Java tutorial
/** * Copyright (C) 2014 The SciGraph authors * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package edu.sdsc.scigraph.owlapi; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.logging.Logger; import javax.inject.Inject; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.AddAxiom; import org.semanticweb.owlapi.model.AxiomType; import org.semanticweb.owlapi.model.OWLAxiom; import org.semanticweb.owlapi.model.OWLClass; import org.semanticweb.owlapi.model.OWLClassExpression; import org.semanticweb.owlapi.model.OWLDataFactory; import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyChange; import org.semanticweb.owlapi.model.OWLOntologyManager; import org.semanticweb.owlapi.model.RemoveAxiom; import org.semanticweb.owlapi.reasoner.OWLReasoner; import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; import com.google.common.collect.Iterables; import edu.sdsc.scigraph.owlapi.loader.OwlLoadConfiguration.ReasonerConfiguration; public class ReasonerUtil { private static final Logger logger = Logger.getLogger(ReasonerUtil.class.getName()); private final static OWLDataFactory factory = OWLManager.getOWLDataFactory(); private final OWLOntologyManager manager; private final OWLOntology ont; private OWLReasoner reasoner; private final ReasonerConfiguration config; private final OWLReasonerFactory reasonerFactory; @Inject public ReasonerUtil(ReasonerConfiguration reasonerConfig, OWLOntologyManager manager, OWLOntology ont) throws InstantiationException, IllegalAccessException, ClassNotFoundException { reasonerFactory = (OWLReasonerFactory) Class.forName(reasonerConfig.getFactory()).newInstance(); logger.info("Creating reasoner for " + ont); reasoner = reasonerFactory.createReasoner(ont); logger.info("Completed creating reasoner for " + ont); this.config = reasonerConfig; this.manager = manager; this.ont = ont; } OWLReasoner getReasoner() { return reasoner; } Collection<OWLOntologyChange> removeAxioms(AxiomType<?> type) { Collection<OWLOntologyChange> removals = new HashSet<>(); for (OWLOntology importedOnt : ont.getImportsClosure()) { Set<? extends OWLAxiom> axioms = importedOnt.getAxioms(type); removals.addAll(manager.removeAxioms(importedOnt, axioms)); } return removals; } /*** * Remove all axioms that would generate extra unsatisfiable classes for the reasoner */ Collection<OWLOntologyChange> removeUnsatisfiableClasses() { Collection<OWLOntologyChange> removals = new HashSet<>(); removals.addAll(removeAxioms(AxiomType.DISJOINT_CLASSES)); removals.addAll(removeAxioms(AxiomType.DATA_PROPERTY_DOMAIN)); removals.addAll(removeAxioms(AxiomType.DATA_PROPERTY_RANGE)); if (removals.size() > 0) { reasoner.flush(); } logger.info("Removed " + removals.size() + " axioms to prevent unsatisfiable classes"); return removals; } Collection<OWLClass> getUnsatisfiableClasses() { return reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom(); } boolean shouldReason() { if (!reasoner.isConsistent()) { logger.warning("Not reasoning on " + ont + " because it is inconsistent."); return false; } Collection<OWLClass> unsatisfiableClasses = getUnsatisfiableClasses(); if (!unsatisfiableClasses.isEmpty()) { logger.warning("Not reasoning on " + ont + " because " + unsatisfiableClasses.size() + " classes are unsatisfiable"); logger.warning("For instance: " + Iterables.getFirst(unsatisfiableClasses, null).getIRI().toString() + " unsatisfiable"); return false; } return true; } AddAxiom getCompleteEquivalence(OWLClass ce) { Set<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(ce).getEntities(); OWLEquivalentClassesAxiom equivalentAxiom = factory.getOWLEquivalentClassesAxiom(equivalentClasses); return new AddAxiom(ont, equivalentAxiom); } //Ticket #42 List<OWLOntologyChange> getDirectInferredEdges(OWLClass ce) { List<OWLOntologyChange> changes = new ArrayList<>(); //find direct inferred superclasses, D Set<OWLClass> directSuperclasses = reasoner.getSuperClasses(ce, true).getFlattened(); //find indirect superclasses, I Set<OWLClass> indirectSuperclasses = reasoner.getSuperClasses(ce, false).getFlattened(); //find asserted superclasses, A Set<OWLClassExpression> assertedSuperclasses = ce.asOWLClass().getSuperClasses(ont); //for each d in D, add an edge subClassOf(x d) for (OWLClass directSuperclass : directSuperclasses) { OWLAxiom axiom = factory.getOWLSubClassOfAxiom(ce, directSuperclass); AddAxiom addAxiom = new AddAxiom(ont, axiom); changes.add(addAxiom); } //for each a in A for (OWLClassExpression assertedSuperclass : assertedSuperclasses) { if (assertedSuperclass.isAnonymous()) { continue; } //if a is in I and not in D, then remove edge subClassOf(x a) if (indirectSuperclasses.contains(assertedSuperclass.asOWLClass()) && !directSuperclasses.contains(assertedSuperclass.asOWLClass())) { OWLAxiom axiom = factory.getOWLSubClassOfAxiom(ce, assertedSuperclass); RemoveAxiom removeAxiom = new RemoveAxiom(ont, axiom); changes.add(removeAxiom); } } return changes; } void flush() { reasoner.flush(); } public boolean reason() { if (config.isRemoveUnsatisfiableClasses()) { removeUnsatisfiableClasses(); } if (!shouldReason()) { return false; } List<OWLOntologyChange> changes = new ArrayList<>(); for (OWLClass ce : ont.getClassesInSignature(true)) { if (config.isAddInferredEquivalences()) { changes.add(getCompleteEquivalence(ce)); } if (config.isAddDirectInferredEdges()) { changes.addAll(getDirectInferredEdges(ce)); } } reasoner.dispose(); logger.info("Applying reasoned axioms: " + changes.size()); manager.applyChanges(changes); logger.info("Completed applying reasoning changes"); return true; } }