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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.api.service;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNull;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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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.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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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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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeByNameComparator;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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/**
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* @author n.hoffmann
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* @since Sep 22, 2009
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*/
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public class ClassificationServiceImplTest extends CdmTransactionalIntegrationTest{
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private static final Logger logger = Logger.getLogger(ClassificationServiceImplTest.class);
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@SpringBeanByType
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private IClassificationService service;
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private ITaxonNodeService taxonNodeService;
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private IClassificationDao classificationDao;
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@SpringBeanByType
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private IReferenceDao referenceDao;
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private static final List<String> NODE_INIT_STRATEGY = Arrays.asList(new String[]{
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"childNodes",
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"childNodes.taxon",
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"childNodes.taxon.name",
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"taxon.sec",
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"taxon.name.*"
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});
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private static final UUID CLASSIFICATION_UUID = UUID.fromString("6c2bc8d9-ee62-4222-be89-4a8e31770878");
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private Comparator<? super TaxonNode> taxonNodeComparator;
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private boolean includeUnpublished;
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@Before
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public void setUp() {
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includeUnpublished = true;
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.ClassificationServiceImpl#loadTaxonNodeByTaxon(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.UUID, java.util.List)}.
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*/
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@Test
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public final void testLoadTaxonNodeByTaxon() {
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logger.warn("testLoadTaxonNodeByTaxon not yet implemented");
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.ClassificationServiceImpl#loadTaxonNode(eu.etaxonomy.cdm.model.taxon.TaxonNode, java.util.List)}.
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*/
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@Test
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public final void testLoadTaxonNode() {
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logger.warn("testLoadTaxonNode not yet implemented");
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}
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@Test
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@DataSet
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public final void testTaxonNodeByNameComparator() {
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taxonNodeComparator = new TaxonNodeByNameComparator();
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List<TaxonNode> nodes = service.getAllNodes();
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Collections.sort(nodes, taxonNodeComparator);
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// logger.setLevel(Level.DEBUG);
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if(logger.isDebugEnabled()){
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logger.debug("-------------");
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for (TaxonNode node: nodes){
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if (node!= null && node.getTaxon() != null && node.getTaxon().getName()!= null){
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logger.debug(node.getTaxon().getName().getTitleCache() + " [" + node.getTaxon().getName().getRank() + "]");
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}
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}
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}
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Assert.assertEquals("Acacia N.Jacobsen, Bastm. & Yuji Sasaki", nodes.get(1).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia subgen. Aculeiferum Pedley", nodes.get(2).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia sect. Botrycephalae Yuji Sasaki", nodes.get(3).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia subgen. Phyllodineae N.Jacobsen, Bastm. & Yuji Sasaki", nodes.get(4).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia acicularis Willd.", nodes.get(5).getTaxon().getName().getTitleCache());
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Assert.assertEquals("×Acacia acicularis Willd. subsp. acicularis", nodes.get(6).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia cuspidifolia Maslin", nodes.get(7).getTaxon().getName().getTitleCache());
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Assert.assertEquals("Acacia mearnsii Benth", nodes.get(8).getTaxon().getName().getTitleCache());
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/*
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((TaxonNodeByNameComparator)taxonNodeComparator).setSortInfraGenericFirst(false);
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Collections.sort(taxonNodes, taxonNodeComparator);
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Assert.assertEquals("Acacia cuspidifolia Maslin", taxonNodes.get(0).getTaxon().getName().getTitleCache());
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System.err.println();
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for (TaxonNode node: taxonNodes){
