cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCodeEdition.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.ArrayList;
  13 import java.util.List;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import javax.xml.bind.annotation.XmlEnum;
  18 import javax.xml.bind.annotation.XmlEnumValue;
  19 import javax.xml.bind.annotation.XmlType;
  20
  21 import org.apache.commons.lang3.StringUtils;
  22 import org.apache.logging.log4j.LogManager;
  23 import org.apache.logging.log4j.Logger;
  24
  25 import eu.etaxonomy.cdm.common.DOI;
  26 import eu.etaxonomy.cdm.common.URI;
  27 import eu.etaxonomy.cdm.model.agent.Person;
  28 import eu.etaxonomy.cdm.model.agent.Team;
  29 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  30 import eu.etaxonomy.cdm.model.common.Language;
  31 import eu.etaxonomy.cdm.model.reference.Reference;
  32 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  33 import eu.etaxonomy.cdm.model.term.EnumeratedTermVoc;
  34 import eu.etaxonomy.cdm.model.term.IEnumTerm;
  35 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
  36
  37 /**
  38  * The class for the nomenclature code edition of the 5 nomenclatural codes (ICNP, ICBN, ICNCP, ICZN and ICVCN)
  39  * ruling {@link TaxonName taxon names}.
  40  * <P>
  41  * See also https://www.wikidata.org/wiki/Q693148
  42  * <P>
  43  * @see NomenclaturalCode
  44  *
  45  * @author a.mueller
  46  * @since 23.07.2019
  47  */
  48
  49 @XmlType(name = "NomenclaturalCodeEdition")
  50 @XmlEnum
  51 public enum NomenclaturalCodeEdition implements IEnumTerm<NomenclaturalCodeEdition> {
  52
  53     //0
  54     /**
  55      * International Code of Nomenclature for algae, fungi, and plants.
  56      * Shenzhen 2017
  57      * Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Kusber, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNeill, J., Monro, A. M., Prado, J., Price, M. J. & Smith, G. F. (eds.) 2018: International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. DOI https://doi.org/10.12705/Code.2018
  58      */
  59     @XmlEnumValue("Shenzhen")
  60     ICN_2017_SHENZHEN(UUID.fromString("87e8ac37-97c4-43c7-a016-43f1a5c3503f"), "ICN", "Shenzhen", 2017, NomenclaturalCode.ICNAFP, "Q56701992","10.12705/Code.2018" ),
  61
  62     //1
  63     /**
  64      * International Code of Nomenclature for algae, fungi, and plants.
  65      * Melbourne 2011
  66      */
  67     @XmlEnumValue("Melbourne")
  68     ICN_2011_MELBOURNE(UUID.fromString("ea2ebf9e-e3eb-4aaf-8007-c6f9f8877451"), "ICN", "Melbourne", 2011, NomenclaturalCode.ICNAFP, "Q15895076", null),
  69
  70     //2
  71     /**
  72      * International Code of Botanical Nomenclature.
  73      * Vienna 2005
  74      */
  75     @XmlEnumValue("Vienna")
  76     ICN_2005_VIENNA(UUID.fromString("d8f9f3d6-96af-4d83-a8d5-04ff62ba4d9c"), "ICBN", "Vienna", 2005, NomenclaturalCode.ICNAFP, "Q15895126", null),
  77
  78     //3
  79     /**
  80      * International Code of Botanical Nomenclature.
  81      * Saint Louis 1999
  82      */
  83     @XmlEnumValue("Saint Louis")
  84     ICN_1999_ST_LOUIS(UUID.fromString("2746b72e-43be-4073-90d0-494a7afac271"), "ICBN", "Saint Louis", 1999, NomenclaturalCode.ICNAFP, "Q15895151", null),
  85
  86     //4
  87     /**
  88      * International Code of Botanical Nomenclature.
  89      * Tokyo 1993
  90      */
  91     @XmlEnumValue("Tokyo")
  92     ICN_1993_TOKYO(UUID.fromString("5a846761-839f-4f77-b614-7181b9b29355"), "ICBN", "Tokyo", 1993, NomenclaturalCode.ICNAFP, "Q15895201", null),
  93
  94     //5
  95     /**
  96      * International Code of Botanical Nomenclature.
  97      * Berlin 1987
  98      */
  99     @XmlEnumValue("Berlin")
 100     ICN_1987_BERLIN(UUID.fromString("5702fc16-e194-4ad2-bdaf-4451af523db2"), "ICBN", "Berlin", 1987, NomenclaturalCode.ICNAFP, null, null),
 101
 102     //6
 103     /**
 104      * International Code of Botanical Nomenclature.
