Examples with AttributeType org.molgenis.data.meta.AttributeType used on opensource projects

Example 31 with AttributeType

use of org.molgenis.data.meta.AttributeType in project molgenis by molgenis.

the class MappingServiceImpl method compareTargetMetadatas.

/**
 * Compares the attributes between the target repository and the mapping target.
 * Applied Rules:
 * - The mapping target can not contain attributes which are not in the target repository
 * - The attributes of the mapping target with the same name as attributes in the target repository should have the same type
 * - If there are reference attributes, the name of the reference entity should be the same in both the target repository as in the mapping target
 *
 * @param targetRepositoryEntityType the target repository EntityType to check
 * @param mappingTargetEntityType    the mapping target EntityType to check
 * @throws MolgenisDataException if the types are not compatible
 */
private void compareTargetMetadatas(EntityType targetRepositoryEntityType, EntityType mappingTargetEntityType) {
    Map<String, Attribute> targetRepositoryAttributeMap = newHashMap();
    targetRepositoryEntityType.getAtomicAttributes().forEach(attribute -> targetRepositoryAttributeMap.put(attribute.getName(), attribute));
    for (Attribute mappingTargetAttribute : mappingTargetEntityType.getAtomicAttributes()) {
        String mappingTargetAttributeName = mappingTargetAttribute.getName();
        Attribute targetRepositoryAttribute = targetRepositoryAttributeMap.get(mappingTargetAttributeName);
        if (targetRepositoryAttribute == null) {
            throw new MolgenisDataException(format("Target repository does not contain the following attribute: %s", mappingTargetAttributeName));
        }
        AttributeType targetRepositoryAttributeType = targetRepositoryAttribute.getDataType();
        AttributeType mappingTargetAttributeType = mappingTargetAttribute.getDataType();
        if (!mappingTargetAttributeType.equals(targetRepositoryAttributeType)) {
            throw new MolgenisDataException(format("attribute %s in the mapping target is type %s while attribute %s in the target repository is type %s. Please make sure the types are the same", mappingTargetAttributeName, mappingTargetAttributeType, targetRepositoryAttribute.getName(), targetRepositoryAttributeType));
        }
        if (isReferenceType(mappingTargetAttribute)) {
            String mappingTargetRefEntityName = mappingTargetAttribute.getRefEntity().getId();
            String targetRepositoryRefEntityName = targetRepositoryAttribute.getRefEntity().getId();
            if (!mappingTargetRefEntityName.equals(targetRepositoryRefEntityName)) {
                throw new MolgenisDataException(format("In the mapping target, attribute %s of type %s has reference entity %s while in the target repository attribute %s of type %s has reference entity %s. " + "Please make sure the reference entities of your mapping target are pointing towards the same reference entities as your target repository", mappingTargetAttributeName, mappingTargetAttributeType, mappingTargetRefEntityName, targetRepositoryAttribute.getName(), targetRepositoryAttributeType, targetRepositoryRefEntityName));
            }
        }
    }
}

Example 32 with AttributeType

use of org.molgenis.data.meta.AttributeType in project molgenis by molgenis.

the class VcfToEntity method createEntityType.

private EntityType createEntityType(String entityTypeId, VcfMeta vcfMeta) {
    Attribute idAttribute = attrMetaFactory.create().setName(INTERNAL_ID).setDataType(STRING);
    idAttribute.setVisible(false);
    EntityType entityType = entityTypeFactory.create(entityTypeId);
    entityType.setLabel(entityTypeId);
    entityType.addAttribute(vcfAttributes.getChromAttribute());
    entityType.addAttribute(vcfAttributes.getAltAttribute());
    entityType.addAttribute(vcfAttributes.getPosAttribute());
    entityType.addAttribute(vcfAttributes.getRefAttribute());
    entityType.addAttribute(vcfAttributes.getFilterAttribute());
    entityType.addAttribute(vcfAttributes.getQualAttribute());
    entityType.addAttribute(vcfAttributes.getIdAttribute());
    entityType.addAttribute(idAttribute, ROLE_ID);
    Attribute infoMetaData = attrMetaFactory.create().setName(INFO).setDataType(COMPOUND).setNillable(true);
    for (VcfMetaInfo info : vcfMeta.getInfoMeta()) {
        String attrName = toAttributeName(info.getId());
        AttributeType attrType = vcfReaderFormatToMolgenisType(info);
        String attrDescription = StringUtils.isBlank(info.getDescription()) ? VcfRepository.DEFAULT_ATTRIBUTE_DESCRIPTION : info.getDescription();
        Attribute attribute = attrMetaFactory.create().setName(attrName).setDataType(attrType).setDescription(attrDescription).setAggregatable(true).setParent(infoMetaData);
        entityType.addAttribute(attribute);
    }
    entityType.addAttribute(infoMetaData);
    if (sampleEntityType != null) {
        Attribute samplesAttributeMeta = attrMetaFactory.create().setName(SAMPLES).setDataType(MREF).setRefEntity(sampleEntityType).setLabel("SAMPLES");
        entityType.addAttribute(samplesAttributeMeta);
    }
    return entityType;
}

