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.util.HashMap;
  13 import java.util.HashSet;
  14 import java.util.Map;
  15 import java.util.Set;
  16
  17 import javax.persistence.Entity;
  18 import javax.persistence.FetchType;
  19 import javax.persistence.Inheritance;
  20 import javax.persistence.InheritanceType;
  21 import javax.persistence.ManyToMany;
  22 import javax.persistence.ManyToOne;
  23 import javax.persistence.OneToMany;
  24 import javax.persistence.Transient;
  25 import javax.validation.constraints.Min;
  26 import javax.validation.constraints.NotNull;
  27 import javax.xml.bind.annotation.XmlAccessType;
  28 import javax.xml.bind.annotation.XmlAccessorType;
  29 import javax.xml.bind.annotation.XmlElement;
  30 import javax.xml.bind.annotation.XmlElementWrapper;
  31 import javax.xml.bind.annotation.XmlIDREF;
  32 import javax.xml.bind.annotation.XmlRootElement;
  33 import javax.xml.bind.annotation.XmlSchemaType;
  34 import javax.xml.bind.annotation.XmlType;
  35 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  36
  37 import org.apache.log4j.Logger;
  38 import org.hibernate.annotations.Cascade;
  39 import org.hibernate.annotations.CascadeType;
  40 import org.hibernate.annotations.Index;
  41 import org.hibernate.annotations.Table;
  42 import org.hibernate.envers.Audited;
  43 import org.hibernate.search.annotations.Field;
  44 import org.hibernate.search.annotations.IndexedEmbedded;
  45
  46 import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
  47 import eu.etaxonomy.cdm.model.common.Language;
  48 import eu.etaxonomy.cdm.model.common.LanguageString;
  49 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  50 import eu.etaxonomy.cdm.model.description.Sex;
  51 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  52 import eu.etaxonomy.cdm.model.description.Stage;
  53 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  54 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  55 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
  56 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  57
  58 /**
  59  * type figures are observations with at least a figure object in media
  60  * @author m.doering
  61  * @version 1.0
  62  * @created 08-Nov-2007 13:06:41
  63  */
  64 @XmlAccessorType(XmlAccessType.FIELD)
  65 @XmlType(name = "SpecimenOrObservationBase", propOrder = {
  66         "sex",
  67     "individualCount",
  68     "lifeStage",
  69     "description",
  70     "descriptions",
  71     "determinations",
  72     "derivationEvents"
  73 })
  74 @XmlRootElement(name = "SpecimenOrObservationBase")
  75 @Entity
  76 @Audited
  77 @Inheritance(strategy=InheritanceType.SINGLE_TABLE)
  78 @Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })
  79 public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S> {
  80
  81         private static final Logger logger = Logger.getLogger(SpecimenOrObservationBase.class);
  82
  83         @XmlElementWrapper(name = "Descriptions")
  84         @XmlElement(name = "Description")
  85         @ManyToMany(fetch = FetchType.LAZY,mappedBy="describedSpecimenOrObservations",targetEntity=DescriptionBase.class)
  86         @Cascade(CascadeType.SAVE_UPDATE)
  87         @NotNull
  88         private Set<DescriptionBase> descriptions = new HashSet<DescriptionBase>();
  89
  90         @XmlElementWrapper(name = "Determinations")
  91         @XmlElement(name = "Determination")
  92         @OneToMany(mappedBy="identifiedUnit")
  93         @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
  94         @IndexedEmbedded(depth = 2)
  95         @NotNull
  96         private Set<DeterminationEvent> determinations = new HashSet<DeterminationEvent>();
  97
  98         @XmlElement(name = "Sex")
  99         @XmlIDREF
 100         @XmlSchemaType(name = "IDREF")
 101         @ManyToOne(fetch = FetchType.LAZY)
 102         private Sex sex;
 103
 104         @XmlElement(name = "LifeStage")
 105         @XmlIDREF
 106         @XmlSchemaType(name = "IDREF")
 107         @ManyToOne(fetch = FetchType.LAZY)
 108         private Stage lifeStage;
 109
 110         @XmlElement(name = "IndividualCount")
 111         @Field(index=org.hibernate.search.annotations.Index.UN_TOKENIZED)
 112         @Min(0)
 113         private Integer individualCount;
 114
 115         // the verbatim description of this occurrence. Free text usable when no atomised data is available.
