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.description;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.Inheritance;

import javax.persistence.InheritanceType;

import javax.persistence.JoinTable;

import javax.persistence.ManyToMany;

import javax.persistence.ManyToOne;

import javax.persistence.MapKeyJoinColumn;

import javax.persistence.OneToMany;

import javax.persistence.OrderColumn;

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.XmlSchemaType;

import javax.xml.bind.annotation.XmlTransient;

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.ListIndexBase;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.IndexedEmbedded;

import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;

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

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

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.TimePeriod;

import eu.etaxonomy.cdm.model.media.Media;

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

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.reference.IOriginalSource;

import eu.etaxonomy.cdm.model.reference.ISourceable;

import eu.etaxonomy.cdm.model.reference.OriginalSourceType;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.taxon.Taxon;

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

import eu.etaxonomy.cdm.model.term.TermVocabulary;

import eu.etaxonomy.cdm.strategy.merge.Merge;

import eu.etaxonomy.cdm.strategy.merge.MergeMode;

/**

 * The upmost (abstract) class for a piece of information) about

 * a {@link SpecimenOrObservationBase specimen}, a {@link Taxon taxon} or even a {@link TaxonName taxon name}.

 * A concrete description element assigns descriptive data to one {@link Feature feature}.<BR>

 * Experts use the word feature for the property itself but not for the actual

 * description element. Therefore naming this class FeatureBase would have

 * leaded to confusion.

 * <P>

 * This class corresponds to: <ul>

 * <li> DescriptionsBaseType according to the the SDD schema

 * <li> InfoItem according to the TDWG ontology

 * <li> MeasurementOrFactAtomised according to the ABCD schema

 * </ul>

 *

 * @author m.doering

 * @since 08-Nov-2007 13:06:24

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

    "feature",

    "inDescription",

    "timeperiod",

    "modifiers",

    "modifyingText",

    "media",

    "sources",

    "sortIndex"

})

@Entity

@Audited

@Inheritance(strategy=InheritanceType.SINGLE_TABLE)

public abstract class DescriptionElementBase extends AnnotatableEntity

        implements ISourceable<DescriptionElementSource>, IModifiable, IMultiLanguageTextHolder{

    private static final long serialVersionUID = 5000910777835755905L;

    @SuppressWarnings("unused")

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

    //type, category of information. In structured descriptions characters

    @XmlElement(name = "Feature")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

//    @Cascade(CascadeType.MERGE)   remove cascade #5755

    @IndexedEmbedded // no depth for terms

    private Feature feature;

    @XmlElementWrapper(name = "Modifiers")

    @XmlElement(name = "Modifier")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToMany(fetch = FetchType.LAZY)

    @JoinTable(name="DescriptionElementBase_Modifier")

    @IndexedEmbedded(depth=1)

    private Set<DefinedTerm> modifiers = new HashSet<>();

    @XmlElement(name = "ModifyingText")

    @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)

    @OneToMany(fetch = FetchType.LAZY)

    @JoinTable(name = "DescriptionElementBase_ModifyingText")

    @MapKeyJoinColumn(name="modifyingtext_mapkey_id")

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

    @IndexedEmbedded

    private Map<Language,LanguageString> modifyingText = new HashMap<>();

    @XmlElementWrapper(name = "Media")

    @XmlElement(name = "Medium")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToMany(fetch = FetchType.LAZY)

    @OrderColumn(name="sortIndex")

    @ListIndexBase(value=0)  //not really needed as this is the default

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

    private List<Media> media = new ArrayList<>();

    @XmlElement(name = "InDescription")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

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

    @IndexedEmbedded(includeEmbeddedObjectId=true)

    private DescriptionBase<?> inDescription;

	@XmlElement(name = "TimePeriod")

    private TimePeriod timeperiod = TimePeriod.NewInstance();

    @XmlElementWrapper(name = "Sources")

    @XmlElement(name = "DescriptionElementSource")

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

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

    @Merge(MergeMode.ADD_CLONE)

    private Set<DescriptionElementSource> sources = new HashSet<>();

    //#8004 optional sortIndex

    private Integer sortIndex = null;

    // ************* CONSTRUCTORS *************/

    /**

     * Class constructor: creates a new empty description element instance.

