cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.java

   1 /**
   2 * Copyright (C) 2009 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.persistence.dao.hibernate.taxon;
  11
  12 import static org.junit.Assert.assertEquals;
  13 import static org.junit.Assert.assertFalse;
  14 import static org.junit.Assert.assertNotNull;
  15 import static org.junit.Assert.assertNull;
  16 import static org.junit.Assert.assertTrue;
  17 import static org.junit.Assert.fail;
  18
  19 import java.io.FileNotFoundException;
  20 import java.util.ArrayList;
  21 import java.util.HashSet;
  22 import java.util.List;
  23 import java.util.Set;
  24 import java.util.UUID;
  25
  26 import org.apache.log4j.Level;
  27 import org.hibernate.Hibernate;
  28 import org.hibernate.envers.query.AuditEntity;
  29 import org.hibernate.envers.query.criteria.AuditCriterion;
  30 import org.hibernate.proxy.HibernateProxy;
  31 import org.junit.After;
  32 import org.junit.Assert;
  33 import org.junit.Before;
  34 import org.junit.Test;
  35 import org.unitils.dbunit.annotation.DataSet;
  36 import org.unitils.dbunit.annotation.ExpectedDataSet;
  37 import org.unitils.spring.annotation.SpringBeanByType;
  38
  39 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  40 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  41 import eu.etaxonomy.cdm.model.common.Marker;
  42 import eu.etaxonomy.cdm.model.common.MarkerType;
  43 import eu.etaxonomy.cdm.model.location.NamedArea;
  44 import eu.etaxonomy.cdm.model.name.NonViralName;
  45 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.taxon.Classification;
  48 import eu.etaxonomy.cdm.model.taxon.Synonym;
  49 import eu.etaxonomy.cdm.model.taxon.SynonymType;
  50 import eu.etaxonomy.cdm.model.taxon.Taxon;
  51 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  53 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  54 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  55 import eu.etaxonomy.cdm.model.view.AuditEvent;
  56 import eu.etaxonomy.cdm.model.view.AuditEventRecord;
  57 import eu.etaxonomy.cdm.model.view.context.AuditEventContextHolder;
  58 import eu.etaxonomy.cdm.persistence.dao.common.AuditEventSort;
  59 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  60 import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
  61 import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
  62 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  63 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  64 import eu.etaxonomy.cdm.persistence.query.GroupByCount;
  65 import eu.etaxonomy.cdm.persistence.query.GroupByDate;
  66 import eu.etaxonomy.cdm.persistence.query.Grouping;
  67 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  68 import eu.etaxonomy.cdm.persistence.query.NativeSqlOrderHint;
  69 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  70 import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
  71 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  72 import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
  73
  74 /**
  75  * @author a.mueller
  76  * @author ben.clark
  77  */
  78 public class TaxonDaoHibernateImplTest extends CdmTransactionalIntegrationTest {
  79
  80     @SpringBeanByType
  81     private ITaxonDao taxonDao;
  82
  83     @SpringBeanByType
  84     private IClassificationDao classificationDao;
  85
  86     @SpringBeanByType
  87     private IReferenceDao referenceDao;
  88
  89     @SpringBeanByType
  90     IDefinedTermDao definedTermDao;
  91
  92     private UUID uuid;
  93     private UUID sphingidae;
  94     private UUID acherontia;
  95     private UUID rethera;
  96     private UUID retheraSecCdmtest;
  97     private UUID atroposAgassiz; // a Synonym
  98     private UUID atroposLeach; // a Synonym
  99     private UUID acherontiaLachesis;
 100
 101     private AuditEvent previousAuditEvent;
 102     private AuditEvent mostRecentAuditEvent;
 103
 104     private UUID northernAmericaUuid;
 105     private UUID southernAmericaUuid;
 106     private UUID antarcticaUuid;
 107
 108     private UUID classificationUuid;
 109
 110     private static final String[] TABLE_NAMES = new String[] {
 111         "HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "TAXONBASE", "TAXONBASE_AUD"
 112         , "TAXONNAMEBASE", "TAXONNAMEBASE_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
 113
 114
 115     @Before
 116     public void setUp() {
 117
 118         uuid = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
 119         sphingidae = UUID.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
 120         acherontia = UUID.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
 121         acherontiaLachesis = UUID.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
 122         atroposAgassiz = UUID.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1");
 123         atroposLeach =  UUID.fromString("3da4ab34-6c50-4586-801e-732615899b07");
 124         rethera = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
 125         retheraSecCdmtest = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
 126
 127         previousAuditEvent = new AuditEvent();
 128         previousAuditEvent.setRevisionNumber(1025);
 129         previousAuditEvent.setUuid(UUID.fromString("a680fab4-365e-4765-b49e-768f2ee30cda"));
 130         mostRecentAuditEvent = new AuditEvent();
 131         mostRecentAuditEvent.setRevisionNumber(1026);
 132         mostRecentAuditEvent.setUuid(UUID.fromString("afe8e761-8545-497b-9134-6a6791fc0b0d"));
 133         AuditEventContextHolder.clearContext(); // By default we're in the current view (i.e. view == null)
 134
 135         northernAmericaUuid = UUID.fromString("2757e726-d897-4546-93bd-7951d203bf6f");
 136         southernAmericaUuid = UUID.fromString("6310b3ba-96f4-4855-bb5b-326e7af188ea");
 137         antarcticaUuid = UUID.fromString("791b3aa0-54dd-4bed-9b68-56b4680aad0c");
 138
 139         classificationUuid = UUID.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
 140     }
 141
 142     @After
 143     public void tearDown() {
 144         AuditEventContextHolder.clearContext();
 145     }
 146
 147     /**
 148      * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#TaxonDaoHibernateImpl()}.
