D-Net

package eu.dnetlib.data.mapreduce.hbase.dataexport;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Collections;

import java.util.List;

import java.util.Map;

import java.util.stream.Collectors;

import com.google.common.collect.Iterables;

import com.google.common.collect.Lists;

import eu.dnetlib.data.mapreduce.util.DedupUtils;

import eu.dnetlib.data.mapreduce.util.OafDecoder;

import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;

import eu.dnetlib.data.proto.OafProtos.OafEntity;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.apache.hadoop.hbase.client.Result;

import org.apache.hadoop.hbase.io.ImmutableBytesWritable;

import org.apache.hadoop.hbase.mapreduce.TableMapper;

import org.apache.hadoop.hbase.util.Bytes;

import org.apache.hadoop.io.Text;

/**

 * Exports the result identifiers as json.

 *

 * @author claudio

 */

public class ExportResultIdentifiersMapper extends TableMapper<Text, Text> {

	/**

	 * logger.

	 */

	private static final Log log = LogFactory.getLog(ExportResultIdentifiersMapper.class); // NOPMD by marko on 11/24/08 5:02 PM

	private static final String CF = "result";

	private Text keyOut;

	private Text valueOut;

	@Override

	protected void setup(final Context context) throws IOException, InterruptedException {

		super.setup(context);

		keyOut = new Text("");

		valueOut = new Text();

	}

	@Override

	protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {

		try {

			final byte[] body = value.getValue(Bytes.toBytes(CF), DedupUtils.BODY_B);

			if (body == null) {

				context.getCounter(CF, "missing body").increment(1);

				return;

			}

			final OpenaireEntityId id = new OpenaireEntityId();

			final OafDecoder d = OafDecoder.decode(body);

			id.setDeleted(d.getOaf().getDataInfo().getDeletedbyinference());

			id.setId(d.getEntityId());

			id.setPids(d.getOaf().getEntity().getPidList().stream()

					.collect(Collectors.groupingBy(

							p -> p.getQualifier().getClassid()

					)).entrySet().stream()

					.collect(Collectors.toMap(

							Map.Entry::getKey,

							e -> e.getValue().stream()

									.map(StructuredProperty::getValue)

									.collect(Collectors.toList()))));

			final List<OafEntity> childrenList = d.getEntity().getChildrenList();

			if (childrenList != null && !childrenList.isEmpty()) {

				id.setMergedIds(childrenList.stream()

						.map(oafEntity -> oafEntity.getId())

						.sorted()

						.collect(Collectors.toList()));

			}

			valueOut.set(id.toString());

			context.write(keyOut, valueOut);

		} catch (final Throwable e) {

			log.error("error exporting the following record from HBase: " + value.toString(), e);

			context.getCounter("error", e.getClass().getName()).increment(1);

			throw new RuntimeException(e);

		}

	}

}