cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/Rank.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 import java.util.HashMap;
  13 import java.util.List;
  14 import java.util.Map;
  15 import java.util.UUID;
  16
  17 import javax.persistence.Entity;
  18 import javax.persistence.Transient;
  19 import javax.validation.constraints.NotNull;
  20 import javax.xml.bind.annotation.XmlAccessType;
  21 import javax.xml.bind.annotation.XmlAccessorType;
  22 import javax.xml.bind.annotation.XmlAttribute;
  23 import javax.xml.bind.annotation.XmlType;
  24
  25 import org.apache.commons.lang.StringUtils;
  26 import org.apache.log4j.Logger;
  27 import org.hibernate.annotations.Type;
  28 import org.hibernate.envers.Audited;
  29 import org.hibernate.search.annotations.Indexed;
  30
  31 import eu.etaxonomy.cdm.common.CdmUtils;
  32 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  33 import eu.etaxonomy.cdm.model.common.Language;
  34 import eu.etaxonomy.cdm.model.common.OrderedTermBase;
  35 import eu.etaxonomy.cdm.model.common.Representation;
  36 import eu.etaxonomy.cdm.model.common.TermType;
  37 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  38 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  39
  40 /**
  41  * The class representing the taxonomical ranks (like "Family", "Genus" or
  42  * "Species") used for {@link TaxonNameBase taxon names} across all {@link NomenclaturalCode nomenclatural codes}
  43  * for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
  44  * cultivars (ICNCP) and animals (ICZN).
  45  * <P>
  46  * A standard (ordered) list of taxonomical rank instances will be automatically
  47  * created as the project starts. But this class allows to extend this standard
  48  * list by creating new instances of additional taxonomical ranks if needed.
  49  * <P>
  50  * This class corresponds to: <ul>
  51  * <li> TaxonRankTerm according to the TDWG ontology
  52  * <li> TaxonomicRankEnum according to the TCS
  53  * <li> Rank according to the ABCD schema
  54  * </ul>
  55  *
  56  * @author m.doering
  57  * @version 1.0
  58  * @created 08-Nov-2007 13:06:46
  59  */
  60 @XmlAccessorType(XmlAccessType.FIELD)
  61 @XmlType(name = "Rank")
  62 @Entity
  63 @Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
  64 @Audited
  65 public class Rank extends OrderedTermBase<Rank> {
  66     private static final long serialVersionUID = -8648081681348758485L;
  67     private static final Logger logger = Logger.getLogger(Rank.class);
  68
  69     private static final UUID uuidEmpire = UUID.fromString("ac470211-1586-4b24-95ca-1038050b618d");
  70     private static final UUID uuidDomain = UUID.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
  71     private static final UUID uuidSuperkingdom = UUID.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
  72     private static final UUID uuidKingdom = UUID.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
  73     private static final UUID uuidSubkingdom = UUID.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
  74     private static final UUID uuidInfrakingdom = UUID.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
  75     private static final UUID uuidSuperphylum = UUID.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
  76     private static final UUID uuidPhylum = UUID.fromString("773430d2-76b4-438c-b817-97a543a33287");
  77     private static final UUID uuidSubphylum = UUID.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
  78     private static final UUID uuidInfraphylum = UUID.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
  79     private static final UUID uuidSuperdivision = UUID.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
  80     private static final UUID uuidDivision = UUID.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
  81     private static final UUID uuidSubdivision = UUID.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
  82     private static final UUID uuidInfradivision = UUID.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
  83     private static final UUID uuidSuperclass = UUID.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
  84     private static final UUID uuidClass = UUID.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
  85     private static final UUID uuidSubclass = UUID.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
  86     private static final UUID uuidInfraclass = UUID.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
  87     private static final UUID uuidSuperorder = UUID.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
  88     private static final UUID uuidOrder = UUID.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
  89     private static final UUID uuidSuborder = UUID.fromString("768ad378-fa85-42ab-b668-763225832f57");
  90     private static final UUID uuidInfraorder = UUID.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
  91     private static final UUID uuidSectionZoology = UUID.fromString("691d371e-10d7-43f0-93db-3d7fa1a62c54");
  92     private static final UUID uuidSubsectionZoology = UUID.fromString("0ed32d28-adc4-4303-a9ca-68e2acd67e33");
  93     private static final UUID uuidSuperfamily = UUID.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
  94     private static final UUID uuidFamily = UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
  95     private static final UUID uuidSubfamily = UUID.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
  96     private static final UUID uuidInfrafamily = UUID.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
  97     private static final UUID uuidSupertribe = UUID.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
  98     private static final UUID uuidTribe = UUID.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
