cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/SpecimenTypeDesignation.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.name;
  11
  12
  13 import javax.persistence.Entity;
  14 import javax.persistence.FetchType;
  15 import javax.persistence.JoinColumn;
  16 import javax.persistence.ManyToOne;
  17 import javax.xml.bind.annotation.XmlAccessType;
  18 import javax.xml.bind.annotation.XmlAccessorType;
  19 import javax.xml.bind.annotation.XmlElement;
  20 import javax.xml.bind.annotation.XmlIDREF;
  21 import javax.xml.bind.annotation.XmlRootElement;
  22 import javax.xml.bind.annotation.XmlSchemaType;
  23 import javax.xml.bind.annotation.XmlType;
  24
  25 import org.apache.logging.log4j.LogManager;
  26 import org.apache.logging.log4j.Logger;
  27 import org.hibernate.annotations.Cascade;
  28 import org.hibernate.annotations.CascadeType;
  29 import org.hibernate.envers.Audited;
  30
  31 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  32 import eu.etaxonomy.cdm.model.reference.Reference;
  33
  34 /**
  35  * The class representing a typification of one or several {@link TaxonName taxon names} by a
  36  * {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or a figure}. All {@link TaxonName taxon names}
  37  * which have a {@link Rank rank} "species aggregate" or lower can only be typified
  38  * by specimens. Moreover each typification by a specimen (or by a figure) has a
  39  * {@link SpecimenTypeDesignationStatus status} like "holotype" or "isotype".
  40  * <P>
  41  * This class corresponds to: <ul>
  42  * <li> NomenclaturalType according to the TDWG ontology
  43  * <li> Typification (partially) according to the TCS
  44  * <li> NomenclaturalTypeDesignation according to the ABCD schema
  45  * </ul>
  46  *
  47  * @see         TypeDesignationBase
  48  * @see         NameTypeDesignation
  49  * @author      m.doering
  50  * @since 08-Nov-2007 13:06:38
  51  */
  52 @XmlRootElement(name = "SpecimenTypeDesignation")
  53 @XmlAccessorType(XmlAccessType.FIELD)
  54 @XmlType(name = "SpecimenTypeDesignation", propOrder = {
  55     "typeSpecimen"
  56 })
  57 @Entity
  58 @Audited
  59 public class SpecimenTypeDesignation
  60         extends TypeDesignationBase<SpecimenTypeDesignationStatus> {
  61
  62         private static final long serialVersionUID = 6481627446997275007L;
  63         private static final Logger logger = LogManager.getLogger();
  64
  65         @XmlElement(name = "TypeSpecimen")
  66         @XmlIDREF
  67         @XmlSchemaType(name = "IDREF")
  68         @ManyToOne(fetch = FetchType.LAZY)
  69         @JoinColumn(name="typeSpecimen_id")
  70         @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
  71         private DerivedUnit typeSpecimen;
  72
  73
  74     public static SpecimenTypeDesignation NewInstance() {
  75         return new SpecimenTypeDesignation();
  76     }
  77
  78 //      /**
  79 //       * Creates a new specimen type designation instance
  80 //       * (including its {@link reference.Reference reference source} and eventually
  81 //       * the taxon name string originally used by this reference when establishing
  82 //       * the former designation) and adds it to the corresponding
  83 //       * {@link HomotypicalGroup#getSpecimenTypeDesignations() specimen type designation set} of the
  84 //       * {@link HomotypicalGroup homotypical group}.
  85 //       *
  86 //       * @param specimen                              the derived unit (specimen or figure) used as type
  87 //       * @param status                                the type designation status
  88 //       * @param citation                              the reference source for the new designation
  89 //       * @param citationMicroReference        the string with the details describing the exact localisation within the reference
  90 //       * @param originalInfo          any information from the original source, might be the name as written in the source (#10097)
  91 //       * @see                                                 #SpecimenTypeDesignation(DerivedUnit, TypeDesignationStatus, Reference, String, String)
  92 //       * @see                                                 HomotypicalGroup#addSpecimenTypeDesignation(SpecimenTypeDesignation, boolean)
  93 //       * @see                                                 occurrence.DerivedUnit
  94 //       */
  95 //      protected static SpecimenTypeDesignation NewInstance2(DerivedUnit specimen, TypeDesignationStatus status,
  96 //                      Reference citation, String citationMicroReference, String originalInfo){
  97 //              SpecimenTypeDesignation specTypeDesig = new SpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalInfo);
  98 //              return specTypeDesig;
  99 //      }
 100
 101 // ************* CONSTRUCTORS *************/
 102         /**
 103          * Class constructor: creates a new empty specimen type designation.
