cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.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.taxon;
  11
  12 import java.lang.reflect.Method;
  13
  14 import javax.persistence.Entity;
  15 import javax.persistence.FetchType;
  16 import javax.persistence.ManyToOne;
  17 import javax.persistence.Transient;
  18 import javax.validation.constraints.NotNull;
  19 import javax.xml.bind.annotation.XmlAccessType;
  20 import javax.xml.bind.annotation.XmlAccessorType;
  21 import javax.xml.bind.annotation.XmlAttribute;
  22 import javax.xml.bind.annotation.XmlElement;
  23 import javax.xml.bind.annotation.XmlIDREF;
  24 import javax.xml.bind.annotation.XmlSchemaType;
  25 import javax.xml.bind.annotation.XmlType;
  26
  27 import org.apache.log4j.Logger;
  28 import org.hibernate.annotations.Cascade;
  29 import org.hibernate.annotations.CascadeType;
  30 import org.hibernate.annotations.Index;
  31 import org.hibernate.annotations.Table;
  32 import org.hibernate.envers.Audited;
  33 import org.hibernate.search.annotations.ClassBridge;
  34 import org.hibernate.search.annotations.ClassBridges;
  35 import org.hibernate.search.annotations.IndexedEmbedded;
  36 import org.hibernate.search.annotations.Store;
  37
  38 import eu.etaxonomy.cdm.hibernate.search.AcceptedTaxonBridge;
  39 import eu.etaxonomy.cdm.hibernate.search.ClassInfoBridge;
  40 import eu.etaxonomy.cdm.model.common.IPublishable;
  41 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  42 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  43 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  44 import eu.etaxonomy.cdm.model.reference.Reference;
  45 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  46 import eu.etaxonomy.cdm.validation.Level2;
  47 import eu.etaxonomy.cdm.validation.Level3;
  48 import eu.etaxonomy.cdm.validation.annotation.TaxonNameCannotBeAcceptedAndSynonym;
  49
  50 /**
  51  * The upmost (abstract) class for the use of a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} in a {@link eu.etaxonomy.cdm.model.reference.Reference reference}
  52  * or within a taxonomic view/treatment either as a {@link Taxon taxon}
  53  * ("accepted" respectively "correct" name) or as a (junior) {@link Synonym synonym}.
  54  * Within a taxonomic view/treatment or a reference a taxon name can be used
  55  * only in one of both described meanings. The reference using the taxon name
  56  * is generally cited with "sec." (secundum, sensu). For instance:
  57  * "<i>Juncus longirostris</i> Kuvaev sec. Kirschner, J. et al. 2002".
  58  * <P>
  59  * This class corresponds to: <ul>
  60  * <li> TaxonConcept according to the TDWG ontology
  61  * <li> TaxonConcept according to the TCS
  62  * </ul>
  63  *
  64  * @author m.doering
  65  * @created 08-Nov-2007 13:06:56
  66  */
  67 @XmlAccessorType(XmlAccessType.FIELD)
  68 @XmlType(name = "TaxonBase", propOrder = {
  69     "name",
  70     "sec",
  71     "doubtful",
  72     "appendedPhrase",
  73     "useNameCache",
  74     "publish"
  75 })
  76 @Entity
  77 @Audited
  78 //@PreFilter("hasPermission(filterObject, 'edit')")
  79 @Table(appliesTo="TaxonBase", indexes = { @Index(name = "taxonBaseTitleCacheIndex", columnNames = { "titleCache" }) })
  80 @TaxonNameCannotBeAcceptedAndSynonym(groups = Level3.class)
  81 @ClassBridges({
  82     @ClassBridge(name="classInfo",
  83             index = org.hibernate.search.annotations.Index.YES,
  84             store = Store.YES,
  85             impl = ClassInfoBridge.class),
  86     @ClassBridge(name="accTaxon", // TODO rename to acceptedTaxon, since we are usually not using abbreviations for field names
  87             index = org.hibernate.search.annotations.Index.YES,
  88             store = Store.YES,
  89             impl = AcceptedTaxonBridge.class),
  90     @ClassBridge(impl = eu.etaxonomy.cdm.hibernate.search.NomenclaturalSortOrderBrigde.class)
  91 })
  92 public abstract class TaxonBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements  IPublishable, Cloneable {
  93     private static final long serialVersionUID = -3589185949928938529L;
  94     private static final Logger logger = Logger.getLogger(TaxonBase.class);
  95
  96     private static Method methodTaxonNameAddTaxonBase;