 105      * Sydney 1981
 106      */
 107     @XmlEnumValue("Sydney")
 108     ICN_1981_Sydney(UUID.fromString("f956c556-6d79-4e0f-adeb-ed9d81f2fa24"), "ICBN", "Sydney", 1981, NomenclaturalCode.ICNAFP, null, null),
 109
 110     //7
 111     /**
 112      * International Code of Botanical Nomenclature.
 113      * Leningrad 1975
 114      */
 115     @XmlEnumValue("Leningrad")
 116     ICN_1975_TOKYO(UUID.fromString("f52e50b4-4c75-42dd-8efe-39cd966da712"), "ICBN", "Leningrad", 1975, NomenclaturalCode.ICNAFP, null, null),
 117
 118     //8
 119     /**
 120      * International Code of Botanical Nomenclature.
 121      * Seattle 1969
 122      */
 123     @XmlEnumValue("Seattle")
 124     ICN_1969_Seattle(UUID.fromString("2d19b5af-27cc-428e-affb-8a06563ff9cd"), "ICBN", "Seattle", 1969, NomenclaturalCode.ICNAFP, null, null),
 125
 126     //9
 127     /**
 128      * International Code of Botanical Nomenclature.
 129      * Stockholm 1952
 130      */
 131     @XmlEnumValue("Stockholm")
 132     ICN_1952_Stockholm(UUID.fromString("a0c07e5f-9b2b-4cd7-9f14-acd4729f175a"), "ICBN", "Stockholm", 1952, NomenclaturalCode.ICNAFP, null, null),
 133
 134     //10
 135     /**
 136      * International Code of Botanical Nomenclature.
 137      * Cambridge Rules 1935
 138      */
 139     @XmlEnumValue("Cambridge")
 140     //TODO abbrev correct?
 141     ICN_1935_CAMBRIDGE(UUID.fromString("e6f7e578-2ce5-434d-9904-aaf2a6e06c43"), "ICBN", "Cambrdige", 1935, NomenclaturalCode.ICNAFP, null, null),
 142
 143     //11
 144     /**
 145      * International Code of Botanical Nomenclature.
 146      * Vienna Rules 1905
 147      */
 148     @XmlEnumValue("Vienna 1905")
 149     //TODO abbrev correct?
 150     ICN_1905_VIENNA(UUID.fromString("23781153-540f-4c54-a5ae-5d6b6f490332"), "ICBN", "Vienna", 1905, NomenclaturalCode.ICNAFP, null, null),
 151
 152     //12
 153     /**
 154      * International Code of Botanical Nomenclature.
 155      * Laws of botanical nomenclature 1867
 156      */
 157     @XmlEnumValue("Laws")
 158     //TODO abbrev correct?
 159     ICN_1867_LAWS(UUID.fromString("230314c3-0bb0-4488-8597-f4ef63d27781"), "ICBN", "Laws of botanical nomenclature", 1867, NomenclaturalCode.ICNAFP, null, null),
 160
 161
 162     //*** ICZN **/
 163     //z1
 164     /**
 165      * International Code of Zoological Nomenclature. Fourth edition. The International Trust for Zoological Nomenclature, London, UK.
 166      * https://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature#Versions
 167      */
 168     @XmlEnumValue("ICZN_1999")
 169     ICZN_1999(UUID.fromString("98f61693-67c5-40e1-a802-4989cb5ac4eb"), "ICZN", null, 1999, NomenclaturalCode.ICZN, null, "10.5962/bhl.title.50608"),
 170
 171     //z2
 172     /**
 173      * International Code of Zoological Nomenclature. Third edition. The International Trust for Zoological Nomenclature, London, UK.
 174      * https://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature#Versions
 175      */
 176     @XmlEnumValue("ICZN_1985")
 177     ICZN_1985(UUID.fromString("093110c8-f7e8-4f86-a794-e8e7b17c99d6"), "ICZN", null, 1985, NomenclaturalCode.ICZN, null, "10.5962/bhl.title.50611"),
 178
 179     //z3
 180     /**
 181      * International Code of Zoological Nomenclature. Second edition. The International Trust for Zoological Nomenclature, London, UK.
 182      * https://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature#Versions
 183      */
 184     @XmlEnumValue("ICZN_1964")
 185     ICZN_1964(UUID.fromString("2b4a9e59-45dd-444b-bf93-741bc727c38c"), "ICZN", null, 1964, NomenclaturalCode.ICZN, null, "10.5962/bhl.title.50606"),
 186
 187     //z4
 188     /**
 189      * International Code of Zoological Nomenclature: adopted by the XV International Congress of Zoology. The International Trust for Zoological Nomenclature, London, UK.