 149      */
 150     @Test
 151     @DataSet
 152     public void testInit() {
 153         logger.warn("testInit()");
 154         assertNotNull("Instance of ITaxonDao expected",taxonDao);
 155         assertNotNull("Instance of IReferenceDao expected",referenceDao);
 156     }
 157
 158     /**
 159      * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
 160      */
 161     @Test
 162     @DataSet
 163     public void testGetTaxaByName() {
 164         Reference sec = referenceDao.findById(1);
 165         assert sec != null : "sec must exist";
 166
 167         List<TaxonBase> results = taxonDao.getTaxaByName("Aus", sec);
 168         assertNotNull("getTaxaByName should return a List", results);
 169         //assertFalse("The list should not be empty", results.isEmpty());
 170         assertEquals(1, results.size());
 171
 172         results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, true, null, null);
 173         assertNotNull("getTaxaByName should return a List", results);
 174
 175         int numberOfTaxaByName_A = 5;
 176
 177         logger.setLevel(Level.DEBUG); //FIXME #######################
 178         if (logger.isDebugEnabled()) {
 179             for (int i = 0; i < results.size(); i++) {
 180                 String nameCache = "";
 181                 TaxonNameBase<?,?> taxonNameBase= results.get(i).getName();
 182                 nameCache = HibernateProxyHelper.deproxy(taxonNameBase, NonViralName.class).getNameCache();
 183                 logger.debug(results.get(i).getClass() + "(" + i +")" +
 184                         ": Name Cache = " + nameCache + ", Title Cache = " + results.get(i).getTitleCache());
 185             }
 186         }
 187
 188         assertEquals(numberOfTaxaByName_A, results.size());
 189
 190
 191         //System.err.println("Species group: " + Rank.SPECIESGROUP().getId() + "Species: " + Rank.SPECIES().getId() + "Section Botany: "+ Rank.SECTION_BOTANY());
 192
 193 //              assertEquals(results.get(0).getTitleCache(), "Abies sec. ???");
 194 //              assertEquals(results.get(1).getTitleCache(), "Abies Mill.");
 195 //              assertEquals(results.get(2).getTitleCache(), "Abies mill. sec. ???");
 196 //              assertEquals(results.get(3).getTitleCache(), "Abies alba sec. ???");
 197 //              assertEquals(results.get(4).getTitleCache(), "Abies alba Michx. sec. ???");
 198 //              assertEquals(results.get(5).getTitleCache(), "Abies alba Mill. sec. ???");
 199
 200         results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, true, null, null);
 201         assertNotNull("getTaxaByName should return a List", results);
 202         assertEquals(numberOfTaxaByName_A, results.size());
 203
 204         results = taxonDao.getTaxaByName("Aus", MatchMode.EXACT, true, null, null);
 205         assertNotNull("getTaxaByName should return a List", results);
 206         assertEquals("Results list should contain one entity",1,results.size());
 207     }
 208
 209
 210     @Test
 211     @DataSet (loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
 212     public void testGetTaxaByNameWithMisappliedNames(){
 213
 214         Classification classification = classificationDao.load(classificationUuid);
 215
 216         /* NOTE:
 217          * The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis), two contained in the classification used in this test,
 218          * the other one is not contained in any classification. This latter case is the more general situation.
 219          * Misapplied names should be found regardless of whether they are contained in a classification or not.
 220          */
 221         //two accepted taxa starting with R in classification "TestBaum"
 222         List<TaxonBase> results = taxonDao.getTaxaByName(true, false, false, "R*", classification, MatchMode.BEGINNING, null, null, null, null);
 223         Assert.assertEquals("There should be 2 Taxa", 2, results.size());
 224
 225         //three taxa, 2 accepted and 1 misapplied name starting with R
 226         results = taxonDao.getTaxaByName(true, false, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
 227         Assert.assertEquals("There should be 3 Taxa", 3, results.size());
 228
 229         //one synonym has no accepted taxon
 230         results = taxonDao.getTaxaByName(true, true, true, "A*", null, MatchMode.BEGINNING, null, null, null, null);
 231         Assert.assertEquals("There should be 11 Taxa",11, results.size());
 232
 233         //two accepted taxa in classification and 1 misapplied name with accepted name in classification
 234         results = taxonDao.getTaxaByName(true, true, true, "R*", classification, MatchMode.BEGINNING, null, null, null, null);
 235         Assert.assertEquals("There should be 3 Taxa", 3, results.size());
 236
 237         //same as above because all taxa, synonyms and misapplied names starting with R are in the classification
 238         results = taxonDao.getTaxaByName(true, true, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
 239         Assert.assertEquals("There should be 3 Taxa", 3, results.size());
 240
 241         //find misapplied names with accepted taxon in the classification, the accepted taxa of two misapplied names are in the classification
 242         results = taxonDao.getTaxaByName(false, false, true, "*", classification, MatchMode.BEGINNING, null, null, null, null);
 243         Assert.assertEquals("There should be 2 Taxa", 2, results.size());
 244
 245         //find misapplied names beginning with R
 246         results = taxonDao.getTaxaByName(false, false, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
 247         Assert.assertEquals("There should be 1 Taxa", 1, results.size());
 248
 249         //find all three misapplied names
 250         results = taxonDao.getTaxaByName(false, false, true, "*", null, MatchMode.BEGINNING, null, null, null, null);
 251         Assert.assertEquals("There should be 3 Taxa", 3, results.size());
 252
 253     }
 254
 255     /**
 256      * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
 257      */
 258     @Test
 259     @DataSet
 260     public void testGetTaxaByNameForEditor() {
 261         Reference sec = referenceDao.findById(1);
 262         assert sec != null : "sec must exist";
 263
 264         List<UuidAndTitleCache<IdentifiableEntity>> results = taxonDao.getTaxaByNameForEditor(true, true, false,false,"Acher", null, MatchMode.BEGINNING, null);
 265         assertNotNull("getTaxaByName should return a List", results);
 266         assertFalse("The list should not be empty", results.isEmpty());
 267         assertEquals(4, results.size());
 268
 269
 270         results = taxonDao.getTaxaByNameForEditor(true, true, false, false,"A",null, MatchMode.BEGINNING, null);
 271         assertNotNull("getTaxaByName should return a List", results);
 272         assertEquals(7, results.size());
 273
 274
 275         results = taxonDao.getTaxaByNameForEditor(true, false,false, false,"A", null,MatchMode.BEGINNING, null);
 276         assertNotNull("getTaxaByName should return a List", results);
 277         assertEquals(5, results.size());
 278         assertEquals(results.get(0).getType(), Taxon.class);
 279
 280         results = taxonDao.getTaxaByNameForEditor(false, true,false,false, "A", null,MatchMode.BEGINNING, null);
 281         assertNotNull("getTaxaByName should return a List", results);
 282         assertEquals(2, results.size());
 283         assertEquals(results.get(0).getType(), Synonym.class);
 284
 285         results = taxonDao.getTaxaByNameForEditor(true, true,false,false,"Aus", null,MatchMode.EXACT,  null);
 286         assertNotNull("getTaxaByName should return a List", results);
 287         assertEquals("Results list should contain one entity",1,results.size());
 288
 289         results = taxonDao.getTaxaByNameForEditor(true, true,true,false,"A", null,MatchMode.BEGINNING,  null);
 290         assertNotNull("getTaxaByName should return a List", results);
 291         assertEquals("Results list should contain one entity", 8, results.size());
 292
 293         //TODO: test the search for misapplied names
 294
 295     }
 296
 297
 298     /**
 299      * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}
 300      * restricting the search by a set of Areas.
