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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.taxon;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotSame;
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import static org.junit.Assert.assertNull;
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import static org.junit.Assert.assertSame;
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import static org.junit.Assert.assertTrue;
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import java.lang.reflect.Field;
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import java.lang.reflect.Method;
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import java.lang.reflect.Modifier;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.springframework.beans.BeanUtils;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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//import eu.etaxonomy.cdm.model.reference.Book;
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//import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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/**
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* @author a.mueller
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* @since 01.04.2009
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*/
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public class ClassificationTest {
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private static final Logger logger = Logger.getLogger(ClassificationTest.class);
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private static String treeName1;
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private static Classification classification1;
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private static TaxonNode taxonNode1;
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private static TaxonNode taxonNode2;
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private static TaxonNode taxonNode3;
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private static TaxonNode taxonNode12;
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private static TaxonNode taxonNode121;
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private static Taxon taxon1;
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private static Taxon taxon2;
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private static Taxon taxon3;
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private static Taxon taxon12;
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private static Taxon taxon121;
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private static TaxonName taxonName1;
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private static TaxonName taxonName2;
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private static TaxonName taxonName3;
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private static TaxonName taxonName12;
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private static TaxonName taxonName121;
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private static Reference ref1;
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private static Reference ref2;
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private static Reference ref3;
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//private ReferenceFactory refFactory;
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/**
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* @throws java.lang.Exception
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*/
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@Before
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public void setUp() throws Exception {
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treeName1 = "Greuther, 1993";
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//refFactory = ReferenceFactory.newInstance();
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classification1 = Classification.NewInstance(treeName1);
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taxonName12 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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taxonName121 = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());
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taxonName1 = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
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taxonName2 = TaxonNameFactory.NewZoologicalInstance(Rank.GENUS());
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taxonName3 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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ref1 = ReferenceFactory.newJournal();
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ref2 = ReferenceFactory.newJournal();
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ref3 = ReferenceFactory.newJournal();
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taxon1 = Taxon.NewInstance(taxonName1, ref1);
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taxon2 = Taxon.NewInstance(taxonName2, ref2);
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taxon3 = Taxon.NewInstance(taxonName3, ref3);
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taxon12 = Taxon.NewInstance(taxonName12, ref3);
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taxon121 = Taxon.NewInstance(taxonName121, ref3);
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//taxonNode1 = new TaxonNode(taxon1, taxonomicView1);
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}
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//****************************** TESTS *****************************************/
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/**
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* Test method for {@link eu.etaxonomy.cdm.model.taxon.Classification#addRoot(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String, eu.etaxonomy.cdm.model.taxon.Synonym)}.
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*/
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@Test
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public void testAddRoot() {
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TaxonName synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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Synonym synonym = Synonym.NewInstance(synonymName, ref1);
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TaxonNode taxonNode1 = classification1.addChildTaxon(taxon1, null, null);
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taxonNode1.setSynonymToBeUsed(synonym);
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//test root node
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List<TaxonNode> rootNodes = classification1.getChildNodes();
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assertFalse("List of root nodes should not be empty", rootNodes.isEmpty());
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assertEquals("Number of root nodes should be 1", 1, rootNodes.size());
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TaxonNode root = rootNodes.iterator().next();
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assertEquals(taxon1, root.getTaxon());
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assertSame(taxonNode1, root);
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assertNull(root.getReference());
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assertNull(root.getMicroReference());
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assertEquals(synonym, root.getSynonymToBeUsed());
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//any node
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List<TaxonNode> allNodes = classification1.getChildNodes();
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assertFalse("List of root nodes should not be empty", allNodes.isEmpty());
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assertEquals("Number of root nodes should be 1", 1, allNodes.size());
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TaxonNode anyNode = allNodes.iterator().next();
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assertSame("Taxon for TaxonNode should be the same added to the view", taxon1, anyNode.getTaxon());
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assertSame("TaxonNode should be the same added to the view", taxonNode1, anyNode);
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}
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@Test
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public void testIsTaxonInTree() {
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classification1.addChildTaxon(taxon1, null, null);
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assertTrue(classification1.isTaxonInTree(taxon1));
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Taxon anyTaxon = Taxon.NewInstance(null, null);
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assertFalse(classification1.isTaxonInTree(anyTaxon));
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}
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@Test
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public void testMakeRootChildOfOtherNode() {
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TaxonNode root1 = classification1.addChildTaxon(taxon1, null, null);
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TaxonNode root2 = classification1.addChildTaxon(taxon2, null, null);
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Taxon taxon3 = Taxon.NewInstance(null, null);
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root2.addChildTaxon(taxon3, null, null);
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String microRef = "p55";
