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/**
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* Copyright (C) 2018 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.cdmLight.out;
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import java.io.BufferedReader;
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import java.io.ByteArrayInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.nio.charset.Charset;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.junit.Assert;
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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.dbunit.annotation.DataSets;
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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.IClassificationService;
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import eu.etaxonomy.cdm.api.service.ICommonService;
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.io.cdmLight.CdmLightExportConfigurator;
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import eu.etaxonomy.cdm.io.cdmLight.CdmLightExportTable;
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import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;
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import eu.etaxonomy.cdm.io.common.ExportDataWrapper;
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import eu.etaxonomy.cdm.io.common.ExportResult;
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import eu.etaxonomy.cdm.io.common.IExportConfigurator.TARGET;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* @author k.luther
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* @since 17.01.2018
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*/
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public class CdmLightExportTest extends CdmTransactionalIntegrationTest{
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(CdmLightExportTest.class);
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@SpringBeanByName
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private CdmApplicationAwareDefaultExport<CdmLightExportConfigurator> defaultExport;
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private ITaxonNodeService taxonNodeService;
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@SpringBeanByType
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private ICommonService commonService;
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@Before
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public void setUp() {
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// DefinedTerm ipniIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("IPNI Identifier", "IPNI Identifier", "IPNI Identifier");
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// ipniIdentifierTerm.setUuid(DefinedTerm.uuidIpniNameIdentifier);
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//
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// DefinedTerm tropicosIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("Tropicos Identifier", "Tropicos Identifier", "Tropicos Identifier");
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// tropicosIdentifierTerm.setUuid(DefinedTerm.uuidTropicosNameIdentifier);
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//
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// DefinedTerm wfoIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("WFO Identifier", "WFO Identifier", "WFO Identifier");
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// wfoIdentifierTerm.setUuid(DefinedTerm.uuidWfoNameIdentifier);
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// List<DefinedTermBase> terms = new ArrayList();
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// terms.add(wfoIdentifierTerm);
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// terms.add(tropicosIdentifierTerm);
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// terms.add(ipniIdentifierTerm);
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// termService.saveOrUpdate(terms);
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createFullTestDataSet();
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}
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@Test
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@DataSets({
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
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})
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public void testSubTree(){
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CdmLightExportConfigurator config = CdmLightExportConfigurator.NewInstance();
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// config.setCreateCondensedDistributionString(false);
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config.setTaxonNodeFilter(TaxonNodeFilter.NewSubtreeInstance(UUID.fromString("f8c9933a-fe3a-42ce-8a92-000e27bfdfac")));
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config.setTarget(TARGET.EXPORT_DATA);
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ExportResult result = defaultExport.invoke(config);
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ExportDataWrapper<?> exportData = result.getExportData();
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testExceptionsErrorsWarnings(result);
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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byte[] taxon = data.get(CdmLightExportTable.TAXON.getTableName());
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Assert.assertNotNull("Taxon table must not be null", taxon);
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String taxonStr = new String(taxon);
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String notExpected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
