cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivedUnit.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.HashSet;
  13 import java.util.Set;
  14
  15 import javax.persistence.Entity;
  16 import javax.persistence.FetchType;
  17 import javax.persistence.ManyToOne;
  18 import javax.persistence.OneToMany;
  19 import javax.persistence.Transient;
  20 import javax.validation.constraints.Size;
  21 import javax.xml.bind.annotation.XmlAccessType;
  22 import javax.xml.bind.annotation.XmlAccessorType;
  23 import javax.xml.bind.annotation.XmlElement;
  24 import javax.xml.bind.annotation.XmlElementWrapper;
  25 import javax.xml.bind.annotation.XmlIDREF;
  26 import javax.xml.bind.annotation.XmlRootElement;
  27 import javax.xml.bind.annotation.XmlSchemaType;
  28 import javax.xml.bind.annotation.XmlType;
  29
  30 import org.apache.log4j.Logger;
  31 import org.hibernate.annotations.Cascade;
  32 import org.hibernate.annotations.CascadeType;
  33 import org.hibernate.envers.Audited;
  34 import org.hibernate.search.annotations.Analyze;
  35 import org.hibernate.search.annotations.Field;
  36 import org.hibernate.search.annotations.Indexed;
  37 import org.hibernate.search.annotations.IndexedEmbedded;
  38 import org.hibernate.validator.constraints.Length;
  39
  40 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  41 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  42 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  43 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  44
  45 /**
  46  * A derived unit is regarded as derived from a field unit,
  47  * so locality and gathering related information is captured as a separate FieldUnit object
  48  * related to a specimen via a derivation event
  49  *
  50  * http://www.bgbm.org/biodivinf/docs/CollectionModel/ReprintTNR.pdf
  51  * http://www.bgbm.org/biodivinf/docs/CollectionModel/
  52  * <BR>
  53  * Type figures are derived units with at least a figure object in media
  54  *
  55  * @author m.doering
  56  * @created 08-Nov-2007 13:06:52
  57  *
  58  */
  59 @XmlAccessorType(XmlAccessType.FIELD)
  60 @XmlType(name = "DerivedUnit", propOrder = {
  61     "collection",
  62     "catalogNumber",
  63     "storedUnder",
  64     "derivedFrom",
  65     "accessionNumber",
  66     "collectorsNumber",
  67     "barcode",
  68         "preservation",
  69         "exsiccatum",
  70     "specimenTypeDesignations"
  71 })
  72 @XmlRootElement(name = "DerivedUnit")
  73 @Entity
  74 @Audited
  75 // even if hibernate complains "Abstract classes can never insert index documents. Remove @Indexed."
  76 // this is needed, otherwise the fields of the also abstract super class are missed during indexing
  77 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  78 public class DerivedUnit extends SpecimenOrObservationBase<IIdentifiableEntityCacheStrategy> implements Cloneable{
  79         private static final long serialVersionUID = -3525746216270843517L;
  80
  81         private static final Logger logger = Logger.getLogger(DnaSample.class);
  82
  83         @XmlElement(name = "Collection")
  84         @XmlIDREF
  85         @XmlSchemaType(name = "IDREF")
  86         @ManyToOne(fetch = FetchType.LAZY)
  87         @Cascade(CascadeType.SAVE_UPDATE)
  88         @IndexedEmbedded
  89         private Collection collection;
  90
  91         @XmlElement(name = "CatalogNumber")
  92         @Field(analyze = Analyze.NO)
  93     //TODO Val #3379
  94 //      @NullOrNotEmpty
  95         @Length(max = 255)
  96         private String catalogNumber;
  97
  98         @XmlElement(name = "AccessionNumber")
  99         @Field(analyze = Analyze.NO)
 100     //TODO Val #3379
 101 //      @NullOrNotEmpty
 102         @Length(max = 255)
 103         private String accessionNumber;
 104
 105         @XmlElement(name = "CollectorsNumber")
 106         @Field(analyze = Analyze.NO)
 107     //TODO Val #3379
 108 //      @NullOrNotEmpty
 109         @Length(max = 255)
 110         private String collectorsNumber;
 111
 112         @XmlElement(name = "Barcode")
 113         @Field(analyze = Analyze.NO)
 114     //TODO Val #3379
 115 //      @NullOrNotEmpty
 116         @Length(max = 255)
 117         private String barcode;
 118
 119         @XmlElement(name = "StoredUnder")
 120         @XmlIDREF
 121         @XmlSchemaType(name = "IDREF")
 122         @ManyToOne(fetch = FetchType.LAZY)
 123         @Cascade(CascadeType.SAVE_UPDATE)
 124         @IndexedEmbedded
 125         private TaxonNameBase storedUnder;
 126
 127         @XmlElement(name = "DerivedFrom")
 128         @XmlIDREF
 129         @XmlSchemaType(name = "IDREF")
 130         @ManyToOne(fetch = FetchType.LAZY)
 131         @Cascade(CascadeType.SAVE_UPDATE)
 132         @IndexedEmbedded(depth = 4)
 133         private DerivationEvent derivedFrom;
 134
 135         @XmlElementWrapper(name = "SpecimenTypeDesignations")
 136         @XmlElement(name = "SpecimenTypeDesignation")
 137         @OneToMany(fetch = FetchType.LAZY, mappedBy = "typeSpecimen")
 138         @Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE })
 139         private final Set<SpecimenTypeDesignation> specimenTypeDesignations = new HashSet<SpecimenTypeDesignation>();
