src/test/java/eu/etaxonomy/cdm/service/SpecimenTypeDesignationWorkingSetServiceImplTest.java

   1 /**
   2 * Copyright (C) 2017 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.service;
  10
  11 import java.io.FileNotFoundException;
  12 import java.net.URISyntaxException;
  13 import java.util.UUID;
  14
  15 import org.junit.Assert;
  16 import org.junit.BeforeClass;
  17 import org.junit.FixMethodOrder;
  18 import org.junit.Test;
  19 import org.junit.runners.MethodSorters;
  20 import org.unitils.database.annotations.Transactional;
  21 import org.unitils.database.util.TransactionMode;
  22 import org.unitils.dbunit.annotation.DataSet;
  23 import org.unitils.dbunit.annotation.ExpectedDataSet;
  24 import org.unitils.spring.annotation.SpringBeanByName;
  25 import org.unitils.spring.annotation.SpringBeanByType;
  26
  27 import eu.etaxonomy.cdm.CdmVaadinIntegrationTest;
  28 import eu.etaxonomy.cdm.api.application.CdmRepository;
  29 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  30 import eu.etaxonomy.cdm.api.util.DerivedUnitConversionException;
  31 import eu.etaxonomy.cdm.common.URI;
  32 import eu.etaxonomy.cdm.model.agent.Team;
  33 import eu.etaxonomy.cdm.model.common.Language;
  34 import eu.etaxonomy.cdm.model.common.LanguageString;
  35 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  36 import eu.etaxonomy.cdm.model.name.Rank;
  37 import eu.etaxonomy.cdm.model.name.Registration;
  38 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  39 import eu.etaxonomy.cdm.model.name.TaxonName;
  40 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  41 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  42 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  43 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  44 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  45 import eu.etaxonomy.cdm.model.reference.Reference;
  46 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  47 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  48 import eu.etaxonomy.cdm.vaadin.model.registration.KindOfUnitTerms;
  49 import eu.etaxonomy.cdm.vaadin.model.registration.SpecimenTypeDesignationDTO;
  50 import eu.etaxonomy.cdm.vaadin.model.registration.SpecimenTypeDesignationWorkingSetDTO;
  51
  52 /**
  53  * @author a.kohlbecker
  54  * @since Nov 17, 2017
  55  */
  56 @Transactional(TransactionMode.DISABLED)
  57 // IMPORTANT: test03_deleteTypeDesignationTest executed not as last would cause the other tests to fail due to changes in the db
  58 @FixMethodOrder(MethodSorters.NAME_ASCENDING)
  59 public class SpecimenTypeDesignationWorkingSetServiceImplTest extends CdmVaadinIntegrationTest{
  60
  61     @SpringBeanByName
  62     private CdmRepository cdmRepository;
  63
  64     @SpringBeanByType
  65     private ISpecimenTypeDesignationWorkingSetService service;
  66
  67     @SpringBeanByType
  68     private IOccurrenceService occurrenceService;
  69
  70     @BeforeClass
  71     public static void setupLoggers()  {
  72        // Logger.getLogger("org.dbunit").setLevel(Level.DEBUG);
  73     }
  74
  75     UUID registrationUuid = UUID.fromString("c8bb4e70-ca85-43c3-ae81-c90a2b41a93f"); // 5000;
  76
  77     private UUID publicationUuid = UUID.fromString("45804c65-7df9-42fd-b43a-818a8958c264"); // 5000;
  78
  79     private UUID typifiedNameUuid = UUID.fromString("47d9263e-b32a-42af-98ea-5528f154384f"); //  5000;
  80
  81     private UUID fieldUnitUuid = UUID.fromString("22be718a-6f21-4b74-aae3-bb7d7d659e1c"); // 5001
  82
  83     private final String[] includeTableNames_create = new String[]{"TAXONNAME", "REFERENCE", "AGENTBASE", "HOMOTYPICALGROUP", "REGISTRATION",
