EDIT

/**

 * Copyright (C) 2014 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See LICENSE.TXT at the top of this package for the full license terms.

 */

package eu.etaxonomy.cdm.api.service;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertNotEquals;

import static org.junit.Assert.assertNotNull;

import static org.junit.Assert.assertNull;

import static org.junit.Assert.assertTrue;

import java.io.FileNotFoundException;

import java.util.Collection;

import java.util.Collections;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import java.util.stream.Collectors;

import org.apache.log4j.Logger;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;

import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;

import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.model.agent.Institution;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.DefinedTerm;

import eu.etaxonomy.cdm.model.common.Identifier;

import eu.etaxonomy.cdm.model.common.TimePeriod;

import eu.etaxonomy.cdm.model.description.DescriptionElementBase;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.IndividualsAssociation;

import eu.etaxonomy.cdm.model.description.SpecimenDescription;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.molecular.Sequence;

import eu.etaxonomy.cdm.model.name.IBotanicalName;

import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.name.TaxonNameFactory;

import eu.etaxonomy.cdm.model.name.TypeDesignationBase;

import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;

import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;

import eu.etaxonomy.cdm.model.occurrence.FieldUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.SynonymType;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;

import eu.etaxonomy.cdm.persistence.query.AssignmentStatus;

import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;

import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;

/**

 * @author pplitzner

 * @since 31.03.2014

 *

 */

public class OccurrenceServiceTest extends CdmTransactionalIntegrationTest {

    @SuppressWarnings("unused")

    private static final Logger logger = Logger.getLogger(OccurrenceServiceTest.class);

    @SpringBeanByType

    private IOccurrenceService occurrenceService;

    @SpringBeanByType

    private ISequenceService sequenceService;

    @SpringBeanByType

    private ITaxonService taxonService;

    @SpringBeanByType

    private ITaxonNodeService taxonNodeService;

    @SpringBeanByType

    private IClassificationService classificationService;

    @SpringBeanByType

    private INameService nameService;

    @SpringBeanByType

    private ITermService termService;

    @SpringBeanByType

    private IDescriptionService descriptionService;

    private Reference getReference() {

        Reference result = ReferenceFactory.newGeneric();

        result.setTitle("some generic reference");

        return result;

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")

    public void testMoveDerivate() {

        DerivedUnit specimenA = (DerivedUnit) occurrenceService.load(UUID

                .fromString("35cfb0b3-588d-4eee-9db6-ac9caa44e39a"));

        DerivedUnit specimenB = (DerivedUnit) occurrenceService.load(UUID

                .fromString("09496534-efd0-44c8-b1ce-01a34a8a0229"));

        DerivedUnit dnaSample = (DnaSample) occurrenceService.load(UUID

                .fromString("5995f852-0e78-405c-b849-d923bd6781d9"));

        occurrenceService.saveOrUpdate(specimenA);

        occurrenceService.saveOrUpdate(specimenB);

        occurrenceService.saveOrUpdate(dnaSample);

        Person derivationActor = Person.NewTitledInstance("Derivation Actor");

        String derivationDescription = "Derivation Description";

        Institution derivationInstitution = Institution.NewInstance();

        TimePeriod derivationTimePeriod = TimePeriod.NewInstance(2015);

        DerivationEvent originalDerivedFromEvent = DerivationEvent.NewSimpleInstance(specimenA, dnaSample,

                DerivationEventType.DNA_EXTRACTION());

        originalDerivedFromEvent.setActor(derivationActor);

        originalDerivedFromEvent.setDescription(derivationDescription);

        originalDerivedFromEvent.setInstitution(derivationInstitution);

        originalDerivedFromEvent.setTimeperiod(derivationTimePeriod);

        occurrenceService.moveDerivate(specimenA, specimenB, dnaSample);

        assertTrue("DerivationEvent not removed from source!", specimenA.getDerivationEvents().isEmpty());

        assertEquals("DerivationEvent not moved to source!", 1, specimenB.getDerivationEvents().size());

