cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/cdmLight/out/CdmLightExportTest.java

   1 /**
   2 * Copyright (C) 2018 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 package eu.etaxonomy.cdm.io.cdmLight.out;
  10
  11 import java.io.BufferedReader;
  12 import java.io.ByteArrayInputStream;
  13 import java.io.FileNotFoundException;
  14 import java.io.IOException;
  15 import java.io.InputStreamReader;
  16 import java.nio.charset.Charset;
  17 import java.util.HashSet;
  18 import java.util.Map;
  19 import java.util.Set;
  20 import java.util.UUID;
  21
  22 import org.apache.log4j.Logger;
  23 import org.junit.Assert;
  24 import org.junit.Before;
  25 import org.junit.Test;
  26 import org.unitils.dbunit.annotation.DataSet;
  27 import org.unitils.dbunit.annotation.DataSets;
  28 import org.unitils.spring.annotation.SpringBeanByName;
  29 import org.unitils.spring.annotation.SpringBeanByType;
  30
  31 import eu.etaxonomy.cdm.api.service.IClassificationService;
  32 import eu.etaxonomy.cdm.api.service.ICommonService;
  33 import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
  34 import eu.etaxonomy.cdm.api.service.ITermService;
  35 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  36 import eu.etaxonomy.cdm.io.cdmLight.CdmLightExportConfigurator;
  37 import eu.etaxonomy.cdm.io.cdmLight.CdmLightExportTable;
  38 import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;
  39 import eu.etaxonomy.cdm.io.common.ExportDataWrapper;
  40 import eu.etaxonomy.cdm.io.common.ExportResult;
  41 import eu.etaxonomy.cdm.io.common.IExportConfigurator.TARGET;
  42 import eu.etaxonomy.cdm.model.common.CdmBase;
  43 import eu.etaxonomy.cdm.model.description.Distribution;
  44 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  45 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  46 import eu.etaxonomy.cdm.model.location.NamedArea;
  47 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  48 import eu.etaxonomy.cdm.model.name.Rank;
  49 import eu.etaxonomy.cdm.model.name.TaxonName;
  50 import eu.etaxonomy.cdm.model.reference.Reference;
  51 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  52 import eu.etaxonomy.cdm.model.taxon.Classification;
  53 import eu.etaxonomy.cdm.model.taxon.Synonym;
  54 import eu.etaxonomy.cdm.model.taxon.Taxon;
  55 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  56 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  57 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  58 import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
  59
  60 /**
  61  * @author k.luther
  62  * @since 17.01.2018
  63  */
  64 public class CdmLightExportTest extends CdmTransactionalIntegrationTest{
  65
  66         @SuppressWarnings("unused")
  67         private static final Logger logger = Logger.getLogger(CdmLightExportTest.class);
  68
  69         @SpringBeanByName
  70         private CdmApplicationAwareDefaultExport<CdmLightExportConfigurator> defaultExport;
  71
  72         @SpringBeanByType
  73         private IClassificationService classificationService;
  74
  75         @SpringBeanByType
  76         private ITermService termService;
  77
  78         @SpringBeanByType
  79         private ITaxonNodeService taxonNodeService;
  80
  81         @SpringBeanByType
  82         private ICommonService commonService;
  83
  84         @Before
  85         public void setUp()  {
  86 //            DefinedTerm ipniIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("IPNI Identifier", "IPNI Identifier", "IPNI Identifier");
  87 //            ipniIdentifierTerm.setUuid(DefinedTerm.uuidIpniNameIdentifier);
  88 //
  89 //            DefinedTerm tropicosIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("Tropicos Identifier", "Tropicos Identifier", "Tropicos Identifier");
  90 //            tropicosIdentifierTerm.setUuid(DefinedTerm.uuidTropicosNameIdentifier);
  91 //
  92 //            DefinedTerm wfoIdentifierTerm = DefinedTerm.NewIdentifierTypeInstance("WFO Identifier", "WFO Identifier", "WFO Identifier");
  93 //            wfoIdentifierTerm.setUuid(DefinedTerm.uuidWfoNameIdentifier);
  94 //            List<DefinedTermBase> terms = new ArrayList();
  95 //            terms.add(wfoIdentifierTerm);
  96 //            terms.add(tropicosIdentifierTerm);
  97 //            terms.add(ipniIdentifierTerm);
  98 //            termService.saveOrUpdate(terms);
  99             createFullTestDataSet();
 100         }
 101
 102         @Test
 103         @DataSets({
 104             @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
 105             @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
 106         })
 107         public void testSubTree(){
 108
