="xs:NCName" />
- <xs:element name="granularPortDepth">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:int">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#integer" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
- <xs:element name="portDepth">
- <xs:complexType>
- <xs:simpleContent>
- <xs:extension base="xs:int">
- <xs:attribute ref="rdf:datatype" use="required"
- fixed="http://www.w3.org/2001/XMLSchema#integer" />
- </xs:extension>
- </xs:simpleContent>
- </xs:complexType>
- </xs:element>
-
-
-</xs:schema>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/8e7b6700/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
----------------------------------------------------------------------
diff --git a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd b/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
deleted file mode 100644
index 0f13678..0000000
--- a/taverna-scufl2-rdfxml/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/xml.xsd
+++ /dev/null
@@ -1,116 +0,0 @@
-<?xml version='1.0'?>
-<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en">
-
- <xs:annotation>
- <xs:documentation>
- See http://www.w3.org/XML/1998/namespace.html and
- http://www.w3.org/TR/REC-xml for information about this namespace.
-
- This schema document describes the XML namespace, in a form
- suitable for import by other schema documents.
-
- Note that local names in this namespace are intended to be defined
- only by the World Wide Web Consortium or its subgroups. The
- following names are currently defined in this namespace and should
- not be used with conflicting semantics by any Working Group,
- specification, or document instance:
-
- base (as an attribute name): denotes an attribute whose value
- provides a URI to be used as the base for interpreting any
- relative URIs in the scope of the element on which it
- appears; its value is inherited. This name is reserved
- by virtue of its definition in the XML Base specification.
-
- lang (as an attribute name): denotes an attribute whose value
- is a language code for the natural language of the content of
- any element; its value is inherited. This name is reserved
- by virtue of its definition in the XML specification.
-
- space (as an attribute name): denotes an attribute whose
- value is a keyword indicating what whitespace processing
- discipline is intended for the content of the element; its
- value is inherited. This name is reserved by virtue of its
- definition in the XML specification.
-
- Father (in any context at all): denotes Jon Bosak, the chair of
- the original XML Working Group. This name is reserved by
- the following decision of the W3C XML Plenary and
- XML Coordination groups:
-
- In appreciation for his vision, leadership and dedication
- the W3C XML Plenary on this 10th day of February, 2000
- reserves for Jon Bosak in perpetuity the XML name
- xml:Father
- </xs:documentation>
- </xs:annotation>
-
- <xs:annotation>
- <xs:documentation>This schema defines attributes and an attribute group
- suitable for use by
- schemas wishing to allow xml:base, xml:lang or xml:space attributes
- on elements they define.
-
- To enable this, such a schema must import this schema
- for the XML namespace, e.g. as follows:
- <schema . . .>
- . . .
- <import namespace="http://www.w3.org/XML/1998/namespace"
- schemaLocation="http://www.w3.org/2001/03/xml.xsd"/>
-
- Subsequently, qualified reference to any of the attributes
- or the group defined below will have the desired effect, e.g.
-
- <type . . .>
- . . .
- <attributeGroup ref="xml:specialAttrs"/>
-
- will define a type which will schema-validate an instance
- element with any of those attributes</xs:documentation>
- </xs:annotation>
-
- <xs:annotation>
- <xs:documentation>In keeping with the XML Schema WG's standard versioning
- policy, this schema document will persist at
- http://www.w3.org/2001/03/xml.xsd.
- At the date of issue it can also be found at
- http://www.w3.org/2001/xml.xsd.
- The schema document at that URI may however change in the future,
- in order to remain compatible with the latest version of XML Schema
- itself. In other words, if the XML Schema namespace changes, the version
- of this document at
- http://www.w3.org/2001/xml.xsd will change
- accordingly; the version at
- http://www.w3.org/2001/03/xml.xsd will not change.
