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package eu.dnetlib.data.mapreduce.hbase.statsExport.mapreduce;
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import com.google.common.collect.ArrayListMultimap;
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import com.google.common.collect.Multimap;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.mapreduce.hbase.index.config.EntityConfigTable;
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import eu.dnetlib.data.mapreduce.hbase.index.config.IndexConfig;
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import eu.dnetlib.data.mapreduce.hbase.index.config.LinkDescriptor;
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import eu.dnetlib.data.mapreduce.hbase.statsExport.utils.ContextTransformer;
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import eu.dnetlib.data.mapreduce.hbase.statsExport.utils.Serializer;
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import eu.dnetlib.data.mapreduce.util.OafDecoder;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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import eu.dnetlib.data.mapreduce.util.RelDescriptor;
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import eu.dnetlib.data.mapreduce.util.UpdateMerger;
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import eu.dnetlib.data.proto.KindProtos;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.OafRel;
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import eu.dnetlib.data.proto.OafProtos.OafRelOrBuilder;
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import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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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.log4j.Logger;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Properties;
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/**
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* Mapper Class that reads HBASE contents and prepares them for the StatsDB
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* export
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*/
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public class StatsMapper extends TableMapper<Text, ImmutableBytesWritable> {
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private Logger log = Logger.getLogger(this.getClass());
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//Index configuratios for OAFs
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private EntityConfigTable entityConfigTable;
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//Counters for produced entities. Visible in the JobTracker monitoring page.
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private enum STATS_COUNTERS {
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datasource,
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organization,
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result,
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person,
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project
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}
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private enum REL_COUNTERS {
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resultProject,
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datasourceOrganization,
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organizationOrganization,
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resultResult,
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personPerson,
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personResult,
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projectOrganization,
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projectPerson,
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resultOrganization
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}
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//Counter for corrupted records.
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private enum ERROR_COUNTERS {
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rottenRecords,
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rottenRelations
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}
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//Init class: Load Index config and mapping for DB tables.
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@Override
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protected void setup(Context context) throws IOException, InterruptedException {
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loadEntityConfig(context);
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}
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//Read HBASE table and decode Protos to OAF entities.
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@Override
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protected void map(final ImmutableBytesWritable keyIn, final Result result, final Context context) throws IOException {
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Oaf oaf = null;
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OafRowKeyDecoder keyDecoder = OafRowKeyDecoder.decode(keyIn.copyBytes());
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try {
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oaf = UpdateMerger.mergeBodyUpdates(context, result.getFamilyMap(Bytes.toBytes(keyDecoder.getType().toString())));
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} catch (Exception e) {
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/*
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System.err.println("Unable to parse proto in row: " + oaf.getEntity().getType().toString() + keyDecoder.getKey());
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log.error("Unable to parse proto in row: " + oaf.getEntity().getType().toString() + keyDecoder.getKey(), e);
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*/
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System.err.println("Unable to parse proto in row: " + keyDecoder.getKey());
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log.error("Unable to parse proto in row: " + keyDecoder.getKey(), e);
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context.getCounter(ERROR_COUNTERS.rottenRecords).increment(1);
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}
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if (isValid(oaf)) {
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emitProtos(context, result, oaf);
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}
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}
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private boolean isValid(Oaf oaf) {
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if (oaf != null && oaf.isInitialized() && !deletedByInference(oaf) && !invisible(oaf)) return true;
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return false;
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}
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private void emitProtos(Context context, Result result, Oaf oaf) {
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Oaf.Builder oafBuilder = Oaf.newBuilder().setKind(oaf.getKind()).
