// $Id$
/**
-* Copyright (C) 2014 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
+ * Copyright (C) 2014 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
package eu.etaxonomy.cdm.api.service;
import static org.junit.Assert.assertEquals;
private IDescriptionService descriptionService;
@Test
- public void testGetNonCascadedAssociatedElements(){
- //Collection
+ public void testGetNonCascadedAssociatedElements() {
+ // Collection
Collection collection = Collection.NewInstance();
Collection subCollection = Collection.NewInstance();
subCollection.setSuperCollection(collection);
Institution institution = Institution.NewInstance();
- institution.addType(DefinedTerm.NewInstitutionTypeInstance("Research and teaching", "botanical garden", "BGBM"));
+ institution
+ .addType(DefinedTerm.NewInstitutionTypeInstance("Research and teaching", "botanical garden", "BGBM"));
collection.setInstitute(institution);
- //Source
- Reference<?> article = ReferenceFactory.newArticle(getReference(), Person.NewInstance(), "title", "pages", "series", "volume", TimePeriod.NewInstance(2014));
+ // Source
+ Reference<?> article = ReferenceFactory.newArticle(getReference(), Person.NewInstance(), "title", "pages",
+ "series", "volume", TimePeriod.NewInstance(2014));
IdentifiableSource source = IdentifiableSource.NewPrimarySourceInstance(article, "microCitation");
- //FieldUnit
+ // FieldUnit
FieldUnit fieldUnit = FieldUnit.NewInstance();
Person primaryCollector = Person.NewInstance();
primaryCollector.setLifespan(TimePeriod.NewInstance(2014));
fieldUnit.setPrimaryCollector(primaryCollector);
fieldUnit.addSource(source);
- //GatheringEvent
+ // GatheringEvent
GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
fieldUnit.setGatheringEvent(gatheringEvent);
gatheringEvent.putLocality(Language.ENGLISH(), "locality");
gatheringEvent.setCountry(Country.GERMANY());
gatheringEvent.addCollectingArea(NamedArea.EUROPE());
- //Derived Unit
+ // Derived Unit
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
mediaSpecimen.setCollection(collection);
BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
mediaSpecimen.setStoredUnder(storedUnder);
PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
- preservation.setMedium(DefinedTerm.NewDnaMarkerInstance("medium", "medium", "medium"));//dummy defined term
+ preservation.setMedium(DefinedTerm.NewDnaMarkerInstance("medium", "medium", "medium"));// dummy
+ // defined
+ // term
mediaSpecimen.setPreservation(preservation);
- //DerivationEvent
+ // DerivationEvent
DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
event.addOriginal(fieldUnit);
event.addDerivative(mediaSpecimen);
- //SpecOrObservationBase
+ // SpecOrObservationBase
fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
fieldUnit.setLifeStage(DefinedTerm.NewStageInstance("Live stage", "stage", null));
fieldUnit.setKindOfUnit(DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null));
fieldUnit.putDefinition(Language.ENGLISH(), "definition");
- //Determination
+ // Determination
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
- determinationEvent.setModifier(DefinedTerm.NewModifierInstance("modifierDescription", "modifierLabel", "mofifierLabelAbbrev"));
+ determinationEvent.setModifier(DefinedTerm.NewModifierInstance("modifierDescription", "modifierLabel",
+ "mofifierLabelAbbrev"));
determinationEvent.setPreferredFlag(true);
Reference<?> reference = getReference();
determinationEvent.addReference(reference);
- /*NonCascaded
- * SOOB
- * - sex (FEMALE)
- * - stage (Live stage)
- * - kindOfUnit (Kind of unit)
- * GatheringEvent
- * - country (GERMANY)
- * - collectingArea (EUROPE)
- * DerivedUnit
- * - storedUnder (botanical name)
- * DerivedUnit-> Collection -> institiute
- * - type (botanical garden)
- *
- * */
-
- assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(fieldUnit).size());
- assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService.getNonCascadedAssociatedElements(mediaSpecimen).size());
+ /*
+ * NonCascaded SOOB - sex (FEMALE) - stage (Live stage) - kindOfUnit
+ * (Kind of unit) GatheringEvent - country (GERMANY) - collectingArea
+ * (EUROPE) DerivedUnit - storedUnder (botanical name) DerivedUnit->
+ * Collection -> institiute - type (botanical garden)
+ */
+
+ assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService
+ .getNonCascadedAssociatedElements(fieldUnit).size());
+ assertEquals("Incorrect number of non cascaded CDM entities", 9, occurrenceService
+ .getNonCascadedAssociatedElements(mediaSpecimen).size());
}
+
private Reference<?> getReference() {
Reference<?> result = ReferenceFactory.newGeneric();
result.setTitle("some generic reference");
return result;
- }
- private Taxon getTaxon() {
- Reference<?> sec = getReference();
- TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
- Taxon taxon = Taxon.NewInstance(name, sec);
- return taxon;
+ }
- }
+ private Taxon getTaxon() {
+ Reference<?> sec = getReference();
+ TaxonNameBase<?, ?> name = BotanicalName.NewInstance(Rank.GENUS());
+ Taxon taxon = Taxon.NewInstance(name, sec);
+ return taxon;
- @Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurenceServiceTest.move.xml")
- public void testMoveDerivate(){
- DerivedUnit specimenA = (DerivedUnit) occurrenceService.load(UUID.fromString("35cfb0b3-588d-4eee-9db6-ac9caa44e39a"));
- DerivedUnit specimenB = (DerivedUnit) occurrenceService.load(UUID.fromString("09496534-efd0-44c8-b1ce-01a34a8a0229"));
- DerivedUnit dnaSample = (DnaSample) occurrenceService.load(UUID.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
+ }
+ @Test
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")
+ public void testMoveDerivate() {
+ DerivedUnit specimenA = (DerivedUnit) occurrenceService.load(UUID
+ .fromString("35cfb0b3-588d-4eee-9db6-ac9caa44e39a"));
+ DerivedUnit specimenB = (DerivedUnit) occurrenceService.load(UUID
+ .fromString("09496534-efd0-44c8-b1ce-01a34a8a0229"));
+ DerivedUnit dnaSample = (DnaSample) occurrenceService.load(UUID
+ .fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
occurrenceService.saveOrUpdate(specimenA);
occurrenceService.saveOrUpdate(specimenB);
Institution derivationInstitution = Institution.NewInstance();
TimePeriod derivationTimePeriod = TimePeriod.NewInstance(2015);
- DerivationEvent originalDerivedFromEvent = DerivationEvent.NewSimpleInstance(specimenA, dnaSample, DerivationEventType.DNA_EXTRACTION());
+ DerivationEvent originalDerivedFromEvent = DerivationEvent.NewSimpleInstance(specimenA, dnaSample,
+ DerivationEventType.DNA_EXTRACTION());
originalDerivedFromEvent.setActor(derivationActor);
originalDerivedFromEvent.setDescription(derivationDescription);
assertEquals("DerivationEvent not moved to source!", 1, specimenB.getDerivationEvents().size());
DerivationEvent derivationEvent = specimenB.getDerivationEvents().iterator().next();
- assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(), derivationEvent.getType());
+ assertEquals("Moved DerivationEvent not of same type!", DerivationEventType.DNA_EXTRACTION(),
+ derivationEvent.getType());
assertEquals(derivationActor, derivationEvent.getActor());
assertEquals(derivationDescription, derivationEvent.getDescription());
assertEquals(derivationInstitution, derivationEvent.getInstitution());
assertEquals("Wrong number of derivatives!", 1, derivationEvent.getDerivatives().size());
DerivedUnit movedDerivate = derivationEvent.getDerivatives().iterator().next();
- assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample, movedDerivate.getRecordBasis());
- assertNotEquals("DerivationEvent 'derivedFrom' has not been changed after moving", originalDerivedFromEvent, movedDerivate.getDerivedFrom());
+ assertEquals("Moved derivate has wrong type", SpecimenOrObservationType.DnaSample,
+ movedDerivate.getRecordBasis());
+ assertNotEquals("DerivationEvent 'derivedFrom' has not been changed after moving", originalDerivedFromEvent,
+ movedDerivate.getDerivedFrom());
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="BlankDataSet.xml")
- public void testMoveDerivateNoParent(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "BlankDataSet.xml")
+ public void testMoveDerivateNoParent() {
DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
FieldUnit fieldUnit = FieldUnit.NewInstance();
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurenceServiceTest.move.xml")
- public void testMoveSequence(){
- DnaSample dnaSampleA = (DnaSample) occurrenceService.load(UUID.fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
- DnaSample dnaSampleB = (DnaSample) occurrenceService.load(UUID.fromString("85fccc2f-c796-46b3-b2fc-6c9a4d68cfda"));
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurenceServiceTest.move.xml")
+ public void testMoveSequence() {
+ DnaSample dnaSampleA = (DnaSample) occurrenceService.load(UUID
+ .fromString("5995f852-0e78-405c-b849-d923bd6781d9"));
+ DnaSample dnaSampleB = (DnaSample) occurrenceService.load(UUID
+ .fromString("85fccc2f-c796-46b3-b2fc-6c9a4d68cfda"));
String consensusSequence = "ATTCG";
Sequence sequence = sequenceService.load(UUID.fromString("6da4f378-9861-4338-861b-7b8073763e7a"));
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteIndividualAssociatedAndTypeSpecimen.xml")
- public void testDeleteIndividualAssociatedAndTypeSpecimen(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testDeleteIndividualAssociatedAndTypeSpecimen.xml")
+ public void testDeleteIndividualAssociatedAndTypeSpecimen() {
final UUID taxonDEscriptionUuid = UUID.fromString("a87a893e-2ea8-427d-a26b-dbd2515d6b8a");
final UUID botanicalNameUuid = UUID.fromString("a604774e-d66a-4d47-b9d1-d0e38a8c787a");
final UUID fieldUnitUuid = UUID.fromString("67e81ca8-ff91-4df6-bf48-e4600c7f15a2");
final UUID derivedUnitUuid = UUID.fromString("d229713b-0123-4f15-bffc-76ae45c37564");
- // //how the XML was generated
-// FieldUnit fieldUnit = FieldUnit.NewInstance();
-// fieldUnit.setUuid(fieldUnitUuid);
-// //sub derivates (DerivedUnit, DnaSample)
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setUuid(derivedUnitUuid);
-//
-// //derivation events
-// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
-//
-// occurrenceService.save(fieldUnit);
-// occurrenceService.save(derivedUnit);
-//
-// //create name with type specimen
-// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
-// name.setUuid(BOTANICAL_NAME_UUID);
-// SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
-// typeDesignation.setTypeSpecimen(derivedUnit);
-// //add type designation to name
-// name.addTypeDesignation(typeDesignation, false);
-//
-// // create taxon with name and two taxon descriptions (one with
-// // IndividualsAssociations and a "described" voucher specimen, and an
-// // empty one)
-// Taxon taxon = Taxon.NewInstance(name, null);
-// taxon.setUuid(taxonUuid);
-// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
-// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);
-// //add voucher
-// taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
-// taxon.addDescription(taxonDescription);
-// //add another taxon description to taxon which is not associated with a specimen thus should not be taken into account
-// taxon.addDescription(TaxonDescription.NewInstance());
-// taxonService.saveOrUpdate(taxon);
-//
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testDeleteIndividualAssociatedAndTypeSpecimen");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
+ // //how the XML was generated
+ // FieldUnit fieldUnit = FieldUnit.NewInstance();
+ // fieldUnit.setUuid(fieldUnitUuid);
+ // //sub derivates (DerivedUnit, DnaSample)
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // derivedUnit.setUuid(derivedUnitUuid);
+ //
+ // //derivation events
+ // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
+ // DerivationEventType.ACCESSIONING());
+ //
+ // occurrenceService.save(fieldUnit);
+ // occurrenceService.save(derivedUnit);
+ //
+ // //create name with type specimen
+ // BotanicalName name =
+ // BotanicalName.PARSED_NAME("Campanula patual sec L.");
+ // name.setUuid(BOTANICAL_NAME_UUID);
+ // SpecimenTypeDesignation typeDesignation =
+ // SpecimenTypeDesignation.NewInstance();
+ // typeDesignation.setTypeSpecimen(derivedUnit);
+ // //add type designation to name
+ // name.addTypeDesignation(typeDesignation, false);
+ //
+ // // create taxon with name and two taxon descriptions (one with
+ // // IndividualsAssociations and a "described" voucher specimen, and an
+ // // empty one)
+ // Taxon taxon = Taxon.NewInstance(name, null);
+ // taxon.setUuid(taxonUuid);
+ // TaxonDescription taxonDescription = TaxonDescription.NewInstance();
+ // taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);
+ // //add voucher
+ // taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
+ // taxon.addDescription(taxonDescription);
+ // //add another taxon description to taxon which is not associated with
+ // a specimen thus should not be taken into account
+ // taxon.addDescription(TaxonDescription.NewInstance());
+ // taxonService.saveOrUpdate(taxon);
+ //
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testDeleteIndividualAssociatedAndTypeSpecimen");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
BotanicalName name = (BotanicalName) nameService.load(botanicalNameUuid);
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDEscriptionUuid);
- //check initial state (IndividualsAssociation)
+ // check initial state (IndividualsAssociation)
DescriptionElementBase descriptionElement = taxonDescription.getElements().iterator().next();
assertTrue("wrong type of description element", descriptionElement.isInstanceOf(IndividualsAssociation.class));
- assertEquals("associated specimen is incorrect", associatedFieldUnit, ((IndividualsAssociation)descriptionElement).getAssociatedSpecimenOrObservation());
- //check initial state (Type Designation)
+ assertEquals("associated specimen is incorrect", associatedFieldUnit,
+ ((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation());
+ // check initial state (Type Designation)
Set<TypeDesignationBase> typeDesignations = name.getTypeDesignations();
TypeDesignationBase<?> typeDesignation = typeDesignations.iterator().next();
assertTrue("wrong type of type designation", typeDesignation.isInstanceOf(SpecimenTypeDesignation.class));
- assertEquals("type specimen is incorrect", typeSpecimen, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
+ assertEquals("type specimen is incorrect", typeSpecimen,
+ ((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen());
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
- //delete type specimen from type designation
+ // delete type specimen from type designation
config.setDeleteFromTypeDesignation(true);
occurrenceService.delete(typeSpecimen, config);
- assertTrue(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen()==null);
+ assertTrue(((SpecimenTypeDesignation) typeDesignation).getTypeSpecimen() == null);
- //delete associated field unit from IndividualsAssociation
+ // delete associated field unit from IndividualsAssociation
config.setDeleteFromIndividualsAssociation(true);
occurrenceService.delete(associatedFieldUnit, config);
- assertTrue(((IndividualsAssociation)descriptionElement).getAssociatedSpecimenOrObservation()==null);
+ assertTrue(((IndividualsAssociation) descriptionElement).getAssociatedSpecimenOrObservation() == null);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceService.loadData.xml")
- public void testLoadData(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceService.loadData.xml")
+ public void testLoadData() {
String fieldUnitUuid = "5a31df5a-2e4d-40b1-8d4e-5754736ae7ef";
String derivedUnitUuid = "18f70977-5d9c-400a-96c4-0cb7a2cd287e";
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(UUID.fromString(derivedUnitUuid));
assertFalse(fieldUnit.getDerivationEvents().iterator().next().getDerivatives().isEmpty());
- assertTrue(derivedUnit.getDerivedFrom()!=null);
+ assertTrue(derivedUnit.getDerivedFrom() != null);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testListAssociatedAndTypedTaxa.xml")
- public void testListAssociatedAndTypedTaxa(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testListAssociatedAndTypedTaxa.xml")
+ public void testListAssociatedAndTypedTaxa() {
UUID fieldUnitUuid = UUID.fromString("b359ff20-98de-46bf-aa43-3e10bb072cd4");
UUID typeSpecimenUuid = UUID.fromString("0f8608c7-ffe7-40e6-828c-cb3382580878");
UUID taxonDescriptionUuid = UUID.fromString("d77db2d4-45a1-4aa1-ab34-f33395f54965");
UUID taxonUuid = UUID.fromString("b0de794c-8cb7-4369-8f83-870ca37abbe0");
-// //how the XML was generated
-// FieldUnit associatedFieldUnit = FieldUnit.NewInstance();
-// associatedFieldUnit.setUuid(fieldUnitUuid);
-// //sub derivates (DerivedUnit, DnaSample)
-// DerivedUnit typeSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// typeSpecimen.setUuid(typeSpecimenUuid);
-//
-// //derivation events
-// DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen, DerivationEventType.ACCESSIONING());
-//
-// occurrenceService.save(associatedFieldUnit);
-// occurrenceService.save(typeSpecimen);
-//
-// //create name with type specimen
-// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
-// SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
-// typeDesignation.setTypeSpecimen(typeSpecimen);
-//
-// // create taxon with name and two taxon descriptions (one with
-// // IndividualsAssociations and a "described" voucher specimen, and an
-// // empty one)
-// Taxon taxon = Taxon.NewInstance(name, null);
-// taxon.setUuid(taxonUuid);
-// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
-// taxonDescription.setUuid(taxonDescriptionUuid);
-// //add voucher
-// taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit));
-// taxon.addDescription(taxonDescription);
-// //add type designation to name
-// name.addTypeDesignation(typeDesignation, false);
-// //add another taxon description to taxon which is not associated with a specimen thus should not be taken into account
-// taxon.addDescription(TaxonDescription.NewInstance());
-// taxonService.saveOrUpdate(taxon);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-// try {
-// writeDbUnitDataSetFile(new String[]{
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"}, "testListAssociatedAndTypedTaxa");
-// } catch (FileNotFoundException e) {
-// // TODO Auto-generated catch block
-// e.printStackTrace();
-// }
-//
-// System.out.println("associatedFieldUnit.getUuid() " + associatedFieldUnit.getUuid());
-// System.out.println("typeSpecimen.getUuid() "+typeSpecimen.getUuid());
-// System.out.println("taxonDescription.getUuid() "+taxonDescription.getUuid());
-// System.out.println("taxon.getUuid() "+taxon.getUuid());
-
+ // //how the XML was generated
+ // FieldUnit associatedFieldUnit = FieldUnit.NewInstance();
+ // associatedFieldUnit.setUuid(fieldUnitUuid);