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assertFalse("Root1 must not yet be child of root 2", root2.getChildNodes().contains(root1));
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assertNotSame("Root2 must not yet be parent of root 1", root2, root1.getParent());
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assertEquals("view must contain 3 nodes", 3, classification1.getAllNodes().size());
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assertEquals("view must still contain 2 root", 2, classification1.getChildNodes().size());
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assertEquals("root2 must have 1 child", 1, root2.getChildNodes().size());
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classification1.makeTopmostNodeChildOfOtherNode(root1, root2, ref1, microRef);
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assertTrue("Root1 must be child of root 2", root2.getChildNodes().contains(root1));
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assertSame("Root2 must be parent of root 1", root2, root1.getParent());
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assertEquals("view must contain 3 nodes", 3, classification1.getAllNodes().size());
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assertEquals("view must contain 1 root", 1, classification1.getChildNodes().size());
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assertEquals("new child node must have the expected reference for parent child relationship", ref1, root1.getReference());
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assertEquals("new child node must have the expected micro reference for parent child relationship", microRef, root1.getMicroReference());
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assertEquals("root2 must have 2 children", 2, root2.getChildNodes().size());
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}
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@Test
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public void testIsTopmostInTree() {
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TaxonNode root = classification1.addChildTaxon(taxon1, null, null);
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assertTrue(classification1.isTaxonInTree(taxon1));
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assertTrue(classification1.isTopmostInTree(taxon1));
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Taxon anyTaxon = Taxon.NewInstance(null, null);
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assertFalse(classification1.isTaxonInTree(anyTaxon));
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assertFalse(classification1.isTopmostInTree(anyTaxon));
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Taxon child = Taxon.NewInstance(null, null);
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root.addChildTaxon(child, null, null);
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assertTrue(classification1.isTaxonInTree(child));
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assertFalse(classification1.isTopmostInTree(child));
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}
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@Test
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public void testGetTopmostNode() {
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TaxonNode root = classification1.addChildTaxon(taxon1, null, null);
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assertEquals(root, classification1.getTopmostNode(taxon1));
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Taxon anyTaxon = Taxon.NewInstance(null, null);
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assertFalse(classification1.isTaxonInTree(anyTaxon));
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assertNull(classification1.getTopmostNode(anyTaxon));
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Taxon child = Taxon.NewInstance(null, null);
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root.addChildTaxon(child, null, null);
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assertTrue(classification1.isTaxonInTree(child));
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assertNull(classification1.getTopmostNode(child));
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}
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@Test
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public void testAddParentChild() {
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TaxonName synonymName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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Synonym synonym = Synonym.NewInstance(synonymName, ref1);
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TaxonNode rootNode = classification1.addChildTaxon(taxon1, null, null);
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rootNode.setSynonymToBeUsed(synonym);
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Assert.assertEquals(0,rootNode.getChildNodes().size());
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//add child to existing root
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classification1.addParentChild(taxon1, taxon2, ref1, "Micro1");
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Assert.assertTrue(classification1.isTaxonInTree(taxon2));
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Assert.assertFalse(classification1.isTopmostInTree(taxon2));
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Assert.assertEquals(1,rootNode.getChildNodes().size());
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TaxonNode childNode = rootNode.getChildNodes().iterator().next();
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Assert.assertEquals(taxon2, childNode.getTaxon());
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//relationship already exists
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classification1.addParentChild(taxon1, taxon2, ref2, "Micro2");
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Assert.assertTrue(classification1.isTaxonInTree(taxon2));
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Assert.assertFalse(classification1.isTopmostInTree(taxon2));
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Assert.assertEquals(2, classification1.getAllNodes().size());
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Assert.assertEquals(1,rootNode.getChildNodes().size());
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childNode = rootNode.getChildNodes().iterator().next();
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Assert.assertEquals(taxon2, childNode.getTaxon());
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Assert.assertEquals(ref2, childNode.getReference());
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Assert.assertEquals("Micro2", childNode.getMicroReference());
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logger.info("testAddParentChild not yet fully implemented");
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}
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@Test
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public void testGenerateTitle() {
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Classification taxonomicViewLocal = Classification.NewInstance(treeName1);
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//Maybe changed if title cache is generated in a different way
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assertEquals(treeName1, taxonomicViewLocal.getTitleCache());
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}
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@Test
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public void play() {
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CdmBase referencedCdmBase = Person.NewInstance();
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Set<Class<? extends CdmBase>> allCdmClasses = findAllCdmClasses();
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Class<? extends CdmBase> referencedClass = referencedCdmBase.getClass();
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Set<CdmBase> result = new HashSet<CdmBase>();
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System.out.println("Referenced Class: " + referencedClass.getName());
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for (Class<? extends CdmBase> cdmClass : allCdmClasses){
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Set<Field> fields = getFields(cdmClass);
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for (Field field: fields){
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Class<?> type = field.getType();
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if (! type.isInterface()){
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if (referencedClass.isAssignableFrom(type)||
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type.isAssignableFrom(referencedClass) && CdmBase.class.isAssignableFrom(type)){
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handleSingleClass(referencedClass, type, field, cdmClass, result, referencedCdmBase);
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}
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}else{ //interface
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if (type.isAssignableFrom(referencedClass)){
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handleSingleClass(referencedClass, type, field, cdmClass, result, referencedCdmBase);
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}
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}
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// Class[] interfaces = referencedClass.getInterfaces();
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// for (Class interfaze: interfaces){