  99     private static final UUID uuidSubtribe = UUID.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
 100     private static final UUID uuidInfratribe = UUID.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
 101     private static final UUID uuidSupragenericTaxon = UUID.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
 102     public static final UUID uuidGenus = UUID.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
 103     private static final UUID uuidSubgenus = UUID.fromString("78786e16-2a70-48af-a608-494023b91904");
 104     private static final UUID uuidInfragenus = UUID.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
 105     private static final UUID uuidSectionBotany = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
 106     private static final UUID uuidSubsectionBotany = UUID.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
 107     private static final UUID uuidSeries = UUID.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
 108     private static final UUID uuidSubseries = UUID.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
 109     private static final UUID uuidSpeciesAggregate = UUID.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
 110     private static final UUID uuidSpeciesGroup = UUID.fromString("d1988a11-292b-46fa-8fb7-bc64ea6d8fc6");
 111     public static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
 112     public static final UUID uuidSpecies = UUID.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
 113     private static final UUID uuidSubspecificAggregate = UUID.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
 114     private static final UUID uuidSubspecies = UUID.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
 115     private static final UUID uuidInfraspecies = UUID.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
 116     private static final UUID uuidNatio = UUID.fromString("965f2f38-7f97-4270-ab5a-1999bf050a22");
 117     private static final UUID uuidVariety = UUID.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
 118     private static final UUID uuidBioVariety = UUID.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
 119     private static final UUID uuidPathoVariety = UUID.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
 120     private static final UUID uuidSubvariety = UUID.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
 121     private static final UUID uuidSubsubvariety = UUID.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
 122
 123     private static final UUID uuidProles = UUID.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");
 124     private static final UUID uuidRace = UUID.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");
 125     private static final UUID uuidSublusus = UUID.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");
 126
 127     private static final UUID uuidConvar = UUID.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
 128     private static final UUID uuidForm = UUID.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
 129     private static final UUID uuidSpecialForm = UUID.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
 130     private static final UUID uuidSubform = UUID.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
 131     private static final UUID uuidSubsubform = UUID.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
 132     public static final UUID uuidInfraspecificTaxon = UUID.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
 133     private static final UUID uuidCandidate = UUID.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
 134     private static final UUID uuidDenominationClass = UUID.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
 135     private static final UUID uuidGrex = UUID.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
 136     private static final UUID uuidGraftChimaera = UUID.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
 137     private static final UUID uuidCultivarGroup = UUID.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
 138     private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
 139     private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
 140
 141     private static Map<String, UUID> abbrevMap = null;
 142     private static Map<String, UUID> labelMap = null;
 143
 144     protected static Map<UUID, Rank> termMap = null;
 145
 146 //*********************** Factory methods ********************************************/
 147
 148 //    /**
 149 //     * Creates a new empty rank.
 150 //     *
 151 //     * @see #NewInstance(String, String, String)
 152 //     */
 153 //    private static Rank NewInstance(){
 154 //        return new Rank();
 155 //    }
 156
 157     /**
 158      * Creates an additional rank with a description (in the {@link Language#DEFAULT() default language}),
 159      * a label and a label abbreviation.
 160      *
 161      * @param   term             the string (in the default language) describing the
 162      *                                           new rank to be created
 163      * @param   label            the string identifying the new rank to be created
 164      * @param   labelAbbrev  the string identifying (in abbreviated form) the
 165      *                                           new rank to be created
 166      * @see                              #NewInstance()
 167      */
 168     public static Rank NewInstance(RankClass rankClass, String term, String label, String labelAbbrev){
 169         return new Rank(rankClass, term, label, labelAbbrev);
 170     }
 171
 172         /**
 173          * The {@link RankClass rank class} of a rank. It is usually needed for correct formatting of a
 174          * rank by using e.g. isSupraGeneric(). Prior to v3.3 this was computed by comparison of ranks.