        DerivationEvent derivationEvent = specimenB.getDerivationEvents().iterator().next();

        assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(),

                derivationEvent.getType());

        assertEquals(derivationActor, derivationEvent.getActor());

        assertEquals(derivationDescription, derivationEvent.getDescription());

        assertEquals(derivationInstitution, derivationEvent.getInstitution());

        assertEquals(derivationTimePeriod, derivationEvent.getTimeperiod());

        assertEquals(DerivationEventType.DNA_EXTRACTION(), derivationEvent.getType());

        assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());

        SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();

        assertEquals("Target of moved object not correct", specimenB, newOriginal);

        assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());

        DerivedUnit movedDerivate = derivationEvent.getDerivatives().iterator().next();

        assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample,

                movedDerivate.getRecordBasis());

        assertNotEquals("DerivationEvent 'derivedFrom' has not been changed after moving", originalDerivedFromEvent,

                movedDerivate.getDerivedFrom());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "../../database/BlankDataSet.xml")

    public void testMoveDerivateNoParent() {

        DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);

        FieldUnit fieldUnit = FieldUnit.NewInstance();

        occurrenceService.saveOrUpdate(fieldUnit);

        occurrenceService.saveOrUpdate(derivedUnit);

        assertEquals("DerivationEvent not moved to source!", 0, fieldUnit.getDerivationEvents().size());

        occurrenceService.moveDerivate(null, fieldUnit, derivedUnit);

        assertEquals("DerivationEvent not moved to source!", 1, fieldUnit.getDerivationEvents().size());

        DerivationEvent derivationEvent = fieldUnit.getDerivationEvents().iterator().next();

        assertNull(derivationEvent.getType());

        assertEquals("Wrong number of derivation originals!", 1, derivationEvent.getOriginals().size());

        SpecimenOrObservationBase<?> newOriginal = derivationEvent.getOriginals().iterator().next();

        assertEquals("Target of moved object not correct", fieldUnit, newOriginal);

        assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")

    public void testMoveSequence() {

        DnaSample dnaSampleA = (DnaSample) occurrenceService.load(UUID

                .fromString("5995f852-0e78-405c-b849-d923bd6781d9"));

        DnaSample dnaSampleB = (DnaSample) occurrenceService.load(UUID

                .fromString("85fccc2f-c796-46b3-b2fc-6c9a4d68cfda"));

        String consensusSequence = "ATTCG";

        Sequence sequence = sequenceService.load(UUID.fromString("6da4f378-9861-4338-861b-7b8073763e7a"));

        occurrenceService.saveOrUpdate(dnaSampleA);

        occurrenceService.saveOrUpdate(dnaSampleB);

        sequenceService.saveOrUpdate(sequence);

        dnaSampleA.addSequence(sequence);

        occurrenceService.moveSequence(dnaSampleA, dnaSampleB, sequence);

        assertEquals("Number of sequences is wrong", 0, dnaSampleA.getSequences().size());

        assertEquals("Number of sequences is wrong", 1, dnaSampleB.getSequences().size());

        Sequence next = dnaSampleB.getSequences().iterator().next();

        assertEquals("Sequences are not equals", sequence, next);

        assertEquals("Sequences are not equals", consensusSequence, next.getSequenceString());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testDeleteIndividualAssociatedAndTypeSpecimen.xml")

    public void testDeleteIndividualAssociatedAndTypeSpecimen() {

        final UUID taxonDEscriptionUuid = UUID.fromString("a87a893e-2ea8-427d-a26b-dbd2515d6b8a");

        final UUID botanicalNameUuid = UUID.fromString("a604774e-d66a-4d47-b9d1-d0e38a8c787a");

        final UUID fieldUnitUuid = UUID.fromString("67e81ca8-ff91-4df6-bf48-e4600c7f15a2");

        final UUID derivedUnitUuid = UUID.fromString("d229713b-0123-4f15-bffc-76ae45c37564");