 104          *
 105          * @see #SpecimenTypeDesignation(DerivedUnit, SpecimenTypeDesignationStatus,
 106          * Reference, String, String, boolean)
 107          */
 108         protected SpecimenTypeDesignation(){
 109         }
 110
 111
 112         /**
 113          * Class constructor: creates a new specimen type designation instance
 114          * (including its {@link eu.etaxonomy.cdm.model.reference.Reference reference source} and
 115          * eventually the taxon name string originally used by this reference when
 116          * establishing the former designation).
 117          *
 118          * @param specimen                              the derived unit (specimen or figure) used
 119          *                                                              as type
 120          * @param status                                the type designation status
 121          * @param citation                              the reference source for the new designation
 122          * @param citationMicroReference        the string with the details describing
 123          *                                                              the exact localisation within the reference
 124          * @param originalInfo          any information from the original source, might be the name as written in the source (#10097)
 125          *                                                              reference source for the new designation
 126          * @param isNotDesignated               the boolean flag indicating whether there is no specimen type at all for
 127          *                                                              <i>this</i> specimen type designation
 128          * @see                                                 #SpecimenTypeDesignation()
 129          * @see                                                 TaxonName#addSpecimenTypeDesignation(Specimen, SpecimenTypeDesignationStatus, Reference, String, String, boolean, boolean)
 130          * @see                                                 TypeDesignationBase#isNotDesignated()
 131          * @see                                                 eu.etaxonomy.cdm.model.occurrence.DerivedUnit
 132          */
 133         protected SpecimenTypeDesignation(DerivedUnit specimen, SpecimenTypeDesignationStatus status, Reference citation, String citationMicroReference,
 134                         String originalInfo, boolean isNotDesignated) {
 135                 super(citation, citationMicroReference, originalInfo, isNotDesignated);
 136                 this.setTypeSpecimen(specimen);
 137                 this.setTypeStatus(status);
 138         }
 139
 140 //********* METHODS **************************************/
 141
 142         @Override
 143         public void removeType() {
 144                 this.setTypeSpecimen(null);
 145         }
 146
 147         /**
 148          * Returns the {@link DerivedUnit.DerivedUnit derived unit} (specimen or figure) that is used
 149          * in <i>this</i> specimen type designation to typify the {@link TaxonName taxon name}.
 150          *
 151          * @see   #getHomotypicalGroup()
 152          */
 153         public DerivedUnit getTypeSpecimen(){
 154                 return this.typeSpecimen;
 155         }
 156
 157         /**
 158          * @see  #getTypeSpecimen()
 159          */
 160         public void setTypeSpecimen(DerivedUnit typeSpecimen){
 161                 if (this.typeSpecimen == typeSpecimen){
 162                         return;
 163                 }
 164                 if (this.typeSpecimen != null){
 165                         this.typeSpecimen.removeSpecimenTypeDesignation(this);
 166                 }
 167                 if (typeSpecimen != null && ! typeSpecimen.getSpecimenTypeDesignations().contains(this)){
 168                         typeSpecimen.addSpecimenTypeDesignation(this);
 169                 }
 170                 this.typeSpecimen = typeSpecimen;
 171         }
 172
 173 //*********************** CLONE ********************************************************/
 174
 175         /**
 176          * Clones <i>this</i> type specimen. This is a shortcut that enables to create
 177          * a new instance that differs only slightly from <i>this</i> type specimen by
 178          * modifying only some of the attributes.
 179          *
 180          * @see eu.etaxonomy.cdm.model.name.TypeDesignationBase#clone()
 181          * @see java.lang.Object#clone()
 182          */
 183         @Override
 184         public SpecimenTypeDesignation clone() {
 185
 186                 SpecimenTypeDesignation result;
 187                 try {
 188                         result = (SpecimenTypeDesignation)super.clone();
 189                         //no changes to: typeSpecimen
 190                         return result;
 191                 } catch (CloneNotSupportedException e) {
 192                         logger.warn("Object does not implement cloneable");
 193                         e.printStackTrace();
 194                         return null;
 195                 }
 196         }
 197 }