     *

     * @see #DescriptionElementBase(Feature)

     */

    protected DescriptionElementBase(){

    }

    /**

     * Class constructor: creates a new description element instance with the

     * given {@link Feature feature} that is described or measured.

     *

     * @param	feature	the feature described or measured

     * @see 			#DescriptionElementBase()

     */

    protected DescriptionElementBase(Feature feature){

        if (feature == null){

            feature = Feature.UNKNOWN();

        }

        this.feature = feature;

    }

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

    /**

     * Returns the list of {@link Media media} (that is pictures, movies,

     * recorded sounds ...) <i>this</i> description element is based on.

     */

    public List<Media> getMedia(){

        return this.media;

    }

    /**

     * Adds a {@link Media media} to the list of {@link #getMedia() media}

     * <i>this</i> description element is based on.

     *

     * @param media	the media to be added to <i>this</i> description element

     * @see    	   	#getMedia()

     */

    public void addMedia(Media media){

        this.media.add(media);

    }

    /**

     * Removes one element from the list of {@link #getMedia() media}

     * <i>this</i> description element is based on.

     *

     * @param  media	the media which should be removed

     * @see     		#getMedia()

     * @see     		#addMedia(Media)

     */

    public void removeMedia(Media media){

        this.media.remove(media);

    }

    /**

     * Returns the {@link DescriptionBase description} that <i>this</i> DescriptionElement is

     * part of.

     * @return

     */

    public DescriptionBase getInDescription() {

        return this.inDescription;

    }

    /**

     * @see	#setInDescription()

     */

    protected void setInDescription(DescriptionBase inDescription) {

        this.inDescription = inDescription;

    }

    /**

     * Returns the {@link Feature feature} <i>this</i> description element is for.

     * A feature is a property that can be described or measured but not the

     * description or the measurement itself.

     */

    public Feature getFeature(){

        return this.feature;

    }

    /**

     * @see	#getFeature()

     */

    public void setFeature(Feature feature){

        this.feature = feature;

    }

    /**

	 * The point in time, the time period or the season for which this description element

	 * is valid. A season may be expressed by not filling the year part(s) of the time period.

	 */

	public TimePeriod getTimeperiod() {

		return timeperiod;

	}

	/**

	 * @see #getTimeperiod()

	 */

	public void setTimeperiod(TimePeriod timeperiod) {

		if (timeperiod == null){

			timeperiod = TimePeriod.NewInstance();

		}

		this.timeperiod = timeperiod;

	}

	/**

     * Returns the set of {@link Modifier modifiers} used to qualify the validity of

     * <i>this</i> description element. This is only metainformation.

     */

    @Override

    public Set<DefinedTerm> getModifiers(){

        return this.modifiers;

    }

    /**

     * Adds a {@link Modifier modifier} to the set of {@link #getModifiers() modifiers}

     * used to qualify the validity of <i>this</i> description element.

     *

     * @param modifier	the modifier to be added to <i>this</i> description element

     * @see    	   		#getModifiers()

     */

    @Override

    public void addModifier(DefinedTerm modifier){

        this.modifiers.add(modifier);

    }

    /**

     * Removes one element from the set of {@link #getModifiers() modifiers}

     * used to qualify the validity of <i>this</i> description element.

     *

     * @param  modifier	the modifier which should be removed

     * @see     		#getModifiers()

     * @see     		#addModifier(Modifier)

     */

    @Override

    public void removeModifier(DefinedTerm modifier){

        this.modifiers.remove(modifier);

    }

    /**

     * Returns the {@link MultilanguageText multilanguage text} used to qualify the validity

     * of <i>this</i> description element.  The different {@link LanguageString language strings}

     * contained in the multilanguage text should all have the same meaning.<BR>

     * A multilanguage text does not belong to a controlled {@link TermVocabulary term vocabulary}

     * as a {@link Modifier modifier} does.