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Assert.assertFalse("Result must not contain root taxon", taxonStr.startsWith(notExpected));
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String expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"4096df99-7274-421e-8843-211b603d832e\",\"CdmLightExportTest Classification\",\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"4b6acca1-959b-4790-b76e-e474a0882990\",\"My sec ref\"";
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Assert.assertTrue(taxonStr.contains(expected));
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byte[] reference = data.get(CdmLightExportTable.REFERENCE.getTableName());
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String referenceString = new String(reference);
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Assert.assertNotNull("Reference table must not be null", reference);
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expected ="\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"Mill. (1804)\",\"\",\"The book of botany\",\"1804\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"3\",\"1804\",\"Mill.\"";
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Assert.assertTrue(referenceString.contains(expected));
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byte[] geographicAreaFact = data.get(CdmLightExportTable.GEOGRAPHIC_AREA_FACT.getTableName());
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String geographicAreaFactString = new String(geographicAreaFact);
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Assert.assertNotNull("Geographical fact table must not be null", geographicAreaFact);
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expected ="\"674e9e27-9102-4166-8626-8cb871a9a89b\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Africa\",\"present\"";
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Assert.assertTrue(geographicAreaFactString.contains(expected));
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byte[] nomenclaturalAuthor = data.get(CdmLightExportTable.NOMENCLATURAL_AUTHOR.getTableName());
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String nomenclaturalAuthorString = new String(nomenclaturalAuthor);
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Assert.assertNotNull("Nomenclatural Author table must not be null", nomenclaturalAuthor);
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expected ="\"Mill.\",\"Mill.\",\"\",\"\",\"\",\"\"";
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Assert.assertTrue(nomenclaturalAuthorString.contains(expected));
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byte[] scientificName = data.get(CdmLightExportTable.SCIENTIFIC_NAME.getTableName());
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String scientificNameString = new String(scientificName);
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Assert.assertNotNull("Scientific Name table must not be null", scientificName);
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expected ="\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"\",\"Subspecies\",\"43\",\"Genus species subsp. subspec Mill.\",\"Genus species subsp. subspec\",\"Genus\",\"\",\"\",\"species\",\"subsp.\",\"subspec\",\"\",\"\",\"\",";
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Assert.assertTrue(scientificNameString.contains(expected));
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if (config.isAddHTML()){
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expected = "\"<i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804\"";
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Assert.assertTrue(scientificNameString.contains(expected));
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}
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expected ="\"Book\",\"The book of botany\",\"The book of botany\",\"Mill.\",\"Mill.\",\"3:22\",\"3\",\"22\",\"1804\",\"1804\",\"\",\"\",\"\",\"\"";
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Assert.assertTrue(scientificNameString.contains(expected));
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byte[] homotypicGroup = data.get(CdmLightExportTable.HOMOTYPIC_GROUP.getTableName());
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String homotypicGroupString = new String(homotypicGroup);
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Assert.assertNotNull("Reference table must not be null", homotypicGroup);
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if (config.isAddHTML()){
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expected ="\"= <i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804\",\"\"";
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}else{
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expected ="\"= Genus species subsp. subspec Mill., The book of botany 3: 22. 1804\",\"\"";
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}
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Assert.assertTrue(homotypicGroupString.contains(expected));
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}
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@Test
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@DataSets({
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
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})
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public void testFullTreeWithUnpublished(){
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CdmLightExportConfigurator config = CdmLightExportConfigurator.NewInstance();
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config.setTarget(TARGET.EXPORT_DATA);
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config.getTaxonNodeFilter().setIncludeUnpublished(true);