 190      * https://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature#Versions
 191      */
 192     @XmlEnumValue("ICZN_1961")
 193     ICZN_1961(UUID.fromString("b9de5507-1171-496c-8a8d-8af47e42724e"), "ICZN", null, 1961, NomenclaturalCode.ICZN, null, "10.5962/bhl.title.50303"),
 194
 195     //TODO older versions, see wikipedia
 196
 197    //bact1
 198     /**
 199      * Parker, C.T., Tindall, B.J. & Garrity, G.M. (2019) International Code of Nomenclature of Prokaryotes. 2008 Revision. Microbiology Society
 200      * https://en.wikipedia.org/wiki/International_Code_of_Nomenclature_of_Prokaryotes#Versions
 201      */
 202     @XmlEnumValue("ICNP_2008")
 203     ICNP_2008(UUID.fromString("1297a8e9-dfde-4db7-9f93-672453e8b3e6"), "ICNP", null, 2008, NomenclaturalCode.ICNP, null, "10.1099/ijsem.0.000778"),
 204
 205     //bact2
 206     /**
 207      * Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. & Clark, W.A. (1992). International Code of Nomenclature of Bacteria. Bacteriological Code. 1990 Revision. American Society for Microbiology, Washington, D.C., ISBN 1-55581-039-X
 208      * https://en.wikipedia.org/wiki/International_Code_of_Nomenclature_of_Prokaryotes#Versions
 209      */
 210     @XmlEnumValue("ICNP_1990")
 211     ICNP_1990(UUID.fromString("fd5d6dd3-de58-4244-8290-c8d89323f163"), "ICNB", null, 1990, NomenclaturalCode.ICNP, null, "10.5962/bhl.title.50303"),
 212
 213     //bact3
 214     /**
 215      * Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. & Clark, W.A. (1975). International Code of Nomenclature of Bacteria. 1975 Revision. American Society of Microbiology, Washington, D.C
 216      * https://en.wikipedia.org/wiki/International_Code_of_Nomenclature_of_Prokaryotes#Versions
 217      */
 218     @XmlEnumValue("ICNP_1975")
 219     ICNP_1975(UUID.fromString("2dafaf3c-abf6-4baf-82db-3332db25d654"), "ICNB", null, 1975, NomenclaturalCode.ICNP, null, null),
 220
 221     //cult plants 1
 222     /**
 223      * ISHS Secretariat: ICNCP - International Code for the Nomenclature for Cultivated Plants (9th edition). International Society for Horticultural Science, 15. Juni 2016
 224      * https://www.ishs.org/news/icncp-international-code-nomenclature-cultivated-plants-9th-edition
 225      */
 226     @XmlEnumValue("ICNCP_2016")
 227     ICNCP_2016(UUID.fromString("e395e7be-405f-4214-a3a2-2b19eef6a055"), "ICNCP", null, 2016, NomenclaturalCode.ICNCP, null, null),
 228
 229     //cult plants 2
 230     /**
 231      * International Code of Nomenclature for Cultivated Plants. 8th edition. [Scripta Horticulturae 10]
 232      * https://www.ishs.org/news/icncp-international-code-nomenclature-cultivated-plants-9th-edition
 233      */
 234     @XmlEnumValue("ICNCP_2009")
 235     ICNCP_2009(UUID.fromString("bc66202a-0ffb-4cf3-a1c9-520efd5e76e9"), "ICNCP", null, 2009, NomenclaturalCode.ICNCP, null, null),
 236
 237     //cult plants 3
 238     /**
 239      * SHS (International Society for Horticultural Science; Hrsg.): International Code of Nomenclature for Cultivated Plants, 7th edition. In: Acta Horticulturae Band 647, 2004. ISBN 90-6605-527-8.
 240      * https://de.wikipedia.org/wiki/Internationaler_Code_der_Nomenklatur_der_Kulturpflanzen
 241      */
 242     @XmlEnumValue("ICNCP_2004")
 243     ICNCP_2004(UUID.fromString("a29abcee-1f34-4320-afad-eb7ee23cc473"), "ICNCP", null, 2004, NomenclaturalCode.ICNCP, null, null),
 244
 245     //virus1
 246     /**
 247      * https://talk.ictvonline.org/ictv-reports/ictv_online_report/
 248      * 10th report
 249      */
 250     @XmlEnumValue("ICVCN_2018")
 251     //TODO abbrev correct?
