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.model.taxon;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertFalse;

import static org.junit.Assert.assertNotNull;

import static org.junit.Assert.assertSame;

import static org.junit.Assert.assertTrue;

import java.util.Set;

import org.apache.log4j.Logger;

import org.junit.Assert;

import org.junit.Before;

import org.junit.BeforeClass;

import org.junit.Test;

import org.springframework.beans.BeanUtils;

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

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

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

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

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

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.Book;

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

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

import eu.etaxonomy.cdm.model.term.DefaultTermInitializer;

import eu.etaxonomy.cdm.test.unit.EntityTestBase;

public class TaxonTest extends EntityTestBase {

	@SuppressWarnings("unused")

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

	private Reference sec;

	private Reference misSec;

	private IZoologicalName name1;

	private IBotanicalName name2;

	private Taxon rootT;

	private Taxon child1;

	private Taxon child2;

	private Synonym syn1;

	private Synonym syn2;

	private IBotanicalName name3;

	private IBotanicalName name4;

	private Taxon freeT;

	private Taxon misTaxon1;

	private Taxon misTaxon2;

	@BeforeClass

	public static void setUpBeforeClass() {

		DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();

		vocabularyStore.initialize();

	}

	@Before

	public void setUp() throws Exception {

		Person linne =new Person("Carl", "Linné", "L.");

		sec= ReferenceFactory.newBook();

		sec.setAuthorship(linne);

		sec.setTitleCache("Schönes saftiges Allgäu", true);

		misSec = ReferenceFactory.newBook();

		misSec.setTitleCache("Stupid book", true);

		name1 = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES(),"Panthera",null,"onca",null,linne,null,"p.1467", null);

		name2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(),"Abies",null,"alba",null,linne,null,"p.317", null);

		name3 = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES(),"Polygala",null,"vulgaris","alpina",linne,null,"p.191", null);

		name4 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(),"Cichoria",null,"carminata",null,linne,null,"p.14", null);

		rootT = Taxon.NewInstance(name1,sec);

		freeT = Taxon.NewInstance(name4,sec);

		// taxonomic children

		child1 = Taxon.NewInstance(name2,sec);

		child2 = Taxon.NewInstance(name3,sec);

//		Classification newTree = Classification.NewInstance("testTree");

//		newTree.addParentChild(rootT, child1, sec, "p.998");

//		newTree.addParentChild(rootT, child2, sec, "p.987");

		// synonymy

		syn1=Synonym.NewInstance(name1,sec);

		syn2=Synonym.NewInstance(name2,sec);

		child1.addSynonym(syn1, SynonymType.HETEROTYPIC_SYNONYM_OF());

		child2.addSynonym(syn2, SynonymType.HOMOTYPIC_SYNONYM_OF());

		//misaplication

		misTaxon1 = Taxon.NewInstance(name4, misSec);

		misTaxon2 = Taxon.NewInstance(name4, misSec);

		rootT.addMisappliedName(misTaxon1, null, "99");

		child1.addMisappliedName(misTaxon2, null, "44");

	}

	@Test

	public void testGenerateTitle() {

		assertTrue(rootT.generateTitle().startsWith(rootT.getName().getTitleCache()));

	}

	@Test

	public void testIsMisappliedName() {

		assertFalse(child2.isMisapplication());

		assertFalse(rootT.isMisapplication());

		assertTrue(misTaxon1.isMisapplication());

		assertTrue(misTaxon2.isMisapplication());

	}

	@Test

	public void testGetSynonyms() {

		assertTrue(child1.getSynonyms().contains(syn1));

		assertTrue(child2.getSynonyms().contains(syn2));

		assertTrue(rootT.getSynonyms().isEmpty());

	}

	@Test

	public void testGetSynonymNames() {

		assertTrue(child1.getSynonymNames().contains(name1));

		assertTrue(child2.getSynonymNames().contains(name2));

		assertTrue(rootT.getSynonymNames().isEmpty());

	}

	@Test

	public void testAddSynonym() {

		freeT.addSynonym(syn1, SynonymType.HETEROTYPIC_SYNONYM_OF());

		assertTrue(freeT.getSynonyms().contains(syn1));

		assertTrue(syn1.getAcceptedTaxon().equals(freeT));

		assertFalse(freeT.getSynonyms().contains(syn2));

	}

	@Test

	public void testAddAndRemoveDescriptionTaxonDescription() {

		TaxonDescription desc = TaxonDescription.NewInstance();

		rootT.addDescription(desc);  //test if reflection method in addDescription() works

		assertTrue("The description has not properly been added to the taxon", rootT.getDescriptions().contains(desc));

		assertEquals("The taxon has not properly been added to the description", rootT, desc.getTaxon());

		rootT.removeDescription(desc); //test if reflection method in removeDescription() works

		assertFalse("The description has not properly been removed from the taxon", rootT.getDescriptions().contains(desc));

		assertEquals("The taxon has not properly been removed from the description", null, desc.getTaxon());

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getTaxonRelations()}.

	 */

	@Test

	public void testGetTaxonRelations() {

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

		taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);

		Set<TaxonRelationship> relationships = taxon.getTaxonRelations();

		assertTrue("There should be exactly one relationship", relationships.size() == 1);

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeTaxonRelation(eu.etaxonomy.cdm.model.taxon.TaxonRelationship)}.

