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package eu.dnetlib.data.mapreduce.hbase.dataexport;
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sandro.lab
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import com.google.gson.Gson;
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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.mapreduce.util.UpdateMerger;
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import eu.dnetlib.data.proto.OafProtos;
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import eu.dnetlib.data.proto.TypeProtos;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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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.io.Text;
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import org.apache.hadoop.mapreduce.lib.output.MultipleOutputs;
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import java.io.IOException;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.NavigableMap;
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/**
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* Exports Oaf objects as their json serialization.
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*
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* @author claudio
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*
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*/
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public class ExportInformationSpaceMapper2DHP extends TableMapper<Text, Text> {
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private Text keyOut;
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private Text valueOut;
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private MultipleOutputs multipleOutputs;
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private Gson g;
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@Override
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protected void setup(final Context context) throws IOException, InterruptedException {
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super.setup(context);
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keyOut = new Text();
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valueOut = new Text();
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multipleOutputs = new MultipleOutputs(context);
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g = new Gson();
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}
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@Override
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protected void cleanup(Context context) throws IOException, InterruptedException {
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multipleOutputs.close();
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}
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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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try {
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final OafRowKeyDecoder rkd = OafRowKeyDecoder.decode(keyIn.get());
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final OafProtos.Oaf oaf = UpdateMerger.mergeBodyUpdates(context, value.getFamilyMap(Bytes.toBytes(rkd.getType().toString())));
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if (oaf == null) {
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return;
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} else {
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emit(context, oaf);
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}
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final Map<byte[], NavigableMap<byte[], byte[]>> row = value.getNoVersionMap();
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for (byte[] cf : row.keySet()) {
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for (Entry<byte[], byte[]> q : row.get(cf).entrySet()) {
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final String key = new String(q.getKey());
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if("update".startsWith(key) || DedupUtils.BODY_S.equals(key)) {
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continue;
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}
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if (new String(q.getValue()).equals("")) {
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context.getCounter("export", "skipped relation " + new String(cf)).increment(1);
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} else {
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emit(context, OafProtos.Oaf.parseFrom(q.getValue()));
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}
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}
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}
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} catch (final Throwable e) {
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context.getCounter("export", "error: " + e.getClass().getName()).increment(1);
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throw new RuntimeException(e);
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}
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}
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private void emit(Context context, OafProtos.Oaf oaf) throws IOException, InterruptedException {
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Oaf result = null;
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try {
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result = ProtoConverter.convert(oaf);
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} catch (Throwable e) {
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context.getCounter("export", "error:" + e.getClass().getName()).increment(1);
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}
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if (result != null) {
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keyOut.set(result.getClass().getName());
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valueOut.set(g.toJson(result));
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final String namedOutput = result.getClass().getSimpleName().toLowerCase();
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multipleOutputs.write(namedOutput, keyOut, valueOut, namedOutput + "/" + namedOutput);
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context.getCounter("export", result.getClass().getName()).increment(1);
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}
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}
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}
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