 175          */
 176         @XmlAttribute(name ="RankClass")
 177         @NotNull
 178         @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
 179                 parameters = {@org.hibernate.annotations.Parameter(name="enumClass", value="eu.etaxonomy.cdm.model.name.RankClass")}
 180         )
 181         private RankClass rankClass;
 182
 183
 184 //********************************** Constructor *********************************/
 185
 186         //for hibernate use only
 187         @Deprecated
 188         protected Rank() {
 189                 super(TermType.Rank);
 190         }
 191
 192     /**
 193      * Class constructor: creates an additional rank instance with a description
 194      * (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
 195      *
 196      * @param   term             the string (in the default language) describing the
 197      *                                           new rank to be created
 198      * @param   label            the string identifying the new rank to be created
 199      * @param   labelAbbrev  the string identifying (in abbreviated form) the
 200      *                                           new rank to be created
 201      * @see     #Rank()
 202      */
 203     protected Rank(RankClass rankClass, String term, String label, String labelAbbrev) {
 204         super(TermType.Rank, term, label, labelAbbrev);
 205         this.rankClass = rankClass;
 206     }
 207
 208
 209 //********* METHODS **************************************/
 210
 211     /* (non-Javadoc)
 212      * @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
 213      */
 214     @Override
 215     public void resetTerms(){
 216         termMap = null;
 217     }
 218
 219
 220
 221     protected static Rank getTermByUuid(UUID uuid){
 222         if (termMap == null){
 223             return null;  //better return null then initialize the termMap in an unwanted way
 224         }
 225         return (Rank)termMap.get(uuid);
 226     }
 227
 228     public static final Rank EMPIRE(){
 229       return getTermByUuid(uuidEmpire);
 230     }
 231     public static final Rank DOMAIN(){
 232           return getTermByUuid(uuidDomain);
 233     }
 234     public static final Rank SUPERKINGDOM(){
 235         return getTermByUuid(uuidSuperkingdom);
 236     }
 237     public static final Rank KINGDOM(){
 238         return getTermByUuid(uuidKingdom);
 239     }
 240     public static final Rank SUBKINGDOM(){
 241         return getTermByUuid(uuidSubkingdom);
 242     }
 243     public static final Rank INFRAKINGDOM(){
 244         return getTermByUuid(uuidInfrakingdom);
 245     }
 246     public static final Rank SUPERPHYLUM(){
 247         return getTermByUuid(uuidSuperphylum);
 248     }
 249     public static final Rank PHYLUM(){
 250         return getTermByUuid(uuidPhylum);
 251     }
 252     public static final Rank SUBPHYLUM(){
 253         return getTermByUuid(uuidSubphylum);
 254     }
 255     public static final Rank INFRAPHYLUM(){
 256         return getTermByUuid(uuidInfraphylum);
 257     }
 258     public static final Rank SUPERDIVISION(){
 259         return getTermByUuid(uuidSuperdivision);
 260     }
 261     public static final Rank DIVISION(){
 262         return getTermByUuid(uuidDivision);
 263     }
 264     public static final Rank SUBDIVISION(){
 265         return getTermByUuid(uuidSubdivision);
 266     }
 267     public static final Rank INFRADIVISION(){
 268         return getTermByUuid(uuidInfradivision);
 269     }
 270     public static final Rank SUPERCLASS(){
 271         return getTermByUuid(uuidSuperclass);
 272     }
 273     public static final Rank CLASS(){
 274         return getTermByUuid(uuidClass);
 275     }
 276     public static final Rank SUBCLASS(){
 277         return getTermByUuid(uuidSubclass);
 278     }
 279     public static final Rank INFRACLASS(){
 280         return getTermByUuid(uuidInfraclass);
 281     }
 282     public static final Rank SUPERORDER(){
 283         return getTermByUuid(uuidSuperorder);
 284     }
 285     public static final Rank ORDER(){
 286         return getTermByUuid(uuidOrder);
 287     }
 288     public static final Rank SUBORDER(){
 289         return getTermByUuid(uuidSuborder);
 290     }
 291     public static final Rank INFRAORDER(){
 292         return getTermByUuid(uuidInfraorder);
 293     }
 294     public static final Rank SUPERFAMILY(){
 295         return getTermByUuid(uuidSuperfamily);
 296     }
 297     public static final Rank FAMILY(){
 298         return getTermByUuid(uuidFamily);
 299     }
 300     public static final Rank SUBFAMILY(){
 301         return getTermByUuid(uuidSubfamily);
 302     }
 303     public static final Rank INFRAFAMILY(){
 304         return getTermByUuid(uuidInfrafamily);
 305     }
 306     public static final Rank SUPERTRIBE(){
 307         return getTermByUuid(uuidSupertribe);
 308     }
 309     public static final Rank TRIBE(){
 310         return getTermByUuid(uuidTribe);
 311     }
 312     public static final Rank SUBTRIBE(){
 313         return getTermByUuid(uuidSubtribe);
 314     }
 315     public static final Rank INFRATRIBE(){
 316         return getTermByUuid(uuidInfratribe);
 317     }
 318     public static final Rank SUPRAGENERICTAXON(){
 319         return getTermByUuid(uuidSupragenericTaxon);
 320     }
 321     public static final Rank GENUS(){
 322         return getTermByUuid(uuidGenus);
 323     }
 324     public static final Rank SUBGENUS(){
 325         return getTermByUuid(uuidSubgenus);
 326     }
 327     public static final Rank INFRAGENUS(){
 328         return getTermByUuid(uuidInfragenus);
 329     }
 330     public static final Rank SECTION_BOTANY(){
 331         return getTermByUuid(uuidSectionBotany);
 332     }
 333     public static final Rank SUBSECTION_BOTANY(){
 334         return getTermByUuid(uuidSubsectionBotany);
 335     }
 336     public static final Rank SECTION_ZOOLOGY(){
 337         return getTermByUuid(uuidSectionZoology);
 338     }
 339     public static final Rank SUBSECTION_ZOOLOGY(){
 340         return getTermByUuid(uuidSubsectionZoology);
 341     }
 342     public static final Rank SERIES(){
 343         return getTermByUuid(uuidSeries);
 344     }
 345     public static final Rank SUBSERIES(){
 346         return getTermByUuid(uuidSubseries);
 347     }
 348     public static final Rank SPECIESAGGREGATE(){
 349         return getTermByUuid(uuidSpeciesAggregate);
 350     }
 351     public static final Rank SPECIESGROUP(){
 352         return getTermByUuid(uuidSpeciesGroup);
 353     }
 354     /**
 355      * 'Unranked infrageneric'. An infrageneric rank which is on purpose not further defined.
