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.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import javax.persistence.Column;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.Inheritance;

import javax.persistence.InheritanceType;

import javax.persistence.ManyToMany;

import javax.persistence.ManyToOne;

import javax.persistence.MapKeyJoinColumn;

import javax.persistence.OneToMany;

import javax.persistence.Transient;

import javax.validation.constraints.Min;

import javax.validation.constraints.NotNull;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlAttribute;

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 javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import org.apache.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.annotations.Index;

import org.hibernate.annotations.Table;

import org.hibernate.annotations.Type;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Analyze;

import org.hibernate.search.annotations.ContainedIn;

import org.hibernate.search.annotations.Field;

import org.hibernate.search.annotations.IndexedEmbedded;

import org.hibernate.search.annotations.NumericField;

import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;

import eu.etaxonomy.cdm.model.common.DefinedTerm;

import eu.etaxonomy.cdm.model.common.IMultiLanguageTextHolder;

import eu.etaxonomy.cdm.model.common.IdentifiableEntity;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.LanguageString;

import eu.etaxonomy.cdm.model.common.MultilanguageText;

import eu.etaxonomy.cdm.model.common.TermType;

import eu.etaxonomy.cdm.model.description.DescriptionBase;

import eu.etaxonomy.cdm.model.description.SpecimenDescription;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.description.TaxonNameDescription;

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

/**

 * type figures are observations with at least a figure object in media

 * @author m.doering

 * @created 08-Nov-2007 13:06:41

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

	"recordBasis",

	"publish",

	"sex",

	"lifeStage",

    "kindOfUnit",

	"individualCount",

    "definition",

    "descriptions",

    "determinations",

    "derivationEvents"

})

@XmlRootElement(name = "SpecimenOrObservationBase")

@Entity

@Audited

@Inheritance(strategy=InheritanceType.SINGLE_TABLE)

@Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })

public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements IMultiLanguageTextHolder{

	private static final long serialVersionUID = 6932680139334408031L;

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

	/**

	 * An indication of what the unit record describes.

	 * 

	 * NOTE: The name of the attribute was chosen against the common naming conventions of the CDM

	 * as it is well known in common standards like ABCD and DarwinCore. According to CDM naming

	 * conventions it would specimenOrObservationType. 

	 * 

	 * @see ABCD: DataSets/DataSet/Units/Unit/RecordBasis

	 * @see Darwin Core: http://wiki.tdwg.org/twiki/bin/view/DarwinCore/BasisOfRecord 

	 */

	@XmlAttribute(name ="RecordBasis")

	@Column(name="recordBasis")

	@NotNull

    @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",

    	parameters = {@org.hibernate.annotations.Parameter(name  = "enumClass", value = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType")}

    )

	private SpecimenOrObservationType recordBasis;

	@XmlElementWrapper(name = "Descriptions")

	@XmlElement(name = "Description")

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

	@Cascade(CascadeType.SAVE_UPDATE)

    @ContainedIn

    @NotNull

	private Set<DescriptionBase> descriptions = new HashSet<DescriptionBase>();

	@XmlElementWrapper(name = "Determinations")

	@XmlElement(name = "Determination")

	@OneToMany(mappedBy="identifiedUnit", orphanRemoval=true)

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

	@IndexedEmbedded(depth = 2)

	@NotNull

	private Set<DeterminationEvent> determinations = new HashSet<DeterminationEvent>();

	@XmlElement(name = "Sex")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	private DefinedTerm sex;

	@XmlElement(name = "LifeStage")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	private DefinedTerm lifeStage;

	/**

	 * Part(s) of organism or class of materials represented by this unit.

	 * Example: fruits, seeds, tissue, gDNA, leaves

	 * 

	 * @see ABCD: DataSets/DataSet/Units/Unit/KindOfUnit

	 * @see TermType#KindOfUnit

	 */

	@XmlElement(name = "KindOfUnit")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

//    @IndexedEmbedded(depth=1)

	private DefinedTerm kindOfUnit;

	@XmlElement(name = "IndividualCount")

	@Field(analyze = Analyze.NO)

	@NumericField

	@Min(0)

	private Integer individualCount;

	// the verbatim description of this occurrence. Free text usable when no atomised data is available.