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ExportResult result = defaultExport.invoke(config);
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testExceptionsErrorsWarnings(result);
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ExportDataWrapper<?> exportData = result.getExportData();
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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ByteArrayInputStream stream = new ByteArrayInputStream( data.get(CdmLightExportTable.TAXON.getTableName()));
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BufferedReader reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
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String line;
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int count = 0;
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try {
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while ((line = reader.readLine()) != null) {
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count ++;
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}
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Assert.assertTrue("There should be 5 taxa", count == 6);// 6 because of the header line
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stream = new ByteArrayInputStream(data.get(CdmLightExportTable.REFERENCE.getTableName()));
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reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
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count = 0;
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while ((line = reader.readLine()) != null) {
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count ++;
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}
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Assert.assertTrue("There should be 7 references (6 nomenclatural references and 1 sec reference)", count == 8);
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stream = new ByteArrayInputStream(data.get(CdmLightExportTable.SYNONYM.getTableName()));
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reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
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count = 0;
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while ((line = reader.readLine()) != null) {
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count ++;
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}
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Assert.assertTrue("There should be 1 synonym", count == 2);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO Exception thrown during test.");
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}
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byte[] taxon = data.get(CdmLightExportTable.TAXON.getTableName());
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Assert.assertNotNull("Taxon table must not be null", taxon);
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String taxonStr = new String(taxon);
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String notExpected = "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
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Assert.assertFalse("Result must not contain root taxon", taxonStr.startsWith(notExpected));
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String expected = "\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"4096df99-7274-421e-8843-211b603d832e\",\"CdmLightExportTest Classification\",\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\",\"4b6acca1-959b-4790-b76e-e474a0882990\",\"My sec ref\"";
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Assert.assertTrue(taxonStr.contains(expected));
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byte[] reference = data.get(CdmLightExportTable.REFERENCE.getTableName());
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String referenceString = new String(reference);
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Assert.assertNotNull("Reference table must not be null", reference);
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expected ="\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"Mill. (1804)\",\"\",\"The book of botany\",\"1804\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"3\",\"1804\",\"Mill.\"";
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Assert.assertTrue(referenceString.contains(expected));
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byte[] geographicAreaFact = data.get(CdmLightExportTable.GEOGRAPHIC_AREA_FACT.getTableName());
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String geographicAreaFactString = new String(geographicAreaFact);
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Assert.assertNotNull("Geographical fact table must not be null", geographicAreaFact);
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expected ="\"674e9e27-9102-4166-8626-8cb871a9a89b\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Africa\",\"present\"";
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Assert.assertTrue(geographicAreaFactString.contains(expected));
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byte[] nomenclaturalAuthor = data.get(CdmLightExportTable.NOMENCLATURAL_AUTHOR.getTableName());
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String nomenclaturalAuthorString = new String(nomenclaturalAuthor);
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Assert.assertNotNull("Nomenclatural Author table must not be null", nomenclaturalAuthor);
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expected ="\"Mill.\",\"Mill.\",\"\",\"\",\"\",\"\"";
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Assert.assertTrue(nomenclaturalAuthorString.contains(expected));
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byte[] scientificName = data.get(CdmLightExportTable.SCIENTIFIC_NAME.getTableName());
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String scientificNameString = new String(scientificName);
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Assert.assertNotNull("Scientific Name table must not be null", scientificName);
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expected ="\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"\",\"Subspecies\",\"43\",\"Genus species subsp. subspec Mill.\",\"Genus species subsp. subspec\",\"Genus\",\"\",\"\",\"species\",\"subsp.\",\"subspec\",\"\",\"\",\"\",";
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Assert.assertTrue(scientificNameString.contains(expected));
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expected ="\"Book\",\"The book of botany\",\"The book of botany\",\"Mill.\",\"Mill.\",\"3:22\",\"3\",\"22\",\"1804\",\"1804\",\"\",\"\",\"\",\"\"";
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Assert.assertTrue(scientificNameString.contains(expected));
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byte[] homotypicGroup = data.get(CdmLightExportTable.HOMOTYPIC_GROUP.getTableName());
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String homotypicGroupString = new String(homotypicGroup);
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Assert.assertNotNull("Reference table must not be null", homotypicGroup);
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if (config.isAddHTML()){
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expected ="\"= <i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804\",\"\",\"\",\"= <i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804 My sec ref\",\"\",\"\"";
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}else{
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expected ="\"= Genus species subsp. subspec Mill., The book of botany 3: 22. (1804)\",\"\",\"\",\"= Genus species subsp. subspec Mill., The book of botany 3: 22. (1804) My sec ref\",\"\",\"\"";
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}
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Assert.assertTrue(homotypicGroupString.contains(expected));
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}
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@Test
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@DataSets({
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
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})
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public void testFullData(){
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CdmLightExportConfigurator config = CdmLightExportConfigurator.NewInstance();
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config.setTarget(TARGET.EXPORT_DATA);
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ExportResult result = defaultExport.invoke(config);
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testExceptionsErrorsWarnings(result);
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ExportDataWrapper<?> exportData = result.getExportData();
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@SuppressWarnings("unchecked")
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Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
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278
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ByteArrayInputStream stream = new ByteArrayInputStream( data.get(CdmLightExportTable.TAXON.getTableName()));
|
|
279
|
BufferedReader reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
|
|
280
|
String line;
|
|
281
|
int count = 0;
|
|
282
|
try {
|
|
283
|
while ((line = reader.readLine()) != null) {
|
|
284
|
count ++;
|
|
285
|
}
|
|
286
|
Assert.assertTrue("There should be 4 taxa", count == 5);// 5 because of the header line
|
|
287
|
|
|
288
|
stream = new ByteArrayInputStream(data.get(CdmLightExportTable.REFERENCE.getTableName()));
|
|
289
|
reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
|
|
290
|
count = 0;
|
|
291
|
while ((line = reader.readLine()) != null) {
|
|
292
|
count ++;
|
|
293
|
}
|
|
294
|
Assert.assertTrue("There should be 5 references", count == 6);
|
|
295
|
try{
|
|
296
|
stream = new ByteArrayInputStream(data.get(CdmLightExportTable.SYNONYM.getTableName()));
|
|
297
|
// now there are always all tables also if empty
|
|
298
|
reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
|
|
299
|
|
|
300
|
boolean dummyLine = true;
|
|
301
|
count = 0;
|
|
302
|
while ((line = reader.readLine()) != null) {
|
|
303
|
if (!(line.startsWith("\"DUMMY") || line.startsWith("\"Synonym_ID"))){
|
|
304
|
dummyLine = dummyLine && false;
|
|
305
|
}
|
|
306
|
count++;
|
|
307
|
}
|
|
308
|
Assert.assertTrue("There should be 0 synomyms", dummyLine && count == 3);
|
|
309
|
// Assert.fail("There should not be a synonym table, because the only synonym is not public.");
|
|
310
|
}catch(NullPointerException e){
|
|
311
|
//OK, should be thrown
|
|
312
|
}
|
|
313
|
} catch (IOException e) {
|
|
314
|
throw new RuntimeException(e);
|
|
315
|
}
|
|
316
|
}
|
|
317
|
|
|
318
|
@Test
|
|
319
|
@DataSets({
|
|
320
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
|
|
321
|
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
|
|
322
|
})
|
|
323
|
public void testFullSampleData(){
|
|
324
|
|
|
325
|
commonService.createFullSampleData();
|
|
326
|
commitAndStartNewTransaction();
|
|
327
|
|
|
328
|
|
|
329
|
CdmLightExportConfigurator config = CdmLightExportConfigurator.NewInstance();
|
|
330
|
config.setTarget(TARGET.EXPORT_DATA);
|
|
331
|
|
|
332
|
ExportResult result = defaultExport.invoke(config);
|
|
333
|
testExceptionsErrorsWarnings(result);
|
|
334
|
}
|
|
335
|
|
|
336
|
