JsonDataReader.java

package org.opencb.opencga.storage.core.io.json;

import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.opencb.commons.io.DataReader;

import java.io.IOException;
import java.io.InputStream;
import java.io.UncheckedIOException;
import java.util.ArrayList;
import java.util.List;

/**
 * Created on 02/12/16.
 *
 * Generic Json writer from an input stream.
 *
 * TODO: Move to Java Common Libs
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class JsonDataReader<T>  implements DataReader<T> {
    private final JsonFactory jsonFactory;
    private final ObjectMapper objectMapper;
    private final Class<T> clazz;
    private final InputStream inputStream;
    private JsonParser parser;
    private long numReads;

    public JsonDataReader(Class<T> clazz, InputStream inputStream) {
        this.clazz = clazz;
        this.inputStream = inputStream;
        jsonFactory = new JsonFactory();
        objectMapper = new ObjectMapper(jsonFactory);
    }

    @Override
    public boolean open() {
        numReads = 0;
        try {
            parser = jsonFactory.createParser(inputStream);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
        return true;
    }

    @Override
    public List<T> read(int batchSize) {
        List<T> batch = new ArrayList<>(batchSize);
        try {
            while (parser.nextToken() != null && batch.size() < batchSize) {
                numReads++;
                batch.add(parser.readValueAs(clazz));
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
        return batch;
    }

    @Override
    public boolean close() {
        try {
            parser.close();
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
        return true;
    }

    public void addMixIn(Class<?> target, Class<?> mixinSource) {
        objectMapper.addMixIn(target, mixinSource);
    }

    public ObjectMapper getObjectMapper() {
        return objectMapper;
    }

    public long getNumReads() {
        return numReads;
    }
}