You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:05:13 UTC
[28/79] [partial] incubator-taverna-language git commit: Revert
"temporarily empty repository"
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/README.md
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/README.md b/taverna-scufl2-examples/README.md
new file mode 100644
index 0000000..429d4e8
--- /dev/null
+++ b/taverna-scufl2-examples/README.md
@@ -0,0 +1,251 @@
+SCUFL2 examples
+===============
+
+Examples of using the [SCUFL2 API](http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API) v0.14.0.
+
+[](https://travis-ci.org/myGrid/scufl2-examples)
+
+As this code is meant only as examples that you can extend and modify, the
+groupId and package name are `org.apache.taverna.examples`, which should be changed
+in your application.
+
+
+
+Download
+--------
+Download the `scufl2-examples-0.x.x-standalone.jar` from the
+[latest build](http://build.mygrid.org.uk/ci/job/scufl2-examples/lastSuccessfulBuild/com.example$scufl2-examples/), or browse the [Maven snapshot repository](http://repository.mygrid.org.uk/artifactory/libs-snapshot-local/com/example/scufl2-examples/).
+
+This is a standalone executable JAR (see below).
+
+
+
+Build
+-----
+
+
+To build, you'll need [Maven](http://maven.apache.org/download.cgi) 3.0.5 or newer, and run
+```mvn clean install```:
+
+ C:\Users\stain\workspace\scufl2-examples> mvn clean install
+
+ [INFO] ------------------------------------------------------------------------
+ [INFO] Building SCUFL2 examples 0.1.1-SNAPSHOT
+ [INFO] ------------------------------------------------------------------------
+ [INFO]
+ [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ scufl2-examples ---
+ [INFO] Deleting C:\Users\stain\workspace\scufl2-examples\target
+ (..)
+ [INFO] Installing C:\Users\stain\workspace\scufl2-examples\target\scufl2-examples-0.1.1-SNAPSHOT.jar to C:\Users\stain\.m2\repository\com\example\scufl2-examples\0.1.1-SNAPSHOT\scufl2-examples-0.1.1-SNAPSHOT.jar
+ [INFO] Installing C:\Users\stain\workspace\scufl2-examples\pom.xml to C:\Users\stain\.m2\repository\com\example\scufl2-examples\0.1.1-SNAPSHOT\scufl2-examples-0.1.1-SNAPSHOT.pom
+ [INFO] ------------------------------------------------------------------------
+ [INFO] BUILD SUCCESS
+ [INFO] ------------------------------------------------------------------------
+ [INFO] Total time: 6.223s
+ [INFO] Finished at: Tue Apr 23 11:00:27 BST 2013
+ [INFO] Final Memory: 15M/243M
+ [INFO] ----------------
+
+To run the examples, see the folder ```target\scufl2-examples``` which has a `bin/` executable for each of the below tools. Note that these tools require the provided `bin/` and `lib/` folder structure.
+
+Alternatively you can use ```java -jar target/scufl2-examples-0.2.0-SNAPSHOT-standalone.jar``` - this is a standalone
+JAR file that can execute any of the tools as the first argument.
+
+Linux users can install this with:
+
+ chmod 755 target/scufl2-examples-*-standalone.jar
+ sudo cp target/scufl2-examples-*-standalone.jar /usr/local/bin/scufl2tool
+
+as long as JAR files are recognized as executables:
+
+ stain@biggie-mint ~/src/scufl2-examples $ target/scufl2-examples-0.2.0-SNAPSHOT-standalone.jar
+ SCUFL2 workflow tool
+ Usage: scufl2tool <tool> [option] ...
+
+ Available tools:
+ t2flowtowfbundle - Convert t2flow workflows to wfbundle
+ jsonexport - Export JSON structure of workflow
+ processornames - List tree of processor names in workflow
+ servicetypes - List service types used in workflow
+ workflowmaker - Create an example workflow programmatically
+
+
+
+processornames
+--------------
+This tool lists a tree of the processor names in the workflows of the given bundle.
+
+ C:\Users\stain\workspace\scufl2-examples> target\scufl2-examples\bin\processornames examples/helloworld.t2flow
+ + Hello_World
+ - hello
+
+
+ C:\Users\stain\workspace\scufl2-examples> target\scufl2-examples\bin\processornames examples/helloanyone.t2flow
+ + Hello_Anyone
+ - Concatenate_two_strings
+ - hello
+
+See the source code for [org.apache.taverna.examples.ProcessorNames](src/main/java/org/apache/taverna/examples/ProcessorNames.java)
+ for how this is implemented.
+
+
+servicetypes
+------------
+This tool lists the URIs of the types of services (activities) used in the workflow.
+
+ C:\Users\stain\workspace\scufl2-examples> target\scufl2-examples\bin\servicetypes examples/helloanyone.t2flow
+ http://ns.taverna.org.uk/2010/activity/beanshell
+ http://ns.taverna.org.uk/2010/activity/constant
+
+See the source code for [org.apache.taverna.examples.ServiceTypes](src/main/java/org/apache/taverna/examples/ServiceTypes.java)
+ for how this is implemented.
+
+
+workflowmaker
+-------------
+This tool shows how to construct a workflow from scratch and save it as a
+[SCUFL2 wfbundle](http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle).
