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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:39:55 UTC
[04/51] [partial] incubator-taverna-language git commit: temporarily
empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow b/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
deleted file mode 100755
index 798a520..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
+++ /dev/null
@@ -1,210 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="819135a3-2a42-4494-a98b-0e25148af91e" 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>1.2</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>a
-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>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>
- <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>logVec</name>
- <symanticType>BOOL_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>numVec</name>
- <symanticType>DOUBLE_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>intVec</name>
- <symanticType>INTEGER_LIST</symanticType>
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>strVec</name>
- <symanticType>STRING_LIST</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>str2</name>
- <symanticType reference="../../net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[3]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </inputSymanticTypes>
- <outputSymanticTypes>
- <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>int</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[2]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>str</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[3]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>logVec</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[4]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>numVec</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[5]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>intVect</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[6]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- <name>strVect</name>
- <symanticType reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[7]/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 reference="../../../inputSymanticTypes/net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean[8]/symanticType" />
- </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
- </outputSymanticTypes>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>num</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>int</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>str</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>logVec</name>
- <depth>1</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>numVec</name>
- <depth>1</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>intVec</name>
- <depth>1</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>strVec</name>
- <depth>1</depth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>txt</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>str2</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>log</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>int</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>str</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>logVec</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>numVec</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>intVect</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>strVect</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>png</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>txt</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></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>819135a3-2a42-4494-a98b-0e25148af91e</identification>
- </annotationBean>
- <date>2011-08-18 17:07:13.164 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/316e4a8a/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
deleted file mode 100644
index f2d5e9c..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
+++ /dev/null
@@ -1,541 +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.
- -->
-<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-2.4.0SNAPSHOT">
- <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="xstream">
- <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/316e4a8a/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow b/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
deleted file mode 100644
index b9cd40e..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
+++ /dev/null
@@ -1,78 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="ce96163a-d930-4e1a-b000-a35b847ef7b4" role="top"><name>Workflow1</name><inputPorts><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>P15409</text>
- </annotationBean>
- <date>2013-07-25 10:20:45.653 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>sequence</name><annotations /></port></outputPorts><processors><processor><name>Get_Protein_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>1.4</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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>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>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputText</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>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=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);
- }
-reader.close();
-outputText = writer.toString();
-</script>
- <dependencies />
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Protein_FASTA</processor><port>id</port></sink><source type="dataflow"><port>ID</port></source></datalink><datalink><sink type="dataflow"><port>sequence</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.ann
otation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>ce96163a-d930-4e1a-b000-a35b847ef7b4</identification>
- </annotationBean>
- <date>2013-07-25 10:20:51.37 UTC</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/316e4a8a/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow b/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
deleted file mode 100755
index 3022c1a..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
+++ /dev/null
@@ -1,215 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="b3701848-309f-4010-8212-166f621d7714" role="top"><name>Workflow8</name><inputPorts /><outputPorts><port><name>third_sleeper_report</name><annotations /></port><port><name>second_sleeper_report</name><annotations /></port><port><name>second_sleeper_2_report</name><annotations /></port><port><name>first_sleeper_report</name><annotations /></port><port><name>first_sleeper_finished</name><annotations /></port><port><name>second_sleeper_started</name><annotations /></port><port><name>second_sleeper_finished</name><annotations /></port><port><name>second_sleeper_2_finished</name><annotations /></port><port><name>second_sleeper_2_started</name><annotations /></port><port><name>third_sleeper_started</name><annotations /></port></outputPorts><processors><processor><name>second_sleeper</name><inputPorts /><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularD
epth></port><port><name>started</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>finished</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>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap><map from="report" to="report" /><map from="finished" to="finished" /><map from="started" to="started" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>report</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>duration</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>started</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>finished</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>started = new Date().getTime();
-Thread.sleep(2500);
-finished = new Date().getTime();
-duration = finished - started;
-
-report = "Started at " + started + "\nFinished at "
- + finished + ", took " + duration + " ms";
-
-</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>1.3</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>first_sleeper</name><inputPorts /><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>finished</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>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap><map from=
"report" to="report" /><map from="finished" to="finished" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>report</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>duration</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>started</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>finished</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>started = new Date().getTime();
-Thread.sleep(1000);
-finished = new Date().getTime();
-duration = finished - started;
-
-report = "Started at " + started + "\nFinished at "
- + finished + ", took " + duration + " ms";
-
-</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>1.3</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>second_sleeper_2</name><inputPorts /><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>finished</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>started</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>1.3</version></raven><class>net.sf.tavern
a.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap><map from="report" to="report" /><map from="finished" to="finished" /><map from="started" to="started" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>report</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>duration</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>started</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>finished</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>started = new Date().getTime();
-Thread.sleep(3500);
-finished = new Date().getTime();
-duration = finished - started;
-
-report = "Started at " + started + "\nFinished at "
- + finished + ", took " + duration + " ms";
-
-</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>1.3</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>third_sleeper</name><inputPorts /><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>started</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>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap><map from="
report" to="report" /><map from="started" to="started" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <inputs />
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>report</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>duration</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>started</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>finished</name>
- <depth>0</depth>
- <mimeTypes />
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>started = new Date().getTime();
-Thread.sleep(2500);
-finished = new Date().getTime();
-duration = finished - started;
-
-report = "Started at " + started + "\nFinished at "
- + finished + ", took " + duration + " ms";
-
-</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>1.3</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><condition control="second_sleeper" target="third_sleeper" /><condition control="first_sleeper" target="second_sleeper_2" /><condition control="first_sleeper" target="second_sleeper" /><condition control="second_sleeper_2" target="third_sleeper" /></conditions><datalinks><datalink><sink type="dataflow"><port>third_sleeper_report</port></sink><source type="processor"><processor>third_sleeper</processor><port>report</port></source></datalink><datalink><sink type="dataflow"
><port>second_sleeper_report</port></sink><source type="processor"><processor>second_sleeper</processor><port>report</port></source></datalink><datalink><sink type="dataflow"><port>second_sleeper_2_report</port></sink><source type="processor"><processor>second_sleeper_2</processor><port>report</port></source></datalink><datalink><sink type="dataflow"><port>first_sleeper_report</port></sink><source type="processor"><processor>first_sleeper</processor><port>report</port></source></datalink><datalink><sink type="dataflow"><port>first_sleeper_finished</port></sink><source type="processor"><processor>first_sleeper</processor><port>finished</port></source></datalink><datalink><sink type="dataflow"><port>second_sleeper_started</port></sink><source type="processor"><processor>second_sleeper</processor><port>started</port></source></datalink><datalink><sink type="dataflow"><port>second_sleeper_finished</port></sink><source type="processor"><processor>second_sleeper</processor><port>finished<
/port></source></datalink><datalink><sink type="dataflow"><port>second_sleeper_2_finished</port></sink><source type="processor"><processor>second_sleeper_2</processor><port>finished</port></source></datalink><datalink><sink type="dataflow"><port>second_sleeper_2_started</port></sink><source type="processor"><processor>second_sleeper_2</processor><port>started</port></source></datalink><datalink><sink type="dataflow"><port>third_sleeper_started</port></sink><source type="processor"><processor>third_sleeper</processor><port>started</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>b3701848-309f-4010-8212-166f621d7714</identification>
- </annotationBean>
- <date>2011-08-25 12:18:38.470 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>57411dbe-9c2d-47c6-a404-2fa43812faa1</identification>
- </annotationBean>
- <date>2011-08-25 12:15:29.11 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/316e4a8a/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
deleted file mode 100644
index 2a3fb45..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
+++ /dev/null
@@ -1,77 +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.