 301      */
 302     @Test
 303     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
 304     public void testGetTaxaByNameAndArea() {
 305
 306         Set<NamedArea> namedAreas = new HashSet<NamedArea>();
 307         namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
 308         //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
 309         //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
 310
 311         Classification taxonmicTree = classificationDao.findByUuid(classificationUuid);
 312
 313         // prepare some synonym relation ships for some tests
 314         Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
 315         Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
 316         taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
 317         logger.warn("addSynonym(..)");
 318
 319         Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
 320         Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
 321         taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
 322         this.taxonDao.save(taxonRetheraSecCdmtest);
 323
 324         Taxon test = (Taxon)this.taxonDao.findByUuid(retheraSecCdmtest);
 325 //        Set<Synonym> synonyms3 = test.getSynonyms();
 326         // 1. searching for a taxon (Rethera)
 327         //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
 328
 329         List<TaxonBase> results = taxonDao.getTaxaByName(true,false, false, "Rethera", null, MatchMode.BEGINNING, namedAreas,
 330             null, null, null);
 331         assertNotNull("getTaxaByName should return a List", results);
 332         assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
 333
 334         // 2. searching for a taxon (Rethera) contained in a specific classification
 335         results = taxonDao.getTaxaByName(true, false, false, "Rethera", taxonmicTree, MatchMode.BEGINNING, namedAreas,
 336             null, null, null);
 337         assertNotNull("getTaxaByName should return a List", results);
 338         assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
 339
 340
 341         // 3. searching for Synonyms
 342         results = taxonDao.getTaxaByName(false, true, false, "Atropo", null, MatchMode.ANYWHERE, null,
 343             null, null, null);
 344         assertNotNull("getTaxaByName should return a List", results);
 345         /*System.err.println(results.get(0).getTitleCache() + " - " +results.get(1).getTitleCache() + " - " +results.get(2).getTitleCache() );
 346
 347
 348         System.err.println(((Synonym)results.get(0)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(1)).getAcceptedTaxa().contains(taxonRethera)+ " - "  +((Synonym)results.get(2)).getAcceptedTaxa().contains(taxonRethera)+ " - "  );
 349         */
 350         assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
 351
 352         // 4. searching for Synonyms
 353         results = taxonDao.getTaxaByName(false, true, false, "Atropo", null, MatchMode.BEGINNING, null,
 354             null, null, null);
 355         assertNotNull("getTaxaByName should return a List", results);
 356         assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
 357
 358
 359         // 5. searching for a Synonyms and Taxa
 360         results = taxonDao.getTaxaByName(true, true, false, "A", null, MatchMode.BEGINNING, namedAreas,
 361             null, null, null);
 362         //only five taxa have a distribution
 363         assertNotNull("getTaxaByName should return a List", results);
 364         assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
 365     }
 366
 367
 368     /**
 369      * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#findByNameTitleCache(Class<? extends TaxonBase>clazz, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths)}
 370      * restricting the search by a set of Areas.
