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// $Id$
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/**
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* Copyright (C) 2014 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.api.service;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import java.io.FileNotFoundException;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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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.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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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 pplitzner
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* @date 31.03.2014
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*
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*/
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public class OccurrenceServiceDeepDeleteTest extends CdmTransactionalIntegrationTest {
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private final UUID FIELD_UNIT_UUID = UUID.fromString("b5f58da5-4442-4001-9d13-33f41518b72a");
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private final UUID DERIVED_UNIT_UUID = UUID.fromString("448be6e7-f19c-4a10-9a0a-97aa005f817d");
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private final UUID DNA_SAMPLE_UUID = UUID.fromString("bee4212b-aff1-484e-845f-065c7d6216af");
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private final UUID SEQUENCE_UUID = UUID.fromString("0b867369-de8c-4837-a708-5b7d9f6091be");
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(OccurrenceServiceDeepDeleteTest.class);
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@SpringBeanByType
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private IOccurrenceService occurrenceService;
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@SpringBeanByType
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private ISequenceService sequenceService;
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml")
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public void testDeepDelete_FieldUnit(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete field unit
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deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeepDelete_DerivedUnit(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete derived unit
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deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeepDelete_DnaSample(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete dna sample
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deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Test
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@DataSet(value="OccurrenceServiceDeepDeleteTest.testDeleteStepByStep.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeleteDerivateHierarchyStepByStep(){
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UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
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UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
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UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
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UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
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UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
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DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
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DerivedUnit tissueSample = (DerivedUnit) occurrenceService.load(tissueSampleUuid);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
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Sequence consensusSequence = sequenceService.load(sequenceUuid);
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//check initial state
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assertNotNull(fieldUnit);
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assertNotNull(derivedUnit);
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assertNotNull(tissueSample);
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assertNotNull(dnaSample);
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assertNotNull(consensusSequence);
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assertEquals(assertMessage, 4, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 3, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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assertEquals("incorrect number of single reads", 1, consensusSequence.getSingleReads().size());
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assertEquals(consensusSequence.getSingleReads().iterator().next(), dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next());
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//delete sequence -> should fail
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deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
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assertFalse(deleteResult.toString(), deleteResult.isOk());
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//allow deletion of molecular data
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config.setDeleteMolecularData(true);
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SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
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deleteResult = occurrenceService.deleteSingleRead(singleRead, consensusSequence);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals("incorrect number of single reads", 0, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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assertEquals("incorrect number of single reads", 0, consensusSequence.getSingleReads().size());
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//delete sequence -> should fail
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deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
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//delete dna sample
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deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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//delete tissue sample
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deleteResult = occurrenceService.deleteDerivateHierarchy(tissueSample, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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//delete derived unit
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deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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//delete field unit
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deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Override
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@Test
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// @Ignore
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public void createTestDataSet() throws FileNotFoundException {
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UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
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UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
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UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
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UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
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UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
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//how the XML was generated
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FieldUnit fieldUnit = FieldUnit.NewInstance();
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fieldUnit.setUuid(fieldUnitUuid);
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//sub derivates (DerivedUnit, DnaSample)
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DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
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derivedUnit.setUuid(derivedUnitUuid);
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DerivedUnit tissueSample = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
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tissueSample.setUuid(tissueSampleUuid);
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DnaSample dnaSample = (DnaSample) DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
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dnaSample.setUuid(dnaSampleUuid);
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Sequence sequence = Sequence.NewInstance("");
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sequence.setUuid(sequenceUuid);
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SingleRead singleRead1 = SingleRead.NewInstance();
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dnaSample.addSequence(sequence);
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sequence.addSingleRead(singleRead1);
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AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
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amplificationResult.addSingleRead(singleRead1);
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//derivation events
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DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
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DerivationEvent.NewSimpleInstance(derivedUnit, tissueSample, DerivationEventType.TISSUE_SAMPLING());
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DerivationEvent.NewSimpleInstance(tissueSample, dnaSample, DerivationEventType.DNA_EXTRACTION());
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occurrenceService.save(fieldUnit);
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occurrenceService.save(derivedUnit);
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occurrenceService.save(tissueSample);
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occurrenceService.save(dnaSample);
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commitAndStartNewTransaction(null);
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setComplete();
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endTransaction();
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try {
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writeDbUnitDataSetFile(new String[] {
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"SpecimenOrObservationBase",
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"SpecimenOrObservationBase_DerivationEvent",
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"DerivationEvent",
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"Sequence",
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"SingleRead",
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"SingleReadAlignment",
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"Amplification",
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"AmplificationResult",
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"DescriptionElementBase",
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"DescriptionBase",
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"TaxonBase",
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"TypeDesignationBase",
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"TaxonNameBase",
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"TaxonNameBase_TypeDesignationBase",
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"HomotypicalGroup"
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}, "testDeleteStepByStep");
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} catch (FileNotFoundException e) {
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e.printStackTrace();
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}
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}
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}
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