	 */

	@Test

	public void testRemoveTaxonRelation() {

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

		taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);

		assertTrue("There should be exactly one taxon relationship", taxon.getTaxonRelations().size() == 1);

		TaxonRelationship relationship = (TaxonRelationship) taxon.getTaxonRelations().toArray()[0];

		assertNotNull("Relationship should not be null", relationship);

		taxon.removeTaxonRelation(relationship);

		assertTrue("There should be no taxon relationships", taxon.getTaxonRelations().size() == 0);

	}

	/**

	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addTaxonRelation(eu.etaxonomy.cdm.model.taxon.TaxonRelationship)}.

	 */

	@Test

	public void testAddTaxonRelationTaxonRelationship() {

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

		taxon.addTaxonRelation(Taxon.NewInstance(null, null), TaxonRelationshipType.CONTRADICTION(), null, null);

		assertTrue("There should be exactly one taxon relationship", taxon.getTaxonRelations().size() == 1);

		TaxonRelationship relationship = (TaxonRelationship) taxon.getTaxonRelations().toArray()[0];

		assertNotNull("Relationship should not be null", relationship);

		taxon.removeTaxonRelation(relationship);

		assertTrue("There should be no taxon relationships", taxon.getTaxonRelations().size() == 0);

		taxon.addTaxonRelation(relationship);

		assertEquals("There should be exactly one taxon relationships", 1, taxon.getTaxonRelations().size());

	}

    @Test

    public void testAddHomotypicSynonymName(){

        TaxonName taxonName = TaxonNameFactory.NewBotanicalInstance(null);

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

        TaxonName synonymName1 = TaxonNameFactory.NewBotanicalInstance(null);

        // add a synonym to the taxon

        Synonym synonym1 = taxon.addHomotypicSynonymName(synonymName1);

        // get the homotypic group of that synonym

        HomotypicalGroup homotypicGroupOfSynonym = synonym1.getHomotypicGroup();

        // everything is fine

        Assert.assertEquals("We should have two names in the homotypic group",

                2, homotypicGroupOfSynonym.getTypifiedNames().size());

    }

    @Test

    public void testAddHomotypicSynonym(){

        TaxonName taxonName = TaxonNameFactory.NewBotanicalInstance(null);

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

        TaxonName synonymName1 = TaxonNameFactory.NewBotanicalInstance(null);

        Synonym synonym = Synonym.NewInstance(synonymName1, null);

        // add a synonym to the taxon

        taxon.addHomotypicSynonym(synonym);

        //synonym type must be homotypic

        Assert.assertEquals("Synonym must be homotypic", SynonymType.HOMOTYPIC_SYNONYM_OF(), synonym.getType());

        // get the homotypic group of that synonym

        HomotypicalGroup homotypicGroupOfSynonym = synonym.getHomotypicGroup();

        // everything is fine

        Assert.assertEquals("We should have two names in the homotypic group",

                2, homotypicGroupOfSynonym.getTypifiedNames().size());

    }

	@Test

	public void testAddRemoveSynonymInSameGroup(){

		TaxonName taxonName = TaxonNameFactory.NewBotanicalInstance(null);

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

		TaxonName synonymName1 = TaxonNameFactory.NewBotanicalInstance(null);

		TaxonName synonymName2 = TaxonNameFactory.NewBotanicalInstance(null);

		// add a synonym to the taxon

		Synonym synonym1 = taxon.addHeterotypicSynonymName(synonymName1);

		// get the homotypic group of that synonym

		HomotypicalGroup homotypicGroupOfSynonym = synonym1.getHomotypicGroup();

		// add another synonym into the homotypic group we just created

		Synonym synonym2 = taxon.addHeterotypicSynonymName(synonymName2, null, null, homotypicGroupOfSynonym);

		// everything is fine

		Assert.assertEquals("We should have two synonyms in the group", 2, taxon.getSynonymsInGroup(homotypicGroupOfSynonym).size());

		// removing the synonym from the taxon

		taxon.removeSynonym(synonym2);

		// get the homotypical group via the methods in Taxon

		HomotypicalGroup homotypicGroupViaTaxon = taxon.getHeterotypicSynonymyGroups().iterator().next();

		// the group is for sure the same as the synonyms one

		Assert.assertSame("Accessing the homotypic group via the taxon methods should result in the same object",

		        homotypicGroupOfSynonym, homotypicGroupViaTaxon);

		// although it might be correct that the synonym is not deleted from the taxonomic group

		// we would not expect it to be here, since we just deleted it from the taxon and are accessing synonyms

		// via methods in Taxon

		Assert.assertEquals("When accessing the homotypic groups via taxon we would not expect the synonym we just deleted",

				1, taxon.getSynonymsInGroup(homotypicGroupViaTaxon).size());

	}

	@Test

	public void testClone(){

		Taxon clone = (Taxon)child2.clone();

		assertNotNull(clone);

		assertEquals(0,clone.getTaxonNodes().size());

		assertSame(clone.getName(), child2.getName());

	}

	@Test

	public void beanTests(){

//	    #5307 Test that BeanUtils does not fail

	    BeanUtils.getPropertyDescriptors(Taxon.class);

	    BeanUtils.getPropertyDescriptors(Synonym.class);

	}

}