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.assertEquals;

import static org.junit.Assert.assertFalse;

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.ArrayList;

import java.util.Collections;

import java.util.Iterator;

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.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

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

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

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.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.TaxonNaturalComparator;

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

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

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

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

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

/**

 * @author n.hoffmann

 * @created Dec 16, 2010

 */

//@SpringApplicationContext("file:./target/test-classes/eu/etaxonomy/cdm/applicationContext-test.xml")

public class TaxonNodeServiceImplTest extends CdmTransactionalIntegrationTest{

	@SpringBeanByType

	private ITaxonNodeService taxonNodeService;

	@SpringBeanByType

	private IClassificationService classificationService;

	@SpringBeanByType

	private IReferenceService referenceService;

	@SpringBeanByType

	private ITermService termService;

	@SpringBeanByType

    private INameService nameService;

	@SpringBeanByType

	private ITaxonService taxonService;

	@SpringBeanByType

	private IPolytomousKeyService polKeyService;

	@SpringBeanByType

	private IPolytomousKeyNodeService polKeyNodeService;

	private static final UUID t1Uuid = UUID.fromString("55c3e41a-c629-40e6-aa6a-ff274ac6ddb1");

	private static final UUID t2Uuid = UUID.fromString("2659a7e0-ff35-4ee4-8493-b453756ab955");

	private static final UUID classificationUuid = UUID.fromString("6c2bc8d9-ee62-4222-be89-4a8e31770878");

	private static final UUID classification2Uuid = UUID.fromString("43d67247-936f-42a3-a739-bbcde372e334");

	private static final UUID referenceUuid = UUID.fromString("de7d1205-291f-45d9-9059-ca83fc7ade14");

	private static final UUID node1Uuid= UUID.fromString("484a1a77-689c-44be-8e65-347d835f47e8");

	private static final UUID node2Uuid = UUID.fromString("2d41f0c2-b785-4f73-a436-cc2d5e93cc5b");

	private static final UUID node4Uuid = UUID.fromString("2fbf7bf5-22dd-4c1a-84e4-c8c93d1f0342");

	private static final UUID node5Uuid = UUID.fromString("c4d5170a-7967-4dac-ab76-ae2019eefde5");

	private static final UUID node6Uuid = UUID.fromString("b419ba5e-9c8b-449c-ad86-7abfca9a7340");

	private static final UUID rootNodeUuid = UUID.fromString("324a1a77-689c-44be-8e65-347d835f4111");

	private Taxon t1;

	private Taxon t2;

	private Taxon t4;

//	private Synonym s1;

	private SynonymType synonymType;

	private Reference reference;

	private String referenceDetail;

	private Classification classification;

	private TaxonNode node1;

	private TaxonNode node2;

    private TaxonNode node4;

	/**

	 * @throws java.lang.Exception

	 */

	@Before

	public void setUp() throws Exception {

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonNodeServiceImpl#makeTaxonNodeASynonymOfAnotherTaxonNode(eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.taxon.SynonymType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.

	 */

	@Test

	@DataSet

	public final void testMakeTaxonNodeASynonymOfAnotherTaxonNode() {

		classification = classificationService.load(classificationUuid);

		node1 = taxonNodeService.load(node1Uuid);

		node2 = taxonNodeService.load(node2Uuid);

		node4 = taxonNodeService.load(node4Uuid);

		reference = referenceService.load(referenceUuid);

//		synonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();

		synonymType = CdmBase.deproxy(termService.load(SynonymType.uuidHomotypicSynonymOf), SynonymType.class) ;

		referenceDetail = "test";

		//

		//TODO

//		printDataSet(System.err, new String [] {"TaxonNode"});

		// descriptions

		t1 = node1.getTaxon();

		PolytomousKey polKey = PolytomousKey.NewInstance();

		PolytomousKeyNode keyNode = PolytomousKeyNode.NewInstance("", "", t1, null);

		keyNode.setKey(polKey);

		polKeyNodeService.save(keyNode);

		polKeyService.save(polKey);

		//nameRelations

		t1.getName().addRelationshipFromName(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), NameRelationshipType.ALTERNATIVE_NAME(), null );

