cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/HomotypicGroupTaxonComparatorTest.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.model.taxon;
  11
  12 import java.util.ArrayList;
  13 import java.util.Calendar;
  14 import java.util.Collections;
  15 import java.util.List;
  16 import java.util.UUID;
  17
  18 import org.apache.log4j.Logger;
  19 import org.junit.Assert;
  20 import org.junit.Before;
  21 import org.junit.BeforeClass;
  22 import org.junit.Test;
  23
  24 import eu.etaxonomy.cdm.model.common.DefaultTermInitializer;
  25 import eu.etaxonomy.cdm.model.common.TimePeriod;
  26 import eu.etaxonomy.cdm.model.name.BotanicalName;
  27 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  28 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  29 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  30 import eu.etaxonomy.cdm.model.name.NonViralName;
  31 import eu.etaxonomy.cdm.model.name.Rank;
  32 //import eu.etaxonomy.cdm.model.reference.Book;
  33 import eu.etaxonomy.cdm.model.reference.Reference;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 04.03.2016
  39  */
  40 public class HomotypicGroupTaxonComparatorTest {
  41     @SuppressWarnings("unused")
  42     private static final Logger logger = Logger.getLogger(HomotypicGroupTaxonComparatorTest.class);
  43
  44     private Reference<?> sec;
  45     private Reference<?> ref1;
  46     private Reference<?> ref2;
  47     private Reference<?> ref3;
  48     private Calendar cal1;
  49     private Calendar cal2;
  50     private Calendar cal3;
  51     private BotanicalName botName1;
  52     private BotanicalName botName2;
  53     private BotanicalName botName3;
  54     private BotanicalName botName4;
  55     private BotanicalName botName5;
  56
  57     private List<TaxonBase<?>> list;
  58
  59     private Taxon taxon1;
  60     private Synonym synonym2;
  61     private Synonym synonym3;
  62
  63     @BeforeClass
  64     public static void setUpBeforeClass() {
  65         DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
  66         vocabularyStore.initialize();
  67     }
  68
  69     /**
  70      * @throws java.lang.Exception
  71      */
  72     @Before
  73     public void setUp() throws Exception {
  74         sec = ReferenceFactory.newBook();
  75
  76         ref1 = ReferenceFactory.newBook();
  77         ref2 = ReferenceFactory.newBook();
  78         ref3 = ReferenceFactory.newBook();
  79         cal1 = Calendar.getInstance();
  80         cal2 = Calendar.getInstance();
  81         cal3 = Calendar.getInstance();
  82         cal1.set(1856, 3, 2);
  83         cal2.set(1943, 3, 2);
  84         cal3.set(1945, 3, 2);
  85
  86         ref1.setDatePublished(TimePeriod.NewInstance(cal1));
  87         ref2.setDatePublished(TimePeriod.NewInstance(cal2));
  88         ref3.setDatePublished(TimePeriod.NewInstance(cal3));
  89
  90         botName1 =  BotanicalName.NewInstance(Rank.SPECIES());
  91         botName2 =  BotanicalName.NewInstance(Rank.SPECIES());
  92         botName3 =  BotanicalName.NewInstance(Rank.SPECIES());
  93         botName4 =  BotanicalName.NewInstance(Rank.SPECIES());
  94         botName5 =  BotanicalName.NewInstance(Rank.SPECIES());
  95
  96         setNameParts(botName1, "Aaa", "aaa");
  97         setNameParts(botName2, "Bbb", "bbb");
  98         setNameParts(botName3, "Ccc", "ccc");
  99         setNameParts(botName4, "Ddd", "ddd");
 100         setNameParts(botName5, "Eee", "eee");
 101
 102 //        zooName1.setPublicationYear(1823);
 103
 104         list = new ArrayList<TaxonBase<?>>();
 105
 106         taxon1 = Taxon.NewInstance(botName1, sec);
 107
 108
 109     }
 110
 111     private void setNameParts(NonViralName<?> name, String genus, String speciesEpi) {
 112         name.setGenusOrUninomial(genus);
 113         name.setSpecificEpithet(speciesEpi);
 114         name.getTitleCache();
 115     }
 116
 117
 118 /******************** TESTS *****************************************************/
 119
 120     @Test
 121     public void testCompare_BasionymGroupsTogether() {
 122         //2 basionym groups
 123
 124         HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
 125         taxon1.addHeterotypicSynonymName(botName3);
 126         taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
 127         botName3.addBasionym(botName5);
 128
 129         synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 130         taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
 131         botName2.addBasionym(botName4);
 132
 133
 134         list.addAll(taxon1.getSynonyms());
 135         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 136
 137         Assert.assertEquals("basionym for first group should come first", botName4, list.get(0).getName());
