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Posted to commits@taverna.apache.org by st...@apache.org on 2016/04/28 00:55:54 UTC
[06/26] incubator-taverna-engine git commit: Moved
taverna-integration-tests to separate branch
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/e68dd99a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow b/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
deleted file mode 100644
index 196a4bc..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
+++ /dev/null
@@ -1,518 +0,0 @@
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ringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=" + id);
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
- <text>GBSeq test</text>
- </annotationBean>
- <date>2009-12-15 20:30:12.959 GMT</date>
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- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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- <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated
-to them given a protein and a nucleotide id.</text>
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- <date>2009-12-15 20:30:23.505 GMT</date>
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- <date>2010-07-04 18:16:42.290 BST</date>
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- <identification>c00b121a-0114-471a-bd29-03597414879c</identification>
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- <date>2011-07-12 14:07:08.97 BST</date>
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- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>af08cba7-dd16-404c-b20b-fd3cb7ccf7aa</identification>
- </annotationBean>
- <date>2011-07-12 14:06:02.422 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
- <text>Franck Tanoh</text>
- </annotationBean>
- <date>2011-07-12 14:07:04.790 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-engine/blob/e68dd99a/taverna-integration-tests/src/test/resources/t2flow/apiconsumer.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/apiconsumer.t2flow b/taverna-integration-tests/src/test/resources/t2flow/apiconsumer.t2flow
deleted file mode 100644
index 66ef4ac..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/apiconsumer.t2flow
+++ /dev/null
@@ -1,178 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="8bf2b5e5-a3e0-4fbd-bfd2-aefc7b2a6b8a" role="top"><name>Workflow4</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>String</name><inputPorts><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>object</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</class><inputMap><map from="string" to="string" /></inputMap><outputMap><map from="object" to="object" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.apic
onsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <inputs />
- <outputs />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>java.lang.String</className>
- <methodName>String</methodName>
- <parameterNames>
- <string>string</string>
- </parameterNames>
- <parameterDimensions>
- <int>0</int>
- </parameterDimensions>
- <parameterTypes>
- <string>java.lang.String</string>
- </parameterTypes>
- <returnType>java.lang.String</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>true</isMethodConstructor>
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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><cross><port name="string" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>toUpperCase</name><inputPorts><port><name>object</name><depth>0</depth></port></inputPorts><outputPorts><port><name>result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>apiconsumer-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity</cl
ass><inputMap><map from="object" to="object" /></inputMap><outputMap><map from="result" to="result" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean xmlns="">
- <inputs />
- <outputs />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <apiConsumerName>No name</apiConsumerName>
- <apiConsumerDescription>No description</apiConsumerDescription>
- <description />
- <className>java.lang.String</className>
- <methodName>toUpperCase</methodName>
- <parameterNames />
- <parameterDimensions />
- <parameterTypes />
- <returnType>java.lang.String</returnType>
- <returnDimension>0</returnDimension>
- <isMethodStatic>false</isMethodStatic>
- <isMethodConstructor>false</isMethodConstructor>
-</net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</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><cross><port name="object" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>String</processor><port>string</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="processor"><processor>toUpperCase</processor><port>object</port></sink><source type="processor"><processor>String</processor><port>object</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="proc
essor"><processor>toUpperCase</processor><port>result</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>483d65c6-98c1-4b94-b628-d5bcbf351e97</identification>
- </annotationBean>
- <date>2011-05-16 13:07:03.385 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>d460e60a-43bb-47fc-a9f4-89e15274b100</identification>
- </annotationBean>
- <date>2011-11-02 12:43:09.911 GMT</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>0d977496-aa5d-4274-9827-85400d5f13a2</identification>
- </annotationBean>
- <date>2011-05-16 13:06:33.69 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>8bf2b5e5-a3e0-4fbd-bfd2-aefc7b2a6b8a</identification>
- </annotationBean>
- <date>2011-11-02 12:46:41.313 GMT</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>58f30a52-57df-46ce-b1bb-b9533984f8dd</identification>
- </annotationBean>
- <date>2011-11-02 12:29:15.575 GMT</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>c2693c41-1373-48cf-afbe-d8bbe0ea9e35</identification>
