development for NIHVIVO-2410 (specific type inference in lieu of moniker)
This commit is contained in:
stellamit
parent
73e0916a04
commit
132cbdce2c
2 changed files with 303 additions and 41 deletions
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@ -9,15 +9,20 @@ 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.datatypes.xsd.XSDDatatype;
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import com.hp.hpl.jena.ontology.AnnotationProperty;
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import com.hp.hpl.jena.ontology.OntClass;
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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.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.vocabulary.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
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@ -28,6 +33,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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private Resource objectProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#ObjectProperty");
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private static final String mostSpecificTypePropertyURI = "http://vivoweb.org/ontology/core#mostSpecificType";
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@Before
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public void suppressErrorOutput() {
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@ -35,7 +41,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Turn off log messages to console
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setLoggerLevel(SimpleReasoner.class, Level.OFF);
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}
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/*
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* Test that when an individual is asserted to be of a type,
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* its asserted type is not added to the inference graph
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@ -46,6 +52,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Create a Tbox with a simple class hierarchy. B is a subclass of A.
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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@ -84,6 +91,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Create a Tbox with a simple class hierarchy. D and E are subclasses
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// of C. B and C are subclasses of A. Pellet will compute TBox inferences.
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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@ -137,6 +145,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -184,6 +193,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -223,6 +233,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -271,6 +282,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// and B is a subclass of A. Pellet will compute TBox inferences.
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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@ -336,6 +348,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -403,6 +416,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -462,6 +476,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -547,6 +562,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -589,6 +605,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -630,6 +647,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -684,6 +702,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -726,6 +745,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -782,6 +802,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -849,6 +870,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
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// Pellet will compute TBox inferences
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OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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Model inf = ModelFactory.createDefaultModel();
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@ -933,6 +955,209 @@ public class SimpleReasonerTest extends AbstractTestClass {
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}
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@Test
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/*
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* Test computation of mostSpecificType annotations in response
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* to an added/removed ABox type assertion.
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*/
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public void mstTest1(){
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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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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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tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
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// Set up the Tbox with a class hierarchy. C is a subclass of A
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// and Y. D and E are subclasses C. B is a subclass of D.
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// Pellet will compute TBox inferences.
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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OntClass classB = tBox.createClass("http://test.vivo/B");
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classB.setLabel("class B", "en-US");
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OntClass classC = tBox.createClass("http://test.vivo/C");
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classC.setLabel("class C", "en-US");
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OntClass classD = tBox.createClass("http://test.vivo/D");
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classD.setLabel("class D", "en-US");
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OntClass classE = tBox.createClass("http://test.vivo/E");
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classE.setLabel("class E", "en-US");
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OntClass classY = tBox.createClass("http://test.vivo/Y");
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classE.setLabel("class Y", "en-US");
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classY.addSubClass(classC);
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classA.addSubClass(classC);
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classC.addSubClass(classD);
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classC.addSubClass(classE);
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classD.addSubClass(classB);
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// Add the statement individual x is of type Y to the ABox
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Resource ind_x = aBox.createResource("http://test.vivo/x");
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aBox.add(ind_x, RDF.type, classD);
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// Verify ind_x mostSpecificType annotation for D
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
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// Verify ind_x doesn't have a mostSpecificType annotation for
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// A, Y, C, E or B.
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classA.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classY.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classC.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classE.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classB.getURI(), XSDDatatype.XSDanyURI)));
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aBox.remove(ind_x, RDF.type, classD); // retract assertion that x is of type D.
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// Verify that D is not longer the most specific type
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
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}
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@Test
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/*
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* Test computation of mostSpecificType annotations in response
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* to an added ABox type assertion.
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*/
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public void mstTest2(){
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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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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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tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
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// Set up the Tbox with a class hierarchy. B is a subclass of A,
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// C is a subclass of B, and A is a subclass of C.
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// Pellet should infer these three classes to be equivalent.
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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OntClass classB = tBox.createClass("http://test.vivo/B");
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classB.setLabel("class B", "en-US");
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OntClass classC = tBox.createClass("http://test.vivo/C");
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classC.setLabel("class C", "en-US");
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classA.addSubClass(classB);
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classB.addSubClass(classC);
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classC.addSubClass(classA);
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// Add the statement individual x is of type B to the ABox
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Resource ind_x = aBox.createResource("http://test.vivo/x");
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aBox.add(ind_x, RDF.type, classB);
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StmtIterator stmtIterator = aBox.listStatements(ind_x, mostSpecificType, (RDFNode)null);
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// Verify ind_x mostSpecificType annotation for A, B and C
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classA.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classB.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classC.getURI(), XSDDatatype.XSDanyURI)));
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}
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@Test
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/*
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* Test computation of mostSpecificType annotations in response
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* to an added/removed TBox assertions.
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*/
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public void mstTest3(){
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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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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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tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
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OntClass OWL_THING = tBox.createClass(OWL.Thing.getURI());
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AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
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// Set up the Tbox with classes A, B, C, D,
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// E, F and G
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OntClass classA = tBox.createClass("http://test.vivo/A");
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classA.setLabel("class A", "en-US");
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OntClass classB = tBox.createClass("http://test.vivo/B");
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classB.setLabel("class B", "en-US");
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OntClass classC = tBox.createClass("http://test.vivo/C");
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classC.setLabel("class C", "en-US");
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OntClass classD = tBox.createClass("http://test.vivo/D");
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classD.setLabel("class D", "en-US");
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OntClass classE = tBox.createClass("http://test.vivo/E");
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classE.setLabel("class E", "en-US");
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OntClass classF = tBox.createClass("http://test.vivo/F");
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classE.setLabel("class F", "en-US");
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OntClass classG = tBox.createClass("http://test.vivo/G");
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classE.setLabel("class G", "en-US");
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// add individuals x, y and z to the aBox
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Resource ind_x = aBox.createResource("http://test.vivo/x");
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Resource ind_y = aBox.createResource("http://test.vivo/y");
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aBox.add(ind_x, RDF.type, OWL_THING);
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aBox.add(ind_y, RDF.type, classD);
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(OWL.Thing.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
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aBox.add(ind_x, RDF.type, classC);
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aBox.add(ind_y, RDF.type, classF);
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Assert.assertFalse(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(OWL.Thing.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_x, mostSpecificType, ResourceFactory.createTypedLiteral(classC.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classF.getURI(), XSDDatatype.XSDanyURI)));
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// Set up a class hierarchy.
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// Pellet will compute TBox inferences.
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classA.addSubClass(classB);
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classA.addSubClass(classC);
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classA.addSubClass(classD);
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classC.addSubClass(classE);
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classD.addSubClass(classF);
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classD.addSubClass(classG);
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Assert.assertFalse(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
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Assert.assertTrue(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classF.getURI(), XSDDatatype.XSDanyURI)));
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// If F is removed as a subclass of D, then D should once again be a most specific type
|
||||
// for y.
|
||||
classD.removeSubClass(classF);
|
||||
Assert.assertTrue(aBox.contains(ind_y, mostSpecificType, ResourceFactory.createTypedLiteral(classD.getURI(), XSDDatatype.XSDanyURI)));
|
||||
|
||||
}
|
||||
// To help in debugging the unit test
|
||||
void printModels(OntModel ontModel) {
|
||||
|
||||
|
|
|
|||
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Add table
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Reference in a new issue