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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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
