EDIT

/**

* Copyright (C) 2007 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.assertFalse;

import static org.junit.Assert.assertNull;

import static org.junit.Assert.assertTrue;

import java.io.FileNotFoundException;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Test;

import org.unitils.spring.annotation.SpringBeanByType;

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

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

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

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

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

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

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

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.TaxonRelationshipType;

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

/**

 * This test checks of all the business logic methods do what they are expected to do.

 *

 * @author n.hoffmann

 * @since Dec 16, 2010

 */

public class TaxonServiceImplBusinessTest extends CdmIntegrationTest {

	private Synonym s1;

	private Synonym s2;

	private Taxon t2;

	private Taxon t1;

	@SpringBeanByType

	private ITaxonService service;

	@SpringBeanByType

	private INameService nameService;

	private String referenceDetail;

	private Reference reference;

	private SynonymType homoTypicSynonymType;

	private SynonymType heteroTypicSynonymType;

	private INonViralName s1n;

	private INonViralName t2n;

	private INonViralName t1n;

	private TaxonName s2n;

	@Before

	public void setUp() throws Exception {

		//service = new TaxonServiceImpl();

		//nameService = new NameServiceImpl();

		t1n = TaxonNameFactory.NewNonViralInstance(null);

		t1 = Taxon.NewInstance(t1n, reference);

		t2n = TaxonNameFactory.NewNonViralInstance(null);

		t2 = Taxon.NewInstance(t2n, reference);

		s1n = TaxonNameFactory.NewNonViralInstance(null);

		s1 = Synonym.NewInstance(s1n, reference);

		s2n = TaxonNameFactory.NewNonViralInstance(null);

		s2 = Synonym.NewInstance(s2n, reference);

		// referencing

		homoTypicSynonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();

		heteroTypicSynonymType = SynonymType.HETEROTYPIC_SYNONYM_OF();

		reference = ReferenceFactory.newGeneric();

		referenceDetail = "test";

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#swapSynonymAndAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.

	 */

	@Test

	public final void testSwapSynonymAndAcceptedTaxon() {

		t1.addSynonym(s1, homoTypicSynonymType);

		UpdateResult result = service.swapSynonymAndAcceptedTaxon(s1, t1, true);

		Synonym syn = (Synonym)service.load(s1.getUuid());

		Assert.assertNull(syn);

		TaxonName name = nameService.load(s1n.getUuid());

		Assert.assertNotNull(name);

		//The name of the new accepted taxon should be the same as from the former synonym

		Assert.assertEquals(((Taxon)result.getCdmEntity()).getName(), name);

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.

	 */

	@Test

	public final void testChangeSynonymToAcceptedTaxon() {

		t1.addSynonym(s1, homoTypicSynonymType);

		HomotypicalGroup oldGroup = s1.getName().getHomotypicalGroup();

		Assert.assertEquals("Homotypical group of new accepted taxon should contain exactly 2 names", 2, oldGroup.getTypifiedNames().size());

		boolean deleteSynonym = false;

		Taxon taxon = null;

		UpdateResult result;

        try {

            result = service.changeSynonymToAcceptedTaxon(s1, t1, deleteSynonym);

            Assert.assertTrue("Change must fail for synonym and taxon in same homotypical group",result.isAbort());

        } catch (HomotypicalGroupChangeException e1) {

            // TODO Auto-generated catch block

            e1.printStackTrace();

        }

		t1.addSynonym(s2, heteroTypicSynonymType);

		Assert.assertEquals("Homotypical group of old accepted taxon should still contain exactly 2 names", 2, oldGroup.getTypifiedNames().size());

		Assert.assertTrue("Old accepted taxon should now have 2 synonyms", t1.getSynonyms().size() == 2);

		try {

			taxon = (Taxon)service.changeSynonymToAcceptedTaxon(s2, t1, deleteSynonym).getCdmEntity();

		} catch (HomotypicalGroupChangeException e) {

			Assert.fail("Change must not throw exception for heterotypic synonym change");

		}

		Assert.assertTrue("Former accepted taxon should still have 1 synonym", t1.getSynonyms().size() == 1);

		Assert.assertNotNull(taxon);

		Assert.assertEquals(s2n, taxon.getName());

		HomotypicalGroup newGroup = taxon.getName().getHomotypicalGroup();

		Assert.assertEquals("Homotypical group of new accepted taxon should contain exactly one name", 1, newGroup.getTypifiedNames().size());

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)}.

