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
  52     @SuppressWarnings("unused")
  53     private static final Logger logger = Logger.getLogger(OccurrenceServiceDeepDeleteTest.class);
  54
  55     @SpringBeanByType
  56     private IOccurrenceService occurrenceService;
  57
  58     @SpringBeanByType
  59     private ISequenceService sequenceService;
  60
  61     @Test
  62     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml")
  63     public void testDeepDelete_FieldUnit(){
  64
  65
  66         String assertMessage = "Incorrect number of specimens after deletion.";
  67         DeleteResult deleteResult = null;
  68         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
  69         config.setDeleteMolecularData(true);
  70         config.setDeleteChildren(true);
  71
  72         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
  73         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
  74
  75         //check initial state
  76         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
  77         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
  78         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
  79         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
  80         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
  81         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
  82         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
  83
  84         //delete field unit
  85         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
  86         assertTrue(deleteResult.toString(), deleteResult.isOk());
  87         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
  88         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
  89         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
  90         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
  91     }
  92
  93     @Test
  94     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
  95     public void testDeepDelete_DerivedUnit(){
  96         String assertMessage = "Incorrect number of specimens after deletion.";
  97         DeleteResult deleteResult = null;
  98         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
  99         config.setDeleteMolecularData(true);
 100         config.setDeleteChildren(true);
 101
 102         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
 103         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 104
 105         //check initial state
 106         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 107         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 108         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 109         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 110         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 111         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 112         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 113
 114         //delete derived unit
 115         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 116         assertTrue(deleteResult.toString(), deleteResult.isOk());
 117         assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 118         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 119         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 120         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 121     }
 122
 123     @Test
 124     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
 125     public void testDeepDelete_DnaSample(){
 126         String assertMessage = "Incorrect number of specimens after deletion.";
 127         DeleteResult deleteResult = null;
 128         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 129         config.setDeleteMolecularData(true);
 130         config.setDeleteChildren(true);
 131
 132         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 133
 134         //check initial state
 135         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 136         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 137         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 138         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 139         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 140         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 141         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 142
 143         //delete dna sample
 144         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 145         assertTrue(deleteResult.toString(), deleteResult.isOk());
 146         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 147         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 148         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 149         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 150     }
 151
 152
 153     @Test
 154     @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
 155     public void testDeleteDerivateHierarchyStepByStep(){
 156         String assertMessage = "Incorrect number of specimens after deletion.";
 157         DeleteResult deleteResult = null;
 158         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 159
 160         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
 161         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
 162         DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
 163         Sequence consensusSequence = sequenceService.load(SEQUENCE_UUID);
 164
 165         //check initial state
 166         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 167         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 168         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 169         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 170         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 171         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 172         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 173
 174         //delete single read -> should fail
 175         SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
 176         deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
 177         assertFalse(deleteResult.toString(), deleteResult.isOk());
 178         //delete sequence -> should fail
 179         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 180         assertFalse(deleteResult.toString(), deleteResult.isOk());
 181
 182         //allow deletion of molecular data
 183         config.setDeleteMolecularData(true);
 184
 185         deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
 186         assertTrue(deleteResult.toString(), deleteResult.isOk());
 187         assertTrue(consensusSequence.getSingleReads().isEmpty());
 188
 189         //delete sequence -> should fail
 190         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 191         assertTrue(deleteResult.toString(), deleteResult.isOk());
 192         assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
 193
 194
 195         //delete dna sample
 196         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 197         assertTrue(deleteResult.toString(), deleteResult.isOk());
 198         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 199         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 200         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 201         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 202
 203         //delete derived unit
 204         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 205         assertTrue(deleteResult.toString(), deleteResult.isOk());
 206         assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 207         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 208         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 209         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 210
 211         //delete field unit
 212         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 213         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 214         assertTrue(deleteResult.toString(), deleteResult.isOk());
 215         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
 216         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
 217         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 218         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 219     }
 220
 221     /* (non-Javadoc)
 222      * @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
 223      */
 224     @Override
 225     @Test
 226     @Ignore
 227     public void createTestDataSet() throws FileNotFoundException {
 228         //how the XML was generated
 229         FieldUnit fieldUnit = FieldUnit.NewInstance();
 230         fieldUnit.setUuid(FIELD_UNIT_UUID);
 231         //sub derivates (DerivedUnit, DnaSample)
 232         DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
 233         derivedUnit.setUuid(DERIVED_UNIT_UUID);
 234         DnaSample dnaSample = DnaSample.NewInstance();
 235         dnaSample.setUuid(DNA_SAMPLE_UUID);
 236
 237         //derivation events
 238         DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
 239         DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
 240
 241         //DNA (Sequence, SingleRead, Amplification)
 242         Sequence sequence = Sequence.NewInstance(dnaSample, "ATTCG", 5);
 243         sequence.setUuid(SEQUENCE_UUID);
 244         SingleRead singleRead = SingleRead.NewInstance();
 245         sequence.addSingleRead(singleRead);
 246         dnaSample.addSequence(sequence);
 247         AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
 248         amplificationResult.addSingleRead(singleRead);
 249         occurrenceService.save(fieldUnit);
 250         occurrenceService.save(derivedUnit);
 251         occurrenceService.save(dnaSample);
 252
 253         commitAndStartNewTransaction(null);
 254
 255         setComplete();
 256         endTransaction();
 257
 258
 259         try {
 260             writeDbUnitDataSetFile(new String[] {
 261                     "SpecimenOrObservationBase",
 262                     "SpecimenOrObservationBase_DerivationEvent",
 263                     "DerivationEvent",
 264                     "Sequence",
 265                     "Sequence_SingleRead",
 266                     "SingleRead",
 267                     "AmplificationResult"
 268             });
 269         } catch (FileNotFoundException e) {
 270             e.printStackTrace();
 271         }
 272     }
 273 }