Examples with TermNode eu.etaxonomy.cdm.model.term.TermNode used on opensource projects

Example 16 with TermNode

use of eu.etaxonomy.cdm.model.term.TermNode in project cdmlib by cybertaxonomy.

the class OwlImportUtil method addCharacterProperties.

static void addCharacterProperties(Character character, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state) {
    addFeatureProperties(character, termResource, repo, model, state);
    // import property
    if (character.getProperty() != null) {
        Statement propertyStatement = termResource.getProperty(OwlUtil.propCharacterHasProperty);
        Resource propertyResource = model.createResource(propertyStatement.getObject().toString());
        TermNode propertyNode = loadNode(propertyResource, repo, model, state);
        if (propertyNode != null) {
            character.setProperty(propertyNode);
        } else {
            logger.error("Property not found for character: " + character);
            return;
        }
    }
    // import structure
    if (character.getStructure() != null) {
        Statement structureStatement = termResource.getProperty(OwlUtil.propCharacterHasStructure);
        Resource structureResource = model.createResource(structureStatement.getObject().toString());
        TermNode structureNode = loadNode(structureResource, repo, model, state);
        if (structureNode != null) {
            character.setStructure(structureNode);
        } else {
            logger.error("Structure not found for character: " + character);
            return;
        }
    }
    // import structure modifier
    if (character.getStructureModifier() != null && termResource.hasProperty(OwlUtil.propCharacterHasStructureModfier)) {
        Statement structureModifierStatement = termResource.getProperty(OwlUtil.propCharacterHasStructureModfier);
        Resource structureModifierResource = model.createResource(structureModifierStatement.getObject().toString());
        DefinedTerm structureModifier = findTerm(DefinedTerm.class, structureModifierResource, repo, model, state);
        character.setStructureModifier(structureModifier);
    }
}

Example 17 with TermNode

use of eu.etaxonomy.cdm.model.term.TermNode in project cdmlib by cybertaxonomy.

the class SDDDocumentBuilder method buildCharacterTrees.

public void buildCharacterTrees(ElementImpl dataset) throws ParseException {
    if (cdmSource.getFeatureData() != null) {
        ElementImpl elChartrees = new ElementImpl(document, CHARACTER_TREES);
        for (int i = 0; i < cdmSource.getFeatureData().size(); i++) {
            VersionableEntity featu = cdmSource.getFeatureData().get(i);
            if (featu instanceof TermTree) {
                TermTree ft = (TermTree) featu;
                ElementImpl elChartree = new ElementImpl(document, CHARACTER_TREE);
                chartreeCount = buildReference(featu, featuretrees, ID, elChartree, "ct", chartreeCount);
                buildRepresentation(elChartree, ft);
                elChartrees.appendChild(elChartree);
                ElementImpl elNodes = new ElementImpl(document, NODES);
                elChartree.appendChild(elNodes);
                List<TermNode> roots = ft.getRootChildren();
                for (Iterator<TermNode> fn = roots.iterator(); fn.hasNext(); ) {
                    TermNode featureNode = fn.next();
                    buildBranches(featureNode, elNodes, true);
                }
            }
        }
        dataset.appendChild(elChartrees);
    }
}

Example 18 with TermNode

use of eu.etaxonomy.cdm.model.term.TermNode in project cdmlib by cybertaxonomy.

the class TermNodeDaoImpl method list.

@Override
public List<TermNode> list() {
    Criteria crit = getSession().createCriteria(type);
    @SuppressWarnings("unchecked") List<TermNode> result = crit.list();
    return result;
}

Example 19 with TermNode

use of eu.etaxonomy.cdm.model.term.TermNode in project cdmlib by cybertaxonomy.

the class TermNodeDaoImpl method list.

// TODO still needs to be tested
@Override
public List<TermNode> list(TermType termType, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
    Criteria criteria = getSession().createCriteria(type);
    if (termType != null) {
        Set<TermType> types = termType.getGeneralizationOf(true);
        types.add(termType);
        criteria.add(Restrictions.in("termType", types));
    }
    addLimitAndStart(criteria, limit, start);
    addOrder(criteria, orderHints);
    @SuppressWarnings("unchecked") List<TermNode> results = criteria.list();
    defaultBeanInitializer.initializeAll(results, propertyPaths);
    return results;
}

Example 20 with TermNode

use of eu.etaxonomy.cdm.model.term.TermNode in project cdmlib by cybertaxonomy.

the class CharacterDto method termDtoListFrom.

