/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* 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 eu.etaxonomy.cdm.model.reference.ReferenceBase;
-import eu.etaxonomy.cdm.model.common.Language;
-import eu.etaxonomy.cdm.model.common.LanguageString;
-import eu.etaxonomy.cdm.model.common.Media;
-import eu.etaxonomy.cdm.model.common.IReferencedEntity;
-import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
-import eu.etaxonomy.cdm.model.common.MultilanguageSet;
-import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
+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.OneToMany;
+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.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.IndexColumn;
+import org.hibernate.envers.Audited;
+import org.hibernate.search.annotations.IndexedEmbedded;
-import java.util.*;
-
-import javax.persistence.*;
+import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
+import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
+import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
+import eu.etaxonomy.cdm.model.common.IMultiLanguageTextHolder;
+import eu.etaxonomy.cdm.model.common.ISourceable;
+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.TermVocabulary;
+import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.strategy.merge.Merge;
+import eu.etaxonomy.cdm.strategy.merge.MergeMode;
/**
- * The upmost (abstract) class for a description element of a specimen
- * or of a taxon. A concrete description element assigns descriptive data to
- * the feature. As experts use the word feature for the property itself but not
- * for the actual description naming this class FeatureBase would make no sense.
- *
- *
+ * The upmost (abstract) class for a piece of information) about
+ * a {@link SpecimenOrObservationBase specimen}, a {@link Taxon taxon} or even a {@link TaxonNameBase 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
* @version 1.0
* @created 08-Nov-2007 13:06:24
*/
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "DescriptionElementBase", propOrder = {
+ "feature",
+ "modifiers",
+ "modifyingText",
+ "media",
+ "inDescription",
+ "sources"
+})
@Entity
+@Audited
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
-public abstract class DescriptionElementBase extends ReferencedEntityBase {
- private static final Logger logger = Logger.getLogger(DescriptionElementBase.class);
-
- //type, category of information. In structured descriptions characters
- private Feature type;
- private Set<Modifier> modifiers = new HashSet<Modifier>();
- private MultilanguageSet modifyingText;
- private Set<Media> media = new HashSet<Media>();
-
-
- @OneToMany
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<Media> getMedia(){
- return this.media;
- }
- protected void setMedia(Set<Media> media) {
- this.media = media;
- }
- public void addMedia(Media media){
- this.media.add(media);
- }
- public void removeMedia(Media media){
- this.media.remove(media);
- }
-
-
- @ManyToOne
- public Feature getType(){
- return this.type;
- }
- public void setType(Feature type){
- this.type = type;
- }
-
-
- @OneToMany
- public Set<Modifier> getModifiers(){
- return this.modifiers;
- }
- protected void setModifiers(Set<Modifier> modifiers){
- this.modifiers = modifiers;
- }
- public void addModifier(Modifier modifier){
- this.modifiers.add(modifier);
- }
- public void removeModifier(Modifier modifier){
- this.modifiers.remove(modifier);
- }
-
-
- public MultilanguageSet getModifyingText(){
- return this.modifyingText;
- }
- protected void setModifyingText(MultilanguageSet modifyingText){
- this.modifyingText = modifyingText;
- }
- public String addModifyingText(LanguageString description){
- return this.modifyingText.add(description);
- }
- public String addModifyingText(String text, Language language){
- return this.modifyingText.put(language, text);
- }
- public String removeModifyingText(Language language){
- return this.modifyingText.remove(language);
- }
+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.SAVE_UPDATE)
+ @Cascade(CascadeType.MERGE)
+ @IndexedEmbedded(depth=3)
+ private Feature feature;
+
+ @XmlElementWrapper(name = "Modifiers")
+ @XmlElement(name = "Modifier")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToMany(fetch = FetchType.LAZY)
+ @JoinTable(name="DescriptionElementBase_Modifier")
+ @IndexedEmbedded(depth=3)
+ private Set<Modifier> modifiers = new HashSet<Modifier>();
+
+ @XmlElement(name = "ModifyingText")
+ @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
+ @OneToMany(fetch = FetchType.LAZY)
+ @JoinTable(name = "DescriptionElementBase_ModifyingText")
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ @IndexedEmbedded
+ private Map<Language,LanguageString> modifyingText = new HashMap<Language,LanguageString>();
+
+ @XmlElementWrapper(name = "Media")
+ @XmlElement(name = "Medium")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToMany(fetch = FetchType.LAZY)
+ @IndexColumn(name="sortIndex", base = 0)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ private List<Media> media = new ArrayList<Media>();
+
+ @XmlElement(name = "InDescription")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.LAZY)
+ @Cascade(CascadeType.SAVE_UPDATE)
+ @IndexedEmbedded
+ private DescriptionBase inDescription;
+
+ @XmlElementWrapper(name = "Sources")
+ @XmlElement(name = "DescriptionElementSource")
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @Merge(MergeMode.ADD_CLONE)
+ private Set<DescriptionElementSource> sources = new HashSet<DescriptionElementSource>();
+
+
+
+ // ************* 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Returns the set of {@link Modifier modifiers} used to qualify the validity of
+ * <i>this</i> description element. This is only metainformation.