 140
 141
 142 //*** attributes valid only for preserved specimen (PreservedSpecimen, Fossil, DnaSample)
 143
 144         @XmlElement(name = "Preservation")
 145         @XmlIDREF
 146         @XmlSchemaType(name = "IDREF")
 147         @ManyToOne(fetch = FetchType.LAZY)
 148     @Cascade(CascadeType.SAVE_UPDATE)
 149         private PreservationMethod preservation;
 150
 151
 152         @XmlElement(name = "Exsiccatum")
 153     //TODO Val #3379
 154 //      @NullOrNotEmpty
 155         @Field
 156         @Size(max = 255)
 157     private String exsiccatum;
 158
 159 // ******************** FACTORY METHOD **********************************/
 160
 161
 162         public static DerivedUnit NewInstance(SpecimenOrObservationType type) {
 163                 return new DerivedUnit(type);
 164         }
 165
 166         /**
 167          * Factory method
 168          * @return
 169          */
 170         public static DerivedUnit NewPreservedSpecimenInstance(){
 171                 DerivedUnit result = new DerivedUnit(SpecimenOrObservationType.PreservedSpecimen);
 172                 return result;
 173         }
 174
 175 //************************** CONSTRUCTOR *********************************/
 176
 177         //Constructor: For hibernate use only
 178         protected DerivedUnit() {super();}
 179
 180
 181         /**
 182          * Constructor
 183          * @param recordBasis
 184          */
 185         protected DerivedUnit(SpecimenOrObservationType recordBasis) {
 186                 super(recordBasis);
 187         }
 188
 189
 190         /**
 191          * Create new unit derived from an existing field unit
 192          * @param fieldUnit existing field unit from where this unit is derived
 193          */
 194         protected DerivedUnit(SpecimenOrObservationType recordBasis, FieldUnit fieldUnit) {
 195                 super(recordBasis);
 196                 DerivationEvent derivedFrom = new DerivationEvent();
 197                 // TODO: should be done in a more controlled way. Probably by making derivation event implement a general relationship interface (for bidirectional add/remove etc)
 198                 fieldUnit.addDerivationEvent(derivedFrom);
 199                 derivedFrom.getOriginals().add(fieldUnit);
 200                 derivedFrom.getDerivatives().add(this);
 201                 this.setDerivedFrom(derivedFrom);
 202         }
 203
 204         /**
 205          * create new unit derived from an existing gathering event,
 206          * thereby creating a new empty field unit
 207          * @param gatheringEvent the gathering event this unit was collected at
 208          */
 209         protected DerivedUnit(SpecimenOrObservationType recordBasis, GatheringEvent gatheringEvent) {
 210                 this(recordBasis, new FieldUnit());
 211                 FieldUnit field = (FieldUnit)this.getOriginalUnit();
 212                 field.setGatheringEvent(gatheringEvent);
 213         }
 214
 215 // ******************** GETTER / SETTER *************************************/
 216
 217         public DerivationEvent getDerivedFrom() {
 218                 return derivedFrom;
 219         }
 220
 221         public void setDerivedFrom(DerivationEvent derivedFrom){
 222                 if (getDerivedFrom() != null){
 223                         getDerivedFrom().getDerivatives().remove(derivedFrom);
 224                 }
 225                 this.derivedFrom = derivedFrom;
 226                 if (derivedFrom != null){
 227                         derivedFrom.addDerivative(this);
 228                 }
 229         }
 230
 231         @Transient
 232         public Set<SpecimenOrObservationBase> getOriginals(){
 233                 if(getDerivedFrom() != null){
 234                         return getDerivedFrom().getOriginals();
 235                 }
 236                 return null;
 237         }
 238
 239         public Collection getCollection(){
 240                 return this.collection;
 241         }
 242
 243         public void setCollection(Collection collection){
 244                 this.collection = collection;
 245         }
 246
 247
 248         public String getCatalogNumber() {
 249                 return catalogNumber;
 250         }
 251
 252         public void setCatalogNumber(String catalogNumber) {
 253                 this.catalogNumber = catalogNumber;
 254         }
 255
 256         public void setBarcode(String barcode) {
 257                 this.barcode = barcode;
 258         }
 259         public String getBarcode() {
 260                 return barcode;
 261         }
 262
 263         public void setStoredUnder(TaxonNameBase storedUnder) {
 264                 this.storedUnder = storedUnder;
 265         }
 266
 267         public String getAccessionNumber() {
 268                 return accessionNumber;
 269         }
 270
 271
 272         public void setAccessionNumber(String accessionNumber) {
 273                 this.accessionNumber = accessionNumber;
 274         }
 275
 276         /**
 277          * Will be removed in future versions as semantics is not clear.
