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Example 1 with QuantitativeData

use of eu.etaxonomy.cdm.model.description.QuantitativeData in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetService method addRowWrapperToDataset.

@Override
@Transactional(readOnly = false)
public UpdateResult addRowWrapperToDataset(Collection<SpecimenRowWrapperDTO> wrappers, UUID datasetUuid, boolean addDatasetSource) {
    UpdateResult result = new UpdateResult();
    DescriptiveDataSet dataSet = load(datasetUuid);
    result.setCdmEntity(dataSet);
    List<UUID> taxonUuids = wrappers.stream().map(wrapper -> wrapper.getTaxonNode().getTaxonUuid()).collect(Collectors.toList());
    List<TaxonBase> taxa = taxonService.load(taxonUuids, Arrays.asList(new String[] { "descriptions" }));
    for (SpecimenRowWrapperDTO wrapper : wrappers) {
        Optional<TaxonBase> findAny = taxa.stream().filter(taxon -> taxon.getUuid().equals(wrapper.getTaxonNode().getTaxonUuid())).findAny();
        if (!findAny.isPresent()) {
            result.addException(new IllegalArgumentException("Could not create wrapper for " + wrapper.getSpecimenDto().getLabel()));
            continue;
        }
        Taxon taxon = (Taxon) findAny.get();
        SpecimenOrObservationBase<?> specimen = occurrenceService.load(wrapper.getSpecimenDto().getUuid());
        TaxonDescription taxonDescription = taxon.getDescriptions().stream().filter(desc -> desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION)).findFirst().orElseGet(() -> {
            TaxonDescription td = TaxonDescription.NewInstance(taxon);
            td.addType(DescriptionType.INDIVIDUALS_ASSOCIATION);
            td.setTitleCache("Specimens used by " + dataSet.getTitleCache() + " for " + getTaxonLabel(taxon), true);
            return td;
        });
        IndividualsAssociation association = null;
        for (DescriptionElementBase el : taxonDescription.getElements()) {
            if (el instanceof IndividualsAssociation) {
                IndividualsAssociation indAss = (IndividualsAssociation) el;
                if (indAss.getAssociatedSpecimenOrObservation().getUuid().equals(specimen.getUuid())) {
                    association = indAss;
                }
            }
        }
        if (association == null) {
            association = IndividualsAssociation.NewInstance(specimen);
            taxonDescription.addElement(association);
            taxonService.saveOrUpdate(taxon);
            result.addUpdatedObject(taxon);
        }
        UUID specimenDescriptionUuid = wrapper.getDescription().getDescriptionUuid();
        DescriptionBaseDto descriptionDto = wrapper.getDescription();
        DescriptionBase<?> specimenDescription = descriptionService.load(specimenDescriptionUuid);
        // if description already exist use the loaded one and add changed data otherwise create a new one and add to specimen
        if (specimenDescription == null) {
            specimenDescription = SpecimenDescription.NewInstance(specimen);
            specimenDescription.setUuid(specimenDescriptionUuid);
            List<DescriptionElementDto> elementDtos = descriptionDto.getElements();
            for (DescriptionElementDto elementDto : elementDtos) {
                if (elementDto instanceof CategoricalDataDto) {
                    eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
                    CategoricalData data = CategoricalData.NewInstance(feature);
                    for (StateDataDto stateDto : ((CategoricalDataDto) elementDto).getStates()) {
                        State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid());
                        data.addStateData(state);
                        specimenDescription.addElement(data);
                    }
                }
                if (elementDto instanceof QuantitativeDataDto) {
                    eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
                    QuantitativeData data = QuantitativeData.NewInstance(feature);
                    if (((QuantitativeDataDto) elementDto).getMeasurementUnit() != null) {
                        MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) elementDto).getMeasurementUnit().getUuid());
                        data.setUnit(unit);
                    }
                    for (StatisticalMeasurementValueDto stateDto : ((QuantitativeDataDto) elementDto).getValues()) {
                        StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, stateDto.getType().getUuid());
                        StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(statMeasure, stateDto.getValue());
                        data.addStatisticalValue(value);
                        specimenDescription.addElement(data);
                    }
                }
            }
        } else {
            List<DescriptionElementDto> elementDtos = descriptionDto.getElements();
            for (DescriptionElementDto elementDto : elementDtos) {
                if (elementDto instanceof CategoricalDataDto) {
                    eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
                    List<DescriptionElementBase> uniqueElementList = specimenDescription.getElements().stream().filter(element -> element.getUuid().equals(elementDto.getElementUuid())).collect(Collectors.toList());
                    List<State> allStates = new ArrayList<>();
                    CategoricalData element = null;
                    if (uniqueElementList.size() == 1) {
                        element = HibernateProxyHelper.deproxy(uniqueElementList.get(0), CategoricalData.class);
                    } else {
                        element = CategoricalData.NewInstance(feature);
                    }
                    for (StateDataDto stateDto : ((CategoricalDataDto) elementDto).getStates()) {
                        State state = DefinedTermBase.getTermByClassAndUUID(State.class, stateDto.getState().getUuid());
                        allStates.add(state);
                    }
                    element.setStateDataOnly(allStates);
                }
                if (elementDto instanceof QuantitativeDataDto) {
                    eu.etaxonomy.cdm.model.description.Character feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, elementDto.getFeatureUuid());
                    QuantitativeData data = QuantitativeData.NewInstance(feature);
                    if (((QuantitativeDataDto) elementDto).getMeasurementUnit() != null) {
                        MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) elementDto).getMeasurementUnit().getUuid());
                        data.setUnit(unit);
                    }
                    for (StatisticalMeasurementValueDto stateDto : ((QuantitativeDataDto) elementDto).getValues()) {
                        StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, stateDto.getType().getUuid());
                        StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(statMeasure, stateDto.getValue());
                        data.addStatisticalValue(value);
                        specimenDescription.addElement(data);
                    }
                }
            }
        }
        if (addDatasetSource) {
            for (IdentifiableSource source : dataSet.getSources()) {
                try {
                    specimenDescription.addSource(source.clone());
                } catch (CloneNotSupportedException e) {
                // nothing
                }
            }
        }
        // add specimen description to data set
        specimenDescription.addDescriptiveDataSet(dataSet);
        // add taxon description with IndividualsAssociation to the specimen to data set
        taxonDescription.addDescriptiveDataSet(dataSet);
        result.addUpdatedObject(specimen);
        result.addUpdatedObject(specimenDescription);
        result.addUpdatedObject(taxonDescription);
    }
    saveOrUpdate(dataSet);
    return result;
}
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Example 2 with QuantitativeData