- </xs:documentation>
- </xs:annotation>
-
- <xs:attribute name="lang" type="xs:language">
- <xs:annotation>
- <xs:documentation>In due course, we should install the relevant ISO 2- and 3-letter
- codes as the enumerated possible values . . .</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attribute name="space" default="preserve">
- <xs:simpleType>
- <xs:restriction base="xs:NCName">
- <xs:enumeration value="default"/>
- <xs:enumeration value="preserve"/>
- </xs:restriction>
- </xs:simpleType>
- </xs:attribute>
-
- <xs:attribute name="base" type="xs:anyURI">
- <xs:annotation>
- <xs:documentation>See http://www.w3.org/TR/xmlbase/ for
- information about this attribute.</xs:documentation>
- </xs:annotation>
- </xs:attribute>
-
- <xs:attributeGroup name="specialAttrs">
- <xs:attribute ref="xml:base"/>
- <xs:attribute ref="xml:lang"/>
- <xs:attribute ref="xml:space"/>
- </xs:attributeGroup>
-
-</xs:schema>
[26/52] [abbrv] incubator-taverna-language git commit: NOTICE file
mentions W3C
Posted by st...@apache.org.
NOTICE file mentions W3C
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/54208546
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/54208546
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/54208546
Branch: refs/heads/master
Commit: 5420854640fe7608044b8214de6d013dbb0fbb60
Parents: 9c347eb
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 10 16:19:43 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 10 16:19:43 2015 +0000
----------------------------------------------------------------------
.../src/main/resources/META-INF/NOTICE.vm | 39 ++++++++++++++++++++
1 file changed, 39 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/54208546/taverna-scufl2-schemas/src/main/resources/META-INF/NOTICE.vm
----------------------------------------------------------------------
diff --git a/taverna-scufl2-schemas/src/main/resources/META-INF/NOTICE.vm b/taverna-scufl2-schemas/src/main/resources/META-INF/NOTICE.vm
new file mode 100644
index 0000000..f8b48e6
--- /dev/null
+++ b/taverna-scufl2-schemas/src/main/resources/META-INF/NOTICE.vm
@@ -0,0 +1,39 @@
+##
+## Licensed to the Apache Software Foundation (ASF) under one
+## or more contributor license agreements. See the NOTICE file
+## distributed with this work for additional information
+## regarding copyright ownership. The ASF licenses this file
+## to you under the Apache License, Version 2.0 (the
+## "License"); you may not use this file except in compliance
+## with the License. You may obtain a copy of the License at
+##
+## http://www.apache.org/licenses/LICENSE-2.0
+##
+## Unless required by applicable law or agreed to in writing,
+## software distributed under the License is distributed on an
+## "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+## KIND, either express or implied. See the License for the
+## specific language governing permissions and limitations
+## under the License.
+##
+
+#if ($projectName)$projectName#else${project.name}#end
+
+Copyright ${projectTimespan}#if($project.organization.name) $project.organization.name#else The Apache Software Foundation#end
+
+
+This product includes software developed at
+The Apache Software Foundation (http://www.apache.org/).
+
+
+# xml.xsd
+
+Copyright © 2008 W3C® (MIT, ERCIM, Keio, Beihang). This software or
+document includes material copied from or derived from:
+
+- Extensible Markup Language (XML) 1.0 (Fifth Edition)
+ W3C Recommendation 26 November 2008
+ http://www.w3.org/2001/xml.xsd
+ http://www.w3.org/TR/xml/
+
+
[37/52] [abbrv] incubator-taverna-language git commit: Merge pull
request #4 from dkfellows/master
Posted by st...@apache.org.