 109             CdmLightExportConfigurator config = new CdmLightExportConfigurator(null);
 110 //            config.setCreateCondensedDistributionString(false);
 111             config.setTaxonNodeFilter(TaxonNodeFilter.NewSubtreeInstance(UUID.fromString("f8c9933a-fe3a-42ce-8a92-000e27bfdfac")));
 112
 113             config.setTarget(TARGET.EXPORT_DATA);
 114             ExportResult result = defaultExport.invoke(config);
 115             ExportDataWrapper<?> exportData = result.getExportData();
 116             testExceptionsErrorsWarnings(result);
 117
 118             @SuppressWarnings("unchecked")
 119             Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
 120
 121             byte[] taxon = data.get(CdmLightExportTable.TAXON.getTableName());
 122             Assert.assertNotNull("Taxon table must not be null", taxon);
 123             String taxonStr = new String(taxon);
 124             String notExpected =  "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
 125             Assert.assertFalse("Result must not contain root taxon", taxonStr.startsWith(notExpected));
 126             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\"";
 127             Assert.assertTrue(taxonStr.contains(expected));
 128
 129             byte[] reference = data.get(CdmLightExportTable.REFERENCE.getTableName());
 130             String referenceString = new String(reference);
 131             Assert.assertNotNull("Reference table must not be null", reference);
 132             expected ="\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"Mill. 1804\",\"\",\"The book of botany\",\"1804\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"3\",\"1804\",\"Mill.\"";
 133             Assert.assertTrue(referenceString.contains(expected));
 134
 135             byte[] geographicAreaFact = data.get(CdmLightExportTable.GEOGRAPHIC_AREA_FACT.getTableName());
 136             String geographicAreaFactString = new String(geographicAreaFact);
 137             Assert.assertNotNull("Geographical fact table must not be null", geographicAreaFact);
 138             expected ="\"674e9e27-9102-4166-8626-8cb871a9a89b\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Africa\",\"present\"";
 139             Assert.assertTrue(geographicAreaFactString.contains(expected));
 140
 141             byte[] nomenclaturalAuthor = data.get(CdmLightExportTable.NOMENCLATURAL_AUTHOR.getTableName());
 142             String nomenclaturalAuthorString = new String(nomenclaturalAuthor);
 143             Assert.assertNotNull("Nomenclatural Author table must not be null", nomenclaturalAuthor);
 144             expected ="\"Mill.\",\"Mill.\",\"\",\"\",\"\",\"\"";
 145             Assert.assertTrue(nomenclaturalAuthorString.contains(expected));
 146
 147             byte[] scientificName = data.get(CdmLightExportTable.SCIENTIFIC_NAME.getTableName());
 148             String scientificNameString = new String(scientificName);
 149             Assert.assertNotNull("Scientific Name table must not be null", scientificName);
 150             expected ="\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"\",\"Subspecies\",\"43\",\"Genus species subsp. subspec Mill.\",\"Genus species subsp. subspec\",\"Genus\",\"\",\"\",\"species\",\"subsp.\",\"subspec\",\"\",\"\",\"\",";
 151             Assert.assertTrue(scientificNameString.contains(expected));
 152             if (config.isAddHTML()){
 153                 expected = "\"<i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804\"";
 154                 Assert.assertTrue(scientificNameString.contains(expected));
 155             }
 156
 157             expected ="\"Book\",\"The book of botany\",\"The book of botany\",\"Mill.\",\"Mill.\",\"3:22\",\"3\",\"22\",\"1804\",\"1804\",\"\",\"\",\"\",\"\"";
 158             Assert.assertTrue(scientificNameString.contains(expected));
 159
 160             byte[] homotypicGroup = data.get(CdmLightExportTable.HOMOTYPIC_GROUP.getTableName());
 161             String homotypicGroupString = new String(homotypicGroup);
 162             Assert.assertNotNull("Reference table must not be null", homotypicGroup);
 163             if (config.isAddHTML()){
 164                 expected ="\"<i>Genus</i> <i>species</i> subsp. <i>subspec</i> Mill., The book of botany 3: 22. 1804\",\"\"";
 165             }else{
 166                 expected ="\"Genus species subsp. subspec Mill., The book of botany 3: 22. 1804\",\"\"";
 167             }
 168             Assert.assertTrue(homotypicGroupString.contains(expected));
 169         }
 170
 171         @Test
 172         @DataSets({
 173             @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
 174             @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
 175         })