public static List<TermDto> termDtoListFrom(List<Object[]> results) {
    // list to ensure order
    List<TermDto> dtos = new ArrayList<>();
    // map to handle multiple representations/media/vocRepresentation because of LEFT JOIN
    Map<UUID, TermDto> dtoMap = new HashMap<>(results.size());
    for (Object[] elements : results) {
        UUID uuid = (UUID) elements[0];
        if (dtoMap.containsKey(uuid)) {
            // multiple results for one term -> multiple (voc) representation/media
            if (elements[1] != null) {
                dtoMap.get(uuid).addRepresentation((Representation) elements[1]);
            }
            // }
            if (elements[8] != null) {
                dtoMap.get(uuid).addMedia(((Media) elements[8]).getUuid());
            }
        } else {
            // term representation
            Set<Representation> representations = new HashSet<>();
            if (elements[1] instanceof Representation) {
                representations = new HashSet<Representation>(1);
                representations.add((Representation) elements[1]);
            }
            // term media
            Set<UUID> mediaUuids = new HashSet<>();
            if (elements[8] instanceof Media) {
                mediaUuids.add(((Media) elements[8]).getUuid());
            }
            // voc representation
            // Set<Representation> vocRepresentations = new HashSet<>();
            // if(elements[6] instanceof Representation) {
            // vocRepresentations = new HashSet<Representation>(7);
            // vocRepresentations.add((Representation)elements[6]);
            // }
            boolean isAvailableForTaxon = false;
            boolean isAvailableForTaxonName = false;
            boolean isAvailableForOccurrence = false;
            EnumSet<CdmClass> availableForString = (EnumSet<CdmClass>) elements[9];
            if (availableForString.contains(CdmClass.TAXON)) {
                isAvailableForTaxon = true;
            }
            if (availableForString.contains(CdmClass.TAXON_NAME)) {
                isAvailableForTaxonName = true;
            }
            if (availableForString.contains(CdmClass.OCCURRENCE)) {
                isAvailableForOccurrence = true;
            }
            boolean isSupportsCategoricalData = false;
            boolean isSupportsQuantitativeData = false;
            EnumSet<CdmClass> supportsString = (EnumSet<CdmClass>) elements[11];
            if (supportsString.contains(CdmClass.CATEGORICAL_DATA)) {
                isSupportsCategoricalData = true;
            }
            if (supportsString.contains(CdmClass.QUANTITATIVE_DATA)) {
                isSupportsQuantitativeData = true;
            }
            Object o = elements[12];
            Set<TermVocabularyDto> recommendedModifierDtos = new HashSet<>();
            if (o instanceof TermVocabulary) {
                recommendedModifierDtos.add(TermVocabularyDto.fromVocabulary((TermVocabulary) o));
            } else if (o instanceof Set) {
                Set<TermVocabulary<DefinedTerm>> recommendedModifierEnumeration = (Set<TermVocabulary<DefinedTerm>>) o;
                if (recommendedModifierEnumeration != null) {
                    for (TermVocabulary<DefinedTerm> voc : recommendedModifierEnumeration) {
                        recommendedModifierDtos.add(TermVocabularyDto.fromVocabulary(voc));
                    }
                }
            }
            o = elements[13];
            Set<TermDto> recommendedStatisticalMeasuresDtos = new HashSet<>();
            if (o instanceof StatisticalMeasure) {
                recommendedStatisticalMeasuresDtos.add(TermDto.fromTerm((StatisticalMeasure) o));
            } else if (o instanceof Set) {
                Set<StatisticalMeasure> recommendedStatisticalMeasures = (Set<StatisticalMeasure>) o;
                if (recommendedStatisticalMeasures != null) {
                    for (StatisticalMeasure term : recommendedStatisticalMeasures) {
                        recommendedStatisticalMeasuresDtos.add(TermDto.fromTerm(term));
                    }
                }
            }
            o = elements[14];
            Set<TermVocabularyDto> supportedCategoricalDtos = new HashSet<>();
            if (o instanceof TermVocabulary) {
                supportedCategoricalDtos.add(TermVocabularyDto.fromVocabulary((TermVocabulary) o));
            } else if (o instanceof Set) {
                Set<TermVocabulary> supportedCategoricalEnumerations = (Set<TermVocabulary>) o;
                for (TermVocabulary<State> voc : supportedCategoricalEnumerations) {
                    supportedCategoricalDtos.add(TermVocabularyDto.fromVocabulary(voc));
                }
            }
            o = elements[15];
            Set<TermDto> recommendedMeasurementUnitsDtos = new HashSet<>();
            if (o instanceof MeasurementUnit) {
                recommendedMeasurementUnitsDtos.add(TermDto.fromTerm((MeasurementUnit) o));
            } else if (o instanceof Set) {
                Set<MeasurementUnit> recommendedMeasurementUnits = (Set<MeasurementUnit>) elements[15];
                for (MeasurementUnit term : recommendedMeasurementUnits) {
                    recommendedMeasurementUnitsDtos.add(TermDto.fromTerm(term));
                }
            }
            o = elements[16];
            TermNodeDto prop = null;
            if (o instanceof TermNode) {
                prop = TermNodeDto.fromNode((TermNode) o, TermTreeDto.fromTree((TermTree) ((TermNode) o).getGraph()));
            }
            o = elements[17];
            TermNodeDto structure = null;
            if (o instanceof TermNode) {
                structure = TermNodeDto.fromNode((TermNode) o, TermTreeDto.fromTree((TermTree) ((TermNode) o).getGraph()));
            }
            o = elements[9];
            TermNodeDto ratioTo = null;
            if (o instanceof TermNode) {
                ratioTo = TermNodeDto.fromNode((TermNode) o, TermTreeDto.fromTree((TermTree) ((TermNode) o).getGraph()));
            }
            TermDto termDto = new CharacterDto(uuid, representations, (UUID) elements[2], (UUID) elements[3], (UUID) elements[4], null, (String) elements[5], // vocRepresentations,
            isAvailableForTaxon, isAvailableForTaxonName, isAvailableForOccurrence, (String) elements[10], structure, null, prop, null, ratioTo, isSupportsCategoricalData, // structure, structureModifier, prop, null, isSupportsCategoricalData,
            isSupportsQuantitativeData, supportedCategoricalDtos, recommendedModifierDtos, recommendedMeasurementUnitsDtos, recommendedStatisticalMeasuresDtos);
            termDto.setUri((URI) elements[7]);
            termDto.setMedia(mediaUuids);
            dtoMap.put(uuid, termDto);
            dtos.add(termDto);
        }
    }
    return dtos;
}