cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/SpecimenOrObservationBase.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.model.occurrence;
  11
  12 import java.lang.reflect.Method;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.Map;
  16 import java.util.Set;
  17
  18 import javax.persistence.Entity;
  19 import javax.persistence.FetchType;
  20 import javax.persistence.Inheritance;
  21 import javax.persistence.InheritanceType;
  22 import javax.persistence.ManyToMany;
  23 import javax.persistence.ManyToOne;
  24 import javax.persistence.OneToMany;
  25 import javax.persistence.Transient;
  26 import javax.xml.bind.annotation.XmlAccessType;
  27 import javax.xml.bind.annotation.XmlAccessorType;
  28 import javax.xml.bind.annotation.XmlElement;
  29 import javax.xml.bind.annotation.XmlElementWrapper;
  30 import javax.xml.bind.annotation.XmlIDREF;
  31 import javax.xml.bind.annotation.XmlRootElement;
  32 import javax.xml.bind.annotation.XmlSchemaType;
  33 import javax.xml.bind.annotation.XmlType;
  34 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  35
  36 import org.apache.log4j.Logger;
  37 import org.hibernate.annotations.Cascade;
  38 import org.hibernate.annotations.CascadeType;
  39 import org.hibernate.annotations.Index;
  40 import org.hibernate.annotations.Table;
  41 import org.hibernate.envers.Audited;
  42 import org.springframework.util.ReflectionUtils;
  43
  44 import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
  45 import eu.etaxonomy.cdm.model.common.Language;
  46 import eu.etaxonomy.cdm.model.common.LanguageString;
  47 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  48 import eu.etaxonomy.cdm.model.description.Sex;
  49 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  50 import eu.etaxonomy.cdm.model.description.Stage;
  51 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
  52 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  53
  54 /**
  55  * type figures are observations with at least a figure object in media
  56  * @author m.doering
  57  * @version 1.0
  58  * @created 08-Nov-2007 13:06:41
  59  */
  60 @XmlAccessorType(XmlAccessType.FIELD)
  61 @XmlType(name = "SpecimenOrObservationBase", propOrder = {
  62         "sex",
  63     "individualCount",
  64     "lifeStage",
  65     "description",
  66     "descriptions",
  67     "determinations",
  68     "derivationEvents"
  69 })
  70 @XmlRootElement(name = "SpecimenOrObservationBase")
  71 @Entity
  72 @Audited
  73 @Inheritance(strategy=InheritanceType.SINGLE_TABLE)
  74 @Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })
  75 public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S> {
  76
  77         private static final Logger logger = Logger.getLogger(SpecimenOrObservationBase.class);
  78
  79         @XmlElementWrapper(name = "Descriptions")
  80         @XmlElement(name = "Description")
  81         @ManyToMany(fetch = FetchType.LAZY,mappedBy="describedSpecimenOrObservations",targetEntity=DescriptionBase.class)
  82         private Set<SpecimenDescription> descriptions = new HashSet<SpecimenDescription>();
  83
  84         @XmlElementWrapper(name = "Determinations")
  85         @XmlElement(name = "Determination")
  86         @OneToMany(mappedBy="identifiedUnit")
  87         @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
  88         private Set<DeterminationEvent> determinations = new HashSet<DeterminationEvent>();
  89
  90         @XmlElement(name = "Sex")
  91         @XmlIDREF
  92         @XmlSchemaType(name = "IDREF")
  93         @ManyToOne(fetch = FetchType.LAZY)
  94         private Sex sex;
  95
  96         @XmlElement(name = "LifeStage")
  97         @XmlIDREF
  98         @XmlSchemaType(name = "IDREF")
  99         @ManyToOne(fetch = FetchType.LAZY)
 100         private Stage lifeStage;
 101
 102         @XmlElement(name = "IndividualCount")
 103         private Integer individualCount;
 104
 105         // the verbatim description of this occurrence. Free text usable when no atomised data is available.