 138         Assert.assertEquals(botName2, list.get(1).getName());
 139         Assert.assertEquals(botName5, list.get(2).getName());
 140         Assert.assertEquals(botName3, list.get(3).getName());
 141
 142         //add replaced synonym relation between basionyms
 143         botName4.addReplacedSynonym(botName5, null, null, null);
 144         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 145         Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
 146                             botName5, list.get(0).getName());
 147         Assert.assertEquals(botName3, list.get(1).getName());
 148         Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
 149                             botName4, list.get(2).getName());
 150         Assert.assertEquals(botName2, list.get(3).getName());
 151
 152         //set a name as first name
 153         Collections.sort(list, new HomotypicGroupTaxonComparator(synonym2));
 154
 155         Assert.assertEquals("name2 should come first now",
 156                             botName2, list.get(0).getName());
 157         Assert.assertEquals("name2 should be followed by its basionym", botName4, list.get(1).getName());
 158         Assert.assertEquals("other basionym group should come later but with basionym first",
 159                             botName5, list.get(2).getName());
 160         Assert.assertEquals(botName3, list.get(3).getName());
 161
 162
 163     }
 164
 165     @Test
 166     public void testCompare_BasionymGroupsSeparated() {
 167
 168         //2 basionym groups in 2 homotypic groups
 169         synonym3 = taxon1.addHeterotypicSynonymName(botName3).getSynonym();
 170         taxon1.addHeterotypicSynonymName(botName5);
 171         botName3.addBasionym(botName5);  //also merges homotypic groups
 172
 173         taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 174         taxon1.addHeterotypicSynonymName(botName4);
 175         botName2.addBasionym(botName4);
 176
 177         list.addAll(taxon1.getSynonyms());
 178
 179         UUID uuidFirst = UUID.fromString("000000972-d164-4cb5-9a1e-d6216cc858f6");
 180         UUID uuidSecond = UUID.fromString("ffffff972-d164-4cb5-9a1e-d6216cc858f6");
 181         Assert.assertTrue(uuidFirst.toString().compareTo(uuidSecond.toString())<-1);
 182
 183         botName4.getHomotypicalGroup().setUuid(uuidFirst);
 184         botName5.getHomotypicalGroup().setUuid(uuidSecond);
 185
 186
 187         //start test
 188         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 189
 190         Assert.assertEquals("basionym for first group should come first", botName4, list.get(0).getName());
 191         Assert.assertEquals(botName2, list.get(1).getName());
 192         Assert.assertEquals(botName5, list.get(2).getName());
 193         Assert.assertEquals(botName3, list.get(3).getName());
 194
 195         //set a name as first name
 196         //TODO
 197         //first taxon in group should have an impact only for the homotypic group to which it belongs
 198         //but this is still under discussion and may change in future
 199         Collections.sort(list, new HomotypicGroupTaxonComparator(synonym3));
 200
 201         Assert.assertEquals(botName4, list.get(0).getName());
 202         Assert.assertEquals(botName2, list.get(1).getName());
 203         Assert.assertEquals(botName3, list.get(2).getName());
 204         Assert.assertEquals(botName5, list.get(3).getName());
 205     }
 206
 207     @Test
 208     public void testCompare_BasionymGroupsSomeWithYears() {
 209
 210         //2 basionym groups, 1 new combination with year (botName2) and 1 basionym with year (botName5)
 211         //The later should come first according to the rules, though alphabetically being
 212         //basionym botName4
 213
 214         botName2.setNomenclaturalReference(ref2);
 215         botName5.setNomenclaturalReference(ref3);
 216
 217         HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
 218         taxon1.addHeterotypicSynonymName(botName3);
 219         taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
 220         botName3.addBasionym(botName5);
 221
 222         synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 223         taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
 224         botName2.addBasionym(botName4);
 225
 226
 227         list.addAll(taxon1.getSynonyms());
 228         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 229
 230         Assert.assertEquals("basionym with date should comes first", botName5, list.get(0).getName());
 231         Assert.assertEquals(botName3, list.get(1).getName());
 232         Assert.assertEquals(botName4, list.get(2).getName());
 233         Assert.assertEquals(botName2, list.get(3).getName());
 234
 235         //even with nom. illeg. the name with date should come first
