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Posted to commits@taverna.apache.org by st...@apache.org on 2015/03/17 10:55:44 UTC
[1/6] incubator-taverna-language git commit: These are all my
workflows - added Apache header
Repository: incubator-taverna-language
Updated Branches:
refs/heads/master d2af1bc5d -> f2972d5b3
These are all my workflows - added Apache header
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/315acb42
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/315acb42
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/315acb42
Branch: refs/heads/master
Commit: 315acb42378b33aad40c78044f5c345d594900ff
Parents: d2af1bc
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:49:18 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:49:18 2015 +0000
----------------------------------------------------------------------
.../resources/annotation_with_backslash.t2flow | 21 +-
.../src/test/resources/as.t2flow | 3 +-
.../src/test/resources/beanshell-deps.t2flow | 21 +-
.../src/test/resources/component_simple.t2flow | 21 +-
.../resources/dataflow_link_then_merge.t2flow | 21 +-
.../src/test/resources/dispatchlayers.t2flow | 21 +-
.../test/resources/iterationstrategies.t2flow | 21 +-
.../src/test/resources/merge_fun.t2flow | 21 +-
.../resources/merge_then_dataflow_link.t2flow | 21 +-
.../src/test/resources/missing_merge.t2flow | 21 +-
.../resources/missing_produced_by_941.t2flow | 247 -------------------
.../src/test/resources/rest-2-2.t2flow | 21 +-
.../src/test/resources/sleepers.t2flow | 21 +-
13 files changed, 222 insertions(+), 259 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/annotation_with_backslash.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/annotation_with_backslash.t2flow b/taverna-scufl2-t2flow/src/test/resources/annotation_with_backslash.t2flow
index b9da130..5be3301 100644
--- a/taverna-scufl2-t2flow/src/test/resources/annotation_with_backslash.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/annotation_with_backslash.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-core-2.5.0"><dataflow id="b550eb5c-d7ad-4a9b-8dea-fc16df39b9f4" role="top"><name>Workflow1</name><inputPorts><port><name>backslash</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>
@@ -20,4 +39,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/as.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/as.t2flow b/taverna-scufl2-t2flow/src/test/resources/as.t2flow
index c52586a..27fa1da 100644
--- a/taverna-scufl2-t2flow/src/test/resources/as.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/as.t2flow
@@ -1,4 +1,4 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0">
+<?xml version="1.0"?>
<!--
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
@@ -17,6 +17,7 @@
* specific language governing permissions and limitations
* under the License.
-->
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0">
<dataflow id="92c5e8d5-8360-4f86-a845-09c9849cbdc5" role="top">
<name>Workflow1</name>
<inputPorts />
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow b/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
index 3d52c25..7c96b03 100755
--- a/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="9a455aad-8690-4a1a-862b-a5d5feee84cf" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>A_C_workflow</name><inputPorts /><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 /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<inputs />
<outputs />
@@ -44,4 +63,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/component_simple.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/component_simple.t2flow b/taverna-scufl2-t2flow/src/test/resources/component_simple.t2flow
index e240e38..88d00e0 100644
--- a/taverna-scufl2-t2flow/src/test/resources/component_simple.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/component_simple.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-digitalpreservation-2.5.0"><dataflow id="b521b6df-57f3-4eed-8536-c4c1a044dfcc" role="top"><name>Workflow1</name><inputPorts><port><name>doc1</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>doc2</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>docOut</name><lastPredictedDepth>0</lastPredictedDepth><annotations /></port></outputPorts><processors><processor><name>combiner</name><inputPorts><port><name>metricDocument1</name><depth>0</depth></port><port><name>metricDocument2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>combinedMetricDocument</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.component</group><artifact>component-activity</artifact><version>1.5</version></raven><class>ne
t.sf.taverna.t2.component.ComponentActivity</class><inputMap><map from="metricDocument1" to="metricDocument1" /><map from="metricDocument2" to="metricDocument2" /></inputMap><outputMap><map from="combinedMetricDocument" to="combinedMetricDocument" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.component.ComponentActivityConfigurationBean xmlns="">
<registryBase>http://www.myexperiment.org</registryBase>
<familyName>SCAPE Utility Components</familyName>
@@ -32,4 +51,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow b/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
index 62206b6..b5aee0b 100644
--- a/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
<script>outputlist = inputlist;</script>
@@ -63,4 +82,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow b/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
index 0c10d59..cb19faf 100644
--- a/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="3805e4de-40e6-4052-a292-8adc6515618c" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>retries</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>retries</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
@@ -150,4 +169,4 @@ if ("true".matches(loop)) {
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow b/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
