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         private PreservationMethod preservation;
 149
 150
 151         @XmlElement(name = "Exsiccatum")
 152     //TODO Val #3379
 153 //      @NullOrNotEmpty
 154         @Field
 155         @Size(max = 255)
 156     private String exsiccatum;
 157
 158 // ******************** FACTORY METHOD **********************************/
 159
 160
 161         public static DerivedUnit NewInstance(SpecimenOrObservationType type) {
 162                 return new DerivedUnit(type);
 163         }
 164
 165         /**
 166          * Factory method
 167          * @return
 168          */
 169         public static DerivedUnit NewPreservedSpecimenInstance(){
 170                 DerivedUnit result = new DerivedUnit(SpecimenOrObservationType.PreservedSpecimen);
 171                 return result;
 172         }
 173
 174 //************************** CONSTRUCTOR *********************************/
 175
 176         //Constructor: For hibernate use only
 177         protected DerivedUnit() {super();}
 178
 179
 180         /**
 181          * Constructor
 182          * @param recordBasis
 183          */
 184         protected DerivedUnit(SpecimenOrObservationType recordBasis) {
 185                 super(recordBasis);
 186         }
 187
 188
 189         /**
 190          * Create new unit derived from an existing field unit
 191          * @param fieldUnit existing field unit from where this unit is derived
 192          */
 193         protected DerivedUnit(SpecimenOrObservationType recordBasis, FieldUnit fieldUnit) {
 194                 super(recordBasis);
 195                 DerivationEvent derivedFrom = new DerivationEvent();
 196                 // TODO: should be done in a more controlled way. Probably by making derivation event implement a general relationship interface (for bidirectional add/remove etc)
 197                 fieldUnit.addDerivationEvent(derivedFrom);
 198                 derivedFrom.getOriginals().add(fieldUnit);
 199                 derivedFrom.getDerivatives().add(this);
 200                 this.setDerivedFrom(derivedFrom);
 201         }
 202
 203         /**
 204          * create new unit derived from an existing gathering event,
 205          * thereby creating a new empty field unit
 206          * @param gatheringEvent the gathering event this unit was collected at
 207          */
 208         protected DerivedUnit(SpecimenOrObservationType recordBasis, GatheringEvent gatheringEvent) {
 209                 this(recordBasis, new FieldUnit());
 210                 FieldUnit field = (FieldUnit)this.getOriginalUnit();
 211                 field.setGatheringEvent(gatheringEvent);
 212         }
 213
 214 // ******************** GETTER / SETTER *************************************/
 215
 216         public DerivationEvent getDerivedFrom() {
 217                 return derivedFrom;
 218         }
 219
 220         public void setDerivedFrom(DerivationEvent derivedFrom){
 221                 if (getDerivedFrom() != null){
 222                         getDerivedFrom().getDerivatives().remove(derivedFrom);
 223                 }
 224                 this.derivedFrom = derivedFrom;
 225                 if (derivedFrom != null){
 226                         derivedFrom.addDerivative(this);
 227                 }
 228         }
 229
 230         @Transient
 231         public Set<SpecimenOrObservationBase> getOriginals(){
 232                 if(getDerivedFrom() != null){
 233                         return getDerivedFrom().getOriginals();
 234                 }
 235                 return null;
 236         }
 237
 238         public Collection getCollection(){
 239                 return this.collection;
 240         }
 241
 242         public void setCollection(Collection collection){
 243                 this.collection = collection;
 244         }
 245
 246
 247         public String getCatalogNumber() {
 248                 return catalogNumber;
 249         }
 250
 251         public void setCatalogNumber(String catalogNumber) {
 252                 this.catalogNumber = catalogNumber;
 253         }
 254
 255         public void setBarcode(String barcode) {
 256                 this.barcode = barcode;
 257         }
 258         public String getBarcode() {
 259                 return barcode;
 260         }
 261
 262         public void setStoredUnder(TaxonNameBase storedUnder) {
 263                 this.storedUnder = storedUnder;
 264         }
 265
 266         public String getAccessionNumber() {
 267                 return accessionNumber;
 268         }
 269
 270
 271         public void setAccessionNumber(String accessionNumber) {
 272                 this.accessionNumber = accessionNumber;
 273         }
 274
 275         /**
 276          * Will be removed in future versions as semantics is not clear.