	// in conjunction with titleCache which serves as the "citation" string for this object

	@XmlElement(name = "Description")

	@XmlJavaTypeAdapter(MultilanguageTextAdapter.class)

	@OneToMany(fetch = FetchType.LAZY, orphanRemoval=true)

	@MapKeyJoinColumn(name="definition_mapkey_id")

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

	@IndexedEmbedded

	@NotNull

	protected Map<Language,LanguageString> definition = new HashMap<Language,LanguageString>();

	// events that created derivedUnits from this unit

	@XmlElementWrapper(name = "DerivationEvents")

	@XmlElement(name = "DerivationEvent")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToMany(fetch=FetchType.LAZY)

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

    @NotNull

	protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();

    @XmlAttribute(name = "publish")

    private boolean publish = true;

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

  	//for hibernate use only

  	@Deprecated

  	protected SpecimenOrObservationBase(){super();}

	protected SpecimenOrObservationBase(SpecimenOrObservationType recordBasis) {

		super();

		if (recordBasis == null){ throw new IllegalArgumentException("RecordBasis must not be null");}

		this.recordBasis = recordBasis;

	}

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

	/**

	 * @see #recordBasis

	 * @return

	 */

	public SpecimenOrObservationType getRecordBasis() {

		return recordBasis;

	}

	/**

     * @see #recordBasis

	 * @param recordBasis

	 */

	public void setRecordBasis(SpecimenOrObservationType recordBasis) {

		this.recordBasis = recordBasis;

	}

	/**

	 * Returns the boolean value indicating if this specimen or observation should be withheld 

	 * (<code>publish=false</code>) or not (<code>publish=true</code>) during any publication

	 * process to the general public.

	 * This publish flag implementation is preliminary and may be replaced by a more general 

	 * implementation of READ rights in future.<BR>

	 * The default value is <code>true</code>.

	 */

	public boolean isPublish() {

		return publish;

	}

	/**

	 * @see #isPublish()

	 * @param publish

	 */

	public void setPublish(boolean publish) {

		this.publish = publish;

	}

	/**

	 * The descriptions this specimen or observation is part of.<BR>

	 * A specimen can not only have it's own {@link SpecimenDescription specimen description }

	 * but can also be part of a {@link TaxonDescription taxon description} or a

	 * {@link TaxonNameDescription taxon name description}.<BR>

	 * @see #getSpecimenDescriptions()

	 * @return

	 */

	public Set<DescriptionBase> getDescriptions() {

		if(descriptions == null) {

			this.descriptions = new HashSet<DescriptionBase>();

		}

		return this.descriptions;

	}

	/**

	 * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.

	 * @see #getDescriptions()

	 * @return

	 */

	@Transient

	public Set<SpecimenDescription> getSpecimenDescriptions() {

		return getSpecimenDescriptions(true);

	}

	/**

	 * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.

	 * @see #getDescriptions()

	 * @return

	 */

	@Transient

	public Set<SpecimenDescription> getSpecimenDescriptions(boolean includeImageGallery) {

		Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();

		for (DescriptionBase descriptionBase : getDescriptions()){

			if (descriptionBase.isInstanceOf(SpecimenDescription.class)){

				if (includeImageGallery || descriptionBase.isImageGallery() == false){

					specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));

				}

			}

		}

		return specimenDescriptions;

	}

	/**

	 * Returns the {@link SpecimenDescription specimen descriptions} which act as an image gallery

	 * and which this specimen is part of.

	 * @see #getDescriptions()

	 * @return

	 */

	@Transient

	public Set<SpecimenDescription> getSpecimenDescriptionImageGallery() {

		Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();

		for (DescriptionBase descriptionBase : getDescriptions()){

			if (descriptionBase.isInstanceOf(SpecimenDescription.class)){

				if (descriptionBase.isImageGallery() == true){

					specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));

				}

			}

		}

		return specimenDescriptions;

	}

	/**

	 * Adds a new description to this specimen or observation

	 * @param description

	 */

	public void addDescription(DescriptionBase description) {

		if (description.getDescribedSpecimenOrObservation() != null){

			description.getDescribedSpecimenOrObservation().removeDescription(description);

		}

		descriptions.add(description);

		description.setDescribedSpecimenOrObservation(this);

	}

	/**

	 * Removes a specimen from a description (removes a description from this specimen)

	 * @param description

	 */

	public void removeDescription(DescriptionBase description) {

        boolean existed = descriptions.remove(description);

        if (existed){

        	description.setDescribedSpecimenOrObservation(null);

        }

	}

	public Set<DerivationEvent> getDerivationEvents() {

		if(derivationEvents == null) {

			this.derivationEvents = new HashSet<DerivationEvent>();