        // //how the XML was generated

        // FieldUnit fieldUnit = FieldUnit.NewInstance();

        // fieldUnit.setUuid(fieldUnitUuid);

        // //sub derivates (DerivedUnit, DnaSample)

        // DerivedUnit derivedUnit =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        // derivedUnit.setUuid(derivedUnitUuid);

        //

        // //derivation events

        // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,

        // DerivationEventType.ACCESSIONING());

        //

        // occurrenceService.save(fieldUnit);

        // occurrenceService.save(derivedUnit);

        //

        // //create name with type specimen

        // BotanicalName name =

        // BotanicalName.PARSED_NAME("Campanula patual sec L.");

        // name.setUuid(BOTANICAL_NAME_UUID);

        // SpecimenTypeDesignation typeDesignation =

        // SpecimenTypeDesignation.NewInstance();

        // typeDesignation.setTypeSpecimen(derivedUnit);

        // //add type designation to name

        // name.addTypeDesignation(typeDesignation, false);

        //

        // // create taxon with name and two taxon descriptions (one with

        // // IndividualsAssociations and a "described" voucher specimen, and an

        // // empty one)

        // Taxon taxon = Taxon.NewInstance(name, null);

        // taxon.setUuid(taxonUuid);

        // TaxonDescription taxonDescription = TaxonDescription.NewInstance();

        // taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);

        // //add voucher

        // taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));

        // taxon.addDescription(taxonDescription);

        // //add another taxon description to taxon which is not associated with

        // a specimen thus should not be taken into account

        // taxon.addDescription(TaxonDescription.NewInstance());

        // taxonService.saveOrUpdate(taxon);

        //

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testDeleteIndividualAssociatedAndTypeSpecimen");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);

        DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);

        IBotanicalName name = nameService.load(botanicalNameUuid);

        TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDEscriptionUuid);

        // check initial state (IndividualsAssociation)

        DescriptionElementBase descriptionElement = taxonDescription.getElements().iterator().next();

        assertTrue("wrong type of description element", descriptionElement.isInstanceOf(IndividualsAssociation.class));

        assertEquals("associated specimen is incorrect", associatedFieldUnit,

                ((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation());

        // check initial state (Type Designation)

        Set<TypeDesignationBase> typeDesignations = name.getTypeDesignations();

        TypeDesignationBase<?> typeDesignation = typeDesignations.iterator().next();

        assertTrue("wrong type of type designation", typeDesignation.isInstanceOf(SpecimenTypeDesignation.class));

        assertEquals("type specimen is incorrect", typeSpecimen,

                ((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen());

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        // delete type specimen from type designation

        config.setDeleteFromTypeDesignation(true);

        occurrenceService.delete(typeSpecimen, config);

        assertTrue(((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen() == null);

        // delete associated field unit from IndividualsAssociation

        config.setDeleteFromIndividualsAssociation(true);

        occurrenceService.delete(associatedFieldUnit, config);

        assertTrue(((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation() == null);

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceService.loadData.xml")

    public void testLoadData() {

        String fieldUnitUuid = "5a31df5a-2e4d-40b1-8d4e-5754736ae7ef";

        String derivedUnitUuid = "18f70977-5d9c-400a-96c4-0cb7a2cd287e";

        FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(UUID.fromString(fieldUnitUuid));

        DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(UUID.fromString(derivedUnitUuid));

        assertFalse(fieldUnit.getDerivationEvents().iterator().next().getDerivatives().isEmpty());

        assertTrue(derivedUnit.getDerivedFrom() != null);

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testListAssociatedAndTypedTaxa.xml")

    public void testListIndividualsAssociatensAndSpecimenTypeDesignations(){

        UUID fieldUnitUuid = UUID.fromString("b359ff20-98de-46bf-aa43-3e10bb072cd4");