+
+ C:\Users\stain\workspace\scufl2-examples> target\scufl2-examples\bin\workflowmaker
+ Written to C:\Users\stain\AppData\Local\Temp\test6264603033381329995.wfbundle
+
+ WorkflowBundle '4fdb73e3-a5c6-41a8-aafb-32f67ca552b2'
+ MainWorkflow 'Echotest'
+ Workflow 'Echotest'
+ In 'in1'
+ Out 'out1'
+ Processor 'p'
+ In 'pIn'
+ Out 'pOut'
+ Links
+ 'in1' -> 'p:pIn'
+ 'p:pOut' -> 'out1'
+ MainProfile 'default'
+ Profile 'default'
+ Activity 'myBeanshell'
+ Type <http://ns.taverna.org.uk/2010/activity/beanshell>
+ In 'in1'
+ Out 'out1'
+ ProcessorBinding '434e7226-1d7f-498d-a19f-75be9f38f266'
+ Activity 'myBeanshell'
+ Processor 'Echotest:p'
+ InputPortBindings
+ 'pIn' -> 'in1'
+ OutputPortBindings
+ 'out1' -> 'pOut'
+ Configuration 'beanshellConf'
+ Type <http://ns.taverna.org.uk/2010/activity/beanshell#Config>
+ Configures 'activity/myBeanshell'
+ Property <http://ns.taverna.org.uk/2010/activity/beanshell#script>
+ '''out1 = in1'''
+
+
+See the source code for [org.apache.taverna.examples.WorkflowMaker](src/main/java/org/apache/taverna/WorkflowMaker.java)
+for how this is implemented.
+
+
+t2flowtowfbundle
+----------------
+
+This tool shows how to convert a *.t2flow* file to a
+[SCUFL2 .wfbundle](http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle).
+
+ C:\Users\stain\workspace\scufl2-examples> rm helloworld.wfbundle
+
+ C:\Users\stain\workspace\scufl2-examples> target\scufl2-examples\bin\t2flowtowfbu
+
+ C:\Users\stain\workspace\scufl2-examples> unzip -t helloworld.wfbundle
+ Archive: helloworld.wfbundle
+ testing: mimetype OK
+ testing: META-INF/ OK
+ testing: META-INF/manifest.xml OK
+ testing: history/ OK
+ testing: history/8781d5f4-d0ba-48a8-a1d1-14281bd8a917.t2flow OK
+ testing: workflow/ OK
+ testing: workflow/Hello_World.rdf OK
+ testing: profile/ OK
+ testing: profile/taverna-2.2.0.rdf OK
+ testing: annotation/ OK
+ testing: annotation/0c2f3c2c-7b5f-49cc-a448-92d707da3795.rdf OK
+ testing: annotation/48c04fe7-90f8-42f2-be61-a0480aa826d1.rdf OK
+ testing: annotation/9558f2e4-b629-4d1d-a62e-8c0dd39d7746.rdf OK
+ testing: workflowBundle.rdf OK
+ testing: META-INF/container.xml OK
+ No errors detected in compressed data of helloworld.wfbundle.
+
+See the source code for
+[org.apache.taverna.examples.ConvertT2flowToWorkflowBundle.java](src/main/java/org/apache/taverna/examples/ConvertT2flowToWorkflowBundle.java)
+for how this is implemented.
+
+The included files [helloworld.wfbundle](helloworld.wfbundle?raw=true) and
+[helloanyone.wfbundle](helloanyone.wfbundle?raw=true) are examples of converting
+[helloworld.t2flow](helloworld.t2flow?raw=true) and [helloanyone.t2flow](helloanyone.t2flow?raw=true)
+
+
+jsonexport
+----------
+This tool exports a JSON structure of the workflow, including basic
+annotations on workflows, ports, processors, nested workflows and
+revision log of the workflows.
+
+Usage:
+
+ c:\Users\stain\src\scufl2-examples> target\scufl2-examples\bin\jsonexport -h
+ Export workflow structore as JSON.
+ Usage: jsonexport [filename] ...
+ If the filename is - the workflow will be read from STDIN and
+ JSON written to STDOUT.
+ Otherwise, the file is read as a workflow (t2flow, workflow bundle)
+ and written as JSON to a file with the .json extension.
+ Multiple filenames can be given. JSON filenames are written to STDOUT
+
+Converting multiple files:
+
+ c:\Users\stain\src\scufl2-examples> target\scufl2-examples\bin\jsonexport examples/helloworld.t2flow examples/helloanyone.wfbundle
+ examples/helloworld.json
+ examples/helloanyone.json
+
+See the converted [examples/helloworld.json](helloworld.json) and
+[examples/helloanyone.json](helloanyone.json).
