README - incubator-taverna-language - Git at Google

 Convert SCUFL2 to wfdesc
 ========================

 This is an extension to Scufl2 [1] which provides the export capability
 to wfdesc ontology from the Wf4Ever [2] RO wfdesc ontology v0.1 [3].

 This is exposed as a command line tool "scufl2-to-wfdesc", but can also
 be accessed programmatically using the SCUFL2 APIs.


 Building
 --------

 Requirements:
  * Java JDK 6 or higher [6], or OpenJDK 7 or higher [7]
  * Maven 2 or higher [9]  (only for building)

 To build, simply use "mvn clean install"

 Example:

     : stain@ralph ~/src/wf4ever/scufl2-wfdesc;mvn clean install
     [INFO] Scanning for projects...
     [INFO]
     [INFO] ------------------------------------------------------------------------
     [INFO] Building SCUFL2 to wfdesc 0.1-SNAPSHOT
     [INFO] ------------------------------------------------------------------------
     [INFO]
     [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ scufl2-wfdesc ---
     [INFO]
     [INFO] --- maven-antrun-plugin:1.6:run (default) @ scufl2-wfdesc ---
     [INFO] Executing tasks

     main:
         [mkdir] Created dir: /home/stain/stuff/src/wf4ever/scufl2-wfdesc/target/generated-sources
     (..)
     [INFO] ------------------------------------------------------------------------
     [INFO] BUILD SUCCESS
     [INFO] ------------------------------------------------------------------------
     [INFO] Total time: 46.734s
     [INFO] Finished at: Wed Jan 04 15:22:58 WET 2012
     [INFO] Final Memory: 18M/129M
     [INFO] ------------------------------------------------------------------------


 Note that the first time you build, Maven will download several
 required dependencies from Maven repositories. Depending on your network
 connection this might take some time to complete.


 Command line tool
 -----------------

 After building, the folder "target/scufl2-wfdesc" contains a
 distribution of the command line tool "scufl2-to-wfdesc", with launchers
 generated for Unix and Windows.

 You may copy and distribute this folder for a standalone usage of the
 conversion tool.

 The command line tool takes a list of Taverna workflow files (supported file
 types are *.t2flow and *.wfbundle)


 Example:

     : stain@ralph ~/src/wf4ever/scufl2-wfdesc; target/scufl2-wfdesc/bin/scufl2-to-wfdesc src/test/resources/helloworld.t2flow
     log4j:WARN No appenders could be found for logger (org.openrdf.sail.memory.MemoryStore).
     log4j:WARN Please initialize the log4j system properly.
     Converted src/test/resources/helloworld.t2flow to src/test/resources/helloworld.wfdesc.ttl


     : stain@ralph ~/src/wf4ever/scufl2-wfdesc; cat src/test/resources/helloworld.wfdesc.ttl

     @base <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/> .
     @prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
     @prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
     @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

     <processor/Concatenate_two_strings/> a wfdesc:Process , wfdesc:Description , <http://www.w3.org/2002/07/owl#Thing> , wf4ever:BeanshellScript ;
         wf4ever:script "output = string1 + string2;" ;
         rdfs:label "Concatenate_two_strings" ;
         wfdesc:hasInput <processor/Concatenate_two_strings/in/string1> , <processor/Concatenate_two_strings/in/string2> ;
         wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> .

     <datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> a wfdesc:DataLink ;
         wfdesc:hasSource <in/name> ;
         wfdesc:hasSink <processor/Concatenate_two_strings/in/string2> .

     <datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> a wfdesc:DataLink ;
         wfdesc:hasSource <processor/Concatenate_two_strings/out/output> ;
         wfdesc:hasSink <out/greeting> .

     <datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> a wfdesc:DataLink ;
         wfdesc:hasSource <processor/hello/out/value> ;
         wfdesc:hasSink <processor/Concatenate_two_strings/in/string1> .

     <> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
         rdfs:label "Hello_Anyone" ;
         wfdesc:hasInput <in/name> ;
         wfdesc:hasOutput <out/greeting> ;
         wfdesc:hasSubProcess <processor/Concatenate_two_strings/> , <processor/hello/> ;
         wfdesc:hasDataLink <datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> , <datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> , <datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> .

     <in/name> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
         rdfs:label "name" .

     <out/greeting> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
         rdfs:label "greeting" .

     <processor/Concatenate_two_strings/in/string1> a wfdesc:Input , wfdesc:Description ;
         rdfs:label "string1" .