 176         public void testFullTreeWithUnpublished(){
 177
 178             CdmLightExportConfigurator config = new CdmLightExportConfigurator(null);
 179             config.setTarget(TARGET.EXPORT_DATA);
 180             config.getTaxonNodeFilter().setIncludeUnpublished(true);
 181
 182             ExportResult result = defaultExport.invoke(config);
 183             testExceptionsErrorsWarnings(result);
 184             ExportDataWrapper<?> exportData = result.getExportData();
 185             @SuppressWarnings("unchecked")
 186             Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
 187
 188             ByteArrayInputStream stream = new ByteArrayInputStream( data.get(CdmLightExportTable.TAXON.getTableName()));
 189             BufferedReader reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
 190             String line;
 191             int count = 0;
 192             try {
 193                 while ((line = reader.readLine()) != null) {
 194                     count ++;
 195                 }
 196                 Assert.assertTrue("There should be 5 taxa", count == 6);// 6 because of the header line
 197
 198                 stream = new ByteArrayInputStream(data.get(CdmLightExportTable.REFERENCE.getTableName()));
 199                 reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
 200                 count = 0;
 201                 while ((line = reader.readLine()) != null) {
 202                     count ++;
 203                 }
 204                 Assert.assertTrue("There should be 7 references (6 nomenclatural references and 1 sec reference)", count == 8);
 205                 stream = new ByteArrayInputStream(data.get(CdmLightExportTable.SYNONYM.getTableName()));
 206                 reader = new BufferedReader(new InputStreamReader(stream, Charset.forName("UTF-8")));
 207                 count = 0;
 208                 while ((line = reader.readLine()) != null) {
 209                     count ++;
 210                 }
 211                 Assert.assertTrue("There should be 1 synonym", count == 2);
 212             } catch (IOException e) {
 213                 e.printStackTrace();
 214                 Assert.fail("IO Exception thrown during test.");
 215             }
 216             byte[] taxon = data.get(CdmLightExportTable.TAXON.getTableName());
 217             Assert.assertNotNull("Taxon table must not be null", taxon);
 218             String taxonStr = new String(taxon);
 219             String notExpected =  "\"9182e136-f2e2-4f9a-9010-3f35908fb5e0\"";
 220             Assert.assertFalse("Result must not contain root taxon", taxonStr.startsWith(notExpected));
 221             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\"";
 222             Assert.assertTrue(taxonStr.contains(expected));
 223
 224             byte[] reference = data.get(CdmLightExportTable.REFERENCE.getTableName());
 225             String referenceString = new String(reference);
 226             Assert.assertNotNull("Reference table must not be null", reference);
 227             expected ="\"b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f\",\"Mill. 1804\",\"\",\"The book of botany\",\"1804\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"3\",\"1804\",\"Mill.\"";
 228             Assert.assertTrue(referenceString.contains(expected));
 229
 230             byte[] geographicAreaFact = data.get(CdmLightExportTable.GEOGRAPHIC_AREA_FACT.getTableName());
 231             String geographicAreaFactString = new String(geographicAreaFact);
 232             Assert.assertNotNull("Geographical fact table must not be null", geographicAreaFact);
 233             expected ="\"674e9e27-9102-4166-8626-8cb871a9a89b\",\"b2c86698-500e-4efb-b9ae-6bb6e701d4bc\",\"Africa\",\"present\"";
 234             Assert.assertTrue(geographicAreaFactString.contains(expected));
 235
 236             byte[] nomenclaturalAuthor = data.get(CdmLightExportTable.NOMENCLATURAL_AUTHOR.getTableName());
 237             String nomenclaturalAuthorString = new String(nomenclaturalAuthor);
 238             Assert.assertNotNull("Nomenclatural Author table must not be null", nomenclaturalAuthor);
 239             expected ="\"Mill.\",\"Mill.\",\"\",\"\",\"\",\"\"";
 240             Assert.assertTrue(nomenclaturalAuthorString.contains(expected));
 241
 242             byte[] scientificName = data.get(CdmLightExportTable.SCIENTIFIC_NAME.getTableName());
 243             String scientificNameString = new String(scientificName);
 244             Assert.assertNotNull("Scientific Name table must not be null", scientificName);
 245             expected ="\"3483cc5e-4c77-4c80-8cb0-73d43df31ee3\",\"\",\"Subspecies\",\"43\",\"Genus species subsp. subspec Mill.\",\"Genus species subsp. subspec\",\"Genus\",\"\",\"\",\"species\",\"subsp.\",\"subspec\",\"\",\"\",\"\",";
 246             Assert.assertTrue(scientificNameString.contains(expected));
 247             expected ="\"Book\",\"The book of botany\",\"The book of botany\",\"Mill.\",\"Mill.\",\"3:22\",\"3\",\"22\",\"1804\",\"1804\",\"\",\"\",\"\",\"\"";
 248             Assert.assertTrue(scientificNameString.contains(expected));
 249
 250             byte[] homotypicGroup = data.get(CdmLightExportTable.HOMOTYPIC_GROUP.getTableName());
 251             String homotypicGroupString = new String(homotypicGroup);
 252             Assert.assertNotNull("Reference table must not be null", homotypicGroup);
 253             if (config.isAddHTML()){
 254                 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\",\"\",\"\"";
 255             }else{
 256                 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\",\"\",\"\"";
 257             }
 258             Assert.assertTrue(homotypicGroupString.contains(expected));
 259         }
 260
 261         @Test
 262         @DataSets({
 263             @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
 264             @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
 265         })
 266         public void testFullData(){
 267
 268             CdmLightExportConfigurator config = new CdmLightExportConfigurator(null);
 269             config.setTarget(TARGET.EXPORT_DATA);
 270
 271             ExportResult result = defaultExport.invoke(config);
 272             testExceptionsErrorsWarnings(result);
 273
 274             ExportDataWrapper<?> exportData = result.getExportData();
 275             @SuppressWarnings("unchecked")
 276             Map<String, byte[]> data = (Map<String, byte[]>) exportData.getExportData();
 277
 278             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                     count = 0;
 300                     while ((line = reader.readLine()) != null) {
 301                         count ++;
 302                     }
 303                     Assert.assertTrue("There should be 0 synomyms", count == 1);
 304 //                    Assert.fail("There should not be a synonym table, because the only synonym is not public.");
 305                 }catch(NullPointerException e){
 306                     //OK, should be thrown
 307                 }
 308             } catch (IOException e) {
 309                 throw new RuntimeException(e);
 310             }
 311         }
 312
 313         @Test
 314         @DataSets({
 315             @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
 316             @DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml")
 317         })
 318         public void testFullSampleData(){
 319
 320             commonService.createFullSampleData();
 321             commitAndStartNewTransaction();
 322
 323
 324             CdmLightExportConfigurator config = new CdmLightExportConfigurator(null);
 325             config.setTarget(TARGET.EXPORT_DATA);
 326
 327             ExportResult result = defaultExport.invoke(config);
 328             testExceptionsErrorsWarnings(result);
 329         }
 330
 331         private void testExceptionsErrorsWarnings(ExportResult result) {
 332             Assert.assertTrue(result.getExceptions().size() == 0);
 333             Assert.assertTrue(result.getErrors().size() == 0);
 334             Assert.assertTrue(result.getWarnings().size() == 0);
 335         }
 336
 337         public void createFullTestDataSet() {
 338             Set<TaxonNode> nodesToSave = new HashSet<>();
 339
 340             Reference sec1 = ReferenceFactory.newGeneric();
 341             setUuid(sec1, "4b6acca1-959b-4790-b76e-e474a0882990");
 342             sec1.setTitle("My sec ref");
 343
 344             Classification classification = Classification.NewInstance("CdmLightExportTest Classification");
 345             setUuid(classification, "4096df99-7274-421e-8843-211b603d832e");
 346
 347             NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
 348             TaxonName familyName = parser.parseReferencedName("Family L., Sp. Pl. 3: 22. 1752",
 349                     NomenclaturalCode.ICNAFP, Rank.FAMILY());
 350             setUuid(familyName,"e983cc5e-4c77-4c80-8cb0-73d43df31ef7");
 351             setUuid(familyName.getNomenclaturalReference(), "b0dd7f4a-0c7f-4372-bc5d-3b676363bc63");
 352             Taxon family = Taxon.NewInstance(familyName, sec1);
 353             setUuid(family,"3162e136-f2e2-4f9a-9010-3f35908fbae1");
 354             TaxonNode node1 = classification.addChildTaxon(family, sec1, "22");
 355             setUuid(node1, "0fae5ad5-ffa2-4100-bcd7-8aa9dda0aebc");