 356      * This sometimes holds for names from the 19th century.
 357      */
 358     public static final Rank INFRAGENERICTAXON(){
 359         return getTermByUuid(uuidInfragenericTaxon);
 360     }
 361     public static final Rank SPECIES(){
 362         return getTermByUuid(uuidSpecies);
 363     }
 364     public static final Rank SUBSPECIFICAGGREGATE(){
 365         return getTermByUuid(uuidSubspecificAggregate);
 366     }
 367     public static final Rank SUBSPECIES(){
 368         return getTermByUuid(uuidSubspecies);
 369     }
 370     public static final Rank INFRASPECIES(){
 371         return getTermByUuid(uuidInfraspecies);
 372     }
 373     public static final Rank VARIETY(){
 374         return getTermByUuid(uuidVariety);
 375     }
 376     public static final Rank BIOVARIETY(){
 377         return getTermByUuid(uuidBioVariety);
 378     }
 379     public static final Rank PATHOVARIETY(){
 380         return getTermByUuid(uuidPathoVariety);
 381     }
 382     public static final Rank SUBVARIETY(){
 383         return getTermByUuid(uuidSubvariety);
 384     }
 385     public static final Rank SUBSUBVARIETY(){
 386         return getTermByUuid(uuidSubsubvariety );
 387     }
 388     public static final Rank PROLES(){
 389         return getTermByUuid(uuidProles);
 390     }
 391     public static final Rank RACE(){
 392         return getTermByUuid(uuidRace);
 393     }
 394     public static final Rank SUBLUSUS(){
 395         return getTermByUuid(uuidSublusus);
 396     }
 397
 398     public static final Rank CONVAR(){
 399         return getTermByUuid(uuidConvar);
 400     }
 401     public static final Rank FORM(){
 402         return getTermByUuid(uuidForm);
 403     }
 404     public static final Rank SPECIALFORM(){
 405         return getTermByUuid(uuidSpecialForm);
 406     }
 407     public static final Rank SUBFORM(){
 408         return getTermByUuid(uuidSubform);
 409     }
 410     public static final Rank SUBSUBFORM(){
 411         return getTermByUuid(uuidSubsubform);
 412     }
 413     /**
 414      * 'Unranked infraspecific'. An infraspecific rank which is on purpose not further defined.
 415      * This sometimes holds for names from the 19th century.
 416      */
 417     public static final Rank INFRASPECIFICTAXON(){
 418         return getTermByUuid(uuidInfraspecificTaxon);
 419     }
 420     public static final Rank CANDIDATE(){
 421         return getTermByUuid(uuidCandidate);
 422     }
 423     public static final Rank DENOMINATIONCLASS(){
 424         return getTermByUuid(uuidDenominationClass);
 425     }
 426     public static final Rank GREX(){
 427         return getTermByUuid(uuidGrex);
 428     }
 429     public static final Rank GRAFTCHIMAERA(){
 430         return getTermByUuid(uuidGraftChimaera);
 431     }
 432     public static final Rank CULTIVARGROUP(){
 433         return getTermByUuid(uuidCultivarGroup);
 434     }
 435     public static final Rank CULTIVAR(){
 436         return getTermByUuid(uuidCultivar);
 437     }
 438     public static final Rank UNKNOWN_RANK(){
 439         return getTermByUuid(uuidUnknownRank);
 440     }
 441     public static final Rank NATIO(){
 442         return getTermByUuid(uuidNatio);
 443     }
 444     /**
 445      * @see #INFRASPECIFICTAXON()
 446      */
 447     public static final Rank UNRANKED_INFRASPECIFIC(){
 448         return getTermByUuid(uuidInfraspecificTaxon);
 449     }
 450     /**
 451      * @see #INFRAGENERICTAXON()
 452      */
 453     public static final Rank UNRANKED_INFRAGENERIC(){
 454         return getTermByUuid(uuidInfragenericTaxon);
 455     }
 456
 457 // ************************ GETTER / SETTER **********************************/
 458
 459     public RankClass getRankClass() {
 460                 return rankClass;
 461         }
 462
 463         public void setRankClass(RankClass rankClass) {
 464                 this.rankClass = rankClass;
 465         }
 466
 467 // ******************************** METHODS ***************************************/
 468
 469     /**
 470      * Returns the boolean value indicating whether <i>this</i> rank is higher than
 471      * the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
 472      *
 473      * @see  #isGenus()
 474      * @see  #isInfraGeneric()
 475      * @see  #isSpecies()
 476      * @see  #isInfraSpecific()
 477      */
 478     @Transient
 479     public boolean isSupraGeneric(){
 480         return this.rankClass.equals(RankClass.Suprageneric); // (this.isHigher(Rank.GENUS()));
 481     }
 482
 483     /**
 484      * Returns the boolean value indicating whether <i>this</i> rank is the genus rank
 485      * (true) or not (false). Returns false if <i>this</i> rank is null.
