OWLAPI loading and saving OWL individiuals using FOAF and PROV

pom.xml

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<groupId>com.example.owlapitest</groupId>
	<artifactId>owlapitest</artifactId>
	<version>0.0.1-SNAPSHOT</version>
	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>2.3.2</version>
				<configuration>
					<source>1.7</source>
					<target>1.7</target>
				</configuration>
			</plugin>
		</plugins>
	</build>
	<dependencies>
		<dependency>
			<groupId>net.sourceforge.owlapi</groupId>
			<artifactId>owlapi-apibinding</artifactId>
			<version>3.4.1</version>	
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.10</version>
			<scope>test</scope>
		</dependency>
	</dependencies>
</project>

TestFOAFPROV.java

package com.example.owlapitest;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Set;

import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.junit.Test;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AddImport;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLImportsDeclaration;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.util.DefaultPrefixManager;

public class TestFOAFPROV {


	private static Path testFile;

	@Test
	public void saveFile() throws Exception {
		if (testFile != null) {
			// Only run once
			return;
		}
		
		OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
		OWLDataFactory factory = manager.getOWLDataFactory();

		// Create ontology with two imports
		IRI ontologyIRI = IRI.create("prov.ttl");
		OWLOntology ontology = manager.createOntology(ontologyIRI);
		IRI provIri = IRI.create("http://www.w3.org/ns/prov");
		OWLOntology prov = manager.loadOntology(provIri);
		IRI foafIri = IRI.create("http://xmlns.com/foaf/0.1");
		OWLOntology foaf = manager.loadOntology(foafIri);

		DefaultPrefixManager pm = new DefaultPrefixManager();
		pm.setDefaultPrefix(ontologyIRI + "#");
		pm.setPrefix("foaf:", "http://xmlns.com/foaf/0.1/");
		pm.setPrefix("prov:", "http://www.w3.org/ns/prov#");

		// NOTE: We can't use the correct URIs (as above) here, as it will
		// wrongly be output as
		// "prov:null" in the Turtle output
		OWLImportsDeclaration provImport = factory
				.getOWLImportsDeclaration(provIri);
		manager.applyChange(new AddImport(ontology, provImport));
		OWLImportsDeclaration foafImport = factory
				.getOWLImportsDeclaration(foafIri);
		manager.applyChange(new AddImport(ontology, foafImport));

		OWLNamedIndividual index = factory.getOWLNamedIndividual(IRI
				.create("index.html"));
		manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(index));

		
		OWLClass entityClass = factory.getOWLClass("prov:Entity", pm);
		manager.addAxiom(ontology,
				factory.getOWLClassAssertionAxiom(entityClass, index));

		OWLObjectProperty wasAttributedTo = factory.getOWLObjectProperty(
				"prov:wasAttributedTo", pm);
		OWLIndividual me = factory.getOWLNamedIndividual(IRI
				.create("http://soiland-reyes.com/stian/#me"));
		// The order of these parameters is a bit odd.. predicate/subject/object
		manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(
				wasAttributedTo, index, me));

		OWLClass personClass = factory.getOWLClass("foaf:Person", pm);
		manager.addAxiom(ontology,
				factory.getOWLClassAssertionAxiom(personClass, me));

		// Note: Using foaf:lastName instead of foaf:name
		// because it is an invalid dataproperty subproperty of annotation property: 
		// 
		// http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Custom-import-ontology-button-problem-td3684903.html
		
		OWLDataProperty name = factory.getOWLDataProperty("foaf:lastName", pm);
		OWLDataPropertyAssertionAxiom dataPropertyAssertion = factory
				.getOWLDataPropertyAssertionAxiom(name, me,
						"Soiland-Reyes");
		manager.addAxiom(ontology, dataPropertyAssertion);

		testFile = Files.createTempFile("prov", ".ttl");
		
		RDFXMLOntologyFormat rdfFormat = new RDFXMLOntologyFormat();
		rdfFormat.copyPrefixesFrom(pm);
		rdfFormat.setDefaultPrefix(ontologyIRI + "#");
		
		TurtleOntologyFormat turtleFormat = new TurtleOntologyFormat();
		turtleFormat.copyPrefixesFrom(pm);
		turtleFormat.setDefaultPrefix(ontologyIRI + "#");
		
		try (OutputStream outputStream = Files.newOutputStream(testFile)) {
			manager.saveOntology(ontology, turtleFormat,				
					outputStream);
		}
		System.out.println(testFile);
	}

	@Test
	public void loadFile() throws Exception {
		if (testFile == null) { 
			// Run save first
			saveFile();
		}
		
		OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
		
		// Create ontology with two imports
		IRI provIri = IRI.create("http://www.w3.org/ns/prov");
		OWLOntology prov = manager.loadOntology(provIri);
		IRI foafIri = IRI.create("http://xmlns.com/foaf/0.1");
		OWLOntology foaf = manager.loadOntology(foafIri);

		
		OWLDataFactory factory = manager.getOWLDataFactory();

		DefaultPrefixManager pm = new DefaultPrefixManager();
		pm.setPrefix("foaf:", "http://xmlns.com/foaf/0.1/");
		pm.setPrefix("prov:", "http://www.w3.org/ns/prov#");

		OWLClass entityClass = factory.getOWLClass("prov:Entity", pm);

		OWLOntology ontology;
		try (InputStream inStream = Files.newInputStream(testFile)) {
			ontology = manager.loadOntologyFromOntologyDocument(inStream);
			// Don't  load from the File - as it will make URIs absolute 
			// when loading from RDF/XML (fine from Turtle..)
		}
		
		for (OWLIndividual entity : entityClass.getIndividuals(ontology)) {
			System.out.println("Entity " + entity);
			assertEquals("index.html", entity.asOWLNamedIndividual().getIRI()
					.toString());
			OWLObjectProperty wasAttributedTo = factory.getOWLObjectProperty(
					"prov:wasAttributedTo", pm);
			Set<OWLIndividual> attributed = entity.getObjectPropertyValues(
					wasAttributedTo, ontology);
			OWLIndividual me = attributed.iterator().next();
			
			System.out.println("  prov:wasAttributedTo " + me);
			assertEquals("http://soiland-reyes.com/stian/#me", me
					.asOWLNamedIndividual().getIRI().toString());

			OWLClass personClass = factory.getOWLClass("foaf:Person", pm);
			assertTrue(me.getTypes(ontology).contains(personClass));

			
		
			OWLDataProperty name = factory.getOWLDataProperty("foaf:lastName", pm);
			assertEquals("Soiland-Reyes",
					me.getDataPropertyValues(name, ontology).iterator().next()
							.getLiteral());

		}		
	}

}