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 import java.util.Set;
  24
  25 import org.junit.Before;
  26 import org.junit.Test;
  27 import org.unitils.dbunit.annotation.DataSet;
  28 import org.unitils.spring.annotation.SpringBeanByName;
  29 import org.unitils.spring.annotation.SpringBeanByType;
  30
  31 import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
  32 import eu.etaxonomy.cdm.api.service.ITermService;
  33 import eu.etaxonomy.cdm.api.service.IVocabularyService;
  34 import eu.etaxonomy.cdm.common.CdmUtils;
  35 import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
  36 import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportConfigurator;
  37 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  38 import eu.etaxonomy.cdm.model.common.Language;
  39 import eu.etaxonomy.cdm.model.media.Media;
  40 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  41 import eu.etaxonomy.cdm.model.media.MediaUtils;
  42 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  43 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  44 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  45 import eu.etaxonomy.cdm.model.term.FeatureNode;
  46 import eu.etaxonomy.cdm.model.term.FeatureTree;
  47 import eu.etaxonomy.cdm.model.term.Representation;
  48 import eu.etaxonomy.cdm.model.term.TermType;
  49 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  50 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  51 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  52
  53 /**
  54  *
  55  * @author pplitzner
  56  * @since Apr 24, 2019
  57  *
  58  */
  59 public class StructureTreeOwlImportTest extends CdmTransactionalIntegrationTest {
  60
  61     @SpringBeanByName
  62     private CdmApplicationAwareDefaultImport<?> defaultImport;
  63
  64     @SpringBeanByType
  65     private ITermService termService;
  66
  67     @SpringBeanByType
  68     private IFeatureTreeService featureTreeService;
  69
  70     @SpringBeanByType
  71     private IVocabularyService vocabularyService;
  72
  73     @Before
  74     public void setUp() {
  75     }
  76
  77     @Test
  78     public void testInit() {
  79         assertNotNull("import should not be null", defaultImport);
  80     }
  81
  82     @Test
  83     @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
  84     public void testImportStructureTree() throws URISyntaxException {
  85         URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/test_structures.owl");
  86         URI uri = url.toURI();
  87         assertNotNull(url);
  88         StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
  89
  90         boolean result = defaultImport.invoke(configurator).isSuccess();
  91         assertTrue("Return value for import.invoke should be true", result);
  92         this.setComplete();
  93         this.endTransaction();
  94
  95         String treeLabel = "test_structures";
  96         List<FeatureTree> trees = featureTreeService.listByTitle(FeatureTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
  97         List<String> nodeProperties = new ArrayList<>();
  98         nodeProperties.add("term");
  99         nodeProperties.add("term.media");
 100         FeatureTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
 101         assertNotNull("featureTree should not be null", tree);
 102
 103         assertEquals("Tree has wrong term type", TermType.Structure, tree.getTermType());
 104         assertEquals("Wrong number of distinct features", 4, tree.getDistinctFeatures().size());
 105         List rootChildren = tree.getRootChildren();
 106         assertEquals("Wrong number of root children", 1, rootChildren.size());
 107         Object entirePlant = rootChildren.iterator().next();
 108         assertTrue("Root is no feature node", entirePlant instanceof FeatureNode);
 109         assertEquals("Root node has wrong term type", TermType.Structure, ((FeatureNode)entirePlant).getTermType());
 110         FeatureNode<DefinedTerm> entirePlantNode = (FeatureNode<DefinedTerm>) entirePlant;
 111         List<FeatureNode<DefinedTerm>> childNodes = entirePlantNode.getChildNodes();
 112         assertEquals("Wrong number of children", 2, childNodes.size());
 113
 114         String inflorescenceLabel = "inflorescence";
 115         String inflorescenceDescription = " the part of the plant that bears the flowers, including all its bracts  branches and flowers  but excluding unmodified leaves               ";
 116         List<DefinedTerm> records = termService.findByRepresentationText(inflorescenceDescription, DefinedTerm.class, null, null).getRecords();
 117         assertEquals("wrong number of terms found for \"inflorescence\"", 1, records.size());
 118         DefinedTerm inflorescence = records.iterator().next();
 119         assertEquals(inflorescenceLabel, inflorescence.getLabel(Language.ENGLISH()));
 120
 121         for (FeatureNode<DefinedTerm> featureNode : childNodes) {
 122             assertTrue("Child node not found. Found node with term: "+featureNode.getTerm().getLabel(),
 123                     featureNode.getTerm().getUuid().equals(inflorescence.getUuid())
 124                     || featureNode.getTerm().getLabel(Language.ENGLISH()).equals("Flower"));
 125             if(featureNode.getTerm().getUuid().equals(inflorescence.getUuid())){
 126                 assertEquals("Term mismatch", inflorescence, featureNode.getTerm());
 127                 inflorescence = featureNode.getTerm();