  84             "HIBERNATE_SEQUENCES"};
  85
  86     @SuppressWarnings("unused")
  87     private final String[] includeTableNames_delete = new String[]{"TAXONNAME", "REFERENCE", "AGENTBASE", "HOMOTYPICALGROUP", "REGISTRATION",
  88             "DERIVATIONEVENT", "GATHERINGEVENT", "LANGUAGESTRING", "SPECIMENOROBSERVATIONBASE", "TYPEDESIGNATIONBASE",
  89             "REGISTRATION_TYPEDESIGNATIONBASE", "TAXONNAME_TYPEDESIGNATIONBASE", "SPECIMENOROBSERVATIONBASE_DERIVATIONEVENT",
  90             "MEDIA", "MEDIA_REPRESENTATION", "MEDIAREPRESENTATION", "MEDIAREPRESENTATIONPART",
  91             "ORIGINALSOURCEBASE",
  92             "AUDITEVENT",
  93             "HIBERNATE_SEQUENCES"
  94             };
  95
  96     @Test
  97     @DataSet("SpecimenTypeDesignationWorkingSetServiceImplTest.xml")
  98     public void test01_createAndEditTest() throws DerivedUnitConversionException, URISyntaxException, FileNotFoundException {
  99
 100 //        printDataSet(System.err, new String[]{"USERACCOUNT", "GROUPS", "USERACCOUNT_GRANTEDAUTHORITYIMPL", "USERACCOUNT_PERMISSIONGROUP"
 101 //                , "PERMISSIONGROUP", "PERMISSIONGROUP_GRANTEDAUTHORITYIMPL", "GRANTEDAUTHORITYIMPL"});
 102
 103 //        printDataSet(System.err, debugTables);
 104 //        writeDbUnitDataSetFile(new String[]{"AUDITEVENT", "DEFINEDTERMBASE", "DEFINEDTERMBASE_AUD", "DEFINEDTERMBASE_REPRESENTATION", "DEFINEDTERMBASE_REPRESENTATION_AUD",
 105 //                "REPRESENTATION", "REPRESENTATION_AUD", "HIBERNATE_SEQUENCES"},
 106 //                "RegistrationTerms");
 107
 108        SpecimenTypeDesignationWorkingSetDTO<Registration> workingset = service.create(registrationUuid, typifiedNameUuid);
 109
 110        Assert.assertNotNull(workingset.getOwner());
 111        Assert.assertEquals(Registration.class, workingset.getOwner().getClass());
 112
 113        workingset.getFieldUnit().setFieldNotes("FieldNotes");
 114        // int baseEntityID = workingset.getFieldUnit().getId();
 115        workingset.getFieldUnit().setFieldNumber("FieldNumber");
 116        workingset.getFieldUnit().getGatheringEvent().setLocality(LanguageString.NewInstance("Somewhere", Language.ENGLISH()));
 117
 118        SpecimenTypeDesignationDTO specimenTypeDesignationDTO = new SpecimenTypeDesignationDTO();
 119        specimenTypeDesignationDTO.setKindOfUnit((DefinedTerm)cdmRepository.getTermService().load(KindOfUnitTerms.PUBLISHED_IMAGE().getUuid()));
 120        specimenTypeDesignationDTO.setMediaUri(new URI("http://foo.bar.com/image1"));
 121        specimenTypeDesignationDTO.setTypeStatus(SpecimenTypeDesignationStatus.HOLOTYPE());
 122        specimenTypeDesignationDTO.setAccessionNumber("TEST_1");
 123
 124        workingset.getSpecimenTypeDesignationDTOs().add(specimenTypeDesignationDTO);
 125
 126        service.save(workingset);
 127
 128        SpecimenOrObservationBase<?> baseEntity = cdmRepository.getOccurrenceService().load(workingset.getFieldUnit().getUuid());
 129
 130 //     printDataSet(System.err, new String[]{"TYPEDESIGNATIONBASE", "SPECIMENOROBSERVATIONBASE"});
 131
 132        workingset = service.load(registrationUuid, baseEntity);
 133
 134        Assert.assertNotNull(specimenTypeDesignationDTO.asSpecimenTypeDesignation().getTypeSpecimen());
 135        Assert.assertEquals(MediaSpecimen.class, specimenTypeDesignationDTO.asSpecimenTypeDesignation().getTypeSpecimen().getClass());
 136        Assert.assertNotNull(specimenTypeDesignationDTO.asSpecimenTypeDesignation().getTypeSpecimen().getOriginals().iterator().next());
 137        Assert.assertEquals(FieldUnit.class, specimenTypeDesignationDTO.asSpecimenTypeDesignation().getTypeSpecimen().getOriginals().iterator().next().getClass());