+
+Example using STDIN/STDOUT:
+
+ c:\Users\stain\src\scufl2-examples> target\scufl2-examples\bin\jsonexport - < examples/helloworld.t2flow
+ {
+ "@context" : [ "https://w3id.org/scufl2/context", {
+ "@base" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/"
+ } ],
+ "id" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/",
+ "workflow" : {
+ "id" : "workflow/Hello_World/",
+ "name" : "Hello_World",
+ "revisions" : [ {
+ "id" : "http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/",
+ "generatedAtTime" : "2012-01-03T15:12:21Z"
+ } ],
+ "inputs" : [ ],
+ "outputs" : [ {
+ "name" : "greeting",
+ "id" : "workflow/Hello_World/out/greeting"
+ } ],
+ "processors" : [ {
+ "id" : "workflow/Hello_World/processor/hello/",
+ "name" : "hello",
+ "inputs" : [ ],
+ "outputs" : [ {
+ "name" : "value",
+ "id" : "workflow/Hello_World/processor/hello/out/value",
+ "depth" : 0
+ } ]
+ } ],
+ "datalinks" : [ {
+ "receivesFrom" : "workflow/Hello_World/processor/hello/out/value",
+ "sendsTo" : "workflow/Hello_World/out/greeting"
+ } ],
+ "controllinks" : [ ],
+ "http://purl.org/dc/terms/description" : "One of the simplest workflows possible. No workflow input ports, a single workflow output port \"greeting\", outputting \"Hello, world!\" as produced by the String Constant \"hello\".",
+ "http://purl.org/dc/elements/1.1/creator" : "Stian Soiland-Reyes",
+ "http://purl.org/dc/terms/title" : "Hello World"
+ }
+ }
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloanyone.json
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloanyone.json b/taverna-scufl2-examples/examples/helloanyone.json
new file mode 100644
index 0000000..477b73c
--- /dev/null
+++ b/taverna-scufl2-examples/examples/helloanyone.json
@@ -0,0 +1,72 @@
+{
+ "@context" : [ "https://w3id.org/scufl2/context", {
+ "@base" : "http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/"
+ } ],
+ "id" : "http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/",
+ "workflow" : {
+ "id" : "workflow/Hello_Anyone/",
+ "name" : "Hello_Anyone",
+ "revisions" : [ {
+ "id" : "http://ns.taverna.org.uk/2010/workflow/01348671-5aaa-4cc2-84cc-477329b70b0d/",
+ "generatedAtTime" : "2012-01-03T15:14:30Z",
+ "wasRevisionOf" : "http://ns.taverna.org.uk/2010/workflow/ca7dba1d-1fdf-476f-b911-714d09227d70/"
+ }, {
+ "id" : "http://ns.taverna.org.uk/2010/workflow/ca7dba1d-1fdf-476f-b911-714d09227d70/",
+ "generatedAtTime" : "2012-01-03T15:14:18Z",
+ "wasRevisionOf" : "http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/"
+ }, {
+ "id" : "http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/",
+ "generatedAtTime" : "2012-01-03T15:12:21Z"
+ } ],
+ "inputs" : [ {
+ "name" : "name",
+ "id" : "workflow/Hello_Anyone/in/name",
+ "depth" : 0
+ } ],
+ "outputs" : [ {
+ "name" : "greeting",
+ "id" : "workflow/Hello_Anyone/out/greeting"
+ } ],
+ "processors" : [ {
+ "id" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/",
+ "name" : "Concatenate_two_strings",
+ "inputs" : [ {
+ "name" : "string1",
+ "id" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/in/string1",
+ "depth" : 0
+ }, {
+ "name" : "string2",
+ "id" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/in/string2",
+ "depth" : 0
+ } ],
+ "outputs" : [ {
+ "name" : "output",
+ "id" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/out/output",
+ "depth" : 0
+ } ]
+ }, {
+ "id" : "workflow/Hello_Anyone/processor/hello/",
+ "name" : "hello",
+ "inputs" : [ ],
+ "outputs" : [ {
+ "name" : "value",
+ "id" : "workflow/Hello_Anyone/processor/hello/out/value",
+ "depth" : 0
+ } ]
+ } ],
+ "datalinks" : [ {
+ "receivesFrom" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/out/output",
+ "sendsTo" : "workflow/Hello_Anyone/out/greeting"
+ }, {
+ "receivesFrom" : "workflow/Hello_Anyone/processor/hello/out/value",
+ "sendsTo" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/in/string1"
+ }, {
+ "receivesFrom" : "workflow/Hello_Anyone/in/name",
+ "sendsTo" : "workflow/Hello_Anyone/processor/Concatenate_two_strings/in/string2"
+ } ],
+ "controllinks" : [ ]
+ },
+ "profile" : {
+ "id" : "profile/taverna-2.2.0/"
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloanyone.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloanyone.t2flow b/taverna-scufl2-examples/examples/helloanyone.t2flow
new file mode 100644
index 0000000..3b625f1
--- /dev/null
+++ b/taverna-scufl2-examples/examples/helloanyone.t2flow
@@ -0,0 +1,196 @@
+<?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="01348671-5aaa-4cc2-84cc-477329b70b0d" role="top"><name>Hello_Anyone</name><inputPorts><port><name>name</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+ <text>World!</text>
+ </annotationBean>
+ <date>2012-01-03 15:13:04.106 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>Your name for the greeting</text>
+ </annotationBean>
+ <date>2012-01-03 15:13:12.530 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>greeting</name><annotations /></port></outputPorts><processors><processor><name>hello</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>Hello, </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="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</name><depth>0</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>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivi
ty</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
+ <script>output = string1 + string2;</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>string1</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>string2</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>output</name>
+ <depth>0</depth>
+ <mimeTypes>
+ <string>'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.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="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>hello</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="dataflow"><port>name</port></source></datalink><datalin
k><sink type="dataflow"><port>greeting</port></sink><source type="processor"><processor>Concatenate_two_strings</processor><port>output</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>8781d5f4-d0ba-48a8-a1d1-14281bd8a917</identification>
+ </annotationBean>
+ <date>2012-01-03 15:12:21.684 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>ca7dba1d-1fdf-476f-b911-714d09227d70</identification>
+ </annotationBean>
+ <date>2012-01-03 15:14:18.734 GMT</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>Stian Soiland-Reyes</text>
