VIVO-778 Use JFact as the TBox reasoner, instead of Pellet.
There are still some differences between the two, and I expect some answers from Jon and Brian regarding irregularities in the ontologies. The Pellet libraries have not yet been removed.
This commit is contained in:
Jim Blake
parent
dad574d33a
commit
8382c2620a
12 changed files with 527 additions and 2804 deletions
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@ -35,7 +35,8 @@ log4j.rootLogger=INFO, AllAppender
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# These classes are too chatty to display INFO messages.
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log4j.logger.edu.cornell.mannlib.vitro.webapp.startup.StartupStatus=WARN
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log4j.logger.edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase=DEBUG
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log4j.logger.edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase=WARN
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log4j.logger.org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer=WARN
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# Spring as a whole is too chatty to display INFO messages.
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log4j.logger.org.springframework=WARN
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webapp/lib/commons-io-2.4.jar
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webapp/lib/commons-io-2.4.jar
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webapp/lib/jfact-4.0.0.jar
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webapp/lib/jfact-4.0.0.jar
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webapp/lib/owlapi-distribution-4.0.1.jar
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webapp/lib/owlapi-distribution-4.0.1.jar
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@ -1,116 +0,0 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletContextEvent;
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import javax.servlet.ServletContextListener;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
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import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
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import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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/**
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* Safety Net:
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*
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* Insure that the inferred TBox is the same as it was before we started messing
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* with things.
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*
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* KLUGE -- this shouldn't go into production.
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*
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* KLUGE -- in production, startup_listeners shouldn't mention this.
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*/
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public class TBoxReasonerSmokeTest implements ServletContextListener {
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private static final Log log = LogFactory
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.getLog(TBoxReasonerSmokeTest.class);
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@Override
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public void contextInitialized(ServletContextEvent sce) {
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ServletContext ctx = sce.getServletContext();
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StartupStatus ss = StartupStatus.getBean(ctx);
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OntModel savedInferencesModel = ModelFactory
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.createOntologyModel(OntModelSpec.OWL_MEM);
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try (InputStream in = new FileInputStream(locateSavedInferencesFile())) {
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savedInferencesModel.read(in, null, "N3");
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} catch (IOException e) {
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ss.fatal(this, "Can't read saved inferences", e);
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}
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OntModel tboxInferencesModel = ModelAccess.on(sce.getServletContext())
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.getOntModel(ModelNames.TBOX_INFERENCES);
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if (savedInferencesModel.isIsomorphicWith(tboxInferencesModel)) {
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ss.info(this, "TBox inferences matches saved.");
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} else {
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dumpDifferences(savedInferencesModel, tboxInferencesModel);
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ss.fatal(this, "TBox inferences does not match saved.");
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}
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}
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private void dumpDifferences(OntModel savedInferencesModel,
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OntModel tboxInferencesModel) {
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Model missingStatements = ModelFactory.createDefaultModel();
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for (Statement stmt : savedInferencesModel.listStatements().toList()) {
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if (!tboxInferencesModel.contains(stmt)) {
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missingStatements.add(stmt);
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}
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}
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Model extraStatements = ModelFactory.createDefaultModel();
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for (Statement stmt : tboxInferencesModel.listStatements().toList()) {
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if (!savedInferencesModel.contains(stmt)) {
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extraStatements.add(stmt);
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}
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}
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log.error("inferences: " + tboxInferencesModel.size() + ", saved: "
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+ savedInferencesModel.size() + ", missing: "
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+ missingStatements.size() + ", extra: "
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+ extraStatements.size());
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String missing = "";
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for (Statement stmt : missingStatements.listStatements().toList()) {
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missing += "\n " + stmt;
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}
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log.error("missing statements:" + missing);
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String extras = "";
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for (Statement stmt : extraStatements.listStatements().toList()) {
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extras += "\n " + stmt;
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}
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log.error("extra statements:" + extras);
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}
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private File locateSavedInferencesFile() {
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String homeDirPath = ApplicationUtils.instance().getHomeDirectory()
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.getPath().toString();
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Path savedInferencesPath = Paths.get(homeDirPath, "rdf", "tbox",
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"savedInferences.n3");
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return savedInferencesPath.toFile();
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}
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@Override
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public void contextDestroyed(ServletContextEvent sce) {
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// Nothing to do
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}
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}
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@ -62,11 +62,11 @@ public class InferenceModelUpdater {
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* to the inferences model.
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*/
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public void update(List<ReasonerStatementPattern> patternList) {
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List<Statement> filteredReasonerModel = reasoner
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List<Statement> filteredReasonerStatements = reasoner
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.filterResults(patternList);
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addNewInferences(filteredReasonerModel);
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addNewInferences(filteredReasonerStatements);
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removeOldInferences(filterInferencesModel(patternList),
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filteredReasonerModel);
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filteredReasonerStatements);
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log.debug("Added: " + addCount + ", Retracted: " + retractCount);
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}
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@ -0,0 +1,340 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl;
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import static com.hp.hpl.jena.rdf.model.ResourceFactory.createProperty;
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import static com.hp.hpl.jena.rdf.model.ResourceFactory.createResource;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.semanticweb.owlapi.model.OWLClass;
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import org.semanticweb.owlapi.model.OWLDataProperty;
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import org.semanticweb.owlapi.model.OWLNamedObject;
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import org.semanticweb.owlapi.model.OWLObjectProperty;
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import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
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import org.semanticweb.owlapi.reasoner.OWLReasoner;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.Resource;
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/**
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* Build a model of inferred statements by walking through the ontology as
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* represented in the reasoner.