+ // //sub derivates (DerivedUnit, DnaSample)
+ // DerivedUnit typeSpecimen =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // typeSpecimen.setUuid(typeSpecimenUuid);
+ //
+ // //derivation events
+ // DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen,
+ // DerivationEventType.ACCESSIONING());
+ //
+ // occurrenceService.save(associatedFieldUnit);
+ // occurrenceService.save(typeSpecimen);
+ //
+ // //create name with type specimen
+ // BotanicalName name =
+ // BotanicalName.PARSED_NAME("Campanula patual sec L.");
+ // SpecimenTypeDesignation typeDesignation =
+ // SpecimenTypeDesignation.NewInstance();
+ // typeDesignation.setTypeSpecimen(typeSpecimen);
+ //
+ // // create taxon with name and two taxon descriptions (one with
+ // // IndividualsAssociations and a "described" voucher specimen, and an
+ // // empty one)
+ // Taxon taxon = Taxon.NewInstance(name, null);
+ // taxon.setUuid(taxonUuid);
+ // TaxonDescription taxonDescription = TaxonDescription.NewInstance();
+ // taxonDescription.setUuid(taxonDescriptionUuid);
+ // //add voucher
+ // taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit));
+ // taxon.addDescription(taxonDescription);
+ // //add type designation to name
+ // name.addTypeDesignation(typeDesignation, false);
+ // //add another taxon description to taxon which is not associated with
+ // a specimen thus should not be taken into account
+ // taxon.addDescription(TaxonDescription.NewInstance());
+ // taxonService.saveOrUpdate(taxon);
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[]{
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"}, "testListAssociatedAndTypedTaxa");
+ // } catch (FileNotFoundException e) {
+ // // TODO Auto-generated catch block
+ // e.printStackTrace();
+ // }
+ //
+ // System.out.println("associatedFieldUnit.getUuid() " +
+ // associatedFieldUnit.getUuid());
+ // System.out.println("typeSpecimen.getUuid() "+typeSpecimen.getUuid());
+ // System.out.println("taxonDescription.getUuid() "+taxonDescription.getUuid());
+ // System.out.println("taxon.getUuid() "+taxon.getUuid());
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(typeSpecimenUuid);
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
- //check for FieldUnit (IndividualsAssociation)
- java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService.listIndividualsAssociations(associatedFieldUnit, null, null, null,null);
+ // check for FieldUnit (IndividualsAssociation)
+ java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService
+ .listIndividualsAssociations(associatedFieldUnit, null, null, null, null);
assertEquals("Number of individuals associations is incorrect", 1, individualsAssociations.size());
IndividualsAssociation individualsAssociation = individualsAssociations.iterator().next();
- assertTrue("association has wrong type", individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class));
- TaxonDescription retrievedTaxonDescription = HibernateProxyHelper.deproxy(individualsAssociation.getInDescription(), TaxonDescription.class);
+ assertTrue("association has wrong type",
+ individualsAssociation.getInDescription().isInstanceOf(TaxonDescription.class));
+ TaxonDescription retrievedTaxonDescription = HibernateProxyHelper.deproxy(
+ individualsAssociation.getInDescription(), TaxonDescription.class);
assertEquals(taxonDescription, retrievedTaxonDescription);
assertEquals("Associated taxon is incorrect", taxon, retrievedTaxonDescription.getTaxon());
-
- //check for DerivedUnit (Type Designation should exist)
- java.util.Collection<SpecimenTypeDesignation> typeDesignations = occurrenceService.listTypeDesignations(typeSpecimen, null, null, null,null);
+ // check for DerivedUnit (Type Designation should exist)
+ java.util.Collection<SpecimenTypeDesignation> typeDesignations = occurrenceService.listTypeDesignations(
+ typeSpecimen, null, null, null, null);
assertEquals("Number of type designations is incorrect", 1, typeDesignations.size());
SpecimenTypeDesignation specimenTypeDesignation = typeDesignations.iterator().next();
Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames();
Set<?> taxonBases = typifiedNames.iterator().next().getTaxonBases();
assertEquals("number of taxa incorrect", 1, taxonBases.size());
Object next = taxonBases.iterator().next();
- assertTrue(next instanceof CdmBase && ((CdmBase)next).isInstanceOf(Taxon.class));
+ assertTrue(next instanceof CdmBase && ((CdmBase) next).isInstanceOf(Taxon.class));
assertEquals("Typed taxon is incorrect", taxon, next);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithSpecimenDescription.xml")
- public void testIsDeletableWithSpecimenDescription(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithSpecimenDescription.xml")
+ public void testIsDeletableWithSpecimenDescription() {
UUID derivedUnitUuid = UUID.fromString("68095c8e-025d-49f0-8bb2-ed36378b75c3");
UUID specimenDescriptionUuid = UUID.fromString("4094f947-ce84-47b1-bad5-e57e33239d3c");
-// //how the XML was generated
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setUuid(derivedUnitUuid);
-// SpecimenDescription specimenDescription = SpecimenDescription.NewInstance();
-// specimenDescription.setUuid(specimenDescriptionUuid);
-// derivedUnit.addDescription(specimenDescription);
-// occurrenceService.save(derivedUnit);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testIsDeletableWithSpecimenDescription");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
-
+ // //how the XML was generated
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // derivedUnit.setUuid(derivedUnitUuid);
+ // SpecimenDescription specimenDescription =
+ // SpecimenDescription.NewInstance();
+ // specimenDescription.setUuid(specimenDescriptionUuid);
+ // derivedUnit.addDescription(specimenDescription);
+ // occurrenceService.save(derivedUnit);
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testIsDeletableWithSpecimenDescription");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
- SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescriptionUuid);
+ SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService
+ .load(specimenDescriptionUuid);
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
DeleteResult deleteResult = null;
- //delete derivedUnit1
+ // delete derivedUnit1