use of eu.etaxonomy.cdm.model.description.QuantitativeData in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetService method findSpecimenDescription.

@Override
@Transactional(readOnly = false)
public DescriptionBaseDto findSpecimenDescription(UUID descriptiveDataSetUuid, SpecimenOrObservationBase specimen) {
    DescriptiveDataSetBaseDto dataSet = this.getDescriptiveDataSetDtoByUuid(descriptiveDataSetUuid);
    // SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);
    TermTreeDto datasetFeatures = dataSet.getDescriptiveSystem();
    List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
    for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
        specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());
        // check if description is already added to data set
        if (dataSet.getDescriptionUuids().contains(specimenDescription.getUuid())) {
            return DescriptionBaseDto.fromDescription(specimenDescription);
        }
        // gather specimen description features and check for match with dataset features
        Set<Feature> specimenDescriptionFeatures = new HashSet<>();
        for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
            Feature feature = specimenDescriptionElement.getFeature();
            specimenDescriptionFeatures.add(feature);
            boolean contains = false;
            for (TermDto featureDto : datasetFeatures.getTerms()) {
                if (featureDto.getUuid().equals(feature.getUuid())) {
                    contains = true;
                    break;
                }
            }
            if (contains && RowWrapperDTO.hasData(specimenDescriptionElement)) {
                matchingDescriptionElements.add(specimenDescriptionElement);
            }
        }
    }
    // Create new specimen description if description has not already been added to the dataset
    SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
    // $NON-NLS-2$
    newDesription.setTitleCache("Dataset " + dataSet.getTitleCache() + ": " + newDesription.generateTitle(), true);
    // check for equals description element (same feature and same values)
    Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
    for (DescriptionElementBase element : matchingDescriptionElements) {
        List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
        if (list == null) {
            list = new ArrayList<>();
        }
        list.add(element);
        featureToElementMap.put(element.getFeature(), list);
    }
    Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
    for (Feature feature : featureToElementMap.keySet()) {
        List<DescriptionElementBase> elements = featureToElementMap.get(feature);
        // no duplicate description elements found for this feature
        if (elements.size() == 1) {
            descriptionElementsToClone.add(elements.get(0));
        } else // duplicates found -> check if all are equal
        {
            DescriptionElementBase match = null;
            for (DescriptionElementBase descriptionElementBase : elements) {
                if (match == null) {
                    match = descriptionElementBase;
                } else if (!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))) {
                    match = null;
                    // String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
                    break;
                }
            }
            if (match != null) {
                descriptionElementsToClone.add(match);
            }
        }
    }
    // clone matching descriptionElements
    for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
        DescriptionElementBase clone;
        clone = descriptionElementBase.clone(newDesription);
        clone.getSources().forEach(source -> {
            if (descriptionElementBase instanceof CategoricalData) {
                TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, Arrays.asList(new Language[] { Language.DEFAULT() }));
                source.setOriginalNameString(label.getText(Language.DEFAULT()));
            } else if (descriptionElementBase instanceof QuantitativeData) {
                TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, Arrays.asList(new Language[] { Language.DEFAULT() }));
                source.setOriginalNameString(label.getText(Language.DEFAULT()));
            }
        });
    }
    // }
    return DescriptionBaseDto.fromDescription(newDesription);
}
Also used : DescriptiveDataSet(eu.etaxonomy.cdm.model.description.DescriptiveDataSet) Set(java.util.Set) HashSet(java.util.HashSet) DefaultCategoricalDescriptionBuilder(eu.etaxonomy.cdm.format.description.DefaultCategoricalDescriptionBuilder) SpecimenDescription(eu.etaxonomy.cdm.model.description.SpecimenDescription) HashMap(java.util.HashMap) ArrayList(java.util.ArrayList) QuantitativeData(eu.etaxonomy.cdm.model.description.QuantitativeData) Feature(eu.etaxonomy.cdm.model.description.Feature) TermDto(eu.etaxonomy.cdm.persistence.dto.TermDto) DescriptionElementBase(eu.etaxonomy.cdm.model.description.DescriptionElementBase) Language(eu.etaxonomy.cdm.model.common.Language) DefaultQuantitativeDescriptionBuilder(eu.etaxonomy.cdm.format.description.DefaultQuantitativeDescriptionBuilder) CategoricalData(eu.etaxonomy.cdm.model.description.CategoricalData) TextData(eu.etaxonomy.cdm.model.description.TextData) TermTreeDto(eu.etaxonomy.cdm.persistence.dto.TermTreeDto) List(java.util.List) ArrayList(java.util.ArrayList) DescriptiveDataSetBaseDto(eu.etaxonomy.cdm.persistence.dto.DescriptiveDataSetBaseDto) HashSet(java.util.HashSet) Transactional(org.springframework.transaction.annotation.Transactional)

Example 3 with QuantitativeData

use of eu.etaxonomy.cdm.model.description.QuantitativeData in project cdmlib by cybertaxonomy.

the class DescriptionServiceImpl method mergeDescriptions.