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*
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* TODO Get rid of the kluges. Either decide that they are not necessary, or
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* give them full status.
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*/
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public class TBoxInferencesAccumulator {
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private static final Log log = LogFactory
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.getLog(TBoxInferencesAccumulator.class);
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private static final Property RDFS_TYPE = createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#type");
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private static final Resource OWL_CLASS = createResource("http://www.w3.org/2002/07/owl#Class");
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private static final Property OWL_EQUIVALENT_CLASS = createProperty("http://www.w3.org/2002/07/owl#equivalentClass");
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private static final Property OWL_DISJOINT_WITH = createProperty("http://www.w3.org/2002/07/owl#disjointWith");
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private static final Property OWL_SUBCLASS_OF = createProperty("http://www.w3.org/2000/01/rdf-schema#subClassOf");
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private static final Property OWL_SUBPROPERTY_OF = createProperty("http://www.w3.org/2000/01/rdf-schema#subPropertyOf");
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private static final Property OWL_INVERSE_OF = createProperty("http://www.w3.org/2002/07/owl#inverseOf");
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public Model populateModelFromReasonerQueries(OWLReasoner reasoner) {
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Model m = ModelFactory.createDefaultModel();
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populateClasses(reasoner, m);
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populateObjectProperties(reasoner, m);
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populateDataProperties(reasoner, m);
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klugeOwlInvariants(m);
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klugeMistakes(m);
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return m;
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}
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private void populateClasses(OWLReasoner r, Model m) {
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OWLClass bottom = r.getBottomClassNode().getRepresentativeElement();
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for (OWLClass c : r.getSuperClasses(bottom, false).getFlattened()) {
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populateClass(c, r, m);
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}
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}
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private void populateClass(OWLClass c, OWLReasoner r, Model m) {
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log.debug("Owl class: " + c);
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populateClassType(c, m);
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populateEquivalentClasses(c, r, m);
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populateDisjointClasses(c, r, m);
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populateSubClasses(c, r, m);
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}
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private void populateClassType(OWLClass c, Model m) {
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log.debug(c + " is a class.");
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m.add(toResource(c), RDFS_TYPE, OWL_CLASS);
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}
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private void populateEquivalentClasses(OWLClass c, OWLReasoner r, Model m) {
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for (OWLClass equiv : r.getEquivalentClasses(c).getEntities()) {
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log.debug("Equivalent class: " + c + ", " + equiv);
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m.add(toResource(c), OWL_EQUIVALENT_CLASS, toResource(equiv));
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}
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}
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private void populateDisjointClasses(OWLClass c, OWLReasoner r, Model m) {
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for (OWLClass d : r.getDisjointClasses(c).getFlattened()) {
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if (!d.isOWLNothing()) {
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log.debug("Disjoint class: " + c + ", " + d);
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m.add(toResource(c), OWL_DISJOINT_WITH, toResource(d));
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}
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}
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}
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private void populateSubClasses(OWLClass c, OWLReasoner r, Model m) {
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for (OWLClass sub : r.getSubClasses(c, false).getFlattened()) {
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log.debug(sub + " is subclass of " + c);
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if (!sub.isOWLNothing()) {
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m.add(toResource(sub), OWL_SUBCLASS_OF, toResource(c));
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}
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}
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}
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private void populateObjectProperties(OWLReasoner r, Model m) {
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OWLObjectPropertyExpression bottom = r.getBottomObjectPropertyNode()
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.getRepresentativeElement();
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populateObjectProperty(bottom, r, m);
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for (OWLObjectPropertyExpression op : r.getSuperObjectProperties(
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bottom, false).getFlattened()) {
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populateObjectProperty(op, r, m);
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}
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}
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private void populateObjectProperty(OWLObjectPropertyExpression ope,
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OWLReasoner r, Model m) {
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if (!ope.isAnonymous()) {
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OWLObjectProperty op = ope.asOWLObjectProperty();
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log.debug("object property: " + op);
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populateObjectSubProperties(op, r, m);
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populateObjectInverseProperties(op, r, m);
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}
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}
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private void populateObjectSubProperties(OWLObjectProperty op,
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OWLReasoner r, Model m) {
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for (OWLObjectPropertyExpression subOPE : r.getSubObjectProperties(op,
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false).getFlattened()) {
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if (!subOPE.isAnonymous()) {
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OWLObjectProperty subOP = subOPE.asOWLObjectProperty();
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log.debug(subOP + " object sub-property of " + op);
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m.add(toResource(subOP), OWL_SUBPROPERTY_OF, toResource(op));
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}
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}
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// getSubObjectProperties is strict, so add the reflexive statement.
