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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:05:48 UTC
[63/79] incubator-taverna-language git commit: taverna-scufl2-rdfxml
-> taverna-scufl2-wfbundle
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaServer.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaServer.rdf b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaServer.rdf
new file mode 100644
index 0000000..a156847
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaServer.rdf
@@ -0,0 +1,87 @@
+<?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/scufl2#"
+ xmlns:beanshell="http://ns.taverna.org.uk/2010/activity/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:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd
+ http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"
+ xsi:type="ProfileDocument" xml:base="tavernaServer/">
+
+ <Profile rdf:about="">
+ <name>tavernaServer</name>
+ <processorBinding rdf:resource="processorbinding/Hello/" />
+ <activateConfiguration rdf:resource="configuration/Hello/" />
+ </Profile>
+
+ <Activity rdf:about="activity/HelloScript/">
+ <rdf:type
+ rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell" />
+ <name>HelloScript</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/HelloScript/in/personName">
+ <name>personName</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/HelloScript/out/hello">
+ <name>hello</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+
+ <ProcessorBinding rdf:about="processorbinding/Hello/">
+ <name>Hello</name>
+ <bindActivity rdf:resource="activity/HelloScript/" />
+ <bindProcessor rdf:resource="../../workflow/HelloWorld/processor/Hello/" />
+ <inputPortBinding>
+ <InputPortBinding rdf:about="processorbinding/Hello/in/name">
+ <bindInputActivityPort rdf:resource="activity/HelloScript/in/personName" />
+ <bindInputProcessorPort
+ rdf:resource="../../workflow/HelloWorld/processor/Hello/in/name" />
+ </InputPortBinding>
+ </inputPortBinding>
+ <outputPortBinding>
+ <OutputPortBinding rdf:about="processorbinding/Hello/out/greeting">
+ <bindOutputActivityPort rdf:resource="activity/HelloScript/out/hello" />
+ <bindOutputProcessorPort
+ rdf:resource="../../workflow/HelloWorld/processor/Hello/out/greeting" />
+ </OutputPortBinding>
+ </outputPortBinding>
+ </ProcessorBinding>
+
+ <Configuration rdf:about="configuration/Hello/">
+ <rdf:type
+ rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config" />
+ <name>Hello</name>
+ <configure rdf:resource="activity/HelloScript/" />
+ <beanshell:script>hello = "Hello, " + personName;
+System.out.println("Server says: " + hello);</beanshell:script>
+ </Configuration>
+
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaWorkbench.rdf
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaWorkbench.rdf b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaWorkbench.rdf
new file mode 100644
index 0000000..3f2b98b
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/profile/tavernaWorkbench.rdf
@@ -0,0 +1,85 @@
+<?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/scufl2#"
+ xmlns:beanshell="http://ns.taverna.org.uk/2010/activity/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:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd
+ http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"
+ xsi:type="ProfileDocument" xml:base="tavernaWorkbench/">
+ <Profile rdf:about="">
+ <name>tavernaWorkbench</name>
+ <processorBinding rdf:resource="processorbinding/Hello/" />
+ <activateConfiguration rdf:resource="configuration/Hello/" />
+ </Profile>
+
+ <Activity rdf:about="activity/HelloScript/">
+ <rdf:type
+ rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell" />
+ <name>HelloScript</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/HelloScript/in/personName">
+ <name>personName</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/HelloScript/out/hello">
+ <name>hello</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+
+ <ProcessorBinding rdf:about="processorbinding/Hello/">
+ <name>Hello</name>
+ <bindActivity rdf:resource="activity/HelloScript/" />
+ <bindProcessor rdf:resource="../../workflow/HelloWorld/processor/Hello/" />
+ <activityPosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">10</activityPosition>
+ <inputPortBinding>
+ <InputPortBinding rdf:about="processorbinding/Hello/in/name">
+ <bindInputActivityPort rdf:resource="activity/HelloScript/in/personName" />
+ <bindInputProcessorPort
+ rdf:resource="../../workflow/HelloWorld/processor/Hello/in/name" />
+ </InputPortBinding>
+ </inputPortBinding>
+ <outputPortBinding>
+ <OutputPortBinding rdf:about="processorbinding/Hello/out/greeting">
+ <bindOutputActivityPort rdf:resource="activity/HelloScript/out/hello" />
+ <bindOutputProcessorPort
+ rdf:resource="../../workflow/HelloWorld/processor/Hello/out/greeting" />
+ </OutputPortBinding>
+ </outputPortBinding>
+ </ProcessorBinding>
+
+ <Configuration rdf:about="configuration/Hello/">
+ <rdf:type
+ rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config" />
+ <name>Hello</name>
+ <configure rdf:resource="activity/HelloScript/" />
+ <beanshell:script>hello = "Hello, " + personName;
+JOptionPane.showMessageDialog(null, hello);</beanshell:script>