 486      *
 487      * @see  #isSupraGeneric()
 488      * @see  #isInfraGeneric()
 489      * @see  #isSpecies()
 490      * @see  #isInfraSpecific()
 491      */
 492     @Transient
 493     public boolean isGenus(){
 494         return this.rankClass.equals(RankClass.Genus); // (this.equals(Rank.GENUS()));
 495     }
 496
 497     /**
 498      * Returns the boolean value indicating whether <i>this</i> rank is higher than the
 499      * species rank and lower than the genus rank (true) or not (false). Species groups or
 500      * aggregates are also handled as infrageneric ranks.
 501      * Returns false if <i>this</i> rank is null.
 502      *
 503      * @see  #isSupraGeneric()
 504      * @see  #isGenus()
 505      * @see  #isSpeciesAggregate()
 506      * @see  #isSpecies()
 507      * @see  #isInfraSpecific()
 508      */
 509     @Transient
 510     public boolean isInfraGeneric(){
 511         return this.rankClass.equals(RankClass.Infrageneric) || this.rankClass.equals(RankClass.SpeciesGroup) ; //(this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
 512     }
 513
 514     /**
 515      * Returns true if this rank indicates a rank that aggregates species
 516      * like species aggregates or species groups, false otherwise. This methods
 517      * currently returns false for all user defined ranks.
 518      * @return
 519      */
 520     @Transient
 521     public boolean isSpeciesAggregate(){
 522         return this.rankClass.equals(RankClass.SpeciesGroup); //(this.equals(Rank.SPECIESAGGREGATE()) || (this.isLower(Rank.SPECIESAGGREGATE()) && this.isHigher(Rank.SPECIES())));
 523     }
 524
 525     /**
 526      * Returns the boolean value indicating whether <i>this</i> rank is the species
 527      * rank (true) or not (false). Returns false if <i>this</i> rank is null.
 528      *
 529      * @see  #isSupraGeneric()
 530      * @see  #isGenus()
 531      * @see  #isInfraGeneric()
 532      * @see  #isInfraSpecific()
 533      */
 534     @Transient
 535     public boolean isSpecies(){
 536         return this.rankClass.equals(RankClass.Species); //(this.equals(Rank.SPECIES()));
 537     }
 538
 539     /**
 540      * Returns the boolean value indicating whether <i>this</i> rank is lower than the
 541      * species rank (true) or not (false). Returns false if <i>this</i> rank is null.
 542      *
 543      * @see  #isSupraGeneric()
 544      * @see  #isGenus()
 545      * @see  #isInfraGeneric()
 546      * @see  #isSpecies()
 547      */
 548     @Transient
 549     public boolean isInfraSpecific(){
 550         return this.rankClass.equals(RankClass.Infraspecific); // (this.isLower(Rank.SPECIES()));
 551     }
 552
 553
 554     /**
 555      * Returns the rank identified through a name (abbreviated or not).
 556      * Preliminary implementation for BotanicalNameParser.
 557      *
 558      * @param   strRank the string identifying the rank
 559      * @return                  the rank
 560      */
 561     public static Rank getRankByNameOrAbbreviation(String strRank) throws UnknownCdmTypeException{
 562         return getRankByNameOrAbbreviation(strRank, false);
 563     }
 564
 565     /**
 566      * Returns the rank identified through a name (abbreviated or not) for a given nomenclatural code.
 567      * Preliminary implementation for BotanicalNameParser.
 568      *
 569      * @param   strRank the string identifying the rank
 570      * @param   nc      the nomenclatural code
 571      * @return                  the rank
 572      */
 573     public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc)
 574                 throws UnknownCdmTypeException{
 575         return getRankByNameOrAbbreviation(strRank, nc, false);
 576     }
 577
 578     // TODO
 579     // Preliminary implementation for BotanicalNameParser.
 580     // not yet complete
 581     /**
 582      * Returns the rank identified through a name (abbreviated or not).
 583      * Preliminary implementation for BotanicalNameParser.
 584      *
 585      * @param   strRank the string identifying the rank
 586      * @param   useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 587      *                  unknown or not yet implemented
 588      * @return                  the rank
 589      */
 590     public static Rank getRankByNameOrAbbreviation(String strRank, boolean useUnknown)
 591             throws UnknownCdmTypeException{
 592         try {
 593             return getRankByAbbreviation(strRank);
 594         } catch (UnknownCdmTypeException e) {
 595             return getRankByName(strRank, useUnknown);
 596         }
 597     }
 598
 599     // TODO
 600     // Preliminary implementation for BotanicalNameParser.
