Examples with UnexpectedEnumException org.molgenis.util.UnexpectedEnumException used on opensource projects

Example 21 with UnexpectedEnumException

use of org.molgenis.util.UnexpectedEnumException in project molgenis by molgenis.

the class PostgreSqlUtils method getPostgreSqlQueryValue.

/**
 * Returns the PostgreSQL query value for the given entity attribute. For query operators requiring a list of
 * values (e.g. IN or RANGE) this method must be called for each individual query value.
 *
 * @param queryValue value of the type that matches the attribute type
 * @param attr       attribute
 * @return PostgreSQL value
 */
static Object getPostgreSqlQueryValue(Object queryValue, Attribute attr) {
    while (true) {
        String attrName = attr.getName();
        AttributeType attrType = attr.getDataType();
        switch(attrType) {
            case BOOL:
                if (queryValue != null && !(queryValue instanceof Boolean)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Boolean.class.getSimpleName()));
                }
                return queryValue;
            case CATEGORICAL:
            // one query value
            case CATEGORICAL_MREF:
            case FILE:
            // one query value
            case MREF:
            case XREF:
            case ONE_TO_MANY:
                // queries values referencing an entity can either be the entity itself or the entity id
                if (queryValue != null) {
                    if (queryValue instanceof Entity) {
                        queryValue = ((Entity) queryValue).getIdValue();
                    }
                    attr = attr.getRefEntity().getIdAttribute();
                    continue;
                } else {
                    return null;
                }
            case DATE:
                if (queryValue != null && !(queryValue instanceof LocalDate)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), LocalDate.class.getSimpleName()));
                }
                return queryValue;
            case DATE_TIME:
                if (queryValue == null) {
                    return null;
                }
                if (!(queryValue instanceof Instant)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Instant.class.getSimpleName()));
                }
                return ((Instant) queryValue).atOffset(UTC);
            case DECIMAL:
                if (queryValue != null && !(queryValue instanceof Double)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Double.class.getSimpleName()));
                }
                return queryValue;
            case ENUM:
                // enum query values can be an enum or enum string
                if (queryValue != null) {
                    if (queryValue instanceof String) {
                        return queryValue;
                    } else if (queryValue instanceof Enum<?>) {
                        return queryValue.toString();
                    } else {
                        throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s] or [%s]", attrName, queryValue.getClass().getSimpleName(), String.class.getSimpleName(), Enum.class.getSimpleName()));
                    }
                } else {
                    return null;
                }
            case EMAIL:
            case HTML:
            case HYPERLINK:
            case SCRIPT:
            case STRING:
            case TEXT:
                if (queryValue != null && !(queryValue instanceof String)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), String.class.getSimpleName()));
                }
                return queryValue;
            case INT:
                if (queryValue != null && !(queryValue instanceof Integer)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Integer.class.getSimpleName()));
                }
                return queryValue;
            case LONG:
                if (queryValue != null && !(queryValue instanceof Long)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Long.class.getSimpleName()));
                }
                return queryValue;
            case COMPOUND:
                throw new RuntimeException(format("Illegal attribute type [%s]", attrType.toString()));
            default:
                throw new UnexpectedEnumException(attrType);
        }
    }
}

Example 22 with UnexpectedEnumException

use of org.molgenis.util.UnexpectedEnumException in project molgenis by molgenis.

the class EmxDataProvider method toEntity.

/**
 * Create an entity from the EMX entity
 *
 * @param entityType entity meta data
 * @param emxEntity  EMX entity
 * @return MOLGENIS entity
 */
private Entity toEntity(EntityType entityType, Entity emxEntity) {
    Entity entity = entityManager.create(entityType, POPULATE);
    for (Attribute attr : entityType.getAtomicAttributes()) {
        if (attr.getExpression() == null && !attr.isMappedBy()) {
            String attrName = attr.getName();
            Object emxValue = emxEntity.get(attrName);
            AttributeType attrType = attr.getDataType();
            switch(attrType) {
                case BOOL:
                case DATE:
                case DATE_TIME:
                case DECIMAL:
                case EMAIL:
                case ENUM:
                case HTML:
                case HYPERLINK:
                case INT:
                case LONG:
                case SCRIPT:
                case STRING:
                case TEXT:
                    Object value = emxValue != null ? DataConverter.convert(emxValue, attr) : null;
                    if ((!attr.isAuto() || value != null) && (!attr.hasDefaultValue() || value != null)) {
                        entity.set(attrName, value);
                    }
                    break;
                case CATEGORICAL:
                case FILE:
                case XREF:
                    // DataConverter.convert performs no conversion for reference types
                    Entity refEntity = toRefEntity(attr, emxValue);
                    // do not set generated auto refEntities to null
                    if ((!attr.isAuto() || refEntity != null) && (!attr.hasDefaultValue() || refEntity != null)) {
                        entity.set(attrName, refEntity);
                    }
                    break;
                case CATEGORICAL_MREF:
                case MREF:
                    // DataConverter.convert performs no conversion for reference types
                    List<Entity> refEntities = toRefEntities(attr, emxValue);
                    // do not set generated auto refEntities to null
                    if (!refEntities.isEmpty()) {
                        entity.set(attrName, refEntities);
                    }
                    break;
                case COMPOUND:
                    throw new RuntimeException(format("Illegal attribute type [%s]", attrType.toString()));
                default:
                    throw new UnexpectedEnumException(attrType);
            }
        }
    }
    return entity;
}

Example 23 with UnexpectedEnumException

use of org.molgenis.util.UnexpectedEnumException in project molgenis by molgenis.

