SampleConverter.java

/*
 * Copyright 2015-2016 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.catalog.db.mongodb.converters;

import org.bson.Document;
import org.opencb.commons.datastore.mongodb.GenericDocumentComplexConverter;
import org.opencb.opencga.catalog.models.Sample;

import java.util.List;

/**
 * Created by pfurio on 19/01/16.
 */
public class SampleConverter extends GenericDocumentComplexConverter<Sample> {

    public SampleConverter() {
        super(Sample.class);
    }

    @Override
    public Sample convertToDataModelType(Document object) {
        if (object.get("individual") != null) {
            if (object.get("individual") instanceof List) {
                if (((List) object.get("individual")).size() > 0) {
                    object.put("individual", ((List) object.get("individual")).get(0));
                } else {
                    object.put("individual", new Document("id", -1));
                }
            }
        } else {
            object.put("individual", new Document("id", -1));
        }
        return super.convertToDataModelType(object);
    }

    @Override
    public Document convertToStorageType(Sample object) {
        Document document = super.convertToStorageType(object);
        document.put("id", document.getInteger("id").longValue());
        long individualId = object.getIndividual() != null
                ? (object.getIndividual().getId() == 0 ? -1L : object.getIndividual().getId()) : -1L;
        document.put("individual", new Document("id", individualId));
        return document;
    }
}