cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceDeepDeleteTest.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.api.service;
  11
  12 import static org.junit.Assert.assertEquals;
  13 import static org.junit.Assert.assertFalse;
  14 import static org.junit.Assert.assertTrue;
  15
  16 import java.io.FileNotFoundException;
  17 import java.util.UUID;
  18
  19 import org.apache.log4j.Logger;
  20 import org.junit.Ignore;
  21 import org.junit.Test;
  22 import org.unitils.dbunit.annotation.DataSet;
  23 import org.unitils.spring.annotation.SpringBeanByType;
  24
  25 import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
  26 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  27 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
  28 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  29 import eu.etaxonomy.cdm.model.molecular.Sequence;
  30 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  31 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  32 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  33 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  34 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  35 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  36 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  37 import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
  38 import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
  39
  40 /**
  41  * @author pplitzner
  42  * @date 31.03.2014
  43  *
  44  */
  45 public class OccurrenceServiceDeepDeleteTest extends CdmTransactionalIntegrationTest {
  46
  47     private final UUID FIELD_UNIT_UUID = UUID.fromString("b5f58da5-4442-4001-9d13-33f41518b72a");
  48     private final UUID DERIVED_UNIT_UUID = UUID.fromString("448be6e7-f19c-4a10-9a0a-97aa005f817d");
  49     private final UUID DNA_SAMPLE_UUID = UUID.fromString("bee4212b-aff1-484e-845f-065c7d6216af");
  50     private final UUID SEQUENCE_UUID = UUID.fromString("0b867369-de8c-4837-a708-5b7d9f6091be");
  51     private final UUID TAXON_UUID = UUID.fromString("e93b3840-326c-446e-89f1-a7611f17c0e8");
  52
  53     @SuppressWarnings("unused")
  54     private static final Logger logger = Logger.getLogger(OccurrenceServiceDeepDeleteTest.class);
  55
  56     @SpringBeanByType
  57     private IOccurrenceService occurrenceService;
  58
  59     @SpringBeanByType
  60     private ISequenceService sequenceService;
  61
  62     @Test
  63     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml")
  64     public void testDeepDelete_FieldUnit(){
  65
  66
  67         String assertMessage = "Incorrect number of specimens after deletion.";
  68         DeleteResult deleteResult = null;
  69         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
  70         config.setDeleteMolecularData(true);
  71         config.setDeleteChildren(true);
  72
  73         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
  74         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
  75
  76         //check initial state
  77         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
  78         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
  79         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
  80         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
  81         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
  82         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
  83         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
  84
  85         //delete field unit
  86         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
  87         assertTrue(deleteResult.toString(), deleteResult.isOk());
  88         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
  89         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
  90         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
  91         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
  92     }
  93
  94     @Test
  95     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
  96     public void testDeepDelete_DerivedUnit(){
  97         String assertMessage = "Incorrect number of specimens after deletion.";
  98         DeleteResult deleteResult = null;
  99         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 100         config.setDeleteMolecularData(true);
 101         config.setDeleteChildren(true);
 102
 103         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
 104         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 105
 106         //check initial state
 107         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 108         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 109         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 110         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 111         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 112         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 113         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 114
 115         //delete derived unit
 116         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 117         assertTrue(deleteResult.toString(), deleteResult.isOk());
 118         assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 119         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 120         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 121         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 122     }
 123
 124     @Test
 125     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
 126     public void testDeepDelete_DnaSample(){
 127         String assertMessage = "Incorrect number of specimens after deletion.";
 128         DeleteResult deleteResult = null;
 129         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 130         config.setDeleteMolecularData(true);
 131         config.setDeleteChildren(true);
 132
 133         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 134
 135         //check initial state
 136         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 137         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 138         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 139         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 140         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 141         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 142         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 143
 144         //delete dna sample
 145         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 146         assertTrue(deleteResult.toString(), deleteResult.isOk());
 147         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 148         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 149         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 150         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 151     }
 152
 153
 154     @Test
 155     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
 156     public void testDeleteDerivateHierarchyStepByStep(){
 157         String assertMessage = "Incorrect number of specimens after deletion.";
 158         DeleteResult deleteResult = null;
 159         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 160
 161         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
 162         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
 163         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 164         Sequence consensusSequence = sequenceService.load(SEQUENCE_UUID);
 165
 166         //check initial state
 167         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 168         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 169         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 170         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 171         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 172         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 173         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 174
 175         //delete single read -> should fail
 176         SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
 177         deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
 178         assertFalse(deleteResult.toString(), deleteResult.isOk());
 179         //delete sequence -> should fail
 180         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 181         assertFalse(deleteResult.toString(), deleteResult.isOk());
 182
 183         //allow deletion of molecular data
 184         config.setDeleteMolecularData(true);
 185
 186         deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
 187         assertTrue(deleteResult.toString(), deleteResult.isOk());
 188         assertTrue(consensusSequence.getSingleReads().isEmpty());
 189
 190         //delete sequence -> should fail
 191         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 192         assertTrue(deleteResult.toString(), deleteResult.isOk());
 193         assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
 194
 195
 196         //delete dna sample
 197         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 198         assertTrue(deleteResult.toString(), deleteResult.isOk());
 199         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 200         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 201         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 202         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 203
 204         //delete derived unit
 205         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 206         assertTrue(deleteResult.toString(), deleteResult.isOk());
 207         assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 208         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 209         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 210         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 211
 212         //delete field unit
 213         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 214         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 215         assertTrue(deleteResult.toString(), deleteResult.isOk());
 216         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
 217         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
 218         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 219         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 220     }
 221
 222     /* (non-Javadoc)
 223      * @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
 224      */
 225     @Override
 226     @Test
 227     @Ignore
 228     public void createTestDataSet() throws FileNotFoundException {
 229         //how the XML was generated
 230         FieldUnit fieldUnit = FieldUnit.NewInstance();
 231         fieldUnit.setUuid(FIELD_UNIT_UUID);
 232         //sub derivates (DerivedUnit, DnaSample)
 233         DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
 234         derivedUnit.setUuid(DERIVED_UNIT_UUID);
 235         DnaSample dnaSample = DnaSample.NewInstance();
 236         dnaSample.setUuid(DNA_SAMPLE_UUID);
 237
 238         //derivation events
 239         DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
 240         DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
 241
 242         //DNA (Sequence, SingleRead, Amplification)
 243         Sequence sequence = Sequence.NewInstance(dnaSample, "ATTCG", 5);
 244         sequence.setUuid(SEQUENCE_UUID);
 245         SingleRead singleRead = SingleRead.NewInstance();
 246         sequence.addSingleRead(singleRead);
 247         dnaSample.addSequence(sequence);
 248         AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
 249         amplificationResult.addSingleRead(singleRead);
 250         occurrenceService.save(fieldUnit);
 251         occurrenceService.save(derivedUnit);
 252         occurrenceService.save(dnaSample);
 253
 254         commitAndStartNewTransaction(null);
 255
 256         setComplete();
 257         endTransaction();
 258
 259
 260         try {
 261             writeDbUnitDataSetFile(new String[] {
 262                     "SpecimenOrObservationBase",
 263                     "SpecimenOrObservationBase_DerivationEvent",
 264                     "DerivationEvent",
 265                     "Sequence",
 266                     "Sequence_SingleRead",
 267                     "SingleRead",
 268                     "AmplificationResult"
 269             });
 270         } catch (FileNotFoundException e) {
 271             e.printStackTrace();
 272         }
 273     }
 274 }