EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.owl.in;

import static org.junit.Assert.assertEquals;

import static org.junit.Assert.assertNotNull;

import static org.junit.Assert.assertTrue;

import java.io.FileNotFoundException;

import java.net.URI;

import java.net.URISyntaxException;

import java.net.URL;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import java.util.List;

import java.util.Set;

import org.junit.Before;

import org.junit.Test;

import org.unitils.dbunit.annotation.DataSet;

import org.unitils.spring.annotation.SpringBeanByName;

import org.unitils.spring.annotation.SpringBeanByType;

import eu.etaxonomy.cdm.api.service.IFeatureTreeService;

import eu.etaxonomy.cdm.api.service.ITermService;

import eu.etaxonomy.cdm.api.service.IVocabularyService;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;

import eu.etaxonomy.cdm.io.descriptive.owl.in.StructureTreeOwlImportConfigurator;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;

import eu.etaxonomy.cdm.model.media.MediaUtils;

import eu.etaxonomy.cdm.model.reference.OriginalSourceType;

import eu.etaxonomy.cdm.model.term.DefinedTerm;

import eu.etaxonomy.cdm.model.term.DefinedTermBase;

import eu.etaxonomy.cdm.model.term.Representation;

import eu.etaxonomy.cdm.model.term.TermNode;

import eu.etaxonomy.cdm.model.term.TermTree;

import eu.etaxonomy.cdm.model.term.TermType;

import eu.etaxonomy.cdm.model.term.TermVocabulary;

import eu.etaxonomy.cdm.persistence.dto.TermDto;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;

/**

 *

 * @author pplitzner

 * @since Apr 24, 2019

 *

 */

public class StructureTreeOwlImportTest extends CdmTransactionalIntegrationTest {

    @SpringBeanByName

    private CdmApplicationAwareDefaultImport<?> defaultImport;

    @SpringBeanByType

    private ITermService termService;

    @SpringBeanByType

    private IFeatureTreeService featureTreeService;

    @SpringBeanByType

    private IVocabularyService vocabularyService;

    @Before

    public void setUp() {

    }

    @Test

    public void testInit() {

        assertNotNull("import should not be null", defaultImport);

    }

    @Test

    @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")

    public void testImportStructureTree() throws URISyntaxException {

        URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/test_structures.owl");

        URI uri = url.toURI();

        assertNotNull(url);

        StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);

        boolean result = defaultImport.invoke(configurator).isSuccess();

        assertTrue("Return value for import.invoke should be true", result);

        this.setComplete();

        this.endTransaction();

        String treeLabel = "test_structures";

        List<TermTree> trees = featureTreeService.listByTitle(TermTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);

        List<String> nodeProperties = new ArrayList<>();

        nodeProperties.add("term");

        nodeProperties.add("term.media");

        TermTree<Feature> tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);

        assertNotNull("featureTree should not be null", tree);

        assertEquals("Tree has wrong term type", TermType.Structure, tree.getTermType());

        assertEquals("Wrong number of distinct features", 4, tree.getDistinctTerms().size());

        List rootChildren = tree.getRootChildren();

        assertEquals("Wrong number of root children", 1, rootChildren.size());

        Object entirePlant = rootChildren.iterator().next();

        assertTrue("Root is no feature node", entirePlant instanceof TermNode);

        assertEquals("Root node has wrong term type", TermType.Structure, ((TermNode)entirePlant).getTermType());

        TermNode<DefinedTerm> entirePlantNode = (TermNode<DefinedTerm>) entirePlant;

        List<TermNode<DefinedTerm>> childNodes = entirePlantNode.getChildNodes();

        assertEquals("Wrong number of children", 2, childNodes.size());

        String inflorescenceLabel = "inflorescence";

        String inflorescenceDescription = " the part of the plant that bears the flowers, including all its bracts  branches and flowers  but excluding unmodified leaves               ";

        List<DefinedTerm> records = termService.findByRepresentationText(inflorescenceDescription, DefinedTerm.class, null, null).getRecords();

        assertEquals("wrong number of terms found for \"inflorescence\"", 1, records.size());

        DefinedTerm inflorescence = records.iterator().next();

        assertEquals(inflorescenceLabel, inflorescence.getLabel(Language.ENGLISH()));

        for (TermNode<DefinedTerm> termNode : childNodes) {

            assertTrue("Child node not found. Found node with term: "+termNode.getTerm().getLabel(),

                    termNode.getTerm().getUuid().equals(inflorescence.getUuid())

                    || termNode.getTerm().getLabel(Language.ENGLISH()).equals("Flower"));

            if(termNode.getTerm().getUuid().equals(inflorescence.getUuid())){

                assertEquals("Term mismatch", inflorescence, termNode.getTerm());

                inflorescence = termNode.getTerm();

                assertEquals("wrong id in vocabulary", "inflorescence", inflorescence.getIdInVocabulary());

                assertEquals("wrong symbol", "infloSymbol", inflorescence.getSymbol());

                assertEquals("wrong symbol2", "infloSymbol2", inflorescence.getSymbol2());

                Set<Media> mediaSet = inflorescence.getMedia();

                assertEquals("wrong number of media", 1, mediaSet.size());

                Media media = mediaSet.iterator().next();

                MediaRepresentationPart part = MediaUtils.getFirstMediaRepresentationPart(media);

                assertNotNull("media part not found", part);

                assertEquals("incorrect URI", URI.create("https://upload.wikimedia.org/wikipedia/commons/8/82/Aloe_hereroensis_Auob_C15.JPG"), part.getUri());

                assertEquals("incorrect title", "Aloe hereroensis", media.getTitle(Language.DEFAULT()).getText());

                Representation englishRepresentation = inflorescence.getRepresentation(Language.ENGLISH());

                assertTrue("Description not found", CdmUtils.isNotBlank(englishRepresentation.getDescription()));

                assertEquals("Description wrong", inflorescenceDescription, englishRepresentation.getDescription());

                assertEquals("wrong plural", "inflorescences", englishRepresentation.getPlural());

                assertEquals("wrong label abbrev", "inflo", englishRepresentation.getAbbreviatedLabel());

                // german representation

                assertEquals("wrong number of representations", 2, inflorescence.getRepresentations().size());

                Representation germanRepresentation = inflorescence.getRepresentation(Language.GERMAN());

                assertNotNull("Representation is null for "+Language.GERMAN(), germanRepresentation);

                assertEquals("wrong description", "Der Teil der Pflanze, der die Bluete traegt", germanRepresentation.getDescription());

                assertEquals("wrong label", "Infloreszenz", germanRepresentation.getLabel());

            }

        }

        assertNotNull("term is null", inflorescence);

        assertEquals("Wrong term type", TermType.Structure, inflorescence.getTermType());

        String vocLabel = "03 Generative Structures";

        List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();

        assertEquals("wrong number of vocabularies", 1, vocs.size());

        TermVocabulary termVoc = vocs.iterator().next();

        assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());

        Collection<TermDto> topLevelTerms = vocabularyService.getTopLevelTerms(termVoc.getUuid());

        assertEquals("wrong number of top level terms", 4, topLevelTerms.size());

    }

    @Test

    @DataSet(value="/eu/etaxonomy/cdm/database/BlankDataSet.xml")

    public void testImportPropertyTreeAndVocabulary() throws URISyntaxException {

        URL url = this.getClass().getResource("/eu/etaxonomy/cdm/io/owl/in/properties.owl");

        URI uri = url.toURI();

        assertNotNull(url);

        StructureTreeOwlImportConfigurator configurator = StructureTreeOwlImportConfigurator.NewInstance(uri);

        boolean result = defaultImport.invoke(configurator).isSuccess();

        assertTrue("Return value for import.invoke should be true", result);

        this.setComplete();

        this.endTransaction();

        String treeLabel = "properties 1.0";

        List<TermTree> trees = featureTreeService.listByTitle(TermTree.class, treeLabel, MatchMode.EXACT, null, null, null, null, null);

        List<String> nodeProperties = new ArrayList<>();

        nodeProperties.add("term");

        TermTree tree = featureTreeService.loadWithNodes(trees.iterator().next().getUuid(), null, nodeProperties);

        assertNotNull("featureTree should not be null", tree);

        assertEquals("Tree has wrong term type", TermType.Property, tree.getTermType());

        assertEquals("Wrong number of distinct features", 12, tree.getDistinctTerms().size());

        List rootChildren = tree.getRootChildren();

        String vocLabel = "Plant Glossary Properties";

        List<TermVocabulary> vocs = vocabularyService.findByTitle(TermVocabulary.class, vocLabel, MatchMode.EXACT, null, null, null, null, Arrays.asList("terms")).getRecords();

        assertEquals("wrong number of vocabularies", 1, vocs.size());

        TermVocabulary termVoc = vocs.iterator().next();

        assertEquals("Wrong vocabulary label", vocLabel, termVoc.getTitleCache());

        assertEquals(82, termVoc.getTerms().size());

        Set<DefinedTermBase> terms = termVoc.getTerms();

        for (DefinedTermBase definedTermBase : terms) {

            List<String> termProperties = new ArrayList<>();

            termProperties.add("sources");

            definedTermBase = termService.load(definedTermBase.getUuid(), termProperties);

            Set<IdentifiableSource> sources = definedTermBase.getSources();

            assertTrue("Import source is missing for term: "+definedTermBase, !sources.isEmpty());

            assertTrue("import source type not found", sources.stream().anyMatch(source->OriginalSourceType.Import.getKey().equals(source.getType().getKey())));

        }

    }

    @Override

    public void createTestDataSet() throws FileNotFoundException {}

}