     <processor/Concatenate_two_strings/in/string2> a wfdesc:Input , wfdesc:Description ;
         rdfs:label "string2" .

     <processor/Concatenate_two_strings/out/output> a wfdesc:Output , wfdesc:Description ;
         rdfs:label "output" .

     <processor/hello/> a wfdesc:Process , wfdesc:Description ;
         rdfs:label "hello" ;
         wfdesc:hasOutput <processor/hello/out/value> .

     <processor/hello/out/value> a wfdesc:Output , wfdesc:Description ;
         rdfs:label "value" .


 Programmatic use
 ----------------

 Add a Maven dependency to "scufl2-wfdesc":

     <dependency>
         <groupId>uk.org.taverna.scufl2</groupId>
         <artifactId>scufl2-wfdesc</artifactId>
         <version>0.1-SNAPSHOT</version>
     </dependency>


 Example:

     import uk.org.taverna.scufl2.api.container.WorkflowBundle;
     import uk.org.taverna.scufl2.api.io.ReaderException;
     import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
     import uk.org.taverna.scufl2.api.io.WriterException;

     ..
     File original = new File("helloworld.t2flow");
     File output = new File("helloworld.wfdesc.ttl");
     String original = null; // to guess filetype
     WorkflowBundle wfBundle = io.readBundle(original, null);
     io.writeBundle(wfBundle, output, "text/vnd.wf4ever.wfdesc+turtle");


 References
 ----------
  * SCUFL2 [4]
  * RO ontologies wfdesc [5]


 [1] https://github.com/mygrid/scufl2/
 [2] http://www.wf4ever-project.org/
 [3] https://github.com/wf4ever/ro/tree/0.1
 [4] http://www.mygrid.org.uk/dev/wiki/display/developer/2010-07+SCUFL2
 [5] http://www.wf4ever-project.org/wiki/display/docs/Research+Object+Vocabulary+Specification+v0.1
 [6] http://www.oracle.com/technetwork/java/javase/downloads/index.html
 [7] http://openjdk.java.net/install/
 [8] http://maven.apache.org/download.html
	Convert SCUFL2 to wfdesc
	========================

	This is an extension to Scufl2 [1] which provides the export capability
	to wfdesc ontology from the Wf4Ever [2] RO wfdesc ontology v0.1 [3].

	This is exposed as a command line tool "scufl2-to-wfdesc", but can also
	be accessed programmatically using the SCUFL2 APIs.






	Building
	--------

	Requirements:
	* Java JDK 6 or higher [6], or OpenJDK 7 or higher [7]
	* Maven 2 or higher [9] (only for building)

	To build, simply use "mvn clean install"

	Example:

	: stain@ralph ~/src/wf4ever/scufl2-wfdesc;mvn clean install
	[INFO] Scanning for projects...
	[INFO]
	[INFO] ------------------------------------------------------------------------
	[INFO] Building SCUFL2 to wfdesc 0.1-SNAPSHOT
	[INFO] ------------------------------------------------------------------------
	[INFO]
	[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ scufl2-wfdesc ---
	[INFO]
	[INFO] --- maven-antrun-plugin:1.6:run (default) @ scufl2-wfdesc ---
	[INFO] Executing tasks

	main:
	[mkdir] Created dir: /home/stain/stuff/src/wf4ever/scufl2-wfdesc/target/generated-sources
	(..)
	[INFO] ------------------------------------------------------------------------
	[INFO] BUILD SUCCESS
	[INFO] ------------------------------------------------------------------------
	[INFO] Total time: 46.734s
	[INFO] Finished at: Wed Jan 04 15:22:58 WET 2012
	[INFO] Final Memory: 18M/129M
	[INFO] ------------------------------------------------------------------------


	Note that the first time you build, Maven will download several
	required dependencies from Maven repositories. Depending on your network
	connection this might take some time to complete.



	Command line tool
	-----------------

	After building, the folder "target/scufl2-wfdesc" contains a
	distribution of the command line tool "scufl2-to-wfdesc", with launchers
	generated for Unix and Windows.

	You may copy and distribute this folder for a standalone usage of the
	conversion tool.