  97
  98     static {
  99         try {
 100             methodTaxonNameAddTaxonBase = TaxonNameBase.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);
 101             methodTaxonNameAddTaxonBase.setAccessible(true);
 102         } catch (Exception e) {
 103             logger.error(e);
 104             for(StackTraceElement ste : e.getStackTrace()) {
 105                 logger.error(ste);
 106             }
 107         }
 108     }
 109
 110     //The assignment to the Taxon or to the Synonym class is not definitive
 111     @XmlAttribute(name = "isDoubtful")
 112     private boolean doubtful;
 113
 114
 115     @XmlElement(name = "Name", required = true)
 116     @XmlIDREF
 117     @XmlSchemaType(name = "IDREF")
 118     @ManyToOne(fetch = FetchType.LAZY)
 119     @IndexedEmbedded
 120     @Cascade(CascadeType.SAVE_UPDATE)
 121     @NotNull(groups = Level2.class)
 122     private TaxonNameBase<?,?> name;
 123
 124     // The concept reference
 125     @XmlElement(name = "Sec")
 126     @XmlIDREF
 127     @XmlSchemaType(name = "IDREF")
 128     @ManyToOne(fetch = FetchType.LAZY)
 129     @Cascade(CascadeType.SAVE_UPDATE)
 130     @NotNull(groups = Level2.class)
 131     @IndexedEmbedded
 132     private Reference<?> sec;
 133
 134
 135     @XmlElement(name = "AppendedPhrase")
 136     private String appendedPhrase;
 137
 138     @XmlAttribute(name= "UseNameCache")
 139     private boolean useNameCache = false;
 140
 141     @XmlAttribute(name = "publish")
 142     private boolean publish = true;
 143
 144
 145 // ************* CONSTRUCTORS *************/
 146     /**
 147      * Class constructor: creates a new empty (abstract) taxon.
 148      *
 149      * @see     #TaxonBase(TaxonNameBase, Reference)
 150      */
 151     protected TaxonBase(){
 152         super();
 153     }
 154
 155     /**
 156      * Class constructor: creates a new (abstract) taxon with the
 157      * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
 158      * using it.
 159      *
 160      * @param  taxonNameBase    the taxon name used
 161      * @param  sec                              the reference using the taxon name
 162      * @see    #TaxonBase()
 163      */
 164     protected TaxonBase(TaxonNameBase taxonNameBase, Reference sec){
 165         super();
 166         if (taxonNameBase != null){
 167             this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonNameBase);
 168         }
 169         this.setSec(sec);
 170     }
 171
 172 //********* METHODS **************************************/
 173
 174     /**
 175      * Generates and returns the string with the full scientific name (including
 176      * authorship) of the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i>
 177      * (abstract) taxon as well as the title of the {@link eu.etaxonomy.cdm.model.reference.Reference reference} using
 178      * this taxon name. This string may be stored in the inherited
 179      * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
 180      * This method overrides the generic and inherited generateTitle() method
 181      * from {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.
 182      *
 183      * @return  the string with the full scientific name of the taxon name
 184      *                  and with the title of the reference involved in <i>this</i> (abstract) taxon
 185      * @see     eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
 186      * @see     eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
 187      */
 188 //      @Override
 189 //      public String generateTitle() {
 190 //              String title;
 191 //              if (name != null && name.getTitleCache() != null){
 192 //                      title = name.getTitleCache() + " sec. ";
 193 //                      if (sec != null){
 194 //                              title += sec.getTitleCache();
 195 //                      }else{
 196 //                              title += "???";
 197 //                      }
 198 //              }else{
 199 //                      title = this.toString();
 200 //              }
 201 //              return title;
 202 //      }
 203
 204     /**
 205      * Returns the {@link TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.