@Override
@Transactional(readOnly = false)
public UpdateResult mergeDescriptions(Collection<DescriptionBaseDto> descriptions, UUID descriptiveDataSetUuid) {
    UpdateResult result = new UpdateResult();
    DescriptiveDataSet dataSet = descriptiveDataSetDao.load(descriptiveDataSetUuid);
    Set<DescriptionBase> descriptionsOfDataSet = dataSet.getDescriptions();
    HashMap<UUID, Set<DescriptionBase>> descriptionSpecimenMap = new HashMap<>();
    Set<DescriptionBase> specimenDescriptions;
    for (DescriptionBase<?> descriptionBase : descriptionsOfDataSet) {
        if (descriptionBase.getDescribedSpecimenOrObservation() != null) {
            specimenDescriptions = descriptionSpecimenMap.get(descriptionBase.getDescribedSpecimenOrObservation().getUuid());
            if (specimenDescriptions == null) {
                specimenDescriptions = new HashSet<>();
            }
            specimenDescriptions.add(descriptionBase);
            descriptionSpecimenMap.put(descriptionBase.getDescribedSpecimenOrObservation().getUuid(), specimenDescriptions);
        }
        if (descriptionBase instanceof TaxonDescription) {
            specimenDescriptions = descriptionSpecimenMap.get(((TaxonDescription) descriptionBase).getTaxon().getUuid());
            if (specimenDescriptions == null) {
                specimenDescriptions = new HashSet<>();
            }
            specimenDescriptions.add(descriptionBase);
            descriptionSpecimenMap.put(((TaxonDescription) descriptionBase).getTaxon().getUuid(), specimenDescriptions);
        }
        if (descriptionBase instanceof TaxonNameDescription) {
            specimenDescriptions = descriptionSpecimenMap.get(((TaxonNameDescription) descriptionBase).getTaxonName().getUuid());
            if (specimenDescriptions == null) {
                specimenDescriptions = new HashSet<>();
            }
            specimenDescriptions.add(descriptionBase);
            descriptionSpecimenMap.put(((TaxonNameDescription) descriptionBase).getTaxonName().getUuid(), specimenDescriptions);
        }
    }
    MergeResult<DescriptionBase> mergeResult = null;
    for (DescriptionBaseDto descDto : descriptions) {
        UUID descriptionUUID = descDto.getDescriptionUuid();
        DescriptionBase<?> description = load(descriptionUUID);
        UUID describedObjectUuid = null;
        if (description instanceof SpecimenDescription) {
            describedObjectUuid = descDto.getSpecimenDto().getUuid();
        } else if (description instanceof TaxonDescription) {
            describedObjectUuid = descDto.getTaxonDto().getUuid();
        } else if (description instanceof TaxonNameDescription) {
            describedObjectUuid = descDto.getNameDto().getUuid();
        }
        Set<DescriptionBase> descSpecimen = descriptionSpecimenMap.get(describedObjectUuid);
        if (descSpecimen != null) {
            // TODO: elements are Dtos now, no cdm entities, needs to get the value and replace or create new description element
            Set<DescriptionElementDto> elements = new HashSet<>();
            for (Object element : descDto.getElements()) {
                elements.add((DescriptionElementDto) element);
            }
            DescriptionBase<?> desc = null;
            for (DescriptionBase<?> tempDesc : descSpecimen) {
                if (tempDesc.getUuid().equals(descDto.getDescriptionUuid())) {
                    desc = tempDesc;
                    break;
                }
            }
            Set<DescriptionElementBase> removeElements = new HashSet<>();
            Set<DescriptionElementBase> descriptionElements = desc.getElements();
            for (DescriptionElementBase elementBase : descriptionElements) {
                UUID descElementUuid = elementBase.getUuid();
                if (descElementUuid != null) {
                    List<DescriptionElementDto> equalUuidsElements = elements.stream().filter(e -> e != null && e.getElementUuid() != null && e.getElementUuid().equals(descElementUuid)).collect(Collectors.toList());
                    if (equalUuidsElements.size() == 0 || (equalUuidsElements.size() == 1 && equalUuidsElements.get(0) instanceof QuantitativeDataDto && ((QuantitativeDataDto) equalUuidsElements.get(0)).getValues().isEmpty())) {
                        removeElements.add(elementBase);
                    }
                }
            }
            if (!removeElements.isEmpty()) {
                for (DescriptionElementBase el : removeElements) {
                    desc.removeElement(el);
                }
            }
            for (DescriptionElementDto descElement : elements) {
                if (descElement == null) {
                    continue;
                }
                UUID descElementUuid = descElement.getElementUuid();
                if (descElement instanceof CategoricalDataDto && ((CategoricalDataDto) descElement).getStates().isEmpty() || descElement instanceof QuantitativeDataDto && ((QuantitativeDataDto) descElement).getValues().isEmpty()) {
                    continue;
                }
                List<DescriptionElementBase> equalUuidsElements = descriptionElements.stream().filter(e -> e.getUuid().equals(descElementUuid)).collect(Collectors.toList());
                eu.etaxonomy.cdm.model.description.Feature feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Feature.class, descElement.getFeatureUuid());
                if (feature == null) {
                    feature = DefinedTermBase.getTermByClassAndUUID(eu.etaxonomy.cdm.model.description.Character.class, descElement.getFeatureUuid());
                }
                if (equalUuidsElements.size() == 0) {
                    if (descElement instanceof CategoricalDataDto) {
                        CategoricalData elementBase = CategoricalData.NewInstance(feature);
                        List<StateDataDto> stateDtos = ((CategoricalDataDto) descElement).getStates();
                        for (StateDataDto dataDto : stateDtos) {
                            // create new statedata
                            State newState = DefinedTermBase.getTermByClassAndUUID(State.class, dataDto.getState().getUuid());
