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.assertNotNull;
  15 import static org.junit.Assert.assertTrue;
  16
  17 import java.io.FileNotFoundException;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  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(value="OccurrenceServiceDeepDeleteTest.testDeleteStepByStep.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
 155     public void testDeleteDerivateHierarchyStepByStep(){
 156         UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
 157         UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
 158         UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
 159         UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
 160         UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
 161
 162         String assertMessage = "Incorrect number of specimens after deletion.";
 163         DeleteResult deleteResult = null;
 164         SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
 165
 166         FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
 167         DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
 168         DerivedUnit tissueSample = (DerivedUnit) occurrenceService.load(tissueSampleUuid);
 169         DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
 170         Sequence consensusSequence = sequenceService.load(sequenceUuid);
 171
 172         //check initial state
 173         assertNotNull(fieldUnit);
 174         assertNotNull(derivedUnit);
 175         assertNotNull(tissueSample);
 176         assertNotNull(dnaSample);
 177         assertNotNull(consensusSequence);
 178
 179         assertEquals(assertMessage, 4, occurrenceService.count(SpecimenOrObservationBase.class));
 180         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 181         assertEquals(assertMessage, 3, occurrenceService.count(DerivedUnit.class));
 182         assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
 183         assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
 184         assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
 185         assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 186         assertEquals("incorrect number of single reads", 1, consensusSequence.getSingleReads().size());
 187         assertEquals(consensusSequence.getSingleReads().iterator().next(), dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next());
 188
 189         //delete sequence -> should fail
 190         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 191         assertFalse(deleteResult.toString(), deleteResult.isOk());
 192
 193         //allow deletion of molecular data
 194         config.setDeleteMolecularData(true);
 195
 196         SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
 197         deleteResult = occurrenceService.deleteSingleRead(singleRead, consensusSequence);
 198         assertTrue(deleteResult.toString(), deleteResult.isOk());
 199         assertEquals("incorrect number of single reads", 0, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
 200         assertEquals("incorrect number of single reads", 0, consensusSequence.getSingleReads().size());
 201
 202         //delete sequence -> should fail
 203         deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
 204         assertTrue(deleteResult.toString(), deleteResult.isOk());
 205         assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
 206
 207
 208         //delete dna sample
 209         deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
 210         assertTrue(deleteResult.toString(), deleteResult.isOk());
 211         assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
 212         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 213         assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
 214         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 215
 216         //delete tissue sample
 217         deleteResult = occurrenceService.deleteDerivateHierarchy(tissueSample, config);
 218         assertTrue(deleteResult.toString(), deleteResult.isOk());
 219         assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
 220         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 221         assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
 222         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 223
 224         //delete derived unit
 225         deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
 226         assertTrue(deleteResult.toString(), deleteResult.isOk());
 227         assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
 228         assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
 229         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 230         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 231
 232         //delete field unit
 233         deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
 234
 235         assertTrue(deleteResult.toString(), deleteResult.isOk());
 236         assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
 237         assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
 238         assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
 239         assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
 240     }
 241
 242     @Override
 243     @Test
 244 //    @Ignore
 245     public void createTestDataSet() throws FileNotFoundException {
 246         UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
 247         UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
 248         UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
 249         UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
 250         UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
 251
 252         //how the XML was generated
 253         FieldUnit fieldUnit = FieldUnit.NewInstance();
 254         fieldUnit.setUuid(fieldUnitUuid);
 255         //sub derivates (DerivedUnit, DnaSample)
 256         DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 257         derivedUnit.setUuid(derivedUnitUuid);
 258         DerivedUnit tissueSample = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
 259         tissueSample.setUuid(tissueSampleUuid);
 260         DnaSample dnaSample = (DnaSample) DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
 261         dnaSample.setUuid(dnaSampleUuid);
 262         Sequence sequence = Sequence.NewInstance("");
 263         sequence.setUuid(sequenceUuid);
 264         SingleRead singleRead1 = SingleRead.NewInstance();
 265
 266         dnaSample.addSequence(sequence);
 267         sequence.addSingleRead(singleRead1);
 268         AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
 269         amplificationResult.addSingleRead(singleRead1);
 270
 271         //derivation events
 272         DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
 273         DerivationEvent.NewSimpleInstance(derivedUnit, tissueSample, DerivationEventType.TISSUE_SAMPLING());
 274         DerivationEvent.NewSimpleInstance(tissueSample, dnaSample, DerivationEventType.DNA_EXTRACTION());
 275
 276         occurrenceService.save(fieldUnit);
 277         occurrenceService.save(derivedUnit);
 278         occurrenceService.save(tissueSample);
 279         occurrenceService.save(dnaSample);
 280
 281         commitAndStartNewTransaction(null);
 282
 283         setComplete();
 284         endTransaction();
 285
 286         try {
 287             writeDbUnitDataSetFile(new String[] {
 288                     "SpecimenOrObservationBase",
 289                     "SpecimenOrObservationBase_DerivationEvent",
 290                     "DerivationEvent",
 291                     "Sequence",
 292                     "SingleRead",
 293                     "SingleReadAlignment",
 294                     "Amplification",
 295                     "AmplificationResult",
 296                     "DescriptionElementBase",
 297                     "DescriptionBase",
 298                     "TaxonBase",
 299                     "TypeDesignationBase",
 300                     "TaxonNameBase",
 301                     "TaxonNameBase_TypeDesignationBase",
 302                     "HomotypicalGroup"
 303             }, "testDeleteStepByStep");
 304         } catch (FileNotFoundException e) {
 305             e.printStackTrace();
 306         }
 307     }
 308 }