cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/occurrence/SpecimenTest.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.occurrence;
  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.assertNotSame;
  16 import static org.junit.Assert.assertNull;
  17 import static org.junit.Assert.assertSame;
  18 import static org.junit.Assert.assertTrue;
  19
  20 import java.util.Calendar;
  21 import java.util.UUID;
  22
  23 import org.apache.log4j.Logger;
  24 import org.joda.time.DateTime;
  25 import org.junit.Assert;
  26 import org.junit.Before;
  27 import org.junit.Test;
  28
  29 import com.ibm.lsid.MalformedLSIDException;
  30
  31 import eu.etaxonomy.cdm.model.agent.Person;
  32 import eu.etaxonomy.cdm.model.common.Annotation;
  33 import eu.etaxonomy.cdm.model.common.Extension;
  34 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  35 import eu.etaxonomy.cdm.model.common.LSID;
  36 import eu.etaxonomy.cdm.model.common.Language;
  37 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  38 import eu.etaxonomy.cdm.model.common.Marker;
  39 import eu.etaxonomy.cdm.model.common.MarkerType;
  40 import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
  41 import eu.etaxonomy.cdm.model.description.Sex;
  42 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  43 import eu.etaxonomy.cdm.model.description.Stage;
  44 import eu.etaxonomy.cdm.model.media.Media;
  45 import eu.etaxonomy.cdm.model.media.Rights;
  46 import eu.etaxonomy.cdm.model.name.BotanicalName;
  47 import eu.etaxonomy.cdm.model.name.Rank;
  48 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  49 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  50
  51 /**
  52  * @author a.mueller
  53  * @created 28.10.2008
  54  * @version 1.0
  55  */
  56 public class SpecimenTest {
  57         private static final Logger logger = Logger.getLogger(SpecimenTest.class);
  58
  59         private Specimen specimen;
  60
  61         @Before
  62         public void setUp() throws Exception {
  63                 specimen = Specimen.NewInstance();
  64         }
  65
  66         /**
  67          * Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#NewInstance()}.
  68          */
  69         @Test
  70         public void testNewInstance() {
  71                 Specimen specimen = Specimen.NewInstance();
  72                 assertNotNull(specimen);
  73                 assertTrue(specimen instanceof Specimen);
  74         }
  75
  76         /**
  77          * Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#Specimen()}.
  78          */
  79         @Test
  80         public void testSpecimen() {
  81                 Specimen specimen = new Specimen();
  82                 assertNotNull(specimen);
  83         }
  84
  85         /**
  86          * Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#getPreservation()} and
  87          * {@link eu.etaxonomy.cdm.model.occurrence.Specimen#setPreservation(eu.etaxonomy.cdm.model.occurrence.PreservationMethod)}.
  88          */
  89         @Test
  90         public void testGetSetPreservation() {
  91                 PreservationMethod preservation = PreservationMethod.NewInstance();
  92                 specimen.setPreservation(preservation);
  93                 assertSame(preservation, specimen.getPreservation());
  94                 specimen.setPreservation(null);
  95         }
  96
  97         @Test
  98         public void testBidirectionalTypeDesignation(){
  99                 SpecimenTypeDesignation desig1 = SpecimenTypeDesignation.NewInstance();
 100                 SpecimenTypeDesignation desig2 = SpecimenTypeDesignation.NewInstance();
 101                 Specimen specimen2 = Specimen.NewInstance();
 102
 103                 specimen.addSpecimenTypeDesignation(desig1);
 104                 Assert.assertEquals("Specimen1 should be the designations specimen", specimen, desig1.getTypeSpecimen());
 105                 Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
 106                 Assert.assertEquals("specimen1's designation should be desig1", desig1, specimen.getSpecimenTypeDesignations().iterator().next());
 107
 108                 specimen.addSpecimenTypeDesignation(desig2);
 109                 Assert.assertEquals("Specimen1 should be the desig2's specimen", specimen, desig2.getTypeSpecimen());
 110                 Assert.assertEquals("specimen1 should have exactly 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
 111
 112                 specimen2.addSpecimenTypeDesignation(desig2);
 113                 Assert.assertEquals("Specimen2 should have replaced specimen1 as desig2's specimen", specimen2, desig2.getTypeSpecimen());
 114                 Assert.assertEquals("Specimen2 should have exactly 1 designation", 1, specimen2.getSpecimenTypeDesignations().size());
 115                 Assert.assertEquals("Specimen1's designation should be desig2", desig2, specimen2.getSpecimenTypeDesignations().iterator().next());
 116                 Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
 117
 118                 specimen2.removeSpecimenTypeDesignation(desig2);
 119                 Assert.assertEquals("Desig2 should not have a specimen anymore", null, desig2.getTypeSpecimen());
 120                 Assert.assertEquals("Specimen2 should have no designation", 0, specimen2.getSpecimenTypeDesignations().size());
 121                 Assert.assertEquals("specimen1 should have exactly 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
 122
 123                 specimen.addSpecimenTypeDesignation(desig2);
 124                 Assert.assertEquals("Specimen1 should be the desig2's specimen", specimen, desig2.getTypeSpecimen());
 125                 Assert.assertEquals("specimen1 should have exactly 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
 126
 127                 desig1.setTypeSpecimen(null);
 128                 Assert.assertEquals("Desig1 should not have a specimen anymore", null, desig1.getTypeSpecimen());
 129                 Assert.assertEquals("Specimen1 should have 1 designation", 1, specimen.getSpecimenTypeDesignations().size());
 130                 Assert.assertEquals("Specimen1's designation should be desig2", desig2, specimen.getSpecimenTypeDesignations().iterator().next());
 131
 132                 desig1.setTypeSpecimen(specimen);
 133                 Assert.assertEquals("Desig1 should have specimen1 as specimen again", specimen, desig1.getTypeSpecimen());
 134                 Assert.assertEquals("Specimen1 should have 2 designation", 2, specimen.getSpecimenTypeDesignations().size());
 135
 136         }
 137
 138
 139         /**
 140          * Test method for {@link eu.etaxonomy.cdm.model.occurrence.Specimen#clone()}.