 116         // in conjunction with titleCache which serves as the "citation" string for this object
 117         @XmlElement(name = "Description")
 118         @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
 119         @OneToMany(fetch = FetchType.LAZY)
 120         @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
 121         @IndexedEmbedded
 122         @NotNull
 123         protected Map<Language,LanguageString> description = new HashMap<Language,LanguageString>();
 124
 125         // events that created derivedUnits from this unit
 126         @XmlElementWrapper(name = "DerivationEvents")
 127         @XmlElement(name = "DerivationEvent")
 128     @XmlIDREF
 129     @XmlSchemaType(name = "IDREF")
 130     @ManyToMany(fetch=FetchType.LAZY)
 131     @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
 132     @NotNull
 133         protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();
 134
 135         /**
 136          * Constructor
 137          */
 138         protected SpecimenOrObservationBase(){
 139                 super();
 140         }
 141
 142         /**
 143          * The descriptions this specimen or observation is part of.<BR>
 144          * A specimen can not only have it's own {@link SpecimenDescription specimen description }
 145          * but can also be part of a {@link TaxonDescription taxon description} or a
 146          * {@link TaxonNameDescription taxon name description}.<BR>
 147          * @see #getSpecimenDescriptions()
 148          * @return
 149          */
 150         public Set<DescriptionBase> getDescriptions() {
 151                 if(descriptions == null) {
 152                         this.descriptions = new HashSet<DescriptionBase>();
 153                 }
 154                 return this.descriptions;
 155         }
 156
 157         /**
 158          * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
 159          * @see #getDescriptions()
 160          * @return
 161          */
 162         public Set<SpecimenDescription> getSpecimenDescriptions() {
 163                 return getSpecimenDescriptions(true);
 164         }
 165
 166         /**
 167          * Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
 168          * @see #getDescriptions()
 169          * @return
 170          */
 171         public Set<SpecimenDescription> getSpecimenDescriptions(boolean includeImageGallery) {
 172                 Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();
 173                 for (DescriptionBase descriptionBase : getDescriptions()){
 174                         if (descriptionBase.isInstanceOf(SpecimenDescription.class)){
 175                                 if (includeImageGallery || descriptionBase.isImageGallery() == false){
 176                                         specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));
 177                                 }
 178
 179                         }
 180                 }
 181                 return specimenDescriptions;
 182         }
 183
 184         /**
 185          * Adds a new description to this specimen or observation
 186          * @param description
 187          */
 188         public void addDescription(DescriptionBase description) {
 189                 this.descriptions.add(description);
 190                 if (! description.getDescribedSpecimenOrObservations().contains(this)){
 191                         description.addDescribedSpecimenOrObservation(this);
 192                 }
 193 //              Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "addDescribedSpecimenOrObservation", new Class[] {SpecimenOrObservationBase.class});
 194 //              ReflectionUtils.makeAccessible(method);
 195 //              ReflectionUtils.invokeMethod(method, description, new Object[] {this});
 196         }
 197
 198         /**
 199          * Removes a specimen from a description (removes a description from this specimen)
 200          * @param description
 201          */
 202         public void removeDescription(DescriptionBase description) {
 203                 this.descriptions.remove(description);
 204                 if (description.getDescribedSpecimenOrObservations().contains(this)){
 205                         description.removeDescribedSpecimenOrObservation(this);
 206                 }
 207 //              Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "removeDescribedSpecimenOrObservations", new Class[] {SpecimenOrObservationBase.class});
 208 //              ReflectionUtils.makeAccessible(method);
 209 //              ReflectionUtils.invokeMethod(method, description, new Object[] {this});
 210         }
 211
 212         public Set<DerivationEvent> getDerivationEvents() {
 213                 if(derivationEvents == null) {
 214                         this.derivationEvents = new HashSet<DerivationEvent>();
 215                 }
 216                 return this.derivationEvents;
 217         }
 218
 219         public void addDerivationEvent(DerivationEvent derivationEvent) {
 220                 if (! this.derivationEvents.contains(derivationEvent)){
