improvements to blank node handling in bulk deletion
This commit is contained in:
brianjlowe
parent
cef7b583e2
commit
b480cb2eea
78 changed files with 5882 additions and 605 deletions
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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.reasoner;
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import org.apache.log4j.Level;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.mindswap.pellet.jena.PelletReasonerFactory;
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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.ontology.OntProperty;
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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.Resource;
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import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
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import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
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public class SimpleReasonerPropertyTest extends AbstractTestClass {
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long delay = 50;
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@Before
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public void suppressErrorOutput() {
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suppressSyserr();
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//Turn off log messages to console
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setLoggerLevel(SimpleReasoner.class, Level.OFF);
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setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
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}
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/*
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* basic scenarios around adding abox data
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*
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* Create a Tbox with property P inverseOf property Q.
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* Pellet will compute TBox inferences. Add a statement
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* a P b, and verify that b Q a is inferred.
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* Add a statement c Q d and verify that d Q c
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* is inferred.
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*/
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@Test
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public void addABoxAssertion1() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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P.addInverseOf(Q);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register the SimpleReasoner listener with it
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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// b Q a is inferred from a P b
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aBox.add(a,P,b);
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Assert.assertTrue(inf.contains(b,Q,a));
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// d P c is inferred from c Q d.
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aBox.add(c,Q,d);
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Assert.assertTrue(inf.contains(d,P,c));
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}
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/*
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* don't infer if it's already in the abox
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*/
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@Test
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public void addABoxAssertion2() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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P.addInverseOf(Q);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and add statement b Q a
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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aBox.add(b,Q,a);
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// register SimpleReasoner
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// b Q a is inferred from a P b, but it is already in the abox
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aBox.add(a,P,b);
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Assert.assertFalse(inf.contains(b,Q,a));
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}
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/*
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* don't infer if it's already in the abox
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*/
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@Test
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public void addABoxAssertion3() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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P.addInverseOf(Q);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register SimpleReasoner
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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// b Q a is inferred from a P b, but it is already in the abox
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aBox.add(a,P,b);
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aBox.add(b,Q,a);
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Assert.assertFalse(inf.contains(b,Q,a));
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}
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/*
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* adding abox data where the property has an inverse and
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* and equivalent property.
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*/
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@Test
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public void addABoxAssertion4() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty R = tBox.createOntProperty("http://test.vivo/R");
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R.setLabel("property R", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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R.addEquivalentProperty(P);
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P.addEquivalentProperty(R);
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P.addInverseOf(Q);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register the SimpleReasoner listener with it
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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// b Q a is inferred from a R b.
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aBox.add(a,R,b);
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Assert.assertTrue(inf.contains(b,Q,a));
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// d P c is inferred from c Q d.
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aBox.add(c,Q,d);
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Assert.assertTrue(inf.contains(d,P,c));
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Assert.assertTrue(inf.contains(d,R,c));
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}
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/*
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* basic scenarios around removing abox data
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*/
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@Test
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public void removedABoxAssertion1() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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OntProperty T = tBox.createOntProperty("http://test.vivo/T");
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Q.setLabel("property T", "en-US");
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P.addInverseOf(Q);
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P.addInverseOf(T);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register the SimpleReasoner listener with it
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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// b Q a is inferred from a P b.
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aBox.add(a,P,b);
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Assert.assertTrue(inf.contains(b,Q,a));
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// d P c is inferred from c Q d and from c T d
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aBox.add(c,Q,d);
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aBox.add(c,T,d);
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Assert.assertTrue(inf.contains(d,P,c));
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aBox.remove(a,P,b);
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Assert.assertFalse(inf.contains(b,Q,a));
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aBox.remove(c,Q,d);
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Assert.assertTrue(inf.contains(d,P,c));
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}
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/*
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* removing abox data with equivalent and inverse properties
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*/
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@Test
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public void removedABoxAssertion2() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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OntProperty T = tBox.createOntProperty("http://test.vivo/T");
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Q.setLabel("property T", "en-US");
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P.addInverseOf(Q);
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Q.addInverseOf(P);
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P.addEquivalentProperty(T);
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T.addEquivalentProperty(P);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register the SimpleReasoner listener with it
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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// b Q a is inferred from a P b and a T b.
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aBox.add(a,P,b);
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aBox.add(a,T,b);
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Assert.assertTrue(inf.contains(b,Q,a));
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Assert.assertFalse(inf.contains(a,P,b));
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aBox.remove(a,P,b);
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Assert.assertTrue(inf.contains(b,Q,a));
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}
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/*
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* removing abox data with equivalent and inverse properties
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*/
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@Test
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public void removedABoxAssertion3() {
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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P.addInverseOf(Q);
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// this is the model to receive inferences
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Model inf = ModelFactory.createDefaultModel();
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// create an ABox and register the SimpleReasoner listener with it
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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aBox.add(a,P,b);
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aBox.register(new SimpleReasoner(tBox, aBox, inf));
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aBox.add(b,Q,a);
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Assert.assertFalse(inf.contains(b,Q,a));
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Assert.assertFalse(inf.contains(a,P,b));
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aBox.remove(a,P,b);
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Assert.assertTrue(inf.contains(a,P,b));
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}
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/*
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* Basic scenario around adding an inverseOf assertion to the
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* TBox
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*/
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@Test
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public void addTBoxInverseAssertion1() throws InterruptedException {
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// Create TBox, ABox and Inference models and register
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// the ABox reasoner listeners with the ABox and TBox
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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OntProperty P = tBox.createOntProperty("http://test.vivo/P");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
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aBox.register(simpleReasoner);
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SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
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tBox.register(simpleReasonerTBoxListener);
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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// abox statements
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aBox.add(a,P,b);
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aBox.add(c,P,d);
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aBox.add(b,Q,a);
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// Assert P and Q as inverses and wait for SimpleReasoner TBox
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// thread to end
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Q.addInverseOf(P);
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tBox.rebind();
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tBox.prepare();
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while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
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Thread.sleep(delay);
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}
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// Verify inferences
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Assert.assertTrue(inf.contains(d,Q,c));
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Assert.assertFalse(inf.contains(b,Q,a));
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simpleReasonerTBoxListener.setStopRequested();
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}
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/*
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* Basic scenario around removing an inverseOf assertion to the
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* TBox
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*/
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@Test
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public void removeTBoxInverseAssertion1() throws InterruptedException {
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// Create TBox, ABox and Inference models and register
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// the ABox reasoner listeners with the ABox and TBox
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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// set up TBox and Abox
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OntProperty P = tBox.createOntProperty("http://test.vivo/propP");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/propQ");
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Q.setLabel("property Q", "en-US");
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Q.addInverseOf(P);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
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aBox.register(simpleReasoner);
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SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
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tBox.register(simpleReasonerTBoxListener);
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// Individuals a, b, c and d
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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// abox statements
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aBox.add(c,P,d);
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Assert.assertTrue(inf.contains(d,Q,c));
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// Remove P and Q inverse relationship and wait for
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// SimpleReasoner TBox thread to end.