 128
 129                 assertEquals("wrong id in vocabulary", "inflorescence", inflorescence.getIdInVocabulary());
 130                 assertEquals("wrong symbol", "infloSymbol", inflorescence.getSymbol());
 131                 assertEquals("wrong symbol2", "infloSymbol2", inflorescence.getSymbol2());
 132
 133                 Set<Media> mediaSet = inflorescence.getMedia();
 134                 assertEquals("wrong number of media", 1, mediaSet.size());
 135                 Media media = mediaSet.iterator().next();
 136                 MediaRepresentationPart part = MediaUtils.getFirstMediaRepresentationPart(media);
 137                 assertNotNull("media part not found", part);
 138                 assertEquals("incorrect URI", URI.create("https://upload.wikimedia.org/wikipedia/commons/8/82/Aloe_hereroensis_Auob_C15.JPG"), part.getUri());
 139                 assertEquals("incorrect title", "Aloe hereroensis", media.getTitle(Language.DEFAULT()).getText());
 140
 141                 Representation englishRepresentation = inflorescence.getRepresentation(Language.ENGLISH());
 142                 assertTrue("Description not found", CdmUtils.isNotBlank(englishRepresentation.getDescription()));
 143                 assertEquals("Description wrong", inflorescenceDescription, englishRepresentation.getDescription());
 144                 assertEquals("wrong plural", "inflorescences", englishRepresentation.getPlural());
 145                 assertEquals("wrong label abbrev", "inflo", englishRepresentation.getAbbreviatedLabel());
 146
 147                 // german representation
 148                 assertEquals("wrong number of representations", 2, inflorescence.getRepresentations().size());
 149                 Representation germanRepresentation = inflorescence.getRepresentation(Language.GERMAN());
 150                 assertNotNull("Representation is null for "+Language.GERMAN(), germanRepresentation);
 151                 assertEquals("wrong description", "Der Teil der Pflanze, der die Bluete traegt", germanRepresentation.getDescription());
 152                 assertEquals("wrong label", "Infloreszenz", germanRepresentation.getLabel());
 153             }
 154         }
 155         assertNotNull("term is null", inflorescence);
 156         assertEquals("Wrong term type", TermType.Structure, inflorescence.getTermType());
 157
 158         String vocLabel = "03 Generative Structures";
 159         List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
 160         assertEquals("wrong number of vocabularies", 1, vocs.size());
 161         TermVocabulary termVoc = vocs.iterator().next();
 162         assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
 163         assertEquals(3, termVoc.getTerms().size());
 164         assertTrue("Term not included in vocabulary", termVoc.getTerms().contains(inflorescence));
 165
 166     }
 167
 168
 169     @Test
 170     @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")
 171     public void testImportPropertyTreeAndVocabulary() throws URISyntaxException {
 172         URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/properties.owl");
 173         URI uri = url.toURI();
 174         assertNotNull(url);
 175         StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);
 176
 177         boolean result = defaultImport.invoke(configurator).isSuccess();
 178         assertTrue("Return value for import.invoke should be true", result);
 179         this.setComplete();
 180         this.endTransaction();
 181
 182         String treeLabel = "properties 1.0";
 183         List<FeatureTree> trees = featureTreeService.listByTitle(FeatureTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);
 184         List<String> nodeProperties = new ArrayList<>();
 185         nodeProperties.add("term");
 186         FeatureTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);
 187         assertNotNull("featureTree should not be null", tree);
 188
 189         assertEquals("Tree has wrong term type", TermType.Property, tree.getTermType());
 190         assertEquals("Wrong number of distinct features", 12, tree.getDistinctFeatures().size());
 191         List rootChildren = tree.getRootChildren();
 192
 193         String vocLabel = "Plant Glossary Properties";
 194         List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();
 195         assertEquals("wrong number of vocabularies", 1, vocs.size());
 196         TermVocabulary termVoc = vocs.iterator().next();
 197         assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());
 198         assertEquals(82, termVoc.getTerms().size());
 199
 200         Set<DefinedTermBase> terms = termVoc.getTerms();
 201         for (DefinedTermBase definedTermBase : terms) {
 202             List<String> termProperties = new ArrayList<>();
 203             termProperties.add("sources");
 204             definedTermBase = termService.load(definedTermBase.getUuid(), termProperties);
 205             Set<IdentifiableSource> sources = definedTermBase.getSources();
 206             assertTrue("Import source is missing for term: "+definedTermBase, !sources.isEmpty());
 207             assertTrue("import source type not found", sources.stream().anyMatch(source->OriginalSourceType.Import.getKey().equals(source.getType().getKey())));
 208         }
 209
 210     }
 211     @Override
 212     public void createTestDataSet() throws FileNotFoundException {}
 213
 214
 215 }