+ </Configuration>
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflow/HelloWorld.rdf
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diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflow/HelloWorld.rdf b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflow/HelloWorld.rdf
new file mode 100644
index 0000000..7c58856
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflow/HelloWorld.rdf
@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<!--
+
+ 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:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://ns.taverna.org.uk/2010/scufl2#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="WorkflowDocument" xml:base="HelloWorld/" xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd">
+ <Workflow rdf:about="">
+ <name>HelloWorld</name>
+ <workflowIdentifier rdf:resource="http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/"/>
+ <inputWorkflowPort>
+ <InputWorkflowPort rdf:about="in/yourName">
+ <name>yourName</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputWorkflowPort>
+ </inputWorkflowPort>
+ <outputWorkflowPort>
+ <OutputWorkflowPort rdf:about="out/results">
+ <name>results</name>
+ </OutputWorkflowPort>
+ </outputWorkflowPort>
+ <processor>
+ <Processor rdf:about="processor/Hello/">
+ <name>Hello</name>
+ <inputProcessorPort>
+ <InputProcessorPort rdf:about="processor/Hello/in/name">
+ <name>name</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputProcessorPort>
+ </inputProcessorPort>
+ <outputProcessorPort>
+ <OutputProcessorPort rdf:about="processor/Hello/out/greeting">
+ <name>greeting</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputProcessorPort>
+ </outputProcessorPort>
+ <dispatchStack>
+ <DispatchStack rdf:about="processor/Hello/dispatchstack/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/DefaultDispatchStack"/>
+ <dispatchStackLayers rdf:parseType="Collection">
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/0/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Parallelise"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/1/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/ErrorBounce"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/2/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Failover"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/3/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Retry"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/4/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Stop"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/Hello/dispatchstack/5/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Invoke"/>
+ </DispatchStackLayer>
+ </dispatchStackLayers>
+ </DispatchStack>
+ </dispatchStack>
+ <iterationStrategyStack>
+ <IterationStrategyStack rdf:about="processor/Hello/iterationstrategy/">
+ <iterationStrategies rdf:parseType="Collection">
+ <CrossProduct rdf:about="processor/Hello/iterationstrategy/0/">
+<productOf rdf:parseType="Collection">
+ <PortNode rdf:about="processor/Hello/iterationstrategy/0/0/">
+ <iterateOverInputPort rdf:resource="processor/Hello/in/name"/>
+ <desiredDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</desiredDepth>
+ </PortNode>
+</productOf>
+ </CrossProduct>
+ </iterationStrategies>
+ </IterationStrategyStack>
+ </iterationStrategyStack>
+ </Processor>
+ </processor>
+ <processor>
+ <Processor rdf:about="processor/wait4me/">
+ <name>wait4me</name>
+ <dispatchStack>
+ <DispatchStack rdf:about="processor/wait4me/dispatchstack/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/DefaultDispatchStack"/>
+ <dispatchStackLayers rdf:parseType="Collection">
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/0/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Parallelise"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/1/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/ErrorBounce"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/2/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Failover"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/3/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Retry"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/4/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Stop"/>
+ </DispatchStackLayer>
+ <DispatchStackLayer rdf:about="processor/wait4me/dispatchstack/5/">
+<rdf:type rdf:resource="http://ns.taverna.org.uk/2010/taverna/2.2/Invoke"/>
+ </DispatchStackLayer>
+ </dispatchStackLayers>
+ </DispatchStack>
+ </dispatchStack>
+ <iterationStrategyStack>
+ <IterationStrategyStack rdf:about="processor/wait4me/iterationstrategy/">
+ <iterationStrategies rdf:parseType="Collection">
+ <CrossProduct rdf:about="processor/wait4me/iterationstrategy/0/">
+<productOf rdf:parseType="Collection"/>
+ </CrossProduct>
+ </iterationStrategies>
+ </IterationStrategyStack>
+ </iterationStrategyStack>
+ </Processor>
+ </processor>
+ <datalink>
+ <DataLink rdf:about="datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0">
+ <receiveFrom rdf:resource="processor/Hello/out/greeting"/>
+ <sendTo rdf:resource="out/results"/>
+ <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</mergePosition>
+ </DataLink>
+ </datalink>