 601     // not yet complete
 602     /**
 603      * Returns the rank identified through a name (abbreviated or not).
 604      * Preliminary implementation for BotanicalNameParser.
 605      *
 606      * @param   strRank the string identifying the rank
 607      * @param   nc      the nomenclatural code
 608      * @param   useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 609      *                  unknown or not yet implemented
 610      * @return                  the rank
 611      */
 612     public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc, boolean useUnknown)
 613             throws UnknownCdmTypeException{
 614         try {
 615             return getRankByAbbreviation(strRank, nc);
 616         } catch (UnknownCdmTypeException e) {
 617             return getRankByName(strRank, nc, useUnknown);
 618         }
 619     }
 620
 621     /**
 622      * Returns the rank identified through an abbreviated name.
 623      * Preliminary implementation for BotanicalNameParser.<BR>
 624      * Note: For abbrev = "[unranked]" the result is undefined.
 625      * It maybe the infrageneric unranked or the infraspecific unranked.
 626      * You need to define by context which one is correct.
 627      *
 628      * @param   abbrev  the string for the name abbreviation
 629      * @return                  the rank
 630      */
 631     public static Rank getRankByAbbreviation(String abbrev)
 632                         throws UnknownCdmTypeException{
 633         return getRankByAbbreviation(abbrev, false);
 634     }
 635
 636     /**
 637      * Returns the rank identified through an abbreviated name for a given nomenclatural code.
 638      * See also {@link #getRankByAbbreviation(String, boolean)}
 639      *
 640      * @param   abbrev  the string for the name abbreviation
 641      * @param   nc          the nomenclatural code
 642      * @return                  the rank
 643      */
 644     public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
 645         return getRankByAbbreviation(abbrev, nc, false);
 646     }
 647
 648     // TODO
 649     // Preliminary implementation for BotanicalNameParser.
 650     // not yet complete
 651     /**
 652      * Returns the rank identified through an abbreviated representation.
 653      * At the moment it uses the English abbreviations (being Latin because
 654      * we do not have Latin representations yet.
 655      * TODO
 656      * If no according abbreviation is available it throws either an UnknownCdmTypeException
 657      * or an #Rank.UNKNOWN() object depending on the useUnknown flag.
 658      *
 659      * @param   abbrev          the string for the name abbreviation
 660      * @param   useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 661      *                  unknown or not yet existent
 662      * @return  the rank
 663      */
 664     public static Rank getRankByAbbreviation(String abbrev, boolean useUnknown) throws UnknownCdmTypeException{
 665         Rank result = null;
 666         if (abbrev == null){
 667             throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
 668         }
 669         if (abbrev.trim().equals("")){
 670             //handle empty abbrev as unknown
 671             abbrev = "oija�m��";
 672         }
 673         if (abbrevMap == null){
 674             return null;
 675         }
 676         UUID uuid = abbrevMap.get(abbrev);
 677         if (uuid != null ){
 678             result = getTermByUuid(uuid);
 679         }
 680         if (result != null){
 681             return result;
 682         }else {
 683             if (abbrev == null){
 684                 abbrev = "(null)";
 685             }
 686             if (useUnknown){
 687                 logger.info("Unknown rank name: " + abbrev + ". Rank 'UNKNOWN_RANK' created instead");
 688                 return Rank.UNKNOWN_RANK();
 689             }else{
 690                 throw new UnknownCdmTypeException("Unknown rank abbreviation: " + abbrev);
 691             }
 692         }
 693     }
 694
 695     // TODO
 696     // Preliminary implementation to cover Botany and Zoology.
 697     /**
 698      * Returns the rank identified through an abbreviated name for a given nomenclatural code.
 699      * Preliminary implementation for ICBN and ICZN.
 700      * See also {@link #getRankByAbbreviation(String, boolean)}
 701
 702      *
 703      * @param   abbrev          the string for the name abbreviation
 704      * @param   nc              the nomenclatural code
 705      * @param   useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 706      *                  unknown or not yet implemented
 707      * @return  the rank
 708      */
 709     public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc, boolean useUnknown)
 710             throws UnknownCdmTypeException{
 711
 712         if (nc != null && nc.equals(NomenclaturalCode.ICZN)) {
 713             if (abbrev != null){
 714                 if (abbrev.equalsIgnoreCase("sect.")) {
 715                     return Rank.SECTION_ZOOLOGY();
 716                 } else if (abbrev.equalsIgnoreCase("subsect.")) {
 717                     return Rank.SUBSECTION_ZOOLOGY();
 718                 }
 719             }
 720         }
 721         return getRankByAbbreviation(abbrev, useUnknown);
 722     }
 723
 724     // TODO
 725     // Preliminary implementation for BotanicalNameParser.