                            StateData newStateData = StateData.NewInstance(newState);
                            elementBase.addStateData(newStateData);
                        }
                        desc.addElement(elementBase);
                    }
                    if (descElement instanceof QuantitativeDataDto) {
                        QuantitativeData data = QuantitativeData.NewInstance(feature);
                        if (((QuantitativeDataDto) descElement).getMeasurementUnit() != null) {
                            MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) descElement).getMeasurementUnit().getUuid());
                            data.setUnit(unit);
                        }
                        Set<StatisticalMeasurementValue> statisticalValues = new HashSet<>();
                        Set<StatisticalMeasurementValueDto> valueDtos = ((QuantitativeDataDto) descElement).getValues();
                        data.getStatisticalValues().clear();
                        for (StatisticalMeasurementValueDto dataDto : valueDtos) {
                            // create new statedata
                            StatisticalMeasurementValue newStatisticalMeasurement = StatisticalMeasurementValue.NewInstance(DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, dataDto.getType().getUuid()), dataDto.getValue());
                            statisticalValues.add(newStatisticalMeasurement);
                            data.addStatisticalValue(newStatisticalMeasurement);
                        }
                        // data.getStatisticalValues().addAll(statisticalValues);
                        data = StructuredDescriptionAggregation.handleMissingMinOrMax(data, MissingMinimumMode.MinToZero, MissingMaximumMode.MaxToMin);
                        desc.addElement(data);
                    }
                // create new element
                } else {
                    DescriptionElementBase elementBase = equalUuidsElements.get(0);
                    if (elementBase.isInstanceOf(CategoricalData.class)) {
                        CategoricalData data = HibernateProxyHelper.deproxy(elementBase, CategoricalData.class);
                        List<StateData> states = new ArrayList<>(data.getStateData());
                        List<StateDataDto> stateDtos = ((CategoricalDataDto) descElement).getStates();
                        data.getStateData().clear();
                        if (stateDtos.isEmpty()) {
                            desc.removeElement(data);
                        } else {
                            for (StateDataDto dataDto : stateDtos) {
                                State newState = DefinedTermBase.getTermByClassAndUUID(State.class, dataDto.getState().getUuid());
                                StateData newStateData = StateData.NewInstance(newState);
                                data.addStateData(newStateData);
                            }
                        }
                    } else if (elementBase.isInstanceOf(QuantitativeData.class)) {
                        QuantitativeData data = HibernateProxyHelper.deproxy(elementBase, QuantitativeData.class);
                        Set<StatisticalMeasurementValue> statisticalValues = new HashSet<>();
                        if (((QuantitativeDataDto) descElement).getMeasurementUnit() != null) {
                            MeasurementUnit unit = DefinedTermBase.getTermByClassAndUUID(MeasurementUnit.class, ((QuantitativeDataDto) descElement).getMeasurementUnit().getUuid());
                            if (data.getUnit() == null || (data.getUnit() != null && !data.getUnit().equals(unit))) {
                                data.setUnit(unit);
                            }
                        }
                        Set<StatisticalMeasurementValueDto> valueDtos = ((QuantitativeDataDto) descElement).getValues();
                        data.getStatisticalValues().clear();
                        if (valueDtos.isEmpty()) {
                            desc.removeElement(data);
                        } else {
                            for (StatisticalMeasurementValueDto dataDto : valueDtos) {
                                // create new statedata
                                StatisticalMeasure statMeasure = DefinedTermBase.getTermByClassAndUUID(StatisticalMeasure.class, dataDto.getType().getUuid());
                                StatisticalMeasurementValue newStatisticalMeasurement = StatisticalMeasurementValue.NewInstance(statMeasure, dataDto.getValue());
                                statisticalValues.add(newStatisticalMeasurement);
                                data.addStatisticalValue(newStatisticalMeasurement);
                            }
                            // data.getStatisticalValues().addAll(statisticalValues);
                            data = StructuredDescriptionAggregation.handleMissingMinOrMax(data, MissingMinimumMode.MinToZero, MissingMaximumMode.MaxToMin);
                        }
                    }
                }
            // remove deleted elements
            }
            descriptionSpecimenMap.get(describedObjectUuid).add(desc);
            description = desc;
        }
        try {
            if (description != null) {
                mergeResult = dao.merge(description, true);
                result.addUpdatedObject(mergeResult.getMergedEntity());
            }
        // if (description instanceof SpecimenDescription){
        // result.addUpdatedObject(mergeResult.getMergedEntity().getDescribedSpecimenOrObservation());
        // }else if (description instanceof TaxonDescription){
        // result.addUpdatedObject(((TaxonDescription)mergeResult.getMergedEntity()).getTaxon());
        // }else if (description instanceof TaxonNameDescription){
        // result.addUpdatedObject(((TaxonNameDescription)mergeResult.getMergedEntity()).getTaxonName());
        // }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    return result;
}
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Example 4 with QuantitativeData