	The command line tool takes a list of Taverna workflow files (supported file
	types are .t2flow and .wfbundle)


	Example:

	: stain@ralph ~/src/wf4ever/scufl2-wfdesc; target/scufl2-wfdesc/bin/scufl2-to-wfdesc src/test/resources/helloworld.t2flow
	log4j:WARN No appenders could be found for logger (org.openrdf.sail.memory.MemoryStore).
	log4j:WARN Please initialize the log4j system properly.
	Converted src/test/resources/helloworld.t2flow to src/test/resources/helloworld.wfdesc.ttl


	: stain@ralph ~/src/wf4ever/scufl2-wfdesc; cat src/test/resources/helloworld.wfdesc.ttl

	@base <http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/> .
	@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
	@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

	<processor/Concatenate_two_strings/> a wfdesc:Process , wfdesc:Description , <http://www.w3.org/2002/07/owl#Thing> , wf4ever:BeanshellScript ;
	wf4ever:script "output = string1 + string2;" ;
	rdfs:label "Concatenate_two_strings" ;
	wfdesc:hasInput <processor/Concatenate_two_strings/in/string1> , <processor/Concatenate_two_strings/in/string2> ;
	wfdesc:hasOutput <processor/Concatenate_two_strings/out/output> .

	<datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> a wfdesc:DataLink ;
	wfdesc:hasSource <in/name> ;
	wfdesc:hasSink <processor/Concatenate_two_strings/in/string2> .

	<datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> a wfdesc:DataLink ;
	wfdesc:hasSource <processor/Concatenate_two_strings/out/output> ;
	wfdesc:hasSink <out/greeting> .

	<datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> a wfdesc:DataLink ;
	wfdesc:hasSource <processor/hello/out/value> ;
	wfdesc:hasSink <processor/Concatenate_two_strings/in/string1> .

	<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
	rdfs:label "Hello_Anyone" ;
	wfdesc:hasInput <in/name> ;
	wfdesc:hasOutput <out/greeting> ;
	wfdesc:hasSubProcess <processor/Concatenate_two_strings/> , <processor/hello/> ;
	wfdesc:hasDataLink <datalink?from=in/name&to=processor/Concatenate_two_strings/in/string2> , <datalink?from=processor/Concatenate_two_strings/out/output&to=out/greeting> , <datalink?from=processor/hello/out/value&to=processor/Concatenate_two_strings/in/string1> .

	<in/name> a wfdesc:Input , wfdesc:Description , wfdesc:Output ;
	rdfs:label "name" .

	<out/greeting> a wfdesc:Output , wfdesc:Description , wfdesc:Input ;
	rdfs:label "greeting" .

	<processor/Concatenate_two_strings/in/string1> a wfdesc:Input , wfdesc:Description ;
	rdfs:label "string1" .

	<processor/Concatenate_two_strings/in/string2> a wfdesc:Input , wfdesc:Description ;
	rdfs:label "string2" .

	<processor/Concatenate_two_strings/out/output> a wfdesc:Output , wfdesc:Description ;
	rdfs:label "output" .

	<processor/hello/> a wfdesc:Process , wfdesc:Description ;
	rdfs:label "hello" ;
	wfdesc:hasOutput <processor/hello/out/value> .

	<processor/hello/out/value> a wfdesc:Output , wfdesc:Description ;
	rdfs:label "value" .



	Programmatic use
	----------------

	Add a Maven dependency to "scufl2-wfdesc":

	<dependency>
	<groupId>uk.org.taverna.scufl2</groupId>
	<artifactId>scufl2-wfdesc</artifactId>
	<version>0.1-SNAPSHOT</version>
	</dependency>


	Example:

	import uk.org.taverna.scufl2.api.container.WorkflowBundle;
	import uk.org.taverna.scufl2.api.io.ReaderException;
	import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
	import uk.org.taverna.scufl2.api.io.WriterException;

	..
	File original = new File("helloworld.t2flow");
	File output = new File("helloworld.wfdesc.ttl");
	String original = null; // to guess filetype
	WorkflowBundle wfBundle = io.readBundle(original, null);
	io.writeBundle(wfBundle, output, "text/vnd.wf4ever.wfdesc+turtle");





	References
	----------
	* SCUFL2 [4]
	* RO ontologies wfdesc [5]



	[1] https://github.com/mygrid/scufl2/
	[2] http://www.wf4ever-project.org/
	[3] https://github.com/wf4ever/ro/tree/0.1
	[4] http://www.mygrid.org.uk/dev/wiki/display/developer/2010-07+SCUFL2
	[5] http://www.wf4ever-project.org/wiki/display/docs/Research+Object+Vocabulary+Specification+v0.1
	[6] http://www.oracle.com/technetwork/java/javase/downloads/index.html
	[7] http://openjdk.java.net/install/
	[8] http://maven.apache.org/download.html