 371      */
 372     @Test
 373     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
 374     public void testFindByNameTitleCache() {
 375
 376         Set<NamedArea> namedAreas = new HashSet<NamedArea>();
 377         namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
 378         //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
 379         //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
 380
 381         Classification classification = classificationDao.findByUuid(classificationUuid);
 382
 383         // prepare some synonym relation ships for some tests
 384         Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
 385         Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
 386         taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
 387         logger.warn("addSynonym(..)");
 388         this.taxonDao.clear();
 389         Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
 390         Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
 391         taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
 392         this.taxonDao.clear();
 393         // 1. searching for a taxon (Rethera)
 394         //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
 395
 396         List<TaxonBase> results = taxonDao.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", null, MatchMode.EXACT, namedAreas,
 397             null, null, null);
 398         assertNotNull("getTaxaByName should return a List", results);
 399         assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
 400
 401         // 2. searching for a taxon (Rethera) contained in a specific classification
 402         results = taxonDao.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", classification, MatchMode.EXACT, namedAreas,
 403             null, null, null);
 404         assertNotNull("getTaxaByName should return a List", results);
 405         assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
 406
 407
 408         // 3. searching for Synonyms
 409         results = taxonDao.findByNameTitleCache(false, true, "*Atropo", null, MatchMode.ANYWHERE, null,
 410             null, null, null);
 411         assertNotNull("getTaxaByName should return a List", results);
 412
 413         assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
 414
 415         // 4. searching for Synonyms
 416         results = taxonDao.findByNameTitleCache(false, true, "Atropo", null, MatchMode.BEGINNING, null,
 417             null, null, null);
 418         assertNotNull("getTaxaByName should return a List", results);
 419         assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
 420
 421
 422         // 5. searching for a Synonyms and Taxa
 423         //   attache a synonym first
 424         Synonym syn = (Synonym)taxonDao.findByUuid(this.atroposLeach);
 425         Taxon tax = (Taxon) taxonDao.findByUuid(rethera);
 426         tax.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
 427
 428         taxonDao.save(tax);
 429         results = taxonDao.findByNameTitleCache(true, true, "A", null, MatchMode.BEGINNING, namedAreas,
 430             null, null, null);
 431         assertNotNull("getTaxaByName should return a List", results);
 432         assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
 433     }
 434
 435     @Test
 436     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
 437     public void testTaxonNameInTwoClassifications(){
 438         int numberOfClassifications = classificationDao.count();
 439         List<String> propertyPaths = new ArrayList<String>();
 440         propertyPaths.add("taxonNodes");
 441         List<TaxonBase> taxa = taxonDao.getTaxaByName(true, true, false, "P", null, MatchMode.BEGINNING, null, null, null, null);
 442         Taxon taxon = (Taxon)taxa.get(0);
 443         Set<TaxonNode> nodes = taxon.getTaxonNodes();
 444         assertTrue(nodes.size() == 1);
 445         //assertNotNull(taxa);
 446         //assertTrue(taxa.size() > 0);
 447     }
 448
 449     @Test
 450     @DataSet
 451     public void testFindByUuid() {
 452         Taxon taxon = (Taxon)taxonDao.findByUuid(uuid);
 453         assertNotNull("findByUuid should return a taxon",taxon);
 454         assertFalse("findByUuid should not return a taxon with it's name initialized",Hibernate.isInitialized(taxon.getName()));
 455     }
 456
 457     @Test
 458     @DataSet
 459     public void testLoad() {
 460         List<String> propertyPaths = new ArrayList<String>();
 461         propertyPaths.add("name");
 462         propertyPaths.add("sec");
 463         Taxon taxon = (Taxon)taxonDao.load(uuid, propertyPaths);
 464         assertNotNull("findByUuid should return a taxon",taxon);
 465         assertTrue("load should return a taxon with it's name initialized, given that the property was specified in the method",Hibernate.isInitialized(taxon.getName()));
 466         assertTrue("load should return a taxon with it's secundum reference initialized, given that the property was specified in the method",Hibernate.isInitialized(taxon.getSec()));
 467     }
 468
 469     @Test
 470     @DataSet
 471     public void testCountTaxonRelationships()   {
 472         Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
 473         assert taxon != null : "taxon must exist";
 474
 475         int numberOfRelatedTaxa = taxonDao.countTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo);
 476         assertEquals("countTaxonRelationships should return 8", 8, numberOfRelatedTaxa);
 477     }
 478
 479     @Test
 480     @DataSet
 481     public void testCountTaxaByName() {
 482         long numberOfTaxa = taxonDao.countTaxaByName(true, false, false, "A", null, MatchMode.BEGINNING, null);
 483         assertEquals(5, numberOfTaxa);
 484         numberOfTaxa = taxonDao.countTaxaByName(true, false, false, "Smerinthus kindermannii", null, MatchMode.EXACT, null);
 485         assertEquals(1, numberOfTaxa);
 486         numberOfTaxa = taxonDao.countTaxaByName(false, true, false, "A", null, MatchMode.BEGINNING, null);
 487         assertEquals(2, numberOfTaxa);
 488         numberOfTaxa = taxonDao.countTaxaByName(true, true, false, "A", null, MatchMode.BEGINNING, null);
 489         assertEquals(7, numberOfTaxa);
 490         numberOfTaxa = taxonDao.countTaxaByName(true, true, false, "Aasfwerfwf fffe", null, MatchMode.BEGINNING, null);
 491         assertEquals(0, numberOfTaxa);
 492 //      FIXME implement test for search in specific classification
 493 //              Reference reference = referenceDao.findByUuid(UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"));
 494 //              numberOfTaxa = taxonDao.countTaxaByName("A*", MatchMode.BEGINNING, SelectMode.ALL, null, null);
 495 //              assertEquals(numberOfTaxa, 2);
 496     }
 497
 498     @Test
 499     @DataSet
 500     public void testRelatedTaxa() {
 501         Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
 502         assert taxon != null : "taxon must exist";
 503
 504         List<String> propertyPaths = new ArrayList<String>();
 505         propertyPaths.add("fromTaxon");
 506         propertyPaths.add("fromTaxon.name");
 507         List<OrderHint> orderHints = new ArrayList<OrderHint>();
 508         orderHints.add(new OrderHint("relatedFrom.name.genusOrUninomial", SortOrder.ASCENDING));
 509         orderHints.add(new OrderHint("relatedFrom.name.specificEpithet", SortOrder.ASCENDING));
 510         orderHints.add(new OrderHint("relatedFrom.name.infraSpecificEpithet", SortOrder.ASCENDING));
 511
 512         List<TaxonRelationship> relatedTaxa = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
 513         assertNotNull("getRelatedTaxa should return a List",relatedTaxa);
