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package eu.dnetlib.data.mapreduce.hbase.statsExport;
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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.Serializer;
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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.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.ProjectProtos;
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import eu.dnetlib.data.proto.RelTypeProtos;
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import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;
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import eu.dnetlib.data.proto.TypeProtos;
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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.hadoop.mapreduce.Mapper.Context;
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import org.apache.log4j.Logger;
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import javax.management.relation.Relation;
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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.*;
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import java.util.Map.Entry;
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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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private Serializer serializer;
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private EntityConfigTable entityConfigTable;
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private Properties tableMappings;
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private long writtenRecs = 0;
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private long threshold = 100000;
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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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@Override
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protected void setup(Context context) throws IOException, InterruptedException {
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loadTableMap(context);
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loadEntityConfig(context);
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serializer = new Serializer(context.getConfiguration().get("stats.delim"), context.getConfiguration().get("stats.nullNum"),
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context.getConfiguration().get("stats.nullString"), context.getConfiguration().get("stats.enclChar"));
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}
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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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final OafRowKeyDecoder decoder = OafRowKeyDecoder.decode(keyIn.copyBytes());
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final Type type = decoder.getType();
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final Oaf oaf = UpdateMerger.mergeBodyUpdates(context, result.getFamilyMap(Bytes.toBytes(type.toString())));
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if (isValid(oaf))
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{
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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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try {
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if (oaf != null && oaf.isInitialized()) {
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return true;
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}
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} catch (Exception e) {
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}
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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()).setDataInfo(oaf.getDataInfo());
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Type type = oaf.getEntity().getType();
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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, type, oafBuilder);
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emitEntity(context, oaf, type, oafBuilder);
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}
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private void emitEntity(Context context, Oaf oaf, Type type, Oaf.Builder oafBuilder) {
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// ONLY EMIT ENTITIES THAT WE WANT TO IMPORT IN STATS DB
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if (tableMappings.containsKey(type.toString())) {
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String serialized = serializer.serialize(oafBuilder.build());
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if (serialized != null) {
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try {
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Text TextKeyOut = new Text(type + "," + serializer.getId(oaf));
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context.write((TextKeyOut), new ImmutableBytesWritable(serialized.getBytes()));
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context.getCounter(STATS_COUNTERS.valueOf(type.toString())).increment(1);
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} catch (IOException e) {
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log.error("Error writing entity to M/R output", e);
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} catch (InterruptedException e) {
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log.error("Error writing entity to M/R output: Job Interrupted.", e);
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}
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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, Type type, Oaf.Builder builder) {
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try {
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// derived relations; ResultLanguages, resultConcepts etc are
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// created here
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HashMap<String, List<String>> relMap = serializer.extractRelations(oaf);
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if (relMap != null && !relMap.isEmpty()) {
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for (Entry<String, List<String>> rel : relMap.entrySet()) {
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Text TextKeyOut = new Text(rel.getKey() + "," + serializer.getId(oaf));
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for (String relVals : rel.getValue()) {
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if (relVals != null && !relVals.isEmpty()) {
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context.write((TextKeyOut), new ImmutableBytesWritable(relVals.getBytes()));
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}
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}
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}
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}
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} catch (Exception 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(type) != null && !entityConfigTable.getDescriptors(type).isEmpty()) {
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for (LinkDescriptor ld : entityConfigTable.getDescriptors(type)) {
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try {
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final Map<byte[], byte[]> columnMap = result.getFamilyMap(Bytes.toBytes(ld.getRelDescriptor().getIt()));
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ArrayList<OafRel> relOaf = decodeRelation(oaf, context, columnMap, ld);
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for (OafRel rel : relOaf) {
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try {
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if (tableMappings.containsKey(rel.getRelType().toString())) {
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builder.getEntityBuilder().addCachedRel(rel);
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Text TextKeyOut = new Text(ld.getRelDescriptor().getRelType().toString() + "," + serializer.getId(rel));
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String buff = serializer.serialize(rel);
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context.write((TextKeyOut), new ImmutableBytesWritable(buff.getBytes()));
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}
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} catch (Exception e) {
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log.error("Error while writing Relation Proto to M/R output", e);
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}
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}
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} catch (Exception e) {
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log.error("Error while decoding Relation Proto from HBase Body", e);
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}
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}
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}
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}
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private ArrayList<OafRel> decodeRelation(final Oaf body, final Context context, Map<byte[], byte[]> columnMap, final LinkDescriptor ld) throws IOException, InterruptedException {
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ArrayList<OafRel> rels = new ArrayList<OafRel>();
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if (hasData(columnMap)) {
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for (Entry<byte[], byte[]> e : columnMap.entrySet()) {
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final Oaf decodedOaf = decodeProto(context, e.getValue());
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if (isValid(decodedOaf) && !deletedByInference(decodedOaf)) {
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OafRel.Builder relBuilder = OafRel.newBuilder(decodedOaf.getRel());
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// skip dedups
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if (ld.getRelDescriptor().getIt().contains(SubRelType.dedup.toString()) && isDedupSelf(relBuilder)) {
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// log.info("avoid to emit dedup self: " +
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// relBuilder.getSource());
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} else {
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OafRel oafRel = relBuilder.setRelType(ld.getRelDescriptor().getRelType()).build();
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relBuilder.setCachedTarget(body.getEntity());
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rels.add(oafRel);
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}
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}
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}
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}
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return rels;
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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 (InvalidProtocolBufferException e) {
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context.getCounter("decodeProto", e.getClass().getName()).increment(1);
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// log.error("Corrupted proto ", e);
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}
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return null;
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}
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private void loadTableMap(Context context) throws IOException {
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tableMappings = new Properties();
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String tables = context.getConfiguration().get("stats.dbTablesMap");
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if (tables == null) {
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log.error("NULL TABLE MAP CONFIG IN MAPPER : ");
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}
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tables = tables.replaceAll(",", "\n");
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InputStream stream = new ByteArrayInputStream(tables.getBytes());
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tableMappings.load(stream);
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stream.close();
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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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@Override
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288 |
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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 Serializer getSerializer() {
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return serializer;
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}
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296 |
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297 |
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public void setSerializer(Serializer serializer) {
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this.serializer = serializer;
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}
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300 |
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301 |
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public EntityConfigTable getEntityConfigTable() {
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return entityConfigTable;
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}
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304 |
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public void setEntityConfigTable(EntityConfigTable entityConfigTable) {
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this.entityConfigTable = entityConfigTable;
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}
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308 |
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309 |
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public Properties getTableMappings() {
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310 |
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return tableMappings;
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}
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312 |
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313 |
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public void setTableMappings(Properties tableMappings) {
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this.tableMappings = tableMappings;
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}
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316 |
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317 |
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public long getWrittenRecs() {
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return writtenRecs;
|
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}
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320 |
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321 |
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public void setWrittenRecs(long writtenRecs) {
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this.writtenRecs = writtenRecs;
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}
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324 |
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325 |
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public long getThreshold() {
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326 |
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return threshold;
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}
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328 |
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public void setThreshold(long threshold) {
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this.threshold = threshold;
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331 |
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}
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332 |
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}
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