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

Example 26 with AttributeType

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

the class EntitySerializer method serialize.

@Override
public JsonElement serialize(Entity entity, Type type, JsonSerializationContext context) {
    JsonObject result = new JsonObject();
    result.addProperty("__entityTypeId", entity.getEntityType().getId());
    for (Attribute attr : entity.getEntityType().getAtomicAttributes()) {
        String attributeName = attr.getName();
        Object value = entity.get(attributeName);
        if (value != null) {
            AttributeType attrType = attr.getDataType();
            switch(attrType) {
                case BOOL:
                    result.addProperty(attributeName, entity.getBoolean(attributeName));
                    break;
                case CATEGORICAL:
                case XREF:
                case FILE:
                    Entity refEntity = entity.getEntity(attributeName);
                    result.add(attributeName, serializeReference(refEntity, context));
                    break;
                case CATEGORICAL_MREF:
                case MREF:
                case ONE_TO_MANY:
                    JsonArray jsonArray = new JsonArray();
                    entity.getEntities(attributeName).forEach(e -> jsonArray.add(serializeReference(e, context)));
                    result.add(attributeName, jsonArray);
                    break;
                case DATE:
                    LocalDate localDateValue = entity.getLocalDate(attributeName);
                    result.add(attributeName, context.serialize(localDateValue));
                    break;
                case DATE_TIME:
                    Instant instantValue = entity.getInstant(attributeName);
                    result.add(attributeName, context.serialize(instantValue));
                    break;
                case DECIMAL:
                    result.addProperty(attributeName, entity.getDouble(attributeName));
                    break;
                case INT:
                    result.addProperty(attributeName, entity.getInt(attributeName));
                    break;
                case LONG:
                    result.addProperty(attributeName, entity.getLong(attributeName));
                    break;
                case ENUM:
                case HTML:
                case HYPERLINK:
                case SCRIPT:
                case EMAIL:
                case STRING:
                case TEXT:
                    result.addProperty(attributeName, value.toString());
                    break;
                case COMPOUND:
                    throw new RuntimeException(format("Illegal attribute type [%s]", attrType.toString()));
                default:
                    throw new UnexpectedEnumException(attrType);
            }
        }
    }
    return result;
}

Example 27 with AttributeType

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

the class PostgreSqlQueryGenerator method getSqlColumn.

private static String getSqlColumn(EntityType entityType, Attribute attr, ColumnMode columnMode) {
    StringBuilder sqlBuilder = new StringBuilder(getColumnName(attr)).append(' ');
    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:
            sqlBuilder.append(getPostgreSqlType(attr));
            break;
        case CATEGORICAL:
        case FILE:
        case XREF:
            sqlBuilder.append(getPostgreSqlType(attr.getRefEntity().getIdAttribute()));
            break;
        case ONE_TO_MANY:
        case COMPOUND:
        case CATEGORICAL_MREF:
        case MREF:
            throw new RuntimeException(format("Illegal attribute type [%s]", attrType.toString()));
        default:
            throw new UnexpectedEnumException(attrType);
    }
    String sqlColumnConstraints = getSqlColumnConstraints(entityType, attr, columnMode);
    if (!sqlColumnConstraints.isEmpty()) {
        sqlBuilder.append(' ').append(sqlColumnConstraints);
    }
    return sqlBuilder.toString();
}

Example 28 with AttributeType

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

the class PostgreSqlRepository method handleBatch.

/**
 * Handles a batch of Entities. Looks up the values for MREF ID attributes and sets them as references in the
 * entities. Then feeds the entities to the {@link Consumer}
 *
 * @param consumer   {@link Consumer} to feed the batch to after setting the MREF ID values
 * @param entityType EntityType for the {@link Entity}s in the batch
 * @param batch      {@link Map} mapping entity ID to entity for all {@link Entity}s in the batch
 */
private void handleBatch(Consumer<List<Entity>> consumer, EntityType entityType, Map<Object, Entity> batch) {
    AttributeType idAttributeDataType = entityType.getIdAttribute().getDataType();
    LOG.debug("Select ID values for a batch of MREF attributes...");
    for (Attribute mrefAttr : entityType.getAtomicAttributes()) {
        if (mrefAttr.getExpression() == null && isMultipleReferenceType(mrefAttr) && !(mrefAttr.getDataType() == ONE_TO_MANY && mrefAttr.isMappedBy())) {
            EntityType refEntityType = mrefAttr.getRefEntity();
            Multimap<Object, Object> mrefIDs = selectMrefIDsForAttribute(entityType, idAttributeDataType, mrefAttr, batch.keySet(), refEntityType.getIdAttribute().getDataType());
            for (Map.Entry entry : batch.entrySet()) {
                batch.get(entry.getKey()).set(mrefAttr.getName(), postgreSqlEntityFactory.getReferences(refEntityType, newArrayList(mrefIDs.get(entry.getKey()))));
            }
        }
    }
    LOG.trace("Feeding batch of {} rows to consumer.", batch.size());
    consumer.accept(batch.values().stream().collect(toList()));
}

Example 29 with AttributeType

use of org.molgenis.data.meta.AttributeType 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 30 with AttributeType

use of org.molgenis.data.meta.AttributeType 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;
}