 206      */
 207     public TaxonNameBase getName(){
 208         return this.name;
 209     }
 210
 211     /*
 212      * @see #getName
 213      */
 214     public void setName(TaxonNameBase name) {
 215         if (this.name != null){
 216             this.name.getTaxonBases().remove(this);
 217         }
 218         if(name != null) {
 219             name.getTaxonBases().add(this);
 220         }
 221         this.name = name;
 222     }
 223
 224     /**
 225      * Returns the {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical group} of the
 226      * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used in <i>this</i> (abstract) taxon.
 227      */
 228     @Transient
 229     public HomotypicalGroup getHomotypicGroup(){
 230         if (this.getName() == null){
 231             return null;
 232         }else{
 233             return this.getName().getHomotypicalGroup();
 234         }
 235     }
 236
 237     /**
 238      * Returns the boolean value indicating whether the assignment of <i>this</i>
 239      * (abstract) taxon to the {@link Taxon Taxon} or to the {@link Synonym Synonym} class
 240      * is definitive (false) or not (true). If this flag is set the use of <i>this</i> (abstract)
 241      * taxon as an "accepted/correct" name or as a (junior) "synonym" might
 242      * still change in the course of taxonomical working process.
 243      */
 244     public boolean isDoubtful(){
 245         return this.doubtful;
 246     }
 247     /**
 248      * @see  #isDoubtful()
 249      */
 250     public void setDoubtful(boolean doubtful){
 251         this.doubtful = doubtful;
 252     }
 253
 254
 255     /**
 256      * Returns the boolean value indicating if this taxon should be withheld (<code>publish=false</code>) or not
 257      * (<code>publish=true</code>) during any publication process to the general public.
 258      * This publish flag implementation is preliminary and may be replaced by a more general
 259      * implementation of READ rights in future.<BR>
 260      * The default value is <code>true</code>.
 261      */
 262     @Override
 263     public boolean isPublish() {
 264         return publish;
 265     }
 266
 267     @Override
 268     public void setPublish(boolean publish) {
 269         this.publish = publish;
 270     }
 271
 272     /**
 273      * Returns the {@link eu.etaxonomy.cdm.model.reference.Reference reference} of <i>this</i> (abstract) taxon.
 274      * This is the reference or the treatment using the {@link TaxonNameBase taxon name}
 275      * in <i>this</i> (abstract) taxon.
 276      */
 277     public Reference getSec() {
 278         return sec;
 279     }
 280
 281     /**
 282      * @see  #getSec()
 283      */
 284     public void setSec(Reference sec) {
 285         this.sec = sec;
 286     }
 287
 288
 289
 290     /**
 291      * An appended phrase is a phrase that is added to the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name}
 292      * 's title cache to be used just in this taxon. E.g. the phrase "sensu latu" may be added
 293      * to the name to describe this taxon more precisely.
 294      * If {@link #isUseNameCache()}
 295      * @return the appendedPhrase
 296      */
 297     public String getAppendedPhrase() {
 298         return appendedPhrase;
 299     }
 300
 301     /**
 302      * @param appendedPhrase the appendedPhrase to set
 303      */
 304     public void setAppendedPhrase(String appendedPhrase) {
 305         this.appendedPhrase = appendedPhrase;
 306     }
 307
 308     /**
 309      * @return the useNameCache
 310      */
 311     public boolean isUseNameCache() {
 312         return useNameCache;
 313     }
 314
 315     /**
 316      * @param useNameCache the useNameCache to set
 317      */
 318     public void setUseNameCache(boolean useNameCache) {
 319         this.useNameCache = useNameCache;
 320     }
 321
 322     @Transient
 323     public abstract boolean isOrphaned();
 324 //*********************** CLONE ********************************************************/
 325
 326     /**
 327      * Clones <i>this</i> taxon. This is a shortcut that enables to create
 328      * a new instance with empty taxon name and sec reference.
 329      *
 330      * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
 331      * @see java.lang.Object#clone()
 332      */
 333     @Override
 334     public Object clone() {
 335         TaxonBase result;
 336         try {
 337             result = (TaxonBase)super.clone();
 338             result.setSec(null);
 339
 340             return result;
 341         } catch (CloneNotSupportedException e) {
 342             logger.warn("Object does not implement cloneable");
 343             e.printStackTrace();
 344             return null;
 345         }
 346
 347
 348     }
 349
 350
 351 }