deleteResult = occurrenceService.isDeletable(derivedUnit, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
- //allow deletion from Descriptions
+ // allow deletion from Descriptions
config.setDeleteFromDescription(true);
deleteResult = occurrenceService.isDeletable(derivedUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
occurrenceService.delete(derivedUnit, config);
- specimenDescription = (SpecimenDescription) descriptionService.find(specimenDescriptionUuid);
+ specimenDescription = (SpecimenDescription) descriptionService.find(specimenDescriptionUuid);
assertNull(specimenDescription);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithDescribedSpecimenInTaxonDescription.xml")
- public void testIsDeletableWithDescribedSpecimenInTaxonDescription(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithDescribedSpecimenInTaxonDescription.xml")
+ public void testIsDeletableWithDescribedSpecimenInTaxonDescription() {
UUID fieldUnitUuid = UUID.fromString("d656a004-38ee-404c-810a-87ffb0ab16c2");
-// //how the XML was generated
-// FieldUnit fieldUnit = FieldUnit.NewInstance();
-// fieldUnit.setUuid(fieldUnitUuid);
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-//
-// //derivation events
-// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
-//
-// occurrenceService.save(fieldUnit);
-// occurrenceService.save(derivedUnit);
-//
-// // create taxon with name and two taxon descriptions
-// //(one with a "described" voucher specimen, and an empty one)
-// Taxon taxon = Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."), null);
-// taxonDescription.setUuid(taxonDescriptionUuid);
-// //add voucher
-// taxonDescription.setDescribedSpecimenOrObservation(derivedUnit);
-// taxon.addDescription(taxonDescription);
-// //add another taxon description to taxon which is not associated with a specimen thus should not be taken into account
-// taxon.addDescription(TaxonDescription.NewInstance());
-// taxonService.saveOrUpdate(taxon);
-//
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testIsDeletableWithDescribedSpecimenInTaxonDescription");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
+ // //how the XML was generated
+ // FieldUnit fieldUnit = FieldUnit.NewInstance();
+ // fieldUnit.setUuid(fieldUnitUuid);
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ //
+ // //derivation events
+ // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
+ // DerivationEventType.ACCESSIONING());
+ //
+ // occurrenceService.save(fieldUnit);
+ // occurrenceService.save(derivedUnit);
+ //
+ // // create taxon with name and two taxon descriptions
+ // //(one with a "described" voucher specimen, and an empty one)
+ // Taxon taxon =
+ // Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),
+ // null);
+ // taxonDescription.setUuid(taxonDescriptionUuid);
+ // //add voucher
+ // taxonDescription.setDescribedSpecimenOrObservation(derivedUnit);
+ // taxon.addDescription(taxonDescription);
+ // //add another taxon description to taxon which is not associated with
+ // a specimen thus should not be taken into account
+ // taxon.addDescription(TaxonDescription.NewInstance());
+ // taxonService.saveOrUpdate(taxon);
+ //
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testIsDeletableWithDescribedSpecimenInTaxonDescription");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
DeleteResult deleteResult = null;
- //check deletion of field unit -> should fail because of voucher specimen (describedSpecimen) in TaxonDescription
+ // check deletion of field unit -> should fail because of voucher
+ // specimen (describedSpecimen) in TaxonDescription
deleteResult = occurrenceService.isDeletable(associatedFieldUnit, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
- //allow deletion from TaxonDescription and deletion of child derivates
+ // allow deletion from TaxonDescription and deletion of child derivates
config.setDeleteFromDescription(true);
config.setDeleteChildren(true);
deleteResult = occurrenceService.isDeletable(associatedFieldUnit, config);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithIndividualsAssociationTaxonDescription.xml")
- public void testIsDeletableWithIndividualsAssociationTaxonDescription(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithIndividualsAssociationTaxonDescription.xml")
+ public void testIsDeletableWithIndividualsAssociationTaxonDescription() {
UUID fieldUnitUuid = UUID.fromString("7978b978-5100-4c7a-82ef-3a23e0f3c723");
UUID taxonDescriptionUuid = UUID.fromString("d4b0d561-6e7e-4fd8-bf3c-925530f949eb");
-// //how the XML was generated
-// FieldUnit fieldUnit = FieldUnit.NewInstance();
-// fieldUnit.setUuid(fieldUnitUuid);
-//
-// occurrenceService.save(fieldUnit);
-//
-// // create taxon with name and two taxon descriptions (one with
-// // IndividualsAssociations and a "described" voucher specimen, and an
-// // empty one)
-// Taxon taxon = Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."), null);
-// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
-// taxonDescription.setUuid(taxonDescriptionUuid);
-// //add voucher
-// taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
-// taxon.addDescription(taxonDescription);
-// //add another taxon description to taxon which is not associated with a specimen thus should not be taken into account
-// taxon.addDescription(TaxonDescription.NewInstance());
-// taxonService.saveOrUpdate(taxon);
-//
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testIsDeletableWithIndividualsAssociationTaxonDescription");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
+ // //how the XML was generated
+ // FieldUnit fieldUnit = FieldUnit.NewInstance();
+ // fieldUnit.setUuid(fieldUnitUuid);
+ //
+ // occurrenceService.save(fieldUnit);
+ //
+ // // create taxon with name and two taxon descriptions (one with
+ // // IndividualsAssociations and a "described" voucher specimen, and an
+ // // empty one)
+ // Taxon taxon =
+ // Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."),
+ // null);
+ // TaxonDescription taxonDescription = TaxonDescription.NewInstance();
+ // taxonDescription.setUuid(taxonDescriptionUuid);
+ // //add voucher
+ // taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit));
+ // taxon.addDescription(taxonDescription);
