cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/integration/SaveCdmEntitiesTest.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.test.integration;
  11
  12 import static org.junit.Assert.assertEquals;
  13
  14 import org.junit.Test;
  15
  16 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  17 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  18 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  19 import eu.etaxonomy.cdm.api.service.INameService;
  20 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  21 import eu.etaxonomy.cdm.api.service.IReferenceService;
  22 import eu.etaxonomy.cdm.api.service.ITermService;
  23 import eu.etaxonomy.cdm.database.CdmDataSource;
  24 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  25 import eu.etaxonomy.cdm.database.ICdmDataSource;
  26 import eu.etaxonomy.cdm.model.agent.Institution;
  27 import eu.etaxonomy.cdm.model.agent.Person;
  28 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  29 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  30 import eu.etaxonomy.cdm.model.common.Language;
  31 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  32 import eu.etaxonomy.cdm.model.common.TimePeriod;
  33 import eu.etaxonomy.cdm.model.location.Country;
  34 import eu.etaxonomy.cdm.model.location.NamedArea;
  35 import eu.etaxonomy.cdm.model.location.Point;
  36 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  37 import eu.etaxonomy.cdm.model.name.BotanicalName;
  38 import eu.etaxonomy.cdm.model.name.Rank;
  39 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  40 import eu.etaxonomy.cdm.model.occurrence.Collection;
  41 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  42 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  43 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  44 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  45 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  46 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  47 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  48 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  49 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  50 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  51 import eu.etaxonomy.cdm.model.reference.Reference;
  52 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  53 import eu.etaxonomy.cdm.model.taxon.Taxon;
  54
  55
  56 /**
  57  * @author pplitzner
  58  * @date Sep 8, 2014
  59  *
  60  */
  61 public class SaveCdmEntitiesTest {
  62
  63     private void persistNonCascadedElements(SpecimenOrObservationBase<?> specimen, ConversationHolder conversation, CdmApplicationController applicationController){
  64         //services
  65         ITermService termService = applicationController.getTermService();
  66         IReferenceService referenceService = applicationController.getReferenceService();
  67         INameService nameService = applicationController.getNameService();
  68
  69         //scan SpecimenOrObservationBase
  70         for(DeterminationEvent determinationEvent:specimen.getDeterminations()){
  71             //modifier
  72             DefinedTerm modifier = determinationEvent.getModifier();
  73             if(termService.find(modifier.getUuid())==null){
  74                 termService.save(modifier);
  75             }
  76             //references DONE with cascading
  77 //            for (Reference reference : determinationEvent.getReferences()) {
  78 //                if(referenceService.find(reference.getUuid())==null){
  79 //                    referenceService.save(reference);
  80 //                }
  81 //                else{
  82 //                    //TODO user interaction??
  83 //                }
  84 //            }
  85         }
  86         //kindOfUnit
  87         persistTerm(termService, specimen.getKindOfUnit());
  88         //lifeStage
  89         persistTerm(termService, specimen.getLifeStage());
  90
  91         //FieldUnit
  92         if(specimen instanceof FieldUnit){
  93             FieldUnit fieldUnit = (FieldUnit)specimen;
  94             GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
  95             if(gatheringEvent!=null){
  96                 //country
  97                 persistTerm(termService, gatheringEvent.getCountry());
  98                 //collecting areas
  99                 for (NamedArea namedArea : gatheringEvent.getCollectingAreas()) {
 100                     persistTerm(termService, namedArea);
 101                 }
 102             }
 103             for (DerivationEvent derivationEvent : fieldUnit.getDerivationEvents()) {
 104                 for (DerivedUnit derivedUnit : derivationEvent.getDerivatives()) {
 105                     persistNonCascadedElements(derivedUnit, conversation, applicationController);
 106                 }
 107             }
 108         }
 109
 110         //DerivedUnit
 111         else if(specimen instanceof DerivedUnit){
 112             DerivedUnit derivedUnit = (DerivedUnit)specimen;
 113             if(derivedUnit.getCollection()!=null && derivedUnit.getCollection().getInstitute()!=null){
 114                 for (DefinedTerm type : derivedUnit.getCollection().getInstitute().getTypes()) {
 115                     persistTerm(termService, type);
 116                 }
 117             }
 118             if(derivedUnit.getPreservation()!=null){
 119                 persistTerm(termService, derivedUnit.getPreservation().getMedium());
 120             }
 121             if(derivedUnit.getStoredUnder()!=null){
 122                 if(nameService.find(derivedUnit.getStoredUnder().getUuid())==null){
 123                     //TODO persist name??
 124                 }
 125                 else{
 126                     //TODO user interaction??
 127                 }
 128             }
 129         }
 130     }
 131
 132     private void persistTerm(ITermService termService, DefinedTermBase<?> term){
 133         if(term!=null){
 134             termService.saveOrUpdate(term);
 135         }
 136     }
 137     //potential fields that are not persisted cascadingly
 138     /*
 139      * SOOB
 140     -DescriptionBase?? how to instantiate?