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System.err.println(node.getTaxon().getName().getTitleCache() );
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/*for (TaxonNode child : node.getChildNodes()){
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System.err.println(child.getTaxon().getName().getTitleCache());
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}
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}*/
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// fail("Not yet implemented");
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}
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@Test
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@DataSet
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public final void testListRankSpecificRootNodes(){
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Classification classification = service.find(UUID.fromString("6c2bc8d9-ee62-4222-be89-4a8e31770878"));
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// classification, see createTestDataSet()
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// ClassificationRoot
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// |- Acacia N.Jacobsen, Bastm. & Yuji Sasaki [Genus]
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// | |-- Acacia subg. Aculeiferum Pedley [Subgenus]
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// | |-- Acacia subg. Phyllodineae N.Jacobsen, Bastm. & Yuji Sasaki [Subgenus]
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// | | |-- Acacia sect. Botrycephalae Yuji Sasaki [Section (Botany)]
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// | |------- Acacia cuspidifolia Maslin [Species]
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// | |------- Acacia mearnsii Benth [Species]
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// |---------- Acacia acicularis Willd. [Species]
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// |-- ×Acacia acicularis Willd. subsp. acicularis [Subspecies]
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//
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// for more historic Acacia taxonomy see http://lexikon.freenet.de/Akazien
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List<TaxonNode> taxonNodes = service.listRankSpecificRootNodes(null, null, null, includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, null, includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(4, taxonNodes.size());
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// also test if the pager works
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 10, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(4, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 1, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 2, NODE_INIT_STRATEGY);
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Assert.assertEquals(0, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(3, taxonNodes.size());
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// also test if the pager works
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, 10, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(3, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, 2, 1, NODE_INIT_STRATEGY);
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Assert.assertEquals(1, taxonNodes.size());
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}
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@Test
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@DataSet
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public final void testListRankSpecificRootNodes_withSubtree(){
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Classification classification = service.find(UUID.fromString("6c2bc8d9-ee62-4222-be89-4a8e31770878"));
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// classification, see createTestDataSet()
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// ClassificationRoot
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// |- Acacia N.Jacobsen, Bastm. & Yuji Sasaki [Genus]
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// | |-- Acacia subg. Aculeiferum Pedley [Subgenus]
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// | |-- Acacia subg. Phyllodineae N.Jacobsen, Bastm. & Yuji Sasaki [Subgenus]
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// | | |-- Acacia sect. Botrycephalae Yuji Sasaki [Section (Botany)]
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// | |------- Acacia cuspidifolia Maslin [Species]
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// | |------- Acacia mearnsii Benth [Species]
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// |---------- Acacia acicularis Willd. [Species]
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// |-- ×Acacia acicularis Willd. subsp. acicularis [Subspecies]
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//
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// for more historic Acacia taxonomy see http://lexikon.freenet.de/Akazien
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TaxonNode subtree = taxonNodeService.find(UUID.fromString("bcdf945f-1f02-423e-883d-fe89e0af93e4"));
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List<TaxonNode> taxonNodes = service.listRankSpecificRootNodes(null, subtree, null, includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, null, includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(4, taxonNodes.size());
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// also test if the pager works
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 10, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(4, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 1, NODE_INIT_STRATEGY);
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Assert.assertEquals(2, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SECTION_BOTANY(), includeUnpublished, 2, 2, NODE_INIT_STRATEGY);
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Assert.assertEquals(0, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, null, null, NODE_INIT_STRATEGY);
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Assert.assertEquals(3, taxonNodes.size());
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// also test if the pager works
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, 10, 0, NODE_INIT_STRATEGY);
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Assert.assertEquals(3, taxonNodes.size());
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taxonNodes = service.listRankSpecificRootNodes(classification, null, Rank.SPECIES(), includeUnpublished, 2, 1, NODE_INIT_STRATEGY);
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Assert.assertEquals(1, taxonNodes.size());
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.api.service.ClassificationServiceImpl#setDao(eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao)}.
