MappingMetadata.java

import java.io.Serializable;
import java.util.Date;
import java.util.UUID;

import org.openrdf.model.URI;
import org.openrdf.model.impl.URIImpl;
import org.openrdf.repository.object.annotations.iri;

@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#Mapping_Metadata")
public class MappingMetadata implements Serializable {

	private static final long serialVersionUID = -1506672559890791939L;

	@iri(Constants.MAPPING_METADATA_PREFIX + "id")
	URI id;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#One_To_One_Mapping")
	URI dependency;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#comment")
	String comment;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#date")
	Date date;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#submitted_by")
	Integer submittedBy;
	
	

	/**
	 * Default no-arg constructor.
	 */
	public MappingMetadata() {
		generateId();
	}

	public MappingMetadata(URI mappingId) {
		this();
		this.dependency = mappingId;
	}

	/**
	 * Generate an id for this mapping.
	 */
	private void generateId() {
		this.id = new URIImpl(Constants.MAPPING_METADATA_PREFIX + UUID.randomUUID().toString());
	}

	/**
	 * @return the id
	 */
	public URI getId() {
		return id;
	}

	/**
	 * @param id
	 *            the id to set
	 */
	public void setId(URI id) {
		this.id = id;
	}

	/**
	 * @return the dependency
	 */
	public URI getDependency() {
		return dependency;
	}

	/**
	 * @param dependency
	 *            the dependency to set
	 */
	public void setDependency(URI dependency) {
		this.dependency = dependency;
	}

	/**
	 * @return the comment
	 */
	public String getComment() {
		return comment;
	}

	/**
	 * @param comment
	 *            the comment to set
	 */
	public void setComment(String comment) {
		this.comment = comment;
	}

	/**
	 * @return the date
	 */
	public Date getDate() {
		return date;
	}

	/**
	 * @param date
	 *            the date to set
	 */
	public void setDate(Date date) {
		this.date = date;
	}

	/**
	 * @return the submittedBy
	 */
	public Integer getSubmittedBy() {
		return submittedBy;
	}

	/**
	 * @param submittedBy2
	 *            the submittedBy to set
	 */
	public void setSubmittedBy(Integer submittedBy2) {
		this.submittedBy = submittedBy2;
	}

}

OneToOneMapping.java

import java.io.Serializable;
import java.util.UUID;

import org.openrdf.model.URI;
import org.openrdf.model.impl.URIImpl;
import org.openrdf.repository.object.annotations.iri;

@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#One_To_One_Mapping")
public class OneToOneMapping implements Serializable {

	private static final long serialVersionUID = 5668752344409465584L;

	@iri(Constants.MAPPING_PREFIX + "id")
	URI id;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#Mapping_metadata")
	MappingMetadata metadata;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#source")
	URI source;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#target")
	URI target;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#relation")
	URI relation;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#source_ontology_id")
	Integer sourceOntologyId;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#target_ontology_id")
	Integer targetOntologyId;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_source_ontology_version")
	Integer createdInSourceOntologyVersion;

	@iri("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_target_ontology_version")
	Integer createdInTargetOntologyVersion;

	/**
	 * Default no-arg constructor.
	 * */
	public OneToOneMapping() {
		generateId();
	}

	/**
	 * Generate an id for this mapping.
	 */
	private void generateId() {
		this.id = new URIImpl(Constants.MAPPING_PREFIX + UUID.randomUUID().toString());
	}

	/**
	 * @return the metadata
	 */
	public MappingMetadata getMetadata() {
		return metadata;
	}

	/**
	 * @param metadata
	 *            the metadata to set
	 */
	public void setMetadata(MappingMetadata metadata) {
		this.metadata = metadata;
	}

	/**
	 * @return the id
	 */
	public URI getId() {
		return id;
	}

	/**
	 * @param id
	 *            the id to set
	 */
	public void setId(URI id) {
		this.id = id;
	}

	/**
	 * @return the source
	 */
	public URI getSource() {
		return source;
	}

	/**
	 * @param source
	 *            the source to set
	 */
	public void setSource(URI source) {
		this.source = source;
	}

	/**
	 * @return the target
	 */
	public URI getTarget() {
		return target;
	}

	/**
	 * @param target
	 *            the target to set
	 */
	public void setTarget(URI target) {
		this.target = target;
	}