private void testExceptionsErrorsWarnings(ExportResult result) {
|
|
337
|
Assert.assertTrue(result.getExceptions().size() == 0);
|
|
338
|
Assert.assertTrue(result.getErrors().size() == 0);
|
|
339
|
Assert.assertTrue(result.getWarnings().size() == 0);
|
|
340
|
}
|
|
341
|
|
|
342
|
public void createFullTestDataSet() {
|
|
343
|
Set<TaxonNode> nodesToSave = new HashSet<>();
|
|
344
|
|
|
345
|
Reference sec1 = ReferenceFactory.newGeneric();
|
|
346
|
setUuid(sec1, "4b6acca1-959b-4790-b76e-e474a0882990");
|
|
347
|
sec1.setTitle("My sec ref");
|
|
348
|
|
|
349
|
Classification classification = Classification.NewInstance("CdmLightExportTest Classification");
|
|
350
|
setUuid(classification, "4096df99-7274-421e-8843-211b603d832e");
|
|
351
|
|
|
352
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
|
353
|
TaxonName familyName = parser.parseReferencedName("Family L., Sp. Pl. 3: 22. 1752",
|
|
354
|
NomenclaturalCode.ICNAFP, Rank.FAMILY());
|
|
355
|
setUuid(familyName,"e983cc5e-4c77-4c80-8cb0-73d43df31ef7");
|
|
356
|
setUuid(familyName.getNomenclaturalReference(), "b0dd7f4a-0c7f-4372-bc5d-3b676363bc63");
|
|
357
|
Taxon family = Taxon.NewInstance(familyName, sec1);
|
|
358
|
setUuid(family,"3162e136-f2e2-4f9a-9010-3f35908fbae1");
|
|
359
|
TaxonNode node1 = classification.addChildTaxon(family, sec1, "22");
|
|
360
|
setUuid(node1, "0fae5ad5-ffa2-4100-bcd7-8aa9dda0aebc");
|
|
361
|
nodesToSave.add(node1);
|
|
362
|
|
|
363
|
TaxonName genusName = parser.parseReferencedName("Genus Humb., The book of botany 3: 22. 1804",
|
|
364
|
NomenclaturalCode.ICNAFP, Rank.GENUS());
|
|
365
|
setUuid(genusName,"5e83cc5e-4c77-4d80-8cb0-73d63df35ee3");
|
|
366
|
setUuid(genusName.getNomenclaturalReference(), "5ed27f4a-6c7f-4372-bc5d-3b67636abc52");
|
|
367
|
Taxon genus = Taxon.NewInstance(genusName, sec1);
|
|
368
|
setUuid(genus,"3f52e136-f2e1-4f9a-9010-2f35908fbd39");
|
|
369
|
|
|
370
|
TaxonNode node2 = node1.addChildTaxon(genus, sec1, "33");
|
|
371
|
setUuid(node2, "43ca733b-fe3a-42ce-8a92-000e27badf44");
|
|
372
|
nodesToSave.add(node2);
|
|
373
|
|
|
374
|
TaxonName speciesName = parser.parseReferencedName("Genus species Mill., The book of botany 3: 22. 1804",
|
|
375
|
NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
|
376
|
setUuid(speciesName,"f983cc5e-4c77-4c80-8cb0-73d43df31ee9");
|
|
377
|
setUuid(speciesName.getNomenclaturalReference(), "a0dd7f4a-0c7f-4372-bc5d-3b676363bc0e");
|
|
378
|
Taxon species = Taxon.NewInstance(speciesName, sec1);
|
|
379
|
setUuid(species,"9182e136-f2e2-4f9a-9010-3f35908fb5e0");
|
|
380
|
TaxonName synonymName = parser.parseReferencedName("Genus synonym Mill., The book of botany 3: 22. 1804", NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
|
381
|
|
|
382
|
setUuid(synonymName, "1584157b-5c43-4150-b271-95b2c99377b2");
|
|
383
|
Synonym synonymUnpublished = Synonym.NewInstance(synonymName, sec1);
|
|
384
|
setUuid(synonymName, "a87c16b7-8299-4d56-a682-ce20973428ea");
|
|
385
|
synonymUnpublished.setPublish(false);
|
|
386
|
species.addHomotypicSynonym(synonymUnpublished);
|
|
387
|
TaxonNode node3 = node2.addChildTaxon(species, sec1, "33");
|
|
388
|
setUuid(node3, "a0c9733a-fe3a-42ce-8a92-000e27bfdfa3");
|
|
389
|
nodesToSave.add(node3);
|
|
390
|
|
|
391
|
TaxonName subspeciesName = parser.parseReferencedName("Genus species subsp. subspec Mill., The book of botany 3: 22. 1804",
|
|
392
|
NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
|
|
393
|
setUuid(subspeciesName,"3483cc5e-4c77-4c80-8cb0-73d43df31ee3");
|
|
394
|
setUuid(subspeciesName.getNomenclaturalReference(), "b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f");
|
|
395
|
|
|
396
|
Taxon subspecies = Taxon.NewInstance(subspeciesName, sec1);
|
|
397
|
setUuid(subspecies, "b2c86698-500e-4efb-b9ae-6bb6e701d4bc");
|
|
398
|
TaxonNode node4 = node3.addChildTaxon(subspecies, sec1, "33");
|
|
399
|
setUuid(node4, "f8c9933a-fe3a-42ce-8a92-000e27bfdfac");
|
|
400
|
nodesToSave.add(node4);
|
|
401
|
|
|
402
|
TaxonName subspeciesNameUnpublished = parser.parseReferencedName("Genus species subsp. unpublished Mill., The book of botany 3: 22. 1804",
|
|
403
|
NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
|
|
404
|
setUuid(subspeciesNameUnpublished,"b6da7ab2-6c67-44b7-9719-2557542f5a23");
|
|
405
|
|
|
406
|
Taxon subspeciesUnpublished = Taxon.NewInstance(subspeciesNameUnpublished, sec1);
|
|
407
|
setUuid(subspeciesUnpublished, "290e295a-9089-4616-a30c-15ded79e064f");
|
|
408
|
subspeciesUnpublished.setPublish(false);
|
|
409
|
TaxonNode node5 = node3.addChildTaxon(subspeciesUnpublished, sec1, "33");
|
|
410
|
setUuid(node5, "81d9c9b2-c8fd-4d4f-a0b4-e7e656dcdc20");
|
|
411
|
nodesToSave.add(node5);
|
|
412
|
|
|
413
|
classificationService.save(classification);
|
|
414
|
taxonNodeService.save(nodesToSave);
|
|
415
|
|
|
416
|
TaxonDescription description = TaxonDescription.NewInstance(species);
|
|
417
|
|
|
418
|
Distribution distribution = Distribution.NewInstance(NamedArea.AFRICA(), PresenceAbsenceTerm.PRESENT());
|
|
419
|
setUuid(distribution,"674e9e27-9102-4166-8626-8cb871a9a89b");
|
|
420
|
description.addElement(distribution);
|
|
421
|
|
|
422
|
subspecies.addDescription(description);
|
|
423
|
commitAndStartNewTransaction(null);
|
|
424
|
}
|
|
425
|
|
|
426
|
private void setUuid(CdmBase cdmBase, String uuidStr) {
|
|
427
|
cdmBase.setUuid(UUID.fromString(uuidStr));
|
|
428
|
}
|
|
429
|
|
|
430
|
@Override
|
|
431
|
public void createTestDataSet() throws FileNotFoundException {
|
|
432
|
// try {
|
|
433
|
// writeDbUnitDataSetFile(new String[] {
|
|
434
|
// "Classification",
|
|
435
|
// }, "testAttachDnaSampleToDerivedUnit");
|
|
436
|
// } catch (FileNotFoundException e) {
|
|
437
|
// e.printStackTrace();
|
|
438
|
// }
|
|
439
|
}
|
|
440
|
}
|