index 412dde9..af10457 100644
--- a/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="87aa4917-46ce-473e-b183-f7d4e1860d30" role="top"><name>Demonstrationofconfigurableiteration</name><inputPorts /><outputPorts><port><name>Output</name><annotations /></port></outputPorts><processors><processor><name>Colours</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>red ,green ,</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
@@ -384,4 +403,4 @@ if (!string.equals("")) {
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow b/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow
index a84b482..2fcd936 100644
--- a/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/merge_fun.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
<script>outputlist = inputlist;</script>
@@ -63,4 +82,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow b/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
index 4968daa..b1c1784 100644
--- a/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
<script>outputlist = inputlist;</script>
@@ -63,4 +82,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow b/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow
index 3cadf5b..84b5ac1 100644
--- a/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/missing_merge.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="aaecfd60-6456-4573-a25c-bcb841050601" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>a</name><annotations /></port><port><name>b</name><annotations /></port></outputPorts><processors><processor><name>Echo_List</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurati
onBean xmlns="">
<localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>
<script>outputlist = inputlist;</script>
@@ -63,4 +82,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/missing_produced_by_941.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/missing_produced_by_941.t2flow b/taverna-scufl2-t2flow/src/test/resources/missing_produced_by_941.t2flow
deleted file mode 100644
index a259a00..0000000
--- a/taverna-scufl2-t2flow/src/test/resources/missing_produced_by_941.t2flow
+++ /dev/null
@@ -1,247 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1"><dataflow id="00c8a793-d305-494b-ba61-a1fd2a0986df" role="top"><name>dataflow0</name><inputPorts /><outputPorts><port><name>mzs</name></port><port><name>intensities</name></port></outputPorts><processors><processor><name>getPeak</name><inputPorts><port><name>parameters</name><depth>0</depth></port></inputPorts><outputPorts><port><name>parameters</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map from="parameters" to="parameters" /></inputMap><outputMap><map from="parameters" to="parameters" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
- <wsdl>http://www.massbank.jp/api/services/MassBankAPI?wsdl</wsdl>
- <operation>getPeak</operation>
-</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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="parameters" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getPeak_input</name><inputPorts><port><name>ids</name><depth>1</depth></port></inputPorts><outputPorts><port><name>output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity</c
lass><inputMap><map from="ids" to="ids" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean xmlns="">
- <wrappedTypeXML><s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getPeak" name="parameters" qname="{http://api.massbank}getPeak"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="string" name="ids" qname="{http://api.massbank}&gt;getPeak&gt;ids"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions></wrappedTypeXML>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <allowsLiteralValues>false</allowsLiteralValues>
- <name>ids</name>
- <depth>1</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">l('text/plain')</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>0</granularDepth>
- <name>output</name>
- <depth>0</depth>
- <mimeTypes class="java.util.Collections$SingletonList">
- <element class="string">'text/xml'</element>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLSplitterConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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="ids" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>String_Constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value"
/></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>KO009304</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>XPath_From_Text</name><inputPorts><port><name>xml-text</name><depth>0</depth></port><port><name>xpath</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>localworker-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><i
nputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals("")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;</script>
- <dependencies>
- <string>dom4j:dom4j:1.6</string>
- </dependencies>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6</version>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xpath</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xml-text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelistAsXML</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>XPath_From_Text0</name><inputPorts><port><name>xml-text</name><depth>0</depth></port><port><name>xpath</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>localworker-activity</artifact><version>0.4</ver
sion></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <script>import org.dom4j.Document;
-import org.dom4j.Node;
-import org.dom4j.io.SAXReader;
-
-SAXReader reader = new SAXReader(false);
-reader.setIncludeInternalDTDDeclarations(false);
-reader.setIncludeExternalDTDDeclarations(false);
-
-Document document = reader.read(new StringReader(xmltext));
-List nodelist = document.selectNodes(xpath);
-
-// Process the elements in the nodelist