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setDataInfo(oaf.getDataInfo()).setLastupdatetimestamp(oaf.getLastupdatetimestamp());
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oafBuilder.setEntity(oaf.getEntity());
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// emit relation first so we can cache them to entity protos
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emitRelation(context, result, oaf, oafBuilder);
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emitEntity(context, oafBuilder.build());
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}
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private void emitEntity(Context context, Oaf oaf) {
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String serialized = Serializer.serialize(oaf, context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.enclChar"));
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if (serialized != null) {
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try {
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Text TextKeyOut = new Text(oaf.getEntity().getType().toString() + "," + Serializer.getId(oaf, context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.enclChar")));
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context.write((TextKeyOut), new ImmutableBytesWritable(serialized.getBytes()));
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context.getCounter(STATS_COUNTERS.valueOf(oaf.getEntity().getType().toString())).increment(1);
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} catch (Exception e) {
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log.error("Error writing entity to M/R output", e);
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}
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}
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}
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// may have multiple relations per each field
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private void emitRelation(Context context, Result result, Oaf oaf, Oaf.Builder builder) {
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try {
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// writing out : personResult,ID,data
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// derived relations; ResultLanguages, resultConcepts etc are
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// created here
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Multimap<String, String> relMap = ArrayListMultimap.create();
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Serializer.extractRelations(oaf, context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.enclChar"), relMap);
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if (!relMap.isEmpty()) {
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for (Entry<String, String> rel : relMap.entries()) {
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Text TextKeyOut = new Text(rel.getKey() + "," + Serializer.getId(oaf, context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.enclChar")));
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//TODO here output
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context.write((TextKeyOut), new ImmutableBytesWritable(rel.getValue().getBytes()));
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}
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}
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} catch (Throwable e) {
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log.error("Error writing relation to M/R output", e);
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}
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// Existing Hbase relations are generated here
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if (entityConfigTable.getDescriptors(oaf.getEntity().getType()) != null) {
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for (LinkDescriptor ld : entityConfigTable.getDescriptors(oaf.getEntity().getType())) {
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try {
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ArrayList<OafRel> oafRels = new ArrayList<OafRel>();
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decodeRelation(oaf, context, result, ld, oafRels);
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for (OafRel rel : oafRels) {
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{
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// builder.getEntityBuilder().addCachedRel(rel);
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Text TextKeyOut = new Text(ld.getRelDescriptor().getRelType().toString()
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+ "," + Serializer.getId(rel, context.getConfiguration().get("stats.delim"),
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context.getConfiguration().get("stats.enclChar")));
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String buff = Serializer.serialize(rel, context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.enclChar"));
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context.write((TextKeyOut), new ImmutableBytesWritable(buff.getBytes()));
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context.getCounter(REL_COUNTERS.valueOf(rel.getRelType().toString())).increment(1);
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}
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}
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} catch (Throwable e) {
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log.error("Error for record ", e);
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context.getCounter(ERROR_COUNTERS.rottenRelations).increment(1);
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}
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}
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}
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}
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private void decodeRelation(final Oaf body, final Context context, Result result, final LinkDescriptor ld, List<OafRel> rels) {
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try {
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final Oaf.Builder oafBuilder = Oaf.newBuilder().setKind(KindProtos.Kind.relation);
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final Map<byte[], byte[]> columnMap = result.getFamilyMap(Bytes.toBytes(ld.getRelDescriptor().getIt()));
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if (hasData(columnMap)) {
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for (Entry<byte[], byte[]> e : columnMap.entrySet()) {
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Oaf decodedOaf = decodeProto(e.getValue(), context);
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OafRel.Builder relBuilder = OafRel.newBuilder(decodedOaf.getRel());
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if (ld.isSymmetric()) {
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RelDescriptor rd = ld.getRelDescriptor();
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relBuilder.setCachedTarget(body.getEntity()).setRelType(rd.getRelType()).setSubRelType(rd.getSubRelType());
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}
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OafRel oafRel = relBuilder.setChild(ld.isChild()).build();
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rels.add(oafBuilder.setDataInfo(decodedOaf.getDataInfo()).setRel(oafRel).build().getRel());
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}
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}
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} catch (Throwable throwable) {
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log.error("Error Decoding relation for: " + body.getRel().getRelType() + " " + body.getEntity().getId() + " ", throwable);
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context.getCounter(ERROR_COUNTERS.rottenRelations).increment(1);
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}
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}
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private Oaf decodeProto(final byte[] body, Context context) {
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try {
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return Oaf.parseFrom(body);
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} catch (Exception e) {
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log.error(e);
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context.getCounter(ERROR_COUNTERS.rottenRecords).increment(1);
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}
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return null;
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}
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private void loadEntityConfig(Context context) {
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String indexConf = context.getConfiguration().get("stats.indexConf");
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if (indexConf == null || indexConf.isEmpty()) {
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log.error("NULL ENTITY CONFIGURATION TABLE IN MAPPER : ");
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}
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entityConfigTable = IndexConfig.load(indexConf).getConfigMap();
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}
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private boolean isDedupSelf(final OafRelOrBuilder rel) {
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return rel.getSource().contains(rel.getTarget());
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}
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private boolean hasData(final Map<byte[], byte[]> columnMap) {
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return columnMap != null && !columnMap.isEmpty();
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}
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private boolean deletedByInference(final Oaf oaf) {
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return oaf.getDataInfo().getDeletedbyinference();
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}
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private boolean invisible(final Oaf oaf) {
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return oaf.getDataInfo().getInvisible();
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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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super.cleanup(context);
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}
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public EntityConfigTable getEntityConfigTable() {
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return entityConfigTable;
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}
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public void setEntityConfigTable(EntityConfigTable entityConfigTable) {
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this.entityConfigTable = entityConfigTable;
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}
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}
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