        UUID typeSpecimenUuid = UUID.fromString("0f8608c7-ffe7-40e6-828c-cb3382580878");

        UUID taxonDescriptionUuid = UUID.fromString("d77db2d4-45a1-4aa1-ab34-f33395f54965");

        UUID taxonUuid = UUID.fromString("b0de794c-8cb7-4369-8f83-870ca37abbe0");

        // //how the XML was generated

        // FieldUnit associatedFieldUnit = FieldUnit.NewInstance();

        // associatedFieldUnit.setUuid(fieldUnitUuid);

        // //sub derivates (DerivedUnit, DnaSample)

        // DerivedUnit typeSpecimen =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        // typeSpecimen.setUuid(typeSpecimenUuid);

        //

        // //derivation events

        // DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen,

        // DerivationEventType.ACCESSIONING());

        //

        // occurrenceService.save(associatedFieldUnit);

        // occurrenceService.save(typeSpecimen);

        //

        // //create name with type specimen

        // BotanicalName name =

        // BotanicalName.PARSED_NAME("Campanula patual sec L.");

        // SpecimenTypeDesignation typeDesignation =

        // SpecimenTypeDesignation.NewInstance();

        // typeDesignation.setTypeSpecimen(typeSpecimen);

        //

        // // create taxon with name and two taxon descriptions (one with

        // // IndividualsAssociations and a "described" voucher specimen, and an

        // // empty one)

        // Taxon taxon = Taxon.NewInstance(name, null);

        // taxon.setUuid(taxonUuid);

        // TaxonDescription taxonDescription = TaxonDescription.NewInstance();

        // taxonDescription.setUuid(taxonDescriptionUuid);

        // //add voucher

        // taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit));

        // taxon.addDescription(taxonDescription);

        // //add type designation to name

        // name.addTypeDesignation(typeDesignation, false);

        // //add another taxon description to taxon which is not associated with

        // a specimen thus should not be taken into account

        // taxon.addDescription(TaxonDescription.NewInstance());

        // taxonService.saveOrUpdate(taxon);

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        // try {

        // writeDbUnitDataSetFile(new String[]{

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"}, "testListAssociatedAndTypedTaxa");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        //

        // System.out.println("associatedFieldUnit.getUuid() " +

        // associatedFieldUnit.getUuid());

        // System.out.println("typeSpecimen.getUuid() "+typeSpecimen.getUuid());

        // System.out.println("taxonDescription.getUuid() "+taxonDescription.getUuid());

        // System.out.println("taxon.getUuid() "+taxon.getUuid());

        FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);

        DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(typeSpecimenUuid);

        Taxon taxon = (Taxon) taxonService.load(taxonUuid);

        TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);

        // check for FieldUnit (IndividualsAssociation)

        java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService

                .listIndividualsAssociations(associatedFieldUnit, null, null, null, null);

        assertEquals("Number of individuals associations is incorrect", 1, individualsAssociations.size());

        IndividualsAssociation individualsAssociation = individualsAssociations.iterator().next();

        assertTrue("association has wrong type",

                individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class));

        TaxonDescription retrievedTaxonDescription = HibernateProxyHelper.deproxy(

                individualsAssociation.getInDescription(), TaxonDescription.class);

        assertEquals(taxonDescription, retrievedTaxonDescription);

        assertEquals("Associated taxon is incorrect", taxon, retrievedTaxonDescription.getTaxon());

        // check for DerivedUnit (Type Designation should exist)

        java.util.Collection<SpecimenTypeDesignation> typeDesignations = occurrenceService.listTypeDesignations(

                typeSpecimen, null, null, null, null);

        assertEquals("Number of type designations is incorrect", 1, typeDesignations.size());

        SpecimenTypeDesignation specimenTypeDesignation = typeDesignations.iterator().next();