-ArrayList outputList = new ArrayList();
-ArrayList outputXmlList = new ArrayList();
-
-String val = null;
-String xmlVal = null;
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
- Node element = (Node) iter.next();
- xmlVal = element.asXML();
- val = element.getStringValue();
- if (val != null && !val.equals("")) {
- outputList.add(val);
- outputXmlList.add(xmlVal);
- }
-
-}
-
-List nodelist=outputList;
-List nodelistAsXML=outputXmlList;</script>
- <dependencies>
- <string>dom4j:dom4j:1.6</string>
- </dependencies>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies>
- <net.sf.taverna.raven.repository.BasicArtifact>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6</version>
- </net.sf.taverna.raven.repository.BasicArtifact>
- </artifactDependencies>
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xpath</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- <name>xml-text</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/xml'</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <granularDepth>1</granularDepth>
- <name>nodelistAsXML</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>String_Constant0</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><o
utputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>//ax21:intensities</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>String_Constant1</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.s
f.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>//ax21:mzs</value>
-</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</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</group><artifact>workflowmodel-impl</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getPeak</processor><port>parameters</port></sink><source type="processor"><processor>getPeak_input</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>getPeak_input</processor><port>ids</port></sink><source type="processor"><processor>String_Constant</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text</processor><port>xml-
text</port></sink><source type="processor"><processor>getPeak</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text</processor><port>xpath</port></sink><source type="processor"><processor>String_Constant0</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text0</processor><port>xml-text</port></sink><source type="processor"><processor>getPeak</processor><port>parameters</port></source></datalink><datalink><sink type="processor"><processor>XPath_From_Text0</processor><port>xpath</port></sink><source type="processor"><processor>String_Constant1</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>mzs</port></sink><source type="processor"><processor>XPath_From_Text0</processor><port>nodelist</port></source></datalink><datalink><sink type="dataflow"><port>intensities</port></sink><source type="processor"><processor>XPath_From_Text</processor>
<port>nodelist</port></source></datalink></datalinks><annotations /></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow b/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow
index d88967e..97f0a51 100755
--- a/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/rest-2-2.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="44e3e7d3-df8c-401b-8b77-9d001343d8c2" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>default</name><inputPorts /><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.ui-activities</group><artifact>rest-activity</artifact><version>0.3.1</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">
<httpMethod>GET</httpMethod>
<urlSignature>http://www.myexperiment.org/user.xml?id={userID}</urlSignature>
@@ -76,4 +95,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/315acb42/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
index 3022c1a..a3e949f 100755
--- a/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/sleepers.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><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>
@@ -212,4 +231,4 @@ report = "Started at " + started + "\nFinished at "
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
[2/6] incubator-taverna-language git commit: Katy Wolstencroft's
workflows from Taverna tutorial
Posted by st...@apache.org.
Katy Wolstencroft's workflows from Taverna tutorial
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/fab2c350
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/fab2c350
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/fab2c350
Branch: refs/heads/master
Commit: fab2c350260675a2ed8503c51b249d33e4a804b7
Parents: 315acb4
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:49:39 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:50:21 2015 +0000
----------------------------------------------------------------------
.../src/test/resources/fasta_and_pscan.t2flow | 21 +++++++++++++++++++-
.../resources/fasta_pscan_and_dbfetch.t2flow | 21 +++++++++++++++++++-
2 files changed, 40 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fab2c350/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow b/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
index 0dfcacb..5aab1d0 100644
--- a/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="a5b440ec-9bc1-4dc6-98b1-6c41fa17a21a" 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>
@@ -98,4 +117,4 @@ outputText = writer.toString();
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/fab2c350/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow b/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
index 83f1404..02cd245 100644
--- a/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="1c78b8e1-9700-43a5-9452-20a77aecfe46" 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>
@@ -147,4 +166,4 @@ outputText = writer.toString();
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
[3/6] incubator-taverna-language git commit: Alan's workflow - Apache
license header
Posted by st...@apache.org.