 236         NomenclaturalStatus illegStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE());
 237         botName5.addStatus(illegStatus);
 238
 239         Assert.assertEquals("basionym with date should comes first", botName5, list.get(0).getName());
 240         Assert.assertEquals(botName3, list.get(1).getName());
 241         Assert.assertEquals(botName4, list.get(2).getName());
 242         Assert.assertEquals(botName2, list.get(3).getName());
 243
 244
 245         //add replaced synonym relation between basionyms
 246         botName5.addReplacedSynonym(botName4, null, null, null);
 247         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 248         Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
 249                             botName4, list.get(0).getName());
 250         Assert.assertEquals(botName2, list.get(1).getName());
 251         Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
 252                             botName5, list.get(2).getName());
 253         Assert.assertEquals(botName3, list.get(3).getName());
 254     }
 255
 256     @Test
 257     public void testCompare_BasionymGroupsWithRanks1() {
 258
 259         botName2.setRank(Rank.VARIETY());
 260         botName2.setInfraSpecificEpithet("varbbbb");
 261
 262         botName3.setRank(Rank.VARIETY());
 263         botName3.setInfraSpecificEpithet("subspccc");
 264
 265         botName4.setRank(Rank.SUBSPECIES());
 266         botName4.setInfraSpecificEpithet("subspddd");
 267
 268
 269         HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
 270         taxon1.addHeterotypicSynonymName(botName3);
 271         taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
 272         botName3.addBasionym(botName5);
 273
 274         synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 275         taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
 276         botName2.addBasionym(botName4);
 277
 278
 279         list.addAll(taxon1.getSynonyms());
 280         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 281
 282         Assert.assertEquals("basionym with rank species should comes first", botName5, list.get(0).getName());
 283         Assert.assertEquals(botName3, list.get(1).getName());
 284         Assert.assertEquals(botName4, list.get(2).getName());
 285         Assert.assertEquals(botName2, list.get(3).getName());
 286
 287         //add replaced synonym relation between basionyms
 288         botName5.addReplacedSynonym(botName4, null, null, null);
 289         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 290         Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
 291                             botName4, list.get(0).getName());
 292         Assert.assertEquals(botName2, list.get(1).getName());
 293         Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
 294                             botName5, list.get(2).getName());
 295         Assert.assertEquals(botName3, list.get(3).getName());
 296     }
 297
 298     @Test
 299     public void testCompare_BasionymGroupsWithRanks2() {
 300
 301
 302         botName2.setRank(Rank.VARIETY());
 303         botName2.setInfraSpecificEpithet("varbbbb");
 304
 305         botName3.setRank(Rank.VARIETY());
 306         botName3.setInfraSpecificEpithet("subspccc");
 307
 308         botName4.setRank(Rank.SUBSPECIES());
 309         botName4.setInfraSpecificEpithet("subspddd");
 310
 311         botName5.setRank(Rank.VARIETY());
 312         botName5.setInfraSpecificEpithet("vareee");
 313
 314
 315         HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
 316         taxon1.addHeterotypicSynonymName(botName3);
 317         taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
 318         botName3.addBasionym(botName5);
 319
 320         synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 321         taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
 322         botName2.addBasionym(botName5);
 323         botName4.addBasionym(botName5);
 324
 325
 326         list.addAll(taxon1.getSynonyms());
 327         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 328
 329         Assert.assertEquals("basionym should comes first", botName5, list.get(0).getName());
 330         Assert.assertEquals("subspecies should come next", botName4, list.get(1).getName());
 331         Assert.assertEquals("variety with b should come next", botName2, list.get(2).getName());
 332         Assert.assertEquals("variety with c should come last", botName3, list.get(3).getName());
 333
 334     }
 335
 336     @Test
 337     public void testCompare_BasionymGroupsWithNomIlleg() {
 338         NomenclaturalStatus illegStatus = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE());
 339         botName4.addStatus(illegStatus);
 340
 341         //2 basionym groups
 342