+ </annotationBean>
+ <date>2012-01-03 15:10:48.73 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Hello Anyone</text>
+ </annotationBean>
+ <date>2012-01-03 15:14:25.703 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Hello World</text>
+ </annotationBean>
+ <date>2012-01-03 15:10:54.167 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>One of the simplest workflows possible, outputting the String Constant "Hello world!"</text>
+ </annotationBean>
+ <date>2012-01-03 15:11:14.557 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".</text>
+ </annotationBean>
+ <date>2012-01-03 15:14:13.847 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".</text>
+ </annotationBean>
+ <date>2012-01-03 15:12:15.643 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>01348671-5aaa-4cc2-84cc-477329b70b0d</identification>
+ </annotationBean>
+ <date>2012-01-03 15:14:30.45 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloanyone.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloanyone.wfbundle b/taverna-scufl2-examples/examples/helloanyone.wfbundle
new file mode 100644
index 0000000..904a40d
Binary files /dev/null and b/taverna-scufl2-examples/examples/helloanyone.wfbundle differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloworld.json
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloworld.json b/taverna-scufl2-examples/examples/helloworld.json
new file mode 100644
index 0000000..24e2f1c
--- /dev/null
+++ b/taverna-scufl2-examples/examples/helloworld.json
@@ -0,0 +1,37 @@
+{
+ "@context" : [ "https://w3id.org/scufl2/context", {
+ "@base" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/"
+ } ],
+ "id" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/",
+ "workflow" : {
+ "id" : "workflow/Hello_World/",
+ "name" : "Hello_World",
+ "revisions" : [ {
+ "id" : "http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/",
+ "generatedAtTime" : "2012-01-03T15:12:21Z"
+ } ],
+ "inputs" : [ ],
+ "outputs" : [ {
+ "name" : "greeting",
+ "id" : "workflow/Hello_World/out/greeting"
+ } ],
+ "processors" : [ {
+ "id" : "workflow/Hello_World/processor/hello/",
+ "name" : "hello",
+ "inputs" : [ ],
+ "outputs" : [ {
+ "name" : "value",
+ "id" : "workflow/Hello_World/processor/hello/out/value",
+ "depth" : 0
+ } ]
+ } ],
+ "datalinks" : [ {
+ "receivesFrom" : "workflow/Hello_World/processor/hello/out/value",
+ "sendsTo" : "workflow/Hello_World/out/greeting"
+ } ],
+ "controllinks" : [ ]
+ },
+ "profile" : {
+ "id" : "profile/taverna-2.2.0/"
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloworld.t2flow
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloworld.t2flow b/taverna-scufl2-examples/examples/helloworld.t2flow
new file mode 100644
index 0000000..2e10ed9
--- /dev/null
+++ b/taverna-scufl2-examples/examples/helloworld.t2flow
@@ -0,0 +1,84 @@
+<?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="8781d5f4-d0ba-48a8-a1d1-14281bd8a917" role="top"><name>Hello_World</name><inputPorts /><outputPorts><port><name>greeting</name><annotations /></port></outputPorts><processors><processor><name>hello</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>Hello, World!</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="">
+ <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="
">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>greeting</port></sink><source type="processor"><processor>hello</processor><port>value</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>8781d5f4-d0ba-48a8-a1d1-14281bd8a917</identification>
+ </annotationBean>
+ <date>2012-01-03 15:12:21.684 GMT</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>Stian Soiland-Reyes</text>
+ </annotationBean>
+ <date>2012-01-03 15:10:48.73 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+ <text>Hello World</text>
+ </annotationBean>
+ <date>2012-01-03 15:10:54.167 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>One of the simplest workflows possible, outputting the String Constant "Hello world!"</text>
+ </annotationBean>
+ <date>2012-01-03 15:11:14.557 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+ <text>One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".</text>
+ </annotationBean>
+ <date>2012-01-03 15:12:15.643 GMT</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/examples/helloworld.wfbundle
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/examples/helloworld.wfbundle b/taverna-scufl2-examples/examples/helloworld.wfbundle
new file mode 100644
index 0000000..ed4cd76
Binary files /dev/null and b/taverna-scufl2-examples/examples/helloworld.wfbundle differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/pom.xml b/taverna-scufl2-examples/pom.xml
new file mode 100644
index 0000000..607b470
--- /dev/null
+++ b/taverna-scufl2-examples/pom.xml
@@ -0,0 +1,154 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-language</artifactId>
+ <version>0.16.1-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-scufl2-examples</artifactId>
+ <name>Apache Taverna Scufl 2 examples</name>
+ <dependencies>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-scufl2-api</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-scufl2-t2flow</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-scufl2-rdfxml</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+
+ <!-- Included to get rid of "Could not set prefix mapper" warning, but
+ should work fine without -->
+ <dependency>
+ <groupId>com.sun.xml.bind</groupId>
+ <artifactId>jaxb-impl</artifactId>
+ <version>2.2.4-1</version>
+ <optional>true</optional>
+ </dependency>
+
+ <!-- For writing out JSON-LD annotations -->
+
+ <dependency>
+ <groupId>org.apache.jena</groupId>
+ <artifactId>jena-arq</artifactId>
+ <version>${jena.version}</version>
+ </dependency>
+
+ <!-- Following only needed by src/test/java -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.4</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>appassembler-maven-plugin</artifactId>
+ <version>1.1.1</version>
+ <executions>
+ <execution>
+ <id>assemble</id>
+ <phase>package</phase>
+ <goals>
+ <goal>assemble</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <repositoryLayout>flat</repositoryLayout>
+ <repositoryName>lib</repositoryName>
+ <assembleDirectory>${project.build.directory}/${project.artifactId}</assembleDirectory>
+ <programs>
+ <program>
+ <mainClass>org.apache.taverna.examples.ConvertT2flowToWorkflowBundle</mainClass>