Merge pull request #4 from dkfellows/master
POM fixes
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/414cd6a0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/414cd6a0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/414cd6a0
Branch: refs/heads/master
Commit: 414cd6a032c8eec68dfdfa9683bd69479bafe71b
Parents: 427d21e 14d0f06
Author: Alan R Williams <al...@manchester.ac.uk>
Authored: Thu Feb 12 11:13:12 2015 +0000
Committer: Alan R Williams <al...@manchester.ac.uk>
Committed: Thu Feb 12 11:13:12 2015 +0000
----------------------------------------------------------------------
pom.xml | 77 +-
taverna-scufl2-examples/pom.xml | 2 +-
.../src/test/resources/annotated2.2-xsd.t2flow | 408 ---------
.../test/resources/annotations_2_4-xsd.t2flow | 456 ----------
.../src/test/resources/annotations_2_4.t2flow | 146 ----
.../defaultActivitiesTaverna2.2-xsd.t2flow | 873 -------------------
.../test/resources/dispatchlayers-xsd.t2flow | 755 ----------------
.../resources/rest-2-2-saved-2-3-xsd.t2flow | 367 --------
.../test/resources/rest-2-2-saved-2-3.t2flow | 85 --
.../src/test/resources/rest-2-2-xsd.t2flow | 361 --------
.../src/test/resources/rest-2-3-xsd.t2flow | 376 --------
.../src/test/resources/rest-2-3.t2flow | 94 --
.../src/test/resources/rshell-2-3.t2flow | 183 ----
.../test/resources/rshell-simple-2-3-xsd.t2flow | 199 -----
.../src/test/resources/rshell-simple-2-3.t2flow | 94 --
.../semantic_annotations__eclipse-xsd.t2flow | 198 -----
.../resources/tool-2-2-resaved-2-3-xsd.t2flow | 222 -----
.../test/resources/tool-2-2-resaved-2-3.t2flow | 193 ----
.../test/resources/tool-2-2-tweaked-xsd.t2flow | 346 --------
.../src/test/resources/tool-2-2.t2flow | 42 -
.../src/test/resources/tool-2-3-xsd.t2flow | 361 --------
.../src/test/resources/tool-2-3.t2flow | 334 -------
taverna-scufl2-wfdesc/pom.xml | 2 +-
23 files changed, 68 insertions(+), 6106 deletions(-)
----------------------------------------------------------------------
[33/52] [abbrv] incubator-taverna-language git commit: Delete unused
testing workflows
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/14d0f060/taverna-scufl2-t2flow/src/test/resources/rest-2-3.t2flow
----------------------------------------------------------------------
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
----------------------------------------------------------------------
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
deleted file mode 100644
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
deleted file mode 100644
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--- a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow
+++ /dev/null
@@ -1,198 +0,0 @@
-<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>
- <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
[48/52] [abbrv] incubator-taverna-language git commit: More removal
of RAT wildcards.
Posted by st...@apache.org.
More removal of RAT wildcards.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/762ae0a7
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/762ae0a7
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/762ae0a7
Branch: refs/heads/master
Commit: 762ae0a791da390784488f12375d7e45d77bc2b4
Parents: ff86717
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Fri Feb 13 11:57:44 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Fri Feb 13 11:57:44 2015 +0000
----------------------------------------------------------------------
pom.xml | 126 ++++++++++++++++++++++++++++++++---------------------------
1 file changed, 68 insertions(+), 58 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/762ae0a7/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 6fce57c..a11fc92 100644
--- a/pom.xml
+++ b/pom.xml
@@ -64,9 +64,17 @@
<!-- META-INF services files can include comments but a license header
would be unecessarily clutter so we exclude these -->
<exclude>**/META-INF/services/*</exclude>
+ <!-- No headers in JSON which haven't got comments ... -->
+ <exclude>**/*.json</exclude>
+ <!-- Really a binary format, but must look like text -->
+ <exclude>**/mimetype</exclude>
+ <!-- Effectively a binary format -->
+ <exclude>**/*.url</exclude>
<!-- The following schemas are W3C; automatic retrieval during build is
blocked by their administrative processes, yet they are explicitly
- standardised documents intended for wide use. -->
+ standardised documents intended for wide use. Their licenses should
+ be standard W3C ones, but that's never stated explicitly by the W3C.