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log.debug(op + " object sub-property of " + op);
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m.add(toResource(op), OWL_SUBPROPERTY_OF, toResource(op));
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}
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private void populateObjectInverseProperties(OWLObjectProperty op,
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OWLReasoner r, Model m) {
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for (OWLObjectPropertyExpression inverseE : r
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.getInverseObjectProperties(op)) {
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if (!inverseE.isAnonymous()
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&& !inverseE.isOWLBottomObjectProperty()
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&& !inverseE.isOWLTopObjectProperty()) {
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OWLObjectProperty inverse = inverseE.asOWLObjectProperty();
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log.debug(inverse + " object inverse of " + op);
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m.add(toResource(inverse), OWL_INVERSE_OF, toResource(op));
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}
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}
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}
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private void populateDataProperties(OWLReasoner r, Model m) {
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OWLDataProperty bottom = r.getBottomDataPropertyNode()
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.getRepresentativeElement();
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populateDataProperty(bottom, r, m);
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for (OWLDataProperty dp : r.getSuperDataProperties(bottom, false)
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.getFlattened()) {
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populateDataProperty(dp, r, m);
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}
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}
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private void populateDataProperty(OWLDataProperty dp, OWLReasoner r, Model m) {
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log.debug("data property: " + dp);
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populateDataSubProperties(dp, r, m);
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}
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private void populateDataSubProperties(OWLDataProperty dp, OWLReasoner r,
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Model m) {
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for (OWLDataProperty subDP : r.getSubDataProperties(dp, false)
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.getFlattened()) {
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log.debug(subDP + " data sub-property of " + dp);
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m.add(toResource(subDP), OWL_SUBPROPERTY_OF, toResource(dp));
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}
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// getSubDataProperties is strict, so add the reflexive statement.
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log.debug(dp + " data sub-property of " + dp);
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m.add(toResource(dp), OWL_SUBPROPERTY_OF, toResource(dp));
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}
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private Resource toResource(OWLNamedObject owlObject) {
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return createResource(owlObject.getIRI().toString());
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}
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private static final Resource OWL_THING = createResource("http://www.w3.org/2002/07/owl#Thing");
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private static final Resource OWL_OBJECT_PROPERTY = createResource("http://www.w3.org/2002/07/owl#ObjectProperty");
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private static final Resource OWL_TOP_OBJECT_PROPERTY = createResource("http://www.w3.org/2002/07/owl#topObjectProperty");
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private static final Resource OWL_BOTTOM_OBJECT_PROPERTY = createResource("http://www.w3.org/2002/07/owl#bottomObjectProperty");
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private static final Resource OWL_DATA_PROPERTY = createResource("http://www.w3.org/2002/07/owl#DatatypeProperty");
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private static final Resource OWL_TOP_DATA_PROPERTY = createResource("http://www.w3.org/2002/07/owl#topDataProperty");
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private static final Resource OWL_BOTTOM_DATA_PROPERTY = createResource("http://www.w3.org/2002/07/owl#bottomDataProperty");
