Examples with IdentifiableSource eu.etaxonomy.cdm.model.common.IdentifiableSource used on opensource projects

Example 1 with IdentifiableSource

use of eu.etaxonomy.cdm.model.common.IdentifiableSource in project cdmlib by cybertaxonomy.

the class OwlImportUtil method addTermProperties.

private static void addTermProperties(DefinedTermBase term, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state) {
    term.setUuid(UUID.fromString(termResource.getProperty(OwlUtil.propUuid).getString()));
    // term URI
    String uriString = termResource.hasProperty(OwlUtil.propUri) ? termResource.getProperty(OwlUtil.propUri).getString() : null;
    if (CdmUtils.isNotBlank(uriString)) {
        term.setUri(URI.create(uriString));
    }
    // symbol
    String symbolString = termResource.hasProperty(OwlUtil.propTermSymbol) ? termResource.getProperty(OwlUtil.propTermSymbol).getString() : null;
    if (CdmUtils.isNotBlank(symbolString)) {
        term.setSymbol(symbolString);
    }
    // symbol2
    String symbol2String = termResource.hasProperty(OwlUtil.propTermSymbol2) ? termResource.getProperty(OwlUtil.propTermSymbol2).getString() : null;
    if (CdmUtils.isNotBlank(symbol2String)) {
        term.setSymbol2(symbol2String);
    }
    // idInVocabulary
    String idInVocabularyString = termResource.hasProperty(OwlUtil.propTermIdInVocabulary) ? termResource.getProperty(OwlUtil.propTermIdInVocabulary).getString() : null;
    if (CdmUtils.isNotBlank(idInVocabularyString)) {
        term.setIdInVocabulary(idInVocabularyString);
    }
    // import representations
    Set<Representation> representations = new HashSet<>();
    termResource.listProperties(OwlUtil.propHasRepresentation).forEachRemaining(r -> representations.add(OwlImportUtil.createRepresentation(repo, r, model)));
    if (representations.isEmpty()) {
        logger.error("No representations found for term: " + termResource.getProperty(OwlUtil.propUuid));
    }
    representations.forEach(rep -> term.addRepresentation(rep));
    // import sources
    Set<IdentifiableSource> sources = new HashSet<>();
    termResource.listProperties(OwlUtil.propTermHasSource).forEachRemaining(sourceStatement -> sources.add(OwlImportUtil.createSource(sourceStatement, repo, model)));
    sources.forEach(source -> term.addSource(source));
    // add import source
    IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(termResource.getURI());
    importSource.setCitation(state.getConfig().getSourceReference());
    term.addSource(importSource);
}

Example 2 with IdentifiableSource

use of eu.etaxonomy.cdm.model.common.IdentifiableSource in project cdmlib by cybertaxonomy.

the class OwlImportUtil method createMedia.

static Media createMedia(Resource mediaResource, StructureTreeOwlImportState state) {
    URI mediaUri = URI.create(mediaResource.getProperty(OwlUtil.propMediaUri).getString());
    // create new media
    Media media = Media.NewInstance(mediaUri, null, null, null);
    media.setUuid(UUID.fromString(mediaResource.getProperty(OwlUtil.propUuid).getString()));
    if (mediaResource.hasProperty(OwlUtil.propMediaTitle)) {
        // TODO: support multiple language titles
        media.putTitle(Language.DEFAULT(), mediaResource.getProperty(OwlUtil.propMediaTitle).getString());
    }
    IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(mediaResource.getURI());
    importSource.setCitation(state.getConfig().getSourceReference());
    media.addSource(importSource);
    return media;
}

Example 3 with IdentifiableSource

use of eu.etaxonomy.cdm.model.common.IdentifiableSource in project cdmlib by cybertaxonomy.

the class OwlImportUtil method createVocabulary.

static TermVocabulary createVocabulary(Resource vocabularyResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state) {
    TermType termType = TermType.getByKey(vocabularyResource.getProperty(OwlUtil.propType).getString());
    // create new vocabulary
    TermVocabulary vocabulary = TermVocabulary.NewInstance(termType);
    vocabulary.setUuid(UUID.fromString(vocabularyResource.getProperty(OwlUtil.propUuid).getString()));
    // voc URI
    String vocUriString = vocabularyResource.hasProperty(OwlUtil.propUri) ? vocabularyResource.getProperty(OwlUtil.propUri).getString() : null;
    if (CdmUtils.isNotBlank(vocUriString)) {
        vocabulary.setUri(URI.create(vocUriString));
    }
    // voc representations
    Set<Representation> vocRepresentations = new HashSet<>();
    vocabularyResource.listProperties(OwlUtil.propHasRepresentation).forEachRemaining(r -> vocRepresentations.add(OwlImportUtil.createRepresentation(repo, r, model)));
    if (vocRepresentations.isEmpty()) {
        logger.error("No representations found for vocabulary: " + vocabularyResource.getProperty(OwlUtil.propUuid));
    }
    vocRepresentations.forEach(rep -> vocabulary.addRepresentation(rep));
    IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(vocabularyResource.getURI());
    importSource.setCitation(state.getConfig().getSourceReference());
    vocabulary.addSource(importSource);
    return vocabulary;
}

Example 4 with IdentifiableSource

use of eu.etaxonomy.cdm.model.common.IdentifiableSource 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 5 with IdentifiableSource

use of eu.etaxonomy.cdm.model.common.IdentifiableSource in project cdmlib by cybertaxonomy.

the class CommonServiceImpl method getReferencingObjectTarget.

private UuidAndTitleCache<CdmBase> getReferencingObjectTarget(CdmBase entity) {
    CdmBase targetEntity;
    entity = CdmBase.deproxy(entity);
    if (entity instanceof SecundumSource) {
        targetEntity = ((SecundumSource) entity).getSourcedTaxon();
    } else if (entity instanceof NomenclaturalSource) {
        targetEntity = ((NomenclaturalSource) entity).getSourcedName();
    } else if (entity instanceof DescriptionElementSource) {
        DescriptionElementBase element = ((DescriptionElementSource) entity).getSourcedElement();
        targetEntity = getTarget(element);
    } else if (entity instanceof DescriptionElementBase) {
        targetEntity = getTarget((DescriptionElementBase) entity);
    } else if (entity instanceof IdentifiableSource) {
        IdentifiableSource source = (IdentifiableSource) entity;
        targetEntity = originalSourceDao.findIdentifiableBySourceId(IdentifiableEntity.class, source.getId());
    } else if (entity instanceof NamedSource) {
        NamedSource source = (NamedSource) entity;
        SingleSourcedEntityBase singleSourced = originalSourceDao.findSingleSourceBySourceId(SingleSourcedEntityBase.class, source.getId());
        if (singleSourced != null) {
            targetEntity = singleSourced;
        } else {
            // TODO
            targetEntity = entity;
        }
    } else if (entity instanceof DescriptionBase) {
        targetEntity = getTarget((DescriptionBase<?>) entity);
    } else {
        targetEntity = entity;
    }
    targetEntity = CdmBase.deproxy(targetEntity);
    if (targetEntity == null) {
        targetEntity = entity;
    }
    String targetLabel = targetEntity instanceof IdentifiableEntity ? ((IdentifiableEntity<?>) targetEntity).getTitleCache() : null;
    UuidAndTitleCache<CdmBase> result = new UuidAndTitleCache<>(targetEntity.getClass(), targetEntity.getUuid(), targetEntity.getId(), targetLabel);
    return result;
}