Examples with IndividualsAssociation eu.etaxonomy.cdm.model.description.IndividualsAssociation used on opensource projects

Example 1 with IndividualsAssociation

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

the class MarkupSpecimenImport method handleMaterialsExamined.

public List<DescriptionElementBase> handleMaterialsExamined(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature feature, TaxonDescription defaultDescription) throws XMLStreamException {
    List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();
    // reset current areas
    state.removeCurrentAreas();
    while (reader.hasNext()) {
        XMLEvent next = readNoWhitespace(reader);
        if (isMyEndingElement(next, parentEvent)) {
            if (result.isEmpty()) {
                fireWarningEvent("Materials examined created empty Individual Associations list", parentEvent, 4);
            }
            state.removeCurrentAreas();
            return result;
        } else if (isStartingElement(next, SUB_HEADING)) {
            // Map<String, Object> inlineMarkup = new HashMap<String, Object>();
            String text = getCData(state, reader, next, true);
            if (isFeatureHeading(state, next, text)) {
                feature = makeHeadingFeature(state, next, text, feature);
            } else {
                String message = "Unhandled subheading: %s";
                fireWarningEvent(String.format(message, text), next, 4);
            }
        // for (String key : inlineMarkup.keySet()){
        // handleInlineMarkup(state, key, inlineMarkup);
        // }
        } else if (isStartingElement(next, BR) || isEndingElement(next, BR)) {
        // do nothing
        } else if (isStartingElement(next, GATHERING)) {
            DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.DerivedUnit);
            addCurrentAreas(state, next, facade);
            handleGathering(state, reader, next, facade);
            SpecimenOrObservationBase<?> specimen;
            if (facade.innerDerivedUnit() != null) {
                specimen = facade.innerDerivedUnit();
            } else {
                specimen = facade.innerFieldUnit();
            }
            IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();
            individualsAssociation.addPrimaryTaxonomicSource(state.getConfig().getSourceReference());
            individualsAssociation.setAssociatedSpecimenOrObservation(specimen);
            result.add(individualsAssociation);
        } else if (isStartingElement(next, GATHERING_GROUP)) {
            List<DescriptionElementBase> list = getGatheringGroupDescription(state, reader, next);
            result.addAll(list);
        } else if (next.isCharacters()) {
            String text = next.asCharacters().getData().trim();
            if (isPunctuation(text)) {
            // do nothing
            } else {
                String message = "Unrecognized text: %s";
                fireWarningEvent(String.format(message, text), next, 6);
            }
        } else {
            handleUnexpectedElement(next);
        }
    }
    throw new IllegalStateException("<String> has no closing tag");
}

Example 2 with IndividualsAssociation

use of eu.etaxonomy.cdm.model.description.IndividualsAssociation 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;
}

Example 3 with IndividualsAssociation

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

the class DescriptiveDataSetService method removeDescriptionFromDataSet.

private void removeDescriptionFromDataSet(DeleteResult result, DescriptiveDataSet dataSet, DescriptionBase<?> description, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {
    if (description == null) {
        return;
    }
    boolean success = dataSet.removeDescription(description);
    // remove taxon description with IndividualsAssociation from data set
    result.addDeletedObject(description);
    if (description instanceof SpecimenDescription) {
        @SuppressWarnings({ "unchecked", "cast" }) Set<IndividualsAssociation> // NOTE: don't remove cast as it does not compile on some systems
        associations = (Set<IndividualsAssociation>) dataSet.getDescriptions().stream().flatMap(// put all description element in one stream
        desc -> desc.getElements().stream()).filter(element -> element instanceof IndividualsAssociation).map(ia -> (IndividualsAssociation) ia).collect(Collectors.toSet());
        for (IndividualsAssociation individualsAssociation : associations) {
            if (individualsAssociation.getAssociatedSpecimenOrObservation().equals(description.getDescribedSpecimenOrObservation())) {
                dataSet.removeDescription(individualsAssociation.getInDescription());
                result.addUpdatedObject(individualsAssociation.getInDescription());
            }
        }
    }
    if (description instanceof TaxonDescription) {
        DeleteResult isDeletable = descriptionService.isDeletable(description.getUuid());
        for (CdmBase relatedCdmBase : isDeletable.getRelatedObjects()) {
            if (relatedCdmBase instanceof CdmLinkSource) {
                CdmLinkSource linkSource = (CdmLinkSource) relatedCdmBase;
                if (linkSource.getTarget().equals(this)) {
                }
            }
        }
    }
    if (!config.isOnlyRemoveDescriptionsFromDataSet()) {
        DeleteResult deleteResult = descriptionService.deleteDescription(description);
        result.includeResult(deleteResult);
        result.addUpdatedObject(dataSet);
    } else {
        MergeResult<DescriptiveDataSet> mergeResult = dao.merge(dataSet, true);
        result.addUpdatedObject(mergeResult.getMergedEntity());
    }
    result.setStatus(success ? Status.OK : Status.ERROR);
}

Example 4 with IndividualsAssociation

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

the class DescriptiveDataSetServiceTest method createSpecimenDescription.

private SpecimenDescription createSpecimenDescription(DescriptiveDataSet dataSet, UUID taxonUuid, String specLabel) {
    Taxon taxon = (Taxon) taxonService.find(taxonUuid);
    TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
    DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
    specimen.setTitleCache(specLabel, true);
    IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance(specimen);
    // TODO this has to be discussed; currently the description with the InidividualsAssociation is
    // needed in the dataset for performance reasons
    taxonDescription.addElement(individualsAssociation);
    dataSet.addDescription(taxonDescription);
    SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen);
    dataSet.addDescription(specDesc);
    return specDesc;
}

Example 5 with IndividualsAssociation

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

the class StructuredDescriptionAggregationTest method createSpecimenDescription.

private SpecimenDescription createSpecimenDescription(DescriptiveDataSet dataSet, UUID taxonUuid, String specLabel, UUID specimenUuid) {
    Taxon taxon = (Taxon) taxonService.find(taxonUuid);
    DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
    specimen.setTitleCache(specLabel, true);
    specimen.setUuid(specimenUuid);
    TaxonDescription taxonDescription = taxon.getDescriptions(DescriptionType.INDIVIDUALS_ASSOCIATION).stream().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 individualsAssociation = IndividualsAssociation.NewInstance(specimen);
    // TODO this has to be discussed; currently the description with the InidividualsAssociation is
    // needed in the dataset for performance reasons
    taxonDescription.addElement(individualsAssociation);
    dataSet.addDescription(taxonDescription);
    SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen);
    dataSet.addDescription(specDesc);
    return specDesc;
}