 726     // not yet complete
 727     /**
 728      * Returns the rank identified through a name.
 729      * Preliminary implementation for BotanicalNameParser.
 730      *
 731      * @param   rankName        the string for the name of the rank
 732      * @return                          the rank
 733      */
 734     public static Rank getRankByName(String rankName) throws UnknownCdmTypeException{
 735         return getRankByName(rankName, false);
 736     }
 737
 738
 739     // TODO
 740     // Preliminary implementation for ICBN and ICZN.
 741     // not yet complete
 742     /**
 743      * Returns the rank identified through a name for a given nomenclatural code.
 744      * Preliminary implementation for ICBN and ICZN.
 745      *
 746      * @param   rankName        the string for the name of the rank
 747      * @param   nc              the nomenclatural code
 748      * @return                          the rank
 749      */
 750     public static Rank getRankByName(String rankName, NomenclaturalCode nc) throws UnknownCdmTypeException{
 751         return getRankByName(rankName, nc, false);
 752     }
 753
 754     /**
 755      * Returns the rank identified through a name.
 756      * Preliminary implementation for BotanicalNameParser.
 757      * TODO At the moment we do not have Latin representations yet.
 758      *
 759      * @param   rankName        the string for the name of the rank
 760      * @param   useUnknown      if true the rank UNKNOWN_RANK is returned if the rank name is
 761      *                  unknown or not yet implemented
 762      * @return                          the rank
 763      */
 764     public static Rank getRankByName(String rankName, boolean useUnknown)
 765             throws UnknownCdmTypeException{
 766         if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
 767         }else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
 768         }else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
 769         }else if (rankName.equalsIgnoreCase("Subphylum")){ return Rank.SUBPHYLUM();
 770         }else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
 771         }else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
 772         }else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
 773         }else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
 774         }else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
 775         }else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
 776         }else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
 777         }else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
 778         }else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
 779         }else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
 780         }else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
 781         }else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
 782         }else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
 783         }else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION_BOTANY();
 784         }else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION_BOTANY();
 785         }else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
 786         }else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
 787         }else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
 788         }else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
 789         }else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
 790         }else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
 791         }else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
 792         }else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
 793         }else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
 794         }else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
 795         }else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
 796         }else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
 797         }else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
 798         }else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
 799         // old ranks
 800         }else if (rankName.equalsIgnoreCase("proles")){ return Rank.PROLES();
 801         }else if (rankName.equalsIgnoreCase("race")){ return Rank.RACE();
 802         }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.SUBLUSUS();
 803
 804         }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put 'taxon' and the infraspeciesepi to the field unnamed namephrase
 805
 806         }else{
 807             if (rankName == null){
 808                 rankName = "(null)";  //see NPE above
 809             }
 810             if (useUnknown){
 811                 logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");
 812                 return Rank.UNKNOWN_RANK();
 813             }else{
 814                 throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
 815             }
 816         }
 817     }
 818
 819     /**
 820      * Defines the rank according to the English name.
 821      * @param rankName English rank name.
 822      * @param nc Defines the handling of the section and subsection ranks. These are in different orders depending on the
 823      * nomenclatural code.
 824      * @param useUnknown if true, the "Unknown" rank is returned as a placeholder.
 825      * @return
 826      * @throws UnknownCdmTypeException never thrown if useUnknown is true
 827      */
 828     public static Rank getRankByEnglishName(String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException{
 829         Rank result = null;
 830         if (rankName == null){
 831             throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
 832         }
 833         if (labelMap == null){
 834             return null;
 835         }
 836         //handle section and subsection (not unique representations)
 837         if (rankName.equalsIgnoreCase("Section")){
 838             if (nc != null && nc.equals(NomenclaturalCode.ICZN)){       return Rank.SECTION_ZOOLOGY();
 839             }else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){return Rank.SECTION_BOTANY();
 840             }else{
 841                 String errorWarning = "Section is only defined for ICZN and ICNAFP at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
 842                 logger.warn(errorWarning);
 843                 throw new UnknownCdmTypeException (errorWarning);
 844             }
 845         }else if (rankName.equalsIgnoreCase("Subsection")){
 846             if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SUBSECTION_ZOOLOGY();
 847             }else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){ return Rank.SUBSECTION_BOTANY();
 848             }else{
 849                 String errorWarning = "Subsection is only defined for ICZN and ICBN at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
 850                 logger.warn(errorWarning);
 851                 throw new UnknownCdmTypeException (errorWarning);
 852             }
 853         }
 854
 855         rankName = rankName.toLowerCase();
 856
 857         UUID uuid = labelMap.get(rankName);
 858         if (uuid != null ){
 859             result = getTermByUuid(uuid);
 860         }
 861         if (result != null){
 862             return result;
 863         }else {
 864             if (rankName == null){
 865                 rankName = "(null)";
 866             }
 867             if (useUnknown){
 868                 logger.info("Unknown rank name: " + rankName + ". Rank 'UNKNOWN_RANK' created instead");
 869                 return Rank.UNKNOWN_RANK();
 870             }else{
 871                 throw new UnknownCdmTypeException("Unknown rank: " + rankName);
 872             }
 873         }
 874     }
 875
 876
 877     public static Rank getRankByName(String rankName, NomenclaturalCode nc, boolean useUnknown)
 878         throws UnknownCdmTypeException {
 879
 880         if (nc.equals(NomenclaturalCode.ICZN)) {
 881             if (rankName.equalsIgnoreCase("Sectio")) { return Rank.SECTION_ZOOLOGY();
 882             }else if (rankName.equalsIgnoreCase("Subsectio")) { return Rank.SUBSECTION_ZOOLOGY();
 883             }
 884         }
 885         return getRankByName(rankName, useUnknown);
 886     }
 887
 888     /**
 889      * Returns the abbreviated rank name for <i>this</i> rank according to the English representation
 890      * abbreviated label.