 252     ICVCN_2018(UUID.fromString("6a0debf3-7932-4b0c-b1b1-46641c273f36"), "ICVCN", null, 2019, NomenclaturalCode.ICVCN, null, null),
 253
 254     //virus2
 255     /**
 256      * https://talk.ictvonline.org/ictv-reports/ictv_9th_report/
 257      * 9th report
 258      */
 259     @XmlEnumValue("ICVCN_2011")
 260     //TODO abbrev correct?
 261     ICVCN_2011(UUID.fromString("b55c0209-59e2-4fa2-9d64-63addfb15d6b"), "ICVCN", null, 2011, NomenclaturalCode.ICVCN, null, null),
 262
 263     ;
 264
 265     @SuppressWarnings("unused")
 266     private static final Logger logger = LogManager.getLogger();
 267
 268     private static final String WIKIDATA_BASE_URL = "https://www.wikidata.org/wiki/";
 269
 270         private String location;
 271
 272         private Integer year;
 273
 274         private NomenclaturalCode code;
 275
 276         private String wikiDataId;
 277
 278         private DOI doi;
 279
 280         private String abbrev;
 281
 282         private Reference citation;
 283
 284         private NomenclaturalCodeEdition(UUID uuid, String abbrev, String location, Integer year, NomenclaturalCode code, String wikiDataId, String strDoi ){
 285                 delegateVocTerm = EnumeratedTermVoc.addTerm(getClass(), this, uuid, makeTitleCache(location, code, year), code.getKey() + year, null);
 286                 this.location = location;
 287                 this.year=year;
 288                 this.code=code;
 289                 this.wikiDataId = wikiDataId;
 290                 this.doi = (strDoi==null) ? null:DOI.fromString(strDoi);
 291         }
 292
 293     /**
 294      * @param location
 295      * @param code
 296      * @param year
 297      * @return
 298      */
 299     private String makeTitleCache(String location, NomenclaturalCode code, Integer year) {
 300         return (StringUtils.isNotBlank(location)? location: code.getTitleCache()) + " " + year;
 301     }
 302
 303     public String getTitleCache() {
 304         return getLabel();
 305     }
 306
 307         @Override
 308         public String toString() {
 309                 return this.name();
 310         }
 311
 312     public boolean isNonViral() {
 313         return this.code.isNonViral();
 314     }
 315     public boolean isZoological() {
 316         return this.code.isZoological();
 317     }
 318     public boolean isBotanical() {
 319         return this.code.isBotanical();
 320     }
 321     public boolean isCultivar() {
 322         return this.code.isCultivar();
 323     }
 324     public boolean isBacterial() {
 325         return this.code.isBacterial();
 326      }
 327      public boolean isViral() {
 328          return this.code.isViral();
 329      }
 330      public boolean isFungus() {
 331          return this.code.isFungus();
 332      }
 333
 334
 335 //      public static NomenclaturalCodeEdition fromString(String string){
 336 //              xx;
 337 //          for(NomenclaturalCodeEdition code : NomenclaturalCodeEdition.values()){
 338 //                      if(code.name().equalsIgnoreCase(string)) {
 339 //                              return code;
 340 //                      }
 341 //              }
 342 //              return null;
 343 //      }
 344
 345     public static List<NomenclaturalCodeEdition> forCode(NomenclaturalCode code){
 346         List<NomenclaturalCodeEdition> result = new ArrayList<>();
 347
 348         Set<NomenclaturalCode> allCodes = code.getGeneralizationOf(true);
 349         allCodes.add(code);
 350
 351         for(NomenclaturalCodeEdition edition : NomenclaturalCodeEdition.values()){
 352             for (NomenclaturalCode nomCode: allCodes){
 353                 if(edition.getCode().equals(nomCode) && !result.contains(nomCode)) {
 354                     result.add(edition);
 355                 }
 356             }
 357         }
 358         return result;
 359     }
 360
 361     public String getAbbrev() {
 362           return abbrev;
 363     }
 364
 365     public String getLocation() {
 366         return location;
 367     }
 368     public Integer getYear() {
 369         return year;
 370     }
 371     public NomenclaturalCode getCode() {
 372         return code;
 373     }
 374     public String getWikiDataId() {
 375         return wikiDataId;
 376     }
 377     public URI getWikiDataUri() {
 378         return StringUtils.isEmpty(wikiDataId)? null: URI.create(WIKIDATA_BASE_URL + wikiDataId);
 379     }
 380     public DOI getDoi() {
