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package eu.dnetlib.data.mapreduce.hbase.dataexport;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import org.apache.commons.lang.StringUtils;
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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.NullWritable;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapreduce.lib.output.LazyOutputFormat;
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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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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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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 ObjectMapper objectMapper;
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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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objectMapper = new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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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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Stream.of(value.raw())
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.filter(kv -> {
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final String q = Bytes.toString(kv.getQualifier());
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boolean skip = q.startsWith("update") || q.equals(DedupUtils.BODY_S);
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if (skip) {
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context.getCounter("export", String.format("skipped %s", StringUtils.substring(q, 0, 6))).increment(1);
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}
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return !skip;
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})
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.filter(kv -> !"".equals(Bytes.toString(kv.getValue())))
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.map(kv -> kv.getValue())
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.forEach(v -> {
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try {
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emit(context, OafProtos.Oaf.parseFrom(v));
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} catch (IOException | InterruptedException 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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} 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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valueOut.set(objectMapper.writeValueAsString(result));
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final String type = result.getClass().getSimpleName();
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final String namedOutput = type.toLowerCase();
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multipleOutputs.write(namedOutput, keyOut, valueOut, namedOutput + "/" + namedOutput);
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boolean deleted = result.getDataInfo().getDeletedbyinference();
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if (result instanceof Relation) {
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Relation r = (Relation) result;
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String reltype = r.getRelType() + "_" + r.getSubRelType() + "_" + r.getRelClass();
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context.getCounter("export", String.format("%s deleted:%s", reltype, deleted)).increment(1);
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} else if (result instanceof OafEntity) {
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context.getCounter("export", String.format("%s deleted:%s", type, deleted)).increment(1);
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}
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}
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}
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}
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