Examples with TaxonRowWrapperDTO eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO used on opensource projects

Example 1 with TaxonRowWrapperDTO

use of eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetService method createSpecimenRowWrapper.

private SpecimenRowWrapperDTO createSpecimenRowWrapper(DescriptionBaseDto description, UUID taxonNodeUuid, UUID datasetUuid) {
    TaxonNodeDto taxonNode = taxonNodeService.dto(taxonNodeUuid);
    DescriptiveDataSetBaseDto descriptiveDataSet = getDescriptiveDataSetDtoByUuid(datasetUuid);
    // UuidAndTitleCache<SpecimenOrObservationBase> specimen = description.getSpecimenDto();
    SpecimenOrObservationBase specimen = occurrenceService.find(description.getSpecimenDto().getUuid());
    // supplemental information
    if (taxonNode == null) {
        taxonNode = findTaxonNodeForDescription(description, descriptiveDataSet);
    }
    FieldUnit fieldUnit = null;
    String identifier = null;
    NamedArea country = null;
    if (taxonNode == null) {
        return null;
    }
    // taxon node was found
    // get field unit
    Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(specimen.getUuid(), Arrays.asList(new String[] { "gatheringEvent", "gatheringEvent.country" }));
    if (fieldUnits.size() > 1) {
        // $NON-NLS-1$
        logger.error("More than one or no field unit found for specimen");
        return null;
    } else {
        if (fieldUnits.size() > 0) {
            fieldUnit = fieldUnits.iterator().next();
        }
    }
    // get identifier
    identifier = occurrenceService.getMostSignificantIdentifier(specimen.getUuid());
    // get country
    if (fieldUnit != null && fieldUnit.getGatheringEvent() != null) {
        country = fieldUnit.getGatheringEvent().getCountry();
    }
    // get default taxon description
    // TaxonDescription defaultTaxonDescription = findDefaultDescription(description.getUuid(), descriptiveDataSet.getUuid());
    DescriptionBaseDto defaultTaxonDescription = recurseDefaultDescription(taxonNode, descriptiveDataSet);
    TaxonRowWrapperDTO taxonRowWrapper = defaultTaxonDescription != null ? createTaxonRowWrapper(defaultTaxonDescription.getDescriptionUuid(), descriptiveDataSet.getUuid()) : null;
    // use description not specimen for specimenRow
    SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(description, SpecimenOrObservationDTOFactory.fromEntity(specimen), specimen.getRecordBasis(), taxonNode, fieldUnit, identifier, country);
    specimenRowWrapperDTO.setDefaultDescription(taxonRowWrapper);
    return specimenRowWrapperDTO;
}

Example 2 with TaxonRowWrapperDTO

use of eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetService method createTaxonRowWrapper.

@Override
public TaxonRowWrapperDTO createTaxonRowWrapper(DescriptionBaseDto description, UUID descriptiveDataSetUuid) {
    Classification classification = null;
    DescriptiveDataSet descriptiveDataSet = dao.load(descriptiveDataSetUuid, null);
    Optional<TaxonNode> first = descriptiveDataSet.getTaxonSubtreeFilter().stream().filter(node -> node.getClassification() != null).findFirst();
    Optional<Classification> classificationOptional = first.map(node -> node.getClassification());
    Set<DescriptionBaseDto> descriptions = new HashSet<>();
    TaxonNodeDto nodeDto = null;
    if (classificationOptional.isPresent()) {
        classification = classificationOptional.get();
        nodeDto = taxonNodeService.dto(description.getTaxonDto().getUuid(), classification.getUuid());
    }
    return new TaxonRowWrapperDTO(description, nodeDto, descriptions);
}

Example 3 with TaxonRowWrapperDTO

use of eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetServiceTest method testGetRowWrapper.