+ <datalink>
+ <DataLink rdf:about="datalink?from=in/yourName&to=processor/Hello/in/name">
+ <receiveFrom rdf:resource="in/yourName"/>
+ <sendTo rdf:resource="processor/Hello/in/name"/>
+ </DataLink>
+ </datalink>
+ <datalink>
+ <DataLink rdf:about="datalink?from=in/yourName&to=out/results&mergePosition=1">
+ <receiveFrom rdf:resource="in/yourName"/>
+ <sendTo rdf:resource="out/results"/>
+ <mergePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</mergePosition>
+ </DataLink>
+ </datalink>
+ <control>
+ <Blocking rdf:about="control?block=processor/Hello/&untilFinished=processor/wait4me/">
+ <block rdf:resource="processor/Hello/"/>
+ <untilFinished rdf:resource="processor/wait4me/"/>
+ </Blocking>
+ </control>
+ </Workflow>
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflowBundle.rdf
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diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflowBundle.rdf b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflowBundle.rdf
new file mode 100644
index 0000000..e39204f
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/workflowBundle.rdf
@@ -0,0 +1,59 @@
+<?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:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"
+ xsi:type="WorkflowBundleDocument" xml:base="./">
+ <WorkflowBundle rdf:about="">
+ <name>HelloWorld</name>
+ <globalBaseURI
+ rdf:resource="http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/" />
+ <mainWorkflow rdf:resource="workflow/HelloWorld/" />
+ <workflow>
+ <Workflow rdf:about="workflow/HelloWorld/">
+ <rdfs:seeAlso rdf:resource="workflow/HelloWorld.rdf" />
+ </Workflow>
+ </workflow>
+ <!--
+ <workflow>
+ <Workflow rdf:about="workflow/SomeNestedWorkflow/">
+ <rdfs:seeAlso rdf:resource="workflow/SomeNestedWorkflow.rdf" />
+ </Workflow>
+ </workflow>
+ -->
+ <mainProfile rdf:resource="profile/tavernaWorkbench/" />
+ <profile>
+ <Profile rdf:about="profile/tavernaServer/">
+ <rdfs:seeAlso rdf:resource="profile/tavernaServer.rdf" />
+ </Profile>
+ </profile>
+ <profile>
+ <Profile rdf:about="profile/tavernaWorkbench/">
+ <rdfs:seeAlso rdf:resource="profile/tavernaWorkbench.rdf" />
+ </Profile>
+ </profile>
+ <rdfs:seeAlso rdf:resource="annotation/workflowBundle.rdf" />
+ </WorkflowBundle>
+
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/megaProfile.rdf
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diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/megaProfile.rdf b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/megaProfile.rdf
new file mode 100644
index 0000000..3e23437
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/megaProfile.rdf
@@ -0,0 +1,696 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<!--
+
+ 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:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ProfileDocument" xml:base="taverna-2.2.0/" xsi:schemaLocation="http://ns.taverna.org.uk/2010/scufl2# http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://ns.taverna.org.uk/2010/scufl2/rdf.xsd">
+ <Profile rdf:about="">
+ <name>taverna-2.2.0</name>
+ <activateConfiguration rdf:resource="configuration/Content_list/"/>
+ <activateConfiguration rdf:resource="configuration/Format_as_GFF/"/>
+ <activateConfiguration rdf:resource="configuration/Get_XML_result/"/>
+ <activateConfiguration rdf:resource="configuration/Get_XML_result_type_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Get_text_result/"/>
+ <activateConfiguration rdf:resource="configuration/Get_text_result_type_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Input_data/"/>
+ <activateConfiguration rdf:resource="configuration/Input_data_type_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Job_params/"/>
+ <activateConfiguration rdf:resource="configuration/Job_params_async_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Job_params_crc_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Job_params_goterms_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Job_params_seqtype_defaultValue/"/>
+ <activateConfiguration rdf:resource="configuration/Unpack_XML_result/"/>
+ <activateConfiguration rdf:resource="configuration/Unpack_text_result/"/>
+ <activateConfiguration rdf:resource="configuration/checkStatus/"/>
+ <activateConfiguration rdf:resource="configuration/runInterProScan/"/>
+ </Profile>
+ <Activity rdf:about="activity/Content_list/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter/in"/>
+ <name>Content_list</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Content_list/in/WSArrayofData">
+ <name>WSArrayofData</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Content_list/out/output">
+ <name>output</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Format_as_GFF/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell"/>
+ <name>Format_as_GFF</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Format_as_GFF/in/interproscan_text">
+ <name>interproscan_text</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Format_as_GFF/out/interproscan_gff">
+ <name>interproscan_gff</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Get_XML_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl"/>