 278          * For accessing the collecting number use
 279          * {@link FieldUnit#getFieldNumber()} instead.
 280          * @return
 281          */
 282         @Deprecated
 283         public String getCollectorsNumber() {
 284                 return collectorsNumber;
 285         }
 286
 287         /**
 288          * Will be removed in future versions as semantics is not clear.
 289          * For editing the collecting number use
 290          * {@link FieldUnit#getFieldNumber()} instead.
 291          * @return
 292          */
 293         @Deprecated
 294         public void setCollectorsNumber(String collectorsNumber) {
 295                 this.collectorsNumber = collectorsNumber;
 296         }
 297
 298         public TaxonNameBase getStoredUnder() {
 299                 return storedUnder;
 300         }
 301
 302         public void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){
 303                 if (specimenTypeDesignation.getTypeSpecimen() == this){
 304                         return ;
 305                 }else if (specimenTypeDesignation.getTypeSpecimen() != null){
 306                         specimenTypeDesignation.getTypeSpecimen().removeSpecimenTypeDesignation(specimenTypeDesignation);
 307
 308                 }
 309                 specimenTypeDesignations.add(specimenTypeDesignation);
 310                 specimenTypeDesignation.setTypeSpecimen(this);
 311         }
 312
 313         public void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){
 314                 if (specimenTypeDesignation == null){
 315                         return;
 316                 }
 317                 if (specimenTypeDesignations.contains(specimenTypeDesignation)){
 318                         specimenTypeDesignations.remove(specimenTypeDesignation);
 319                         specimenTypeDesignation.setTypeSpecimen(null);
 320                 }
 321         }
 322
 323 // ******* GETTER / SETTER for preserved specimen only ******************/
 324
 325         public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations(){
 326                 return specimenTypeDesignations;
 327         }
 328
 329         public PreservationMethod getPreservation(){
 330                 return this.preservation;
 331         }
 332
 333         public void setPreservation(PreservationMethod preservation){
 334                 this.preservation = preservation;
 335         }
 336
 337
 338         public void setExsiccatum(String exsiccatum) {
 339                 this.exsiccatum = exsiccatum;
 340         }
 341
 342         public String getExsiccatum() {
 343                 return exsiccatum;
 344         }
 345
 346 //*********** CLONE **********************************/
 347
 348         /**
 349          * Clones <i>this</i> derivedUnit. This is a shortcut that enables to
 350          * create a new instance that differs only slightly from <i>this</i> specimen
 351          * by modifying only some of the attributes.<BR>
 352          * This method overrides the clone method from {@link SpecimenOrObservationBase SpecimenOrObservationBase}.
 353          *
 354          * @see SpecimenOrObservationBase#clone()
 355          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 356          * @see java.lang.Object#clone()
 357          */
 358         @Override
 359         public Object clone() {
 360                 try{
 361                         DerivedUnit result = (DerivedUnit)super.clone();
 362                         //collection
 363                         result.setCollection(this.collection);
 364                         //derivedFrom
 365                         result.setDerivedFrom(this.derivedFrom);
 366                         //storedUnder
 367                         result.setStoredUnder(this.storedUnder);
 368                         //preservation
 369                         result.setPreservation(this.preservation);
 370                         //no changes to: accessionNumber, catalogNumber, collectorsNumber
 371                         return result;
 372                 } catch (CloneNotSupportedException e) {
 373                         logger.warn("Object does not implement cloneable");
 374                         e.printStackTrace();
 375                         return null;
 376                 }
 377         }
 378
 379
 380 }