the class VcfToEntity method vcfReaderFormatToMolgenisType.

private static AttributeType vcfReaderFormatToMolgenisType(VcfMetaInfo vcfMetaInfo) {
    String number = vcfMetaInfo.getNumber();
    boolean isListValue;
    try {
        isListValue = number.equals("A") || number.equals("R") || number.equals("G") || number.equals(".") || Integer.parseInt(number) > 1;
    } catch (NumberFormatException ex) {
        throw new GenotypeDataException("Error parsing length of vcf info field. " + number + " is not a valid int or expected preset (A, R, G, .)", ex);
    }
    switch(vcfMetaInfo.getType()) {
        case CHARACTER:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return STRING;
        case FLAG:
            return BOOL;
        case FLOAT:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return DECIMAL;
        case INTEGER:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return INT;
        case STRING:
            if (isListValue) {
                // TODO support list of primitives datatype
                return TEXT;
            }
            return TEXT;
        default:
            throw new UnexpectedEnumException(vcfMetaInfo.getType());
    }
}

Example 24 with UnexpectedEnumException

use of org.molgenis.util.UnexpectedEnumException in project molgenis by molgenis.

the class VcfToEntity method vcfFieldTypeToMolgenisFieldType.

private static AttributeType vcfFieldTypeToMolgenisFieldType(VcfMetaFormat format) {
    String number = format.getNumber();
    boolean isListValue;
    try {
        isListValue = number.equals("A") || number.equals("R") || number.equals("G") || number.equals(".") || Integer.parseInt(number) > 1;
    } catch (NumberFormatException ex) {
        throw new GenotypeDataException("Error parsing length of vcf info field. " + number + " is not a valid int or expected preset (A, R, G, .)", ex);
    }
    switch(format.getType()) {
        case CHARACTER:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return STRING;
        case FLOAT:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return DECIMAL;
        case INTEGER:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return INT;
        case STRING:
            if (isListValue) {
                // TODO support list of primitives datatype
                return STRING;
            }
            return STRING;
        default:
            throw new UnexpectedEnumException(format.getType());
    }
}

Example 25 with UnexpectedEnumException

use of org.molgenis.util.UnexpectedEnumException in project molgenis by molgenis.

the class EntityUtils method equals.

/**
 * Returns true if entity equals another entity. For referenced entities compares the referenced entity ids.
 *
 * @return true if entity equals another entity
 */
public static boolean equals(Entity entity, Entity otherEntity) {
    if (entity == null && otherEntity != null)
        return false;
    if (entity != null && otherEntity == null)
        return false;
    if (entity == null)
        return true;
    if (!entity.getEntityType().getId().equals(otherEntity.getEntityType().getId()))
        return false;
    for (Attribute attr : entity.getEntityType().getAtomicAttributes()) {
        String attrName = attr.getName();
        switch(attr.getDataType()) {
            case BOOL:
                if (!Objects.equals(entity.getBoolean(attrName), otherEntity.getBoolean(attrName)))
                    return false;
                break;
            case CATEGORICAL:
            case FILE:
            case XREF:
                Entity xrefValue = entity.getEntity(attrName);
                Entity otherXrefValue = otherEntity.getEntity(attrName);
                if (xrefValue == null && otherXrefValue != null)
                    return false;
                if (xrefValue != null && otherXrefValue == null)
                    return false;
                if (xrefValue != null && otherXrefValue != null && !xrefValue.getIdValue().equals(otherXrefValue.getIdValue()))
                    return false;
                break;
            case CATEGORICAL_MREF:
            case ONE_TO_MANY:
            case MREF:
                List<Entity> entities = newArrayList(entity.getEntities(attrName));
                List<Entity> otherEntities = newArrayList(otherEntity.getEntities(attrName));
                if (entities.size() != otherEntities.size())
                    return false;
                for (int i = 0; i < entities.size(); ++i) {
                    Entity mrefValue = entities.get(i);
                    Entity otherMrefValue = otherEntities.get(i);
                    if (mrefValue == null && otherMrefValue != null)
                        return false;
                    if (mrefValue != null && otherMrefValue == null)
                        return false;
                    if (mrefValue != null && otherMrefValue != null && !mrefValue.getIdValue().equals(otherMrefValue.getIdValue()))
                        return false;
                }
                break;
            case COMPOUND:
                throw new RuntimeException(format("Invalid data type [%s]", attr.getDataType()));
            case DATE:
                if (!Objects.equals(entity.getLocalDate(attrName), otherEntity.getLocalDate(attrName)))
                    return false;
                break;
            case DATE_TIME:
                if (!Objects.equals(entity.getInstant(attrName), otherEntity.getInstant(attrName)))
                    return false;
                break;
            case DECIMAL:
                if (!Objects.equals(entity.getDouble(attrName), otherEntity.getDouble(attrName)))
                    return false;
                break;
            case EMAIL:
            case ENUM:
            case HTML:
            case HYPERLINK:
            case SCRIPT:
            case STRING:
            case TEXT:
                if (!Objects.equals(entity.getString(attrName), otherEntity.getString(attrName)))
                    return false;
                break;
            case INT:
                if (!Objects.equals(entity.getInt(attrName), otherEntity.getInt(attrName)))
                    return false;
                break;
            case LONG:
                if (!Objects.equals(entity.getLong(attrName), otherEntity.getLong(attrName)))
                    return false;
                break;
            default:
                throw new UnexpectedEnumException(attr.getDataType());
        }
    }
    return true;
}