+ <name>t2flowtowfbundle</name>
+ </program>
+ <program>
+ <mainClass>org.apache.taverna.examples.ProcessorNames</mainClass>
+ <name>processornames</name>
+ </program>
+ <program>
+ <mainClass>org.apache.taverna.examples.ServiceTypes</mainClass>
+ <name>servicetypes</name>
+ </program>
+ <program>
+ <mainClass>org.apache.taverna.examples.WorkflowMaker</mainClass>
+ <name>workflowmaker</name>
+ </program>
+ <program>
+ <mainClass>org.apache.taverna.examples.JsonExport</mainClass>
+ <name>jsonexport</name>
+ </program>
+ </programs>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <!--<version>2.0</version> does not work with Maven 2 :( -->
+ <version>1.7.1</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ <configuration>
+ <shadedArtifactAttached>true</shadedArtifactAttached>
+ <shadedClassifierName>standalone</shadedClassifierName>
+ <transformers>
+ <transformer
+ implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <mainClass>org.apache.taverna.examples.Scufl2Tool</mainClass>
+ </transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer" />
+ <transformer
+ implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
+ <transformer
+ implementation="org.apache.maven.plugins.shade.resource.XmlAppendingTransformer">
+ <resource>META-INF/spring</resource>
+ </transformer>
+ </transformers>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ConvertT2flowToWorkflowBundle.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ConvertT2flowToWorkflowBundle.java b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ConvertT2flowToWorkflowBundle.java
new file mode 100644
index 0000000..ae57665
--- /dev/null
+++ b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ConvertT2flowToWorkflowBundle.java
@@ -0,0 +1,57 @@
+package org.apache.taverna.examples;
+
+/*
+ * 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.
+ */
+
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.xml.bind.JAXBException;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+public class ConvertT2flowToWorkflowBundle {
+ public static void main(String[] args) throws Exception, ReaderException,
+ WriterException {
+ new ConvertT2flowToWorkflowBundle().convert(args);
+ }
+
+ public void convert(String[] filepaths) throws ReaderException, IOException, WriterException {
+
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ for (String filepath : filepaths) {
+ File t2File = new File(filepath);
+
+ String filename = t2File.getName();
+ filename = filename.replaceFirst("\\..*", ".wfbundle");
+ File scufl2File = new File(t2File.getParentFile(), filename);
+
+ WorkflowBundle wfBundle = io.readBundle(t2File,
+ "application/vnd.taverna.t2flow+xml");
+ io.writeBundle(wfBundle, scufl2File,
+ "application/vnd.taverna.scufl2.workflow-bundle");
+ }
+
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/JsonExport.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/JsonExport.java b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/JsonExport.java
new file mode 100644
index 0000000..17e8e5b
--- /dev/null
+++ b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/JsonExport.java
@@ -0,0 +1,319 @@
+package org.apache.taverna.examples;
+
+/*
+ * 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.
+ */
+
+
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.taverna.scufl2.api.annotation.Annotation;
+import org.apache.taverna.scufl2.api.annotation.Revision;
+import org.apache.taverna.scufl2.api.common.Child;
+import org.apache.taverna.scufl2.api.common.Ported;
+import org.apache.taverna.scufl2.api.common.Scufl2Tools;
+import org.apache.taverna.scufl2.api.common.URITools;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.BlockingControlLink;
+import org.apache.taverna.scufl2.api.core.ControlLink;
+import org.apache.taverna.scufl2.api.core.DataLink;
+import org.apache.taverna.scufl2.api.core.Processor;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleWriter;
+import org.apache.taverna.scufl2.api.io.WriterException;
+import org.apache.taverna.scufl2.api.port.DepthPort;
+import org.apache.taverna.scufl2.api.port.GranularDepthPort;
+import org.apache.taverna.scufl2.api.port.Port;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.util.ISO8601DateFormat;
+
+public class JsonExport {
+ public class JsonWriter implements WorkflowBundleWriter {
+
+ @Override
+ public Set<String> getMediaTypes() {
+ return new HashSet<String>(Arrays.asList("application/ld+json",
+ "application/json"));
+ }
+ @Override
+ public void writeBundle(WorkflowBundle wfBundle, File destination,
+ String mediaType) throws WriterException, IOException {
+ ObjectNode json = toJson(wfBundle);
+ mapper.writeValue(destination, json);
+ }
+
+ @Override
+ public void writeBundle(WorkflowBundle wfBundle,
+ OutputStream output, String mediaType)
+ throws WriterException, IOException {
+ ObjectNode json = toJson(wfBundle);
+ mapper.writeValue(output, json);
+ }
+
+ }
+
+ public static void main(String[] args) throws ReaderException, IOException,
+ WriterException {
+ new JsonExport().convert(args);
+ }
+
+
+ private WorkflowBundleIO io = new WorkflowBundleIO();;
+
+ private WorkflowBundleWriter jsonWriter = new JsonWriter();
+
+ private ObjectMapper mapper = new ObjectMapper();
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private URITools uriTools = new URITools();
+
+ public JsonExport() {
+ mapper.enable(SerializationFeature.INDENT_OUTPUT);
+ mapper.disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
+ mapper.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS);
+
+ mapper.setDateFormat(new ISO8601DateFormat());
+
+ // Adding custom writer dynamically
+ List<WorkflowBundleWriter> writers = io.getWriters();
+ writers.add(jsonWriter);
+ io.setWriters(writers);
+ }
+
+ protected void addPorts(Ported ported, ObjectNode p) {
+ ArrayNode inputs = mapper.createArrayNode();
+ for (Port port : ported.getInputPorts()) {
+ inputs.add(toJson(port));
+ }
+ p.put("inputs", inputs);
+
+ ArrayNode outputs = mapper.createArrayNode();
+ for (Port port : ported.getOutputPorts()) {
+ outputs.add(toJson(port));
+ // FIXME: Do we need the id for ports? Needed if we add datalinks
+ }
+ p.put("outputs", outputs);
+ }
+
+ protected ObjectNode annotations(Child<?> bean) {
+ ObjectNode node = mapper.createObjectNode();
+ for (Annotation ann : scufl2Tools.annotationsFor(bean)) {
+ URI annUri = uriTools.uriForBean(ann);
+
+ // TODO: include annotation body?
