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.Column;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.Lob;

import javax.persistence.ManyToOne;

import javax.persistence.OneToMany;

import javax.persistence.Transient;

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 eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

import eu.etaxonomy.cdm.strategy.cache.occurrence.DerivedUnitDefaultCacheStrategy;

/**

 * 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

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

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "collection",

    "catalogNumber",

    "storedUnder",

    "derivedFrom",

    "accessionNumber",

    "collectorsNumber",

    "barcode",

	"preservation",

	"exsiccatum",

	"originalLabelInfo",

    "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<? extends DerivedUnit>> {

    private static final long serialVersionUID = -3525746216270843517L;

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

	@XmlElement(name = "Collection")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

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

	@IndexedEmbedded

	private Collection collection;

	@XmlElement(name = "CatalogNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Column(length=255)

	private String catalogNumber;

	@XmlElement(name = "AccessionNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Column(length=255)

	private String accessionNumber;

	@XmlElement(name = "CollectorsNumber")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Column(length=255)

	private String collectorsNumber;

	@XmlElement(name = "Barcode")

	@Field(analyze = Analyze.NO)

    //TODO Val #3379

//	@NullOrNotEmpty

	@Column(length=255)

	private String barcode;

	@XmlElement(name = "StoredUnder")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

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

	@IndexedEmbedded(includeEmbeddedObjectId=true)

	private TaxonName storedUnder;

	@XmlElement(name = "DerivedFrom")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

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

	@IndexedEmbedded(depth = 4)

	private DerivationEvent derivedFrom;

	@XmlElement(name = "OriginalLabelInfo")

	@Lob

    private String originalLabelInfo;

	@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)

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

	private PreservationMethod preservation;

	@XmlElement(name = "Exsiccatum")

    //TODO Val #3379

//	@NullOrNotEmpty

	@Field

    @Column(length=255)

    private String exsiccatum;

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

	public static DerivedUnit NewInstance(SpecimenOrObservationType type) {

		if (type.isMedia()){

			return MediaSpecimen.NewInstance(type);

		}else if (type.equals(SpecimenOrObservationType.DnaSample) || type.isKindOf(SpecimenOrObservationType.DnaSample)){

			return DnaSample.NewInstance();

		}else if (type.equals(SpecimenOrObservationType.TissueSample) || type.isKindOf(SpecimenOrObservationType.TissueSample)){

            //for now we store TissueSample as DnaSample to allow adding sequences and other DnaSample data to it directly

		    //this is because sometimes explicit DnaSample data does not exist as it is not preserved

		    //In this case a Sequence or Amplification is directly added to the Tissue Sample.

		    //In theory also TissueSample could be missing so this should be possible also for other

		    //SpecimenOrObservationType units.

		    //This is a reason why DnaSample and DerivedUnit should be unified.

		    return DnaSample.NewInstance();

        }else{

			return new DerivedUnit(type);

		}

	}

	public static DerivedUnit NewPreservedSpecimenInstance(){

		DerivedUnit result = new DerivedUnit(SpecimenOrObservationType.PreservedSpecimen);

		return result;

	}

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

	//Constructor: For hibernate use only

	@SuppressWarnings("deprecation")

    protected DerivedUnit() {

	    super();

        initDefaultCacheStrategy();

	}

    /**

	 * Constructor

	 * @param recordBasis

	 */

	protected DerivedUnit(SpecimenOrObservationType recordBasis) {

		super(recordBasis);

        initDefaultCacheStrategy();

	}

	/**

	 * 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) {

		this(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);

	}

    /**

     * Sets the default cache strategy

     */

	@Override

    protected void initDefaultCacheStrategy() {

        this.cacheStrategy = new DerivedUnitDefaultCacheStrategy();

    }

    @Override

    public String getTitleCache() {

        //specimen are complex and changes in other objects often, therefore we compute titleCache each time from scratch

        if (!this.protectedTitleCache){

            this.titleCache = null;

        }

        return super.getTitleCache();

    }

// ******************** 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 new HashSet<>();

	}

	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 = isBlank(catalogNumber)?null:catalogNumber;