Example 33 with AttributeType

use of org.molgenis.data.meta.AttributeType in project molgenis by molgenis.

the class AttributeValidator method validateUpdate.

private static void validateUpdate(Attribute newAttr, Attribute currentAttr) {
    // data type
    AttributeType currentDataType = currentAttr.getDataType();
    AttributeType newDataType = newAttr.getDataType();
    if (!Objects.equals(currentDataType, newDataType)) {
        validateUpdateDataType(currentDataType, newDataType);
        if (newAttr.isInversedBy()) {
            throw new MolgenisDataException(format("Attribute data type change not allowed for bidirectional attribute [%s]", newAttr.getName()));
        }
    }
    // orderBy
    Sort currentOrderBy = currentAttr.getOrderBy();
    Sort newOrderBy = newAttr.getOrderBy();
    if (!Objects.equals(currentOrderBy, newOrderBy)) {
        validateOrderBy(newAttr, newOrderBy);
    }
// note: mappedBy is a readOnly attribute, no need to verify for updates
}

Example 34 with AttributeType

use of org.molgenis.data.meta.AttributeType in project molgenis by molgenis.

the class AttributeValidator method validateDefaultValue.

void validateDefaultValue(Attribute attr, boolean validateEntityReferences) {
    String value = attr.getDefaultValue();
    if (value != null) {
        if (attr.isUnique()) {
            throw new MolgenisDataException("Unique attribute " + attr.getName() + " cannot have default value");
        }
        if (attr.getExpression() != null) {
            throw new MolgenisDataException("Computed attribute " + attr.getName() + " cannot have default value");
        }
        AttributeType fieldType = attr.getDataType();
        if (fieldType.getMaxLength() != null && value.length() > fieldType.getMaxLength()) {
            throw new MolgenisDataException("Default value for attribute [" + attr.getName() + "] exceeds the maximum length for datatype " + attr.getDataType().name());
        }
        if (fieldType == AttributeType.EMAIL) {
            checkEmail(value);
        }
        if (fieldType == AttributeType.HYPERLINK) {
            checkHyperlink(value);
        }
        if (fieldType == AttributeType.ENUM) {
            checkEnum(attr, value);
        }
        // Get typed value to check if the value is of the right type.
        Object typedValue;
        try {
            typedValue = EntityUtils.getTypedValue(value, attr, entityManager);
        } catch (NumberFormatException e) {
            throw new MolgenisValidationException(new ConstraintViolation(format("Invalid default value [%s] for data type [%s]", value, attr.getDataType())));
        }
        if (validateEntityReferences) {
            if (isSingleReferenceType(attr)) {
                Entity refEntity = (Entity) typedValue;
                EntityType refEntityType = attr.getRefEntity();
                if (dataService.query(refEntityType.getId()).eq(refEntityType.getIdAttribute().getName(), refEntity.getIdValue()).count() == 0) {
                    throw new MolgenisValidationException(new ConstraintViolation(format("Default value [%s] refers to an unknown entity", value)));
                }
            } else if (isMultipleReferenceType(attr)) {
                Iterable<Entity> refEntitiesValue = (Iterable<Entity>) typedValue;
                EntityType refEntityType = attr.getRefEntity();
                if (dataService.query(refEntityType.getId()).in(refEntityType.getIdAttribute().getName(), StreamSupport.stream(refEntitiesValue.spliterator(), false).map(Entity::getIdValue).collect(toList())).count() < Iterables.size(refEntitiesValue)) {
                    throw new MolgenisValidationException(new ConstraintViolation(format("Default value [%s] refers to one or more unknown entities", value)));
                }
            }
        }
    }
}

Example 35 with AttributeType

use of org.molgenis.data.meta.AttributeType in project molgenis by molgenis.

the class EffectStructureConverter method parseEffectAttributeDescription.

// Create a map of attributes based on the pipe separated attribute names in the description
private ArrayList<Attribute> parseEffectAttributeDescription(String attributesString, List<Attribute> annotatorAttributes) {
    String[] attributeStrings = attributesString.replaceAll("^\\s'|'$", "").split("\\|");
    ArrayList<Attribute> attributeList = new ArrayList<>();
    Map<String, Attribute> annotatorAttributeMap = VcfUtils.getAttributesMapFromList(annotatorAttributes);
    for (String attribute : attributeStrings) {
        AttributeType type = annotatorAttributeMap.containsKey(attribute) ? annotatorAttributeMap.get(attribute).getDataType() : STRING;
        Attribute attr = attributeFactory.create().setName(StringUtils.deleteWhitespace(attribute)).setDataType(type).setLabel(attribute);
        attributeList.add(attr);
    }
    return attributeList;
}