@BeforeClass
public static void beforeClass() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	OWLOntologyIRIMapper mapper = new CatalogXmlIRIMapper("src/test/resources/rules/ontology/extensions/catalog-v001.xml");
	pw.addIRIMapper(mapper);
	all = new OWLGraphWrapper(pw.parseOWL(IRI.create("http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl")));
	classes = new HashSet<OWLClass>();
	for(OWLClass cls : all.getSourceOntology().getClassesInSignature(true)) {
		String id = all.getIdentifier(cls);
		if (id.startsWith("GO:")) {
			classes.add(cls);
		}
	}
	rat = all.getOWLClassByIdentifier(TaxonTools.NCBI + "10114");
	yeast = all.getOWLClassByIdentifier(TaxonTools.NCBI + "4932");
}
 

@BeforeClass
public static void setUpBeforeClass() throws Exception {
	elkLogger = Logger.getLogger("org.semanticweb.elk");
	elkLogLevel = elkLogger.getLevel();
	elkLogger.setLevel(Level.ERROR);
	
	String qcfile = LOCATION + "annotation_qc.xml";
	String xrfabbslocation = LOCATION + "GO.xrf_abbs";
	ParserWrapper p = new ParserWrapper();
	
	OWLOntologyIRIMapper mapper = new CatalogXmlIRIMapper(getResource("rules/ontology/extensions/catalog-v001.xml"));
	p.addIRIMapper(mapper);
	
	OWLOntology goTaxon = p.parse("http://purl.obolibrary.org/obo/go/extensions/go-plus.owl");
	OWLOntology gorel = p.parse("http://purl.obolibrary.org/obo/go/extensions/gorel.owl");
	OWLGraphWrapper graph = new OWLGraphWrapper(goTaxon);
	graph.addImport(gorel);
	eco = EcoMapperFactory.createTraversingEcoMapper(p, getResourceIRIString("eco.obo")).getMapper();
	
	AnnotationRulesFactory rulesFactory = new GoAnnotationRulesFactoryImpl(
			qcfile, xrfabbslocation, graph, eco, null);
	engine = new AnnotationRulesEngine(rulesFactory, true, false);
}
 

@BeforeClass
public static void setUpBeforeClass() throws Exception {
	elkLogger = Logger.getLogger("org.semanticweb.elk");
	elkLogLevel = elkLogger.getLevel();
	elkLogger.setLevel(Level.ERROR);
	
	String qcfile = LOCATION + "annotation_qc.xml";
	String xrfabbslocation = LOCATION + "GO.xrf_abbs";
	
	ParserWrapper p = new ParserWrapper();
	
	OWLOntologyIRIMapper mapper = new CatalogXmlIRIMapper(getResource("rules/ontology/extensions/catalog-v001.xml"));
	p.addIRIMapper(mapper);
	
	OWLOntology goTaxon = p.parse("http://purl.obolibrary.org/obo/go/extensions/go-plus.owl");
	OWLOntology gorel = p.parse("http://purl.obolibrary.org/obo/go/extensions/gorel.owl");
	OWLGraphWrapper graph = new OWLGraphWrapper(goTaxon);
	graph.addImport(gorel);
	eco = EcoMapperFactory.createTraversingEcoMapper(p, getResourceIRIString("eco.obo")).getMapper();
	
	AnnotationRulesFactory rulesFactory = new GoAnnotationRulesFactoryImpl(
			qcfile, xrfabbslocation, graph, eco, null);
	engine = new AnnotationRulesEngine(rulesFactory, true, false);
}
 

@BeforeClass
public static void beforeClass() throws Exception {
	owltoolsLogger = Logger.getLogger("owltools");
	owltoolsLogLevel = owltoolsLogger.getLevel();
	owltoolsLogger.setLevel(Level.ERROR);
	AbstractEcoRuleTestHelper.beforeClass();
	if (graph == null) {
		ParserWrapper p = new ParserWrapper();
		OWLOntologyIRIMapper mapper = new CatalogXmlIRIMapper(getResource("rules/ontology/extensions/catalog-v001.xml"));
		p.addIRIMapper(mapper);
		OWLOntology goTaxon = p.parse("http://purl.obolibrary.org/obo/go/extensions/go-plus.owl");
		OWLOntology gorel = p.parse("http://purl.obolibrary.org/obo/go/extensions/gorel.owl");
		
		graph = new OWLGraphWrapper(goTaxon);
		graph.addImport(gorel);
	}
}
 

public void addIRIMappers(List<OWLOntologyIRIMapper> mappers) {
    List<OWLOntologyIRIMapper> reverse = new ArrayList<OWLOntologyIRIMapper>(mappers);
    Collections.reverse(reverse);
    for (OWLOntologyIRIMapper mapper : reverse) {
        addIRIMapper(mapper);
    }
}
 