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*/
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@Test
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public final void testSetDaoIClassificationDao() {
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Assert.assertNotNull(service);
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}
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@Test
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@DataSet
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public final void testGroupTaxaByHigherTaxon(){
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Rank minRank = Rank.GENUS();
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Rank maxRank = Rank.KINGDOM();
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List<UUID> taxonUuids = new ArrayList<>();
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taxonUuids.add(acacia_acicularis_uuid);
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taxonUuids.add(acacia_cuspidifolia_uuid);
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taxonUuids.add(acacia_sect_botrycephalae_uuid);
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List<GroupedTaxonDTO> result = this.service.groupTaxaByHigherTaxon(taxonUuids, CLASSIFICATION_UUID, minRank, maxRank);
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System.out.println(result);
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Assert.assertEquals(3, result.size());
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//acacia_acicularis_uuid //is a root taxon with no parents
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Assert.assertEquals(acacia_acicularis_uuid, result.get(0).getTaxonUuid());
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Assert.assertNull(result.get(0).getGroupTaxonUuid());
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Assert.assertTrue(StringUtils.isBlank(result.get(0).getGroupTaxonName()));
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//acacia_cuspidifolia_uuid
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Assert.assertEquals(acacia_cuspidifolia_uuid, result.get(1).getTaxonUuid());
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Assert.assertNotNull(result.get(1).getGroupTaxonUuid());
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Assert.assertFalse(StringUtils.isBlank(result.get(1).getGroupTaxonName()));
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//acacia_sect_botrycephalae_uuid
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Assert.assertEquals(acacia_sect_botrycephalae_uuid, result.get(2).getTaxonUuid());
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Assert.assertNotNull(result.get(2).getGroupTaxonUuid());
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Assert.assertFalse(StringUtils.isBlank(result.get(2).getGroupTaxonName()));
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}
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@Test
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@DataSet
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public final void testCloneClassification(){
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Classification classification = classificationDao.load(CLASSIFICATION_UUID);
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Reference sec = ReferenceFactory.newGeneric();
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sec.setTitle("cloned sec");
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Classification clone = (Classification) classificationService.cloneClassification(CLASSIFICATION_UUID, "Cloned classification", sec, TaxonRelationshipType.CONGRUENT_TO()).getCdmEntity();
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List<TaxonNode> childNodes = classification.getChildNodes();
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for (TaxonNode taxonNode : childNodes) {
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System.out.println(taxonNode.getTaxon().getTitleCache());
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}
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childNodes = clone.getChildNodes();
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for (TaxonNode taxonNode : childNodes) {
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System.out.println(taxonNode.getTaxon().getTitleCache());
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}
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Set<TaxonNode> allNodes = classification.getAllNodes();
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assertEquals("# of direct children does not match", classification.getChildNodes().size(), clone.getChildNodes().size());
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assertEquals("# of all nodes does not match", allNodes.size(), clone.getAllNodes().size());
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//check that original taxon does not appear in cloned classification
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313
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for (TaxonNode taxonNode : allNodes) {
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314