	 */

	@Test

	public final void testChangeSynonymWithMultipleSynonymsInHomotypicalGroupToAcceptedTaxon() {

		t1.addSynonym(s1, heteroTypicSynonymType);

		TaxonName otherHeteroSynonymName = TaxonNameFactory.NewNonViralInstance(null);

		t1.addHeterotypicSynonymName(otherHeteroSynonymName);

		TaxonName homotypicSynonymName = TaxonNameFactory.NewNonViralInstance(null);

		Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());

		t1.addHomotypicSynonym(homotypicSynonym);

		HomotypicalGroup group = s1.getHomotypicGroup();

		Reference citation1 = ReferenceFactory.newBook();

		String microReference1 = "p. 55";

		Synonym s2 = t1.addHeterotypicSynonymName(s2n, citation1, microReference1, group);

		HomotypicalGroup homoGroup2 = s1.getHomotypicGroup();

		Assert.assertEquals("Homotypical group must be the same group as for the old synonym", group, homoGroup2);

		//run

		Taxon newTaxon = null;

		try {

			newTaxon = (Taxon)service.changeSynonymToAcceptedTaxon(s1, t1, false).getCdmEntity();

		} catch (HomotypicalGroupChangeException e1) {

			Assert.fail("Invocation of change method should not throw an exception");

		}

		Assert.assertEquals("Former accepted taxon should now have 2 synonyms left", 2, t1.getSynonyms().size());

		Assert.assertEquals("Former accepted taxon should now have 1 heterotypic synonym group left", 1, t1.getHeterotypicSynonymyGroups().size());

		Assert.assertNotNull(newTaxon);

		Assert.assertEquals(s1n, newTaxon.getName());

		Assert.assertEquals("New accepted taxon should have 1 synonym", 1, newTaxon.getSynonyms().size());

		Assert.assertEquals("The new synonym must be the homotypic synonym of the old synonym", s2, newTaxon.getSynonyms().iterator().next());

		HomotypicalGroup homoGroup = newTaxon.getHomotypicGroup();

		Assert.assertEquals("Homotypical group must be the same group as for the old synonym", group, homoGroup);

		List<Synonym> synonymsInNewTaxonsGroup = newTaxon.getSynonymsInGroup(homoGroup);

		String message = "New accepted taxon should have 1 synonym in its homotypic group: s2. The old synonym may still exist (or not) but not as a synonym of the new taxon";

		Assert.assertEquals(message, 1, synonymsInNewTaxonsGroup.size());

		Assert.assertTrue("The old synonym's homotypic 'partner' must be a synonym of the new accepted taxon, too.", synonymsInNewTaxonsGroup.contains(s2));

		Assert.assertTrue("The old synonym must be in the new accepted taxons homotypic group as it has not been deleted ", newTaxon.getName().getHomotypicalGroup().equals(s2.getName().getHomotypicalGroup()));

		boolean iWasHere = false;

		for (Synonym syn : synonymsInNewTaxonsGroup){

			if (syn.equals(s2) ){

				Assert.assertEquals("s2 relationship needs to have the same citation as the former relation to the given accepted taxon.", citation1, s2.getSec());

				iWasHere = true;

			}

		}

		Assert.assertTrue("Relationship to s2 must have been concidered in 'for'-loop", iWasHere);

		try {

			UpdateResult result = service.changeSynonymToAcceptedTaxon(homotypicSynonym, t1, false);

			Assert.assertTrue("The method should throw an exception when invoked on taxa in the same homotypical group", !result.getExceptions().isEmpty());

		} catch (HomotypicalGroupChangeException e) {

			//OK

		}

//		Assert.assertNull("Synonym should not be used in a name anymore", s1.getName());

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonServiceImpl#changeSynonymToRelatedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.

