001/* 
002 * Copyright 2018 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
003 *
004 * Licensed under the Apache License, Version 2.0 (the "License");
005 * you may not use this file except in compliance with the License.
006 * You may obtain a copy of the License at
007 *
008 *      http://www.apache.org/licenses/LICENSE-2.0
009 *
010 * Unless required by applicable law or agreed to in writing, software
011 * distributed under the License is distributed on an "AS IS" BASIS,
012 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
013 * See the License for the specific language governing permissions and
014 * limitations under the License.
015 */
016package de.isas.mztab2.io.serialization;
017
018import com.fasterxml.jackson.core.JsonGenerator;
019import com.fasterxml.jackson.databind.SerializerProvider;
020import com.fasterxml.jackson.databind.jsontype.TypeSerializer;
021import com.fasterxml.jackson.databind.ser.std.StdSerializer;
022import static de.isas.mztab2.io.serialization.Serializers.addLineWithProperty;
023import static de.isas.mztab2.io.serialization.Serializers.addSubElementParameters;
024import de.isas.mztab2.model.Sample;
025import java.io.IOException;
026import lombok.extern.slf4j.Slf4j;
027import uk.ac.ebi.pride.jmztab2.model.Section;
028
029/**
030 * <p>SampleSerializer implementation for {@link de.isas.mztab2.model.Sample}.</p>
031 *
032 * @author nilshoffmann
033 * 
034 */
035@Slf4j
036public class SampleSerializer extends StdSerializer<Sample> {
037
038    /**
039     * <p>Constructor for SampleSerializer.</p>
040     */
041    public SampleSerializer() {
042        this(null);
043    }
044
045    /**
046     * <p>Constructor for SampleSerializer.</p>
047     *
048     * @param t a {@link java.lang.Class} object.
049     */
050    public SampleSerializer(Class<Sample> t) {
051        super(t);
052    }
053    
054    @Override
055    public void serializeWithType(Sample value, JsonGenerator gen,
056        SerializerProvider serializers, TypeSerializer typeSer) throws IOException {
057        typeSer.writeTypePrefixForObject(value, gen);
058        serialize(value, gen, serializers);
059        typeSer.writeTypeSuffixForObject(value, gen);
060    }
061
062    /** {@inheritDoc} */
063    @Override
064    public void serialize(Sample sample, JsonGenerator jg,
065        SerializerProvider sp) throws IOException {
066        if (sample != null) {
067            Serializers.checkIndexedElement(sample);
068            addLineWithProperty(jg, Section.Metadata.getPrefix(), null, sample,
069                sample.
070                    getName());
071            addLineWithProperty(jg, Section.Metadata.getPrefix(), Sample.Properties.description.getPropertyName(),
072                sample,
073                sample.getDescription());
074            addSubElementParameters(jg, Section.Metadata.getPrefix(), sample,
075                Sample.Properties.species.getPropertyName(),
076                sample.getSpecies(), false);
077            addSubElementParameters(jg, Section.Metadata.getPrefix(), sample,
078                Sample.Properties.cellType.getPropertyName(),
079                sample.getCellType(), false);
080            addSubElementParameters(jg, Section.Metadata.getPrefix(), sample,
081                Sample.Properties.disease.getPropertyName(),
082                sample.getDisease(), false);
083            addSubElementParameters(jg, Section.Metadata.getPrefix(), sample,
084                Sample.Properties.tissue.getPropertyName(),
085                sample.getTissue(), false);
086            addSubElementParameters(jg, Section.Metadata.getPrefix(), sample,
087                Sample.Properties.custom.getPropertyName(),
088                sample.getCustom(), false);
089        } else {
090            log.debug(Sample.class.getSimpleName()+" is null!");
091        }
092    }
093}