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Q.removeInverseProperty(P);
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tBox.rebind();
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tBox.prepare();
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while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
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Thread.sleep(delay);
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}
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// Verify inferences
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Assert.assertFalse(inf.contains(d,Q,c));
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simpleReasonerTBoxListener.setStopRequested();
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}
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/*
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* Basic scenario around recomputing the ABox inferences
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*/
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@Test
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public void recomputeABox1() throws InterruptedException {
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// Create TBox, ABox and Inference models and register
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// the ABox reasoner listeners with the ABox and TBox
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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// set up TBox and Abox
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OntProperty P = tBox.createOntProperty("http://test.vivo/propP");
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P.setLabel("property P", "en-US");
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OntProperty Q = tBox.createOntProperty("http://test.vivo/propQ");
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Q.setLabel("property Q", "en-US");
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Q.addInverseOf(P);
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OntProperty X = tBox.createOntProperty("http://test.vivo/propX");
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P.setLabel("property X", "en-US");
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OntProperty Y = tBox.createOntProperty("http://test.vivo/propY");
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Q.setLabel("property Y", "en-US");
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X.addInverseOf(Y);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
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aBox.register(simpleReasoner);
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SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
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tBox.register(simpleReasonerTBoxListener);
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// Individuals a, b, c and d
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Resource a = aBox.createResource("http://test.vivo/a");
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Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
// abox statements
|
||||
aBox.add(a,P,b);
|
||||
aBox.add(c,X,d);
|
||||
|
||||
simpleReasoner.recompute();
|
||||
|
||||
while (simpleReasoner.isRecomputing()) {
|
||||
Thread.sleep(delay);
|
||||
}
|
||||
|
||||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,Q,a));
|
||||
Assert.assertTrue(inf.contains(d,Y,c));
|
||||
|
||||
simpleReasonerTBoxListener.setStopRequested();
|
||||
}
|
||||
|
||||
//==================================== Utility methods ====================
|
||||
SimpleReasonerTBoxListener getTBoxListener(SimpleReasoner simpleReasoner) {
|
||||
return new SimpleReasonerTBoxListener(simpleReasoner, new Exception().getStackTrace()[1].getMethodName());
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(Model model, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + model.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
model.write(System.out);
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(OntModel ontModel, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + ontModel.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
ontModel.writeAll(System.out,"N3",null);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -26,6 +26,7 @@ public class DataPropertyDaoStub implements DataPropertyDao {
|
|||
// ----------------------------------------------------------------------
|
||||
|
||||
private final Map<String, DataProperty> dpMap = new HashMap<String, DataProperty>();
|
||||
private final Map<String, String> configFilesMap = new HashMap<String, String>();
|
||||
|
||||
public void addDataProperty(DataProperty dataProperty) {
|
||||
if (dataProperty == null) {
|
||||
|
|
@ -40,6 +41,18 @@ public class DataPropertyDaoStub implements DataPropertyDao {
|
|||
dpMap.put(uri, dataProperty);
|
||||
}
|
||||
|
||||
public void setCustomListViewConfigFileName(DataProperty property, String filename) {
|
||||
if (property == null) {
|
||||
throw new NullPointerException("property may not be null.");
|
||||
}
|
||||
|
||||
String uri = property.getURI();
|
||||
if (uri == null) {
|
||||
throw new NullPointerException("uri may not be null.");
|
||||
}
|
||||
|
||||
configFilesMap.put(uri, filename);
|
||||
}
|
||||
// ----------------------------------------------------------------------
|
||||
// Stub methods
|
||||
// ----------------------------------------------------------------------
|
||||
|
|
@ -49,6 +62,17 @@ public class DataPropertyDaoStub implements DataPropertyDao {
|
|||
return dpMap.get(dataPropertyURI);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getCustomListViewConfigFileName(DataProperty dataProperty) {
|
||||
if (dataProperty == null) {
|
||||
return null;
|
||||
}
|
||||
String uri = dataProperty.getURI();
|
||||
if (uri == null) {
|
||||
return null;
|
||||
}
|
||||
return configFilesMap.get(uri);
|
||||
}
|
||||
// ----------------------------------------------------------------------
|
||||
// Un-implemented methods
|
||||
// ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package stubs.edu.cornell.mannlib.vitro.webapp.dao;
|
||||
|
||||
import java.util.HashMap;
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue