cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/owl/in/StructureTreeOwlImportTest.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.owl.in;
  11
  12 import static org.junit.Assert.assertEquals;
  13 import static org.junit.Assert.assertNotNull;
  14 import static org.junit.Assert.assertTrue;
  15
  16 import java.io.FileNotFoundException;
  17 import java.net.URI;
  18 import java.net.URISyntaxException;
  19 import java.net.URL;
  20 import java.util.ArrayList;
  21 import java.util.Arrays;
  22 import java.util.List;
  23
  24 import org.junit.Before;
  25 import org.junit.Test;
  26 import org.unitils.dbunit.annotation.DataSet;
  27 import org.unitils.spring.annotation.SpringBeanByType;
  28
  29 import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
  30 import eu.etaxonomy.cdm.api.service.ITermService;
  31 import eu.etaxonomy.cdm.api.service.IVocabularyService;
  32 import eu.etaxonomy.cdm.common.CdmUtils;
  33 import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImport;
  34 import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportConfigurator;
  35 import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportState;
  36 import eu.etaxonomy.cdm.model.common.Language;
  37 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  38 import eu.etaxonomy.cdm.model.term.FeatureNode;
  39 import eu.etaxonomy.cdm.model.term.FeatureTree;
  40 import eu.etaxonomy.cdm.model.term.Representation;
  41 import eu.etaxonomy.cdm.model.term.TermType;
  42 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  43 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  44 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  45
  46 /**
  47  *
  48  * @author pplitzner
  49  * @since Apr 24, 2019
  50  *
  51  */
  52 public class StructureTreeOwlImportTest extends CdmTransactionalIntegrationTest {
  53
  54     @SpringBeanByType
  55     private StructureTreeOwlImport structureTreeImport;
  56
  57     @SpringBeanByType
  58     private ITermService termService;
  59
  60     @SpringBeanByType
  61     private IFeatureTreeService featureTreeService;
  62
  63     @SpringBeanByType
  64     private IVocabularyService vocabularyService;
  65
  66     private StructureTreeOwlImportConfigurator configurator;
  67
  68     private FeatureTree tree;
  69
  70     @Before
  71     public void setUp() throws URISyntaxException {
  72         URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/test_structures.owl");
  73                 URI uri = url.toURI();
  74                 assertNotNull(url);
  75                 configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
  76     }
  77
  78     @Test
  79     public void testInit() {
  80         assertNotNull("structureTreeImport should not be null", structureTreeImport);
  81     }
  82
  83     @Test
  84     @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
  85     public void testDoInvoke() {
  86         StructureTreeOwlImportState state = configurator.getNewState();
  87         structureTreeImport.doInvoke(state);
  88         this.setComplete();
  89         this.endTransaction();
  90
  91         String treeLabel = "test_structures";
  92         List<FeatureTree> trees = featureTreeService.listByTitle(FeatureTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
  93         List<String> nodeProperties = new ArrayList<>();
  94         nodeProperties.add("term");
  95         tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
  96         assertNotNull("featureTree should not be null", tree);
  97
  98         assertEquals("Tree has wrong term type", TermType.Structure, tree.getTermType());
  99         assertEquals("Wrong number of distinct features", 4, tree.getDistinctFeatures().size());
 100         List rootChildren = tree.getRootChildren();
 101         assertEquals("Wrong number of root children", 1, rootChildren.size());
 102         Object entirePlant = rootChildren.iterator().next();
 103         assertTrue("Root is no feature node", entirePlant instanceof FeatureNode);
 104         assertEquals("Root node has wrong term type", TermType.Structure, ((FeatureNode)entirePlant).getTermType());
 105         FeatureNode<DefinedTerm> entirePlantNode = (FeatureNode<DefinedTerm>) entirePlant;
 106         List<FeatureNode<DefinedTerm>> childNodes = entirePlantNode.getChildNodes();
 107         assertEquals("Wrong number of children", 2, childNodes.size());
 108
 109         String inflorescenceLabel = "inflorescence";
 110         String inflorescenceDescription = " the part of the plant that bears the flowers, including all its bracts  branches and flowers  but excluding unmodified leaves               ";
 111         List<DefinedTerm> records = termService.findByRepresentationText(inflorescenceDescription, DefinedTerm.class, null, null).getRecords();
 112         assertEquals("wrong number of terms found for \"inflorescence\"", 1, records.size());
 113         DefinedTerm inflorescence = records.iterator().next();
 114         assertEquals(inflorescenceLabel, inflorescence.getLabel(Language.ENGLISH()));
 115
 116         for (FeatureNode<DefinedTerm> featureNode : childNodes) {
 117             assertTrue("Child node not found. Found node with term: "+featureNode.getTerm().getLabel(),
 118                     featureNode.getTerm().getUuid().equals(inflorescence.getUuid())
 119                     || featureNode.getTerm().getLabel(Language.ENGLISH()).equals("Flower"));
 120             if(featureNode.getTerm().getUuid().equals(inflorescence.getUuid())){
 121                 assertEquals("Term mismatch", inflorescence, featureNode.getTerm());
 122                 inflorescence = featureNode.getTerm();
 123
 124                 String englishDescription = inflorescence.getDescription(Language.ENGLISH());
 125                 assertTrue("Description not found", CdmUtils.isNotBlank(englishDescription));
 126                 assertEquals("Description wrong", inflorescenceDescription, englishDescription);
 127                 assertEquals("wrong number of representations", 2, inflorescence.getRepresentations().size());
 128                 Representation germanRepresentation = inflorescence.getRepresentation(Language.GERMAN());
 129                 assertNotNull("Representation is null for "+Language.GERMAN(), germanRepresentation);
 130                 assertEquals("wrong description", "Der Teil der Pflanze, der die Bluete traegt", germanRepresentation.getDescription());
 131                 assertEquals("wrong label", "Infloreszenz", germanRepresentation.getLabel());
 132             }
 133         }
 134         assertNotNull("term is null", inflorescence);
 135         assertEquals("Wrong term type", TermType.Structure, inflorescence.getTermType());
 136
 137         String vocLabel = "03 Generative Structures";
 138         List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
 139         assertEquals("wrong number of vocabularies", 1, vocs.size());
 140         TermVocabulary termVoc = vocs.iterator().next();
 141         assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
 142         assertEquals(3, termVoc.getTerms().size());
 143         assertTrue("Term not included in vocabulary", termVoc.getTerms().contains(inflorescence));
 144
 145     }
 146
 147     @Override
 148     public void createTestDataSet() throws FileNotFoundException {}
 149
 150
 151 }