+ "Thanks!" -->
<exclude>**/xml.xsd</exclude>
<exclude>**/xenc-schema.xsd</exclude>
<exclude>**/xmldsig-core-schema.xsd</exclude>
@@ -76,64 +84,66 @@
has no copyright statement at all in it. -->
<exclude>**/foaf.rdf</exclude>
<!-- The following contain a mix of licenses. PROBLEM! -->
- <exclude>**/src/main/resources/ontologies/*.owl</exclude>
- <exclude>**/src/main/resources/ontologies/*.rdf</exclude>
- <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl</exclude>
- <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl</exclude>
- <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl</exclude>
- <exclude>**/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl</exclude>
- <exclude>**/src/main/resources/org/w3/prov-o.ttl</exclude>
- <!-- No headers in JSON which haven't got comments .. -->
- <exclude>**/*.json</exclude>
+ <exclude>/src/main/resources/ontologies/*.owl</exclude>
+ <exclude>/src/main/resources/ontologies/*.rdf</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/roterms.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wf4ever.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wfdesc.ttl</exclude>
+ <exclude>/src/main/resources/org/purl/wf4ever/wfdesc/wfprov.ttl</exclude>
+ <exclude>/src/main/resources/org/w3/prov-o.ttl</exclude>
<!-- Various files used for testing and test support only. -->
- <exclude>**/src/test/resources/annotated2.2.t2flow</exclude>
- <exclude>**/src/test/resources/annotation_with_backslash.t2flow</exclude>
- <exclude>**/src/test/resources/as.t2flow</exclude>
- <exclude>**/src/test/resources/beanshell-deps.t2flow</exclude>
- <exclude>**/src/test/resources/component_simple.t2flow</exclude>
- <exclude>**/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
- <exclude>**/src/test/resources/defaultActivitiesTaverna2.2.t2flow</exclude>
- <exclude>**/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
- <exclude>**/src/test/resources/dispatchlayers.t2flow</exclude>
- <exclude>**/src/test/resources/fasta_and_pscan.t2flow</exclude>
- <exclude>**/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
- <exclude>**/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
- <exclude>**/src/test/resources/interaction_multiple_choice.t2flow</exclude>
- <exclude>**/src/test/resources/interaction_simple_tell.t2flow</exclude>
- <exclude>**/src/test/resources/iterationstrategies.t2flow</exclude>
- <exclude>**/src/test/resources/merge_fun.t2flow</exclude>
- <exclude>**/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
- <exclude>**/src/test/resources/missing_merge.t2flow</exclude>
- <exclude>**/src/test/resources/missing_produced_by_941.t2flow</exclude>
- <exclude>**/src/test/resources/random.t2flow</exclude>
- <exclude>**/src/test/resources/rest-2-2.t2flow</exclude>
- <exclude>**/src/test/resources/rshell-2-2.t2flow</exclude>
- <exclude>**/src/test/resources/semantic_annotations__eclipse.t2flow</exclude>
- <exclude>**/src/test/resources/simple_fasta.t2flow</exclude>
- <exclude>**/src/test/resources/sleepers.t2flow</exclude>
- <exclude>**/src/test/resources/spreadsheet_activity_defaults_892.t2flow</exclude>
- <exclude>**/src/test/resources/T3-1226-annotations-with-quotes.t2flow</exclude>
- <exclude>**/src/test/resources/xpath_workflow.t2flow</exclude>
- <exclude>**/examples/helloanyone.t2flow</exclude>
- <exclude>**/examples/helloworld.t2flow</exclude>
- <exclude>**/src/test/resources/apiconsumer.t2flow</exclude>
- <exclude>**/src/test/resources/rest.t2flow</exclude>
- <exclude>**/src/test/resources/helloanyone.t2flow</exclude>
- <exclude>**/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
- <exclude>**/src/test/resources/allTypes.t2flow</exclude>
- <exclude>**/src/test/resources/enm-v21.t2flow</exclude>
- <exclude>**/src/test/resources/helloworld.t2flow</exclude>
- <exclude>**/src/test/resources/helloworld.wfdesc.ttl</exclude>
- <exclude>**/src/test/resources/localdependency.t2flow</exclude>