 141     -determinations
 142     --modifier TERM
 143     --setOfReferences CDM
 144     -kindOfUnit TERM
 145     -lifeStage TERM
 146     - sex TERM
 147
 148     FieldUnit
 149     -GatheringEvent
 150     --Country TERM
 151     --CollectingAreas TERM
 152
 153     DerivedUnit
 154     -collection
 155     --institute
 156     ---types TERM
 157     -preservationMethod
 158     --medium TERM
 159     -storedUnder CDM TaxonNameBase
 160     */
 161
 162     @Test
 163     public void testSaveSpecimen(){
 164         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE_DROP;
 165 //        ICdmDataSource datasource = CdmDataSource.NewMySqlInstance("localhost", "test_db", "root", "root");
 166         ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("test_db", "root", "root");
 167         CdmApplicationController applicationController = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 168
 169         ConversationHolder conversation = applicationController.NewConversation();
 170         conversation.startTransaction();
 171         conversation.bind();
 172
 173         IOccurrenceService occurrenceService = applicationController.getOccurrenceService();
 174         for(int i=0;i<10;i++){
 175             DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 176             derivedUnitFacade.setAccessionNumber(Double.toString(Math.random()));
 177             derivedUnitFacade.setCountry(NamedArea.AFRICA());
 178             derivedUnitFacade.addSource(OriginalSourceType.Unknown, ReferenceFactory.newArticle(), "microReference", "originalNameString");
 179
 180             //save specimen
 181             occurrenceService.saveOrUpdate(derivedUnitFacade.innerDerivedUnit());
 182             conversation.commit();
 183
 184           //Collection
 185             Collection collection = Collection.NewInstance();
 186             Collection subCollection = Collection.NewInstance();
 187             subCollection.setSuperCollection(collection);
 188
 189             collection.setCode("coll code");
 190             collection.setCodeStandard("codeStandard");
 191             collection.setName("coll name");
 192             collection.setTownOrLocation("townOrLocation");
 193             Institution institution = Institution.NewInstance();
 194             collection.setInstitute(institution);
 195
 196             //FieldUnit
 197             FieldUnit fieldUnit = FieldUnit.NewInstance();
 198             fieldUnit.setFieldNumber("fieldNumber");
 199             fieldUnit.setFieldNotes("fieldNotes");
 200             Person primaryCollector = Person.NewInstance();
 201             primaryCollector.setLifespan(TimePeriod.NewInstance(2014));
 202             fieldUnit.setPrimaryCollector(primaryCollector);
 203
 204             GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
 205             fieldUnit.setGatheringEvent(gatheringEvent);
 206             gatheringEvent.putLocality(Language.ENGLISH(), "locality");
 207             gatheringEvent.setExactLocation(Point.NewInstance(22.4, -34.2,
 208                     ReferenceSystem.WGS84(), 33));
 209             gatheringEvent.setCountry(Country.GERMANY());
 210             gatheringEvent.addCollectingArea(NamedArea.EUROPE());
 211             gatheringEvent.setCollectingMethod("collectingMethod");
 212             gatheringEvent.setAbsoluteElevation(10);
 213             gatheringEvent.setAbsoluteElevationMax(100);
 214             gatheringEvent.setAbsoluteElevationText("elevation text");
 215
 216             gatheringEvent.setDistanceToGround(10.4);
 217             gatheringEvent.setDistanceToGroundMax(100.3);
 218             gatheringEvent.setDistanceToGroundText("distance to ground text");
 219
 220             gatheringEvent.setDistanceToWaterSurface(10.4);
 221             gatheringEvent.setDistanceToWaterSurfaceMax(100.3);
 222             gatheringEvent.setDistanceToWaterSurfaceText("distance to water text");
 223
 224
 225             //Derived Unit
 226             MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
 227             mediaSpecimen.setCollection(collection);
 228             mediaSpecimen.setCatalogNumber("catalogNumber");
 229             mediaSpecimen.setAccessionNumber("accessionNumber");
 230 //          mediaSpecimen.setCollectorsNumber("collectorsNumber");
 231             mediaSpecimen.setBarcode("barcode");
 232             BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
 233             storedUnder.setTitleCache("Stored under", true);
 234             mediaSpecimen.setStoredUnder(storedUnder);
 235             mediaSpecimen.setExsiccatum("exsiccatum");
 236             PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
 237             preservation.setTemperature(22.4);
 238             mediaSpecimen.setPreservation(preservation);
 239
 240             //DerivationEvent
 241             DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
 242             event.addOriginal(fieldUnit);
 243             event.addDerivative(mediaSpecimen);
 244
 245
 246             //SpecOrObservationBase
 247             fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
 248             fieldUnit.setLifeStage(DefinedTerm.NewStageInstance("Live stage", "stage", null));
 249             fieldUnit.setKindOfUnit(DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null));
 250             fieldUnit.setIndividualCount(3);
 251             fieldUnit.putDefinition(Language.ENGLISH(), "definition");
 252             fieldUnit.setPublish(true);
 253
 254             //Determination
 255             DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
 256             determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
 257             determinationEvent.setPreferredFlag(true);
 258             Reference<?> reference = getReference();
 259             determinationEvent.addReference(reference);
 260
 261
 262             //save specimen
 263             persistNonCascadedElements(fieldUnit, conversation, applicationController);
 264             occurrenceService.saveOrUpdate(fieldUnit);
 265             try{
 266                 conversation.commit();
 267             }
 268             catch (Exception e){
 269                 e.printStackTrace();
 270             }
 271         }
 272         assertEquals("Incorrect number of DerivedUnits in DB", 20, occurrenceService.getDerivedUnitUuidAndTitleCache().size());
 273
 274     }
 275     private Reference<?> getReference() {
 276         Reference<?> result = ReferenceFactory.newGeneric();
 277         result.setTitle("some generic reference");
 278         return result;
 279    }
 280
 281    private Taxon getTaxon() {
 282        Reference<?> sec = getReference();
 283        TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 284        Taxon taxon = Taxon.NewInstance(name, sec);
 285        return taxon;
 286
 287    }
 288
 289 }