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import java.io.IOException;
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import java.util.*;
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import com.google.common.base.Function;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.mapreduce.JobParams;
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import eu.dnetlib.data.mapreduce.util.DedupUtils;
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import eu.dnetlib.data.mapreduce.util.StreamUtils;
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import eu.dnetlib.data.proto.OafProtos;
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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 eu.dnetlib.pace.clustering.NGramUtils;
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| ... | ... | |
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import eu.dnetlib.pace.config.WfConfig;
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import eu.dnetlib.pace.distance.PaceDocumentDistance;
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import eu.dnetlib.pace.distance.eval.ScoreResult;
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import eu.dnetlib.pace.model.Field;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.model.MapDocumentComparator;
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import eu.dnetlib.pace.model.MapDocumentSerializer;
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import eu.dnetlib.pace.model.*;
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import eu.dnetlib.pace.util.BlockProcessor;
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import eu.dnetlib.pace.util.Reporter;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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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 javax.annotation.Nullable;
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public class DedupReducer extends TableReducer<Text, ImmutableBytesWritable, ImmutableBytesWritable> {
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private static final Log log = LogFactory.getLog(DedupReducer.class);
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| ... | ... | |
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}
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@Override
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protected void reduce(final Text key, final Iterable<ImmutableBytesWritable> values, final Context context) throws IOException, InterruptedException {
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protected void reduce(final Text key, final Iterable<ImmutableBytesWritable> values, final Context context) {
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final Queue<MapDocument> q = prepare(context, key, values);
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if (q.size() > 1) {
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log.info("reducing key: '" + key + "' records: " + q.size());
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final Type type = Type.valueOf(dedupConf.getWf().getEntityType());
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switch (type) {
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case result:
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process(simplifyQueue(q, key.toString(), context), context);
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break;
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case organization:
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process(q, context);
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break;
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default:
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throw new IllegalArgumentException("process not implemented for type: " + dedupConf.getWf().getEntityType());
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final Iterable<MapDocument> docs = Iterables.transform(values, new Function<ImmutableBytesWritable, MapDocument>() {
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@Nullable
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@Override
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public MapDocument apply(@Nullable ImmutableBytesWritable b) {
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return MapDocumentSerializer.decode(b.copyBytes());
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}
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} else {
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context.getCounter(dedupConf.getWf().getEntityType(), "records per hash key = 1").increment(1);
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}
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}
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});
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private Queue<MapDocument> prepare(final Context context, final Text key, final Iterable<ImmutableBytesWritable> values) {
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final Queue<MapDocument> queue = new PriorityQueue<MapDocument>(100, new MapDocumentComparator(dedupConf.getWf().getOrderField()));
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new BlockProcessor(dedupConf).process(key.toString(), docs, new Reporter() {
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final Set<String> seen = new HashSet<String>();
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final int queueMaxSize = dedupConf.getWf().getQueueMaxSize();
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boolean logged = false;
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for (final ImmutableBytesWritable i : values) {
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if (queue.size() <= queueMaxSize) {
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final MapDocument doc = MapDocumentSerializer.decode(i.copyBytes());
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final String id = doc.getIdentifier();
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if (!seen.contains(id)) {
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seen.add(id);
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queue.add(doc);
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}
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} else {
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if (!logged) {
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// context.getCounter("ngram size > " + LIMIT, "'" + key.toString() + "', --> " + context.getTaskAttemptID()).increment(1);
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context.getCounter("ngram size > " + queueMaxSize, "N").increment(1);
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log.info("breaking out after limit (" + queueMaxSize + ") for ngram '" + key + "'");
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logged = true;
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}
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@Override
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public void incrementCounter(String counterGroup, String counterName, long delta) {
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context.getCounter(counterGroup, counterName).increment(delta);
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}
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}
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return queue;
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}
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@Override
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public void emit(String type, String from, String to) {
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private Queue<MapDocument> simplifyQueue(final Queue<MapDocument> queue, final String ngram, final Context context) {
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final Queue<MapDocument> q = new LinkedList<MapDocument>();
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String fieldRef = "";
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final List<MapDocument> tempResults = Lists.newArrayList();
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while (!queue.isEmpty()) {
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final MapDocument result = queue.remove();
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final String orderFieldName = dedupConf.getWf().getOrderField();
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final Field orderFieldValue = result.values(orderFieldName);
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if (!orderFieldValue.isEmpty()) {
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final String field = NGramUtils.cleanupForOrdering(orderFieldValue.stringValue());
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if (field.equals(fieldRef)) {
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tempResults.add(result);
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} else {
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populateSimplifiedQueue(q, tempResults, context, fieldRef, ngram);
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tempResults.clear();
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tempResults.add(result);
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fieldRef = field;
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}
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} else {
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context.getCounter(dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField()).increment(1);
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emitRel(context, type, from, to);
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emitRel(context, type, to, from);
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}
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}
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populateSimplifiedQueue(q, tempResults, context, fieldRef, ngram);
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return q;
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}
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private void populateSimplifiedQueue(final Queue<MapDocument> q,
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final List<MapDocument> tempResults,
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final Context context,
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final String fieldRef,
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final String ngram) {
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final WfConfig wfConf = dedupConf.getWf();
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if (tempResults.size() < wfConf.getGroupMaxSize()) {
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q.addAll(tempResults);
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} else {
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context.getCounter(wfConf.getEntityType(),
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"Skipped records for count(" + wfConf.getOrderField() + ") >= " + wfConf.getGroupMaxSize())
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.increment(tempResults.size());
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log.info("Skipped field: " + fieldRef + " - size: " + tempResults.size() + " - ngram: " + ngram);
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}
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}
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private void process(final Queue<MapDocument> queue, final Context context) throws IOException, InterruptedException {