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private static final Resource OWL_FUNCTIONAL_PROPERTY = createResource("http://www.w3.org/2002/07/owl#FunctionalProperty");
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private static final Resource OWL_INVERSE_FUNCTIONAL_PROPERTY = createResource("http://www.w3.org/2002/07/owl#InverseFunctionalProperty");
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private static final Resource OWL_TRANSITIVE_PROPERTY = createResource("http://www.w3.org/2002/07/owl#TransitiveProperty");
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private static final Resource OWL_SYMMETRIC_PROPERTY = createResource("http://www.w3.org/2002/07/owl#SymmetricProperty");
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private static final Resource OWL_ASYMMETRIC_PROPERTY = createResource("http://www.w3.org/2002/07/owl#AsymmetricProperty");
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private static final Resource OWL_REFLEXIVE_PROPERTY = createResource("http://www.w3.org/2002/07/owl#ReflexiveProperty");
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private static final Resource OWL_IRREFLEXIVE_PROPERTY = createResource("http://www.w3.org/2002/07/owl#IrreflexiveProperty");
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private static final Resource OWL_ANNOTATION_PROPERTY = createResource("http://www.w3.org/2002/07/owl#AnnotationProperty");
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private static final Resource OWL_VERSION_INFO = createResource("http://www.w3.org/2002/07/owl#versionInfo");
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private static final Resource OWL_BACKWARD_COMPATIBLE_WITH = createResource("http://www.w3.org/2002/07/owl#backwardCompatibleWith");
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private static final Resource OWL_INCOMPATIBLE_WITH = createResource("http://www.w3.org/2002/07/owl#incompatibleWith");
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private static final Resource OWL_PRIOR_VERSION = createResource("http://www.w3.org/2002/07/owl#priorVersion");
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private static final Resource RDFS_SEE_ALSO = createResource("http://www.w3.org/2000/01/rdf-schema#seeAlso");
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private static final Resource RDFS_COMMENT = createResource("http://www.w3.org/2000/01/rdf-schema#comment");
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private static final Resource RDFS_IS_DEFINED_BY = createResource("http://www.w3.org/2000/01/rdf-schema#isDefinedBy");
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private static final Resource RDFS_LABEL = createResource("http://www.w3.org/2000/01/rdf-schema#label");
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private void klugeOwlInvariants(Model m) {
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m.add(OWL_BOTTOM_DATA_PROPERTY, RDFS_TYPE, OWL_DATA_PROPERTY);
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m.add(OWL_BOTTOM_DATA_PROPERTY, RDFS_TYPE, OWL_FUNCTIONAL_PROPERTY);
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m.add(OWL_TOP_DATA_PROPERTY, RDFS_TYPE, OWL_DATA_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_OBJECT_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_FUNCTIONAL_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE,
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OWL_INVERSE_FUNCTIONAL_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_TRANSITIVE_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_SYMMETRIC_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_ASYMMETRIC_PROPERTY);
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m.add(OWL_BOTTOM_OBJECT_PROPERTY, RDFS_TYPE, OWL_IRREFLEXIVE_PROPERTY);
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m.add(OWL_TOP_OBJECT_PROPERTY, RDFS_TYPE, OWL_OBJECT_PROPERTY);
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m.add(OWL_TOP_OBJECT_PROPERTY, RDFS_TYPE, OWL_TRANSITIVE_PROPERTY);
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m.add(OWL_TOP_OBJECT_PROPERTY, RDFS_TYPE, OWL_REFLEXIVE_PROPERTY);
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m.add(OWL_TOP_OBJECT_PROPERTY, RDFS_TYPE, OWL_SYMMETRIC_PROPERTY);
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m.add(OWL_THING, RDFS_TYPE, OWL_CLASS);
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m.add(OWL_VERSION_INFO, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
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m.add(OWL_BACKWARD_COMPATIBLE_WITH, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(OWL_PRIOR_VERSION, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(OWL_INCOMPATIBLE_WITH, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(RDFS_SEE_ALSO, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(RDFS_COMMENT, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(RDFS_IS_DEFINED_BY, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
m.add(RDFS_LABEL, RDFS_TYPE, OWL_ANNOTATION_PROPERTY);
|
||||
}
|
||||
|
||||
private void klugeMistakes(Model m) {
|
||||
Property ISF_DEPRECATED = createProperty("http://isf/deprecated_op");
|
||||