+ <name>Get_XML_result</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Get_XML_result/in/jobid">
+ <name>jobid</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Get_XML_result/in/type">
+ <name>type</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_XML_result/out/attachmentList">
+ <name>attachmentList</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_XML_result/out/result">
+ <name>result</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Get_XML_result_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Get_XML_result_type_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_XML_result_type_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Get_text_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl"/>
+ <name>Get_text_result</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Get_text_result/in/jobid">
+ <name>jobid</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Get_text_result/in/type">
+ <name>type</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_text_result/out/attachmentList">
+ <name>attachmentList</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_text_result/out/result">
+ <name>result</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Get_text_result_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Get_text_result_type_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Get_text_result_type_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Input_data/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter/in"/>
+ <name>Input_data</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Input_data/in/content">
+ <name>content</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Input_data/in/type">
+ <name>type</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Input_data/out/output">
+ <name>output</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Input_data_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Input_data_type_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Input_data_type_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Job_params/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter/in"/>
+ <name>Job_params</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/app">
+ <name>app</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/async">
+ <name>async</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/crc">
+ <name>crc</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/email">
+ <name>email</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/goterms">
+ <name>goterms</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/outformat">
+ <name>outformat</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/seqtype">
+ <name>seqtype</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/trlen">
+ <name>trlen</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Job_params/in/trtable">
+ <name>trtable</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Job_params/out/output">
+ <name>output</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Job_params_async_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Job_params_async_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Job_params_async_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Job_params_crc_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Job_params_crc_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Job_params_crc_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Job_params_goterms_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Job_params_goterms_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Job_params_goterms_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Job_params_seqtype_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant"/>
+ <name>Job_params_seqtype_defaultValue</name>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Job_params_seqtype_defaultValue/out/value">
+ <name>value</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Unpack_XML_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell"/>
+ <name>Unpack_XML_result</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Unpack_XML_result/in/bytes">
+ <name>bytes</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Unpack_XML_result/out/string">
+ <name>string</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/Unpack_text_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell"/>
+ <name>Unpack_text_result</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/Unpack_text_result/in/bytes">
+ <name>bytes</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/Unpack_text_result/out/string">
+ <name>string</name>
+ <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</portDepth>
+ <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</granularPortDepth>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/checkStatus/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl"/>
+ <name>checkStatus</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/checkStatus/in/jobid">
+ <name>jobid</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/checkStatus/out/status">
+ <name>status</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Activity rdf:about="activity/runInterProScan/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl"/>