		//taxonRelations

		t1.addTaxonRelation(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null), TaxonRelationshipType.CONGRUENT_OR_EXCLUDES(), null, null);

		Synonym synonym = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);

		UUID uuidSynonym = taxonService.save(synonym).getUuid();

		t1.addHomotypicSynonym(synonym);

		UUID uuidT1 = taxonService.saveOrUpdate(t1);

		t1 = null;

		t1 =(Taxon) taxonService.load(uuidT1);

		t1 = HibernateProxyHelper.deproxy(t1);

		TaxonName nameT1 = t1.getName();

		UUID t1UUID = t1.getUuid();

		t2 = node2.getTaxon();

		assertEquals(2, t1.getDescriptions().size());

		Assert.assertTrue(t2.getSynonyms().isEmpty());

		Assert.assertTrue(t2.getDescriptions().size() == 0);

		assertEquals(2,t1.getSynonyms().size());

		UUID synUUID = null;

		DeleteResult result;

		t4 = node4.getTaxon();

        UUID uuidT4 = t4.getUuid();

        t4 = (Taxon) taxonService.find(uuidT4);

        TaxonName name4 = nameService.find(t4.getName().getUuid());

        result = taxonNodeService.makeTaxonNodeASynonymOfAnotherTaxonNode(node4, node2, synonymType, reference, referenceDetail);

        if (result.isError() || result.isAbort()){

            Assert.fail();

        }

        t4 = (Taxon)taxonService.find(uuidT4);

        assertNull(t4);

		//Taxon can't be deleted because of the polytomous key node

		result = taxonNodeService.makeTaxonNodeASynonymOfAnotherTaxonNode(node1, node2, synonymType, reference, referenceDetail);

		if (result.isError() || result.isAbort()){

			Assert.fail();

		}

		commitAndStartNewTransaction(new String[]{/*"TaxonNode"*/});

		t1 = (Taxon)taxonService.find(t1Uuid);

		assertNotNull(t1);//because of the polytomous key node

		node1 = taxonNodeService.load(node1Uuid);

		assertNull(node1);

		Set<CdmBase> updatedObjects = result.getUpdatedObjects();

		Iterator<CdmBase> it = updatedObjects.iterator();

		Taxon taxon;

		while (it.hasNext()) {

			CdmBase updatedObject = it.next();

			if(updatedObject.isInstanceOf(Taxon.class)){

				taxon = HibernateProxyHelper.deproxy(updatedObject, Taxon.class);

				Set<Synonym> syns =  taxon.getSynonyms();

				assertNotNull(syns);

				if (taxon.equals(t2)){

				    assertEquals(4,syns.size());

				    Set<TaxonName> typifiedNames =taxon.getHomotypicGroup().getTypifiedNames();

	                assertEquals(typifiedNames.size(),4);

	                assertTrue(taxon.getHomotypicGroup().equals( nameT1.getHomotypicalGroup()));

	                assertEquals(taxon, t2);

				}

			}

		}

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.api.service.TaxonNodeServiceImpl#makeTaxonNodeASynonymOfAnotherTaxonNode(eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.taxon.SynonymType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.

	 */

	@Test

	@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)

	public final void testMakeTaxonNodeAHeterotypicSynonymOfAnotherTaxonNode() {

	    //create data

	    classification = classificationService.load(classificationUuid);

		node1 = taxonNodeService.load(node1Uuid);

		node2 = taxonNodeService.load(node2Uuid);

		reference = referenceService.load(referenceUuid);

		synonymType = CdmBase.deproxy(termService.load(SynonymType.uuidHeterotypicSynonymOf), SynonymType.class) ;

		referenceDetail = "test";

		// descriptions

		t1 = node1.getTaxon();

		PolytomousKey polKey = PolytomousKey.NewInstance();

		PolytomousKeyNode keyNode = PolytomousKeyNode.NewInstance("", "", t1, null);

		keyNode.setKey(polKey);

		polKeyNodeService.save(keyNode);

		polKeyService.save(polKey);

		//nameRelations

		t1.getName().addRelationshipFromName(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), NameRelationshipType.ALTERNATIVE_NAME(), null );

		TaxonName name1 = t1.getName();

		UUID name1UUID = name1.getUuid();

		//taxonRelations

		t1.addTaxonRelation(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null), TaxonRelationshipType.CONGRUENT_OR_EXCLUDES(), null, null);

		Synonym t1HomotypSynonym = Synonym.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);

		t1.addHomotypicSynonym(t1HomotypSynonym);

		TaxonName nameT1 = t1.getName();

		t2 = node2.getTaxon();

		assertEquals("taxon 1 must have 2 descriptions", 2, t1.getDescriptions().size());

		assertEquals("taxon 1 must have 2 synonyms", 2, t1.getSynonyms().size());

		Assert.assertTrue("taxon 2 must have no synonyms", t2.getSynonyms().isEmpty());

		Assert.assertTrue("taxon 2 must have no descriptions", t2.getDescriptions().size() == 0);

		//save

		UUID uuidSynonym = taxonService.save(t1HomotypSynonym).getUuid();

		//do it

		DeleteResult result = taxonNodeService.makeTaxonNodeASynonymOfAnotherTaxonNode

		        (node1, node2, synonymType, reference, referenceDetail);

		//post conditions

		if (!result.getUpdatedObjects().iterator().hasNext()){

			Assert.fail("Some updates must have taken place");

		}

		assertEquals(3,result.getUpdatedObjects().size());

		assertNotNull("Old taxon should not have been deleted as it is referenced by key node", taxonService.find(t1Uuid));

		assertNull("Old taxon node should not exist anymore", taxonNodeService.find(node1Uuid));

		t1HomotypSynonym = (Synonym)taxonService.find(uuidSynonym);

		assertNotNull(t1HomotypSynonym);

		keyNode.setTaxon(null);

		polKeyNodeService.saveOrUpdate(keyNode);

		t2 =HibernateProxyHelper.deproxy(t2);

		HibernateProxyHelper.deproxy(t2.getHomotypicGroup());

		t2.setName(HibernateProxyHelper.deproxy(t2.getName()));

		termService.saveOrUpdate(synonymType);

		assertFalse("taxon 2 must have a synonym now", t2.getSynonyms().isEmpty());

		assertEquals("taxon 2 must have 3 synonyms now, the old taxon 1 and it's 2 synonyms", 3, t2.getSynonyms().size());

		assertEquals("taxon 2 must have 2 descriptions now, taken form taxon 1", 2, t2.getDescriptions().size());

		result = taxonService.deleteTaxon(t1.getUuid(), null, null);

		if (result.isAbort() || result.isError()){

			Assert.fail();

		}

		assertNull(taxonService.find(t1Uuid));

		assertNull(taxonNodeService.find(node1Uuid));

		name1 = nameService.find(name1UUID);

		assertNotNull("taxon name 1 should still exist", name1);

		assertEquals("... but being used for the new synonym only as taxon 1 is deleted", 1, name1.getTaxonBases().size());

		t1HomotypSynonym = (Synonym)taxonService.find(uuidSynonym);

		assertNotNull(t1HomotypSynonym);

		Synonym newSynonym =(Synonym) name1.getTaxonBases().iterator().next();

		Taxon newAcceptedTaxon = CdmBase.deproxy(taxonService.find(t2.getUuid()), Taxon.class);

		assertEquals("The new synonym (old accepted taxon) and it's homotypic synonym should still be homotypic", newSynonym.getHomotypicGroup(), t1HomotypSynonym.getName().getHomotypicalGroup());

		assertFalse("The new accepted taxon must not be homotypic to ", newAcceptedTaxon.getHomotypicGroup().equals(newSynonym.getName().getHomotypicalGroup()));

		assertEquals("The new accepted taxon is taxon 2", newAcceptedTaxon, t2);

		assertEquals("The new synonyms name must be the same as the old accepted taxon's name", newSynonym.getName(), nameT1);

	}

	@Test

	@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonNodeServiceImplTest-indexing.xml")

	public final void testIndexCreateNode() {

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

		classification = classificationService.load(classificationUuid);

		node2 = taxonNodeService.load(node2Uuid);

		String oldTreeIndex = node2.treeIndex();

		TaxonNode newNode = node2.addChildTaxon(taxon, null, null);

		taxonNodeService.saveOrUpdate(newNode);

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		newNode = taxonNodeService.load(newNode.getUuid());

		Assert.assertEquals("", oldTreeIndex + newNode.getId() + "#", newNode.treeIndex());

	}

	@Test

	@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonNodeServiceImplTest-indexing.xml")

	public final void testIndexMoveNode() {

		//in classification

		classification = classificationService.load(classificationUuid);

		node1 = taxonNodeService.load(node1Uuid);

		node2 = taxonNodeService.load(node2Uuid);

		node2.addChildNode(node1, null, null);

		taxonNodeService.saveOrUpdate(node1);

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		TaxonNode node6 = taxonNodeService.load(node6Uuid);

		Assert.assertEquals("Node6 treeindex is not correct", node2.treeIndex() + "2#4#6#", node6.treeIndex());

		//root of new classification

		Classification classification2 = classificationService.load(classification2Uuid);

		node1 = taxonNodeService.load(node1Uuid);

		classification2.setRootNode(HibernateProxyHelper.deproxy(classification2.getRootNode(),TaxonNode.class));

		classification2.addChildNode(node1, null, null);

		taxonNodeService.saveOrUpdate(node1);

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		node1 = taxonNodeService.load(node1Uuid);

		Assert.assertEquals("Node1 treeindex is not correct", "#t2#8#2#", node1.treeIndex());

		node6 = taxonNodeService.load(node6Uuid);

		Assert.assertEquals("Node6 treeindex is not correct", "#t2#8#2#4#6#", node6.treeIndex());

		//into new classification

		node2 = taxonNodeService.load(node2Uuid);

		TaxonNode node5 = taxonNodeService.load(node5Uuid);

		node2 =node5.addChildNode(node2, null, null);

		taxonNodeService.saveOrUpdate(node2);

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		node2 = taxonNodeService.load(node2Uuid);

		Assert.assertEquals("Node3 treeindex is not correct", "#t2#8#2#5#3#", node2.treeIndex());

}

	@Test

	@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonNodeServiceImplTest-indexing.xml")

	public final void testIndexDeleteNode() {

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		node1 = taxonNodeService.load(node1Uuid);

		TaxonNode node4 = taxonNodeService.load(node4Uuid);

		String treeIndex = node1.treeIndex();

		TaxonNode node6 = taxonNodeService.load(node6Uuid);

		treeIndex= node6.treeIndex();

		HibernateProxyHelper.deproxy(node1, TaxonNode.class);

		node1.deleteChildNode(node4, false);

		TaxonNode node5 = taxonNodeService.load(node5Uuid);

		treeIndex = node5.treeIndex();

		node6 = taxonNodeService.load(node6Uuid);

		treeIndex = node6.treeIndex();

		Taxon newTaxon= Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);

		UUID taxonNewUuid = taxonService.save(newTaxon).getUuid();

		node5.addChildTaxon(newTaxon, null, null);

		String node5TreeIndex =node5.treeIndex();

		taxonNodeService.saveOrUpdate(node5);

		commitAndStartNewTransaction(new String[]{"TaxonNode"});

		node5 = taxonNodeService.load(node5Uuid);

		List<TaxonNode> children =  node5.getChildNodes();

		TaxonNode node = children.get(0);

		int id = node.getId();

		Assert.assertEquals("Node6 treeindex is not correct", "#t1#1#2#6#", treeIndex);

		Assert.assertEquals("new node treeindex is not correct", node5TreeIndex + id +"#", node.treeIndex());

	}

	@Test

	@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)

	public final void testDeleteNode(){

		classification = classificationService.load(classificationUuid);

		node1 = taxonNodeService.load(node1Uuid);

		node2 = taxonNodeService.load(rootNodeUuid);

		node1 = HibernateProxyHelper.deproxy(node1);

		TaxonNode newNode = node1.addChildTaxon(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null), null, null);

		UUID uuidNewNode = taxonNodeService.save(newNode).getUuid();

		newNode = taxonNodeService.load(uuidNewNode);

		UUID taxUUID = newNode.getTaxon().getUuid();

		UUID nameUUID = newNode.getTaxon().getName().getUuid();