/**
 * Loading ontologies from the test resources
 * 
 * @param man
 * @param name
 * @return the loaded ontology
 * @throws URISyntaxException
 * @throws OWLOntologyCreationException
 */
private OWLOntology loadOntology(OWLOntologyManager man, String name)
		throws URISyntaxException, OWLOntologyCreationException {

	final URI ontologyRoot = getClass().getClassLoader()
			.getResource("empty_import").toURI();

	OWLOntologyIRIMapper iriMapper = new ThisIRIMapper(ontologyRoot.toString());
	
	man.setIRIMappers(Collections.singleton(iriMapper));

	final URI mainOntology = getClass().getClassLoader()
			.getResource("empty_import/" + name).toURI();

	return man.loadOntologyFromOntologyDocument(new File(mainOntology));

}
 

/**
 * Loading ontologies from the test resources
 * 
 * @param man
 * @param name
 * @return the loaded ontology
 * @throws URISyntaxException
 * @throws OWLOntologyCreationException
 */
private OWLOntology loadOntology(OWLOntologyManager man, String name)
		throws URISyntaxException, OWLOntologyCreationException {

	final URI ontologyRoot = getClass().getClassLoader()
			.getResource("ontologies").toURI();

	OWLOntologyIRIMapper iriMapper = new ThisIRIMapper(
			ontologyRoot.toString());

	man.setIRIMappers(Collections.singleton(iriMapper));

	final URI mainOntology = getClass().getClassLoader()
			.getResource("ontologies/" + name).toURI();

	return man.loadOntologyFromOntologyDocument(new File(mainOntology));

}
 

/**
 * Loading ontologies from the test resources
 * 
 * @param man
 * @param name
 * @return the loaded ontology
 * @throws URISyntaxException
 * @throws OWLOntologyCreationException
 */
private OWLOntology loadOntology(OWLOntologyManager man, String name)
		throws URISyntaxException, OWLOntologyCreationException {

	final URI ontologyRoot = getClass().getClassLoader()
			.getResource("ontologies").toURI();

	OWLOntologyIRIMapper iriMapper = new ThisIRIMapper(ontologyRoot.toString());
	man.setIRIMappers(Collections.singleton(iriMapper));

	final InputStream mainOntology = getClass().getClassLoader()
			.getResourceAsStream("ontologies/" + name);

	return man.loadOntologyFromOntologyDocument(mainOntology);

}
 

public void addIRIMapper(OWLOntologyIRIMapper mapper) {
    manager.getIRIMappers().add(mapper);
    mappers.add(0, mapper);
}
 

public void removeIRIMapper(OWLOntologyIRIMapper mapper) {
    manager.getIRIMappers().remove(mapper);
    mappers.remove(mapper);
}
 

public List<OWLOntologyIRIMapper> getIRIMappers() {
    return Collections.unmodifiableList(mappers);
}
 

public void initOntology()
{
	try
	{
		//Auxiliar structures
		//map_owl_relexwords = new HashMap<String,OWLIndividual>();
		map_owl_properties = new HashMap<String,OWLProperty>();

		// OWLOntologyManager that manages a set of ontologies
		manager = OWLManager.createOWLOntologyManager();

		// URI of the ontology
		ontologyURI = URI.create("http://student.dei.uc.pt/~racosta/relex/owl_format.owl");

		// Pphysical URI
		physicalURI = URI.create("file:/media/Docs/uc/MSc-2/SW/Project/ontologies/relex2.owl");

		// Set up a mapping, which maps the ontology URI to the physical URI
		OWLOntologyIRIMapper mapper = new SimpleIRIMapper(IRI.create(ontologyURI),IRI.create(physicalURI));
		manager.addIRIMapper(mapper);