        Set<TaxonName> typifiedNames = specimenTypeDesignation.getTypifiedNames();

        assertEquals("number of typified names is incorrect", 1, typifiedNames.size());

        Set<?> taxonBases = typifiedNames.iterator().next().getTaxonBases();

        assertEquals("number of taxa incorrect", 1, taxonBases.size());

        Object next = taxonBases.iterator().next();

        assertTrue(next instanceof CdmBase && ((CdmBase) next).isInstanceOf(Taxon.class));

        assertEquals("Typed taxon is incorrect", taxon, next);

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithSpecimenDescription.xml")

    public void testIsDeletableWithSpecimenDescription() {

        UUID derivedUnitUuid = UUID.fromString("68095c8e-025d-49f0-8bb2-ed36378b75c3");

        UUID specimenDescriptionUuid = UUID.fromString("4094f947-ce84-47b1-bad5-e57e33239d3c");

        // //how the XML was generated

        // DerivedUnit derivedUnit =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        // derivedUnit.setUuid(derivedUnitUuid);

        // SpecimenDescription specimenDescription =

        // SpecimenDescription.NewInstance();

        // specimenDescription.setUuid(specimenDescriptionUuid);

        // derivedUnit.addDescription(specimenDescription);

        // occurrenceService.save(derivedUnit);

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testIsDeletableWithSpecimenDescription");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);

        SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService

                .load(specimenDescriptionUuid);

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        DeleteResult deleteResult = null;

        // delete derivedUnit1

        deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);

        //deletion of specimen description should always work because there are no

        //specimen description without a specimen

        assertTrue(deleteResult.toString(), deleteResult.isOk());

        occurrenceService.delete(derivedUnit, config);

        specimenDescription = (SpecimenDescription) descriptionService.find(specimenDescriptionUuid);

        assertNull(specimenDescription);

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithDescribedSpecimenInTaxonDescription.xml")

    public void testIsDeletableWithDescribedSpecimenInTaxonDescription() {

        UUID fieldUnitUuid = UUID.fromString("d656a004-38ee-404c-810a-87ffb0ab16c2");

        // //how the XML was generated

        // FieldUnit fieldUnit = FieldUnit.NewInstance();

        // fieldUnit.setUuid(fieldUnitUuid);

        // DerivedUnit derivedUnit =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        //

        // //derivation events

        // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,

        // DerivationEventType.ACCESSIONING());

        //

        // occurrenceService.save(fieldUnit);

        // occurrenceService.save(derivedUnit);

        //

        // // create taxon with name and two taxon descriptions

        // //(one with a "described" voucher specimen, and an empty one)

        // Taxon taxon =

        // Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),

        // null);

        // taxonDescription.setUuid(taxonDescriptionUuid);

        // //add voucher

        // taxonDescription.setDescribedSpecimenOrObservation(derivedUnit);

        // taxon.addDescription(taxonDescription);

        // //add another taxon description to taxon which is not associated with

        // a specimen thus should not be taken into account

        // taxon.addDescription(TaxonDescription.NewInstance());

        // taxonService.saveOrUpdate(taxon);

        //

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testIsDeletableWithDescribedSpecimenInTaxonDescription");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        DeleteResult deleteResult = null;

        // check deletion of field unit -> should fail because of voucher

        // specimen (describedSpecimen) in TaxonDescription

        deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);

        assertFalse(deleteResult.toString(), deleteResult.isOk());

        // allow deletion from TaxonDescription and deletion of child derivates

        config.setDeleteFromDescription(true);

        config.setDeleteChildren(true);

        deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithIndividualsAssociationTaxonDescription.xml")

    public void testIsDeletableWithIndividualsAssociationTaxonDescription() {

        UUID fieldUnitUuid = UUID.fromString("7978b978-5100-4c7a-82ef-3a23e0f3c723");

        UUID taxonDescriptionUuid = UUID.fromString("d4b0d561-6e7e-4fd8-bf3c-925530f949eb");

