EDIT

/**

* Copyright (C) 2018 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.name;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

import java.util.ArrayList;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Test;

import eu.etaxonomy.cdm.api.service.exception.RegistrationValidationException;

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

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

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

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

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

import eu.etaxonomy.cdm.model.media.Media;

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

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

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

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

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

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.name.TypeDesignationStatusBase;

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

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.FieldUnit;

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

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.ref.TypedEntityReference;

import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;

import eu.etaxonomy.cdm.test.TermTestBase;

/**

 * @author a.kohlbecker, k.luther, a.mueller

 * @since 03.09.2018

 */

public class TypeDesignationSetManagerTest extends TermTestBase{

        private static final boolean WITH_CITATION = true;

        private static final boolean WITH_NAME = true;

        private static final boolean WITH_TYPE_LABEL = true;

        private NameTypeDesignation ntd;

        private NameTypeDesignation ntd_LT;

        private SpecimenTypeDesignation std_IT;

        private SpecimenTypeDesignation std_HT;

        private SpecimenTypeDesignation std_LT;

        private SpecimenTypeDesignation std_IT_2;

        private SpecimenTypeDesignation std_IT_3;

        private SpecimenTypeDesignation mtd_HT_published;

        private SpecimenTypeDesignation mtd_IT_unpublished;

        private Reference book;

        private Team team;

        @Before

        public void init(){

            Person person1 = Person.NewInstance("DC", "Decandolle", "A.", null);

            Person person2 = Person.NewInstance("Hab.", "Haber", "M.", null);

            Person person3 = Person.NewInstance("Moler", "Moler", "A.P.", null);

            team = Team.NewInstance(person1, person2, person3);

            book = ReferenceFactory.newBook();

            book.setAuthorship(team);

            book.setDatePublished(TimePeriodParser.parseStringVerbatim("11 Apr 1962"));

            ntd = NameTypeDesignation.NewInstance();

            ntd.setId(1);

            TaxonName typeName = TaxonNameFactory.NewBacterialInstance(Rank.SPECIES());

            typeName.setTitleCache("Prionus coriatius L.", true);

            ntd.setTypeName(typeName);

//            Reference citation = ReferenceFactory.newGeneric();

//            citation.setTitleCache("Species Plantarum", true);

//            ntd.setCitation(citation);

//          ntd.addPrimaryTaxonomicSource(citation, null);

            ntd_LT = NameTypeDesignation.NewInstance();

            ntd_LT.setTypeStatus(NameTypeDesignationStatus.LECTOTYPE());

            TaxonName typeName2 = TaxonNameFactory.NewBacterialInstance(Rank.SPECIES());

            typeName2.setTitleCache("Prionus arealus L.", true);

            ntd_LT.setTypeName(typeName2);

            ntd_LT.setCitation(book);

            FieldUnit fu_1 = FieldUnit.NewInstance();

            fu_1.setId(1);

            fu_1.setTitleCache("Testland, near Bughausen, A.Kohlbecker 81989, 2017", true);

            FieldUnit fu_2 = FieldUnit.NewInstance();

            fu_2.setId(2);

            fu_2.setTitleCache("Dreamland, near Kissingen, A.Kohlbecker 66211, 2017", true);

            std_HT = SpecimenTypeDesignation.NewInstance();

            std_HT.setId(1);

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

            specimen_HT.setTitleCache("OHA", true);

            createDerivationEvent(fu_1, specimen_HT);

            specimen_HT.getOriginals().add(fu_1);

            std_HT.setTypeSpecimen(specimen_HT);

            std_HT.setTypeStatus(SpecimenTypeDesignationStatus.HOLOTYPE());

            std_IT = SpecimenTypeDesignation.NewInstance();

            std_IT.setId(2);

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

            specimen_IT.setTitleCache("BER", true);

            createDerivationEvent(fu_1, specimen_IT);

            std_IT.setTypeSpecimen(specimen_IT);

            std_IT.setTypeStatus(SpecimenTypeDesignationStatus.ISOTYPE());

            std_LT = SpecimenTypeDesignation.NewInstance();

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

            specimen_LT.setTitleCache("LEC", true);

            createDerivationEvent(fu_1, specimen_LT);

            std_LT.setTypeSpecimen(specimen_LT);

            std_LT.setTypeStatus(SpecimenTypeDesignationStatus.LECTOTYPE());

            std_LT.setCitation(book);

            std_IT_2 = SpecimenTypeDesignation.NewInstance();

            std_IT_2.setId(3);