	}

	public void setBarcode(String barcode) {

		this.barcode = isBlank(barcode)? null : barcode;

	}

	public String getBarcode() {

		return barcode;

	}

	public void setStoredUnder(TaxonName storedUnder) {

		this.storedUnder = storedUnder;

	}

	public String getAccessionNumber() {

		return accessionNumber;

	}

	public void setAccessionNumber(String accessionNumber) {

		this.accessionNumber = isBlank(accessionNumber)? null : accessionNumber;

	}

	/**

	 * Original label information may present the exact original text

	 * or any other text which fully or partly represents the text available

	 * on the specimens label. This information may differ from the information

	 * available in the derived unit itself.

	 * @return the original label information

	 */

	//#4218

	public String getOriginalLabelInfo() {

		return originalLabelInfo;

	}

	public void setOriginalLabelInfo(String originalLabelInfo) {

		this.originalLabelInfo = originalLabelInfo;

	}

	/**

	 * 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 = isBlank(collectorsNumber)? null : collectorsNumber;

	}

	public TaxonName 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);

		}

	}

    public String getMostSignificantIdentifier() {

        if (isNotBlank(getAccessionNumber())) {

            return getAccessionNumber();

        }

        else if(isNotBlank(getBarcode())){

            return getBarcode();

        }

        else if(isNotBlank(getCatalogNumber())){

            return getCatalogNumber();

        }

        return null;

    }

    /**

     * Collects all top most units (FieldUnits, DerivedUnits) in the parent branches of the derivation graph.

     * <p>

     * <b>NOTE:</b> As this method walks the derivation graph it should only be used in a transactional context or

     * it must be assured that the whole graph is initialized.

     *

     * @param typeRestriction

     *  Restricts the returned entities to a specific type of unit.

     */

    public <T extends SpecimenOrObservationBase> java.util.Collection<T> collectRootUnits(Class<T> typeRestriction) {

        return collectRootUnits(typeRestriction, new HashSet<>());

    }

    private <T extends SpecimenOrObservationBase> java.util.Collection<T> collectRootUnits(Class<T> typeRestriction, Set<SpecimenOrObservationBase<?>> cycleDetection) {

        if(typeRestriction == null) {

            typeRestriction = (Class<T>) SpecimenOrObservationBase.class;

        }

        cycleDetection.add(this);

        java.util.Collection<T> rootUnits = new HashSet<>();

        Set<SpecimenOrObservationBase> originals = getOriginals();

        if (originals != null && !originals.isEmpty()) {

            for (SpecimenOrObservationBase<?> original : originals) {

                if (original.isInstanceOf(FieldUnit.class)) {

                    if(typeRestriction.isAssignableFrom(FieldUnit.class)) {

                        if(logger.isTraceEnabled()) {logger.trace(" [" + original + "] <-- " + this );}

                        rootUnits.add(HibernateProxyHelper.deproxy(original, typeRestriction));

                    }

                    // otherwise this entity can be ignored

                } else if(original.isInstanceOf(DerivedUnit.class)){

                    DerivedUnit originalDerivedUnit = HibernateProxyHelper.deproxy(original, DerivedUnit.class);

                    if(!cycleDetection.contains(originalDerivedUnit)) {

                        rootUnits.addAll(originalDerivedUnit.collectRootUnits(typeRestriction, cycleDetection));

                    } else {

                        // circular graph path found, this should not exist but is not prevented by the cdmlib

                        // using this as rootNode

                        if(logger.isTraceEnabled()) {logger.trace("CYCLE! "+ originalDerivedUnit + " <-- [" + this + "] <-- ...");}

                        rootUnits.add((T)this);

                    }

                }

            }

        } else {

            // no more originals for this DerivedUnit.

            // Potential FieldUnits have been filtered out one call before in the recursion

            if(isInstanceOf(typeRestriction)) {

                rootUnits.add(HibernateProxyHelper.deproxy(this, typeRestriction));

            }

        }

        return rootUnits;

    }

// ******* 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 = isBlank(exsiccatum)? null : 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 java.lang.Object#clone()

	 */

	@Override

	public DerivedUnit 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;

		}

	}

}