cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurenceServiceTest.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.api.service;
  11
  12 import static org.junit.Assert.assertEquals;
  13 import static org.junit.Assert.assertTrue;
  14
  15 import org.apache.log4j.Logger;
  16 import org.junit.Test;
  17 import org.unitils.spring.annotation.SpringBeanByType;
  18
  19 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  20 import eu.etaxonomy.cdm.model.agent.Institution;
  21 import eu.etaxonomy.cdm.model.agent.Person;
  22 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  23 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  24 import eu.etaxonomy.cdm.model.common.Language;
  25 import eu.etaxonomy.cdm.model.common.TimePeriod;
  26 import eu.etaxonomy.cdm.model.location.Country;
  27 import eu.etaxonomy.cdm.model.location.NamedArea;
  28 import eu.etaxonomy.cdm.model.location.Point;
  29 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  30 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  31 import eu.etaxonomy.cdm.model.molecular.Sequence;
  32 import eu.etaxonomy.cdm.model.name.BotanicalName;
  33 import eu.etaxonomy.cdm.model.name.Rank;
  34 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  35 import eu.etaxonomy.cdm.model.occurrence.Collection;
  36 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  37 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  38 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  39 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  40 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  41 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  42 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  43 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  44 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  48 import eu.etaxonomy.cdm.model.taxon.Taxon;
  49 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  50
  51 /**
  52  * @author pplitzner
  53  * @date 31.03.2014
  54  *
  55  */
  56 public class OccurenceServiceTest extends CdmTransactionalIntegrationTest {
  57     private static final Logger logger = Logger.getLogger(OccurenceServiceTest.class);
  58
  59     @SpringBeanByType
  60     private IOccurrenceService occurrenceService;
  61
  62     @SpringBeanByType
  63     private ISequenceService sequenceService;
  64
  65     @Test
  66     public void testGetNonCascadedAssociatedElements(){
  67         //Collection
  68         Collection collection = Collection.NewInstance();
  69         Collection subCollection = Collection.NewInstance();
  70         subCollection.setSuperCollection(collection);
  71
  72         Institution institution = Institution.NewInstance();
  73         institution.addType(DefinedTerm.NewInstitutionTypeInstance("Research and teaching", "botanical garden", "BGBM"));
  74         collection.setInstitute(institution);
  75
  76         //Source
  77         Reference<?> article = ReferenceFactory.newArticle(getReference(), Person.NewInstance(), "title", "pages", "series", "volume", TimePeriod.NewInstance(2014));
  78         IdentifiableSource source = IdentifiableSource.NewPrimarySourceInstance(article, "microCitation");
  79
  80         //FieldUnit
  81         FieldUnit fieldUnit = FieldUnit.NewInstance();
  82         Person primaryCollector = Person.NewInstance();
  83         primaryCollector.setLifespan(TimePeriod.NewInstance(2014));
  84         fieldUnit.setPrimaryCollector(primaryCollector);
  85         fieldUnit.addSource(source);
  86
  87         //GatheringEvent
  88         GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
  89         fieldUnit.setGatheringEvent(gatheringEvent);
  90         gatheringEvent.putLocality(Language.ENGLISH(), "locality");
  91         gatheringEvent.setExactLocation(Point.NewInstance(22.4, -34.2,
  92                 ReferenceSystem.NewInstance("MyReferenceSystem", "label", "labelAbbrev"), 33));
  93         gatheringEvent.setCountry(Country.GERMANY());
  94         gatheringEvent.addCollectingArea(NamedArea.EUROPE());
  95
  96         //Derived Unit
  97         MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
  98         mediaSpecimen.setCollection(collection);
  99         BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
 100         mediaSpecimen.setStoredUnder(storedUnder);
 101         PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
 102         preservation.setMedium(DefinedTerm.NewDnaMarkerInstance("medium", "medium", "medium"));//dummy defined term
 103         mediaSpecimen.setPreservation(preservation);
 104
 105         //DerivationEvent
 106         DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