            DerivedUnit specimen_IT_2 = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);

            specimen_IT_2.setTitleCache("KEW", true);

            createDerivationEvent(fu_1, specimen_IT_2);

            std_IT_2.setTypeSpecimen(specimen_IT_2);

            std_IT_2.setTypeStatus(SpecimenTypeDesignationStatus.ISOTYPE());

            std_IT_3 = SpecimenTypeDesignation.NewInstance();

            std_IT_3.setId(4);

            DerivedUnit specimen_IT_3 = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);

            specimen_IT_3.setTitleCache("M", true);

            createDerivationEvent(fu_2, specimen_IT_3);

            std_IT_3.setTypeSpecimen(specimen_IT_3);

            std_IT_3.setTypeStatus(SpecimenTypeDesignationStatus.ISOTYPE());

            mtd_HT_published = SpecimenTypeDesignation.NewInstance();

            mtd_HT_published.setId(5);

            MediaSpecimen mediaSpecimen_published = (MediaSpecimen)DerivedUnit.NewInstance(SpecimenOrObservationType.Media);

            Media media = Media.NewInstance();

            Reference ref = ReferenceFactory.newBook();

            ref.setTitle("Algae of the BGBM");

            ref.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(2008));

            ref.setAuthorship(Team.NewInstance(Person.NewInstance(null, "Kohlbecker", "A.", null), Person.NewInstance(null, "Kusber", "W.-H.", null)));

            media.addSource(IdentifiableSource.NewPrimaryMediaSourceInstance(ref, "33"));

            mediaSpecimen_published.setMediaSpecimen(media);

            createDerivationEvent(fu_1, mediaSpecimen_published);

            mtd_HT_published.setTypeSpecimen(mediaSpecimen_published);

            mtd_HT_published.setTypeStatus(SpecimenTypeDesignationStatus.HOLOTYPE());

            mtd_IT_unpublished = SpecimenTypeDesignation.NewInstance();

            mtd_IT_unpublished.setId(6);

            MediaSpecimen mediaSpecimen_unpublished = (MediaSpecimen)DerivedUnit.NewInstance(SpecimenOrObservationType.Media);

            eu.etaxonomy.cdm.model.occurrence.Collection collection = eu.etaxonomy.cdm.model.occurrence.Collection.NewInstance();

            collection.setCode("B");

            mediaSpecimen_unpublished.setCollection(collection);

            mediaSpecimen_unpublished.setAccessionNumber("Slide A565656");

            createDerivationEvent(fu_1, mediaSpecimen_unpublished);

            mtd_IT_unpublished.setTypeSpecimen(mediaSpecimen_unpublished);

            mtd_IT_unpublished.setTypeStatus(SpecimenTypeDesignationStatus.ISOTYPE());

        }

        protected void createDerivationEvent(FieldUnit fu_1, DerivedUnit specimen_IT_2) {

            DerivationEvent derivationEvent_3 = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());

            derivationEvent_3.addOriginal(fu_1);

            derivationEvent_3.addDerivative(specimen_IT_2);

        }

        @Test

        public void test1() throws RegistrationValidationException{

            @SuppressWarnings("rawtypes")

            List<TypeDesignationBase> tds = new ArrayList<>();

            tds.add(ntd);

            tds.add(std_IT);

            tds.add(std_HT);

            tds.add(std_IT_2);

            tds.add(std_IT_3);

            TaxonName typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());

            typifiedName.setTitleCache("Prionus L.", true);

            typifiedName.addTypeDesignation(ntd, false);

            typifiedName.addTypeDesignation(std_HT, false);

            typifiedName.addTypeDesignation(std_IT, false);

            typifiedName.addTypeDesignation(std_IT_2, false);

            typifiedName.addTypeDesignation(std_IT_3, false);

            TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(tds);

            String result = typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME);

//            Logger.getLogger(this.getClass()).debug(result);

            assertNotNull(result);

            assertEquals(

                    "Prionus L.\u202F\u2013\u202FTypes: Dreamland, near Kissingen, A.Kohlbecker 66211, 2017 (isotype: M);"

                    + " Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: OHA; isotypes: BER, KEW);"

                    + " nametype: Prionus coriatius L."

                    , result

                    );

            Map<TypedEntityReference<? extends VersionableEntity>, TypeDesignationWorkingSet> orderedTypeDesignations =

                    typeDesignationManager.getOrderedTypeDesignationWorkingSets();

            Iterator<TypeDesignationWorkingSet> byStatusMapIterator = orderedTypeDesignations.values().iterator();

            Iterator<TypeDesignationStatusBase<?>> keyIt_1 = byStatusMapIterator.next().keySet().iterator();

            Iterator<TypeDesignationStatusBase<?>> keyIt_2 = byStatusMapIterator.next().keySet().iterator();

            assertEquals("isotype", keyIt_1.next().getLabel());

            assertEquals("holotype", keyIt_2.next().getLabel());

            assertEquals("isotype", keyIt_2.next().getLabel());

        }

        @Test

        public void test2() {

            TaxonName typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());

            typifiedName.setTitleCache("Prionus L.", true);

            TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            String result = typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME);

            assertEquals(

                    "Prionus L."