 381         return this.doi;
 382     }
 383
 384     private Reference getCitation() {
 385         if (this.citation == null) {
 386             if (this == NomenclaturalCodeEdition.ICN_2017_SHENZHEN) {
 387                 citation = ReferenceFactory.newBook();
 388                 citation.setTitle("International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code), adopted by the Nineteenth International Botanical Congress, Shenzhen, China, July 2017.");
 389                 Team team = Team.NewInstance();
 390                 citation.setAuthorship(team);
 391                 team.addTeamMember(Person.NewInstance(null, "Turland", "N.J.", null));
 392                 team.addTeamMember(Person.NewInstance(null, "Wiersema", "J.H.", null));
 393                 team.addTeamMember(Person.NewInstance(null, "Barrie", "F.R.", null));
 394                 team.addTeamMember(Person.NewInstance(null, "Greuter", "W.", null));
 395                 team.addTeamMember(Person.NewInstance(null, "Hawksworth", "D.L.", null));
 396                 team.addTeamMember(Person.NewInstance(null, "Herendeen", "P.S.", null));
 397                 team.addTeamMember(Person.NewInstance(null, "Knapp", "S.", null));
 398                 team.addTeamMember(Person.NewInstance(null, "Kusber", "W.-H.", null));
 399                 team.addTeamMember(Person.NewInstance(null, "Li", "D.-Z.", null));
 400                 team.addTeamMember(Person.NewInstance(null, "Marhold", "K.", null));
 401                 team.addTeamMember(Person.NewInstance(null, "May", "T.W.", null));
 402                 team.addTeamMember(Person.NewInstance(null, "McNeill", "J.", null));
 403                 team.addTeamMember(Person.NewInstance(null, "Monro", "A.M.", null));
 404                 team.addTeamMember(Person.NewInstance(null, "Prado", "J.", null));
 405                 team.addTeamMember(Person.NewInstance(null, "Price", "M.J.", null));
 406                 //TODO eds.
 407                 team.addTeamMember(Person.NewInstance(null, "Smith", "G.F. (eds.)", null));
 408                 citation.setDatePublished(TimePeriodParser.parseStringVerbatim("2018"));
 409                 citation.setPlacePublished("Glashütten");
 410                 citation.setPublisher("Koeltz Botanical Books", "Glashütten");
 411                 citation.setDoi(ICN_2017_SHENZHEN.getDoi());
 412                 citation.setSeriesPart("Regnum Vegetabile 159");
 413             }else {
 414                 //TODO other nom codes not yet implemented
 415             }
 416         }
 417         return citation;
 418     }
 419
 420     public IdentifiableSource getSource() {
 421         if (getCitation() != null) {
 422             return IdentifiableSource.NewPrimaryMediaSourceInstance(getCitation(), null);
 423         } else {
 424             return null;
 425         }
 426     }
 427
 428 // *************************** DELEGATE **************************************/
 429
 430         private static EnumeratedTermVoc<NomenclaturalCodeEdition> delegateVoc;
 431         private IEnumTerm<NomenclaturalCodeEdition> delegateVocTerm;
 432
 433         static {
 434                 delegateVoc = EnumeratedTermVoc.getVoc(NomenclaturalCodeEdition.class);
 435         }
 436
 437         @Override
 438         public String getKey(){return delegateVocTerm.getKey();}
 439
 440         @Override
 441     public String getLabel(){return delegateVocTerm.getLabel();}
 442
 443         @Override
 444     public String getLabel(Language language){return delegateVocTerm.getLabel(language);}
 445
 446
 447         @Override
 448     public UUID getUuid() {return delegateVocTerm.getUuid();}
 449
 450         @Override
 451     public NomenclaturalCodeEdition getKindOf() {return delegateVocTerm.getKindOf();}
 452
 453         @Override
 454     public Set<NomenclaturalCodeEdition> getGeneralizationOf() {return delegateVocTerm.getGeneralizationOf();}
 455
 456         @Override
 457         public boolean isKindOf(NomenclaturalCodeEdition ancestor) {return delegateVocTerm.isKindOf(ancestor);  }
 458
 459         @Override
 460     public Set<NomenclaturalCodeEdition> getGeneralizationOf(boolean recursive) {return delegateVocTerm.getGeneralizationOf(recursive);}
 461
 462
 463         public static NomenclaturalCodeEdition getByKey(String key){return delegateVoc.getByKey(key);}
 464     public static NomenclaturalCodeEdition getByUuid(UUID uuid) {return delegateVoc.getByUuid(uuid);}
 465 }