		}

		return this.derivationEvents;

	}

	public void addDerivationEvent(DerivationEvent derivationEvent) {

		if (! this.derivationEvents.contains(derivationEvent)){

			this.derivationEvents.add(derivationEvent);

			derivationEvent.addOriginal(this);

		}

	}

	public void removeDerivationEvent(DerivationEvent derivationEvent) {

		this.derivationEvents.remove(derivationEvent);

	}

	public Set<DeterminationEvent> getDeterminations() {

		if(determinations == null) {

			this.determinations = new HashSet<DeterminationEvent>();

		}

		return this.determinations;

	}

	public void addDetermination(DeterminationEvent determination) {

		// FIXME bidirectional integrity. Use protected Determination setter

		this.determinations.add(determination);

	}

	public void removeDetermination(DeterminationEvent determination) {

		// FIXME bidirectional integrity. Use protected Determination setter

		this.determinations.remove(determination);

	}

	public DefinedTerm getSex() {

		return sex;

	}

	public void setSex(DefinedTerm sex) {

		this.sex = sex;

	}

	public DefinedTerm getLifeStage() {

		return lifeStage;

	}

	public void setLifeStage(DefinedTerm lifeStage) {

		this.lifeStage = lifeStage;

	}

	/**

	 * @see #kindOfUnit

	 * @return

	 */

	public DefinedTerm getKindOfUnit() {

		return kindOfUnit;

	}

	/**

	 * @see #kindOfUnit

	 * @param kindOfUnit

	 */

	public void setKindOfUnit(DefinedTerm kindOfUnit) {

		this.kindOfUnit = kindOfUnit;

	}

	public Integer getIndividualCount() {

		return individualCount;

	}

	public void setIndividualCount(Integer individualCount) {

		this.individualCount = individualCount;

	}

	public Map<Language,LanguageString> getDefinition(){

		return this.definition;

	}

	/**

	 * adds the {@link LanguageString description} to the {@link MultilanguageText multilanguage text}

	 * used to define <i>this</i> specimen or observation.

	 *

	 * @param description	the languageString in with the title string and the given language

	 *

	 * @see    	   		#getDefinition()

	 * @see    	   		#putDefinition(Language, String)

	 */

	public void putDefinition(LanguageString description){

		this.definition.put(description.getLanguage(),description);

	}

	/**

	 * Creates a {@link LanguageString language string} based on the given text string

	 * and the given {@link Language language} and adds it to the {@link MultilanguageText multilanguage text}

	 * used to define <i>this</i> specimen or observation.

	 *

	 * @param language	the language in which the title string is formulated

	 * @param text		the definition in a particular language

	 *

	 * @see    	   		#getDefinition()

	 * @see    	   		#putDefinition(LanguageString)

	 */

	public void putDefinition(Language language, String text){

		this.definition.put(language, LanguageString.NewInstance(text, language));

	}

	public void removeDefinition(Language lang){

		this.definition.remove(lang);

	}

	/**

	 * for derived units get the single next higher parental/original unit.

	 * If multiple original units exist throw error

	 * @return

	 */

	@Transient

	public SpecimenOrObservationBase getOriginalUnit(){

		logger.warn("GetOriginalUnit not yet implemented");

		return null;

	}

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

	/* (non-Javadoc)

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

	 * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()

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

	 */

	@Override

	public Object clone() throws CloneNotSupportedException {

		SpecimenOrObservationBase result = null;

		result = (SpecimenOrObservationBase)super.clone();

		//defininion (description, languageString)

		result.definition = new HashMap<Language,LanguageString>();

		for(LanguageString languageString : this.definition.values()) {

			LanguageString newLanguageString = (LanguageString)languageString.clone();

			result.putDefinition(newLanguageString);

		}

		//sex

		result.setSex(this.sex);

		//life stage

		result.setLifeStage(this.lifeStage);

		//Descriptions

		for(DescriptionBase description : this.descriptions) {

			result.addDescription(description);

		}

		//DeterminationEvent FIXME should clone() the determination

		// as the relationship is OneToMany

		for(DeterminationEvent determination : this.determinations) {

			result.addDetermination(determination);

		}

		//DerivationEvent

		for(DerivationEvent derivationEvent : this.derivationEvents) {

			result.addDerivationEvent(derivationEvent);

		}

		//no changes to: individualCount

		return result;

	}

}