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assertNull(clone.getNode(taxonNode.getTaxon()));
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315
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}
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316
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}
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317
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318
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319
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private UUID acacia_acicularis_uuid = UUID.fromString("90ad2d8f-19a9-4a10-bab3-7d1de5ce1968");
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320
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private UUID acacia_cuspidifolia_uuid = UUID.fromString("94123e4d-da49-4ed0-9d59-f52a9f7a3618");
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321
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private UUID acacia_sect_botrycephalae_uuid = UUID.fromString("2c73a166-35d1-483d-b8e8-209214cb6193");
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322
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323
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324
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/**
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325
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* {@inheritDoc}
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326
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*/
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327
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@Override
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328
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// @Test
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329
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public void createTestDataSet() throws FileNotFoundException {
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330
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331
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// ClassificationRoot
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332
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// |- Acacia N.Jacobsen, Bastm. & Yuji Sasaki [Genus]
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333
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// | |-- Acacia subg. Aculeiferum Pedley [Subgenus]
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334
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// | |-- Acacia subg. Phyllodineae N.Jacobsen, Bastm. & Yuji Sasaki [Subgenus]
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335
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// | | |-- Acacia sect. Botrycephalae Yuji Sasaki [Section (Botany)]
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336
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// | |------- Acacia cuspidifolia Maslin [Species]
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337
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// | |------- Acacia mearnsii Benth [Species]
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338
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// |---------- Acacia acicularis Willd. [Species]
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339
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// |-- ×Acacia acicularis Willd. subsp. acicularis [Subspecies]
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340
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//
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341
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// for more historic Acacia taxonomy see http://lexikon.freenet.de/Akazien
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342
|
|
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343
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// 1. create the entities and save them
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344
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Classification classification = Classification.NewInstance("Acacia Classification");
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345
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classification.setUuid(CLASSIFICATION_UUID);
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346
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classificationDao.save(classification);
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347
|
|
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348
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Reference sec = ReferenceFactory.newBook();
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349
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sec.setTitleCache("Sp. Pl.", true);
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|
350
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referenceDao.save(sec);
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351
|
|
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352
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IBotanicalName acacia_n = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS(), "Acacia", null, null, null, null, sec, null, null);