                    , result

                    );

            typifiedName.addTypeDesignation(ntd, false);

            typeDesignationManager.addTypeDesigations(ntd);

            assertEquals(

                    "Prionus L.\u202F\u2013\u202FNametype: Prionus coriatius L."

                    , typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME)

                    );

            typifiedName.addTypeDesignation(std_HT, false);

            typeDesignationManager.addTypeDesigations(std_HT);

            assertEquals(

                    "Prionus L.\u202F\u2013\u202FTypes: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: OHA); nametype: Prionus coriatius L."

                    , typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME)

                    );

            DerivedUnit specimen = std_HT.getTypeSpecimen();

            specimen.setProtectedTitleCache(false);

            Collection collection = Collection.NewInstance();

            collection.setName("My collection");

            specimen.setCollection(collection);

            assertEquals(

                    "Prionus L.\u202F\u2013\u202FTypes: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: My collection); nametype: Prionus coriatius L."

                    , typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME)

                    );

        }

        //see #9262

        @Test

        public void test_desigby_fide(){

            //specimen types

            TaxonName typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.SPECIES());

            typifiedName.setTitleCache("Prionus coriatius L.", true);

            TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            typeDesignationManager.addTypeDesigations(std_LT);

            Reference citation = ReferenceFactory.newBook();

            Reference inRef = ReferenceFactory.newBookSection();

            inRef.setInBook(citation);

            citation.setDatePublished(TimePeriodParser.parseStringVerbatim("1989"));

            inRef.setAuthorship(Team.NewTitledInstance("Miller", "Mill."));

            std_LT.addPrimaryTaxonomicSource(inRef, "55");

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FTestland, near Bughausen, A.Kohlbecker 81989, 2017 (lectotype: LEC designated by Decandolle & al. 1962 [fide Miller 1989: 55])",

                    typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FTestland, near Bughausen, A.Kohlbecker 81989, 2017 (lectotype: LEC)",

                    typeDesignationManager.print(!WITH_CITATION,!WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Testland, near Bughausen, A.Kohlbecker 81989, 2017 (lectotype: LEC)",

                    typeDesignationManager.print(!WITH_CITATION, !WITH_TYPE_LABEL, !WITH_NAME));

            //name types

            typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());

            typifiedName.setTitleCache("Prionus L.", true);

            typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            typeDesignationManager.addTypeDesigations(ntd_LT);

            ntd_LT.addPrimaryTaxonomicSource(inRef, "66");

            assertEquals("Prionus L.\u202F\u2013\u202FLectotype: Prionus arealus L. designated by Decandolle & al. 1962 [fide Miller 1989: 66]",

                    typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Prionus L.\u202F\u2013\u202FLectotype: Prionus arealus L.",

                    typeDesignationManager.print(!WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

        }

        @Test

        public void test_mediaType(){

            for(int i = 0; i < 10; i++ ){

                init();

                // repeat 10 times to assure the order of typedesignations is fix in the representations

                TaxonName typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.SPECIES());

                typifiedName.setTitleCache("Prionus coriatius L.", true);

                typifiedName.addTypeDesignation(mtd_HT_published, false);

                typifiedName.addTypeDesignation(mtd_IT_unpublished, false);

                TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(typifiedName);

                typeDesignationManager.addTypeDesigations(mtd_HT_published);

                typeDesignationManager.addTypeDesigations(mtd_IT_unpublished);

                assertEquals("failed after repeating " + i + " times",

                        "Prionus coriatius L.\u202F\u2013\u202FTypes: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: [icon] in Kohlbecker & Kusber 2008: 33; isotype: [icon] B Slide A565656)"

                        , typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME)

                        );

                Media media = ((MediaSpecimen)mtd_HT_published.getTypeSpecimen()).getMediaSpecimen();

                Reference ref2 = ReferenceFactory.newBook();

                ref2.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(2009));

                ref2.setAuthorship(Person.NewInstance(null, "Mueller", "A.", null));

                IdentifiableSource newSource = IdentifiableSource.NewPrimaryMediaSourceInstance(ref2, "tab. 4");

                media.addSource(newSource);

                String with2Sources = typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME);

                Assert.assertTrue("failed after repeating " + i + " times",

                        //the order of the sources is currently not yet defined (rare case), therefore 2 possibilities

                        with2Sources.equals("Prionus coriatius L.\u202F\u2013\u202FTypes: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: [icon] in Mueller 2009: tab. 4, Kohlbecker & Kusber 2008: 33; isotype: [icon] B Slide A565656)")