+ // //add another taxon description to taxon which is not associated with
+ // a specimen thus should not be taken into account
+ // taxon.addDescription(TaxonDescription.NewInstance());
+ // taxonService.saveOrUpdate(taxon);
+ //
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testIsDeletableWithIndividualsAssociationTaxonDescription");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
- IndividualsAssociation individualsAssociation = (IndividualsAssociation) taxonDescription.getElements().iterator().next();
+ IndividualsAssociation individualsAssociation = (IndividualsAssociation) taxonDescription.getElements()
+ .iterator().next();
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
DeleteResult deleteResult = null;
- //check deletion of field unit -> should fail because of IndividualAssociation
+ // check deletion of field unit -> should fail because of
+ // IndividualAssociation
deleteResult = occurrenceService.isDeletable(associatedFieldUnit, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(individualsAssociation));
- //allow deletion of individuals association
+ // allow deletion of individuals association
config.setDeleteFromIndividualsAssociation(true);
deleteResult = occurrenceService.isDeletable(associatedFieldUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithTypeDesignation.xml")
- public void testIsDeletableWithTypeDesignation(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithTypeDesignation.xml")
+ public void testIsDeletableWithTypeDesignation() {
UUID derivedUnitUuid = UUID.fromString("f7fd1dc1-3c93-42a7-8279-cde5bfe37ea0");
UUID botanicalNameUuid = UUID.fromString("7396430c-c932-4dd3-a45a-40c2808b132e");
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setUuid(derivedUnitUuid);
-//
-// occurrenceService.save(derivedUnit);
-//
-// //create name with type specimen
-// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
-// name.setUuid(botanicalNameUuid);
-// SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
-// typeDesignation.setTypeSpecimen(derivedUnit);
-// //add type designation to name
-// name.addTypeDesignation(typeDesignation, false);
-//
-// nameService.saveOrUpdate(name);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "Sequence_SingleRead",
-// "SingleRead",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testIsDeletableWithTypeDesignation");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
-
-
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // derivedUnit.setUuid(derivedUnitUuid);
+ //
+ // occurrenceService.save(derivedUnit);
+ //
+ // //create name with type specimen
+ // BotanicalName name =
+ // BotanicalName.PARSED_NAME("Campanula patual sec L.");
+ // name.setUuid(botanicalNameUuid);
+ // SpecimenTypeDesignation typeDesignation =
+ // SpecimenTypeDesignation.NewInstance();
+ // typeDesignation.setTypeSpecimen(derivedUnit);
+ // //add type designation to name
+ // name.addTypeDesignation(typeDesignation, false);
+ //
+ // nameService.saveOrUpdate(name);
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "Sequence_SingleRead",
+ // "SingleRead",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testIsDeletableWithTypeDesignation");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
- //create name with type specimen
+ // create name with type specimen
BotanicalName name = (BotanicalName) nameService.load(botanicalNameUuid);
- SpecimenTypeDesignation typeDesignation = (SpecimenTypeDesignation) name.getTypeDesignations().iterator().next();
+ SpecimenTypeDesignation typeDesignation = (SpecimenTypeDesignation) name.getTypeDesignations().iterator()
+ .next();
- //add type designation to name
+ // add type designation to name
name.addTypeDesignation(typeDesignation, false);
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
DeleteResult deleteResult = null;
- //check deletion of specimen
+ // check deletion of specimen
deleteResult = occurrenceService.isDeletable(typeSpecimen, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(typeDesignation));
- //allow deletion of type designation
+ // allow deletion of type designation
config.setDeleteFromTypeDesignation(true);
deleteResult = occurrenceService.isDeletable(typeSpecimen, config);
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithChildren.xml")
-
- public void testIsDeletableWithChildren(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testIsDeletableWithChildren.xml")
+ public void testIsDeletableWithChildren() {
UUID fieldUnitUuid = UUID.fromString("92ada058-4c14-4131-8ecd-b82dc1dd2882");
UUID derivedUnitUuid = UUID.fromString("896dffdc-6809-4914-8950-5501fee1c0fd");
UUID dnaSampleUuid = UUID.fromString("7efd1d66-ac7f-4202-acdf-a72cbb9c3a21");
- //if this test fails be sure to check if there are left-over elements in the DB
- //e.g. clear by adding "<AMPLIFICATIONRESULT/>" to the data set XML
-
-// //how the XML was generated
-// FieldUnit fieldUnit = FieldUnit.NewInstance();
-// fieldUnit.setUuid(fieldUnitUuid);
-// //sub derivates (DerivedUnit, DnaSample)
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setUuid(derivedUnitUuid);
-// DnaSample dnaSample = DnaSample.NewInstance();
-// dnaSample.setUuid(dnaSampleUuid);
-//
-// //derivation events
-// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
-// DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
-//
-// occurrenceService.save(fieldUnit);
-// occurrenceService.save(derivedUnit);
-// occurrenceService.save(dnaSample);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "Sequence",
-// "SingleRead",
-// "SingleReadAlignment",
-// "Amplification",
-// "AmplificationResult",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup"
-// }, "testIsDeletableWithChildren");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
+ // if this test fails be sure to check if there are left-over elements
+ // in the DB
+ // e.g. clear by adding "<AMPLIFICATIONRESULT/>" to the data set XML
+
+ // //how the XML was generated
+ // FieldUnit fieldUnit = FieldUnit.NewInstance();
+ // fieldUnit.setUuid(fieldUnitUuid);
+ // //sub derivates (DerivedUnit, DnaSample)
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // derivedUnit.setUuid(derivedUnitUuid);
+ // DnaSample dnaSample = DnaSample.NewInstance();
+ // dnaSample.setUuid(dnaSampleUuid);
+ //
+ // //derivation events
+ // DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit,
+ // DerivationEventType.ACCESSIONING());
+ // DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample,
+ // DerivationEventType.DNA_EXTRACTION());
+ //
+ // occurrenceService.save(fieldUnit);
+ // occurrenceService.save(derivedUnit);
+ // occurrenceService.save(dnaSample);
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "Sequence",
+ // "SingleRead",
+ // "SingleReadAlignment",
+ // "Amplification",
+ // "AmplificationResult",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup"
+ // }, "testIsDeletableWithChildren");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
- //sub derivates (DerivedUnit, DnaSample)
+ // sub derivates (DerivedUnit, DnaSample)
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
- //derivation events
+ // derivation events
DerivationEvent fieldUnitToDerivedUnitEvent = fieldUnit.getDerivationEvents().iterator().next();
DerivationEvent derivedUnitToDnaSampleEvent = derivedUnit.getDerivationEvents().iterator().next();
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
DeleteResult deleteResult = null;
- //check deletion of DnaSample
+ // check deletion of DnaSample
deleteResult = occurrenceService.isDeletable(dnaSample, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
- //check deletion of Specimen
+ // check deletion of Specimen
deleteResult = occurrenceService.isDeletable(derivedUnit, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));
- //check deletion of fieldUnit
+ // check deletion of fieldUnit
deleteResult = occurrenceService.isDeletable(fieldUnit, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(fieldUnitToDerivedUnitEvent));
-
-
- //check deletion of Specimen
+ // check deletion of Specimen
config.setDeleteChildren(true);
deleteResult = occurrenceService.isDeletable(derivedUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent));
- //check deletion of fieldUnit
+ // check deletion of fieldUnit
config.setDeleteFromDescription(true);
deleteResult = occurrenceService.isDeletable(fieldUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
}
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testFindOcurrences.xml")
- public void testFindOccurrences(){
+ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "OccurrenceServiceTest.testFindOcurrences.xml")
+ public void testFindOccurrences() {
UUID derivedUnit1Uuid = UUID.fromString("843bc8c9-c0fe-4735-bf40-82f1996dcefb");
UUID derivedUnit2Uuid = UUID.fromString("40cd9cb1-7c74-4e7d-a1f8-8a1e0314e940");
UUID dnaSampleUuid = UUID.fromString("364969a6-2457-4e2e-ae1e-29a6fcaa741a");
UUID taxonUuid = UUID.fromString("dfca7629-8a60-4d51-998d-371897f725e9");
-// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
-// derivedUnit.setTitleCache("testUnit1");
-// derivedUnit.setAccessionNumber("ACC1");
-// DerivedUnit derivedUnit2 = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
-// derivedUnit2.setTitleCache("testUnit2");
-// derivedUnit2.setBarcode("ACC2");
-// DerivedUnit dnaSample = DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
-// dnaSample.setTitleCache("dna");
-// dnaSample.setCatalogNumber("ACC1");
-// DerivedUnit tissue = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
-// tissue.setTitleCache("tissue");
-//
-// DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
-//
-// derivedUnit.setUuid(derivedUnit1Uuid);
-// derivedUnit2.setUuid(derivedUnit2Uuid);
-// dnaSample.setUuid(dnaSampleUuid);
-// tissue.setUuid(tissueUuid);
-//
-// occurrenceService.save(derivedUnit);
-// occurrenceService.save(derivedUnit2);
-// occurrenceService.save(dnaSample);
-// occurrenceService.save(tissue);
-//
-// Taxon taxon = Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual"), null);
-// taxon.setUuid(taxonUuid);
-// TaxonDescription taxonDescription = TaxonDescription.NewInstance();
-// taxonDescription.setUuid(UUID.fromString("272d4d28-662c-468e-94d8-16993fab91ba"));
-// //add voucher
-// taxonDescription.addElement(IndividualsAssociation.NewInstance(derivedUnit));
-// taxonDescription.addElement(IndividualsAssociation.NewInstance(tissue));
-// taxon.addDescription(taxonDescription);
-// taxonService.saveOrUpdate(taxon);
-//
-// commitAndStartNewTransaction(null);
-//
-// setComplete();
-// endTransaction();
-//
-//
-// try {
-// writeDbUnitDataSetFile(new String[] {
-// "SpecimenOrObservationBase",
-// "SpecimenOrObservationBase_DerivationEvent",
-// "DerivationEvent",
-// "DescriptionElementBase",
-// "DescriptionBase",
-// "TaxonBase",
-// "TypeDesignationBase",
-// "TaxonNameBase",
-// "TaxonNameBase_TypeDesignationBase",
-// "HomotypicalGroup",
-// "TeamOrPersonBase"
-// }, "testFindOcurrences");
-// } catch (FileNotFoundException e) {
-// e.printStackTrace();
-// }
+ // DerivedUnit derivedUnit =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
+ // derivedUnit.setTitleCache("testUnit1");
+ // derivedUnit.setAccessionNumber("ACC1");
+ // DerivedUnit derivedUnit2 =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
+ // derivedUnit2.setTitleCache("testUnit2");
+ // derivedUnit2.setBarcode("ACC2");
+ // DerivedUnit dnaSample =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
+ // dnaSample.setTitleCache("dna");
+ // dnaSample.setCatalogNumber("ACC1");
+ // DerivedUnit tissue =
+ // DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
+ // tissue.setTitleCache("tissue");
+ //
+ // DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample,
+ // DerivationEventType.DNA_EXTRACTION());
+ //
+ // derivedUnit.setUuid(derivedUnit1Uuid);
+ // derivedUnit2.setUuid(derivedUnit2Uuid);
+ // dnaSample.setUuid(dnaSampleUuid);
+ // tissue.setUuid(tissueUuid);
+ //
+ // occurrenceService.save(derivedUnit);
+ // occurrenceService.save(derivedUnit2);
+ // occurrenceService.save(dnaSample);
+ // occurrenceService.save(tissue);
+ //
+ // Taxon taxon =
+ // Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual"),
+ // null);
+ // taxon.setUuid(taxonUuid);
+ // TaxonDescription taxonDescription = TaxonDescription.NewInstance();
+ // taxonDescription.setUuid(UUID.fromString("272d4d28-662c-468e-94d8-16993fab91ba"));
+ // //add voucher
+ // taxonDescription.addElement(IndividualsAssociation.NewInstance(derivedUnit));
+ // taxonDescription.addElement(IndividualsAssociation.NewInstance(tissue));
