@Override
public void visit(OWLSubClassAxiom owlSubClassAxiom) {
// get the complex description out of the axiom
List<OWLDescription> descriptions =
new ArrayList<OWLDescription>(owlSubClassAxiom.getDescriptions());
for (OWLDescription description : descriptions) {
// visit the description and record replacment
description.accept(descriptionVisitor);
}
// construct new Axiom
OWLDescription subReplace =
descriptionVisitor.getReplacements().get(owlSubClassAxiom.getSubClass());
OWLDescription superReplace =
descriptionVisitor.getReplacements().get(owlSubClassAxiom.getSuperClass());
if (subReplace == null) {
subReplace = owlSubClassAxiom.getSubClass();
}
if (superReplace == null) {
superReplace = owlSubClassAxiom.getSuperClass();
}
OWLSubClassAxiom replacementAxiom =
owlDataFactory.getOWLSubClassAxiom(subReplace, superReplace);
// create the changeevents that have to be performed on the ontology
try {
List<OWLAxiomChange> replaceEvent =
OWLUtils.createReplaceAxiomEvents(owlOntology, owlSubClassAxiom, replacementAxiom);
axiomChanges.addAll(replaceEvent);
} catch (OWLOntologyChangeException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
// clear the description visitor
descriptionVisitor.clear();
super.visit(owlSubClassAxiom);
}
private void _createNewOntology() throws Exception {
assert namespace.matches(".*(/|#)");
String baseUri = namespace.replaceAll("(/|#)+$", ""); // removing any trailing slash/hash
manager = new SKOSManager();
if (namespace.endsWith("#")) {
// Ok, OWLAPI v2 works fine with hash separator:
dataset = manager.createSKOSDataset(URI.create(baseUri));
} else {
/////////////////////////////////////////////////////////////////////////////////////////////
// TODO NOTE: workaround for bug in OWLAPI v2:
// Instead of using a baseUri without separator,
// use the namespace itself (ie, w/ fragment separator):
dataset = manager.createSKOSDataset(URI.create(namespace));
// In this way, the resulting ontology looks OK except that the xml:base is
// written with the separator:
//
// <rdf:RDF xmlns="http://mmisw.org/ont/mmi/cf/parameter/"
// xml:base="http://mmisw.org/ont/mmi/cf/parameter/" <<<--- WITH trailing slash
// xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
// xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
// xmlns:owl2="http://www.w3.org/2006/12/owl2#"
// xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
// xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
// xmlns:owl="http://www.w3.org/2002/07/owl#"
// xmlns:skos="http://www.w3.org/2004/02/skos/core#">
// <owl:Ontology rdf:about=""/>
// ...
// <!-- http://mmisw.org/ont/mmi/cf/parameter/CfStdName -->
//
// <skos:ConceptScheme rdf:about="CfStdName"/>
//
//
// <!-- http://mmisw.org/ont/mmi/cf/parameter/age_of_stratospheric_air -->
//
// <skos:Concept rdf:about="age_of_stratospheric_air">
// <skos:inScheme rdf:resource="CfStdName"/>
// </skos:Concept>
//
//
// <!-- http://mmisw.org/ont/mmi/cf/parameter/air_density -->
//
// <skos:Concept rdf:about="air_density">
// <skos:inScheme rdf:resource="CfStdName"/>
// </skos:Concept>
//
// ...
/////////////////////////////////////////////////////////////////////////////////////////////
}
SAXBuilder builder = new SAXBuilder();
Document document = builder.build(new StringReader(inputContents));
standard_name_table = document.getRootElement();
_getProperty(standard_name_table, "version_number");
_getProperty(standard_name_table, "last_modified");
_getProperty(standard_name_table, "institution");
_getProperty(standard_name_table, "contact");
// TODO assign version_number, last_modified as some properties to the ontology itself.