+ }
+ return node;
+ }
+
+ public void convert(String[] filepaths) throws ReaderException,
+ IOException, WriterException {
+ if (filepaths.length == 0 || filepaths[0].equals("-h")) {
+ System.out.println("Export workflow structore as JSON.");
+ System.out.println("Usage: jsonexport [filename] ...");
+ System.out.println("If the filename is - the workflow will be read from STDIN and");
+ System.out.println("JSON written to STDOUT. ");
+ System.out.println("Otherwise, the file is read as a workflow (t2flow, workflow bundle)");
+ System.out.println("and written as JSON to a file with the .json extension.");
+ System.out.println("Multiple filenames can be given. JSON filenames are written to STDOUT");
+ return;
+ }
+ if (filepaths[0].equals("-")) {
+ // Do piped Stdin/Stdout instead
+ WorkflowBundle wfBundle = io.readBundle(System.in, null);
+ io.writeBundle(wfBundle, System.err, "application/ld+json");
+ return;
+ }
+
+ for (String filepath : filepaths) {
+ File workflow = new File(filepath);
+
+ String filename = workflow.getName();
+ filename = filename.replaceFirst("\\..*", ".json");
+ File workflowFile = new File(workflow.getParentFile(), filename);
+
+ WorkflowBundle wfBundle = io.readBundle(workflow, null);
+ io.writeBundle(wfBundle, workflowFile, "application/ld+json");
+ System.out.println(workflowFile);
+ }
+ }
+
+ protected ObjectNode toJson(Port port) {
+ ObjectNode p = mapper.createObjectNode();
+ p.put("name", port.getName());
+ p.putPOJO("id", uriTools.relativeUriForBean(port,
+ scufl2Tools.findParent(WorkflowBundle.class, ((Child<?>)port))));
+
+ if (port instanceof DepthPort) {
+ DepthPort depthPort = (DepthPort) port;
+ if (depthPort.getDepth() != null) {
+ p.put("depth", depthPort.getDepth());
+ }
+ }
+ if (port instanceof GranularDepthPort) {
+ GranularDepthPort granularDepthPort = (GranularDepthPort) port;
+ if (granularDepthPort.getGranularDepth() != null &&
+ ! granularDepthPort.getGranularDepth().equals(granularDepthPort.getDepth())) {
+ p.put("granularDepth", granularDepthPort.getGranularDepth());
+ }
+ }
+ p.putAll(annotations((Child<?>)port));
+ return p;
+ }
+
+ protected JsonNode toJson(Processor proc) {
+ ObjectNode p = mapper.createObjectNode();
+ p.putPOJO("id", uriTools.relativeUriForBean(proc, proc.getParent().getParent()));
+ p.put("name", proc.getName());
+ addPorts(proc, p);
+ p.putAll(annotations(proc));
+
+ List<Workflow> nested = scufl2Tools.nestedWorkflowsForProcessor(proc,
+ proc.getParent().getParent().getMainProfile());
+ if (! nested.isEmpty()) {
+ if (nested.size() == 1) {
+ p.put("nestedWorkflow", toJson(nested.iterator().next()));
+ } else {
+ ArrayNode list = mapper.createArrayNode();
+ for (Workflow w : nested) {
+ list.add(toJson(w));
+ }
+ p.put("nestedWorkflow", list);
+ }
+ }
+ return p;
+ }
+
+ protected JsonNode toJson(Revision currentRevision) {
+ ArrayNode revisions = mapper.createArrayNode();
+ while (currentRevision != null) {
+ ObjectNode rev = mapper.createObjectNode();
+ rev.putPOJO("id", currentRevision.getIdentifier());
+ if (currentRevision.getGeneratedAtTime() != null) {
+ rev.putPOJO("generatedAtTime", currentRevision.getGeneratedAtTime());
+ }
+ currentRevision = currentRevision.getPreviousRevision();
+ if (currentRevision != null) {
+ rev.putPOJO("wasRevisionOf", currentRevision.getIdentifier());
+ }
+ revisions.add(rev);
+ }
+ return revisions;
+ }
+
+ protected ObjectNode toJson(Workflow workflow) {
+ ObjectNode wf = mapper.createObjectNode();
+
+ wf.putPOJO("id", uriTools.relativeUriForBean(workflow, workflow.getParent()));
+
+ wf.put("name", workflow.getName());
+ wf.put("revisions", toJson(workflow.getCurrentRevision()));
+
+ ArrayNode processors = mapper.createArrayNode();
+ for (Processor p : workflow.getProcessors()) {
+ processors.add(toJson(p));
+ }
+ addPorts(workflow, wf);
+ wf.put("processors", processors);
+
+ ArrayNode datalinks = mapper.createArrayNode();
+ for (DataLink link : workflow.getDataLinks()) {
+ datalinks.add(toJson(link));
+ }
+ wf.put("datalinks", datalinks);
+
+ ArrayNode controlLinks = mapper.createArrayNode();
+ for (ControlLink link : workflow.getControlLinks()) {
+ controlLinks.add(toJson(link));
+ }
+ wf.put("controllinks", controlLinks);
+
+
+ wf.putAll(annotations(workflow));
+
+ return wf;
+ }
+
+ protected JsonNode toJson(ControlLink link) {
+ ObjectNode l = mapper.createObjectNode();
+ if (link instanceof BlockingControlLink) {
+ BlockingControlLink controlLink = (BlockingControlLink) link;
+ l.putPOJO("block", uriTools.relativeUriForBean(controlLink.getBlock(),
+ link.getParent().getParent()));
+ l.putPOJO("untilFinished", uriTools.relativeUriForBean(controlLink.getUntilFinished(),