+ */
+ public Set<Modifier> 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()
+ */
+ public void addModifier(Modifier 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)
+ */
+ public void removeModifier(Modifier 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
+ */
+ 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
+ */
+ 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);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.ISourceable#getSources()
+ */
+ public Set<DescriptionElementSource> getSources() {
+ return this.sources;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.ISourceable#addSource(eu.etaxonomy.cdm.model.common.IOriginalSource)
+ */
+ public void addSource(DescriptionElementSource source) {
+ if (source != null){
+ DescriptionElementBase oldSourcedObj = source.getSourcedObj();
+ if (oldSourcedObj != null && oldSourcedObj != this){
+ oldSourcedObj.getSources().remove(source);
+ }
+ this.sources.add(source);
+ source.setSourcedObj(this);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.ISourceable#addSource(java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
+ */
+ public DescriptionElementSource addSource(String id, String idNamespace, Reference citation, String microCitation) {
+ if (id == null && idNamespace == null && citation == null && microCitation == null){
+ return null;
+ }
+ DescriptionElementSource source = DescriptionElementSource.NewInstance(id, idNamespace, citation, microCitation);
+ addSource(source);
+ return source;
+ }
+
+ public void addSource(String id, String idNamespace, Reference citation, String microReference, TaxonNameBase nameUsedInSource, String originalNameString){
+ DescriptionElementSource newSource = DescriptionElementSource.NewInstance(id, idNamespace, citation, microReference, nameUsedInSource, originalNameString);
+ addSource(newSource);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.ISourceable#removeSource(eu.etaxonomy.cdm.model.common.IOriginalSource)
+ */
+ public void removeSource(DescriptionElementSource source) {
+ this.sources.remove(source);
+ }
+
+// ******************* METHODS *************************************************************/
+
+ protected Map<TermVocabulary, List<Modifier>> makeModifierMap(){
+ Map<TermVocabulary, List<Modifier>> result = new HashMap<TermVocabulary, List<Modifier>>();
+ for (Modifier modifier : getModifiers()){
+ TermVocabulary<Modifier> voc = modifier.getVocabulary();
+ if (result.get(voc) == null){
+ result.put(voc, new ArrayList<Modifier>());
+ }
+ result.get(voc).add(modifier);
+ }
+ return result;
+ }
+
+ public List<Modifier> getModifiers(TermVocabulary voc){
+ List<Modifier> result = makeModifierMap().get(voc);
+ if (result == null){
+ result = new ArrayList<Modifier>();
+ }
+ return result;
+ }
+
+
+
+//************************** 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
+ result.inDescription = null;
+
+ //Sources
+ result.sources = new HashSet<DescriptionElementSource>();
+ for (DescriptionElementSource source : getSources()){
+ DescriptionElementSource newSource = (DescriptionElementSource)source.clone();
+ result.addSource(newSource);
+ }
+
+ //media
+ result.media = new ArrayList<Media>();
+ for (Media media : getMedia()){
+ result.media.add(media);
+ }
+
+ //modifying text
+ result.modifyingText = new HashMap<Language, LanguageString>();
+ for (Language language : getModifyingText().keySet()){
+ //TODO clone needed? See also IndividualsAssociation
+ LanguageString newLanguageString = (LanguageString)getModifyingText().get(language).clone();
+ result.modifyingText.put(language, newLanguageString);
+ }
+
+ //modifiers
+ result.modifiers = new HashSet<Modifier>();
+ for (Modifier 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;
+ }
+
+
}
\ No newline at end of file
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