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353
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acacia_n.setAuthorshipCache("N.Jacobsen, Bastm. & Yuji Sasaki", true);
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354
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Taxon acacia_t = Taxon.NewInstance(acacia_n, sec);
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|
355
|
acacia_t.setUuid(UUID.fromString("2fc779ee-7a9d-4586-92ba-1cd774ac77f0"));
|
|
356
|
|
|
357
|
IBotanicalName acacia_subg_aculeiferum_n = TaxonNameFactory.NewBotanicalInstance(Rank.SUBGENUS(), "Acacia", "Aculeiferum", null, null, null, sec, null, null);
|
|
358
|
acacia_subg_aculeiferum_n.setAuthorshipCache("Pedley", true);
|
|
359
|
Taxon acacia_subg_aculeiferum_t = Taxon.NewInstance(acacia_subg_aculeiferum_n, sec);
|
|
360
|
acacia_subg_aculeiferum_t.setUuid(UUID.fromString("169fea08-6b7a-4315-b111-a774c7fafe30"));
|
|
361
|
|
|
362
|
IBotanicalName acacia_subg_phyllodineae_n = TaxonNameFactory.NewBotanicalInstance(Rank.SUBGENUS(), "Acacia", "Phyllodineae", null, null, null, sec, null, null);
|
|
363
|
acacia_subg_phyllodineae_n.setAuthorshipCache("N.Jacobsen, Bastm. & Yuji Sasaki", true);
|
|
364
|
Taxon acacia_subg_phyllodineae_t = Taxon.NewInstance(acacia_subg_phyllodineae_n, sec);
|
|
365
|
acacia_subg_phyllodineae_t.setUuid(UUID.fromString("a9da5d43-517e-4ca5-a490-b6a5cd637e9e"));
|
|
366
|
|
|
367
|
IBotanicalName acacia_setc_botrycephalae_n = TaxonNameFactory.NewBotanicalInstance(Rank.SECTION_BOTANY(), "Acacia", "Botrycephalae", null, null, null, sec, null, null);
|
|
368
|
acacia_setc_botrycephalae_n.setAuthorshipCache("Yuji Sasaki", true);
|
|
369
|
Taxon acacia_sect_botrycephalae_t = Taxon.NewInstance(acacia_setc_botrycephalae_n, sec);
|
|
370
|
acacia_sect_botrycephalae_t.setUuid(acacia_sect_botrycephalae_uuid);
|
|
371
|
|
|
372
|
IBotanicalName acacia_cuspidifolia_n = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(), "Acacia", null,"cuspidifolia", null, null, sec, null, null);
|
|
373
|
acacia_cuspidifolia_n.setAuthorshipCache("Maslin", true);
|
|
374
|
Taxon acacia_cuspidifolia_t = Taxon.NewInstance(acacia_cuspidifolia_n, sec);
|
|
375
|
acacia_cuspidifolia_t.setUuid(acacia_cuspidifolia_uuid);
|
|
376
|
|
|
377
|
IBotanicalName acacia_mearnsii_n = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(), "Acacia", null,"mearnsii", null, null, sec, null, null);
|
|
378
|
acacia_mearnsii_n.setAuthorshipCache("Benth", true);
|
|
379
|
Taxon acacia_mearnsii_t = Taxon.NewInstance(acacia_mearnsii_n, sec);
|
|
380
|
acacia_mearnsii_t.setUuid(UUID.fromString("2e55dc01-71f5-4d42-9bb0-a2448e46dd18"));
|
|
381
|
|
|
382
|
IBotanicalName acacia_acicularis_n = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(), "Acacia", null,"acicularis", null, null, sec, null, null);
|
|
383
|
acacia_acicularis_n.setAuthorshipCache("Willd.", true);
|
|
384
|
Taxon acacia_acicularis_t = Taxon.NewInstance(acacia_acicularis_n, sec);
|
|
385
|
acacia_acicularis_t.setUuid(acacia_acicularis_uuid);
|
|
386
|
|
|
387
|
IBotanicalName xacacia_acicularis_n = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES(), "Acacia", null,"acicularis", "acicularis", null, sec, null, null);
|
|
388
|
xacacia_acicularis_n.setAuthorshipCache("Willd.", true);
|
|
389
|
xacacia_acicularis_n.setMonomHybrid(true);
|
|
390
|
System.out.println(xacacia_acicularis_n.getTitleCache());
|
|
391
|
Taxon xacacia_acicularis_t = Taxon.NewInstance(xacacia_acicularis_n, sec);
|
|
392
|
xacacia_acicularis_t.setUuid(UUID.fromString("04d125a6-6adf-4900-97ff-82729618086a"));
|
|
393
|
|
|
394
|
TaxonNode acacia_tn = classification.addChildTaxon(acacia_t, sec, null);
|
|
395
|
TaxonNode acacia_subg_phyllodineae_tn = acacia_tn.addChildTaxon(acacia_subg_phyllodineae_t, sec, null);
|
|
396
|
acacia_subg_phyllodineae_tn.addChildTaxon(acacia_sect_botrycephalae_t, sec, null);
|
|
397
|
acacia_tn.addChildTaxon(acacia_subg_aculeiferum_t, sec, null);
|
|
398
|
acacia_tn.addChildTaxon(acacia_mearnsii_t, sec, null).addChildTaxon(xacacia_acicularis_t, sec, null);
|
|
399
|
acacia_tn.addChildTaxon(acacia_cuspidifolia_t, sec, null);
|
|
400
|
classification.addChildTaxon(acacia_acicularis_t, sec, null);
|
|
401
|
|
|
402
|
classificationDao.save(classification);
|
|
403
|
|
|
404
|
// 2. end the transaction so that all data is actually written to the db
|
|
405
|
setComplete();
|
|
406
|
endTransaction();
|
|
407
|
|
|
408
|
// use the fileNameAppendix if you are creating a data set file which need to be named differently
|
|
409
|
// from the standard name. For example if a single test method needs different data then the other
|
|
410
|
// methods the test class you may want to set the fileNameAppendix when creating the data for this method.
|
|
411
|
String fileNameAppendix = null;
|
|
412
|
|
|
413
|
// 3.
|
|
414
|
writeDbUnitDataSetFile(new String[] {
|
|
415
|
"TAXONBASE", "TAXONNAME",
|
|
416
|
"REFERENCE",
|
|
417
|
"CLASSIFICATION", "TAXONNODE",
|
|
418
|
"LANGUAGESTRING", "HOMOTYPICALGROUP",
|
|
419
|
"HIBERNATE_SEQUENCES" // IMPORTANT!!!
|
|
420
|
},
|
|
421
|
fileNameAppendix, true );
|
|
422
|
|
|
423
|
}
|
|
424
|
}
|