- <exclude>**/src/test/resources/nested.t2flow</exclude>
- <exclude>**/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
- <exclude>**/mimetype</exclude><!-- really a binary format -->
- <exclude>**/src/test/resources/*starterpacklist</exclude>
- <exclude>**/src/test/resources/**/*.txt</exclude>
- <exclude>**/src/test/resources/**/*.url</exclude>
- <exclude>**/src/test/resources/**/workflow*.xml</exclude>
- <exclude>**/resources/sample-output/outputs/**</exclude>
- <exclude>**/src/test/resources/full-example/**</exclude>
+ <!-- THESE SUPPORT COMMENTS with # --><!--taverna-integration-test-->
+ <exclude>/src/test/resources/t172starterpacklist</exclude>
+ <exclude>/src/test/resources/t230starterpacklist</exclude>
+ <!-- THESE ARE XML AND SUPPORT COMMENTS -->
+ <exclude>/src/test/resources/annotated2.2.t2flow</exclude>
+ <exclude>/src/test/resources/annotation_with_backslash.t2flow</exclude>
+ <exclude>/src/test/resources/as.t2flow</exclude>
+ <exclude>/src/test/resources/beanshell-deps.t2flow</exclude>
+ <exclude>/src/test/resources/component_simple.t2flow</exclude>
+ <exclude>/src/test/resources/dataflow_link_then_merge.t2flow</exclude>
+ <exclude>/src/test/resources/defaultActivitiesTaverna2.2.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers-xsd.t2flow</exclude>
+ <exclude>/src/test/resources/dispatchlayers.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_and_pscan.t2flow</exclude>
+ <exclude>/src/test/resources/fasta_pscan_and_dbfetch.t2flow</exclude>
+ <exclude>/src/test/resources/interaction-with-strange-loop.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_multiple_choice.t2flow</exclude>
+ <exclude>/src/test/resources/interaction_simple_tell.t2flow</exclude>
+ <exclude>/src/test/resources/iterationstrategies.t2flow</exclude>
+ <exclude>/src/test/resources/merge_fun.t2flow</exclude>
+ <exclude>/src/test/resources/merge_then_dataflow_link.t2flow</exclude>
+ <exclude>/src/test/resources/missing_merge.t2flow</exclude>
+ <exclude>/src/test/resources/missing_produced_by_941.t2flow</exclude>
+ <exclude>/src/test/resources/random.t2flow</exclude>
+ <exclude>/src/test/resources/rest-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/rshell-2-2.t2flow</exclude>
+ <exclude>/src/test/resources/semantic_annotations__eclipse.t2flow</exclude>
+ <exclude>/src/test/resources/simple_fasta.t2flow</exclude>
+ <exclude>/src/test/resources/sleepers.t2flow</exclude>
+ <exclude>/src/test/resources/spreadsheet_activity_defaults_892.t2flow</exclude>
+ <exclude>/src/test/resources/T3-1226-annotations-with-quotes.t2flow</exclude>
+ <exclude>/src/test/resources/xpath_workflow.t2flow</exclude>
+ <exclude>/examples/helloanyone.t2flow</exclude>
+ <exclude>/examples/helloworld.t2flow</exclude>
+ <exclude>/src/test/resources/apiconsumer.t2flow</exclude>
+ <exclude>/src/test/resources/rest.t2flow</exclude>
+ <exclude>/src/test/resources/helloanyone.t2flow</exclude>
+ <exclude>/src/test/resources/valid_component_imagemagickconvert.t2flow</exclude>
+ <exclude>/src/test/resources/allTypes.t2flow</exclude>
+ <exclude>/src/test/resources/enm-v21.t2flow</exclude>
+ <exclude>/src/test/resources/helloworld.t2flow</exclude>
+ <exclude>/src/test/resources/helloworld.wfdesc.ttl</exclude>
+ <exclude>/src/test/resources/localdependency.t2flow</exclude>
+ <exclude>/src/test/resources/nested.t2flow</exclude>
+ <exclude>/src/test/resources/rdf-in-example-annotation.t2flow</exclude>
+ <exclude>/src/test/resources/workflow10.xml</exclude>
+ <exclude>/src/test/resources/full-example/ebi_interproscan_newservices_900329.t2flow</exclude>
+ <!-- Cannot contain comments; content must match program output. -->
+ <exclude>/src/test/resources/org/apache/taverna/scufl2/api/io/HelloWorld.txt</exclude>
+ <exclude>/src/test/resources/as.txt</exclude>
+ <!-- Expanded data bundle. Generated. -->
+ <exclude>/src/test/resources/full-example/ebi-wfrun-2013-05-31/</exclude>
</excludes>
</configuration>
</plugin>