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comparison OPPL/src/GalaxyOWLAPI.java @ 17:c9e01f86b07c draft

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New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 20 Aug 2012 11:39:56 +0200
parents 622cde484f4c
children d3616fac4ca5
comparison
equal deleted inserted replaced
16:6c25e717c896 17:c9e01f86b07c
47 import org.semanticweb.owlapi.util.InferredOntologyGenerator; 47 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
48 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; 48 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
49 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator; 49 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
50 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator; 50 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
51 import org.semanticweb.owlapi.util.OWLEntityRenamer; 51 import org.semanticweb.owlapi.util.OWLEntityRenamer;
52 import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider;
52 import org.semanticweb.owlapi.util.OWLOntologyMerger; 53 import org.semanticweb.owlapi.util.OWLOntologyMerger;
53 import org.semanticweb.owlapi.util.SimpleShortFormProvider; 54 import org.semanticweb.owlapi.util.SimpleShortFormProvider;
54 import org.semanticweb.owlapi.vocab.OWL2Datatype; 55 import org.semanticweb.owlapi.vocab.OWL2Datatype;
55 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; 56 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
56 import org.semanticweb.owlapi.reasoner.Node; 57 import org.semanticweb.owlapi.reasoner.Node;
60 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; 61 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
61 62
62 /** 63 /**
63 * A wrapper of the OWL API 64 * A wrapper of the OWL API
64 * 65 *
65 * @author Mikel Ega��a Aranguren 66 * @author Mikel Egana Aranguren
66 */ 67 */
67 public class GalaxyOWLAPI { 68 public class GalaxyOWLAPI {
68 private OWLOntologyManager manager; 69 private OWLOntologyManager manager;
69 private OWLOntology ontology; 70 private OWLOntology ontology;
70 private OWLReasonerFactory reasonerFactory; 71 private OWLReasonerFactory reasonerFactory;
107 } 108 }
108 public void setReasonerHermit (){ 109 public void setReasonerHermit (){
109 reasonerFactory = new Reasoner.ReasonerFactory(); 110 reasonerFactory = new Reasoner.ReasonerFactory();
110 reasoner = reasonerFactory.createReasoner(ontology); 111 reasoner = reasonerFactory.createReasoner(ontology);
111 } 112 }
112 public void merge () throws OWLOntologyCreationException{ 113 public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{
113 OWLOntologyMerger merger = new OWLOntologyMerger(manager); 114 OWLOntologyMerger merger = new OWLOntologyMerger(manager);
114 IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl"); 115 // OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology));
116 IRI mergedOntologyIRI = IRI.create(ontologyIRI);
117 // OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
115 ontology = merger.createMergedOntology(manager, mergedOntologyIRI); 118 ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
119 // manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
116 } 120 }
117 121
118 public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{ 122 public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
119 Set<OWLOntology> importsClosure = ontology.getImportsClosure(); 123 Set<OWLOntology> importsClosure = ontology.getImportsClosure();
120 BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider()); 124 BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());