- -->
-<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>
- <end>1</end>
- <excludes />
- </columnRange>
- <rowRange>
- <start>0</start>
- <end>-1</end>
- <excludes />
- </rowRange>
- <emptyCellValue />
- <columnNames />
- <allRows>true</allRows>
- <excludeFirstRow>false</excludeFirstRow>
- <ignoreBlankRows>true</ignoreBlankRows>
- <emptyCellPolicy>EMPTY_STRING</emptyCellPolicy>
-</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>0.8</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <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>0.8</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <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>0.8</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="fileurl" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>SpreadsheetImport</processor><port>fileurl</port></sink><source type="dataflow"><port>file_url</port></source></datalink><datalink><sink type="dataflow"><port>A_column</port></sink><source type="processor"><processor>SpreadsheetImport</processor><port>A</port></source></datalink><datalink><sink type="dataflow"><port>B_column</port></sink><source type="process
or"><processor>SpreadsheetImport</processor><port>B</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>Paul Fisher</text>
- </annotationBean>
- <date>2009-08-24 13:19:15.753 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>This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.</text>
- </annotationBean>
- <date>2009-08-24 13:20:49.43 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.DescriptiveTitle">
- <text>Spreadsheet Importer</text>
- </annotationBean>
- <date>2009-08-24 13:19:23.773 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/316e4a8a/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
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diff --git a/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow b/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
deleted file mode 100644
index be46489..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
+++ /dev/null
@@ -1,108 +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.
- -->
-<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>
- <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
-<localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation>
-</mechanismXML>
- <externaltoolid>efc67bc3-a02c-437f-a525-8557642cb77b</externaltoolid>
- <useCaseDescription>
- <usecaseid />
- <description />
- <command>jpylyzer %%input_file%%</command>
- <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
- <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
- <tags>
- <string>input_file</string>
- </tags>
- <REs />
- <queue__preferred />
- <queue__deny />
- <static__inputs />
- <inputs>
- <entry>
- <string>input_file</string>
- <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
- <tag>input_file</tag>
- <file>false</file>
- <tempFile>false</tempFile>
- <binary>false</binary>
- <charsetName>MacRoman</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>
- <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>1.4</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="input_file" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>XPath_width</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><input
Map><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">
- <xmlDocument><?xml version="1.0" encoding="UTF-8"?>
-<input>
- <width>42</width>
- <height>24</height>
-</input></xmlDocument>
- <xpathExpression>//width/text()</xpathExpression>
- <xpathNamespaceMap />
-</net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean></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_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>XPath_height</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputM
ap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">
- <xpathExpression>//height/text()</xpathExpression>
- <xpathNamespaceMap />
-</net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean></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_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>jpylyzer</processor><port>input_file</port></sink><source type="dataflow"><port>input_file</port></source></datalink><datalink><sink type="processor"><processor>XPath_width</processor><port>xml_text</port></sink><source type="processor"><processor>jpylyzer</processor><port>STDOUT</port></source></datalink><datalink><sink type="processor"><processor>XPath_hei
ght</processor><port>xml_text</port></sink><source type="processor"><processor>jpylyzer</processor><port>STDOUT</port></source></datalink><datalink><sink type="dataflow"><port>STDERR</port></sink><source type="processor"><processor>jpylyzer</processor><port>STDERR</port></source></datalink><datalink><sink type="dataflow"><port>width</port></sink><source type="processor"><processor>XPath_width</processor><port>nodelist</port></source></datalink><datalink><sink type="dataflow"><port>height</port></sink><source type="processor"><processor>XPath_height</processor><port>nodelist</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>1345660e-8b56-407c-9d3f-c2fd3489d26d</identification>
- </annotationBean>
- <date>2013-04-04 09:22:11.660 UTC</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/316e4a8a/taverna-scufl2-ucfpackage/.gitignore
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diff --git a/taverna-scufl2-ucfpackage/.gitignore b/taverna-scufl2-ucfpackage/.gitignore
deleted file mode 100644
index ea8c4bf..0000000
--- a/taverna-scufl2-ucfpackage/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target