		DeleteResult result = taxonNodeService.deleteTaxonNode(node1, null);

		if (!result.isOk()){

			Assert.fail();

		}

		newNode = taxonNodeService.load(uuidNewNode);

		node1 = taxonNodeService.load(node1Uuid);

		assertNull(newNode);

		assertNull(node1);

		t1 = (Taxon) taxonService.load(t1Uuid);

		assertNull(t1);

		Taxon newTaxon = (Taxon)taxonService.load(taxUUID);

		assertNull(newTaxon);

		IBotanicalName name = nameService.load(nameUUID);

		assertNull(name);

	}

	@Test

    @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)

    public final void testDeleteNodeWithReusedTaxon(){

        classification = classificationService.load(classificationUuid);

        node1 = taxonNodeService.load(node1Uuid);

        node2 = taxonNodeService.load(rootNodeUuid);

        node1 = HibernateProxyHelper.deproxy(node1);

        Classification classification2 = Classification.NewInstance("Classification2");

        TaxonNode nodeClassification2 =classification2.addChildTaxon(node1.getTaxon(), null, null);

        assertEquals(node1.getTaxon().getUuid(), t1Uuid);

        classificationService.save(classification2);

        List<TaxonNode> nodesOfClassification2 = taxonNodeService.listAllNodesForClassification(classification2, null, null);

        UUID nodeUUID = nodesOfClassification2.get(0).getUuid();

        assertEquals(nodeUUID, nodeClassification2.getUuid());

        Taxon newTaxon = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()),  null);

        taxonService.save(newTaxon);

        TaxonNode newNode = node1.addChildTaxon(newTaxon,null, null);

        UUID uuidNewNode = taxonNodeService.save(newNode).getUuid();

        newNode = taxonNodeService.load(uuidNewNode);

        UUID taxUUID = newNode.getTaxon().getUuid();

        UUID nameUUID = newNode.getTaxon().getName().getUuid();

        DeleteResult result = taxonNodeService.deleteTaxonNode(node1, null);

        if (!result.isOk()){

            Assert.fail();

        }

        //taxonService.getSession().flush();

        newNode = taxonNodeService.load(uuidNewNode);

        node1 = taxonNodeService.load(node1Uuid);

        assertNull(newNode);

        assertNull(node1);

        assertNotNull(taxonNodeService.load(nodeUUID));

        t1 = (Taxon) taxonService.load(t1Uuid);

        assertNotNull(t1);

        newTaxon = (Taxon)taxonService.load(taxUUID);

        assertNull(newTaxon);

        IBotanicalName name = nameService.load(nameUUID);

        assertNull(name);

    }

	@Test

	@DataSet

	public final void testDeleteNodes(){

		classification = classificationService.load(classificationUuid);

		node1 = taxonNodeService.load(node1Uuid);

		node2 = taxonNodeService.load(rootNodeUuid);

		node1 = HibernateProxyHelper.deproxy(node1);

		node2 = HibernateProxyHelper.deproxy(node2);

		TaxonNode newNode = node1.addChildTaxon(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null), null, null);

		UUID uuidNewNode = taxonNodeService.save(newNode).getUuid();

		List<TaxonNode> treeNodes = new ArrayList<TaxonNode>();

		treeNodes.add(node1);

		treeNodes.add(node2);

		DeleteResult result = taxonNodeService.deleteTaxonNodes(treeNodes, null);

		newNode = taxonNodeService.load(uuidNewNode);

		node1 = taxonNodeService.load(node1Uuid);

		assertNull(newNode);

		assertNull(node1);

		//taxonService.getSession().flush();

		t1 = (Taxon) taxonService.load(t1Uuid);

		assertNull(t1);

		t2 = (Taxon) taxonService.load(t2Uuid);

		assertNull(t2);

	}

	@Test

	@DataSet

	public void testMoveTaxonNode(){

	    classification = classificationService.load(classificationUuid);

	  //  Set<TaxonNode>  nodes = classification.getAllNodes();

	    List<TaxonNode>  nodes = classification.getChildNodes();

	    System.out.println(nodes.size());

	    classification.addChildTaxon(Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null), nodes.size(), null, null);

	   nodes =  classification.getChildNodes();