 514         assertEquals("getRelatedTaxa should return all 8 related taxa", 8, relatedTaxa.size());
 515         assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon()));
 516         assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon().getName()));
 517
 518         assertEquals("Acherontia should appear first in the list of related taxa", relatedTaxa.get(0).getFromTaxon().getTitleCache(), "Acherontia Laspeyres, 1809 sec. cate-sphingidae.org");
 519         assertEquals("Sphingonaepiopsis should appear last in the list of related taxa", "Sphingonaepiopsis Wallengren, 1858 sec. cate-sphingidae.org", relatedTaxa.get(relatedTaxa.size()-1).getFromTaxon().getTitleCache());
 520     }
 521
 522     @Test
 523     @DataSet
 524     public void testGetRelatedTaxaPaged()       {
 525         Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
 526         assert taxon != null : "taxon must exist";
 527
 528         List<String> propertyPaths = new ArrayList<String>();
 529         propertyPaths.add("fromTaxon");
 530         propertyPaths.add("fromTaxon.name");
 531
 532         List<OrderHint> orderHints = new ArrayList<OrderHint>();
 533         orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
 534
 535         int pageSize = 3;
 536         List<TaxonRelationship> firstPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), pageSize, 0, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
 537         List<TaxonRelationship> secondPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),pageSize, 1, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
 538         List<TaxonRelationship> thirdPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), pageSize, 2, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
 539
 540         assertNotNull("getRelatedTaxa: 3, 0 should return a List",firstPage);
 541         assertEquals("getRelatedTaxa: 3, 0 should return a List with 3 elements", pageSize,firstPage.size());
 542         assertNotNull("getRelatedTaxa: 3, 1 should return a List",secondPage);
 543         assertEquals("getRelatedTaxa: 3, 1 should return a List with 3 elements", pageSize, secondPage.size());
 544         assertNotNull("getRelatedTaxa: 3, 2 should return a List",thirdPage);
 545         assertEquals("getRelatedTaxa: 3, 2 should return a List with 2 elements", 2, thirdPage.size());
 546     }
 547
 548     @Test
 549     @DataSet
 550     public void testCountSynonyms() {
 551         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 552         assert taxon != null : "taxon must exist";
 553
 554         int numberOfRelatedSynonym = taxonDao.countSynonyms(taxon,null);
 555         assertEquals("countSynonyms should return 3", 3, numberOfRelatedSynonym);
 556     }
 557
 558     @Test
 559     @DataSet
 560     public void testGetSynonyms()       {
 561         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 562         assert taxon != null : "taxon must exist";
 563         List<String> propertyPaths = new ArrayList<String>();
 564         propertyPaths.add("synonym");
 565         propertyPaths.add("synonym.name");
 566
 567         List<OrderHint> orderHints = new ArrayList<OrderHint>();
 568         orderHints.add(new OrderHint("titleCache", SortOrder.ASCENDING));
 569
 570         List<Synonym> synonyms = taxonDao.getSynonyms(taxon, null, null, null,orderHints,propertyPaths);
 571
 572         assertNotNull("getSynonyms should return a List", synonyms);
 573         assertEquals("getSynonyms should return 3 synonyms", 3, synonyms.size());
 574         assertTrue("getSynonyms should return synonym objects with the synonym initialized", Hibernate.isInitialized(synonyms.get(0)));
 575     }
 576
 577     @Test
 578     @DataSet
 579     public void testCountSynonymsByType()       {
 580         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 581         assert taxon != null : "taxon must exist";
 582
 583         int numberOfTaxonomicSynonyms = taxonDao.countSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF());
 584         assertEquals("countSynonyms should return 4", 3, numberOfTaxonomicSynonyms);
 585     }
 586
 587     @Test
 588     @DataSet
 589     public void testSynonymsByType() {
 590         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 591         assert taxon != null : "taxon must exist";
 592
 593         List<Synonym> synonyms = taxonDao.getSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
 594
 595         assertNotNull("getSynonyms should return a List", synonyms);
 596         assertEquals("getSynonyms should return 4 Synonyms", 3, synonyms.size());
 597     }
 598
 599     @Test
 600     @DataSet
 601     public void testPageSynonyms(){
 602         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 603         assert taxon != null : "taxon must exist";
 604
 605         int pageSize = 2;
 606         List<Synonym> firstPage = taxonDao.getSynonyms(taxon, null, pageSize, 0,null,null);
 607         List<Synonym> secondPage = taxonDao.getSynonyms(taxon, null, pageSize, 1,null,null);
 608
 609         assertNotNull("getSynonyms: 2, 0 should return a List",firstPage);
 610         assertEquals("getSynonyms: 2, 0 should return 2 synonyms", pageSize,firstPage.size());
 611         assertNotNull("getSynonyms: 2, 1 should return a List",secondPage);
 612         assertEquals("getSynonyms: 2, 1 should return 1 synonym", 1, secondPage.size());
 613     }
 614
 615     @Test
 616     @DataSet("TaxonNodeDaoHibernateImplTest.xml")
 617     public void testListAcceptedTaxaFor()  {
 618         UUID acheontitia_ciprosus = UUID.fromString("3ef145f7-bd92-4a64-8afd-2b8203e00e02");
 619
 620         Synonym synonym = (Synonym)taxonDao.findByUuid(acheontitia_ciprosus);
 621         assertNotNull("synonym must exist", synonym);
 622
 623         Taxon taxon = taxonDao.acceptedTaxonFor(synonym, null, null);
 624         assertNotNull("listAcceptedTaxaFor should return a taxon", taxon);
 625
 626         Classification classification = classificationDao.load(classificationUuid);
 627         assertNotNull("classification must exist", classification);
 628
 629         taxon = taxonDao.acceptedTaxonFor(synonym, classification, null);
 630         assertNull("listAcceptedTaxaFor should return not taxon due to classification filter", taxon);
 631     }
 632
 633
 634     @Test
 635     @DataSet
 636     public void testGetTaxonMatchingUninomial() {
 637         List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*","*",null,null,null);
 638
 639         assertNotNull("findTaxaByName should return a List", result);
 640         assertEquals("findTaxaByName should return two Taxa",2,result.size());
 641         assertEquals("findTaxaByName should return a Taxon with id 5",5,result.get(0).getId());
 642     }
 643
 644     @Test
 645     @DataSet
 646     public void testGetTaxonMatchingSpeciesBinomial() {
 647         List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", null, "kindermannii", null,"*",null,null,null);
 648
 649         assertNotNull("findTaxaByName should return a List", result);
 650         assertEquals("findTaxaByName should return one Taxon",1,result.size());
 651         assertEquals("findTaxaByName should return a Taxon with id 8",8,result.get(0).getId());
 652     }
 653
 654     @Test
 655     @DataSet
 656     public void testGetTaxonMatchingTrinomial() {
 657         List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis","*",null,null,null);
 658
 659         assertNotNull("findTaxaByName should return a List", result);
 660         assertEquals("findTaxaByName should return one Taxon",1,result.size());
 661         assertEquals("findTaxaByName should return a Taxon with id 38",38,result.get(0).getId());
 662     }
 663
 664     @Test