 138        Assert.assertEquals("FieldNumber", ((FieldUnit)specimenTypeDesignationDTO.asSpecimenTypeDesignation().getTypeSpecimen().getOriginals().iterator().next()).getFieldNumber());
 139
 140        SpecimenTypeDesignationDTO specimenTypeDesignationDTO2 = new SpecimenTypeDesignationDTO();
 141        specimenTypeDesignationDTO2.setKindOfUnit((DefinedTerm)cdmRepository.getTermService().load(KindOfUnitTerms.SPECIMEN().getUuid()));
 142        specimenTypeDesignationDTO2.setTypeStatus(SpecimenTypeDesignationStatus.HOLOTYPE());
 143        specimenTypeDesignationDTO2.setAccessionNumber("TEST_2");
 144
 145        workingset.getSpecimenTypeDesignationDTOs().add(specimenTypeDesignationDTO2);
 146
 147        service.save(workingset);
 148
 149        workingset = service.load(registrationUuid, baseEntity);
 150        Assert.assertTrue(workingset.getSpecimenTypeDesignationDTOs().size() == 2);
 151
 152        //FIXME this fails: Assert.assertEquals("There must only be one FieldUnit and one MediaSpecimen", 2, cdmRepository.getOccurrenceService().count(DerivedUnit.class));
 153
 154        // write test data for delete test
 155        /*
 156        // printDataSet(System.err, includeTableNames_delete);
 157         writeDbUnitDataSetFile(includeTableNames_delete, "deleteTest");
 158         */
 159        /* The following audit table fix needs also to be added to the test data:
 160            <!-- Test data is being used by more than one test - need to reset a couple of *_AUD tables -->
 161           <AUDITEVENT />
 162           <TAXONNAME_AUD />
 163           <DERIVATIONEVENT_AUD />
 164           <GATHERINGEVENT_AUD />
 165           <LANGUAGESTRING_AUD />
 166           <TYPEDESIGNATIONBASE_AUD />
 167           <SPECIMENOROBSERVATIONBASE_DERIVATIONEVENT_AUD />
 168           <REGISTRATION_AUD />
 169           <SPECIMENOROBSERVATIONBASE_AUD />
 170           <TAXONNAME_TYPEDESIGNATIONBASE_AUD />
 171         */
 172
 173     }
 174
 175     @Test
 176     @DataSet("SpecimenTypeDesignationWorkingSetServiceImplTest-deleteTest.xml")
 177     @ExpectedDataSet("SpecimenTypeDesignationWorkingSetServiceImplTest.deleteTypeDesignationTest-result.xml")
 178     public void test03_deleteTypeDesignationTest() {
 179
 180         FieldUnit baseEntity = (FieldUnit)occurrenceService.load(fieldUnitUuid);
 181
 182         // FieldUnit" ID="5001
 183 //        TypedEntityReference<FieldUnit> baseEntityRef = new TypedEntityReference<>(FieldUnit.class, fieldUnitUuid, "Somewhere, FieldNumber.");
 184         SpecimenTypeDesignationWorkingSetDTO<Registration> workingset = service.load(registrationUuid, baseEntity);
 185         Assert.assertTrue(workingset.getSpecimenTypeDesignationDTOs().size() == 2);
 186
 187         SpecimenTypeDesignationDTO deleteDTO = null;
 188         for(SpecimenTypeDesignationDTO stdDTO : workingset.getSpecimenTypeDesignationDTOs()){
 189             if(stdDTO.getAccessionNumber().equals("TEST_1")){
 190                 deleteDTO = stdDTO;
 191                 break;
 192             }
 193         }
 194         workingset.getSpecimenTypeDesignationDTOs().remove(deleteDTO);
 195
 196         service.save(workingset);
 197
 198         // printDataSet(System.err, includeTableNames_delete);
 199
 200         workingset = service.load(registrationUuid, baseEntity);
 201         Registration reg = workingset.getOwner();
 202         Assert.assertEquals(1, workingset.getSpecimenTypeDesignationDTOs().size());
 203         reg = workingset.getOwner();
 204         Assert.assertEquals(1, reg.getTypeDesignations().size());
 205     }
 206
 207     @Test