                        || with2Sources.equals("Prionus coriatius L.\u202F\u2013\u202FTypes: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (holotype: [icon] in Kohlbecker & Kusber 2008: 33, Mueller 2009: tab. 4; isotype: [icon] B Slide A565656)"))

                        ;

            }

        }

        @Test

        public void test_withoutFieldUnit(){

            TaxonName typifiedName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

            typifiedName.setTitleCache("Prionus coriatius L.", true);

            DerivedUnit protectedSpecimen = DerivedUnit.NewPreservedSpecimenInstance();

            protectedSpecimen.setTitleCache("Mexico. Oaxaca: Coixtlahuaca, Tepelmeme Villa de Morelos, aproximadamente 1 km S del Río Santa Lucía, 1285 m, 27 March 1994, U. Guzmán Cruz 1065 (MEXU 280206)", true);

            Reference citation = ReferenceFactory.newBook();

            citation.setTitle("The book of types");

            SpecimenTypeDesignation protectedDesignation = typifiedName.addSpecimenTypeDesignation(protectedSpecimen, SpecimenTypeDesignationStatus.NEOTYPE(), citation, "55", null, false, false);

            TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            typeDesignationManager.addTypeDesigations(protectedDesignation);

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FNeotype: Mexico. Oaxaca: Coixtlahuaca, Tepelmeme Villa de Morelos, aproximadamente 1 km S del Río Santa Lucía, 1285 m, 27 March 1994, U. Guzmán Cruz 1065 (MEXU 280206) designated by The book of types: 55"

                    , typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME)

                    );

            protectedDesignation.setTypeStatus(null);

            typeDesignationManager.addTypeDesigations(protectedDesignation);

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FMexico. Oaxaca: Coixtlahuaca, Tepelmeme Villa de Morelos, aproximadamente 1 km S del Río Santa Lucía, 1285 m, 27 March 1994, U. Guzmán Cruz 1065 (MEXU 280206) designated by The book of types: 55"

                    , typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME)

                    );

            DerivedUnit withoutFieldUnit = DerivedUnit.NewPreservedSpecimenInstance();

            withoutFieldUnit.setAccessionNumber("280207");

            withoutFieldUnit.setCollection(Collection.NewInstance("B", "Herbarium Berolinense"));

            SpecimenTypeDesignation withoutFieldUnitDesignation = typifiedName.addSpecimenTypeDesignation(withoutFieldUnit, SpecimenTypeDesignationStatus.HOLOTYPE(), null, null, null, false, false);

            typeDesignationManager.addTypeDesigations(withoutFieldUnitDesignation);

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FMexico. Oaxaca: Coixtlahuaca, Tepelmeme Villa de Morelos, aproximadamente 1 km S del Río Santa Lucía, 1285 m, 27 March 1994, U. Guzmán Cruz 1065 (MEXU 280206) designated by The book of types: 55; holotype: B 280207"

                    , typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME)

                    );

        }

        @Test

        public void test_withoutStatus(){

            //for another important test without status see also test_withoutFieldUnit()

            TaxonName typifiedName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

            typifiedName.setTitleCache("Prionus coriatius L.", true);

            TypeDesignationSetManager typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            std_LT.setTypeStatus(null);

            typeDesignationManager.addTypeDesigations(std_LT);

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FType: Testland, near Bughausen, A.Kohlbecker 81989, 2017 (LEC designated by Decandolle & al. 1962)",

                    typeDesignationManager.print(WITH_CITATION, WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Prionus coriatius L.\u202F\u2013\u202FTestland, near Bughausen, A.Kohlbecker 81989, 2017 (LEC)",

                    typeDesignationManager.print(!WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Testland, near Bughausen, A.Kohlbecker 81989, 2017 (LEC)",

                    typeDesignationManager.print(!WITH_CITATION, !WITH_TYPE_LABEL, !WITH_NAME));

            //name types

            typifiedName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());

            typifiedName.setTitleCache("Prionus L.", true);

            typeDesignationManager = new TypeDesignationSetManager(typifiedName);

            typeDesignationManager.addTypeDesigations(ntd_LT);

//            ntd_LT.addPrimaryTaxonomicSource(inRef, "66");

            assertEquals("Prionus L.\u202F\u2013\u202FLectotype: Prionus arealus L. designated by Decandolle & al. 1962",

                    typeDesignationManager.print(WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

            assertEquals("Prionus L.\u202F\u2013\u202FLectotype: Prionus arealus L.",

                    typeDesignationManager.print(!WITH_CITATION, !WITH_TYPE_LABEL, WITH_NAME));

        }

}