 221                         this.derivationEvents.add(derivationEvent);
 222                         derivationEvent.addOriginal(this);
 223                 }
 224         }
 225
 226         public void removeDerivationEvent(DerivationEvent derivationEvent) {
 227                 this.derivationEvents.remove(derivationEvent);
 228         }
 229
 230         public Set<DeterminationEvent> getDeterminations() {
 231                 if(determinations == null) {
 232                         this.determinations = new HashSet<DeterminationEvent>();
 233                 }
 234                 return this.determinations;
 235         }
 236
 237         public void addDetermination(DeterminationEvent determination) {
 238                 // FIXME bidirectional integrity. Use protected Determination setter
 239                 this.determinations.add(determination);
 240         }
 241
 242         public void removeDetermination(DeterminationEvent determination) {
 243                 // FIXME bidirectional integrity. Use protected Determination setter
 244                 this.determinations.remove(determination);
 245         }
 246
 247         public Sex getSex() {
 248                 return sex;
 249         }
 250
 251         public void setSex(Sex sex) {
 252                 this.sex = sex;
 253         }
 254
 255         public Stage getLifeStage() {
 256                 return lifeStage;
 257         }
 258
 259         public void setLifeStage(Stage lifeStage) {
 260                 this.lifeStage = lifeStage;
 261         }
 262
 263         @Override
 264         public String generateTitle(){
 265                 return getCacheStrategy().getTitleCache(this);
 266         }
 267
 268         public Integer getIndividualCount() {
 269                 return individualCount;
 270         }
 271
 272         public void setIndividualCount(Integer individualCount) {
 273                 this.individualCount = individualCount;
 274         }
 275
 276         public Map<Language,LanguageString> getDefinition(){
 277                 return this.description;
 278         }
 279
 280         public void addDefinition(LanguageString description){
 281                 this.description.put(description.getLanguage(),description);
 282         }
 283
 284         public void addDefinition(String text, Language language){
 285                 this.description.put(language, LanguageString.NewInstance(text, language));
 286         }
 287         public void removeDefinition(Language lang){
 288                 this.description.remove(lang);
 289         }
 290
 291         /**
 292          * for derived units get the single next higher parental/original unit.
 293          * If multiple original units exist throw error
 294          * @return
 295          */
 296         @Transient
 297         public SpecimenOrObservationBase getOriginalUnit(){
 298                 logger.warn("GetOriginalUnit not yet implemented");
 299                 return null;
 300         }
 301
 302         @Transient
 303         public abstract GatheringEvent getGatheringEvent();
 304
 305
 306 //******************** CLONE **********************************************/
 307
 308         /* (non-Javadoc)
 309          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 310          * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
 311          * @see java.lang.Object#clone()
 312          */
 313         @Override
 314         public Object clone() throws CloneNotSupportedException {
 315                 SpecimenOrObservationBase result = null;
 316                 result = (SpecimenOrObservationBase)super.clone();
 317
 318                 //defininion (description, languageString)
 319                 result.description = new HashMap<Language,LanguageString>();
 320                 for(LanguageString languageString : this.description.values()) {
 321                         LanguageString newLanguageString = (LanguageString)languageString.clone();
 322                         result.addDefinition(newLanguageString);
 323                 }
 324
 325                 //sex
 326                 result.setSex(this.sex);
 327                 //life stage
 328                 result.setLifeStage(this.lifeStage);
 329
 330                 //Descriptions
 331                 for(DescriptionBase description : this.descriptions) {
 332                         result.addDescription((SpecimenDescription)description);
 333                 }
 334
 335                 //DeterminationEvent FIXME should clone() the determination
 336                 // as the relationship is OneToMany
 337                 for(DeterminationEvent determination : this.determinations) {
 338                         result.addDetermination(determination);
 339                 }
 340
 341                 //DerivationEvent
 342                 for(DerivationEvent derivationEvent : this.derivationEvents) {
 343                         result.addDerivationEvent(derivationEvent);
 344                 }
 345
 346                 //no changes to: individualCount
 347                 return result;
 348         }
 349 }