 107         event.addOriginal(fieldUnit);
 108         event.addDerivative(mediaSpecimen);
 109
 110         //SpecOrObservationBase
 111         fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
 112         fieldUnit.setLifeStage(DefinedTerm.NewStageInstance("Live stage", "stage", null));
 113         fieldUnit.setKindOfUnit(DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null));
 114         fieldUnit.putDefinition(Language.ENGLISH(), "definition");
 115
 116         //Determination
 117         DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
 118         determinationEvent.setModifier(DefinedTerm.NewModifierInstance("modifierDescription", "modifierLabel", "mofifierLabelAbbrev"));
 119         determinationEvent.setPreferredFlag(true);
 120         Reference<?> reference = getReference();
 121         determinationEvent.addReference(reference);
 122
 123         /*NonCascaded
 124          * SOOB
 125          *  - sex (FEMALE)
 126          *  - stage (Live stage)
 127          *  - kindOfUnit (Kind of unit)
 128          * GatheringEvent
 129          *  - country (GERMANY)
 130          *  - collectingArea (EUROPE)
 131          *  DerivedUnit
 132          *  - storedUnder (botanical name)
 133          *  DerivedUnit-> Collection -> institiute
 134          *  - type (botanical garden)
 135          *
 136          * */
 137
 138         assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(fieldUnit).size());
 139         assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(mediaSpecimen).size());
 140
 141     }
 142     private Reference<?> getReference() {
 143         Reference<?> result = ReferenceFactory.newGeneric();
 144         result.setTitle("some generic reference");
 145         return result;
 146    }
 147    private Taxon getTaxon() {
 148        Reference<?> sec = getReference();
 149        TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 150        Taxon taxon = Taxon.NewInstance(name, sec);
 151        return taxon;
 152
 153    }
 154
 155     @Test
 156     public void testMoveDerivate(){
 157         DerivedUnit specimenA = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 158         DerivedUnit specimenB = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 159         DerivedUnit dnaSample = DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
 160
 161         occurrenceService.saveOrUpdate(specimenA);
 162         occurrenceService.saveOrUpdate(specimenB);
 163         occurrenceService.saveOrUpdate(dnaSample);
 164
 165         DerivationEvent.NewSimpleInstance(specimenA, dnaSample, DerivationEventType.DNA_EXTRACTION());
 166
 167         occurrenceService.moveDerivate(specimenA, specimenB, dnaSample);
 168         assertTrue("DerivationEvent not removed from source!", specimenA.getDerivationEvents().isEmpty());
 169         assertEquals("DerivationEvent not moved to source!", 1, specimenB.getDerivationEvents().size());
 170         DerivationEvent derivationEvent = specimenB.getDerivationEvents().iterator().next();
 171         assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(), derivationEvent.getType());
 172         assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());
 173         SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();
 174         assertEquals("Origin of moved object not correct", specimenB, newOriginal);
 175         assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());
 176         DerivedUnit derivedUnit = derivationEvent.getDerivatives().iterator().next();
 177         assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample, derivedUnit.getRecordBasis());
 178
 179     }
 180
 181     @Test
 182     public void testMoveSequence(){
 183         DnaSample dnaSampleA = DnaSample.NewInstance();
 184         DnaSample dnaSampleB = DnaSample.NewInstance();
 185         String consensusSequence = "ATTCG";
 186         Sequence sequence = Sequence.NewInstance(consensusSequence);
 187
 188         occurrenceService.saveOrUpdate(dnaSampleA);
 189         occurrenceService.saveOrUpdate(dnaSampleB);
 190         sequenceService.saveOrUpdate(sequence);
 191
 192         dnaSampleA.addSequence(sequence);
 193
 194         occurrenceService.moveSequence(dnaSampleA, dnaSampleB, sequence);
 195         assertEquals("Number of sequences is wrong", 0, dnaSampleA.getSequences().size());
 196         assertEquals("Number of sequences is wrong", 1, dnaSampleB.getSequences().size());
 197         Sequence next = dnaSampleB.getSequences().iterator().next();
 198         assertEquals("Sequences are not equals", sequence, next);
 199         assertEquals("Sequences are not equals", consensusSequence, next.getSequenceString());
 200     }
 201 }