m.add(ISF_DEPRECATED, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
m.add(ISF_DEPRECATED, OWL_SUBPROPERTY_OF, ISF_DEPRECATED);
|
||||
m.add(ISF_DEPRECATED, OWL_SUBPROPERTY_OF, OWL_TOP_OBJECT_PROPERTY);
|
||||
m.add(OWL_BOTTOM_OBJECT_PROPERTY, OWL_SUBPROPERTY_OF, ISF_DEPRECATED);
|
||||
|
||||
Resource OWL_DEPRECATED = createResource("http://www.w3.org/2002/07/owl#DeprecatedProperty");
|
||||
m.add(OWL_DEPRECATED, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
m.add(OWL_DEPRECATED, OWL_SUBPROPERTY_OF, OWL_DEPRECATED);
|
||||
m.add(OWL_DEPRECATED, OWL_SUBPROPERTY_OF, OWL_TOP_OBJECT_PROPERTY);
|
||||
m.add(OWL_BOTTOM_OBJECT_PROPERTY, OWL_SUBPROPERTY_OF, OWL_DEPRECATED);
|
||||
|
||||
Property DCT_CONTRIBUTOR = createProperty("http://purl.org/dc/terms/contributor");
|
||||
m.add(DCT_CONTRIBUTOR, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
m.add(DCT_CONTRIBUTOR, OWL_SUBPROPERTY_OF, DCT_CONTRIBUTOR);
|
||||
m.add(DCT_CONTRIBUTOR, OWL_SUBPROPERTY_OF, OWL_TOP_OBJECT_PROPERTY);
|
||||
m.add(OWL_BOTTOM_OBJECT_PROPERTY, OWL_SUBPROPERTY_OF, DCT_CONTRIBUTOR);
|
||||
|
||||
Resource ARG_2000400 = createResource("http://purl.obolibrary.org/obo/ARG_2000400");
|
||||
Resource BFO_0000001 = createResource("http://purl.obolibrary.org/obo/BFO_0000001");
|
||||
Resource BFO_0000002 = createResource("http://purl.obolibrary.org/obo/BFO_0000002");
|
||||
Resource BFO_0000031 = createResource("http://purl.obolibrary.org/obo/BFO_0000031");
|
||||
Resource IAO_0000003 = createResource("http://purl.obolibrary.org/obo/IAO_0000003");
|
||||
Resource IAO_0000009 = createResource("http://purl.obolibrary.org/obo/IAO_0000009");
|
||||
Resource IAO_0000030 = createResource("http://purl.obolibrary.org/obo/IAO_0000030");
|
||||
m.add(ARG_2000400, RDFS_TYPE, BFO_0000001);
|
||||
m.add(ARG_2000400, RDFS_TYPE, BFO_0000002);
|
||||
m.add(ARG_2000400, RDFS_TYPE, BFO_0000031);
|
||||
m.add(ARG_2000400, RDFS_TYPE, IAO_0000003);
|
||||
m.add(ARG_2000400, RDFS_TYPE, IAO_0000009);
|
||||
m.add(ARG_2000400, RDFS_TYPE, IAO_0000030);
|
||||
m.add(ARG_2000400, RDFS_TYPE, OWL_THING);
|
||||
|
||||
Resource BIBO_ACCEPTED = createResource("http://purl.org/ontology/bibo/accepted");
|
||||
Resource BIBO_DRAFT = createResource("http://purl.org/ontology/bibo/draft");
|
||||
Resource BIBO_PEER_REVIEWED = createResource("http://purl.org/ontology/bibo/peerReviewed");
|
||||
Resource BIBO_PUBLISHED = createResource("http://purl.org/ontology/bibo/published");
|
||||
Resource BIBO_REJECTED = createResource("http://purl.org/ontology/bibo/rejected");
|
||||
Resource BIBO_UNPUBLISHED = createResource("http://purl.org/ontology/bibo/unpublished");
|
||||
m.add(BIBO_ACCEPTED, RDFS_TYPE, OWL_THING);
|
||||
m.add(BIBO_DRAFT, RDFS_TYPE, OWL_THING);
|
||||
m.add(BIBO_PEER_REVIEWED, RDFS_TYPE, OWL_THING);
|
||||
m.add(BIBO_PUBLISHED, RDFS_TYPE, OWL_THING);
|
||||
m.add(BIBO_REJECTED, RDFS_TYPE, OWL_THING);
|
||||
m.add(BIBO_UNPUBLISHED, RDFS_TYPE, OWL_THING);
|
||||
|
||||
Resource CORE_YMDT_PRECISION = createResource("http://vivoweb.org/ontology/core#yearMonthDayTimePrecision");
|
||||
Resource CORE_YMD_PRECISION = createResource("http://vivoweb.org/ontology/core#yearMonthDayPrecision");
|
||||
Resource CORE_YM_PRECISION = createResource("http://vivoweb.org/ontology/core#yearMonthPrecision");
|
||||
Resource CORE_Y_PRECISION = createResource("http://vivoweb.org/ontology/core#yearPrecision");
|
||||
Resource SKOS_CONCEPT = createResource("http://www.w3.org/2004/02/skos/core#Concept");
|
||||
m.add(CORE_YMDT_PRECISION, RDFS_TYPE, OWL_THING);
|
||||
m.add(CORE_YMDT_PRECISION, RDFS_TYPE, SKOS_CONCEPT);
|
||||
m.add(CORE_YMD_PRECISION, RDFS_TYPE, OWL_THING);
|
||||
m.add(CORE_YMD_PRECISION, RDFS_TYPE, SKOS_CONCEPT);
|
||||
m.add(CORE_YM_PRECISION, RDFS_TYPE, OWL_THING);
|
||||
m.add(CORE_YM_PRECISION, RDFS_TYPE, SKOS_CONCEPT);
|
||||
m.add(CORE_Y_PRECISION, RDFS_TYPE, OWL_THING);
|
||||
m.add(CORE_Y_PRECISION, RDFS_TYPE, SKOS_CONCEPT);
|
||||
|
||||
Resource CORE_CONTACT_INFO = createResource("http://vivoweb.org/ontology/core#contactInformation");
|
||||
m.add(CORE_CONTACT_INFO, RDFS_TYPE, OWL_DATA_PROPERTY);
|
||||
|
||||
Resource CORE_HAS_FACILITY = createResource("http://vivoweb.org/ontology/core#hasFacility");
|
||||
m.add(CORE_HAS_FACILITY, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
|
||||
Resource CORE_HAS_FUNDING = createResource("http://vivoweb.org/ontology/core#hasFundingVehicle");
|
||||
m.add(CORE_HAS_FUNDING, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
|
||||
Resource CORE_HAS_GOV_AUTH = createResource("http://vivoweb.org/ontology/core#hasGoverningAuthority");
|
||||
m.add(CORE_HAS_GOV_AUTH, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
|
||||
Resource CORE_IN_PRESS = createResource("http://vivoweb.org/ontology/core#inPress");
|
||||
m.add(CORE_IN_PRESS, RDFS_TYPE, OWL_THING);
|
||||
|
||||
Resource CORE_INVITED = createResource("http://vivoweb.org/ontology/core#invited");
|
||||
m.add(CORE_INVITED, RDFS_TYPE, OWL_THING);
|
||||
|
||||
Resource CORE_SUBMITTED = createResource("http://vivoweb.org/ontology/core#submitted");
|
||||
m.add(CORE_SUBMITTED, RDFS_TYPE, OWL_THING);
