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 _convert() throws Exception {
List<?> list = standard_name_table.getChildren("entry");
for (Iterator<?> iterator = list.iterator(); iterator.hasNext(); ) {
Element ele = (Element) iterator.next();
numEntries++;
String id = ele.getAttribute("id").getValue().trim();
String canonicalUnits = ele.getChildTextNormalize("canonical_units");
String grib = ele.getChildTextNormalize("grib");
String amip = ele.getChildTextNormalize("amip");
String description = ele.getChildTextNormalize("description");
String prefLabel = id.replace('_', ' ');
URI conceptUri = URI.create(namespace + id);
SKOSConcept concept = dataFactory.getSKOSConcept(conceptUri);
concepts.add(concept);
// skos:narrower
objectRelationAssertions.add(
dataFactory.getSKOSObjectRelationAssertion(
topConcept, dataFactory.getSKOSNarrowerProperty(), concept));
// skos:prefLabel
dataRelationAssertions.add(
dataFactory.getSKOSDataRelationAssertion(
concept, dataFactory.getSKOSPrefLabelProperty(), prefLabel));
////////////////////////////////////////////////
// OWL API stuff
_addOwlChange(conceptUri, id, description, canonicalUnits, grib, amip);
}
props.put("entries", String.valueOf(numEntries));
props.put("concepts", String.valueOf(concepts.size()));
allEntities.add(conceptScheme);
allEntities.addAll(concepts);
List<SKOSChange> skosChanges = new ArrayList<SKOSChange>();
// entities:
List<SKOSEntityAssertion> entityAssertions = dataFactory.getSKOSEntityAssertions(allEntities);
for (SKOSEntityAssertion ass : entityAssertions) {
skosChanges.add(new AddAssertion(dataset, ass));
}
// skos:inScheme
objectRelationAssertions.addAll(
dataFactory.getSKOSObjectRelationAssertions(
concepts, dataFactory.getSKOSInSchemeProperty(), conceptScheme));
// object relations:
for (SKOSObjectRelationAssertion assertion : objectRelationAssertions) {
skosChanges.add(new AddAssertion(dataset, assertion));
}
// data relations:
for (SKOSDataRelationAssertion assertion : dataRelationAssertions) {
skosChanges.add(new AddAssertion(dataset, assertion));
}
manager.applyChanges(skosChanges);
////////////////////////////////////////////////////
// OWL API assertions
owlManager.applyChanges(owlChanges);
}