in taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java [96:310]
protected OntModel save(final WorkflowBundle bundle) {
final OntModel model = ModelFactory.createOntologyModel();
bundle.accept(new VisitorWithPath() {
Scufl2Tools scufl2Tools = new Scufl2Tools();
public boolean visit() {
WorkflowBean node = getCurrentNode();
// System.out.println(node);
if (node instanceof WorkflowBundle) {
return true;
}
// @SuppressWarnings("rawtypes")
if (node instanceof org.apache.taverna.scufl2.api.core.Workflow) {
entityForBean(node, wfdesc.Workflow);
} else if (node instanceof Processor) {
Processor processor = (Processor) node;
Individual process = entityForBean(processor, wfdesc.Process);
Individual wf = entityForBean(processor.getParent(), wfdesc.Workflow);
wf.addProperty(wfdesc.hasSubProcess, process);
} else if (node instanceof InputPort) {
WorkflowBean parent = ((Child) node).getParent();
Individual input = entityForBean(node, wfdesc.Input);
Individual process = entityForBean(parent, wfdesc.Process);
process.addProperty(wfdesc.hasInput, input);
} else if (node instanceof OutputPort) {
WorkflowBean parent = ((Child) node).getParent();
Individual output = entityForBean(node, wfdesc.Output);
Individual process = entityForBean(parent, wfdesc.Process);
process.addProperty(wfdesc.hasOutput, output);
} else if (node instanceof DataLink) {
WorkflowBean parent = ((Child) node).getParent();
DataLink link = (DataLink) node;
Individual dl = entityForBean(link, wfdesc.DataLink);
Individual source = entityForBean(link.getReceivesFrom(), wfdesc.Output);
dl.addProperty(wfdesc.hasSource, source);
Individual sink = entityForBean(link.getSendsTo(), wfdesc.Input);
dl.addProperty(wfdesc.hasSink, sink);
Individual wf = entityForBean(parent, wfdesc.Workflow);
wf.addProperty(wfdesc.hasDataLink, dl);
} else if (node instanceof Profile) {
// So that we can get at the ProcessorBinding - buy only if
// it is the main Profile
return node == bundle.getMainProfile();
} else if (node instanceof ProcessorBinding) {
ProcessorBinding b = (ProcessorBinding) node;
Activity a = b.getBoundActivity();
Processor boundProcessor = b.getBoundProcessor();
Individual process = entityForBean(boundProcessor, wfdesc.Process);
// Note: We don't describe the activity and processor
// binding in wfdesc. Instead we
// assign additional types and attributes to the parent
// processor
try {
URI type = a.getType();
Configuration c = scufl2Tools.configurationFor(a, b.getParent());
JsonNode json = c.getJson();
if (type.equals(BEANSHELL)) {
process.addRDFType(wf4ever.BeanshellScript);
String s = json.get("script").asText();
process.addProperty(wf4ever.script, s);
JsonNode localDep = json.get("localDependency");
if (localDep != null && localDep.isArray()) {
for (int i = 0; i < localDep.size(); i++) {
String depStr = localDep.get(i).asText();
// FIXME: Better class for dependency?
Individual dep = model.createIndividual(OWL.Thing);
dep.addLabel(depStr, null);
dep.addComment("JAR dependency", "en");
process.addProperty(roterms.requiresSoftware, dep);
// Somehow this gets the whole thing to fall
// out of the graph!