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// if (interfaze == type){
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//// if(interfaze.isAssignableFrom(returnType)){
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// }
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// }
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}
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}
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return ;
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// find(cdmClass, )
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}
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private boolean handleSingleClass(Class<?> classToBeSearchedFor, Class<?> type, Field field, Class<?> cdmClass, Set<CdmBase> result, CdmBase value){
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if (! Modifier.isStatic(field.getModifiers())){
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String methodName = StringUtils.rightPad(field.getName(), 30);
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String className = StringUtils.rightPad(cdmClass.getSimpleName(), 30);
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String returnTypeName = StringUtils.rightPad(type.getSimpleName(), 30);
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System.out.println(methodName + "\t\t" + className + "\t\t" + returnTypeName);
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// result_old.add(method);
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result.addAll(getCdmBasesByFieldAndClass(field, cdmClass, value));
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}
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return true;
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}
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private Set<Field> getFields(Class<?> clazz){
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Set<Field> result = new HashSet<Field>();
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for (Field field: clazz.getDeclaredFields()){
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if (!Modifier.isStatic(field.getModifiers())){
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result.add(field);
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}
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}
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Class<?> superclass = clazz.getSuperclass();
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if (CdmBase.class.isAssignableFrom(superclass)){
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result.addAll(getFields(superclass));
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}
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return result;
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}
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private Set<CdmBase> getCdmBasesByFieldAndClass(Field field, Class<?> clazz, CdmBase value){
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//FIXME make not dummy but use dao
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Set<CdmBase> result = new HashSet<>();
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//genericDao.getCdmBasesByFieldAndClass(clazz, field.getName(), value);
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
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name.setTitleCache("A dummy name", true);
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result.add(name);
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Reference ref = ReferenceFactory.newBook();
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ref.setTitleCache("A dummy book", true);
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result.add(ref);
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return result;
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}
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private Set<Class<? extends CdmBase>> findAllCdmClasses(){
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//init
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Set<Class<? extends CdmBase>> allCdmClasses = new HashSet<>();
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allCdmClasses.add(TaxonBase.class);
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allCdmClasses.add(TaxonName.class);
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int count;
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do{
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count = allCdmClasses.size();
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Set<Class<? extends CdmBase>> iteratorSet = new HashSet<>();
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iteratorSet.addAll(allCdmClasses);
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for (Class<? extends CdmBase> cdmClass : iteratorSet){
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Method[] methods = cdmClass.getMethods();
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for (Method method: methods){
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Class<?> returnType = method.getReturnType();
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handleClass(allCdmClasses,returnType);
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Class<?>[] params = method.getParameterTypes();
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for (Class<?> paramClass : params){
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handleClass(allCdmClasses, paramClass);
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}
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}
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}
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}
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while (allCdmClasses.size() > count);
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boolean withAbstract = false;
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if (! withAbstract){
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Iterator<Class<? extends CdmBase>> iterator = allCdmClasses.iterator();
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while (iterator.hasNext()){
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Class<?> clazz = iterator.next();
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if (Modifier.isAbstract(clazz.getModifiers())){
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iterator.remove();
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}
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}
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}
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return allCdmClasses;
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}
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private void handleClass(Set<Class<? extends CdmBase>> allCdmClasses, Class<?> returnType){
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if (CdmBase.class.isAssignableFrom(returnType)){
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if (! allCdmClasses.contains(returnType)){
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//System.out.println(returnType.getSimpleName());
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allCdmClasses.add((Class)returnType);
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Class<?> superClass = returnType.getSuperclass();
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handleClass(allCdmClasses, superClass);
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}
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}
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}
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@Test
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public void testCloneClassification(){
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taxonNode1 = classification1.addChildTaxon(taxon1, null, null);
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taxonName1.setTitleCache("name1", true);
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taxonName12.setTitleCache("name12", true);
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taxonName121.setTitleCache("name121", true);
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taxonName2.setTitleCache("name2", true);
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taxonName3.setTitleCache("name3", true);
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taxonNode12 = taxonNode1.addChildTaxon(taxon12, null, null);
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taxonNode121 = taxonNode12.addChildTaxon(taxon121, null, null);
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taxonNode2 = classification1.addChildTaxon(taxon2, null, null);
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taxonNode2.addChildTaxon(taxon3, null, null);
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Classification clone = (Classification)classification1.clone();
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assertEquals(classification1.getAllNodes().size(), clone.getAllNodes().size());
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TaxonNode cloneNode = clone.getNode(taxon1);
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assertNotSame(cloneNode, taxonNode1);
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}
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@Test
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public void beanTests(){
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// #5307 Test that BeanUtils does not fail
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BeanUtils.getPropertyDescriptors(Classification.class);
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}
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}
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