+ // taxon.addDescription(taxonDescription);
+ // taxonService.saveOrUpdate(taxon);
+ //
+ // commitAndStartNewTransaction(null);
+ //
+ // setComplete();
+ // endTransaction();
+ //
+ //
+ // try {
+ // writeDbUnitDataSetFile(new String[] {
+ // "SpecimenOrObservationBase",
+ // "SpecimenOrObservationBase_DerivationEvent",
+ // "DerivationEvent",
+ // "DescriptionElementBase",
+ // "DescriptionBase",
+ // "TaxonBase",
+ // "TypeDesignationBase",
+ // "TaxonNameBase",
+ // "TaxonNameBase_TypeDesignationBase",
+ // "HomotypicalGroup",
+ // "TeamOrPersonBase"
+ // }, "testFindOcurrences");
+ // } catch (FileNotFoundException e) {
+ // e.printStackTrace();
+ // }
SpecimenOrObservationBase derivedUnit1 = occurrenceService.load(derivedUnit1Uuid);
SpecimenOrObservationBase derivedUnit2 = occurrenceService.load(derivedUnit2Uuid);
assertNotNull(dnaSample);
assertNotNull(taxon);
- //wildcard search => all derivates
+ // wildcard search => all derivates
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
config.setTitleSearchString("*");
assertEquals(4, occurrenceService.countOccurrences(config));
assertTrue(allDerivates.contains(tissue));
assertTrue(allDerivates.contains(dnaSample));
- //queryString search => 2 derivates
+ // queryString search => 2 derivates
config = new FindOccurrencesConfigurator();
config.setTitleSearchString("test*");
-// config.setClazz(SpecimenOrObservationBase.class);
+ // config.setClazz(SpecimenOrObservationBase.class);
assertEquals(2, occurrenceService.countOccurrences(config));
List<SpecimenOrObservationBase> queryStringDerivates = occurrenceService.findByTitle(config).getRecords();
assertEquals(2, queryStringDerivates.size());
assertTrue(queryStringDerivates.contains(derivedUnit1));
assertTrue(queryStringDerivates.contains(derivedUnit2));
- //class search => 0 results
+ // class search => 0 results
config = new FindOccurrencesConfigurator();
config.setClazz(FieldUnit.class);
assertEquals(0, occurrenceService.countOccurrences(config));
List<SpecimenOrObservationBase> fieldUnits = occurrenceService.findByTitle(config).getRecords();
assertEquals(0, fieldUnits.size());
- //class search => 4 results
+ // class search => 4 results
config = new FindOccurrencesConfigurator();
config.setClazz(DerivedUnit.class);
assertEquals(4, occurrenceService.countOccurrences(config));
assertTrue(derivedUnits.contains(tissue));
assertTrue(derivedUnits.contains(dnaSample));
- //significant identifier search
+ // significant identifier search
config = new FindOccurrencesConfigurator();
config.setClazz(DerivedUnit.class);
config.setSignificantIdentifier("ACC1");
assertFalse(barcodedUnits.contains(tissue));
assertFalse(barcodedUnits.contains(dnaSample));
-
- //recordBasis search => 1 Fossil
+ // recordBasis search => 1 Fossil
config = new FindOccurrencesConfigurator();
config.setSpecimenType(SpecimenOrObservationType.Fossil);
assertEquals(1, occurrenceService.countOccurrences(config));
assertEquals(1, fossils.size());
assertTrue(fossils.contains(derivedUnit1));
- //taxon determination search => 2 associated specimens
+ // taxon determination search => 2 associated specimens
config = new FindOccurrencesConfigurator();
config.setClazz(DerivedUnit.class);
config.setAssociatedTaxonUuid(taxon.getUuid());
assertTrue(associatedSpecimens.contains(derivedUnit1));
assertTrue(associatedSpecimens.contains(tissue));
- //taxon determination search (indirectly associated) => 3 associated specimens
+ // taxon determination search (indirectly associated) => 3 associated
+ // specimens
config = new FindOccurrencesConfigurator();
config.setClazz(DerivedUnit.class);
config.setAssociatedTaxonUuid(taxon.getUuid());
config.setRetrieveIndirectlyAssociatedSpecimens(true);
assertEquals(3, occurrenceService.countOccurrences(config));
- List<SpecimenOrObservationBase> indirectlyAssociatedSpecimens = occurrenceService.findByTitle(config).getRecords();
+ List<SpecimenOrObservationBase> indirectlyAssociatedSpecimens = occurrenceService.findByTitle(config)
+ .getRecords();
assertEquals(3, indirectlyAssociatedSpecimens.size());
assertTrue(indirectlyAssociatedSpecimens.contains(derivedUnit1));
assertTrue(indirectlyAssociatedSpecimens.contains(dnaSample));
assertTrue(indirectlyAssociatedSpecimens.contains(tissue));
- //using the super class will lead to 0 results because listByAssociatedTaxon does type matching which obviously does not understand inheritance
+ // using the super class will lead to 0 results because
+ // listByAssociatedTaxon does type matching which obviously does not
+ // understand inheritance
config = new FindOccurrencesConfigurator();
config.setClazz(SpecimenOrObservationBase.class);
config.setAssociatedTaxonUuid(taxon.getUuid());
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
*/
@Override
-// @Test
+ // @Test
public void createTestDataSet() throws FileNotFoundException {
UUID derivedUnit1Uuid = UUID.fromString("843bc8c9-c0fe-4735-bf40-82f1996dcefb");
UUID derivedUnit2Uuid = UUID.fromString("40cd9cb1-7c74-4e7d-a1f8-8a1e0314e940");
taxon.setUuid(taxonUuid);
TaxonDescription taxonDescription = TaxonDescription.NewInstance();
taxonDescription.setUuid(UUID.fromString("272d4d28-662c-468e-94d8-16993fab91ba"));
- //add voucher
+ // add voucher
taxonDescription.addElement(IndividualsAssociation.NewInstance(derivedUnit));
taxonDescription.addElement(IndividualsAssociation.NewInstance(tissue));
taxon.addDescription(taxonDescription);
setComplete();
endTransaction();
-
try {
- writeDbUnitDataSetFile(new String[] {
- "SpecimenOrObservationBase",
- "SpecimenOrObservationBase_DerivationEvent",
- "DerivationEvent",
- "DescriptionElementBase",
- "DescriptionBase",
- "TaxonBase",
- "TypeDesignationBase",
- "TaxonNameBase",
- "TaxonNameBase_TypeDesignationBase",
- "HomotypicalGroup",
- "TeamOrPersonBase"
- }, "testFindOcurrences");
+ writeDbUnitDataSetFile(new String[] { "SpecimenOrObservationBase",
+ "SpecimenOrObservationBase_DerivationEvent", "DerivationEvent", "DescriptionElementBase",
+ "DescriptionBase", "TaxonBase", "TypeDesignationBase", "TaxonNameBase",
+ "TaxonNameBase_TypeDesignationBase", "HomotypicalGroup", "TeamOrPersonBase" }, "testFindOcurrences");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
BGBM BDI Projects / cdmlib.git / commitdiff