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