--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/GalaxyOWLAPI.java	Sat Oct 06 21:50:39 2012 +0200
@@ -0,0 +1,331 @@
+/**
+ * 
+ */
+package es.upm.fi.dia.oeg.oppl.galaxy;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+import java.util.Set;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
+import org.coode.owlapi.obo.parser.OBOOntologyFormat;
+import org.coode.parsers.BidirectionalShortFormProviderAdapter;
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.elk.owlapi.ElkReasonerFactory;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.expression.OWLEntityChecker;
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
+import org.semanticweb.owlapi.model.AddAxiom;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.InferenceType;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
+import org.semanticweb.owlapi.util.InferredAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredOntologyGenerator;
+import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
+import org.semanticweb.owlapi.util.OWLEntityRenamer;
+import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider;
+import org.semanticweb.owlapi.util.OWLOntologyMerger;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+import org.semanticweb.owlapi.reasoner.Node;
+
+import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+
+/**
+ * A wrapper of the OWL API 
+ * 
+ * @author Mikel Egana Aranguren
+ */
+public class GalaxyOWLAPI {
+	private OWLOntologyManager manager;
+	private OWLOntology ontology;
+	private OWLReasonerFactory reasonerFactory;
+	private OWLReasoner reasoner;
+	
+	public GalaxyOWLAPI (){
+		manager = OWLManager.createOWLOntologyManager();
+	}
+	public OWLOntologyManager getOWLManager(){
+		return manager;
+	}
+	public OWLOntology getMainOntology(){
+		return ontology;
+	}
+	public OWLReasoner getReasoner(){
+		return reasoner;
+	}
+	
+	public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{
+		File owl_file = new File(OWLFilePath);
+		ontology = manager.loadOntologyFromOntologyDocument(owl_file);
+	}
+	
+//	public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{
+//		manager.loadOntologyFromOntologyDocument(importedOntologyIRI);
+//	}
+	
+	// OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy
+	// I have to change Racer settings and OWLLink settings
+//		OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
+//		reasoner = factory.createReasoner(OWL_ontology);
+	
+	public void setReasonerPellet (){
+		reasonerFactory = new PelletReasonerFactory(); 
+		reasoner = reasonerFactory.createReasoner(ontology);
+	}
+	public void setReasonerFaCT (){
+		reasonerFactory = new FaCTPlusPlusReasonerFactory();
+		reasoner = reasonerFactory.createReasoner(ontology);
+	}
+	public void setReasonerHermit (){
+		reasonerFactory = new Reasoner.ReasonerFactory();
+		reasoner = reasonerFactory.createReasoner(ontology);
+	}
+	public void setReasonerElk (){
+	    reasonerFactory = new ElkReasonerFactory();	    
+		Logger.getLogger("org.semanticweb.elk").setLevel(Level.OFF);
+	    reasoner = reasonerFactory.createReasoner(ontology);
+	}
+	public void disposeReasoner(){
+		reasoner.dispose();
+	}
+	public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{
+		OWLOntologyMerger merger = new OWLOntologyMerger(manager);
+//		OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology));
+		IRI mergedOntologyIRI = IRI.create(ontologyIRI);
+//		OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
+		ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
+//		manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
+	}
+	
+	public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
+		Set<OWLOntology> importsClosure = ontology.getImportsClosure();
+		BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());
+        OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
+		ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr);
+		MOSparser.setOWLEntityChecker(entityChecker);
+		return MOSparser.parseClassExpression();
+	}
+	
+	public Set<OWLNamedIndividual> getIndividuals (OWLClassExpression expr){
+		return (reasoner.getInstances(expr, false)).getFlattened();
+	}
+	public Set<OWLClass> getEquivalentClasses (OWLClassExpression expr){
+		Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(expr);
+	    Set<OWLClass> result;
+	    if (expr.isAnonymous()) {
+	        result = equivalentClasses.getEntities();
+	    }
+	    else {
+	        result = equivalentClasses.getEntitiesMinus(expr.asOWLClass());
+	    }
+	    return result;
+	}
+	
+	public Set<OWLClass> getDirectSuperClasses (OWLClassExpression expr){		
+		 return (reasoner.getSuperClasses(expr, true)).getFlattened();
+	}
+	
+	public Set<OWLClass> getAncestors (OWLClassExpression expr){		
+		 return (reasoner.getSuperClasses(expr, false)).getFlattened();
+	}
+	
+	public Set<OWLClass> getDirectSubClasses (OWLClassExpression expr){		
+		 return (reasoner.getSubClasses(expr, true)).getFlattened();
+	}
+	
+	public Set<OWLClass> getDescendants (OWLClassExpression expr){		
+		 return (reasoner.getSubClasses(expr, false)).getFlattened();
+	}
+	
+	//	CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.	