 141          */
 142         @Test
 143         public void testClone() {
 144                 logger.debug("Start testClone");
 145
 146                 //Null test is not full implemented, but an error is thrown if null throws
 147                 //null pointer exception somewhere
 148                 Specimen specimenNullClone = (Specimen)specimen.clone();
 149
 150                 String accessionNumber = "accNumber";
 151                 String catalogNumber = "catNumber";
 152                 Collection collection = Collection.NewInstance();
 153                 collection.setCode("code");
 154                 DateTime created = new DateTime();
 155                 Person createdBy = Person.NewTitledInstance("creator");
 156                 DerivationEvent derivedFrom = DerivationEvent.NewInstance(null);
 157                 int id = 22;
 158                 int individualCount = 25;
 159                 Stage lifeStage = Stage.NewInstance();
 160                 LSID lsid = null;
 161                 try {
 162                         lsid = new LSID("urn:lsid:example.com:foo:1");
 163                 } catch (MalformedLSIDException e) {
 164                         // TODO Auto-generated catch block
 165                         e.printStackTrace();
 166                 }
 167                 Specimen nextVersion = Specimen.NewInstance();
 168                 Specimen previousVersion = Specimen.NewInstance();
 169                 PreservationMethod preservation = PreservationMethod.NewInstance();
 170                 boolean protectedTitleCache = true;
 171                 Sex sex = Sex.FEMALE();
 172                 TaxonNameBase<?, ?> storedUnder = BotanicalName.NewInstance(Rank.GENUS());
 173                 String titleCache = "title";
 174                 Calendar updated = Calendar.getInstance();
 175                 Person updatedBy = Person.NewTitledInstance("updatedPerson");
 176                 UUID uuid = UUID.randomUUID();
 177
 178                 Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
 179                 String definition = "definition";
 180                 //TODO
 181                 DerivationEvent derivationEvent = DerivationEvent.NewInstance(null);
 182                 SpecimenDescription description = SpecimenDescription.NewInstance();
 183                 DeterminationEvent determination = DeterminationEvent.NewInstance();
 184                 Extension extension = Extension.NewInstance();
 185                 extension.setValue("extension");
 186                 Marker marker = Marker.NewInstance(MarkerType.COMPLETE(), false);
 187                 Rights right = Rights.NewInstance("right", Language.DEFAULT());
 188                 Media media = Media.NewInstance();
 189                 IdentifiableSource source = IdentifiableSource.NewDataImportInstance("12", "idNamespace");
 190
 191                 specimen.setAccessionNumber(accessionNumber);
 192                 specimen.setCatalogNumber(catalogNumber);
 193                 specimen.setCollection(collection);
 194                 specimen.setCreated(created);
 195 //              specimen.setCreatedBy(createdBy);
 196                 specimen.setDerivedFrom(derivedFrom);
 197                 specimen.setId(id);
 198                 specimen.setIndividualCount(individualCount);
 199                 specimen.setLifeStage(lifeStage);
 200                 specimen.setLsid(lsid);
 201                 specimen.setPreservation(preservation);
 202                 specimen.setProtectedTitleCache(protectedTitleCache);
 203                 specimen.setSex(sex);
 204                 specimen.setStoredUnder(storedUnder);
 205                 specimen.setTitleCache(titleCache, protectedTitleCache);
 206 //              specimen.setUpdated(updated);
 207 //              specimen.setUpdatedBy(updatedBy);
 208                 specimen.setUuid(uuid);
 209
 210                 specimen.addAnnotation(annotation);
 211                 specimen.putDefinition(Language.DEFAULT(), definition);
 212                 specimen.addDerivationEvent(derivationEvent);
 213                 specimen.addDescription(description);
 214                 specimen.addDetermination(determination);
 215                 specimen.addExtension(extension);
 216                 specimen.addMarker(marker);
 217                 specimen.addMedia(media);
 218                 specimen.addRights(right);
 219                 specimen.addSource(source);