+ <name>runInterProScan</name>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/runInterProScan/in/content">
+ <name>content</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <inputActivityPort>
+ <InputActivityPort rdf:about="activity/runInterProScan/in/params">
+ <name>params</name>
+ </InputActivityPort>
+ </inputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/runInterProScan/out/attachmentList">
+ <name>attachmentList</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ <outputActivityPort>
+ <OutputActivityPort rdf:about="activity/runInterProScan/out/jobid">
+ <name>jobid</name>
+ </OutputActivityPort>
+ </outputActivityPort>
+ </Activity>
+ <Configuration rdf:about="configuration/Content_list/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter#Config"/>
+ <name>Content_list</name>
+ <configure rdf:resource="activity/Content_list/"/>
+ <wrappedType:wrappedType xmlns:wrappedType="http://ns.taverna.org.uk/2010/activity/xml-splitter#" rdf:parseType="Literal">
+ <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
+ <s:arraytype name="content" optional="false" qname="{http://www.ebi.ac.uk/WSInterProScan}WSArrayofData" typename="WSArrayofData" unbounded="false" wrapped="false">
+ <s:elementtype>
+ <s:complextype name="" optional="false" qname="{http://www.ebi.ac.uk/WSInterProScan}data" typename="data" unbounded="false">
+ <s:elements>
+<s:basetype name="type" optional="false" qname="data>type" typename="string" unbounded="false"/>
+<s:basetype name="content" optional="false" qname="data>content" typename="string" unbounded="false"/>
+ </s:elements>
+ </s:complextype>
+ </s:elementtype>
+ </s:arraytype>
+ </s:extensions>
+ </wrappedType:wrappedType>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Content_list/in/WSArrayofData"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/xml"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Content_list/out/output"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/xml"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/Format_as_GFF/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config"/>
+ <name>Format_as_GFF</name>
+ <configure rdf:resource="activity/Format_as_GFF/"/>
+ <script:script xmlns:script="http://ns.taverna.org.uk/2010/activity/beanshell#">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:script>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Format_as_GFF/in/interproscan_text"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Format_as_GFF/out/interproscan_gff"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/Get_XML_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl#Config"/>
+ <name>Get_XML_result</name>
+ <configure rdf:resource="activity/Get_XML_result/"/>
+ <operation:operation xmlns:operation="http://ns.taverna.org.uk/2010/activity/wsdl#">
+ <ns6:operation xmlns:ns6="http://ns.taverna.org.uk/2010/activity/wsdl/">
+ <name:name xmlns:name="http://ns.taverna.org.uk/2010/activity/wsdl/operation#">poll</name:name>
+ <wsdl:wsdl xmlns:wsdl="http://ns.taverna.org.uk/2010/activity/wsdl/operation#" rdf:resource="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl"/>
+ </ns6:operation>
+ </operation:operation>
+ </Configuration>
+ <Configuration rdf:about="configuration/Get_XML_result_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Get_XML_result_type_defaultValue</name>
+ <configure rdf:resource="activity/Get_XML_result_type_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">toolxml</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Get_text_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl#Config"/>
+ <name>Get_text_result</name>
+ <configure rdf:resource="activity/Get_text_result/"/>
+ <operation:operation xmlns:operation="http://ns.taverna.org.uk/2010/activity/wsdl#">
+ <ns6:operation xmlns:ns6="http://ns.taverna.org.uk/2010/activity/wsdl/">
+ <name:name xmlns:name="http://ns.taverna.org.uk/2010/activity/wsdl/operation#">poll</name:name>
+ <wsdl:wsdl xmlns:wsdl="http://ns.taverna.org.uk/2010/activity/wsdl/operation#" rdf:resource="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl"/>
+ </ns6:operation>
+ </operation:operation>
+ </Configuration>
+ <Configuration rdf:about="configuration/Get_text_result_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Get_text_result_type_defaultValue</name>
+ <configure rdf:resource="activity/Get_text_result_type_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">toolraw</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Input_data/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter#Config"/>
+ <name>Input_data</name>
+ <configure rdf:resource="activity/Input_data/"/>
+ <wrappedType:wrappedType xmlns:wrappedType="http://ns.taverna.org.uk/2010/activity/xml-splitter#" rdf:parseType="Literal">
+ <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
+ <s:complextype name="" optional="false" qname="{http://www.ebi.ac.uk/WSInterProScan}data" typename="data" unbounded="false">
+ <s:elements>
+ <s:basetype name="type" optional="false" qname="data>type" typename="string" unbounded="false"/>
+ <s:basetype name="content" optional="false" qname="data>content" typename="string" unbounded="false"/>
+ </s:elements>
+ </s:complextype>
+ </s:extensions>