dataFactory = manager.getSKOSDataFactory();
allEntities = new ArrayList<SKOSEntity>();
conceptScheme = dataFactory.getSKOSConceptScheme(URI.create(namespace + CONCEPT_SCHEME));
concepts = new HashSet<SKOSConcept>();
URI topConceptUri = URI.create(namespace + TOP_CONCEPT);
topConcept = dataFactory.getSKOSConcept(topConceptUri);
concepts.add(topConcept);
objectRelationAssertions = new ArrayList<SKOSObjectRelationAssertion>();
dataRelationAssertions = new ArrayList<SKOSDataRelationAssertion>();
// skos:hasTopConcept
objectRelationAssertions.add(
dataFactory.getSKOSObjectRelationAssertion(
conceptScheme, dataFactory.getSKOSHasTopConceptProperty(), topConcept));
/////////////////////////////////////////////////
// OWL API stuff
owlManager = manager.getOWLManger();
owlOntology = owlManager.getOntology(URI.create(namespace));
owlDataFactory = owlManager.getOWLDataFactory();
canonicalUnitsProp =
owlDataFactory.getOWLDataProperty(URI.create(namespace + "canonical_units"));
gribProp = owlDataFactory.getOWLDataProperty(URI.create(namespace + "grib"));
amipProp = owlDataFactory.getOWLDataProperty(URI.create(namespace + "amip"));
rdfsLabel =
owlDataFactory.getOWLDataProperty(URI.create("http://www.w3.org/2000/01/rdf-schema#label"));
rdfsComment =
owlDataFactory.getOWLDataProperty(
URI.create("http://www.w3.org/2000/01/rdf-schema#comment"));
owlChanges = new ArrayList<AddAxiom>();
_addOwlChange(topConceptUri, TOP_CONCEPT.replace('_', ' '), "", null, null, null);
}
private void _addOwlChange(
URI conceptUri,
String id,
String description,
String canonicalUnits,
String grib,
String amip) {
OWLIndividual conceptOwlIndiv = owlDataFactory.getOWLIndividual(conceptUri);
// rdfs:label
if (id.trim().length() > 0) {
OWLTypedConstant owlc = owlDataFactory.getOWLTypedConstant(id.trim());
OWLDataPropertyAssertionAxiom addProp =
owlDataFactory.getOWLDataPropertyAssertionAxiom(conceptOwlIndiv, rdfsLabel, owlc);
owlChanges.add(new AddAxiom(owlOntology, addProp));
}
// rdfs:comment
if (description.trim().length() > 0) {
OWLTypedConstant owlc = owlDataFactory.getOWLTypedConstant(description.trim());
OWLDataPropertyAssertionAxiom addProp =
owlDataFactory.getOWLDataPropertyAssertionAxiom(conceptOwlIndiv, rdfsComment, owlc);
owlChanges.add(new AddAxiom(owlOntology, addProp));
}
// canonicalUnits
if (canonicalUnits != null && canonicalUnits.trim().length() > 0) {
OWLTypedConstant owlc = owlDataFactory.getOWLTypedConstant(canonicalUnits.trim());
OWLDataPropertyAssertionAxiom addProp =
owlDataFactory.getOWLDataPropertyAssertionAxiom(
conceptOwlIndiv, canonicalUnitsProp, owlc);
owlChanges.add(new AddAxiom(owlOntology, addProp));
}
// grib
if (grib != null && grib.trim().length() > 0) {
OWLTypedConstant owlc = owlDataFactory.getOWLTypedConstant(grib.trim());
OWLDataPropertyAssertionAxiom addProp =
owlDataFactory.getOWLDataPropertyAssertionAxiom(conceptOwlIndiv, gribProp, owlc);
owlChanges.add(new AddAxiom(owlOntology, addProp));
}
// amip
if (amip != null && amip.trim().length() > 0) {
OWLTypedConstant owlc = owlDataFactory.getOWLTypedConstant(amip.trim());
OWLDataPropertyAssertionAxiom addProp =
owlDataFactory.getOWLDataPropertyAssertionAxiom(conceptOwlIndiv, amipProp, owlc);
owlChanges.add(new AddAxiom(owlOntology, addProp));
}
}