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.SpringBeanByName;
  28 import org.unitils.spring.annotation.SpringBeanByType;
  29
  30 import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
  31 import eu.etaxonomy.cdm.api.service.ITermService;
  32 import eu.etaxonomy.cdm.api.service.IVocabularyService;
  33 import eu.etaxonomy.cdm.common.CdmUtils;
  34 import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
  35 import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportConfigurator;
  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     @SpringBeanByName
  55     private CdmApplicationAwareDefaultImport<?> defaultImport;
  56
  57     @SpringBeanByType
  58     private ITermService termService;
  59
  60     @SpringBeanByType
  61     private IFeatureTreeService featureTreeService;
  62
  63     @SpringBeanByType
  64     private IVocabularyService vocabularyService;
  65
  66     @Before
  67     public void setUp() {
  68     }
  69
  70     @Test
  71     public void testInit() {
  72         assertNotNull("import should not be null", defaultImport);
  73     }
  74
  75     @Test
  76     @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
  77     public void testImportStructureTree() throws URISyntaxException {
  78         URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/test_structures.owl");
  79         URI uri = url.toURI();
  80         assertNotNull(url);
  81         StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
  82
  83         boolean result = defaultImport.invoke(configurator).isSuccess();
  84         assertTrue("Return value for import.invoke should be true", result);
  85         this.setComplete();
  86         this.endTransaction();
  87
  88         String treeLabel = "test_structures";
  89         List<FeatureTree> trees = featureTreeService.listByTitle(FeatureTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
  90         List<String> nodeProperties = new ArrayList<>();
  91         nodeProperties.add("term");
  92         FeatureTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
  93         assertNotNull("featureTree should not be null", tree);
  94
  95         assertEquals("Tree has wrong term type", TermType.Structure, tree.getTermType());
  96         assertEquals("Wrong number of distinct features", 4, tree.getDistinctFeatures().size());
  97         List rootChildren = tree.getRootChildren();
  98         assertEquals("Wrong number of root children", 1, rootChildren.size());
  99         Object entirePlant = rootChildren.iterator().next();
 100         assertTrue("Root is no feature node", entirePlant instanceof FeatureNode);
 101         assertEquals("Root node has wrong term type", TermType.Structure, ((FeatureNode)entirePlant).getTermType());
 102         FeatureNode<DefinedTerm> entirePlantNode = (FeatureNode<DefinedTerm>) entirePlant;
 103         List<FeatureNode<DefinedTerm>> childNodes = entirePlantNode.getChildNodes();
 104         assertEquals("Wrong number of children", 2, childNodes.size());
 105
 106         String inflorescenceLabel = "inflorescence";
 107         String inflorescenceDescription = " the part of the plant that bears the flowers, including all its bracts  branches and flowers  but excluding unmodified leaves               ";
 108         List<DefinedTerm> records = termService.findByRepresentationText(inflorescenceDescription, DefinedTerm.class, null, null).getRecords();
 109         assertEquals("wrong number of terms found for \"inflorescence\"", 1, records.size());
 110         DefinedTerm inflorescence = records.iterator().next();
 111         assertEquals(inflorescenceLabel, inflorescence.getLabel(Language.ENGLISH()));
 112
 113         for (FeatureNode<DefinedTerm> featureNode : childNodes) {
 114             assertTrue("Child node not found. Found node with term: "+featureNode.getTerm().getLabel(),
 115                     featureNode.getTerm().getUuid().equals(inflorescence.getUuid())
 116                     || featureNode.getTerm().getLabel(Language.ENGLISH()).equals("Flower"));
 117             if(featureNode.getTerm().getUuid().equals(inflorescence.getUuid())){
 118                 assertEquals("Term mismatch", inflorescence, featureNode.getTerm());
 119                 inflorescence = featureNode.getTerm();
 120
 121                 assertEquals("wrong id in vocabulary", "inflorescence", inflorescence.getIdInVocabulary());
 122                 assertEquals("wrong symbol", "infloSymbol", inflorescence.getSymbol());
 123                 assertEquals("wrong symbol2", "infloSymbol2", inflorescence.getSymbol2());
 124
 125                 Representation englishRepresentation = inflorescence.getRepresentation(Language.ENGLISH());
 126                 assertTrue("Description not found", CdmUtils.isNotBlank(englishRepresentation.getDescription()));
 127                 assertEquals("Description wrong", inflorescenceDescription, englishRepresentation.getDescription());
 128                 assertEquals("wrong plural", "inflorescences", englishRepresentation.getPlural());
 129                 assertEquals("wrong label abbrev", "inflo", englishRepresentation.getAbbreviatedLabel());
 130
 131                 // german representation
 132                 assertEquals("wrong number of representations", 2, inflorescence.getRepresentations().size());
 133                 Representation germanRepresentation = inflorescence.getRepresentation(Language.GERMAN());
 134                 assertNotNull("Representation is null for "+Language.GERMAN(), germanRepresentation);
 135                 assertEquals("wrong description", "Der Teil der Pflanze, der die Bluete traegt", germanRepresentation.getDescription());
 136                 assertEquals("wrong label", "Infloreszenz", germanRepresentation.getLabel());
 137             }
 138         }
 139         assertNotNull("term is null", inflorescence);
 140         assertEquals("Wrong term type", TermType.Structure, inflorescence.getTermType());
 141
 142         String vocLabel = "03 Generative Structures";
 143         List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
 144         assertEquals("wrong number of vocabularies", 1, vocs.size());
 145         TermVocabulary termVoc = vocs.iterator().next();
 146         assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
 147         assertEquals(3, termVoc.getTerms().size());
 148         assertTrue("Term not included in vocabulary", termVoc.getTerms().contains(inflorescence));
 149
 150     }
 151
 152
 153     @Test
 154     @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
 155     public void testImportPropertyTreeAndVocabulary() throws URISyntaxException {
 156         URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/properties.owl");
 157         URI uri = url.toURI();
 158         assertNotNull(url);
 159         StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
 160
 161         boolean result = defaultImport.invoke(configurator).isSuccess();
 162         assertTrue("Return value for import.invoke should be true", result);
 163         this.setComplete();
 164         this.endTransaction();
 165
 166         String treeLabel = "properties 1.0";
 167         List<FeatureTree> trees = featureTreeService.listByTitle(FeatureTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
 168         List<String> nodeProperties = new ArrayList<>();
 169         nodeProperties.add("term");
 170         FeatureTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
 171         assertNotNull("featureTree should not be null", tree);
 172
 173         assertEquals("Tree has wrong term type", TermType.Property, tree.getTermType());
 174         assertEquals("Wrong number of distinct features", 12, tree.getDistinctFeatures().size());
 175         List rootChildren = tree.getRootChildren();
 176
 177         String vocLabel = "Plant Glossary Properties";
 178         List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
 179         assertEquals("wrong number of vocabularies", 1, vocs.size());
 180         TermVocabulary termVoc = vocs.iterator().next();
 181         assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
 182         assertEquals(82, termVoc.getTerms().size());
 183
 184     }
 185     @Override
 186     public void createTestDataSet() throws FileNotFoundException {}
 187
 188
 189 }