 106         // in conjunction with titleCache which serves as the "citation" string for this object
 107         @XmlElement(name = "Description")
 108         @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
 109         @OneToMany(fetch = FetchType.LAZY)
 110         protected Map<Language,LanguageString> description = new HashMap<Language,LanguageString>();
 111
 112         // events that created derivedUnits from this unit
 113         @XmlElementWrapper(name = "DerivationEvents")
 114         @XmlElement(name = "DerivationEvent")
 115     @XmlIDREF
 116     @XmlSchemaType(name = "IDREF")
 117     @ManyToMany(fetch=FetchType.LAZY)
 118         protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();
 119
 120         /**
 121          * Constructor
 122          */
 123         protected SpecimenOrObservationBase(){
 124                 super();
 125         }
 126
 127         public Set<SpecimenDescription> getDescriptions() {
 128                 return this.descriptions;
 129         }
 130
 131         public void addDescription(SpecimenDescription description) {
 132                 this.descriptions.add(description);
 133                 Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "addDescribedSpecimenOrObservations", new Class[] {SpecimenOrObservationBase.class});
 134                 ReflectionUtils.makeAccessible(method);
 135                 ReflectionUtils.invokeMethod(method, description, new Object[] {this});
 136         }
 137
 138         public void removeDescription(SpecimenDescription description) {
 139                 this.descriptions.remove(description);
 140                 Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "removeDescribedSpecimenOrObservations", new Class[] {SpecimenOrObservationBase.class});
 141                 ReflectionUtils.makeAccessible(method);
 142                 ReflectionUtils.invokeMethod(method, description, new Object[] {this});
 143         }
 144
 145         public Set<DerivationEvent> getDerivationEvents() {
 146                 return this.derivationEvents;
 147         }
 148
 149         public void addDerivationEvent(DerivationEvent derivationEvent) {
 150                 if (! this.derivationEvents.contains(derivationEvent)){
 151                         this.derivationEvents.add(derivationEvent);
 152                         derivationEvent.addOriginal(this);
 153                 }
 154         }
 155
 156         public void removeDerivationEvent(DerivationEvent derivationEvent) {
 157                 this.derivationEvents.remove(derivationEvent);
 158         }
 159
 160         public Set<DeterminationEvent> getDeterminations() {
 161                 return this.determinations;
 162         }
 163
 164         public void addDetermination(DeterminationEvent determination) {
 165                 // FIXME bidirectional integrity. Use protected Determination setter
 166                 this.determinations.add(determination);
 167         }
 168
 169         public void removeDetermination(DeterminationEvent determination) {
 170                 // FIXME bidirectional integrity. Use protected Determination setter
 171                 this.determinations.remove(determination);
 172         }
 173
 174         public Sex getSex() {
 175                 return sex;
 176         }
 177
 178         public void setSex(Sex sex) {
 179                 this.sex = sex;
 180         }
 181
 182         public Stage getLifeStage() {
 183                 return lifeStage;
 184         }
 185
 186         public void setLifeStage(Stage lifeStage) {
 187                 this.lifeStage = lifeStage;
 188         }
 189
 190         @Override
 191         public String generateTitle(){
 192                 return "";
 193         }
 194
 195         public Integer getIndividualCount() {
 196                 return individualCount;
 197         }
 198
 199         public void setIndividualCount(Integer individualCount) {
 200                 this.individualCount = individualCount;
 201         }
 202
 203         public Map<Language,LanguageString> getDefinition(){
 204                 return this.description;
 205         }
 206
 207         public void addDefinition(LanguageString description){
 208                 this.description.put(description.getLanguage(),description);
 209         }
 210
 211         public void addDefinition(String text, Language language){
 212                 this.description.put(language, LanguageString.NewInstance(text, language));
 213         }
 214         public void removeDefinition(Language lang){
 215                 this.description.remove(lang);
 216         }
 217
 218         /**
 219          * for derived units get the single next higher parental/original unit.
 220          * If multiple original units exist throw error
 221          * @return
 222          */
 223         @Transient
 224         public SpecimenOrObservationBase getOriginalUnit(){
 225                 return null;
 226         }
 227
 228         @Transient
 229         public abstract GatheringEvent getGatheringEvent();
 230
 231
 232 //******************** CLONE **********************************************/
 233
 234         /* (non-Javadoc)
 235          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 236          * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
 237          * @see java.lang.Object#clone()
 238          */
 239         @Override
 240         public Object clone() throws CloneNotSupportedException {
 241                 SpecimenOrObservationBase result = null;
 242                 result = (SpecimenOrObservationBase)super.clone();
 243
 244                 //defininion (description, languageString)
 245                 result.description = new HashMap<Language,LanguageString>();
 246                 for(LanguageString languageString : this.description.values()) {
 247                         LanguageString newLanguageString = (LanguageString)languageString.clone();
 248                         result.addDefinition(newLanguageString);
 249                 }
 250
 251                 //sex
 252                 result.setSex(this.sex);
 253                 //life stage
 254                 result.setLifeStage(this.lifeStage);
 255
 256                 //Descriptions
 257                 for(DescriptionBase description : this.descriptions) {
 258                         result.addDescription((SpecimenDescription)description);
 259                 }
 260
 261                 //DeterminationEvent FIXME should clone() the determination
 262                 // as the relationship is OneToMany
 263                 for(DeterminationEvent determination : this.determinations) {
 264                         result.addDetermination(determination);
 265                 }
 266
 267                 //DerivationEvent
 268                 for(DerivationEvent derivationEvent : this.derivationEvents) {
 269                         result.addDerivationEvent(derivationEvent);
 270                 }
 271
 272                 //no changes to: individualCount
 273                 return result;
 274         }
 275 }