        // //how the XML was generated

        // FieldUnit fieldUnit = FieldUnit.NewInstance();

        // fieldUnit.setUuid(fieldUnitUuid);

        //

        // occurrenceService.save(fieldUnit);

        //

        // // create taxon with name and two taxon descriptions (one with

        // // IndividualsAssociations and a "described" voucher specimen, and an

        // // empty one)

        // Taxon taxon =

        // Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),

        // null);

        // TaxonDescription taxonDescription = TaxonDescription.NewInstance();

        // taxonDescription.setUuid(taxonDescriptionUuid);

        // //add voucher

        // taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));

        // taxon.addDescription(taxonDescription);

        // //add another taxon description to taxon which is not associated with

        // a specimen thus should not be taken into account

        // taxon.addDescription(TaxonDescription.NewInstance());

        // taxonService.saveOrUpdate(taxon);

        //

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testIsDeletableWithIndividualsAssociationTaxonDescription");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);

        TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);

        IndividualsAssociation individualsAssociation = (IndividualsAssociation) taxonDescription.getElements()

                .iterator().next();

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        DeleteResult deleteResult = null;

        // check deletion of field unit -> should fail because of

        // IndividualAssociation

        deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);

        assertFalse(deleteResult.toString(), deleteResult.isOk());

        assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(individualsAssociation));

        // allow deletion of individuals association

        config.setDeleteFromIndividualsAssociation(true);

        deleteResult = occurrenceService.isDeletable(associatedFieldUnit.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithTypeDesignation.xml")

    public void testIsDeletableWithTypeDesignation() {

        UUID derivedUnitUuid = UUID.fromString("f7fd1dc1-3c93-42a7-8279-cde5bfe37ea0");

        UUID botanicalNameUuid = UUID.fromString("7396430c-c932-4dd3-a45a-40c2808b132e");

        // DerivedUnit derivedUnit =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        // derivedUnit.setUuid(derivedUnitUuid);

        //

        // occurrenceService.save(derivedUnit);

        //

        // //create name with type specimen

        // BotanicalName name =

        // BotanicalName.PARSED_NAME("Campanula patual sec L.");

        // name.setUuid(botanicalNameUuid);

        // SpecimenTypeDesignation typeDesignation =

        // SpecimenTypeDesignation.NewInstance();

        // typeDesignation.setTypeSpecimen(derivedUnit);

        // //add type designation to name

        // name.addTypeDesignation(typeDesignation, false);

        //

        // nameService.saveOrUpdate(name);

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "Sequence_SingleRead",

        // "SingleRead",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testIsDeletableWithTypeDesignation");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);

        // create name with type specimen

        IBotanicalName name = nameService.load(botanicalNameUuid);

        SpecimenTypeDesignation typeDesignation = (SpecimenTypeDesignation) name.getTypeDesignations().iterator()

                .next();

        // add type designation to name

        name.addTypeDesignation(typeDesignation, false);

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        DeleteResult deleteResult = null;

        // check deletion of specimen

        deleteResult = occurrenceService.isDeletable(typeSpecimen.getUuid(), config);

        assertFalse(deleteResult.toString(), deleteResult.isOk());

        assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(typeDesignation));

        // allow deletion of type designation

        config.setDeleteFromTypeDesignation(true);

        deleteResult = occurrenceService.isDeletable(typeSpecimen.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithChildren.xml")

    public void testIsDeletableWithChildren() {

        UUID fieldUnitUuid = UUID.fromString("92ada058-4c14-4131-8ecd-b82dc1dd2882");

        UUID derivedUnitUuid = UUID.fromString("896dffdc-6809-4914-8950-5501fee1c0fd");

        UUID dnaSampleUuid = UUID.fromString("7efd1d66-ac7f-4202-acdf-a72cbb9c3a21");