	/**
	 * @return the relation
	 */
	public URI getRelation() {
		return relation;
	}

	/**
	 * @param relation
	 *            the relation to set
	 */
	public void setRelation(URI relation) {
		this.relation = relation;
	}

	/**
	 * @return the sourceOntologyId
	 */
	public Integer getSourceOntologyId() {
		return sourceOntologyId;
	}

	/**
	 * @param sourceOntologyId
	 *            the sourceOntologyId to set
	 */
	public void setSourceOntologyId(Integer sourceOntologyId) {
		this.sourceOntologyId = sourceOntologyId;
	}

	/**
	 * @return the targetOntologyId
	 */
	public Integer getTargetOntologyId() {
		return targetOntologyId;
	}

	/**
	 * @param targetOntologyId
	 *            the targetOntologyId to set
	 */
	public void setTargetOntologyId(Integer targetOntologyId) {
		this.targetOntologyId = targetOntologyId;
	}

	/**
	 * @return the createdInSourceOntologyVersion
	 */
	public Integer getCreatedInSourceOntologyVersion() {
		return createdInSourceOntologyVersion;
	}

	/**
	 * @param createdInSourceOntologyVersion
	 *            the createdInSourceOntologyVersion to set
	 */
	public void setCreatedInSourceOntologyVersion(
			Integer createdInSourceOntologyVersion) {
		this.createdInSourceOntologyVersion = createdInSourceOntologyVersion;
	}

	/**
	 * @return the createdInTargetOntologyVersion
	 */
	public Integer getCreatedInTargetOntologyVersion() {
		return createdInTargetOntologyVersion;
	}

	/**
	 * @param createdInTargetOntologyVersion
	 *            the createdInTargetOntologyVersion to set
	 */
	public void setCreatedInTargetOntologyVersion(
			Integer createdInTargetOntologyVersion) {
		this.createdInTargetOntologyVersion = createdInTargetOntologyVersion;
	}

}

RemoveMapping.java

Repository repository = new VirtuosoRepository("jdbc:virtuoso://localhost:1111/", "dba", "dba");
repository.initialize();

ObjectRepositoryFactory objectRepositoryFactory = new ObjectRepositoryFactory();
ObjectRepository objectRepository = objectRepositoryFactory.createRepository(repository);

ObjectConnection con = objectRepository.getConnection();
con.setAddContexts(new URIImpl("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs"));

OneToOneMapping mapping = new OneToOneMapping();

// Instantiate a MappingMetadata object for the mapping
mapping.setMetadata(new MappingMetadata(mapping.getId()));

// Set Mapping properties
mapping.setSource(new URIImpl("http://purl.bioontology.org/ontology/ATMO/ATM_00000"));
mapping.setTarget(new URIImpl("http://purl.org/obo/owl/UBERON#UBERON_0001062"));
mapping.setRelation(new URIImpl("http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#owl:sameAs"));
mapping.setSourceOntologyId(1099);
mapping.setTargetOntologyId(1404);
mapping.setCreatedInSourceOntologyVersion(44203);
mapping.setCreatedInTargetOntologyVersion(44301);

// Set metadata properties
mapping.getMetadata().setSubmittedBy(99);

try {
        con.addObject(mapping.getId(), mapping);
} catch (RepositoryException e) {
	// TODO Auto-generated catch block
	e.printStackTrace();
}

try {
	OneToOneMapping mappingToDelete = con.getObject(OneToOneMapping.class, mapping.getId());

	mappingToDelete.setId(null);
	mappingToDelete.setMetadata(null);
	mappingToDelete.setSource(null);
	mappingToDelete.setTarget(null);
	mappingToDelete.setRelation(null);
	mappingToDelete.setSourceOntologyId(null);
	mappingToDelete.setTargetOntologyId(null);
	mappingToDelete.setCreatedInSourceOntologyVersion(null);
	mappingToDelete.setCreatedInTargetOntologyVersion(null);

	// Delete the mapping
	con.removeDesignation(mappingToDelete, OneToOneMapping.class);
} catch (RepositoryException e) {
	// TODO Auto-generated catch block
	e.printStackTrace();
} catch (QueryEvaluationException e) {
	// TODO Auto-generated catch block
	e.printStackTrace();
}