+ </wrappedType:wrappedType>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Input_data/in/content"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Input_data/in/type"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Input_data/out/output"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/xml"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/Input_data_type_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Input_data_type_defaultValue</name>
+ <configure rdf:resource="activity/Input_data_type_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">sequence</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Job_params/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/xml-splitter#Config"/>
+ <name>Job_params</name>
+ <configure rdf:resource="activity/Job_params/"/>
+ <wrappedType:wrappedType xmlns:wrappedType="http://ns.taverna.org.uk/2010/activity/xml-splitter#" rdf:parseType="Literal">
+ <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">
+ <s:complextype name="params" optional="false" qname="{http://www.ebi.ac.uk/WSInterProScan}inputParams" typename="inputParams" unbounded="false">
+ <s:elements>
+ <s:basetype name="app" optional="false" qname="inputParams>app" typename="string" unbounded="false"/>
+ <s:basetype name="crc" optional="false" qname="inputParams>crc" typename="boolean" unbounded="false"/>
+ <s:basetype name="seqtype" optional="false" qname="inputParams>seqtype" typename="string" unbounded="false"/>
+ <s:basetype name="trlen" optional="false" qname="inputParams>trlen" typename="int" unbounded="false"/>
+ <s:basetype name="trtable" optional="false" qname="inputParams>trtable" typename="int" unbounded="false"/>
+ <s:basetype name="goterms" optional="false" qname="inputParams>goterms" typename="boolean" unbounded="false"/>
+ <s:basetype name="async" optional="false" qname="inputParams>async" typename="boolean" unbounded="false"/>
+ <s:basetype name="outformat" optional="false" qname="inputParams>outformat" typename="string" unbounded="false"/>
+ <s:basetype name="email" optional="false" qname="inputParams>email" typename="string" unbounded="false"/>
+ </s:elements>
+ </s:complextype>
+ </s:extensions>
+ </wrappedType:wrappedType>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/app"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/async"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/crc"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/email"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/goterms"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/outformat"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/seqtype"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/trlen"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:java.lang.String"/>
+ <definesInputPort rdf:resource="../../activity/Job_params/in/trtable"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Job_params/out/output"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/xml"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/Job_params_async_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Job_params_async_defaultValue</name>
+ <configure rdf:resource="activity/Job_params_async_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">1</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Job_params_crc_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Job_params_crc_defaultValue</name>
+ <configure rdf:resource="activity/Job_params_crc_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">1</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Job_params_goterms_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Job_params_goterms_defaultValue</name>
+ <configure rdf:resource="activity/Job_params_goterms_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">1</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Job_params_seqtype_defaultValue/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/constant#Config"/>
+ <name>Job_params_seqtype_defaultValue</name>
+ <configure rdf:resource="activity/Job_params_seqtype_defaultValue/"/>
+ <string:string xmlns:string="http://ns.taverna.org.uk/2010/activity/constant#">p</string:string>
+ </Configuration>
+ <Configuration rdf:about="configuration/Unpack_XML_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config"/>
+ <name>Unpack_XML_result</name>
+ <configure rdf:resource="activity/Unpack_XML_result/"/>
+ <script:script xmlns:script="http://ns.taverna.org.uk/2010/activity/beanshell#">string = new String(bytes);
+</script:script>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:[B"/>
+ <definesInputPort rdf:resource="../../activity/Unpack_XML_result/in/bytes"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/application/octet-stream"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Unpack_XML_result/out/string"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/Unpack_text_result/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/beanshell#Config"/>
+ <name>Unpack_text_result</name>
+ <configure rdf:resource="activity/Unpack_text_result/"/>
+ <script:script xmlns:script="http://ns.taverna.org.uk/2010/activity/beanshell#">string = new String(bytes);
+</script:script>
+ <inputPortDefinition>
+ <InputPortDefinition>
