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package eu.dnetlib.data.mapreduce.hbase.dedup.gt;
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import java.io.IOException;
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import java.util.Map;
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import org.apache.hadoop.hbase.client.Delete;
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import org.apache.hadoop.hbase.client.Result;
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
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import org.apache.hadoop.hbase.mapreduce.TableMapper;
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import org.apache.hadoop.hbase.util.Bytes;
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import org.apache.hadoop.mapreduce.Counter;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.mapreduce.util.DedupUtils;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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import eu.dnetlib.data.proto.KindProtos.Kind;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.proto.PersonProtos.Person;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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/**
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* Removes the Non-root rows
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*
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*
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* @author claudio
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*
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*/
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public class GTCleanerMapper extends TableMapper<ImmutableBytesWritable, Delete> {
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@Override
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protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {
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final OafRowKeyDecoder keyDecoder = OafRowKeyDecoder.decode(keyIn.copyBytes());
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final Type type = keyDecoder.getType();
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if (!type.equals(Type.person)) {
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incrementCounter(context, "wrong entity type", type.toString(), 1);
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return;
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}
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final Map<byte[], byte[]> map = value.getFamilyMap(Bytes.toBytes(type.toString()));
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final byte[] bodyB = map.get(DedupUtils.BODY_B);
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if (bodyB == null) {
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incrementCounter(context, "missing body (map)", type.toString(), 1);
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return;
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}
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final Oaf oaf = decodeProto(context, bodyB);
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if (!isValid(oaf)) {
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incrementCounter(context, "missing body (map)", type.toString(), 1);
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return;
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}
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if (mergedSize(oaf, 0) || mergedSize(oaf, 1)) {
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context.write(keyIn, new Delete(keyIn.copyBytes()));
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incrementCounter(context, Kind.entity.toString(), "deleted", 1);
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}
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}
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private boolean mergedSize(final Oaf oaf, final int size) {
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final OafEntity entity = oaf.getEntity();
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if (entity == null) return false;
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final Person person = entity.getPerson();
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return (person.getMergedpersonList() != null) && (person.getMergedpersonList().size() == size);
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}
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private boolean isValid(final Oaf oaf) {
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return (oaf != null) && oaf.isInitialized();
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}
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private Oaf decodeProto(final Context context, final byte[] body) {
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try {
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return Oaf.parseFrom(body);
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} catch (final InvalidProtocolBufferException e) {
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e.printStackTrace(System.err);
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context.getCounter("decodeProto", e.getClass().getName()).increment(1);
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}
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return null;
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}
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private void incrementCounter(final Context context, final String k, final String t, final int n) {
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getCounter(context, k, t).increment(n);
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}
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private Counter getCounter(final Context context, final String k, final String t) {
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return context.getCounter(k, t);
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}
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}
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