+ link.getParent().getParent()));
+ }
+ return l;
+ }
+
+ protected JsonNode toJson(DataLink link) {
+ ObjectNode l = mapper.createObjectNode();
+ l.putPOJO("receivesFrom", uriTools.relativeUriForBean(link.getReceivesFrom(),
+ link.getParent().getParent()));
+ l.putPOJO("sendsTo", uriTools.relativeUriForBean(link.getSendsTo(),
+ link.getParent().getParent()));
+ if (link.getMergePosition() != null) {
+ l.put("mergePosition", link.getMergePosition());
+ }
+ return l;
+ }
+
+ public ObjectNode toJson(WorkflowBundle wfBundle) {
+
+ ObjectNode root = mapper.createObjectNode();
+ ArrayNode contextList = root.arrayNode();
+ root.put("@context", contextList);
+ ObjectNode context = root.objectNode();
+ contextList.add("https://w3id.org/scufl2/context");
+ contextList.add(context);
+ URI base = wfBundle.getGlobalBaseURI();
+ context.put("@base", base.toASCIIString());
+ root.put("id", base.toASCIIString());
+
+// root.put("name", wfBundle.getName());
+// root.put("revisions", toJson(wfBundle.getCurrentRevision()));
+
+ root.put("workflow", toJson(wfBundle.getMainWorkflow()));
+ root.put("profile", toJson(wfBundle.getMainProfile()));
+
+ return root;
+ }
+
+ private JsonNode toJson(Profile profile) {
+ ObjectNode pf = mapper.createObjectNode();
+
+ pf.putPOJO("id", uriTools.relativeUriForBean(profile, profile.getParent()));
+ // TODO: Activities and configurations
+ return pf;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ProcessorNames.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ProcessorNames.java b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ProcessorNames.java
new file mode 100644
index 0000000..0a57af5
--- /dev/null
+++ b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ProcessorNames.java
@@ -0,0 +1,132 @@
+package org.apache.taverna.examples;
+
+/*
+ * 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.
+ */
+
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreeModel;
+import javax.xml.bind.JAXBException;
+
+import org.apache.taverna.scufl2.api.common.Scufl2Tools;
+import org.apache.taverna.scufl2.api.common.URITools;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.Processor;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+public class ProcessorNames {
+
+ public static void main(String[] args) throws JAXBException, IOException,
+ ReaderException {
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ ProcessorNames processorNames = new ProcessorNames();
+ for (String filename : args) {
+ // NOTE: We give 'null' as filetype so it will guess based on filename
+ WorkflowBundle ro = io.readBundle(new File(filename), null);
+// System.out.print(filename + ": ");
+// System.out.println(processorNames.showProcessorNames(ro));
+ System.out.println(processorNames.showProcessorTree(ro));
+ }
+ }
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private URITools uriTools = new URITools();
+
+ private Workflow findNestedWorkflow(Processor processor) {
+ Profile profile = processor.getParent().getParent().getMainProfile();
+ return scufl2Tools.nestedWorkflowForProcessor(processor, profile);
+ }
+
+ private void findProcessors(WorkflowBundle ro, Workflow workflow,
+ DefaultMutableTreeNode parent) {
+ for (Processor processor : workflow.getProcessors()) {
+ DefaultMutableTreeNode processorNode = new DefaultMutableTreeNode(
+ processor.getName());
+ parent.add(processorNode);
+ Workflow wf = findNestedWorkflow(processor);
+ if (wf != null) {
+ findProcessors(ro, wf, processorNode);
+ }
+ }
+
+ }
+
+ public TreeModel makeProcessorTree(WorkflowBundle workflowBundle)
+ throws JAXBException, IOException {
+ Workflow workflow = workflowBundle.getMainWorkflow();
+ TreeModel treeModel = new DefaultTreeModel(new DefaultMutableTreeNode(
+ workflow.getName()));
+ DefaultMutableTreeNode parent = (DefaultMutableTreeNode) treeModel
+ .getRoot();
+
+ findProcessors(workflowBundle, workflow, parent);
+ return treeModel;
+ }
+
+ public List<String> showProcessorNames(WorkflowBundle ro)
+ throws JAXBException, IOException {
+ ArrayList<String> names = new ArrayList<String>();
+ for (Processor processor : ro.getMainWorkflow().getProcessors()) {
+ names.add(processor.getName());
+ }
+ Collections.sort(names);
+ return names;
+ }
+
+ public String showProcessorTree(WorkflowBundle ro) throws JAXBException,
+ IOException {
+ TreeModel treeModel = makeProcessorTree(ro);
+ return treeModelAsString(treeModel);
+ }
+
+ public String treeModelAsString(TreeModel treeModel) {
+ StringBuffer sb = new StringBuffer();
+ Object root = treeModel.getRoot();
+ treeModelAsString(treeModel, root, sb, "");
+ return sb.toString();
+ }
+
+ protected void treeModelAsString(TreeModel treeModel, Object parent,
