createOntology.java

package plugins.harmonizationPlugin;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.semanticweb.owlapi.apibinding.OWLManager;
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.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
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.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.util.OWLEntityRenamer;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;

import plugins.HarmonizationComponent.OWLFunction;

public class createOntology
{

	private OWLOntologyManager manager;
	private OWLOntology referenceOntology;
	private OWLOntology createdOntology;
	private OWLDataFactory factory;
	private OWLFunction owlFunction;
	private HashMap<String, OWLClass> labelToOWLClass;
	private HashMap<String, OWLClass> synonymsToOWLClass;

	public createOntology() throws OWLOntologyCreationException, OWLOntologyStorageException
	{

		manager = OWLManager.createOWLOntologyManager();

		factory = manager.getOWLDataFactory();

		owlFunction = new OWLFunction(factory, manager);

		referenceOntology = this.loadOntology("/Users/pc_iverson/Desktop/Input/Thesaurus.owl");

		System.out.println(referenceOntology.getOntologyID().getOntologyIRI().toString());

		createdOntology = this.loadOntology("/Users/pc_iverson/Desktop/Input/PredictionModel.owl");

		this.labelToOWLClass = labelMapURI(referenceOntology, OWLRDFVocabulary.RDFS_LABEL.getIRI());

		this.synonymsToOWLClass = labelMapURI(referenceOntology,
				IRI.create("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#FULL_SYN"));

		this.addingClassHierarchy(referenceOntology, createdOntology);

		this.OntologySave(createdOntology);

	}

	public void OntologySave(OWLOntology ontology) throws OWLOntologyStorageException
	{
		manager.saveOntology(ontology);
	}

	private void addingClassHierarchy(OWLOntology referenceOntology, OWLOntology createdOntology)
	{

		Set<OWLOntology> setOfOntologies = new HashSet<OWLOntology>();

		setOfOntologies.add(createdOntology);

		OWLEntityRenamer renamer = new OWLEntityRenamer(manager, setOfOntologies);

		HashMap<String, OWLClass> labelToClassCreated = labelMapURI(createdOntology,
				OWLRDFVocabulary.RDFS_LABEL.getIRI());

		List<String> allChildren = owlFunction.getAllChildren(createdOntology,
				labelToClassCreated.get("prediction model"), new ArrayList<String>(), 1);

		System.out.println(allChildren);

		for (String className : allChildren)
		{

			List<OWLClass> composites = getClassesFromExpression(labelToClassCreated.get(className.toLowerCase()),
					createdOntology);

			OWLClass replacedClass = null;

			for (OWLClass buildingBlock : composites)
			{

				String classLabel = getLabel(buildingBlock, createdOntology);

				if (labelToOWLClass.containsKey(classLabel.toLowerCase()))
				{
					replacedClass = labelToOWLClass.get(classLabel.toLowerCase());
				}
				if (synonymsToOWLClass.containsKey(classLabel.toLowerCase()))
				{
					replacedClass = labelToOWLClass.get(classLabel.toLowerCase());
				}

				if (replacedClass != null)
				{

					// Add the mapped class and its ancestry and descendant
					// classes.
					List<OWLOntologyChange> changes = renamer.changeIRI(
							labelToClassCreated.get(classLabel.toLowerCase()), replacedClass.getIRI());
					manager.applyChanges(changes);

					addAnnotation(replacedClass, referenceOntology, createdOntology);

					recursiveAddingSuperClass(replacedClass, referenceOntology, createdOntology);

					recursiveAddingSubClass(replacedClass, referenceOntology, createdOntology);

					addSiblingsClass(replacedClass, referenceOntology, createdOntology);
				}

			}

			if (labelToOWLClass.containsKey(className.toLowerCase()))
			{
				replacedClass = labelToOWLClass.get(className.toLowerCase());
			}
			if (synonymsToOWLClass.containsKey(className.toLowerCase()))
			{
				replacedClass = labelToOWLClass.get(className.toLowerCase());
			}

			if (replacedClass != null)
			{

				// Add the mapped class and its ancestry and descendant classes.
				List<OWLOntologyChange> changes = renamer.changeIRI(labelToClassCreated.get(className.toLowerCase()),
						replacedClass.getIRI());
				manager.applyChanges(changes);

				addAnnotation(replacedClass, referenceOntology, createdOntology);

				recursiveAddingSuperClass(replacedClass, referenceOntology, createdOntology);

				recursiveAddingSubClass(replacedClass, referenceOntology, createdOntology);
			}

		}

		// for (OWLClass cls : createdOntology.getClassesInSignature()) {
		//
		// String className = this.getLabel(cls, createdOntology);
		//
		// OWLClass replacedClass = null;
		//
		// if (labelToOWLClass.containsKey(className.toLowerCase())) {
		// replacedClass = labelToOWLClass.get(className.toLowerCase());
		// }
		// if (synonymsToOWLClass.containsKey(className.toLowerCase())) {
		// replacedClass = labelToOWLClass.get(className.toLowerCase());
		// }
		// if (replacedClass != null) {
		//
		// // Add the mapped class and its ancestry and descendant classes.
		// List<OWLOntologyChange> changes = renamer.changeIRI(cls,
		// replacedClass.getIRI());
		// manager.applyChanges(changes);
		//
		// addAnnotation(replacedClass, referenceOntology, createdOntology);
		//
		// recursiveAddingSuperClass(replacedClass, referenceOntology,
		// createdOntology);
		//
		// recursiveAddingSubClass(replacedClass, referenceOntology,
		// createdOntology);
		//
		// // Add the siblings
		// addSiblingsClass(replacedClass, referenceOntology,
		// createdOntology);
		// }
		// }
	}

	private List<OWLClass> getClassesFromExpression(OWLClass owlClass, OWLOntology createdOntology)
	{