+ <dataType rdf:resource="java:[B"/>
+ <definesInputPort rdf:resource="../../activity/Unpack_text_result/in/bytes"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/application/octet-stream"/>
+ </InputPortDefinition>
+ </inputPortDefinition>
+ <outputPortDefinition>
+ <OutputPortDefinition>
+ <definesOutputPort rdf:resource="../../activity/Unpack_text_result/out/string"/>
+ <expectedMimeType rdf:resource="http://purl.org/NET/mediatypes/text/plain"/>
+ </OutputPortDefinition>
+ </outputPortDefinition>
+ </Configuration>
+ <Configuration rdf:about="configuration/checkStatus/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl#Config"/>
+ <name>checkStatus</name>
+ <configure rdf:resource="activity/checkStatus/"/>
+ <operation:operation xmlns:operation="http://ns.taverna.org.uk/2010/activity/wsdl#">
+ <ns6:operation xmlns:ns6="http://ns.taverna.org.uk/2010/activity/wsdl/">
+ <name:name xmlns:name="http://ns.taverna.org.uk/2010/activity/wsdl/operation#">checkStatus</name:name>
+ <wsdl:wsdl xmlns:wsdl="http://ns.taverna.org.uk/2010/activity/wsdl/operation#" rdf:resource="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl"/>
+ </ns6:operation>
+ </operation:operation>
+ </Configuration>
+ <Configuration rdf:about="configuration/runInterProScan/">
+ <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/wsdl#Config"/>
+ <name>runInterProScan</name>
+ <configure rdf:resource="activity/runInterProScan/"/>
+ <operation:operation xmlns:operation="http://ns.taverna.org.uk/2010/activity/wsdl#">
+ <ns6:operation xmlns:ns6="http://ns.taverna.org.uk/2010/activity/wsdl/">
+ <name:name xmlns:name="http://ns.taverna.org.uk/2010/activity/wsdl/operation#">runInterProScan</name:name>
+ <wsdl:wsdl xmlns:wsdl="http://ns.taverna.org.uk/2010/activity/wsdl/operation#" rdf:resource="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl"/>
+ </ns6:operation>
+ </operation:operation>
+ </Configuration>
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/roevo-test.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/roevo-test.xml b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/roevo-test.xml
new file mode 100644
index 0000000..4b2415c
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/roevo-test.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<!--
+
+ 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://purl.org/wf4ever/roevo#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:prov="http://www.w3.org/ns/prov#"
+ xmlns:dcterms="http://purl.org/dc/terms/" xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RoEvoDocument"
+ xml:base="http://example.com/test/base"
+ xsi:schemaLocation="http://purl.org/wf4ever/roevo# ../../../../../../../main/resources/uk/org/taverna/scufl2/rdfxml/xsd/roevo.xsd">
+ <VersionableResource rdf:about="v3">
+ <wasChangedBy>
+ <ChangeSpecification>
+ <rdf:type rdf:resource="http://example.com/InsertNestedWorkflow"/>
+ <fromVersion rdf:resource="v2" />
+ <hasChange>
+ <Removal>
+ <relatedResource rdf:resource="http://example.net/removed-item"/>
+ <relatedResource rdf:resource="removed-item2"/>
+ </Removal>
+ </hasChange>
+ <hasChange>
+ <Addition>
+ <relatedResource rdf:resource="nested-workflow1" />
+ <relatedResource rdf:resource="http://example.net/nested-workflow2" />
+ </Addition>
+ </hasChange>
+ <hasChange>
+ <Modification>
+ <relatedResource rdf:resource="modified"/>
+ <relatedResource rdf:resource="http://example.net/modified2"/>
+ </Modification>
+ </hasChange>
+ </ChangeSpecification>
+ </wasChangedBy>
+ <prov:generatedAtTime rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-12-24T18:00:00+01:00</prov:generatedAtTime>
+ <prov:wasRevisionOf rdf:resource="v2" />
+ <prov:hadOriginalSource rdf:resource="http://example.org/originalSource1"/>
+ <prov:hadOriginalSource rdf:resource="originalSource2"/>
+ <prov:wasAttributedTo rdf:resource="../Fred" />
+ <prov:wasAttributedTo rdf:resource="http://example.net/SomeoneElse#me" />
+ </VersionableResource>
+ <VersionableResource rdf:about="v2">
+ <prov:generatedAtTime rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2010-01-15T11:00:00+01:00</prov:generatedAtTime>
+ <prov:wasRevisionOf rdf:resource="http://example.net/v1" />
+ </VersionableResource>
+ <VersionableResource rdf:about="http://example.net/v1">
+ <prov:generatedAtTime rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2010-01-15T11:00:00+01:00</prov:generatedAtTime>
+ <prov:wasRevisionOf rdf:resource="http://example.net/v0" />
+ </VersionableResource>
+</rdf:RDF>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e27d1dbe/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/update-bundle.sh
----------------------------------------------------------------------
diff --git a/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/update-bundle.sh b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/update-bundle.sh
new file mode 100644
index 0000000..8e422b3
--- /dev/null
+++ b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/update-bundle.sh
@@ -0,0 +1,26 @@
+#!/bin/sh
+#
+#
+# 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.
+#
+#
+set -e
+rm example.scufl2
+cd example
+zip -0 -X ../example.scufl2 mimetype
+zip -r ../example.scufl2 . -x mimetype