        // if this test fails be sure to check if there are left-over elements

        // in the DB

        // e.g. clear by adding "<AMPLIFICATIONRESULT/>" to the data set XML

        // //how the XML was generated

        // FieldUnit fieldUnit = FieldUnit.NewInstance();

        // fieldUnit.setUuid(fieldUnitUuid);

        // //sub derivates (DerivedUnit, DnaSample)

        // DerivedUnit derivedUnit =

        // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

        // derivedUnit.setUuid(derivedUnitUuid);

        // DnaSample dnaSample = DnaSample.NewInstance();

        // dnaSample.setUuid(dnaSampleUuid);

        //

        // //derivation events

        // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,

        // DerivationEventType.ACCESSIONING());

        // DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample,

        // DerivationEventType.DNA_EXTRACTION());

        //

        // occurrenceService.save(fieldUnit);

        // occurrenceService.save(derivedUnit);

        // occurrenceService.save(dnaSample);

        //

        // commitAndStartNewTransaction(null);

        //

        // setComplete();

        // endTransaction();

        //

        // try {

        // writeDbUnitDataSetFile(new String[] {

        // "SpecimenOrObservationBase",

        // "SpecimenOrObservationBase_DerivationEvent",

        // "DerivationEvent",

        // "Sequence",

        // "SingleRead",

        // "SingleReadAlignment",

        // "Amplification",

        // "AmplificationResult",

        // "DescriptionElementBase",

        // "DescriptionBase",

        // "TaxonBase",

        // "TypeDesignationBase",

        // "TaxonName",

        // "TaxonName_TypeDesignationBase",

        // "HomotypicalGroup"

        // }, "testIsDeletableWithChildren");

        // } catch (FileNotFoundException e) {

        // e.printStackTrace();

        // }

        FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);

        // sub derivates (DerivedUnit, DnaSample)

        DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);

        DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);

        // derivation events

        DerivationEvent fieldUnitToDerivedUnitEvent = fieldUnit.getDerivationEvents().iterator().next();

        DerivationEvent derivedUnitToDnaSampleEvent = derivedUnit.getDerivationEvents().iterator().next();

        SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();

        DeleteResult deleteResult = null;

        // check deletion of DnaSample

        deleteResult = occurrenceService.isDeletable(dnaSample.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

        // check deletion of Specimen

        deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);

        assertFalse(deleteResult.toString(), deleteResult.isOk());

        assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));

        // check deletion of fieldUnit

        deleteResult = occurrenceService.isDeletable(fieldUnit.getUuid(), config);

        assertFalse(deleteResult.toString(), deleteResult.isOk());

        assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(fieldUnitToDerivedUnitEvent));

        // check deletion of Specimen

        config.setDeleteChildren(true);

        deleteResult = occurrenceService.isDeletable(derivedUnit.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

        assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));

        // check deletion of fieldUnit

        config.setDeleteFromDescription(true);

        deleteResult = occurrenceService.isDeletable(fieldUnit.getUuid(), config);

        assertTrue(deleteResult.toString(), deleteResult.isOk());

    }

    @Test

    @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testListAssociatedTaxaAndListByAssociatedTaxon.xml")

    public void testListAssociatedTaxaAndListByAssociatedTaxon(){

        UUID associatedSpecimenUuid = UUID.fromString("6478a387-bc77-4f1b-bfab-671ad786a27e");

        UUID unassociatedSpecimenUuid = UUID.fromString("820e1af6-9bff-4244-97d3-81fd9a49c91c");

        UUID typeSpecimenUuid = UUID.fromString("b6f31b9f-f9e2-4bc7-883e-35bd6a9978b4");

        UUID taxonUuid = UUID.fromString("5613698d-840b-4034-b9b1-1302938e183b");

//      DerivedUnit typeSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);

//      DerivedUnit associatedSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);

//      DerivedUnit unassociatedSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);

//      typeSpecimen.setUuid(typeSpecimenUuid);

//      associatedSpecimen.setUuid(associatedSpecimenUuid);