 665     @DataSet
 666     public void testNegativeMatch() {
 667         List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
 668
 669         assertNotNull("findTaxaByName should return a List", result);
 670         assertTrue("findTaxaByName should return an empty List",result.isEmpty());
 671     }
 672
 673     @Test
 674     @DataSet
 675     public void testCountAllTaxa() {
 676         int numberOfTaxa = taxonDao.count(Taxon.class);
 677         assertEquals("count should return 14 taxa", 14, numberOfTaxa);
 678     }
 679
 680     @Test
 681     @DataSet
 682     public void testListAllTaxa() {
 683         List<Taxon> taxa = taxonDao.list(Taxon.class,100, 0);
 684         assertNotNull("list should return a List", taxa);
 685         assertEquals("list should return 14 taxa", 14, taxa.size());
 686     }
 687
 688     @Test
 689     @DataSet
 690    // @ExpectedDataSet
 691     public void testDelete() {
 692         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 693         assert taxon != null : "taxon must exist";
 694         taxonDao.delete(taxon);
 695         taxon = (Taxon)taxonDao.findByUuid(acherontia);
 696         assert taxon == null : "taxon must not exist";
 697         setComplete();
 698         endTransaction();
 699 //        try {
 700 //            printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
 701 //        } catch (FileNotFoundException e) {
 702 //            e.printStackTrace();
 703 //        }
 704     }
 705
 706     @Test
 707     @DataSet
 708     @ExpectedDataSet("TaxonDaoHibernateImplTest.testDelete-result.xml")
 709     public void testDeleteWithMarker() {
 710         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 711         taxon.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
 712         taxonDao.save(taxon);
 713         assert taxon != null : "taxon must exist";
 714
 715         taxonDao.delete(taxon);
 716         commitAndStartNewTransaction(null);
 717         taxon = (Taxon)taxonDao.findByUuid(acherontia);
 718         assert taxon == null : "taxon must not exist";
 719         setComplete();
 720         endTransaction();
 721 //        try {
 722 //            printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
 723 //        } catch (FileNotFoundException e) {
 724 //            e.printStackTrace();
 725 //        }
 726     }
 727
 728     @Test
 729     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 730     public void testFindDeleted() {
 731         TaxonBase<?> taxon = taxonDao.findByUuid(acherontia);
 732         assertNull("findByUuid should return null in this view", taxon);
 733         assertFalse("exist should return false in this view",taxonDao.exists(acherontia));
 734     }
 735
 736     @Test
 737     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 738     public void testFindDeletedInPreviousView() {
 739         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 740         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
 741         assertNotNull("findByUuid should return a taxon in this view",taxon);
 742         assertTrue("exists should return true in this view", taxonDao.exists(acherontia));
 743
 744         try{
 745             assertEquals("There should be 3 relations to this taxon in this view",3,taxon.getRelationsToThisTaxon().size());
 746         } catch(Exception e) {
 747             fail("We should not experience any problems initializing proxies with envers");
 748         }
 749     }
 750
 751     @Test
 752     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 753     public void testGetAuditEvents() {
 754         TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
 755         assert taxon != null : "taxon cannot be null";
 756
 757         List<String> propertyPaths = new ArrayList<String>();
 758         propertyPaths.add("name");
 759         propertyPaths.add("createdBy");
 760         propertyPaths.add("updatedBy");
 761
 762         List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,null,propertyPaths);
 763         assertNotNull("getAuditEvents should return a list",auditEvents);
 764         assertFalse("the list should not be empty",auditEvents.isEmpty());
 765         assertEquals("There should be two AuditEventRecords in the list",2, auditEvents.size());
 766     }
 767
 768     @Test
 769     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 770     public void testGetAuditEventsFromNow() {
 771         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 772         TaxonBase<?> taxon =  taxonDao.findByUuid(sphingidae);
 773         assert taxon != null : "taxon cannot be null";
 774
 775         List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,AuditEventSort.FORWARDS,null);
 776         assertNotNull("getAuditEvents should return a list",auditEvents);
 777         assertFalse("the list should not be empty",auditEvents.isEmpty());
 778         assertEquals("There should be one audit event in the list",1,auditEvents.size());
 779     }
 780
 781     @Test
 782     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 783     public void testCountAuditEvents() {
 784         TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
 785         assert taxon != null : "taxon cannot be null";
 786
 787         int numberOfAuditEvents = taxonDao.countAuditEvents(taxon,null);
 788         assertEquals("countAuditEvents should return 2",numberOfAuditEvents,2);
 789     }
 790
 791     @Test
 792     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 793     public void getPreviousAuditEvent() {
 794         TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
 795         assert taxon != null : "taxon cannot be null";
 796
 797         AuditEventRecord<TaxonBase> auditEvent = taxonDao.getPreviousAuditEvent(taxon);
 798         assertNotNull("getPreviousAuditEvent should not return null as there is at least one audit event prior to the current one",auditEvent);
 799     }
 800
 801     @Test
 802     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 803     public void getPreviousAuditEventAtBeginning() {
 804         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 805         TaxonBase taxon = taxonDao.findByUuid(sphingidae);
 806         assert taxon != null : "taxon cannot be null";
 807
 808         AuditEventRecord<TaxonBase> auditEvent = taxonDao.getPreviousAuditEvent(taxon);
 809         assertNull("getPreviousAuditEvent should return null if we're at the first audit event anyway",auditEvent);
 810     }
 811
 812     @Test
 813     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 814     public void getNextAuditEvent() {
 815         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 816         TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
 817         assert taxon != null : "taxon cannot be null";
 818
 819         AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
 820         assertNotNull("getNextAuditEvent should not return null as there is at least one audit event after the current one",auditEvent);
 821     }
 822
 823     @Test
 824     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 825     public void getNextAuditEventAtEnd() {
 826         AuditEventContextHolder.getContext().setAuditEvent(mostRecentAuditEvent);
 827         TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
 828         assert taxon != null : "taxon cannot be null";
 829
 830         AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
 831         assertNull("getNextAuditEvent should return null as there no more audit events after the current one",auditEvent);
 832     }
 833
 834     @Test
 835     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 836     public void testFind() {