	    System.out.println(nodes.size());

	}

    @Test

    public void testCompareNaturalOrder() {

    	/*

    	 * Classification

    	 *  * Abies

    	 *  `- Abies alba

    	 *   - Abies balsamea

    	 *  * Pinus

    	 *  `- Pinus pampa

    	 */

    	Classification classification = Classification.NewInstance("Classification");

    	IBotanicalName abiesName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

    	abiesName.setGenusOrUninomial("Abies");

    	Taxon abies = Taxon.NewInstance(abiesName, null);

    	IBotanicalName abiesAlbaName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

    	abiesAlbaName.setGenusOrUninomial("Abies");

    	abiesAlbaName.setSpecificEpithet("alba");

    	Taxon abiesAlba = Taxon.NewInstance(abiesAlbaName, null);

    	IBotanicalName pinusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

    	pinusName.setGenusOrUninomial("Pinus");

    	Taxon pinus = Taxon.NewInstance(pinusName, null);

    	IBotanicalName pinusPampaName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

    	pinusPampaName.setGenusOrUninomial("Pinus");

    	pinusPampaName.setSpecificEpithet("pampa");

    	Taxon pinusPampa = Taxon.NewInstance(pinusPampaName, null);

        IBotanicalName abiesBalsameaName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

        abiesBalsameaName.setGenusOrUninomial("Abies");

        abiesBalsameaName.setSpecificEpithet("balsamea");

        Taxon abiesBalsamea = Taxon.NewInstance(abiesBalsameaName, null);

        List<TaxonNode> nodes = new ArrayList<TaxonNode>();

    	nodes.add(classification.addChildTaxon(abies, null, null));

    	TaxonNode abiesAlbaNode = classification.addParentChild(abies, abiesAlba, null, null);

    	TaxonNode balsameaNode = classification.addParentChild(abies, abiesBalsamea, null, null);

    	nodes.add(balsameaNode);

    	nodes.add(abiesAlbaNode);

    	nodes.add(classification.addChildTaxon(pinus, null, null));

    	nodes.add(classification.addParentChild(pinus, pinusPampa, null, null));

    	classificationService.saveClassification(classification);

    	//this.taxonNodeService.save(nodes);

    	TaxonNaturalComparator comparator = new TaxonNaturalComparator();

    	List<TaxonNode> allNodes = new ArrayList<>(classification.getAllNodes());

    	Collections.sort(allNodes, comparator);

    	Assert.assertEquals(allNodes.get(0).getTaxon(), abies );

    	Assert.assertEquals(allNodes.get(2).getTaxon(), abiesBalsamea );

    	Assert.assertEquals(allNodes.get(1).getTaxon(), abiesAlba );

    	taxonNodeService.moveTaxonNode(balsameaNode, abiesAlbaNode,1);

    	classification = classificationService.load(classification.getUuid());

    	allNodes = new ArrayList<>(classification.getAllNodes());

        Collections.sort(allNodes, comparator);

        Assert.assertEquals(allNodes.get(0).getTaxon(), abies );

        Assert.assertEquals(allNodes.get(1).getTaxon(), abiesBalsamea );

        Assert.assertEquals(allNodes.get(2).getTaxon(), abiesAlba );

    }

    @Test

    @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "TaxonNodeServiceImplTest.testGetUuidAndTitleCacheHierarchy.xml")

    public void testGetUuidAndTitleCacheHierarchy(){

        UUID classificationUuid = UUID.fromString("029b4c07-5903-4dcf-87e8-406ed0e0285f");

        UUID abiesUuid = UUID.fromString("f8306fd3-9825-41bf-94aa-a7b5790b553e");

        UUID abiesAlbaUuid = UUID.fromString("c70f76e5-2dcb-41c5-ae6f-d756e0a0fae0");

        UUID abiesAlbaSubBrotaUuid = UUID.fromString("06d58161-7707-44b5-b720-6c0eb916b37c");

        UUID abiesPalmaUuid = UUID.fromString("6dfd30dd-e589-493a-b66a-19c4cb374f92");