use of eu.etaxonomy.cdm.model.description.QuantitativeData in project cdmlib by cybertaxonomy.

the class StructuredDescriptionAggregationTest method verifyQuantitativeData.

private void verifyQuantitativeData(UUID featureUuid, BigDecimal sampleSize, BigDecimal min, BigDecimal max, BigDecimal avg, TaxonDescription aggrDesc) {
    List<QuantitativeData> quantitativeDatas = aggrDesc.getElements().stream().filter(element -> element.getFeature().getUuid().equals(featureUuid)).map(catData -> CdmBase.deproxy(catData, QuantitativeData.class)).collect(Collectors.toList());
    Assert.assertEquals(1, quantitativeDatas.size());
    QuantitativeData leafLength = quantitativeDatas.iterator().next();
    Assert.assertEquals(sampleSize, leafLength.getSampleSize());
    Assert.assertEquals(min, leafLength.getMin());
    Assert.assertEquals(max, leafLength.getMax());
    Assert.assertEquals(avg, leafLength.getAverage());
    Assert.assertEquals(MeasurementUnit.METER(), leafLength.getUnit());
    Assert.assertNotNull(leafLength.getUnit());
}
Also used : DeleteResult(eu.etaxonomy.cdm.api.service.DeleteResult) SpringBeanByType(org.unitils.spring.annotation.SpringBeanByType) TermVocabulary(eu.etaxonomy.cdm.model.term.TermVocabulary) IProgressMonitor(eu.etaxonomy.cdm.common.monitor.IProgressMonitor) CategoricalData(eu.etaxonomy.cdm.model.description.CategoricalData) DerivedUnit(eu.etaxonomy.cdm.model.occurrence.DerivedUnit) IDescriptionService(eu.etaxonomy.cdm.api.service.IDescriptionService) BigDecimal(java.math.BigDecimal) Logger(org.apache.log4j.Logger) DescriptiveDataSet(eu.etaxonomy.cdm.model.description.DescriptiveDataSet) Classification(eu.etaxonomy.cdm.model.taxon.Classification) IClassificationService(eu.etaxonomy.cdm.api.service.IClassificationService) Map(java.util.Map) DataSet(org.unitils.dbunit.annotation.DataSet) TaxonNodeFilter(eu.etaxonomy.cdm.filter.TaxonNodeFilter) ReferenceFactory(eu.etaxonomy.cdm.model.reference.ReferenceFactory) CdmTransactionalIntegrationTest(eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest) TermNode(eu.etaxonomy.cdm.model.term.TermNode) DescriptionElementBase(eu.etaxonomy.cdm.model.description.DescriptionElementBase) Set(java.util.Set) UUID(java.util.UUID) QuantitativeData(eu.etaxonomy.cdm.model.description.QuantitativeData) Collectors(java.util.stream.Collectors) FileNotFoundException(java.io.FileNotFoundException) ITaxonNodeService(eu.etaxonomy.cdm.api.service.ITaxonNodeService) IDescribable(eu.etaxonomy.cdm.model.description.IDescribable) IVocabularyService(eu.etaxonomy.cdm.api.service.IVocabularyService) List(java.util.List) IReferenceService(eu.etaxonomy.cdm.api.service.IReferenceService) DescriptionType(eu.etaxonomy.cdm.model.description.DescriptionType) SpecimenOrObservationBase(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase) DescriptionBase(eu.etaxonomy.cdm.model.description.DescriptionBase) ITermService(eu.etaxonomy.cdm.api.service.ITermService) IBotanicalName(eu.etaxonomy.cdm.model.name.IBotanicalName) SpecimenDescription(eu.etaxonomy.cdm.model.description.SpecimenDescription) IDescriptiveDataSetService(eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService) DataSets(org.unitils.dbunit.annotation.DataSets) Reference(eu.etaxonomy.cdm.model.reference.Reference) StatisticalMeasure(eu.etaxonomy.cdm.model.description.StatisticalMeasure) Taxon(eu.etaxonomy.cdm.model.taxon.Taxon) IndividualsAssociation(eu.etaxonomy.cdm.model.description.IndividualsAssociation) Function(java.util.function.Function) IOccurrenceService(eu.etaxonomy.cdm.api.service.IOccurrenceService) CleanSweepInsertLoadStrategy(eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy) TaxonNameFactory(eu.etaxonomy.cdm.model.name.TaxonNameFactory) TermTree(eu.etaxonomy.cdm.model.term.TermTree) StateData(eu.etaxonomy.cdm.model.description.StateData) State(eu.etaxonomy.cdm.model.description.State) StatisticalMeasurementValue(eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue) Before(org.junit.Before) TaxonNode(eu.etaxonomy.cdm.model.taxon.TaxonNode) CdmBase(eu.etaxonomy.cdm.model.common.CdmBase) Rank(eu.etaxonomy.cdm.model.name.Rank) Test(org.junit.Test) MeasurementUnit(eu.etaxonomy.cdm.model.description.MeasurementUnit) TaxonDescription(eu.etaxonomy.cdm.model.description.TaxonDescription) ICdmRepository(eu.etaxonomy.cdm.api.application.ICdmRepository) ITermTreeService(eu.etaxonomy.cdm.api.service.ITermTreeService) TermType(eu.etaxonomy.cdm.model.term.TermType) ITaxonService(eu.etaxonomy.cdm.api.service.ITaxonService) DefaultProgressMonitor(eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor) Feature(eu.etaxonomy.cdm.model.description.Feature) Assert(org.junit.Assert) QuantitativeData(eu.etaxonomy.cdm.model.description.QuantitativeData)