 891      * TODO Needs to be changed to Latin as soon as Latin representations are available.
 892      *
 893      * @return  the abbreviation string for <i>this</i> rank
 894      */
 895     public String getAbbreviation(){
 896         Language language = Language.ENGLISH();
 897         String result = this.getRepresentation(language).getAbbreviatedLabel();
 898         if (result== null) {
 899             logger.warn("Abbreviation for this Rank " + this.toString() +  " not yet implemented");
 900             return "no abbreviation available.";
 901         }else{
 902             return result;
 903         }
 904     }
 905     @Transient
 906     public String getInfraGenericMarker() throws UnknownCdmTypeException{
 907         String result = null;
 908         if (! this.isInfraGeneric()){
 909             throw new IllegalStateException("An infrageneric marker is only available for a infrageneric rank but was asked for rank: " + this.toString());
 910         }else{
 911             result = this.getAbbreviation();
 912         }
 913         if (result == null){
 914             throw new UnknownCdmTypeException("Abbreviation for rank unknown: " + this.toString());
 915         }
 916         return result;
 917     }
 918
 919
 920
 921     @Override
 922     public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms, boolean abbrevAsId) {
 923         Rank rank = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
 924         RankClass rankClass = RankClass.getByKey(csvLine.get(5));
 925         assert rankClass != null: "XXXXXXXXXXXXXXXXXXXXX  Rank class must not be null: " + csvLine ;
 926         rank.setRankClass(rankClass);
 927         return rank;
 928     }
 929
 930     @Override
 931     protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
 932         termMap = new HashMap<UUID, Rank>();
 933         for (Rank term : termVocabulary.getTerms()){
 934             termMap.put(term.getUuid(), (Rank)term);
 935             addRank(term);
 936         }
 937     }
 938
 939     /**
 940      * @param term
 941      */
 942     private void addRank(Rank rank) {
 943         if (rank == null){
 944             logger.warn("rank is NULL");
 945             return;
 946         }
 947         if (rank.getUuid().equals(uuidSectionZoology) || rank.getUuid().equals(uuidSubsectionZoology )){
 948             //sect./subsect. is used for botanical sections, see also #getRankByAbbreviation(String, NomenclaturalCode, boolean)
 949             return;
 950         }
 951         Language lang = Language.DEFAULT();  //TODO should be Latin but at the moment we have only English representations
 952         Representation representation = rank.getRepresentation(lang);
 953         String abbrevLabel = representation.getAbbreviatedLabel();
 954         String label = representation.getLabel();
 955
 956         //initialize maps
 957         if (abbrevMap == null){
 958             abbrevMap = new HashMap<String, UUID>();
 959         }
 960         if (labelMap == null){
 961             labelMap = new HashMap<String, UUID>();
 962         }
 963         labelMap.put(label.toLowerCase(), rank.getUuid());
 964         //add to map
 965         if (StringUtils.isBlank(abbrevLabel)){
 966             logger.info("Abbreviated label for rank is NULL or empty.Can't add rank to abbrevLabel map: " + CdmUtils.Nz(rank.getLabel()));
 967         }else{
 968                 abbrevMap.put(abbrevLabel, rank.getUuid());
 969         }
 970     }
 971
 972
 973     /**
 974      * It is necessary to skip the vocabulary check, otherwise we would have
 975      * problems in some CacheStrategies, due to uninitialized Vocabularies.
 976      *
 977      * @see eu.etaxonomy.cdm.model.common.OrderedTermBase#compareTo(eu.etaxonomy.cdm.model.common.OrderedTermBase)
 978      */
 979     @Override
 980     public int compareTo(Rank orderedTerm) {
 981         return performCompareTo(orderedTerm, true);
 982     }
 983
 984 }