EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.model.occurrence;

import java.util.HashSet;

import java.util.Set;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

import javax.persistence.OneToMany;

import javax.persistence.Transient;

import javax.validation.constraints.Size;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlElementWrapper;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import org.apache.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Analyze;

import org.hibernate.search.annotations.Field;

import org.hibernate.search.annotations.Indexed;

import org.hibernate.search.annotations.IndexedEmbedded;

import org.hibernate.validator.constraints.Length;

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;

import eu.etaxonomy.cdm.model.name.TaxonNameBase;

import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;

/**

 * A derived unit is regarded as derived from a field unit,

 * so locality and gathering related information is captured as a separate FieldUnit object

 * related to a specimen via a derivation event

 * 

 * http://www.bgbm.org/biodivinf/docs/CollectionModel/ReprintTNR.pdf

 * http://www.bgbm.org/biodivinf/docs/CollectionModel/

 * <BR>

 * Type figures are derived units with at least a figure object in media

 *

 * @author m.doering

 * @created 08-Nov-2007 13:06:52

 *

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "DerivedUnit", propOrder = {

    "collection",

    "catalogNumber",

    "storedUnder",

    "derivedFrom",

    "accessionNumber",

    "collectorsNumber",

    "barcode",

	"preservation",

	"exsiccatum",

    "specimenTypeDesignations"

})

@XmlRootElement(name = "DerivedUnit")

@Entity

@Audited

// even if hibernate complains "Abstract classes can never insert index documents. Remove @Indexed."

// this is needed, otherwise the fields of the also abstract super class are missed during indexing

@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")

public class DerivedUnit extends SpecimenOrObservationBase<IIdentifiableEntityCacheStrategy> implements Cloneable{

	private static final long serialVersionUID = -3525746216270843517L;

	private static final Logger logger = Logger.getLogger(DnaSample.class);

	@XmlElement(name = "Collection")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	@Cascade(CascadeType.SAVE_UPDATE)

	@IndexedEmbedded

	private Collection collection;

	@XmlElement(name = "CatalogNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Length(max = 255)

	private String catalogNumber;

	@XmlElement(name = "AccessionNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Length(max = 255)

	private String accessionNumber;

	@XmlElement(name = "CollectorsNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Length(max = 255)

	private String collectorsNumber;

	@XmlElement(name = "Barcode")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Length(max = 255)

	private String barcode;

	@XmlElement(name = "StoredUnder")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	@Cascade(CascadeType.SAVE_UPDATE)

	@IndexedEmbedded

	private TaxonNameBase storedUnder;

	@XmlElement(name = "DerivedFrom")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	@Cascade(CascadeType.SAVE_UPDATE)

	@IndexedEmbedded(depth = 4)

	private DerivationEvent derivedFrom;

	@XmlElementWrapper(name = "SpecimenTypeDesignations")

	@XmlElement(name = "SpecimenTypeDesignation")

	@OneToMany(fetch = FetchType.LAZY, mappedBy = "typeSpecimen")

	@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE })

	private final Set<SpecimenTypeDesignation> specimenTypeDesignations = new HashSet<SpecimenTypeDesignation>();

//*** attributes valid only for preserved specimen (PreservedSpecimen, Fossil, DnaSample)

	@XmlElement(name = "Preservation")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	private PreservationMethod preservation;

	@XmlElement(name = "Exsiccatum")

    //TODO Val #3379

//	@NullOrNotEmpty

	@Field

	@Size(max = 255)

    private String exsiccatum;

// ******************** FACTORY METHOD **********************************/

	public static DerivedUnit NewInstance(SpecimenOrObservationType type) {

		return new DerivedUnit(type);

	}

	/**

	 * Factory method

	 * @return

	 */

	public static DerivedUnit NewPreservedSpecimenInstance(){

		DerivedUnit result = new DerivedUnit(SpecimenOrObservationType.PreservedSpecimen);

		return result;

	}

//************************** CONSTRUCTOR *********************************/	

	//Constructor: For hibernate use only

	protected DerivedUnit() {super();}

	/**

	 * Constructor

	 * @param recordBasis

	 */

	protected DerivedUnit(SpecimenOrObservationType recordBasis) {

		super(recordBasis);

	}

	/**

	 * Create new unit derived from an existing field unit

	 * @param fieldUnit existing field unit from where this unit is derived

	 */

	protected DerivedUnit(SpecimenOrObservationType recordBasis, FieldUnit fieldUnit) {

		super(recordBasis);

		DerivationEvent derivedFrom = new DerivationEvent();

		// TODO: should be done in a more controlled way. Probably by making derivation event implement a general relationship interface (for bidirectional add/remove etc)

		fieldUnit.addDerivationEvent(derivedFrom);

		derivedFrom.getOriginals().add(fieldUnit);

		derivedFrom.getDerivatives().add(this);

		this.setDerivedFrom(derivedFrom);