Example 5 with QuantitativeData

use of eu.etaxonomy.cdm.model.description.QuantitativeData in project cdmlib by cybertaxonomy.

the class DescriptiveDataSetServiceTest method addQuantitativeData.

private void addQuantitativeData(DescriptionBase<?> desc, UUID uuidFeature, StatisticalMeasure type, BigDecimal value) {
    Feature feature = (Feature) termService.find(uuidFeature);
    QuantitativeData qd = QuantitativeData.NewInstance(feature);
    StatisticalMeasurementValue smv = StatisticalMeasurementValue.NewInstance(type, value);
    qd.addStatisticalValue(smv);
    desc.addElement(qd);
}
Also used : QuantitativeData(eu.etaxonomy.cdm.model.description.QuantitativeData) Feature(eu.etaxonomy.cdm.model.description.Feature) StatisticalMeasurementValue(eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue)

Aggregations

QuantitativeData (eu.etaxonomy.cdm.model.description.QuantitativeData)25 Feature (eu.etaxonomy.cdm.model.description.Feature)19 CategoricalData (eu.etaxonomy.cdm.model.description.CategoricalData)13 StatisticalMeasurementValue (eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue)12 BigDecimal (java.math.BigDecimal)12 ArrayList (java.util.ArrayList)10 DescriptionElementBase (eu.etaxonomy.cdm.model.description.DescriptionElementBase)9 MeasurementUnit (eu.etaxonomy.cdm.model.description.MeasurementUnit)9 TaxonDescription (eu.etaxonomy.cdm.model.description.TaxonDescription)9 TextData (eu.etaxonomy.cdm.model.description.TextData)9 Taxon (eu.etaxonomy.cdm.model.taxon.Taxon)8 HashSet (java.util.HashSet)8 Set (java.util.Set)7 DescriptiveDataSet (eu.etaxonomy.cdm.model.description.DescriptiveDataSet)6 SpecimenDescription (eu.etaxonomy.cdm.model.description.SpecimenDescription)6 State (eu.etaxonomy.cdm.model.description.State)6 StateData (eu.etaxonomy.cdm.model.description.StateData)6 StatisticalMeasure (eu.etaxonomy.cdm.model.description.StatisticalMeasure)6 TermDto (eu.etaxonomy.cdm.persistence.dto.TermDto)5 UUID (java.util.UUID)5