Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/src/GalaxyOWLAPI.java @ 13:7e6604a5ee55

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New query tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 29 Mar 2012 14:49:22 +0200
parents 6ca67b155e32
children 622cde484f4c
comparison
equal deleted inserted replaced
12:d0722148cb59 13:7e6604a5ee55
8 import java.io.IOException; 8 import java.io.IOException;
9 import java.io.OutputStreamWriter; 9 import java.io.OutputStreamWriter;
10 import java.util.ArrayList; 10 import java.util.ArrayList;
11 import java.util.List; 11 import java.util.List;
12 import java.util.Scanner; 12 import java.util.Scanner;
13 13 import java.util.Set;
14
15 import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
14 import org.coode.owlapi.obo.parser.OBOOntologyFormat; 16 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
17 import org.coode.parsers.BidirectionalShortFormProviderAdapter;
15 import org.semanticweb.HermiT.Reasoner; 18 import org.semanticweb.HermiT.Reasoner;
16 import org.semanticweb.owlapi.apibinding.OWLManager; 19 import org.semanticweb.owlapi.apibinding.OWLManager;
20 import org.semanticweb.owlapi.expression.OWLEntityChecker;
21 import org.semanticweb.owlapi.expression.ParserException;
22 import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
17 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; 23 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
18 import org.semanticweb.owlapi.io.SystemOutDocumentTarget; 24 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
19 import org.semanticweb.owlapi.model.AddAxiom; 25 import org.semanticweb.owlapi.model.AddAxiom;
20 import org.semanticweb.owlapi.model.IRI; 26 import org.semanticweb.owlapi.model.IRI;
21 import org.semanticweb.owlapi.model.OWLAnnotation; 27 import org.semanticweb.owlapi.model.OWLAnnotation;
22 import org.semanticweb.owlapi.model.OWLAnnotationProperty; 28 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
23 import org.semanticweb.owlapi.model.OWLAxiom; 29 import org.semanticweb.owlapi.model.OWLAxiom;
24 import org.semanticweb.owlapi.model.OWLClass; 30 import org.semanticweb.owlapi.model.OWLClass;
31 import org.semanticweb.owlapi.model.OWLClassExpression;
25 import org.semanticweb.owlapi.model.OWLDataFactory; 32 import org.semanticweb.owlapi.model.OWLDataFactory;
26 import org.semanticweb.owlapi.model.OWLLiteral; 33 import org.semanticweb.owlapi.model.OWLLiteral;
34 import org.semanticweb.owlapi.model.OWLNamedIndividual;
27 import org.semanticweb.owlapi.model.OWLOntology; 35 import org.semanticweb.owlapi.model.OWLOntology;
28 import org.semanticweb.owlapi.model.OWLOntologyChange; 36 import org.semanticweb.owlapi.model.OWLOntologyChange;
29 import org.semanticweb.owlapi.model.OWLOntologyCreationException; 37 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
30 import org.semanticweb.owlapi.model.OWLOntologyManager; 38 import org.semanticweb.owlapi.model.OWLOntologyManager;
31 import org.semanticweb.owlapi.model.OWLOntologyStorageException; 39 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
32 import org.semanticweb.owlapi.reasoner.InferenceType; 40 import org.semanticweb.owlapi.reasoner.InferenceType;
41 import org.semanticweb.owlapi.reasoner.NodeSet;
33 import org.semanticweb.owlapi.reasoner.OWLReasoner; 42 import org.semanticweb.owlapi.reasoner.OWLReasoner;
34 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; 43 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
44 import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
35 import org.semanticweb.owlapi.util.InferredAxiomGenerator; 45 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
36 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator; 46 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
37 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator; 47 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
38 import org.semanticweb.owlapi.util.InferredOntologyGenerator; 48 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
39 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; 49 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
40 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator; 50 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
41 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator; 51 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
42 import org.semanticweb.owlapi.util.OWLEntityRenamer; 52 import org.semanticweb.owlapi.util.OWLEntityRenamer;
43 import org.semanticweb.owlapi.util.OWLOntologyMerger; 53 import org.semanticweb.owlapi.util.OWLOntologyMerger;
54 import org.semanticweb.owlapi.util.SimpleShortFormProvider;
44 import org.semanticweb.owlapi.vocab.OWL2Datatype; 55 import org.semanticweb.owlapi.vocab.OWL2Datatype;
45 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary; 56 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
57 import org.semanticweb.owlapi.reasoner.Node;
46 58
47 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory; 59 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
48 60
49 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; 61 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
50 62
101 public void merge () throws OWLOntologyCreationException{ 113 public void merge () throws OWLOntologyCreationException{
102 OWLOntologyMerger merger = new OWLOntologyMerger(manager); 114 OWLOntologyMerger merger = new OWLOntologyMerger(manager);
103 IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl"); 115 IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl");
104 ontology = merger.createMergedOntology(manager, mergedOntologyIRI); 116 ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
105 } 117 }
106 118
119 public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
120 Set<OWLOntology> importsClosure = ontology.getImportsClosure();
121 BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());
122 OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
123 ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr);
124 MOSparser.setOWLEntityChecker(entityChecker);
125 return MOSparser.parseClassExpression();
126 }
127
128 public Set<OWLNamedIndividual> getIndividuals (OWLClassExpression expr){
129 return (reasoner.getInstances(expr, false)).getFlattened();
130 }
131 public Set<OWLClass> getEquivalentClasses (OWLClassExpression expr){
132 Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(expr);
133 Set<OWLClass> result;
134 if (expr.isAnonymous()) {
135 result = equivalentClasses.getEntities();
136 }
137 else {
138 result = equivalentClasses.getEntitiesMinus(expr.asOWLClass());
139 }
140 return result;
141 }
142
143 public Set<OWLClass> getDirectSuperClasses (OWLClassExpression expr){
144 return (reasoner.getSuperClasses(expr, true)).getFlattened();
145 }
146
147 public Set<OWLClass> getAncestors (OWLClassExpression expr){
148 return (reasoner.getSuperClasses(expr, false)).getFlattened();
149 }
150
151 public Set<OWLClass> getDirectSubClasses (OWLClassExpression expr){
152 return (reasoner.getSubClasses(expr, true)).getFlattened();
153 }
154
155 public Set<OWLClass> getDescendants (OWLClassExpression expr){
156 return (reasoner.getSubClasses(expr, false)).getFlattened();
157 }
158
107 // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. 159 // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.
108 160
109 public void addCLASS_ASSERTIONS(){ 161 public void addCLASS_ASSERTIONS(){
110 reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS); 162 reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
111 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>(); 163 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();