 837         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 838         assert taxon != null : "taxon cannot be null";
 839
 840        assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
 841     }
 842
 843     @Test
 844     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 845     public void testFindInPreviousView() {
 846         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 847         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 848         assert taxon != null : "taxon cannot be null";
 849
 850         assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon.getRelationsToThisTaxon().isEmpty());
 851     }
 852
 853     @Test
 854     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 855     public void testGetRelations() {
 856         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 857         assert taxon != null : "taxon cannot be null";
 858
 859         List<String> propertyPaths = new ArrayList<String>();
 860          propertyPaths.add("fromTaxon");
 861          propertyPaths.add("fromTaxon.name");
 862
 863          List<OrderHint> orderHints = new ArrayList<OrderHint>();
 864          orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
 865
 866         List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
 867         assertNotNull("getRelatedTaxa should return a list", taxonRelations);
 868         assertEquals("there should be one TaxonRelationship in the list in the current view",1,taxonRelations.size());
 869         assertTrue("TaxonRelationship.relatedFrom should be initialized",Hibernate.isInitialized(taxonRelations.get(0).getFromTaxon()));
 870         assertTrue("TaxonRelationship.relatedFrom.name should be initialized",Hibernate.isInitialized(taxonRelations.get(0).getFromTaxon().getName()));
 871     }
 872
 873     @Test
 874     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 875     public void testCountRelations() {
 876         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 877         assert taxon != null : "taxon cannot be null";
 878         assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo));
 879     }
 880
 881     @Test
 882     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 883     public void testGetRelationsInPreviousView() {
 884        AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 885        Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 886        assert taxon != null : "taxon cannot be null";
 887
 888        List<String> propertyPaths = new ArrayList<String>();
 889        propertyPaths.add("relatedFrom");
 890        propertyPaths.add("relatedFrom.name");
 891
 892        List<OrderHint> orderHints = new ArrayList<OrderHint>();
 893        orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
 894
 895        List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
 896        assertNotNull("getRelatedTaxa should return a list",taxonRelations);
 897        assertTrue("there should be no TaxonRelationships in the list in the prior view",taxonRelations.isEmpty());
 898     }
 899
 900     @Test
 901     @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
 902     public void testCountRelationsInPreviousView() {
 903         AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
 904         Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
 905         assert taxon != null : "taxon cannot be null";
 906         assertEquals("countRelatedTaxa should return 0 in the current view",0, taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo));
 907     }
 908
 909     @Test
 910     @DataSet
 911     public void testGroupTaxa() {
 912         List<Grouping> groups = new ArrayList<Grouping>();
 913         groups.add(new GroupByCount("count",SortOrder.DESCENDING));
 914         groups.add(new Grouping("name.genusOrUninomial", "genus", "n", SortOrder.ASCENDING));
 915         List<Object[]> results = taxonDao.group(null, null, null, groups,null);
 916         System.out.println("count\tname.genuOrUninomial");
 917         for(Object[] result : results) {
 918             System.out.println(result[0] + "\t" + result[1]);
 919         }
 920     }
 921
 922     @Test
 923     @DataSet
 924     public void testGroupTaxaByClass() {
 925         List<Grouping> groups = new ArrayList<Grouping>();
 926         groups.add(new GroupByCount("count",SortOrder.DESCENDING));
 927         groups.add(new Grouping("class", "class",null, SortOrder.ASCENDING));
 928         List<Object[]> results = taxonDao.group(null, null, null, groups,null);
 929         System.out.println("count\tclass");
 930         for(Object[] result : results) {
 931             System.out.println(result[0] + "\t" + result[1]);
 932         }
 933     }
 934
 935     @Test
 936     @DataSet
 937     public void testNativeSQLOrder() {
 938         List<OrderHint> orderHints = new ArrayList<OrderHint>();
 939         orderHints.add(new NativeSqlOrderHint("case when {alias}.titleCache like 'C%' then 0 else 1 end",SortOrder.ASCENDING));
 940
 941         List<TaxonBase> results = taxonDao.list(null, null, orderHints);
 942         System.out.println("native SQL order");
 943         for(TaxonBase<?> result : results) {
 944             System.out.println(result.getTitleCache());
 945         }
 946     }
 947
 948     @Test
 949     @DataSet
 950     public void testGroupByDateTaxa() {
 951         List<Grouping> groups = new ArrayList<Grouping>();
 952         groups.add(new GroupByCount("count",null));
 953         groups.add(new GroupByDate("created", "dateGroup", SortOrder.ASCENDING, GroupByDate.Resolution.MONTH));
 954         List<Object[]> results = taxonDao.group(null, null, null, groups,null);
 955         System.out.println("count\tyear\tmonth");
 956         for(Object[] result : results) {
 957             System.out.println(result[0] + "\t" + result[1] + "\t" + result[2]);
 958         }
 959     }
 960
 961     @Test
 962     @DataSet ("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
 963     public final void testGetTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(){
 964         Classification classification = classificationDao.findByUuid(classificationUuid);
 965         List<UuidAndTitleCache<TaxonNode>> result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  null, null);
 966         assertNotNull(result);
 967         assertEquals(5, result.size());
 968
 969         //test exclude
 970         UUID excludeUUID = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
 971         List<UUID> excludeUUids = new ArrayList<UUID>();
 972         excludeUUids.add(excludeUUID);
 973         result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  null, null);
 974         assertEquals(5, result.size());
 975
 976         //test limit
 977         int limit = 2;
 978         result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification,  limit, null);
 979         assertEquals(2, result.size());
 980
 981         //test pattern
 982         String pattern = "*Rothschi*";
 983         result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, 2, pattern);
 984         assertNotNull(result);
 985         assertEquals(1, result.size());
 986         assertEquals("0b5846e5-b8d2-4ca9-ac51-099286ea4adc", result.get(0).getUuid().toString());
 987
 988     }
 989
 990
 991     @Test
 992     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
 993     //NOTE: There is a problem with loading AuditEvents if this test runs
 994     //stand alone or as first (one of the first) in the test suite. For some reason
 995     //the AuditEvent records from the @DataSet are not inserted into the database then,
 996     //while those inserted by the terms dataset are inserted as well as a completely new one.