|
||||
|
||||
Resource OBO_HAS_AGENT = createResource("http://www.obofoundry.org/ro/ro.owl#has_agent");
|
||||
m.add(OBO_HAS_AGENT, RDFS_TYPE, OWL_OBJECT_PROPERTY);
|
||||
|
||||
Resource OBI_0000066 = createResource("http://purl.obolibrary.org/obo/OBI_0000066");
|
||||
m.remove(OBI_0000066, RDFS_TYPE, OWL_CLASS);
|
||||
m.remove(OBI_0000066, OWL_SUBCLASS_OF, OWL_THING);
|
||||
m.remove(OBI_0000066, OWL_EQUIVALENT_CLASS, OBI_0000066);
|
||||
|
||||
Resource OBI_0000086 = createResource("http://purl.obolibrary.org/obo/OBI_0000086");
|
||||
m.remove(OBI_0000086, RDFS_TYPE, OWL_CLASS);
|
||||
m.remove(OBI_0000086, OWL_SUBCLASS_OF, OWL_THING);
|
||||
m.remove(OBI_0000086, OWL_EQUIVALENT_CLASS, OBI_0000086);
|
||||
|
||||
Resource OBI_0000094 = createResource("http://purl.obolibrary.org/obo/OBI_0000094");
|
||||
m.remove(OBI_0000094, RDFS_TYPE, OWL_CLASS);
|
||||
m.remove(OBI_0000094, OWL_SUBCLASS_OF, OWL_THING);
|
||||
m.remove(OBI_0000094, OWL_EQUIVALENT_CLASS, OBI_0000094);
|
||||
|
||||
Resource OBI_0000571 = createResource("http://purl.obolibrary.org/obo/OBI_0000571");
|
||||
m.remove(OBI_0000571, RDFS_TYPE, OWL_CLASS);
|
||||
m.remove(OBI_0000571, OWL_SUBCLASS_OF, OWL_THING);
|
||||
m.remove(OBI_0000571, OWL_EQUIVALENT_CLASS, OBI_0000571);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,159 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.jfact;
|
||||
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.ByteArrayOutputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.semanticweb.owlapi.apibinding.OWLManager;
|
||||
import org.semanticweb.owlapi.model.OWLOntology;
|
||||
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
|
||||
import org.semanticweb.owlapi.reasoner.InferenceType;
|
||||
import org.semanticweb.owlapi.reasoner.OWLReasoner;
|
||||
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
|
||||
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
|
||||
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
|
||||
|
||||
import uk.ac.manchester.cs.jfact.JFactFactory;
|
||||
|
||||
import com.hp.hpl.jena.ontology.DatatypeProperty;
|
||||
import com.hp.hpl.jena.ontology.ObjectProperty;
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
||||
import com.hp.hpl.jena.ontology.Restriction;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.Statement;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerStatementPattern;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.TBoxChanges;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.TBoxReasoner;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.TBoxInferencesAccumulator;
|
||||
|
||||
/**
|
||||
* An implementation of the JFact reasoner for the TBox.
|
||||
*
|
||||
* It maintains a model of all the assertions it has been given, adding or
|
||||
* removing statements as change sets are received.
|
||||
*
|
||||
* Each time a change is received, it will create a fresh ontology from the
|
||||
* assertions model, and apply a reasoner to that ontology. A model of
|
||||
* inferences is built by querying the reasoner.
|
||||
*
|
||||
* The assertions and inferences are combined into an OntModel, which is kept to
|
||||
* answer queries.
|
||||
*
|
||||
* -----------------
|
||||
*
|
||||
* This class it not thread-safe.
|
||||
*/
|
||||
public class JFactTBoxReasoner implements
|
||||
TBoxReasoner {
|
||||
private static final Log log = LogFactory.getLog(JFactTBoxReasoner.class);
|
||||
|
||||
private final OWLReasonerFactory reasonerFactory;
|
||||
private final TBoxInferencesAccumulator accumulator;
|
||||
|
||||
private final Model filteredAssertionsModel;
|
||||
private final OntModel combinedInferencedModel;
|
||||
|
||||
public JFactTBoxReasoner() {
|
||||
this.filteredAssertionsModel = ModelFactory.createDefaultModel();
|
||||
this.combinedInferencedModel = ModelFactory
|
||||
.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
|
||||
this.reasonerFactory = new JFactFactory();
|
||||
this.accumulator = new TBoxInferencesAccumulator();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void updateReasonerModel(TBoxChanges changes) {
|
||||
log.debug("Adding " + changes.getAddedStatements().size()
|
||||
+ ", removing " + changes.getRemovedStatements().size());
|
||||
filteredAssertionsModel.add(changes.getAddedStatements());
|
||||
filteredAssertionsModel.remove(changes.getRemovedStatements());
|
||||
}
|
||||
|
||||
@Override
|
||||
public Status performReasoning() {
|
||||
try {
|
||||
OWLOntology ont = copyModelToOntology(filteredAssertionsModel);
|
||||
|
||||
OWLReasoner reasoner = createReasoner(ont);
|
||||
reasoner.precomputeInferences(InferenceType.values());
|
||||
|
||||
try {
|
||||
if (!reasoner.isConsistent()) {
|
||||
return Status.inconsistent("Reasoner axioms are not "
|
||||
+ "consistent");
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error(e);
|
||||
return Status.ERROR;
|
||||
}
|
||||
|
||||
Model inferences = accumulator.populateModelFromReasonerQueries(reasoner);
|
||||
mergeModels(filteredAssertionsModel, inferences);
|
||||
return Status.SUCCESS;
|
||||
} catch (Exception e) {
|
||||
log.error(e);
|
||||