		// Now create the ontology - we use the ontology URI
		ontology = manager.createOntology(IRI.create(physicalURI));
		//Data factory, allows to manipulate ontology data
		factory = manager.getOWLDataFactory();

		sentence = factory.getOWLClass(IRI.create(ontologyURI + "#Sentence"));
		word = factory.getOWLClass(IRI.create(ontologyURI + "#Word"));
		//relex_word = factory.getOWLClass(IRI.create(ontologyURI + "#Relex_word"));

		//Generic properties for classes
		has = factory.getOWLObjectProperty(IRI.create(ontologyURI + "#relex_has"));
		//map_owl_properties.put("type",factory.getOWLObjectProperty(IRI.create(ontologyURI + "#type")));

		// word is subclass of phrase
		//OWLAxiom subclassing = factory.getOWLSubClassAxiom(word, sentence);

		// Add the axiom to the ontology
		//AddAxiom addAxiom = new AddAxiom(ontology, subclassing);
		// We now use the manager to apply the change
		//manager.applyChange(addAxiom);

		//2º Add the predefined properties

		/*map_owl_properties.put("tense",factory.getOWLObjectProperty(IRI.create(ontologyURI + * "#p_tense")));
		map_owl_properties.put("index",factory.getOWLDataProperty(IRI.create(ontologyURI + "#p_index")));
		//Add possible relex words
		map_owl_relexwords.put("masculine",factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_masculine")));
		map_owl_relexwords.put("feminine",factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_feminine")));
		map_owl_relexwords.put("person",factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_person")));
		map_owl_relexwords.put("neuter",factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_neuter")));*/

		/*OWLObjectProperty number = factory.getOWLObjectProperty(IRI.create(ontologyURI + "#number"));
		OWLObjectProperty tense = factory.getOWLObjectProperty(IRI.create(ontologyURI + "#tense"));
		OWLObjectProperty query = factory.getOWLObjectProperty(IRI.create(ontologyURI + "#query"));
		OWLObjectProperty quantification = factory.getOWLObjectProperty(IRI.create(ontologyURI + "#quantification"));*/

		// Add axioms to the ontology
		//OWLAxiom genderax = factory.getOWLObjectProperty(infinitive);

		//Phrase Individuals
		/*phr_type_map_owl = new HashMap<String,OWLIndividual>();
		phr_type_map_owl.put("Adverbial Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_adjective")));
		phr_type_map_owl.put("Adverbial Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_adverb")));
		phr_type_map_owl.put("Noun Phrase",      factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_noun")));
		phr_type_map_owl.put("Prepositional Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_prepositional")));
		phr_type_map_owl.put("Particle",         factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_particle")));
		phr_type_map_owl.put("Quantifier Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_quantifier")));
		phr_type_map_owl.put("Clause",           factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_clause")));
		phr_type_map_owl.put("Subordinate Clause", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_subordinate")));
		phr_type_map_owl.put("Subject Inverted", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_inverted")));
		phr_type_map_owl.put("Sentence",         factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_root")));
		phr_type_map_owl.put("Verb Phrase",      factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_verb")));
		phr_type_map_owl.put("Wh-Adverb Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_wh-adverb")));
		phr_type_map_owl.put("Wh-Noun Phrase",   factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_wh-noun")));
		phr_type_map_owl.put("Wh-Prepositional Phrase", factory.getOWLNamedIndividual(IRI.create(ontologyURI + "#rw_wh-prep")));*/

		//Add all the phr_type_map_owl Individuals to the Relex_word Class
		/*Set<String> s = phr_type_map_owl.keySet();
		for (Iterator<String> it = s.iterator(); it.hasNext();)
		{
			manager.applyChange(new AddAxiom(ontology, factory.getOWLClassAssertionAxiom(phr_type_map_owl.get(it.next()), relex_word)));
		}

		//Add all the map_owl_relexwords Individuals to the Relex_word Class
		s = map_owl_relexwords.keySet();
		for (Iterator<String> it = s.iterator(); it.hasNext();)
		{
			manager.applyChange(new AddAxiom(ontology, factory.getOWLClassAssertionAxiom(map_owl_relexwords.get(it.next()), relex_word)));
		}*/

	}
	catch (OWLException e)
	{
		e.printStackTrace();
	}
}