Alan's workflow - Apache license header
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/bb3463a8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/bb3463a8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/bb3463a8
Branch: refs/heads/master
Commit: bb3463a88540c733de5d10862bbc117084baad8f
Parents: fab2c35
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:51:12 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:51:12 2015 +0000
----------------------------------------------------------------------
.../interaction_multiple_choice.t2flow | 21 +++++++++++++++++++-
1 file changed, 20 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/bb3463a8/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow b/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow
index e41c969..b3e07ec 100644
--- a/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/interaction_multiple_choice.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-biodiversity-2.5.0"><dataflow id="da58acd5-937d-419d-aaf4-79ade8491adf" role="top"><name>Workflow3</name><inputPorts /><outputPorts><port><name>answers</name><lastPredictedDepth>1</lastPredictedDepth><annotations /></port></outputPorts><processors><processor><name>Interaction</name><inputPorts><port><name>selectionValues</name><depth>1</depth></port></inputPorts><outputPorts><port><name>answers</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>1.5</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap><map from="selectionValues" to="selectionValues" /></inputMap><outputMap><map from="answers" to="answers" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.
InteractionActivityConfigurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
@@ -106,4 +125,4 @@ if (!string.equals("")) {
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
[5/6] incubator-taverna-language git commit: my rshell-test workflow
Posted by st...@apache.org.
my rshell-test workflow
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/b82bb4c5
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/b82bb4c5
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/b82bb4c5
Branch: refs/heads/master
Commit: b82bb4c5b1e0069f1b7072775c7210e8749f58b9
Parents: 04704cc
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:54:04 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:54:04 2015 +0000
----------------------------------------------------------------------
.../src/test/resources/rshell-2-2.t2flow | 21 +++++++++++++++++++-
1 file changed, 20 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/b82bb4c5/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
index 798a520..7093a1c 100755
--- a/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="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
@@ -207,4 +226,4 @@ script</script>
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
[4/6] incubator-taverna-language git commit: Alan's interaction
workflows
Posted by st...@apache.org.
Alan's interaction workflows
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/04704cc7
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/04704cc7
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/04704cc7
Branch: refs/heads/master
Commit: 04704cc76ea738456b4d8f06e9e730852035ad95
Parents: bb3463a
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:53:32 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:53:32 2015 +0000
----------------------------------------------------------------------
.../interaction-with-strange-loop.t2flow | 21 +++++++++++++++++++-
.../resources/interaction_simple_tell.t2flow | 21 +++++++++++++++++++-
2 files changed, 40 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/04704cc7/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow b/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
index 39c2d0c..75154f3 100644
--- a/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="185649fa-f9da-48a2-8941-dc6354091db4" role="top"><name>Workflow74</name><inputPorts><port><name>flag</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>mask_id</name><annotations /></port><port><name>created</name><annotations /></port></outputPorts><processors><processor><name>BioSTIFInteraction</name><inputPorts /><outputPorts><port><name>maskID</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>1.0.0</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap /><outputMap><map from="maskID" to="maskID" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfi
gurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
@@ -209,4 +228,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/04704cc7/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow b/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow
index 563908a..86766df 100644
--- a/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/interaction_simple_tell.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ -->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-biodiversity-2.5.0"><dataflow id="a2922e48-9c02-4edd-adbf-b2ebfd4fd5ce" role="top"><name>Workflow1</name><inputPorts /><outputPorts><port><name>answer</name><lastPredictedDepth>0</lastPredictedDepth><annotations /></port></outputPorts><processors><processor><name>tell</name><inputPorts><port><name>message</name><depth>0</depth></port></inputPorts><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>1.5</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap><map from="message" to="message" /></inputMap><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBea
n xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
@@ -50,4 +69,4 @@
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
[6/6] incubator-taverna-language git commit: Example workflow by Katy
Wolstencroft
Posted by st...@apache.org.
Example workflow by Katy Wolstencroft
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f2972d5b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f2972d5b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f2972d5b
Branch: refs/heads/master
Commit: f2972d5b31ba9b000345580839d8ee2668be05e0
Parents: b82bb4c
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Mar 17 09:55:29 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Mar 17 09:55:29 2015 +0000
----------------------------------------------------------------------
.../src/test/resources/simple_fasta.t2flow | 21 +++++++++++++++++++-
1 file changed, 20 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/f2972d5b/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
index b9cd40e..44f6448 100644
--- a/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
+++ b/taverna-scufl2-t2flow/src/test/resources/simple_fasta.t2flow
@@ -1,3 +1,22 @@
+<?xml version="1.0"?>
+<!--
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+-->
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="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>
@@ -75,4 +94,4 @@ outputText = writer.toString();
<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
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>