	}

	/**

	 * create new unit derived from an existing gathering event,

	 * thereby creating a new empty field unit

	 * @param gatheringEvent the gathering event this unit was collected at

	 */

	protected DerivedUnit(SpecimenOrObservationType recordBasis, GatheringEvent gatheringEvent) {

		this(recordBasis, new FieldUnit());

		FieldUnit field = (FieldUnit)this.getOriginalUnit();

		field.setGatheringEvent(gatheringEvent);

	}

// ******************** GETTER / SETTER *************************************/

	public DerivationEvent getDerivedFrom() {

		return derivedFrom;

	}

	public void setDerivedFrom(DerivationEvent derivedFrom){

		if (getDerivedFrom() != null){

			getDerivedFrom().getDerivatives().remove(derivedFrom);

		}

		this.derivedFrom = derivedFrom;

		if (derivedFrom != null){

			derivedFrom.addDerivative(this);

		}

	}

	@Transient

	public Set<SpecimenOrObservationBase> getOriginals(){

		if(getDerivedFrom() != null){

			return getDerivedFrom().getOriginals();

		}

		return null;

	}

	public Collection getCollection(){

		return this.collection;

	}

	public void setCollection(Collection collection){

		this.collection = collection;

	}

	public String getCatalogNumber() {

		return catalogNumber;

	}

	public void setCatalogNumber(String catalogNumber) {

		this.catalogNumber = catalogNumber;

	}

	public void setBarcode(String barcode) {

		this.barcode = barcode;

	}

	public String getBarcode() {

		return barcode;

	}

	public void setStoredUnder(TaxonNameBase storedUnder) {

		this.storedUnder = storedUnder;

	}

	public String getAccessionNumber() {

		return accessionNumber;

	}

	public void setAccessionNumber(String accessionNumber) {

		this.accessionNumber = accessionNumber;

	}

	/**

	 * Will be removed in future versions as semantics is not clear.

	 * For accessing the collecting number use

	 * {@link FieldUnit#getFieldNumber()} instead.

	 * @return

	 */

	@Deprecated

	public String getCollectorsNumber() {

		return collectorsNumber;

	}

	/**

	 * Will be removed in future versions as semantics is not clear.

	 * For editing the collecting number use

	 * {@link FieldUnit#getFieldNumber()} instead.

	 * @return

	 */

	@Deprecated

	public void setCollectorsNumber(String collectorsNumber) {

		this.collectorsNumber = collectorsNumber;

	}

	public TaxonNameBase getStoredUnder() {

		return storedUnder;

	}

	public void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){

		if (specimenTypeDesignation.getTypeSpecimen() == this){

			return ;

		}else if (specimenTypeDesignation.getTypeSpecimen() != null){

			specimenTypeDesignation.getTypeSpecimen().removeSpecimenTypeDesignation(specimenTypeDesignation);

		}

		specimenTypeDesignations.add(specimenTypeDesignation);

		specimenTypeDesignation.setTypeSpecimen(this);

	}

	public void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){

		if (specimenTypeDesignation == null){

			return;

		}

		if (specimenTypeDesignations.contains(specimenTypeDesignation)){

			specimenTypeDesignations.remove(specimenTypeDesignation);

			specimenTypeDesignation.setTypeSpecimen(null);

		}

	}

// ******* GETTER / SETTER for preserved specimen only ******************/

	public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations(){

		return specimenTypeDesignations;

	}

	public PreservationMethod getPreservation(){

		return this.preservation;

	}

	public void setPreservation(PreservationMethod preservation){

		this.preservation = preservation;

	}

	public void setExsiccatum(String exsiccatum) {

		this.exsiccatum = exsiccatum;

	}

	public String getExsiccatum() {

		return exsiccatum;

	}

//*********** CLONE **********************************/

	/**

	 * Clones <i>this</i> derivedUnit. This is a shortcut that enables to

	 * create a new instance that differs only slightly from <i>this</i> specimen

	 * by modifying only some of the attributes.<BR>

	 * This method overrides the clone method from {@link SpecimenOrObservationBase SpecimenOrObservationBase}.

	 *

	 * @see SpecimenOrObservationBase#clone()

	 * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()

	 * @see java.lang.Object#clone()

	 */

	@Override

	public Object clone() {

		try{

			DerivedUnit result = (DerivedUnit)super.clone();

			//collection

			result.setCollection(this.collection);

			//derivedFrom

			result.setDerivedFrom(this.derivedFrom);

			//storedUnder

			result.setStoredUnder(this.storedUnder);

			//preservation

			result.setPreservation(this.preservation);

			//no changes to: accessionNumber, catalogNumber, collectorsNumber

			return result;

		} catch (CloneNotSupportedException e) {

			logger.warn("Object does not implement cloneable");

			e.printStackTrace();

			return null;

		}

	}

}