comparison OPPL/src/OWLQueryGalaxy.java @ 18:d3616fac4ca5 draft

Elk support added

17:c9e01f86b07c

	 * @throws ParserException 
	 */
	public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
		// Get the arguments from command-line
		String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
		String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
		
		String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
		String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
		String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
		

		}
		// FaCTPlusPlus
		else if (reasoner_type.equals("FaCTPlusPlus")){
			galaxyowlapi.setReasonerFaCT();
		}
		// HermiT
		else{
			galaxyowlapi.setReasonerHermit();
		}

		OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
		
		// Execute query and print results
		if(Answer_type.equals("Individuals")){
			Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
			for(OWLNamedIndividual ind : inds){
				print_result_entity(ind.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("EquivalentClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("DirectSuperClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("Ancestors")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("DirectSubClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		// Descendants
		else {
			Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}	
	}

18:d3616fac4ca5

	 * @throws ParserException 
	 */
	public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
		// Get the arguments from command-line
		String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
		String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
		
		String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
		String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
		String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
		

		}
		// FaCTPlusPlus
		else if (reasoner_type.equals("FaCTPlusPlus")){
			galaxyowlapi.setReasonerFaCT();
		}
		// Elk
		else if (reasoner_type.equals("Elk")){
			galaxyowlapi.setReasonerElk();
		}
		// HermiT
		else{
			galaxyowlapi.setReasonerHermit();
		}

		OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
		
		// Execute query and print results
		if(Answer_type.equals("Individuals")){
			Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLNamedIndividual ind : inds){
				print_result_entity(ind.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("EquivalentClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("DirectSuperClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("Ancestors")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		else if (Answer_type.equals("DirectSubClasses")) {
			Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}
		// Descendants
		else {
			Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
			galaxyowlapi.disposeReasoner();
			for(OWLClass cls : answer_classes){
				print_result_entity(cls.getIRI(), Answer_render);
			}
		}	
	}