     * <P>

     * NOTE: the actual content of <i>this</i> description element is NOT

     * stored in the modifying text. This is only metainformation

     * (like "Some experts express doubt about this assertion").

     */

    public Map<Language,LanguageString> getModifyingText(){

        return this.modifyingText;

    }

    /**

     * Adds a translated {@link LanguageString text in a particular language}

     * to the {@link MultilanguageText multilanguage text} used to qualify the validity

     * of <i>this</i> description element.

     *

     * @param description	the language string describing the validity

     * 						in a particular language

     * @see    	   			#getModifyingText()

     * @see    	   			#putModifyingText(Language, String)

     * @deprecated 			should follow the put semantic of maps, this method will be removed in v4.0

     * 						Use the {@link #putModifyingText(LanguageString) putModifyingText} method

     */

    @Deprecated

    public LanguageString addModifyingText(LanguageString description){

        return this.putModifyingText(description);

    }

    /**

     * Adds a translated {@link LanguageString text in a particular language}

     * to the {@link MultilanguageText multilanguage text} used to qualify the validity

     * of <i>this</i> description element.

     *

     * @param description	the language string describing the validity

     * 						in a particular language

     * @see    	   			#getModifyingText()

     * @see    	   			#putModifyingText(Language, String)

     */

    public LanguageString putModifyingText(LanguageString description){

        return this.modifyingText.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 qualify the validity of <i>this</i> description element.

     *

     * @param text		the string describing the validity

     * 					in a particular language

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

     * @see    	   		#getModifyingText()

     * @see    	   		#putModifyingText(LanguageString)

     * @deprecated 		should follow the put semantic of maps, this method will be removed in v4.0

     * 					Use the {@link #putModifyingText(Language, String) putModifyingText} method

     */

    @Deprecated

    public LanguageString addModifyingText(String text, Language language){

        return this.putModifyingText(language, text);

    }

    /**

     * 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 qualify the validity of <i>this</i> description element.

     *

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

     * @param text		the string describing the validity

     * 					in a particular language

     *

     * @see    	   		#getModifyingText()

     * @see    	   		#putModifyingText(LanguageString)

     *

     */

    public LanguageString putModifyingText(Language language, String text){

        return this.modifyingText.put(language, LanguageString.NewInstance(text, language));

    }

    /**

     * Removes from the {@link MultilanguageText multilanguage text} used to qualify the validity

     * of <i>this</i> description element the one {@link LanguageString language string}

     * with the given {@link Language language}.

     *

     * @param  language	the language in which the language string to be removed

     * 					has been formulated

     * @see     		#getModifyingText()

     */

    public LanguageString removeModifyingText(Language language){

        return this.modifyingText.remove(language);

    }

    @Override

    public Set<DescriptionElementSource> getSources() {

        return this.sources;

    }

    @Override

    public void addSource(DescriptionElementSource source) {

        if (source != null){

            this.sources.add(source);

        }

    }

    @Override

    public DescriptionElementSource addSource(OriginalSourceType type, String id, String idNamespace, Reference citation, String microCitation) {

        if (id == null && idNamespace == null && citation == null && microCitation == null){

            return null;

        }

        DescriptionElementSource source = DescriptionElementSource.NewInstance(type, id, idNamespace, citation, microCitation);

        addSource(source);

        return source;

    }

    @Override

    public void addSources(Set<DescriptionElementSource> sources){

    	for (DescriptionElementSource source:sources){

    		addSource(source);

    	}

    }

    @Override

    public DescriptionElementSource addImportSource(String id, String idNamespace, Reference citation, String microCitation) {

        if (id == null && idNamespace == null && citation == null && microCitation == null){

            return null;