        UUID pinusUuid = UUID.fromString("5d8e8341-f5e9-4616-96cf-f0351dda42f4");

//        /*

//         * Checklist

//         *  - Abies

//         *   - Abies alba

//         *    - Abieas alba subs. brota

//         *   - Abies palma

//         *  -Pinus

//         */

//        Classification checklist = Classification.NewInstance("Checklist");

//        checklist.setUuid(classificationUuid);

//

//        BotanicalName abiesName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

//        abiesName.setGenusOrUninomial("Abies");

//        Taxon abies = Taxon.NewInstance(abiesName, null);

//

//        BotanicalName abiesAlbaName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

//        abiesAlbaName.setGenusOrUninomial("Abies");

//        abiesAlbaName.setSpecificEpithet("alba");

//        Taxon abiesAlba = Taxon.NewInstance(abiesAlbaName, null);

//

//        BotanicalName abiesAlbaSubBrotaName = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());

//        abiesAlbaSubBrotaName.setGenusOrUninomial("Abies");

//        abiesAlbaSubBrotaName.setSpecificEpithet("alba");

//        abiesAlbaSubBrotaName.setInfraSpecificEpithet("brota");

//        Taxon abiesAlbaSubBrota = Taxon.NewInstance(abiesAlbaSubBrotaName, null);

//

//        BotanicalName abiesPalmaName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

//        abiesPalmaName.setGenusOrUninomial("Abies");

//        abiesPalmaName.setSpecificEpithet("palma");

//        Taxon abiesPalma = Taxon.NewInstance(abiesPalmaName, null);

//

//        BotanicalName pinusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

//        pinusName.setGenusOrUninomial("Pinus");

//        Taxon pinus = Taxon.NewInstance(pinusName, null);

//

//        checklist.addParentChild(null, abies, null, null);

//        checklist.addParentChild(abies, abiesAlba, null, null);

//        checklist.addParentChild(abiesAlba, abiesAlbaSubBrota, null, null);

//        checklist.addParentChild(abies, abiesPalma, null, null);

//        checklist.addParentChild(null, pinus, null, null);

//

//

//        setComplete();

//        endTransaction();

//

//        String fileNameAppendix = "testGetUuidAndTitleCacheHierarchy";

//

//        writeDbUnitDataSetFile(new String[] {

//            "TAXONBASE", "TAXONNAME",

//            "TAXONRELATIONSHIP",

//            "HOMOTYPICALGROUP",

//            "CLASSIFICATION", "TAXONNODE",

//            "HIBERNATE_SEQUENCES" // IMPORTANT!!!

//            },

//            fileNameAppendix );

        Classification classification = classificationService.load(classificationUuid);

        List<TaxonNode> expectedChildTaxonNodes = classification.getChildNodes();

        List<UuidAndTitleCache<TaxonNode>> childNodesUuidAndTitleCache = taxonNodeService.listChildNodesAsUuidAndTitleCache(classification.getRootNode());

        assertNotNull("child UuidAndTitleCache list is null", childNodesUuidAndTitleCache);

        compareChildren(expectedChildTaxonNodes, childNodesUuidAndTitleCache);

        //test taxon parent of sub species

        Taxon abiesAlbaSubBrota = HibernateProxyHelper.deproxy(taxonService.load(abiesAlbaSubBrotaUuid), Taxon.class);

        TaxonNode abiesAlbaSubBrotaNode = abiesAlbaSubBrota.getTaxonNodes().iterator().next();

        TaxonNode expectedTaxonParent = HibernateProxyHelper.deproxy(abiesAlbaSubBrotaNode.getParent(), TaxonNode.class);

        UuidAndTitleCache<TaxonNode> taxonParent = taxonNodeService.getParentUuidAndTitleCache(abiesAlbaSubBrotaNode);

        assertEquals("Taxon Nodes do not match. ", expectedTaxonParent.getUuid(), taxonParent.getUuid());

        assertEquals("Taxon Nodes do not match. ", (Integer)expectedTaxonParent.getId(), taxonParent.getId());

        assertEquals("Taxon Nodes do not match. ", expectedTaxonParent.getTaxon().getTitleCache(), taxonParent.getTitleCache());

        assertEquals("Taxon Nodes do not match. ", expectedTaxonParent, taxonNodeService.load(taxonParent.getUuid()));