+ StringBuffer sb, String indentation) {
+ sb.append(indentation);
+ int childCount = treeModel.getChildCount(parent);
+ if (childCount == 0) {
+ sb.append("- ");
+ } else {
+ sb.append("+ ");
+ indentation = indentation + " ";
+ }
+ sb.append(parent);
+ sb.append("\n");
+ for (int i = 0; i < childCount; i++) {
+ Object child = treeModel.getChild(parent, i);
+ treeModelAsString(treeModel, child, sb, indentation);
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/Scufl2Tool.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/Scufl2Tool.java b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/Scufl2Tool.java
new file mode 100644
index 0000000..1f2a842
--- /dev/null
+++ b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/Scufl2Tool.java
@@ -0,0 +1,101 @@
+package org.apache.taverna.examples;
+
+/*
+ * 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.
+ */
+
+
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * A wrapper around the other example main() methods
+ *
+ * This in order to make a single executable JAR file.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ */
+public class Scufl2Tool {
+
+ public enum Tool {
+ t2flowtowfbundle(ConvertT2flowToWorkflowBundle.class, "Convert t2flow workflows to wfbundle"),
+ jsonexport(JsonExport.class, "Export JSON structure of workflow"),
+ processornames(ProcessorNames.class, "List tree of processor names in workflow"),
+ servicetypes(ServiceTypes.class, "List service types used in workflow"),
+ workflowmaker(WorkflowMaker.class, "Create an example workflow programmatically");
+
+ private final String description;
+ private final Class<?> mainClass;
+
+ Tool(Class<?> mainClass, String description) {
+ this.mainClass = mainClass;
+ this.description = description;
+ }
+
+ @Override
+ public String toString() {
+ return name() + " - " + description;
+ }
+
+ public Class<?> getMainClass() {
+ return mainClass;
+ }
+ }
+
+ public static void main(String[] args) throws IllegalAccessException,
+ IllegalArgumentException, InvocationTargetException,
+ NoSuchMethodException, SecurityException {
+ List<String> argsList = Arrays.asList(args);
+ if (argsList.isEmpty() || argsList.get(0).equals("-h")) {
+ help();
+ return;
+ }
+ Tool tool;
+ try {
+ tool = Tool.valueOf(argsList.get(0).toLowerCase());
+ } catch (IllegalArgumentException e) {
+ System.err.println("Invalid tool: " + argsList.get(0));
+ help();
+ return;
+ }
+
+ // Find and invoke the main method
+ Class<?> mainCls = tool.getMainClass();
+ Method main = mainCls.getMethod("main", String[].class);
+ // But stripping out the first argument
+ args = argsList.subList(1, argsList.size()).toArray(new String[0]);
+ // Array of arrays!
+ Object[] mainArgs = new Object[]{args};
+ main.invoke(null, mainArgs);
+ }
+
+ public static void help() {
+ System.out.println("SCUFL2 workflow tool");
+ System.out.println("Usage: scufl2tool <tool> [option] ...");
+ System.out.println();
+ System.out.println("Available tools:");
+ for (Tool tool : Tool.values()) {
+ System.out.println(tool);
+ }
+
+ }
+}
+;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/c08405cb/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ServiceTypes.java
----------------------------------------------------------------------
diff --git a/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ServiceTypes.java b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ServiceTypes.java
new file mode 100644
index 0000000..2dcf4fb
--- /dev/null
+++ b/taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/ServiceTypes.java
@@ -0,0 +1,62 @@
+package org.apache.taverna.examples;
+
+/*
+ * 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.
+ */
+
+
+import java.io.File;
+import java.io.IOException;
+import java.util.LinkedHashSet;
+import java.util.Set;
+
+import org.apache.taverna.scufl2.api.activity.Activity;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+public class ServiceTypes {
+ public static void main(String[] args) throws Exception, ReaderException,
+ WriterException {
+ for (String type : new ServiceTypes().serviceTypes(args)) {
+ System.out.println(type);
+ }
+ }
+
+ public Set<String> serviceTypes(String[] filepaths) throws ReaderException, IOException, WriterException {
+
+ Set<String> types = new LinkedHashSet<String>();
+
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ for (String filepath : filepaths) {
+ File file = new File(filepath);
+ // mediaType = null --> guess
+ WorkflowBundle wfBundle = io.readBundle(file, null);
+
+ for (Profile profile : wfBundle.getProfiles()) {
+ for (Activity activity : profile.getActivities()) {
+ types.add(activity.getType().toASCIIString());
+ }
+ }
+ }
+ return types;
+ }
+
+}