- </annotationBean>
- <date>2011-11-02 12:31:01.678 GMT</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>1ce7f3a0-71f4-4794-8bbd-dbb6de42442d</identification>
- </annotationBean>
- <date>2011-05-16 12:57:01.975 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
- <annotationAssertions>
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
- <identification>4c2b6995-eecb-47a7-b72c-63cfb96b6852</identification>
- </annotationBean>
- <date>2011-11-02 12:43:51.355 GMT</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>225db881-4e07-4cdb-920c-343dc1536edc</identification>
- </annotationBean>
- <date>2011-05-16 13:10:54.588 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>404e203c-ce51-4a9f-907c-1dab7f2eaaa2</identification>
- </annotationBean>
- <date>2011-05-16 12:44:02.533 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>0b6881f1-aa8d-483e-a7bb-7ad38b1da778</identification>
- </annotationBean>
- <date>2011-05-16 12:26:38.721 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-engine/blob/e68dd99a/taverna-integration-tests/src/test/resources/t2flow/beanshell.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/beanshell.t2flow b/taverna-integration-tests/src/test/resources/t2flow/beanshell.t2flow
deleted file mode 100644
index 8c5968c..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/beanshell.t2flow
+++ /dev/null
@@ -1,137 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="78cb1427-d57f-42c2-a385-1d20c1580f3b" role="top"><name>Workflow13</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Echo</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><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfi
gurationBean xmlns="">
- <script>out=in;</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>out</name>
- <depth>0</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>ListGenerator</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><
map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
- <script>out = new ArrayList();
-
-for (int i = 0; i < 1000; i++) {
- out.add(in + ":" + i);
-}</script>
- <dependencies />
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>in</name>
- <depth>0</depth>
- <mimeTypes>
- <string>text/plain</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>out</name>
- <depth>1</depth>
- <mimeTypes />
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Echo</processor><port>in</port></sink><source type="processor"><processor>ListGenerator</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>ListGenerator</processor><port>in</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><
processor>Echo</processor><port>out</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>13c70169-dfaa-4ea6-b6ab-3551dae7fa84</identification>
- </annotationBean>
- <date>2010-08-19 12:28:57.881 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>7ef10e93-7376-41a9-9255-552149094142</identification>
- </annotationBean>
- <date>2010-08-31 13:06:57.536 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>3b7c0b9c-572d-466b-af6d-0fb40699e8a5</identification>
- </annotationBean>
- <date>2010-08-31 12:50:40.306 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>eb6a550d-f34e-4de9-b0fc-1b3df8ab36c4</identification>
- </annotationBean>
- <date>2010-08-31 14:32:44.634 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>78cb1427-d57f-42c2-a385-1d20c1580f3b</identification>
- </annotationBean>
- <date>2010-08-31 14:36:00.297 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>ad638364-a6e0-4852-abca-9f609c9553d2</identification>
- </annotationBean>
- <date>2010-08-19 13:43:43.797 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-engine/blob/e68dd99a/taverna-integration-tests/src/test/resources/t2flow/biomart.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/biomart.t2flow b/taverna-integration-tests/src/test/resources/t2flow/biomart.t2flow
deleted file mode 100644
index f82f340..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/biomart.t2flow
+++ /dev/null
@@ -1,30 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="4a959e22-8166-4e8b-ae94-6e85c8807e35" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>btaurus_gene_ensembl</name><inputPorts /><outputPorts><port><name>btaurus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="btaurus_gene_ensembl.ensembl_gene_id" to="btaurus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Bos taurus genes (UMD3.1)" nam
e="btaurus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2011-09-07 22:16:01"><MartURLLocation database="ensembl_mart_64" default="1" displayName="ENSEMBL GENES 64 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="1" softwareVersion="0.6" requestId="taverna"><Dataset name="btaurus_gene_ensembl"><Attribute name="ensembl_gene_id" /><Filter name="chromosome_name" value="1" /><Filter name="with_affy_bovine" excluded="0" /><Filter name="go_evidence_code" value="IDA" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><cla
ss>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
- <maxJobs>1</maxJobs>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
- <backoffFactor>1.0</backoffFactor>
- <initialDelay>1000</initialDelay>
- <maxDelay>5000</maxDelay>
- <maxRetries>0</maxRetries>
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>btaurus_gene_ensembl</processor><port>btaurus_gene_ensembl.ensembl_gene_id</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>4a959e22-8166-4e8b-ae94-6e85c8807e35</identification>
- </annotationBean>
- <date>2011-10-27 14:33:16.228 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>5859741c-a0ba-4dae-8b81-1dd7c928562f</identification>
- </annotationBean>
- <date>2011-10-27 14:32:47.106 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