	 */

	@Test

	public final void testChangeSynonymToRelatedTaxon() {

		t1.addSynonym(s1, homoTypicSynonymType);

		t1.addSynonym(s2, homoTypicSynonymType);

		Set<TaxonBase> newInstances = new HashSet<>();

		newInstances.add(s1);

		newInstances.add(t1);

		newInstances.add(t2);

		service.save(newInstances);

		TaxonName synonymName = s1.getName();

		UUID synNameUUID = synonymName.getUuid();

		Taxon newTaxon = (Taxon) service.changeSynonymToRelatedTaxon(s1, t2, TaxonRelationshipType.CONGRUENT_OR_EXCLUDES(), reference, referenceDetail).getCdmEntity();

		//check removeTaxonBase()

		//UUID s1UUID = service.update(s1);

		UUID newTaxonUUID = service.save(newTaxon).getUuid();

		s1 =(Synonym)service.find(s1.getUuid());

		newTaxon = (Taxon)service.find(newTaxonUUID);

		assertNull(s1);

		synonymName = nameService.find(synNameUUID);

		assertFalse(synonymName.getTaxonBases().contains(s1));

		assertTrue(synonymName.getTaxonBases().contains(newTaxon));

		synonymName = s2.getName();

        newTaxon = (Taxon)service.changeSynonymToRelatedTaxon(s2, t1, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), reference, referenceDetail).getCdmEntity();

        //check removeTaxonBase()

        //UUID s1UUID = service.update(s1);

        newTaxonUUID = service.save(newTaxon).getUuid();

        s2 =(Synonym)service.find(s2.getUuid());

        newTaxon = (Taxon)service.find(newTaxonUUID);

        assertNull(s2);

        assertFalse(synonymName.getTaxonBases().contains(s2));

        assertTrue(synonymName.getTaxonBases().contains(newTaxon));

	}

	@Test

	public void changeHomotypicalGroupOfSynonym(){

		//s1 - Heterotypic

		t1.addSynonym(s1, heteroTypicSynonymType);

		//s2 - heterotypic

		TaxonName otherHeteroSynonymName = TaxonNameFactory.NewNonViralInstance(null);

		Synonym s2 = Synonym.NewInstance(otherHeteroSynonymName, t1.getSec());

		t1.addSynonym(s2, heteroTypicSynonymType);

		TaxonName otherHeteroSynonymNameB = TaxonNameFactory.NewNonViralInstance(null);

		otherHeteroSynonymName.addBasionym(otherHeteroSynonymNameB);

		Synonym s2b = Synonym.NewInstance(otherHeteroSynonymNameB, t1.getSec());

		t1.addSynonym(s2b, heteroTypicSynonymType);

		//homotypic

		TaxonName homotypicSynonymName = TaxonNameFactory.NewNonViralInstance(null);

		Synonym homotypicSynonym = Synonym.NewInstance(homotypicSynonymName, t1.getSec());

		t1.addHomotypicSynonym(homotypicSynonym);

		t1.getName().addBasionym(homotypicSynonymName);

		//Preconditions test

		Assert.assertFalse("s2 must not be in s1 homotypic group", s2.getHomotypicGroup().equals(s1.getHomotypicGroup()));

		Assert.assertFalse("s2 must not be in t1 homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));

		Assert.assertNotNull("s2 must have exactly 1 synonym relationship/ must have accepted taxon", s2.getAcceptedTaxon());

		Assert.assertEquals("s2 must have heterotypic relationship type", heteroTypicSynonymType, s2.getType());

		Assert.assertEquals("s2 must have exactly 1 basionym relationships", 1, s2.getName().getBasionyms().size());

		//do it

		service.changeHomotypicalGroupOfSynonym(s2, s1.getHomotypicGroup(), t1, true);

		//postconditions

		Assert.assertEquals("s2 must be in s1 homotypic group", s2.getHomotypicGroup(), s1.getHomotypicGroup());

		Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());

		Assert.assertEquals("s2 must have heterotypic relationship", heteroTypicSynonymType, s2.getType());

		Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());

		//Preconditions test

		Assert.assertEquals("'homotypicSynonym' must have exactly 1 basionym relationships", 1, homotypicSynonym.getName().getNameRelations().size());

		Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());

		Assert.assertFalse("s2 must not be in t1 homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));

		//do it

		service.changeHomotypicalGroupOfSynonym(s2, homotypicSynonym.getHomotypicGroup(), null, true);

		//postconditions

		Assert.assertEquals("s2 must be in 'homotypicSynonym' homotypic group", s2.getHomotypicGroup(), homotypicSynonym.getHomotypicGroup());

		Assert.assertEquals("s2 must be in 't1' homotypic group", s2.getHomotypicGroup(), t1.getHomotypicGroup());

		Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());

		Assert.assertEquals("s2 must have homotypic relationship", this.homoTypicSynonymType, s2.getType());

		Assert.assertEquals("s2 must have exactly 1 basionym relationships", 1, s2.getName().getBasionyms().size());

		Assert.assertEquals("'homotypicSynonym' must have exactly 2 basionym relationships", 2, homotypicSynonym.getName().getNameRelations().size());

		Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());

		Assert.assertEquals("'t1' must have exactly 2 homotypic synonyms", 2, t1.getHomotypicSynonymsByHomotypicSynonymType().size());

		Assert.assertEquals("'t1' must have exactly 2 names in homotypic group", 2, t1.getHomotypicSynonymsByHomotypicGroup(null).size());

		Assert.assertEquals("'t1' homotypic group must include 3 names (t1, s2, homotypicSynonym)", 3, t1.getHomotypicGroup().getTypifiedNames().size());

		//do it

		service.changeHomotypicalGroupOfSynonym(s2, t2.getHomotypicGroup(), t2, false);

		//postconditions

		Assert.assertEquals("s2 must be in 't2' homotypic group", t2.getHomotypicGroup(), s2.getHomotypicGroup());

		Assert.assertFalse("s2 must not be in 't1' homotypic group", s2.getHomotypicGroup().equals(t1.getHomotypicGroup()));

		Assert.assertNotNull("s2 must have exactly 1 synonym relationship/accepted taxon", s2.getAcceptedTaxon());

		Assert.assertEquals("s2 must have homotypic relationship", this.homoTypicSynonymType, s2.getType());

		Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());

		Assert.assertEquals("'homotypicSynonym' must have exactly 1 basionym relationships", 1, homotypicSynonym.getName().getNameRelations().size());

		Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());

		Assert.assertEquals("'t1' must have exactly 1 homotypic synonyms", 1, t1.getHomotypicSynonymsByHomotypicSynonymType().size());

		Assert.assertEquals("'t1' must have exactly 1 names in homotypic group", 1, t1.getHomotypicSynonymsByHomotypicGroup().size());

		Assert.assertEquals("'t1' homotypic group must include 2 names (t1, homotypicSynonym)", 2, t1.getHomotypicGroup().getTypifiedNames().size());

		//do it

		service.changeHomotypicalGroupOfSynonym(s2, s1.getHomotypicGroup(), t1, false);

		//postconditions

		Assert.assertEquals("s2 must be in s1 homotypic group", s2.getHomotypicGroup(), s1.getHomotypicGroup());

		Assert.assertFalse("s2 must not be in 't2' homotypic group", t2.getHomotypicGroup().equals(s2.getHomotypicGroup()));

		//had 2 accepted taxa when synonym relationships still existed

		Assert.assertNotNull("s2 must have accepted taxon", s2.getAcceptedTaxon());

		Assert.assertEquals("Both relationships of s2 must be heterotypic", heteroTypicSynonymType, s2.getType());

		Assert.assertEquals("s2 must have exactly 0 basionym relationships", 0, s2.getName().getBasionyms().size());

	}

    @Override

    public void createTestDataSet() throws FileNotFoundException {}

}