+	
+	public void addCLASS_ASSERTIONS(){
+		reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
+		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+		gens.add(new InferredClassAssertionAxiomGenerator());
+		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+		iog.fillOntology(manager, ontology);
+	}
+	
+	//	CLASS_HIERARCHY Denotes the computation of the class hierarchy.	
+	
+	public void addCLASS_HIERARCHY(){
+		reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
+		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+		gens.add(new InferredSubClassAxiomGenerator());
+		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+		iog.fillOntology(manager, ontology);
+	}
+	
+	//	DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology.
+//	public void addDATA_PROPERTY_ASSERTIONS(){
+//		reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS);
+//		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+//		gens.add(new InferredDataPropertyAxiomGenerator()); 
+//		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+//		iog.fillOntology(manager, ontology);
+//	}
+	
+	//	DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy.
+	
+	public void addDATA_PROPERTY_HIERARCHY(){
+		reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY);
+		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+		gens.add(new InferredSubDataPropertyAxiomGenerator());
+		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+		iog.fillOntology(manager, ontology);
+	}
+	
+	//	DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology.
+	
+//	public void addDIFFERENT_INDIVIDUALS(){
+//		reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS);
+//		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+//		gens.add(new Inferred);
+//		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+//		iog.fillOntology(manager, ontology);
+//	}
+	
+	//	DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology.
+	
+	public void addDISJOINT_CLASSES(){
+		reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES);
+		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+		gens.add(new InferredDisjointClassesAxiomGenerator());
+		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+		iog.fillOntology(manager, ontology);
+	}
+	
+	//	OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology.
+	
+//	public void addOBJECT_PROPERTY_ASSERTIONS(){
+//		reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS);
+//		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+//		gens.add(new InferredObjectPropertyAxiomGenerator<OWLAxiom>() {
+//		};());
+//		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+//		iog.fillOntology(manager, ontology);
+//	}
+	
+	//	OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy.
+	
+	public void addOBJECT_PROPERTY_HIERARCHY(){
+		reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);
+		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+		gens.add(new InferredSubObjectPropertyAxiomGenerator());
+		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+		iog.fillOntology(manager, ontology);
+	}
+	
+	//	SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology.
+	
+//	public void addSAME_INDIVIDUAL(){
+//		reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL);
+//		List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+//		gens.add(new Infer);
+//		InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+//		iog.fillOntology(manager, ontology);
+//	}
+	
+	public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{
+		// OWL format
+		if(OWL){
+			manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
+		}
+		// OBO format
+		else{
+			// OWL API generates bad OBO but OBOformat doesn't work either so I correct the OWL API problems (More predictable) in a temporary file
+			// Very inefficient but no time for another solution
+						
+			OWLDataFactory factory = manager.getOWLDataFactory();
+			OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());
+			OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
+			for(OWLClass cls : ontology.getClassesInSignature()){
+			// Remove annotations (OWL API generates bad OBO annotations)
+							
+			// Keep rdfs:label
+			String class_name = null;
+			for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){
+				if (annotation.getValue() instanceof OWLLiteral) {
+					OWLLiteral val = (OWLLiteral) annotation.getValue();
+					class_name = val.getLiteral();
+				}
+			}
+										
+//			I have to remove all the annotations cause I don't know which ones are rendered properly
+			manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));
+							
+			// Add rdfs:label again
+			OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(
+			OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));
+			OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);
+			manager.applyChange(new AddAxiom(ontology, ax));
+							
+			// Rename entities
+			String cls_IRI = cls.getIRI().toString();
+			String cls_proper_IRI = cls_IRI.replace("_", ":");
+			List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));
+			manager.applyChanges(changes);
+			}
+						
+			File file = new File("tmp.obo");
+			manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));
+			BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));		
+			Scanner input = new Scanner(file);
+			String buffer = "";
+
+			while(input.hasNext()){
+				String nextLine = input.nextLine();
+				if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){
+					if(buffer.isEmpty()){
+						bw.write(buffer);
+						bw.newLine();
+					}
+				}
+				if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){
+					if(!nextLine.isEmpty() && !buffer.contains("relationship:")){
+						bw.write(nextLine);
+						bw.newLine();
+					}
+				}
+				buffer = nextLine;
+			}
+			input.close();
+			bw.close();
+			file.delete();
+		}
+	}	
+}