 208     @DataSet("SpecimenTypeDesignationWorkingSetServiceImplTest-deleteTest.xml")
 209     public void test02_deleteWorkingset() {
 210
 211 //        printDataSet(System.err, includeTableNames_delete);
 212
 213         FieldUnit baseEntity = (FieldUnit)occurrenceService.load(fieldUnitUuid);
 214
 215 //        TypedEntityReference<FieldUnit> baseEntityRef = new TypedEntityReference<>(FieldUnit.class, fieldUnitUuid, null);
 216
 217         SpecimenTypeDesignationWorkingSetDTO<Registration> workingset = service.load(registrationUuid, baseEntity);
 218         Assert.assertNotNull(workingset.getOwner());
 219         Assert.assertEquals(2, workingset.getSpecimenTypeDesignationDTOs().size());
 220         service.delete(workingset, true);
 221
 222 //        UUID gatheringEventUUID = UUID.fromString("23d40440-38bb-46c1-af11-6e25dcfa0145");
 223 //        UUID fieldUnitUUID = UUID.fromString("22be718a-6f21-4b74-aae3-bb7d7d659e1c");
 224 //        UUID mediaSpecimenUUID = UUID.fromString("10eceb2c-9b51-458e-8dcd-2cb92cc558a9");
 225 //        UUID specimenUUID = UUID.fromString("2e384f8e-fbb0-44eb-9d5f-1b7235493932");
 226 //        UUID typeDesignation1UUID = UUID.fromString("a1896ae2-4396-4243-988e-3d74058b44ab");
 227 //        UUID typeDesignation2UUID = UUID.fromString("a1896ae2-4396-4243-988e-3d74058b44ab");
 228
 229         Assert.assertEquals("All TypeDesignations should have been deleted", 0, cdmRepository.getNameService().getAllTypeDesignations(10, 0).size());
 230         Assert.assertEquals("All derived units should have been deleted", 0, cdmRepository.getOccurrenceService().count(DerivedUnit.class));
 231         Assert.assertEquals("FieldUnit should have been deleted", 0, cdmRepository.getOccurrenceService().count(FieldUnit.class));
 232         Assert.assertEquals("Gathering event should have been deleted by orphan remove", 0, cdmRepository.getEventBaseService().count(GatheringEvent.class));
 233         // FIXME Assert.assertEquals("Media should have been deleted ", 0, cdmRepository.getMediaService().count(null));
 234
 235         // printDataSet(System.err, includeTableNames_delete);
 236     }
 237
 238     // ---------------------- TestData -------------------------------------------
 239
 240
 241     @Override
 242     // @Test
 243     public void createTestDataSet() throws FileNotFoundException {
 244         createRegistration();
 245     }
 246
 247     private void createRegistration() throws FileNotFoundException {
 248
 249         Team team = Team.NewTitledInstance("Novis, Braidwood & Kilroy", "Novis, Braidwood & Kilroy");
 250         Reference nomRef = ReferenceFactory.newArticle();
 251         nomRef.setUuid(publicationUuid);
 252         nomRef = cdmRepository.getReferenceService().save(nomRef);
 253
 254         nomRef.setAuthorship(team);
 255         nomRef.setTitle("P.M. Novis, J. Braidwood & C. Kilroy, Small diatoms (Bacillariophyta) in cultures from the Styx River, New Zealand, including descriptions of three new species in Phytotaxa 64");
 256         TaxonName name = TaxonName.NewInstance(NomenclaturalCode.ICNAFP, Rank.SPECIES(), "Planothidium", null,  "victori", null, null, nomRef, "11-45", null);
 257         name.setUuid(typifiedNameUuid);
 258         name = cdmRepository.getNameService().save(name);
 259
 260         Registration reg = Registration.NewInstance();
 261         reg.setName(name);
 262         reg.setUuid(registrationUuid);
 263         reg = cdmRepository.getRegistrationService().save(reg);
 264
 265         //printDataSet(System.err, includeTableNames_create);
 266
 267         writeDbUnitDataSetFile(includeTableNames_create);
 268     }
 269 }