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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.ontology;
import junit.framework.TestCase;
import org.biojava.utils.ChangeVetoException;
/**
* Tests for Ontology.
*
* @author Thomas Down
* @author Matthew Pocock
* @author Moses Hohman
* @since 1.4
*/
public class OntologyTest extends TestCase {
private String name;
private String description;
private Ontology onto;
private Term animal;
private Term fish;
private Term mammal;
private Term human;
private Term isa;
private Triple fish_isa_animal;
private Triple mammal_isa_animal;
private Triple human_isa_mammal;
protected void setUp() throws Exception {
name = "Tester";
description = "Our Description";
onto = OntoTools.getDefaultFactory().createOntology(name, description);
isa = onto.importTerm(OntoTools.IS_A, null);
animal = onto.createTerm("Animal", "An animal");
fish = onto.createTerm("Fish", "A swimming, cold-blooded thingy");
mammal = onto.createTerm("Mammal", "A milk-producing quadraped");
human = onto.createTerm("Human", "Us");
fish_isa_animal = onto.createTriple(fish, animal, isa, null, null);
mammal_isa_animal = onto.createTriple(mammal, animal, isa, null, null);
human_isa_mammal = onto.createTriple(human, mammal, isa, null, null);
}
// basic properties
public void testName() {
assertEquals(onto.getName(), name);
}
public void testDescription() {
assertEquals(onto.getDescription(), description);
}
//terms
public void testTermsSize() {
assertEquals(8, onto.getTerms().size());
}
public void testTermsContainAnimal() {
assertTrue(onto.getTerms().contains(animal));
}
public void testTermsContainFish() {
assertTrue(onto.getTerms().contains(fish));
}
public void testTermsContainMammal() {
assertTrue(onto.getTerms().contains(mammal));
}
public void testTermsContainHuman() {
assertTrue(onto.getTerms().contains(human));
}
//terms by name
public void testGetAnimalByName() {
assertEquals(animal, onto.getTerm("Animal"));
}
// triples
public void testGetAllTriplesSize() {
assertEquals(3, onto.getTriples(null, null, null).size());
}
public void testGetAllTriplesContainsFishIsaAnimal() {
assertTrue(onto.getTriples(null, null, null).contains(fish_isa_animal));
}
public void testGetAllTriplesContainsMammalIsaAnimal() {
assertTrue(onto.getTriples(null, null, null).contains(mammal_isa_animal));
}
public void testGetAllTriplesContainsHumanIsaMammal() {
assertTrue(onto.getTriples(null, null, null).contains(human_isa_mammal));
}
// triple searching
public void testTripleSearchingByObject() {
assertEquals(2, onto.getTriples(null, animal, null).size());
assertEquals(1, onto.getTriples(null, mammal, null).size());
assertEquals(0, onto.getTriples(null, human, null).size());
}
public void testTripleSearchBySubject() {
assertEquals(1, onto.getTriples(onto.getTerm("Human"), null, null).size());
}
public void testTripleSearchingByRelation() {
assertEquals(3, onto.getTriples(null, null, isa).size());
}
public void testTripleSearchingWithAllTerms() {
assertEquals(1, onto.getTriples(human, mammal, isa).size());
assertEquals(0, onto.getTriples(human, animal, isa).size());
}
public void testTripleSearchForSameTermWithDifferentCriteria() {
assertEquals(onto.getTriples(human, null, isa), onto.getTriples(null, mammal, isa));
}
public void testCannotCreateDuplicateTerm() throws ChangeVetoException {
try {
onto.createTerm("Human", "Us");
fail("should have thrown an AlreadyExistsException");
} catch (AlreadyExistsException expected) {
}
}
public void testCannotCreateTripleTermWithForeignSubject() throws OntologyException, ChangeVetoException {
try {
Ontology onto2 = OntoTools.getDefaultFactory().createOntology("other", "");
onto.createTriple(onto2.createTerm("foreign term", ""), human, isa, null, null);
fail("Should have thrown an IllegalArgumentException");
} catch (IllegalArgumentException expected) {
}
}
public void testCannotCreateTripleTermWithForeignObject() throws OntologyException, ChangeVetoException {
try {
Ontology onto2 = OntoTools.getDefaultFactory().createOntology("other", "");
onto.createTriple(fish, onto2.createTerm("foreign term", ""), isa, null, null);
fail("Should have thrown an IllegalArgumentException");
} catch (IllegalArgumentException expected) {
}
}
public void testCannotCreateTripleTermWithForeignRelation() throws OntologyException, ChangeVetoException {
try {
Ontology onto2 = OntoTools.getDefaultFactory().createOntology("other", "");
onto.createTriple(human, fish, onto2.createTerm("wants a", ""), null, null);
fail("Should have thrown an IllegalArgumentException");
} catch (IllegalArgumentException expected) {
}
}
}
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