        }

        DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.Import, id, idNamespace, citation, microCitation);

        addSource(source);

        return source;

    }

    @Override

    public DescriptionElementSource addPrimaryTaxonomicSource(Reference citation, String microCitation) {

        if (citation == null && microCitation == null){

            return null;

        }

        DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(citation, microCitation);

        addSource(source);

        return source;

    }

    @Override

    public DescriptionElementSource addPrimaryTaxonomicSource(Reference citation) {

        return addPrimaryTaxonomicSource(citation, null);

    }

    /**

     * Adds a {@link IOriginalSource source} to this description element.

     * @param type the type of the source

     * @param idInSource the id used in the source

     * @param idNamespace the namespace for the id in the source

     * @param citation the source as a {@link Reference reference}

     * @param microReference the details (e.g. page number) in the reference

     * @param nameUsedInSource the taxon name used in the source

     * @param originalNameString the name as text used in the source

     */

    public void addSource(OriginalSourceType type, String idInSource, String idNamespace, Reference citation, String microReference, TaxonName nameUsedInSource, String originalNameString){

        DescriptionElementSource newSource = DescriptionElementSource.NewInstance(type, idInSource, idNamespace, citation, microReference, nameUsedInSource, originalNameString);

        addSource(newSource);

    }

    @Override

    public void removeSource(DescriptionElementSource source) {

        this.sources.remove(source);

    }

    public Integer getSortIndex() {

        return sortIndex;

    }

    public void setSortIndex(Integer sortIndex) {

        this.sortIndex = sortIndex;

    }

// ******************* METHODS *************************************************************/

    protected Map<TermVocabulary, List<DefinedTerm>> makeModifierMap(){

        Map<TermVocabulary, List<DefinedTerm>> result = new HashMap<>();

        for (DefinedTerm modifier : getModifiers()){

            TermVocabulary<DefinedTerm> voc = modifier.getVocabulary();

            if (result.get(voc) == null){

                result.put(voc, new ArrayList<>());

            }

            result.get(voc).add(modifier);

        }

        return result;

    }

    public List<DefinedTerm> getModifiers(TermVocabulary voc){

        List<DefinedTerm> result = makeModifierMap().get(voc);

        if (result == null){

            result = new ArrayList<>();

        }

        return result;

    }

    /**

     * Is this description item of a class type which is considere to

     * represent character data? These classes are {@link QuantitativeData}

     * and {@link CategoricalData}.

     * To be overriden by these classes.

     */

    @Transient

    @XmlTransient

    public boolean isCharacterData() {

        return false;

    }

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

    /**

     * Clones the description element. The element is <b>not</b> added to the same

     * description as the orginal element (inDescription is set to <code>null</null>).

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

     */

    @Override

    public Object clone() throws CloneNotSupportedException{

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

        //inDescription

        if (result.inDescription != null){

            result.inDescription.removeElement(result);

            result.inDescription = null;

        }

        //Sources

        result.sources = new HashSet<>();

        for (DescriptionElementSource source : getSources()){

            DescriptionElementSource newSource = (DescriptionElementSource)source.clone();

            result.addSource(newSource);

        }

        //media

        result.media = new ArrayList<>();

        for (Media media : getMedia()){

            result.media.add(media);

        }

        //modifying text

        result.modifyingText = cloneLanguageString(getModifyingText());

        //modifiers

        result.modifiers = new HashSet<>();

        for (DefinedTerm modifier : getModifiers()){

            result.modifiers.add(modifier);

        }

        //no changes to: feature

        return result;

    }

    /**

     * Clones the description element.<BR>

     * The new element is added to the <code>description</code>.<BR>

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

     */

    public DescriptionElementBase clone(DescriptionBase description) throws CloneNotSupportedException{

        DescriptionElementBase result = (DescriptionElementBase)clone();

        description.addElement(result);

        return result;

    }

}