return Status.ERROR;
|
||||
}
|
||||
}
|
||||
|
||||
private OWLOntology copyModelToOntology(Model m)
|
||||
throws OWLOntologyCreationException {
|
||||
ByteArrayOutputStream out = new ByteArrayOutputStream();
|
||||
m.write(out, "RDF/XML");
|
||||
|
||||
ByteArrayInputStream in = new ByteArrayInputStream(out.toByteArray());
|
||||
return OWLManager.createOWLOntologyManager()
|
||||
.loadOntologyFromOntologyDocument(in);
|
||||
}
|
||||
|
||||
private OWLReasoner createReasoner(OWLOntology ont) {
|
||||
OWLReasonerConfiguration config = new SimpleConfiguration(50000);
|
||||
OWLReasoner reasoner = this.reasonerFactory.createReasoner(ont, config);
|
||||
return reasoner;
|
||||
}
|
||||
|
||||
private void mergeModels(Model assertions, Model inferences) {
|
||||
combinedInferencedModel.removeAll();
|
||||
combinedInferencedModel.add(assertions);
|
||||
combinedInferencedModel.add(inferences);
|
||||
log.debug("Assertions: " + assertions.size() + ", inferences: "
|
||||
+ inferences.size() + ", combined: "
|
||||
+ combinedInferencedModel.size());
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<ObjectProperty> listObjectProperties() {
|
||||
return combinedInferencedModel.listObjectProperties().toList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<DatatypeProperty> listDatatypeProperties() {
|
||||
return combinedInferencedModel.listDatatypeProperties().toList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Restriction> listRestrictions() {
|
||||
return combinedInferencedModel.listRestrictions().toList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Statement> filterResults(
|
||||
List<ReasonerStatementPattern> patternList) {
|
||||
List<Statement> filtered = new ArrayList<>();
|
||||
for (ReasonerStatementPattern pattern : patternList) {
|
||||
filtered.addAll(pattern
|
||||
.matchStatementsFromModel(combinedInferencedModel));
|
||||
}
|
||||
return filtered;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,6 +1,6 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.pellet;
|
||||
package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.jfact;
|
||||
|
||||
import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames.TBOX_ASSERTIONS;
|
||||
import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames.TBOX_INFERENCES;
|
||||
|
|
@ -13,9 +13,7 @@ import javax.servlet.ServletContext;
|
|||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
import com.hp.hpl.jena.ontology.Restriction;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccess;
|
||||
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
|
||||
|
|
@ -27,13 +25,16 @@ import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerConfiguration;
|
|||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.BasicTBoxReasonerDriver;
|
||||
|
||||
/**
|
||||
* Configure a Pellet reasoner on the TBox.
|
||||
* Configure a JFact reasoner on the TBox.
|
||||
*
|
||||
* Create a JFactTBoxReasoner and pass it as the strategy to a
|
||||
* BasicTBoxReasonerDriver.
|
||||
*/
|
||||
public class PelletTBoxReasonerModule implements TBoxReasonerModule {
|
||||
public class JFactTBoxReasonerModule implements TBoxReasonerModule {
|
||||
private static final Log log = LogFactory
|
||||
.getLog(PelletTBoxReasonerModule.class);
|
||||
.getLog(JFactTBoxReasonerModule.class);
|
||||
|
||||
private PelletTBoxReasoner reasoner;
|
||||
private JFactTBoxReasoner reasoner;
|
||||
private BasicTBoxReasonerDriver driver;
|
||||
|
||||
@Override
|
||||
|
|
@ -41,18 +42,14 @@ public class PelletTBoxReasonerModule implements TBoxReasonerModule {
|
|||
ServletContext ctx = application.getServletContext();
|
||||
|
||||
ContextModelAccess contextModels = ModelAccess.on(ctx);
|
||||
OntModel tboxAssertionsModel = contextModels
|
||||
.getOntModel(TBOX_ASSERTIONS);
|
||||
Model tboxInferencesModel = contextModels.getOntModel(TBOX_INFERENCES)
|
||||
.getBaseModel();
|
||||
OntModel tboxUnionModel = contextModels.getOntModel(TBOX_UNION);
|
||||
|
||||
reasoner = new PelletTBoxReasoner(ReasonerConfiguration.DEFAULT);
|
||||
driver = new BasicTBoxReasonerDriver(tboxAssertionsModel,
|
||||
tboxInferencesModel, tboxUnionModel, reasoner,
|
||||
reasoner = new JFactTBoxReasoner();
|
||||
driver = new BasicTBoxReasonerDriver(
|
||||
contextModels.getOntModel(TBOX_ASSERTIONS), contextModels
|
||||
.getOntModel(TBOX_INFERENCES).getBaseModel(),
|
||||
contextModels.getOntModel(TBOX_UNION), reasoner,
|
||||
ReasonerConfiguration.DEFAULT);
|
||||
|
||||
ss.info("Pellet reasoner connected for the TBox");
|
||||
ss.info("JFact reasoner connected for the TBox");
|
||||
|
||||
waitForTBoxReasoning();
|
||||
}
|
||||
|
|
@ -61,7 +58,7 @@ public class PelletTBoxReasonerModule implements TBoxReasonerModule {
|
|||
public TBoxReasonerStatus getStatus() {
|
||||
if (driver == null) {
|
||||
throw new IllegalStateException(
|
||||
"PelletTBoxReasonerModule has not been started.");
|
||||
"JFactTBoxReasonerModule has not been started.");
|
||||
}
|
||||
return driver.getStatus();
|
||||
}
|
||||
|
|
@ -70,22 +67,16 @@ public class PelletTBoxReasonerModule implements TBoxReasonerModule {
|
|||