 277          * For accessing the collecting number use
 278          * {@link FieldUnit#getFieldNumber()} instead.
 279          * @return
 280          */
 281         @Deprecated
 282         public String getCollectorsNumber() {
 283                 return collectorsNumber;
 284         }
 285
 286         /**
 287          * Will be removed in future versions as semantics is not clear.
 288          * For editing the collecting number use
 289          * {@link FieldUnit#getFieldNumber()} instead.
 290          * @return
 291          */
 292         @Deprecated
 293         public void setCollectorsNumber(String collectorsNumber) {
 294                 this.collectorsNumber = collectorsNumber;
 295         }
 296
 297         public TaxonNameBase getStoredUnder() {
 298                 return storedUnder;
 299         }
 300
 301         public void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){
 302                 if (specimenTypeDesignation.getTypeSpecimen() == this){
 303                         return ;
 304                 }else if (specimenTypeDesignation.getTypeSpecimen() != null){
 305                         specimenTypeDesignation.getTypeSpecimen().removeSpecimenTypeDesignation(specimenTypeDesignation);
 306
 307                 }
 308                 specimenTypeDesignations.add(specimenTypeDesignation);
 309                 specimenTypeDesignation.setTypeSpecimen(this);
 310         }
 311
 312         public void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation){
 313                 if (specimenTypeDesignation == null){
 314                         return;
 315                 }
 316                 if (specimenTypeDesignations.contains(specimenTypeDesignation)){
 317                         specimenTypeDesignations.remove(specimenTypeDesignation);
 318                         specimenTypeDesignation.setTypeSpecimen(null);
 319                 }
 320         }
 321
 322 // ******* GETTER / SETTER for preserved specimen only ******************/
 323
 324         public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations(){
 325                 return specimenTypeDesignations;
 326         }
 327
 328         public PreservationMethod getPreservation(){
 329                 return this.preservation;
 330         }
 331
 332         public void setPreservation(PreservationMethod preservation){
 333                 this.preservation = preservation;
 334         }
 335
 336
 337         public void setExsiccatum(String exsiccatum) {
 338                 this.exsiccatum = exsiccatum;
 339         }
 340
 341         public String getExsiccatum() {
 342                 return exsiccatum;
 343         }
 344
 345 //*********** CLONE **********************************/
 346
 347         /**
 348          * Clones <i>this</i> derivedUnit. This is a shortcut that enables to
 349          * create a new instance that differs only slightly from <i>this</i> specimen
 350          * by modifying only some of the attributes.<BR>
 351          * This method overrides the clone method from {@link SpecimenOrObservationBase SpecimenOrObservationBase}.
 352          *
 353          * @see SpecimenOrObservationBase#clone()
 354          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 355          * @see java.lang.Object#clone()
 356          */
 357         @Override
 358         public Object clone() {
 359                 try{
 360                         DerivedUnit result = (DerivedUnit)super.clone();
 361                         //collection
 362                         result.setCollection(this.collection);
 363                         //derivedFrom
 364                         result.setDerivedFrom(this.derivedFrom);
 365                         //storedUnder
 366                         result.setStoredUnder(this.storedUnder);
 367                         //preservation
 368                         result.setPreservation(this.preservation);
 369                         //no changes to: accessionNumber, catalogNumber, collectorsNumber
 370                         return result;
 371                 } catch (CloneNotSupportedException e) {
 372                         logger.warn("Object does not implement cloneable");
 373                         e.printStackTrace();
 374                         return null;
 375                 }
 376         }
 377
 378
 379 }