//      unassociatedSpecimen.setUuid(unassociatedSpecimenUuid);

//

//      occurrenceService.save(typeSpecimen);

//      occurrenceService.save(associatedSpecimen);

//      occurrenceService.save(unassociatedSpecimen);

//

//      BotanicalName name = BotanicalName.PARSED_NAME("Campanula patula");

//      SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();

//      typeDesignation.setTypeSpecimen(typeSpecimen);

//      name.addTypeDesignation(typeDesignation, false);

//

//      Taxon taxon = Taxon.NewInstance(name, null);

//      taxon.setUuid(taxonUuid);

//      TaxonDescription taxonDescription = TaxonDescription.NewInstance();

////      taxonDescription.setUuid(taxonDescriptionUuid);

//

//      taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedSpecimen));

//      taxon.addDescription(taxonDescription);

//

//      taxonService.saveOrUpdate(taxon);

//

//      commitAndStartNewTransaction(null);

//

//      setComplete();

//      endTransaction();

//

//      try {

//          writeDbUnitDataSetFile(new String[]{

//                                 "SpecimenOrObservationBase",

//                  "SpecimenOrObservationBase_DerivationEvent",

//                  "DerivationEvent",

//                  "Sequence",

//                  "Sequence_SingleRead",

//                  "SingleRead",

//                  "AmplificationResult",

//                  "DescriptionElementBase",

//                  "DescriptionBase",

//                  "TaxonBase",

//                  "TypeDesignationBase",

//                  "TaxonName",

//                  "TaxonName_TypeDesignationBase",

//                  "TeamOrPersonBase",

//                  "HomotypicalGroup"}, "testListAssociatedTaxaAndListByAssociatedTaxon");

//      } catch (FileNotFoundException e) {

//          e.printStackTrace();

//      }

        //check initial state

        SpecimenOrObservationBase typeSpecimen = occurrenceService.load(typeSpecimenUuid);

        SpecimenOrObservationBase associatedSpecimen = occurrenceService.load(associatedSpecimenUuid);

        SpecimenOrObservationBase unassociatedSpecimen = occurrenceService.load(unassociatedSpecimenUuid);

        Taxon taxon = (Taxon) taxonService.load(taxonUuid);

        assertNotNull(typeSpecimen);

        assertNotNull(associatedSpecimen);

        assertNotNull(unassociatedSpecimen);

        assertNotNull(taxon);

        //check association (IndividualsAssociations + TypeDesignations) specimen -> taxon (name)

        //unassociated specimen

        java.util.Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(unassociatedSpecimen, null, null, null, null);

        assertNotNull(associatedTaxa);

        assertTrue(associatedTaxa.isEmpty());

        //type specimen

        associatedTaxa = occurrenceService.listAssociatedTaxa(typeSpecimen, null, null, null, null);

        assertNotNull(associatedTaxa);

        assertEquals(1, associatedTaxa.size());

        assertEquals(taxon, associatedTaxa.iterator().next());

        //associated specimen

        associatedTaxa = occurrenceService.listAssociatedTaxa(associatedSpecimen, null, null, null, null);

        assertNotNull(associatedTaxa);

        assertEquals(1, associatedTaxa.size());

        assertEquals(taxon, associatedTaxa.iterator().next());

        //check association (IndividualsAssociations + TypeDesignations) taxon (name) -> specimen

        List<DerivedUnit> byAssociatedTaxon = occurrenceService.listByAssociatedTaxon(DerivedUnit.class, null, taxon, null, null, null, null, null);

        assertNotNull(byAssociatedTaxon);

        assertEquals(2, byAssociatedTaxon.size());

        assertTrue(byAssociatedTaxon.contains(associatedSpecimen));

        assertTrue(byAssociatedTaxon.contains(typeSpecimen));

        assertTrue(!byAssociatedTaxon.contains(unassociatedSpecimen));

    }