 997     //This problem for some reason does not happen if not running at first place
 998     public void testGetAuditEventsByTypeWithRestrictions() {
 999         commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
1000
1001         List<String> propertyPaths = new ArrayList<String>();
1002         propertyPaths.add("name");
1003         propertyPaths.add("createdBy");
1004         propertyPaths.add("updatedBy");
1005
1006         List<AuditCriterion> criteria = new ArrayList<AuditCriterion>();
1007         criteria.add(AuditEntity.property("lsid_lsid").isNotNull());
1008
1009         int count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
1010
1011         List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, criteria,null, null, AuditEventSort.FORWARDS, propertyPaths);
1012         assertNotNull("getAuditEvents should return a list",auditEvents);
1013         assertFalse("the list should not be empty",auditEvents.isEmpty());
1014         assertEquals("There should be one AuditEventRecord in the list",1, auditEvents.size());
1015     }
1016
1017
1018     @Test
1019     @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
1020 //    @DataSets({  //for testing only
1021 //        @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml"),
1022 //        @DataSet("TaxonDaoHibernateImplTest.testFindDeletedAuditEvents.xml")
1023 //    })
1024     //NOTE: There is a problem with loading AuditEvents if this test runs
1025     //stand alone or as first (one of the first) in the test suite. For some reason
1026     //the AuditEvent records from the @DataSet are not inserted into the database then,
1027     //while those inserted by the terms dataset are inserted as well as a completely new one.
1028     //This problem for some reason does not happen if not running at first place
1029     public void testGetAuditEventsByTypeWithNoRestrictions() {
1030         printDataSet(System.out, new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
1031         commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
1032
1033         List<String> propertyPaths = new ArrayList<String>();
1034         propertyPaths.add("name");
1035         propertyPaths.add("createdBy");
1036         propertyPaths.add("updatedBy");
1037         int count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
1038         List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, null,null, null, AuditEventSort.FORWARDS, propertyPaths);
1039         assertNotNull("getAuditEvents should return a list", auditEvents);
1040         assertFalse("the list should not be empty", auditEvents.isEmpty());
1041         assertEquals("There should be thirty eight AuditEventRecords in the list", 2, auditEvents.size());
1042     }
1043
1044
1045     @Test
1046     @DataSet("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
1047     public void testGetCommonName(){
1048        List<Taxon> commonNameResults = taxonDao.getTaxaByCommonName("common%", null,
1049                 MatchMode.BEGINNING, null, null, null, null);
1050
1051         assertNotNull("getTaxaByCommonName should return a list", commonNameResults);
1052         assertFalse("the list should not be empty", commonNameResults.isEmpty());
1053         assertEquals("There should be one Taxon with common name", 1,commonNameResults.size());
1054         assertEquals(" sec. ???", ((TaxonBase)commonNameResults.get(0)).getTitleCache());
1055     }
1056
1057     @Test
1058     @DataSet
1059     public void testGetTitleCache(){
1060         UUID uuid = UUID.fromString("7b8b5cb3-37ba-4dba-91ac-4c6ffd6ac331");
1061         String titleCache = taxonDao.getTitleCache(uuid, false);
1062         Assert.assertEquals("Acherontia styx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
1063         titleCache = taxonDao.getTitleCache(uuid, true);
1064         Assert.assertEquals("Acherontia styxx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
1065    }
1066
1067
1068     @Test
1069     @DataSet("TaxonDaoHibernateImplTest.testPropertyPath.xml")
1070     public void testPropertyPath(){
1071         //Test that BeanInitializer also works on HiberanteProxys
1072         Classification c = classificationDao.load(UUID.fromString("4bceea53-893f-4685-8c63-6dcec6e85ab1"));
1073         TaxonNode singleNode = c.getRootNode().getChildNodes().iterator().next();
1074         Taxon taxonProxy = singleNode.getTaxon();
1075         Assert.assertTrue("Object to test should be a proxy ", taxonProxy instanceof HibernateProxy);
1076
1077         List<String> propertyPaths = new ArrayList<String>();
1078         propertyPaths.add("taxonNodes");
1079         Taxon taxon = (Taxon)this.taxonDao.load(
1080                 UUID.fromString("4a5bc930-844f-45ec-aea8-dd155e1ab25f"),
1081                 propertyPaths);
1082         Assert.assertSame("Returned object should be the same proxy to assure that we ran initialization on this proxy", taxonProxy, taxon);
1083     }
1084
1085     /**
1086      * {@inheritDoc}
1087      */
1088     @Override
1089 //    @Test
1090     public void createTestDataSet() throws FileNotFoundException {
1091 //        Classification classification  = Classification.NewInstance("Test");
1092 //        BotanicalName taxonNameBase = null;
1093 //        Reference sec = null;
1094 //        Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);
1095 //        classification.addChildTaxon(taxon, sec, null);
1096 //
1097 //        classificationDao.save(classification);
1098 //        this.commitAndStartNewTransaction(null);
1099 //
1100 //        writeDbUnitDataSetFile(new String[] {
1101 //                "CLASSIFICATION", "TAXONNAMEBASE",
1102 //                "REFERENCE","TAXONNODE",
1103 //                "TAXONBASE","LANGUAGESTRING",
1104 //                "HIBERNATE_SEQUENCES" // IMPORTANT!!!
1105 //                },
1106 //                "testPropertyPath" );
1107     }
1108
1109 }