 356             nodesToSave.add(node1);
 357
 358             TaxonName genusName = parser.parseReferencedName("Genus Humb., The book of botany 3: 22. 1804",
 359                     NomenclaturalCode.ICNAFP, Rank.GENUS());
 360             setUuid(genusName,"5e83cc5e-4c77-4d80-8cb0-73d63df35ee3");
 361             setUuid(genusName.getNomenclaturalReference(), "5ed27f4a-6c7f-4372-bc5d-3b67636abc52");
 362             Taxon genus = Taxon.NewInstance(genusName, sec1);
 363             setUuid(genus,"3f52e136-f2e1-4f9a-9010-2f35908fbd39");
 364
 365             TaxonNode node2 = node1.addChildTaxon(genus, sec1, "33");
 366             setUuid(node2, "43ca733b-fe3a-42ce-8a92-000e27badf44");
 367             nodesToSave.add(node2);
 368
 369             TaxonName speciesName = parser.parseReferencedName("Genus species Mill., The book of botany 3: 22. 1804",
 370                     NomenclaturalCode.ICNAFP, Rank.SPECIES());
 371             setUuid(speciesName,"f983cc5e-4c77-4c80-8cb0-73d43df31ee9");
 372             setUuid(speciesName.getNomenclaturalReference(), "a0dd7f4a-0c7f-4372-bc5d-3b676363bc0e");
 373             Taxon species = Taxon.NewInstance(speciesName, sec1);
 374             setUuid(species,"9182e136-f2e2-4f9a-9010-3f35908fb5e0");
 375             TaxonName synonymName = parser.parseReferencedName("Genus synonym Mill., The book of botany 3: 22. 1804", NomenclaturalCode.ICNAFP, Rank.SPECIES());
 376
 377             setUuid(synonymName, "1584157b-5c43-4150-b271-95b2c99377b2");
 378             Synonym  synonymUnpublished = Synonym.NewInstance(synonymName, sec1);
 379             setUuid(synonymName, "a87c16b7-8299-4d56-a682-ce20973428ea");
 380             synonymUnpublished.setPublish(false);
 381             species.addHomotypicSynonym(synonymUnpublished);
 382             TaxonNode node3 = node2.addChildTaxon(species, sec1, "33");
 383             setUuid(node3, "a0c9733a-fe3a-42ce-8a92-000e27bfdfa3");
 384             nodesToSave.add(node3);
 385
 386             TaxonName subspeciesName = parser.parseReferencedName("Genus species subsp. subspec Mill., The book of botany 3: 22. 1804",
 387                     NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
 388             setUuid(subspeciesName,"3483cc5e-4c77-4c80-8cb0-73d43df31ee3");
 389             setUuid(subspeciesName.getNomenclaturalReference(), "b8dd7f4a-0c7f-4372-bc5d-3b676363bc0f");
 390
 391             Taxon subspecies = Taxon.NewInstance(subspeciesName, sec1);
 392             setUuid(subspecies, "b2c86698-500e-4efb-b9ae-6bb6e701d4bc");
 393             TaxonNode node4 = node3.addChildTaxon(subspecies, sec1, "33");
 394             setUuid(node4, "f8c9933a-fe3a-42ce-8a92-000e27bfdfac");
 395             nodesToSave.add(node4);
 396
 397             TaxonName subspeciesNameUnpublished = parser.parseReferencedName("Genus species subsp. unpublished Mill., The book of botany 3: 22. 1804",
 398                     NomenclaturalCode.ICNAFP, Rank.SUBSPECIES());
 399             setUuid(subspeciesNameUnpublished,"b6da7ab2-6c67-44b7-9719-2557542f5a23");
 400
 401             Taxon subspeciesUnpublished = Taxon.NewInstance(subspeciesNameUnpublished, sec1);
 402             setUuid(subspeciesUnpublished, "290e295a-9089-4616-a30c-15ded79e064f");
 403             subspeciesUnpublished.setPublish(false);
 404             TaxonNode node5 = node3.addChildTaxon(subspeciesUnpublished, sec1, "33");
 405             setUuid(node5, "81d9c9b2-c8fd-4d4f-a0b4-e7e656dcdc20");
 406             nodesToSave.add(node5);
 407
 408             classificationService.save(classification);
 409             taxonNodeService.save(nodesToSave);
 410
 411             TaxonDescription description = TaxonDescription.NewInstance(species);
 412
 413             Distribution distribution = Distribution.NewInstance(NamedArea.AFRICA(), PresenceAbsenceTerm.PRESENT());
 414             setUuid(distribution,"674e9e27-9102-4166-8626-8cb871a9a89b");
 415             description.addElement(distribution);
 416
 417             subspecies.addDescription(description);
 418             commitAndStartNewTransaction(null);
 419         }
 420
 421         private void setUuid(CdmBase cdmBase, String uuidStr) {
 422             cdmBase.setUuid(UUID.fromString(uuidStr));
 423         }
 424
 425         @Override
 426         public void createTestDataSet() throws FileNotFoundException {
 427             //      try {
 428             //      writeDbUnitDataSetFile(new String[] {
 429             //              "Classification",
 430             //      }, "testAttachDnaSampleToDerivedUnit");
 431             //  } catch (FileNotFoundException e) {
 432             //      e.printStackTrace();
 433             //  }
 434         }
 435 }