        //test classification parent

        Taxon abies = HibernateProxyHelper.deproxy(taxonService.load(abiesUuid), Taxon.class);

        TaxonNode abiesNode = abies.getTaxonNodes().iterator().next();

        TaxonNode expectedClassificationParent = HibernateProxyHelper.deproxy(abiesNode.getParent(), TaxonNode.class);

        UuidAndTitleCache<TaxonNode> classificationParent= taxonNodeService.getParentUuidAndTitleCache(abiesNode);

        assertEquals("Taxon Nodes do not match. ", expectedClassificationParent.getUuid(), classificationParent.getUuid());

        assertEquals("Taxon Nodes do not match. ", (Integer)expectedClassificationParent.getId(), classificationParent.getId());

        assertEquals("Taxon Nodes do not match. ", expectedClassificationParent.getClassification().getTitleCache(), classificationParent.getTitleCache());

        assertEquals("Taxon Nodes do not match. ", expectedClassificationParent, taxonNodeService.load(classificationParent.getUuid()));

    }

    private void compareChildren(List<TaxonNode> expectedChildTaxonNodes, List<UuidAndTitleCache<TaxonNode>> childNodesUuidAndTitleCache){

        assertEquals("Number of children does not match", expectedChildTaxonNodes.size(), childNodesUuidAndTitleCache.size());

        UuidAndTitleCache<TaxonNode> foundMatch = null;

        for (TaxonNode taxonNode : expectedChildTaxonNodes) {

            foundMatch = null;

            for (UuidAndTitleCache<TaxonNode> uuidAndTitleCache : childNodesUuidAndTitleCache) {

                if(uuidAndTitleCache.getUuid().equals(taxonNode.getUuid())){

                    String titleCache = taxonNode.getTaxon().getTitleCache();

                    if(uuidAndTitleCache.getTitleCache().equals(titleCache)){

                        foundMatch = uuidAndTitleCache;

                        break;

                    }

                }

            }

            assertTrue(String.format("no matching UuidAndTitleCache found for child %s", taxonNode), foundMatch!=null);

            compareChildren(taxonNode.getChildNodes(), taxonNodeService.listChildNodesAsUuidAndTitleCache(foundMatch));

        }

    }

    private UuidAndTitleCache<TaxonNode> findMatchingUuidAndTitleCache(List<UuidAndTitleCache<TaxonNode>> childNodesUuidAndTitleCache,

            UuidAndTitleCache<TaxonNode> foundMatch, TaxonNode taxonNode) {

        for (UuidAndTitleCache<TaxonNode> uuidAndTitleCache : childNodesUuidAndTitleCache) {

            if(uuidAndTitleCache.getUuid().equals(taxonNode.getUuid())){

                String titleCache = taxonNode.getTaxon().getTitleCache();

                if(uuidAndTitleCache.getTitleCache().equals(titleCache)){

                    foundMatch = uuidAndTitleCache;

                    break;

                }

            }

        }

        return foundMatch;

    }

    @Test

    @DataSet("TaxonNodeServiceImplTest.testSetSecundumForSubtree.xml")

    public void testSetSecundumForSubtree(){

        UUID subTreeUuid = UUID.fromString("484a1a77-689c-44be-8e65-347d835f47e8");

//        UUID taxon1uuid = UUID.fromString("55c3e41a-c629-40e6-aa6a-ff274ac6ddb1");

//        UUID taxon5uuid = UUID.fromString("d0b99fee-a783-4dda-b8a2-8960703cfcc2");

        Reference newSec = referenceService.find(UUID.fromString("1d3fb074-d7ba-47e4-be94-b4cb1a99afa7"));

        //assert current state

        Assert.assertNotNull(newSec);

        Assert.assertNull(taxonService.find(1).getSec());

        Assert.assertNull(taxonService.find(2).getSec());

        Assert.assertNull(taxonService.find(3).getSec());

        Assert.assertNull(taxonService.find(4).getSec());

        TaxonBase<?> taxon5 = taxonService.find(5);

        Assert.assertNotNull(taxon5.getSec());