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

Example 1 with COMPOUND

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

the class EntityUtils method getTypedValue.

/**
 * Convert a string value to a typed value based on the attribute data type.
 *
 * @param valueStr      string value
 * @param attr          attribute
 * @param entityManager entity manager used to convert referenced entity values
 * @return typed value
 */
public static Object getTypedValue(String valueStr, Attribute attr, EntityManager entityManager) {
    if (valueStr == null)
        return null;
    switch(attr.getDataType()) {
        case BOOL:
            return Boolean.valueOf(valueStr);
        case CATEGORICAL:
        case FILE:
        case XREF:
            EntityType xrefEntity = attr.getRefEntity();
            Object xrefIdValue = getTypedValue(valueStr, xrefEntity.getIdAttribute(), entityManager);
            return entityManager.getReference(xrefEntity, xrefIdValue);
        case CATEGORICAL_MREF:
        case MREF:
        case ONE_TO_MANY:
            EntityType mrefEntity = attr.getRefEntity();
            List<String> mrefIdStrValues = ListEscapeUtils.toList(valueStr);
            return mrefIdStrValues.stream().map(mrefIdStrValue -> getTypedValue(mrefIdStrValue, mrefEntity.getIdAttribute(), entityManager)).map(mrefIdValue -> entityManager.getReference(mrefEntity, mrefIdValue)).collect(toList());
        case COMPOUND:
            throw new IllegalArgumentException("Compound attribute has no value");
        case DATE:
            try {
                return parseLocalDate(valueStr);
            } catch (DateTimeParseException e) {
                throw new MolgenisDataException(format(FAILED_TO_PARSE_ATTRIBUTE_AS_DATE_MESSAGE, attr.getName(), valueStr), e);
            }
        case DATE_TIME:
            try {
                return parseInstant(valueStr);
            } catch (DateTimeParseException e) {
                throw new MolgenisDataException(format(FAILED_TO_PARSE_ATTRIBUTE_AS_DATETIME_MESSAGE, attr.getName(), valueStr), e);
            }
        case DECIMAL:
            return Double.valueOf(valueStr);
        case EMAIL:
        case ENUM:
        case HTML:
        case HYPERLINK:
        case SCRIPT:
        case STRING:
        case TEXT:
            return valueStr;
        case INT:
            return Integer.valueOf(valueStr);
        case LONG:
            return Long.valueOf(valueStr);
        default:
            throw new UnexpectedEnumException(attr.getDataType());
    }
}

Example 2 with COMPOUND

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

the class AnnotatorUtils method createCompoundForAnnotator.

private static void createCompoundForAnnotator(EntityType entityType, AttributeFactory attributeFactory, RepositoryAnnotator annotator, List<Attribute> attributes, String compoundName) {
    Attribute compound;
    compound = attributeFactory.create().setName(compoundName).setLabel(annotator.getFullName()).setDataType(COMPOUND).setLabel(annotator.getSimpleName());
    attributes.stream().filter(part -> entityType.getAttribute(part.getName()) == null).forEachOrdered(part -> part.setParent(compound));
    entityType.addAttribute(compound);
    // Only add attributes that do not already exist. We assume existing attributes are added in a previous annotation run.
    // This is a potential risk if an attribute with that name already exist that was not added by the annotator.
    // This risk is relatively low since annotator attributes are prefixed.
    attributes = attributes.stream().filter(attribute -> entityType.getAttribute(attribute.getName()) == null).collect(toList());
    entityType.addAttributes(attributes);
}