 220
 221                 try {
 222                         Thread.sleep(200);
 223                 } catch (InterruptedException e) {
 224                         //ignore
 225                 }
 226                 Specimen specimenClone = (Specimen)specimen.clone();
 227
 228                 assertFalse(id == specimenClone.getId());
 229                 assertFalse(created.equals(specimenClone.getCreated()));
 230                 assertFalse(createdBy.equals(specimenClone.getCreatedBy()));
 231                 assertFalse(updated.equals(specimenClone.getUpdated()));
 232                 assertFalse(updatedBy.equals(specimenClone.getUpdatedBy()));
 233                 assertNull(specimenClone.getUpdatedBy());
 234                 assertNull(specimenClone.getCreatedBy());
 235                 assertFalse(uuid.equals(specimenClone.getUuid()));
 236
 237
 238                 assertEquals(accessionNumber, specimenClone.getAccessionNumber());
 239                 assertEquals(catalogNumber, specimenClone.getCatalogNumber());
 240                 assertEquals(collection, specimenClone.getCollection());
 241                 assertEquals(derivedFrom, specimenClone.getDerivedFrom());
 242                 assertEquals(lifeStage, specimenClone.getLifeStage());
 243                 assertEquals(lsid, specimenClone.getLsid());
 244                 assertEquals(preservation, specimenClone.getPreservation());
 245                 assertEquals(protectedTitleCache, specimenClone.isProtectedTitleCache());
 246                 assertEquals(storedUnder, specimenClone.getStoredUnder());
 247                 assertEquals(sex, specimenClone.getSex());
 248                 assertEquals(titleCache, specimenClone.getTitleCache());
 249
 250                 Annotation clonedAnnotation = specimenClone.getAnnotations().iterator().next();
 251                 assertFalse(annotation.equals(clonedAnnotation));
 252                 assertEquals(annotation.getText(), ((LanguageStringBase)specimenClone.getAnnotations().iterator().next()).getText() );
 253                 assertNotSame(annotation, specimenClone.getAnnotations().iterator().next() );
 254
 255                 assertEquals(definition, specimenClone.getDefinition().get(Language.DEFAULT()).getText());
 256 //TODO
 257 //              assertNotSame(definition, specimenClone.getDefinition().getText(Language.DEFAULT()));
 258
 259                 assertEquals(derivationEvent, specimenClone.getDerivationEvents().iterator().next());
 260                 assertSame(derivationEvent, specimenClone.getDerivationEvents().iterator().next());
 261
 262                 assertEquals(description, specimenClone.getDescriptions().iterator().next());
 263                 // TODO ?
 264                 assertSame(description, specimenClone.getDescriptions().iterator().next());
 265
 266                 assertEquals(determination, specimenClone.getDeterminations().iterator().next());
 267                 // TODO ?
 268                 assertSame(determination, specimenClone.getDeterminations().iterator().next());
 269
 270                 assertFalse(extension.equals(specimenClone.getExtensions().iterator().next()));
 271                 assertEquals(extension.getValue(), ((Extension)specimenClone.getExtensions().iterator().next()).getValue());
 272                 assertNotSame(extension, specimenClone.getExtensions().iterator().next());
 273                 assertEquals(1, specimen.getExtensions().size());
 274
 275                 assertFalse(marker.equals(specimenClone.getMarkers().iterator().next()));
 276                 assertEquals(marker.getFlag(), ((Marker)specimenClone.getMarkers().iterator().next()).getFlag());
 277                 assertNotSame(marker, specimenClone.getMarkers().iterator().next());
 278                 assertEquals(1, specimenClone.getMarkers().size());
 279
 280                 assertEquals(media, specimenClone.getMedia().iterator().next());
 281                 assertEquals(right, specimenClone.getRights().iterator().next());
 282
 283                 assertFalse(source.equals(specimenClone.getSources().iterator().next()));
 284                 assertEquals(source.getId(), ((OriginalSourceBase)specimenClone.getSources().iterator().next()).getId());
 285                 assertNotSame(source, specimenClone.getSources().iterator().next());
 286                 assertEquals(1, specimenClone.getSources().size());
 287         }
 288 }