 343         HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup();
 344         taxon1.addHeterotypicSynonymName(botName3);
 345         taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null);
 346         botName3.addBasionym(botName5);
 347
 348         synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym();
 349         taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null);
 350 //        botName2.addBasionym(botName4);
 351
 352
 353         list.addAll(taxon1.getSynonyms());
 354         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 355
 356         Assert.assertEquals("basionym for non nom. illeg. group should come first", botName2, list.get(0).getName());
 357         Assert.assertEquals(botName5, list.get(1).getName());
 358         Assert.assertEquals(botName3, list.get(2).getName());
 359         Assert.assertEquals("Nom illeg should come last", botName4, list.get(3).getName());
 360
 361         //name having a nom. illeg. as basionym should stay in its basionym group
 362         //NOTE: this is dirty data as nom. illeg. is not allowed as basionym by the code
 363         botName2.addBasionym(botName4);
 364         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 365
 366         Assert.assertEquals("basionym for non nom. illeg. group should come first", botName5, list.get(0).getName());
 367         Assert.assertEquals(botName3, list.get(1).getName());
 368         Assert.assertEquals("Nom illeg basionym group should come last", botName4, list.get(2).getName());
 369         Assert.assertEquals("Names with nom. illeg. as basionym should stay in basionym group", botName2, list.get(3).getName());
 370
 371         //non basionym nom. illeg. should not change the order
 372         botName4.removeStatus(illegStatus);
 373         botName2.addStatus(illegStatus);
 374         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 375
 376         Assert.assertEquals("basionym for non nom. illeg. group should come first", botName4, list.get(0).getName());
 377         Assert.assertEquals(botName2, list.get(1).getName());
 378         Assert.assertEquals("Nom illeg basionym group should come last", botName5, list.get(2).getName());
 379         Assert.assertEquals("Names with nom. illeg. as basionym should stay in basionym group", botName3, list.get(3).getName());
 380
 381     }
 382
 383     @Test
 384     public void testCompare_NoCircularProblemsWithBasionyms() {
 385
 386         taxon1.addHomotypicSynonymName(botName3, null, null);
 387         taxon1.addHomotypicSynonymName(botName5, null, null);
 388         botName3.addBasionym(botName5);
 389
 390         Assert.assertEquals(botName1.getHomotypicalGroup(), botName5.getHomotypicalGroup());
 391         botName5.addBasionym(botName1);
 392         botName1.addBasionym(botName3);
 393
 394         list.addAll(taxon1.getSynonyms());
 395         list.add(taxon1);
 396         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 397
 398         Assert.assertEquals(botName1, list.get(0).getName());
 399         Assert.assertEquals(botName3, list.get(1).getName());
 400         Assert.assertEquals(botName5, list.get(2).getName());
 401
 402         //additional basionym for botName3
 403         taxon1.addHomotypicSynonymName(botName2, null, null);
 404         Assert.assertEquals(botName1.getHomotypicalGroup(), botName2.getHomotypicalGroup());
 405         botName3.addBasionym(botName2);
 406         list.clear();
 407         list.addAll(taxon1.getSynonyms());
 408         list.add(taxon1);
 409         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 410
 411         Assert.assertEquals(botName1, list.get(0).getName());
 412         Assert.assertEquals(botName2, list.get(1).getName());
 413         Assert.assertEquals(botName3, list.get(2).getName());
 414         Assert.assertEquals(botName5, list.get(3).getName());
 415
 416     }
 417
 418     @Test
 419     public void testCompare_NoCircularProblemsWithReplacedSynonyms() {
 420
 421         taxon1.addHomotypicSynonymName(botName3, null, null);
 422         taxon1.addHomotypicSynonymName(botName5, null, null);
 423         botName3.addReplacedSynonym(botName5, null, null, null);
 424
 425         Assert.assertEquals(botName1.getHomotypicalGroup(), botName5.getHomotypicalGroup());
 426         botName5.addReplacedSynonym(botName1, null, null, null);
 427         botName1.addReplacedSynonym(botName3, null, null, null);
 428
 429         list.addAll(taxon1.getSynonyms());
 430         list.add(taxon1);
 431         Collections.sort(list, new HomotypicGroupTaxonComparator(null));
 432
 433         Assert.assertEquals(botName1, list.get(0).getName());
 434         Assert.assertEquals(botName3, list.get(1).getName());
 435         Assert.assertEquals(botName5, list.get(2).getName());
 436
 437
 438     }
 439
 440 }