		List<OWLClass> lisfOfOWLClasses = new ArrayList<OWLClass>();

		for (OWLSubClassOfAxiom axiom : createdOntology.getSubClassAxiomsForSubClass(owlClass))
		{

			OWLClassExpression expression = axiom.getSuperClass();

			if (expression.isAnonymous())
			{
				lisfOfOWLClasses.addAll(expression.getClassesInSignature());
			}
		}

		return lisfOfOWLClasses;
	}

	private void addSiblingsClass(OWLClass cls, OWLOntology referenceOntology, OWLOntology createdOntology)
	{

		for (OWLSubClassOfAxiom axiom : referenceOntology.getSubClassAxiomsForSubClass(cls))
		{

			OWLClassExpression expression = axiom.getSuperClass();

			if (!expression.isAnonymous())
			{

				manager.applyChange(new AddAxiom(createdOntology, axiom));

				addAnnotation(expression.asOWLClass(), referenceOntology, createdOntology);

				recursiveAddingSuperClass(expression.asOWLClass(), referenceOntology, createdOntology);

				recursiveAddingSubClass(expression.asOWLClass(), referenceOntology, createdOntology);
			}
		}

	}

	private void recursiveAddingSuperClass(OWLClass cls, OWLOntology referenceOntology, OWLOntology createdOntology)
	{

		for (OWLSubClassOfAxiom axiom : referenceOntology.getSubClassAxiomsForSubClass(cls))
		{

			OWLClassExpression expression = axiom.getSuperClass();

			if (!expression.isAnonymous())
			{
				manager.applyChange(new AddAxiom(createdOntology, axiom));
				addAnnotation(expression.asOWLClass(), referenceOntology, createdOntology);
				recursiveAddingSuperClass(expression.asOWLClass(), referenceOntology, createdOntology);
			}
		}
	}

	private void recursiveAddingSubClass(OWLClass cls, OWLOntology referenceOntology, OWLOntology createdOntology)
	{

		for (OWLSubClassOfAxiom axiom : referenceOntology.getSubClassAxiomsForSuperClass(cls))
		{

			OWLClassExpression expression = axiom.getSubClass();

			if (!expression.isAnonymous())
			{
				manager.applyChange(new AddAxiom(createdOntology, axiom));
				addAnnotation(expression.asOWLClass(), referenceOntology, createdOntology);
				recursiveAddingSubClass(expression.asOWLClass(), referenceOntology, createdOntology);
			}
		}
	}

	public static void main(String args[]) throws OWLOntologyCreationException, OWLOntologyStorageException
	{

		new createOntology();
	}

	public void openSpreadSheet(String fileName)
	{

	}

	public OWLOntology loadOntology(String ontologyFileName) throws OWLOntologyCreationException
	{

		System.out.println("Loading the ontology file!");

		File file = new File(ontologyFileName);

		OWLOntology ontology = manager.loadOntologyFromOntologyDocument(file);

		System.out.println("The ontology is loaded!");

		return ontology;
	}

	/**
	 * Copy and paste annotation of OWL class from reference ontology to the new
	 * ontology
	 * 
	 * @param cls
	 * @param referenceOntology
	 * @param createdOntology
	 */
	public void addAnnotation(OWLClass cls, OWLOntology referenceOntology, OWLOntology createdOntology)
	{

		for (OWLAnnotation annotation : cls.getAnnotations(referenceOntology))
		{
			OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), annotation);
			manager.applyChange(new AddAxiom(createdOntology, ax));
		}
	}

	public HashMap<String, OWLClass> labelMapURI(OWLOntology owlontology, IRI AnnotataionProperty)
	{

		HashMap<String, OWLClass> mapURI = new HashMap<String, OWLClass>();
		OWLAnnotationProperty label = factory.getOWLAnnotationProperty(AnnotataionProperty);
		OWLAnnotationProperty synonym = factory.getOWLAnnotationProperty(IRI
				.create("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#FULL_SYN"));
		for (OWLClass cls : owlontology.getClassesInSignature())
		{
			// Get the annotations on the class that use the label property
			for (OWLAnnotation annotation : cls.getAnnotations(owlontology, label))
			{
				if (annotation.getValue() instanceof OWLLiteral)
				{
					OWLLiteral val = (OWLLiteral) annotation.getValue();
					String labelString = val.getLiteral();
					mapURI.put(labelString.toLowerCase(), cls);
				}
			}
		}
		return mapURI;
	}// end of labelMapURI method

	/*
	 * This method is used to get a label of corresponding OWLClass.
	 * 
	 * @param cls is the class we want to get label
	 * 
	 * @return the label of the class
	 */
	public String getLabel(OWLEntity cls, OWLOntology owlontology)
	{
		String labelValue = "";
		try
		{
			OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
			for (OWLAnnotation annotation : cls.getAnnotations(owlontology, label))
			{
				if (annotation.getValue() instanceof OWLLiteral)
				{
					OWLLiteral val = (OWLLiteral) annotation.getValue();
					labelValue = val.getLiteral().toString();
				}
			}
		}
		catch (Exception e)
		{
			System.out.println("The annotation is null!");
		}
		return labelValue;
	}// end of the getLabel method
}