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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.io.owl.in;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import java.io.FileNotFoundException;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.List;
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import java.util.Set;
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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.SpringBeanByName;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.ITermTreeService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
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import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportConfigurator;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.persistence.dto.TermDto;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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/**
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* @author pplitzner
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* @since Apr 24, 2019
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*/
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public class StructureTreeOwlImportTest extends CdmTransactionalIntegrationTest {
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@SpringBeanByName
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private CdmApplicationAwareDefaultImport<?> defaultImport;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private ITermTreeService featureTreeService;
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@SpringBeanByType
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private IVocabularyService vocabularyService;
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@Before
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public void setUp() {
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}
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@Test
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public void testInit() {
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assertNotNull("import should not be null", defaultImport);
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}
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@Test
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@DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
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public void testImportStructureTree() throws URISyntaxException {
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URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/test_structures.owl");
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URI uri = URI.fromUrl(url);
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assertNotNull(url);
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StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
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boolean result = defaultImport.invoke(configurator).isSuccess();
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assertTrue("Return value for import.invoke should be true", result);
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this.setComplete();
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this.endTransaction();
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String treeLabel = "test_structures";
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List<TermTree> trees = featureTreeService.listByTitle(TermTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
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List<String> nodeProperties = new ArrayList<>();
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nodeProperties.add("term");
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nodeProperties.add("term.media");
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TermTree<Feature> tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
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assertNotNull("featureTree should not be null", tree);
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assertEquals("Tree has wrong term type", TermType.Structure, tree.getTermType());
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assertEquals("Wrong number of distinct features", 4, tree.getDistinctTerms().size());
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List rootChildren = tree.getRootChildren();
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assertEquals("Wrong number of root children", 1, rootChildren.size());
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Object entirePlant = rootChildren.iterator().next();
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assertTrue("Root is no feature node", entirePlant instanceof TermNode);
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assertEquals("Root node has wrong term type", TermType.Structure, ((TermNode)entirePlant).getTermType());
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TermNode<DefinedTerm> entirePlantNode = (TermNode<DefinedTerm>) entirePlant;
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List<TermNode<DefinedTerm>> childNodes = entirePlantNode.getChildNodes();
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assertEquals("Wrong number of children", 2, childNodes.size());
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String inflorescenceLabel = "inflorescence";
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String inflorescenceDescription = " the part of the plant that bears the flowers, including all its bracts branches and flowers but excluding unmodified leaves ";
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List<DefinedTerm> records = termService.findByRepresentationText(inflorescenceDescription, DefinedTerm.class, null, null).getRecords();
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assertEquals("wrong number of terms found for \"inflorescence\"", 1, records.size());
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DefinedTerm inflorescence = records.iterator().next();
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assertEquals(inflorescenceLabel, inflorescence.getLabel(Language.ENGLISH()));
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for (TermNode<DefinedTerm> termNode : childNodes) {
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assertTrue("Child node not found. Found node with term: "+termNode.getTerm().getLabel(),
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termNode.getTerm().getUuid().equals(inflorescence.getUuid())
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|| termNode.getTerm().getLabel(Language.ENGLISH()).equals("Flower"));
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if(termNode.getTerm().getUuid().equals(inflorescence.getUuid())){
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assertEquals("Term mismatch", inflorescence, termNode.getTerm());
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inflorescence = termNode.getTerm();
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assertEquals("wrong id in vocabulary", "inflorescence", inflorescence.getIdInVocabulary());
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assertEquals("wrong symbol", "infloSymbol", inflorescence.getSymbol());
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assertEquals("wrong symbol2", "infloSymbol2", inflorescence.getSymbol2());
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Set<Media> mediaSet = inflorescence.getMedia();
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assertEquals("wrong number of media", 1, mediaSet.size());
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Media media = mediaSet.iterator().next();
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MediaRepresentationPart part = MediaUtils.getFirstMediaRepresentationPart(media);
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assertNotNull("media part not found", part);
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assertEquals("incorrect URI", URI.create("https://upload.wikimedia.org/wikipedia/commons/8/82/Aloe_hereroensis_Auob_C15.JPG"), part.getUri());
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assertEquals("incorrect title", "Aloe hereroensis", media.getTitle(Language.DEFAULT()).getText());
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Representation englishRepresentation = inflorescence.getRepresentation(Language.ENGLISH());
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assertTrue("Description not found", CdmUtils.isNotBlank(englishRepresentation.getDescription()));
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assertEquals("Description wrong", inflorescenceDescription, englishRepresentation.getDescription());
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assertEquals("wrong plural", "inflorescences", englishRepresentation.getPlural());
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assertEquals("wrong label abbrev", "inflo", englishRepresentation.getAbbreviatedLabel());
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// german representation
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assertEquals("wrong number of representations", 2, inflorescence.getRepresentations().size());
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Representation germanRepresentation = inflorescence.getRepresentation(Language.GERMAN());
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assertNotNull("Representation is null for "+Language.GERMAN(), germanRepresentation);
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assertEquals("wrong description", "Der Teil der Pflanze, der die Bluete traegt", germanRepresentation.getDescription());
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assertEquals("wrong label", "Infloreszenz", germanRepresentation.getLabel());
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}
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}
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assertNotNull("term is null", inflorescence);
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assertEquals("Wrong term type", TermType.Structure, inflorescence.getTermType());
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String vocLabel = "03 Generative Structures";
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List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
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assertEquals("wrong number of vocabularies", 1, vocs.size());
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TermVocabulary termVoc = vocs.iterator().next();
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assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
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Collection<TermDto> topLevelTerms = vocabularyService.getTopLevelTerms(termVoc.getUuid());
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assertEquals("wrong number of top level terms", 4, topLevelTerms.size());
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}
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@Test
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@DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
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public void testImportPropertyTreeAndVocabulary() throws URISyntaxException {
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URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/properties.owl");
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URI uri = URI.fromUrl(url);
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assertNotNull(url);
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StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
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boolean result = defaultImport.invoke(configurator).isSuccess();
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assertTrue("Return value for import.invoke should be true", result);
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this.setComplete();
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this.endTransaction();
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String treeLabel = "properties 1.0";
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List<TermTree> trees = featureTreeService.listByTitle(TermTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
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List<String> nodeProperties = new ArrayList<>();
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nodeProperties.add("term");
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TermTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
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assertNotNull("featureTree should not be null", tree);
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assertEquals("Tree has wrong term type", TermType.Property, tree.getTermType());
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assertEquals("Wrong number of distinct features", 12, tree.getDistinctTerms().size());
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List rootChildren = tree.getRootChildren();
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String vocLabel = "Plant Glossary Properties";
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List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
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assertEquals("wrong number of vocabularies", 1, vocs.size());
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TermVocabulary termVoc = vocs.iterator().next();
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assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
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assertEquals(82, termVoc.getTerms().size());
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Set<DefinedTermBase> terms = termVoc.getTerms();
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for (DefinedTermBase definedTermBase : terms) {
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List<String> termProperties = new ArrayList<>();
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termProperties.add("sources");
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definedTermBase = termService.load(definedTermBase.getUuid(), termProperties);
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Set<IdentifiableSource> sources = definedTermBase.getSources();
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assertTrue("Import source is missing for term: "+definedTermBase, !sources.isEmpty());
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assertTrue("import source type not found", sources.stream().anyMatch(source->OriginalSourceType.Import.getKey().equals(source.getType().getKey())));
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}
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}
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@Override
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public void createTestDataSet() throws FileNotFoundException {}
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}
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