// the tesat fails when running in suite because no dataset is available, running the test in eclipse works as expected.
@Ignore
@Test
@DataSets({ @DataSet(loadStrategy = CleanSweepInsertLoadStrategy.class, value = "/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), @DataSet(value = "/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), @DataSet(value = "StructuredDescriptionAggregationTest.xml") })
public void testGetRowWrapper() {
    createDefaultFeatureTree();
    DescriptiveDataSet dataSet = createTestDataset();
    commitAndStartNewTransaction();
    List<RowWrapperDTO<?>> rowWrappers = datasetService.getRowWrapper(dataSet.getUuid(), monitor);
    // There are 4 specimen descriptions and one literature description (taxon association)
    assertTrue(rowWrappers.size() == 5);
    // check rowWrapper
    // specimen_1 2 categorical and 1 quantitative
    List<SpecimenRowWrapperDTO> alpinaSpec1List = rowWrappers.stream().filter(r -> r instanceof SpecimenRowWrapperDTO).map(r -> (SpecimenRowWrapperDTO) r).filter(s -> s.getSpecimenDto().getLabel().equals("alpina specimen1")).collect(Collectors.toList());
    Assert.assertEquals(1, alpinaSpec1List.size());
    SpecimenRowWrapperDTO alpinaSpec1Dto = alpinaSpec1List.get(0);
    // leafColor
    Set<DescriptionElementDto> leafColorElements = alpinaSpec1Dto.getDataValueForFeature(uuidFeatureLeafColor);
    Assert.assertNotNull(leafColorElements);
    Assert.assertTrue(leafColorElements.size() == 1);
    DescriptionElementDto dto = leafColorElements.iterator().next();
    Assert.assertTrue(dto instanceof CategoricalDataDto);
    CategoricalDataDto cDto = (CategoricalDataDto) dto;
    assertTrue("The states should contain one element", cDto.getStates().size() == 1);
    StateDataDto stateData = cDto.getStates().iterator().next();
    assertEquals(uuidLeafColorBlue, stateData.getState().getUuid());
    // leaf length
    Set<DescriptionElementDto> leafLengthElements = alpinaSpec1Dto.getDataValueForFeature(uuidFeatureLeafLength);
    Assert.assertNotNull(leafLengthElements);
    Assert.assertTrue(leafLengthElements.size() == 1);
    dto = leafLengthElements.iterator().next();
    Assert.assertTrue(dto instanceof QuantitativeDataDto);
    QuantitativeDataDto qDto = (QuantitativeDataDto) dto;
    assertTrue("The statistical values should contain one element", qDto.getValues().size() == 1);
    StatisticalMeasurementValueDto statValue = qDto.getValues().iterator().next();
    assertEquals(new BigDecimal("5.0"), statValue.getValue());
    Set<DescriptionElementDto> leafPAElements = alpinaSpec1Dto.getDataValueForFeature(uuidFeatureLeafPA);
    Assert.assertNotNull(leafPAElements);
    Assert.assertTrue(leafPAElements.size() == 1);
    dto = leafPAElements.iterator().next();
    Assert.assertTrue(dto instanceof CategoricalDataDto);
    cDto = (CategoricalDataDto) dto;
    assertTrue("The statistical values should contain one element", cDto.getStates().size() == 1);
    stateData = cDto.getStates().iterator().next();
    assertEquals(State.uuidPresent, stateData.getState().getUuid());
    // taxon descriptions
    List<TaxonRowWrapperDTO> taxonDescList = rowWrappers.stream().filter(r -> r instanceof TaxonRowWrapperDTO).map(r -> (TaxonRowWrapperDTO) r).collect(Collectors.toList());
    Assert.assertEquals(1, taxonDescList.size());
    // .filter(s->s.getTaxonDto().getLabel().equals("alpina specimen1")).collect(Collectors.toList());
    TaxonRowWrapperDTO taxonDto = taxonDescList.get(0);
    leafLengthElements = taxonDto.getDataValueForFeature(uuidFeatureLeafLength);
    Assert.assertNotNull(leafLengthElements);
    Assert.assertTrue(leafLengthElements.size() == 1);
    dto = leafLengthElements.iterator().next();
    Assert.assertTrue(dto instanceof QuantitativeDataDto);
    qDto = (QuantitativeDataDto) dto;
    assertTrue("The statistical values should contain one element", qDto.getValues().size() == 2);
    List<StatisticalMeasurementValueDto> minList = qDto.getValues().stream().filter(vs -> vs.getValue().equals(new BigDecimal("4.5"))).collect(Collectors.toList());
    Assert.assertEquals(1, minList.size());
    TermDto minDtoType = minList.get(0).getType();
    Assert.assertTrue(minDtoType.getUuid().equals(StatisticalMeasure.MIN().getUuid()));
    Assert.assertTrue(minDtoType.getTermType().equals(TermType.StatisticalMeasure));
}