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| 150 |
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final PaceDocumentDistance algo = new PaceDocumentDistance();
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while (!queue.isEmpty()) {
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final MapDocument pivot = queue.remove();
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final String idPivot = pivot.getIdentifier();
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final Field fieldsPivot = pivot.values(dedupConf.getWf().getOrderField());
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final String fieldPivot = (fieldsPivot == null) || fieldsPivot.isEmpty() ? null : fieldsPivot.stringValue();
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if (fieldPivot != null) {
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// System.out.println(idPivot + " --> " + fieldPivot);
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int i = 0;
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for (final MapDocument curr : queue) {
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final String idCurr = curr.getIdentifier();
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if (mustSkip(idCurr)) {
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context.getCounter(dedupConf.getWf().getEntityType(), "skip list").increment(1);
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break;
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}
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| 173 |
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if (i > dedupConf.getWf().getSlidingWindowSize()) {
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| 174 |
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break;
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| 175 |
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}
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| 177 |
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final Field fieldsCurr = curr.values(dedupConf.getWf().getOrderField());
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final String fieldCurr = (fieldsCurr == null) || fieldsCurr.isEmpty() ? null : fieldsCurr.stringValue();
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| 180 |
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if (!idCurr.equals(idPivot) && (fieldCurr != null)) {
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| 181 |
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| 182 |
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final ScoreResult sr = similarity(algo, pivot, curr);
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emitOutput(sr, idPivot, idCurr, context);
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i++;
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}
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private void emitRel(final Context context, final String type, final String from, final String to) {
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79 |
final Put put = new Put(Bytes.toBytes(from)).add(DedupUtils.getSimilarityCFBytes(type), Bytes.toBytes(to), Bytes.toBytes(""));
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80 |
put.setDurability(Durability.SKIP_WAL);
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81 |
ibw.set(Bytes.toBytes(from));
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82 |
try {
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83 |
context.write(ibw, put);
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84 |
} catch (IOException | InterruptedException e) {
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85 |
e.printStackTrace();
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| 186 |
86 |
}
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| 187 |
87 |
}
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| 188 |
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}
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88 |
});
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| 189 |
89 |
}
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| 190 |
90 |
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| 191 |
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private void emitOutput(final ScoreResult sr, final String idPivot, final String idCurr, final Context context) throws IOException, InterruptedException {
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| 192 |
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final double d = sr.getScore();
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| 193 |
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| 194 |
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if (d >= dedupConf.getWf().getThreshold()) {
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| 195 |
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writeSimilarity(context, idPivot, idCurr, d);
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| 196 |
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context.getCounter(dedupConf.getWf().getEntityType(), SubRelType.dedupSimilarity.toString() + " (x2)").increment(1);
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| 197 |
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} else {
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| 198 |
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context.getCounter(dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold()).increment(1);
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| 199 |
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}
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| 200 |
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}
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| 201 |
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|
| 202 |
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private ScoreResult similarity(final PaceDocumentDistance algo, final MapDocument a, final MapDocument b) {
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| 203 |
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try {
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| 204 |
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return algo.between(a, b, dedupConf);
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| 205 |
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} catch(Throwable e) {
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| 206 |
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log.error(String.format("\nA: %s\n----------------------\nB: %s", a, b), e);
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| 207 |
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throw new IllegalArgumentException(e);
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| 208 |
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}
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| 209 |
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}
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| 210 |
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| 211 |
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private boolean mustSkip(final String idPivot) {
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| 212 |
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return dedupConf.getWf().getSkipList().contains(getNsPrefix(idPivot));
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| 213 |
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}
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| 214 |
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| 215 |
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private String getNsPrefix(final String id) {
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| 216 |
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return StringUtils.substringBetween(id, "|", "::");
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| 217 |
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}
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| 218 |
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| 219 |
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private void writeSimilarity(final Context context, final String idPivot, final String id, final double d) throws IOException, InterruptedException {
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| 220 |
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final byte[] rowKey = Bytes.toBytes(idPivot);
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| 221 |
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final byte[] target = Bytes.toBytes(id);
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| 222 |
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| 223 |
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//log.info("writing similarity: " + idPivot + " <-> " + id);
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| 224 |
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| 225 |
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emitRel(context, rowKey, target, d);
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| 226 |
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emitRel(context, target, rowKey, d);
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| 227 |
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}
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| 228 |
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| 229 |
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private void emitRel(final Context context, final byte[] from, final byte[] to, final double d) throws IOException, InterruptedException {
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| 230 |
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final Type type = Type.valueOf(dedupConf.getWf().getEntityType());
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| 231 |
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| 232 |
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//final OafRel.Builder rel = DedupUtils.getDedupSimilarity(dedupConf, new String(from), new String(to));
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| 233 |
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//final Oaf.Builder oaf = DedupUtils.buildRel(dedupConf, rel, d);
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| 234 |
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| 235 |
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//final Put put = new Put(from).add(DedupUtils.getSimilarityCFBytes(type), to, oaf.build().toByteArray());
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| 236 |
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final Put put = new Put(from).add(DedupUtils.getSimilarityCFBytes(type), to, Bytes.toBytes(""));
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| 237 |
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put.setDurability(Durability.SKIP_WAL);
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| 238 |
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ibw.set(from);
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| 239 |
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context.write(ibw, put);
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| 240 |
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}
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| 241 |
91 |
}
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Added by Claudio Atzori almost 6 years ago
introduced use of BlockProcessor