// QName depQ = new
// QName("http://google.com/", ""+
// UUID.randomUUID());
// sesameManager.rename(dep, depQ);
}
}
}
if (type.equals(RSHELL)) {
process.addRDFType(wf4ever.RScript);
String s = json.get("script").asText();
process.addProperty(wf4ever.script, s);
}
if (type.equals(WSDL)) {
process.addRDFType(wf4ever.SOAPService);
JsonNode operation = json.get("operation");
URI wsdl = URI.create(operation.get("wsdl").asText());
process.addProperty(wf4ever.wsdlURI, wsdl.toASCIIString());
process.addProperty(wf4ever.wsdlOperationName, operation.get("name").asText());
process.addProperty(wf4ever.rootURI, wsdl.resolve("/").toASCIIString());
}
if (type.equals(REST)) {
process.addRDFType(wf4ever.RESTService);
// System.out.println(json);
JsonNode request = json.get("request");
String absoluteURITemplate = request.get("absoluteURITemplate").asText();
String uriTemplate = absoluteURITemplate.replace("{", "");
uriTemplate = uriTemplate.replace("}", "");
// TODO: Detect {}
try {
URI root = new URI(uriTemplate).resolve("/");
process.addProperty(wf4ever.rootURI, root.toASCIIString());
} catch (URISyntaxException e) {
logger.warning("Potentially invalid URI template: " + absoluteURITemplate);
// Uncomment to temporarily break
// TestInvalidURITemplate:
// rest.getWfRootURI().add(URI.create("http://example.com/FRED"));
}
}
if (type.equals(TOOL)) {
process.addRDFType(wf4ever.CommandLineTool);
JsonNode desc = json.get("toolDescription");
// System.out.println(json);
JsonNode command = desc.get("command");
if (command != null) {
process.addProperty(wf4ever.command, command.asText());
}
}
if (type.equals(NESTED_WORKFLOW)) {
Workflow nestedWf = scufl2Tools.nestedWorkflowForProcessor(boundProcessor, b.getParent());
// The parent process is a specialization of the
// nested workflow
// (because the nested workflow could exist as
// several processors)
specializationOf(boundProcessor, nestedWf);
process.addRDFType(wfdesc.Workflow);
// Just like the Processor specializes the nested
// workflow, the
// ProcessorPorts specialize the WorkflowPort
for (ProcessorPortBinding portBinding : b.getInputPortBindings()) {
// Map from activity port (not in wfdesc) to
// WorkflowPort
WorkflowPort wfPort = nestedWf.getInputPorts()
.getByName(portBinding.getBoundActivityPort().getName());
if (wfPort == null) {
continue;
}
specializationOf(portBinding.getBoundProcessorPort(), wfPort);
}
for (ProcessorPortBinding portBinding : b.getOutputPortBindings()) {
WorkflowPort wfPort = nestedWf.getOutputPorts()
.getByName(portBinding.getBoundActivityPort().getName());
if (wfPort == null) {
continue;
}
specializationOf(portBinding.getBoundProcessorPort(), wfPort);
}
}
} catch (IndexOutOfBoundsException ex) {
}
return false;
} else {
// System.out.println("--NO!");
return false;
}
for (Annotation ann : scufl2Tools.annotationsFor(node, bundle)) {
String annotationBody = ann.getBody().toASCIIString();
String baseURI = bundle.getGlobalBaseURI().resolve(ann.getBody()).toASCIIString();
InputStream annotationStream;
try {
annotationStream = bundle.getResources().getResourceAsInputStream(annotationBody);
try {
// FIXME: Don't just assume Lang.TURTLE
RDFDataMgr.read(model, annotationStream, baseURI, Lang.TURTLE);
} catch (RiotException e) {
logger.log(Level.WARNING, "Can't parse RDF Turtle from " + annotationBody, e);
} finally {
annotationStream.close();
}
} catch (IOException e) {
logger.log(Level.WARNING, "Can't read " + annotationBody, e);
}
}
if (node instanceof Named) {
Named named = (Named) node;
entityForBean(node, OWL.Thing).addLabel(named.getName(), null);
}
return true;
}
private void specializationOf(WorkflowBean special, WorkflowBean general) {
Individual specialEnt = entityForBean(special, prov.Entity);
Individual generalEnt = entityForBean(general, prov.Entity);
specialEnt.addProperty(prov.specializationOf, generalEnt);
}
private Individual entityForBean(WorkflowBean bean, Resource thing) {
return model.createIndividual(uriForBean(bean), thing);
}
// @Override
// public boolean visitEnter(WorkflowBean node) {
// if (node instanceof Processor
// || node instanceof org.apache.taverna.scufl2.api.core.Workflow
// || node instanceof Port || node instanceof DataLink) {
// visit(node);
// return true;
// }
// // The other node types (e.g. dispatch stack, configuration) are
// // not (directly) represented in wfdesc
//// System.out.println("Skipping " + node);
// return false;
// };
});
return model;
}