taverna-scufl2-wfdesc

Convert SCUFL2 to wfdesc

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

You can use the tavlang convert command line tool for converting Taverna workflows to wfdesc.

Example

The output is a RDF Turtle document containing statements about the workflow structure according to the RO ontology wfdesc ontology, with additional service descriptions using the wf4ever ontology where supported.

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

	@base <http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/workflow/Hello_World/> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
	@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
	@prefix owl: <http://www.w3.org/2002/07/owl#> .
	@prefix prov: <http://www.w3.org/ns/prov#> .
	@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
	@prefix wf4ever: <http://purl.org/wf4ever/wf4ever#> .
	@prefix roterms: <http://purl.org/wf4ever/roterms#> .
	@prefix dc: <http://purl.org/dc/elements/1.1/> .
	@prefix dcterms: <http://purl.org/dc/terms/> .
	@prefix comp: <http://purl.org/DP/components#> .
	@prefix dep: <http://scape.keep.pt/vocab/dependencies#> .
	@prefix biocat: <http://biocatalogue.org/attribute/> .
	@prefix : <#> .

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

	<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
		dc:creator "Stian Soiland-Reyes" ;
		dcterms: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\"." ;
		dcterms:title "Hello World" ;
		rdfs:label "Hello_World" ;
		wfdesc:hasOutput <out/greeting> ;
		wfdesc:hasSubProcess <processor/hello/> ;
		wfdesc:hasDataLink <datalink?from=processor/hello/out/value&to=out/greeting> .

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

	<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" .

Extracted annotations

Annotations in the workflow are also extracted for the workflow, processors and input ports (see namespaces above):

• dc:creator
• dcterms:description
• dcterms:title
• biocat:exampleData

Richer semantic annotations (e.g. on Taverna Components) are extracted verbatim, e.g.:

	<> a wfdesc:Workflow , wfdesc:Description , wfdesc:Process ;
		comp:fits comp:MigrationAction ;
		comp:migrates _:node18musbm56x1 .

	_:node18musbm56x1 a comp:MigrationPath ;
		comp:fromMimetype "image/tiff" ;
		comp:toMimetype "image/tiff" .

See valid_component_imagemagickconvert.wfdesc.ttl for the complete example.

Example:

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;

..
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");

Common queries

These queries can be executed using SPARQL on the returned wfdesc Turtle, and assume these PREFIXes:

PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX wfdesc: <http://purl.org/wf4ever/wfdesc#>
PREFIX wfprov: <http://purl.org/wf4ever/wfprov#>
PREFIX tavernaprov: <http://ns.taverna.org.uk/2012/tavernaprov/>
PREFIX cnt:  <http://www.w3.org/2011/content#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX wf4ever: <http://purl.org/wf4ever/wf4ever#>
PREFIX comp: <http://purl.org/DP/components#>

How do I exclude nested workflows from a query?

The wfdesc model does not have a concept of "top-level" workflow, however you can use a SPARQL NOT EXISTS filter to skip any nested workflows:

SELECT ?wf WHERE {
  ?wf a wfdesc:Workflow .

  FILTER NOT EXISTS {
      ?processInParent prov:specializationOf ?wf .
      ?parent wfdesc:hasSubProcess ?processInParent
  } .
}

Thus any workflow ?wf which (specialization) has been used as a sub-process in ?parent are excluded from the result. As SCUFL2 workflows have unique URIs within each workflow bundle, e.g. http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/ - the above would not be excluding a workflow just because its structure has been reused elsewhere.

How do I select processors in the top-level workflows?

A variant of the above is if you are only interested in processors in top-level workflows:

SELECT ?proc WHERE {
  ?wf a wfdesc:Workflow ;
      wfdesc:hasSubProcess ?proc .

  FILTER NOT EXISTS {
      ?processInParent prov:specializationOf ?wf .
      ?parent wfdesc:hasSubProcess ?processInParent
  } .
}