public List<Restriction> listRestrictions() {
|
||||
if (reasoner == null) {
|
||||
throw new IllegalStateException(
|
||||
"PelletTBoxReasonerModule has not been started.");
|
||||
"JFactTBoxReasonerModule has not been started.");
|
||||
}
|
||||
return reasoner.listRestrictions();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown(Application application) {
|
||||
driver.shutdown();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void waitForTBoxReasoning() {
|
||||
public void waitForTBoxReasoning() {
|
||||
int sleeps = 0;
|
||||
// sleep at least once to make sure the TBox reasoning gets started
|
||||
while ((0 == sleeps)
|
||||
|| ((sleeps < 1000) && getStatus().isReasoning())) {
|
||||
while ((0 == sleeps) || ((sleeps < 1000) && getStatus().isReasoning())) {
|
||||
if (((sleeps - 1) % 10) == 0) { // print message at 10 second
|
||||
// intervals
|
||||
log.info("Waiting for initial TBox reasoning to complete");
|
||||
|
|
@ -99,4 +90,9 @@ public class PelletTBoxReasonerModule implements TBoxReasonerModule {
|
|||
sleeps++;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void shutdown(Application application) {
|
||||
driver.shutdown();
|
||||
}
|
||||
}
|
||||
|
|
@ -1,114 +0,0 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.pellet;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.mindswap.pellet.exceptions.InconsistentOntologyException;
|
||||
import org.mindswap.pellet.jena.PelletInfGraph;
|
||||
|
||||
import com.hp.hpl.jena.ontology.DatatypeProperty;
|
||||
import com.hp.hpl.jena.ontology.ObjectProperty;
|
||||
import com.hp.hpl.jena.ontology.Restriction;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.Statement;
|
||||
import com.hp.hpl.jena.vocabulary.OWL;
|
||||
import com.hp.hpl.jena.vocabulary.RDFS;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerConfiguration;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerStatementPattern;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.TBoxChanges;
|
||||
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.TBoxReasoner;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockableOntModel;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.jena.criticalsection.LockedOntModel;
|
||||
|
||||
/**
|
||||
* An implementation the TBoxReasonerWrapper for Pellet.
|
||||
*/
|
||||
public class PelletTBoxReasoner implements TBoxReasoner {
|
||||
private static final Log log = LogFactory
|
||||
.getLog(PelletTBoxReasoner.class);
|
||||
|
||||
private final LockableOntModel lockablePelletModel;
|
||||
|
||||
public PelletTBoxReasoner(ReasonerConfiguration reasonerConfiguration) {
|
||||
this.lockablePelletModel = new LockableOntModel(
|
||||
ModelFactory.createOntologyModel(reasonerConfiguration
|
||||
.getOntModelSpec()));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void updateReasonerModel(TBoxChanges changes) {
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.write()) {
|
||||
pelletModel.remove(changes.getRemovedStatements());
|
||||
pelletModel.add(changes.getAddedStatements());
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public Status performReasoning() {
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.write()) {
|
||||
try {
|
||||
pelletModel.rebind();
|
||||
pelletModel.prepare();
|
||||
return Status.SUCCESS;
|
||||
} catch (InconsistentOntologyException ioe) {
|
||||
String explanation = ((PelletInfGraph) pelletModel.getGraph())
|
||||
.getKB().getExplanation();
|
||||
log.error(ioe);
|
||||
log.error(explanation);
|
||||
return Status.inconsistent(explanation);
|
||||
} catch (Exception e) {
|
||||
log.error("Exception during inference", e);
|
||||
return Status.ERROR;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<ObjectProperty> listObjectProperties() {
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.read()) {
|
||||
return pelletModel.listObjectProperties().toList();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<DatatypeProperty> listDatatypeProperties() {
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.read()) {
|
||||
return pelletModel.listDatatypeProperties().toList();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Statement> filterResults(
|
||||
List<ReasonerStatementPattern> patternList) {
|
||||
List<Statement> filtered = new ArrayList<>();
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.read()) {
|
||||
for (ReasonerStatementPattern pattern : patternList) {
|
||||
filtered.addAll(pattern.matchStatementsFromModel(pelletModel));
|
||||
}
|
||||
}
|
||||
for (Iterator<Statement> fit = filtered.iterator(); fit.hasNext(); ) {
|
||||
Statement stmt = fit.next();
|
||||
if (stmt.getObject().equals(RDFS.Resource)) {
|
||||
fit.remove();
|
||||
} else if (stmt.getSubject().equals(OWL.Nothing)) {
|
||||
fit.remove();
|
||||
} else if (stmt.getObject().equals(OWL.Nothing)) {
|
||||
fit.remove();
|
||||
}
|
||||
}
|
||||
return filtered;
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Restriction> listRestrictions() {
|
||||
try (LockedOntModel pelletModel = lockablePelletModel.read()) {
|
||||
return pelletModel.listRestrictions().toList();
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue