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package eu.dnetlib.data.mapreduce.hbase.dedup;
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import java.io.IOException;
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import java.util.List;
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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 eu.dnetlib.data.mapreduce.JobParams;
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import eu.dnetlib.data.mapreduce.hbase.index.config.RelClasses;
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import eu.dnetlib.data.mapreduce.util.DedupUtils;
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import eu.dnetlib.data.mapreduce.util.OafDecoder;
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import eu.dnetlib.data.mapreduce.util.OafHbaseUtils;
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import eu.dnetlib.data.mapreduce.util.OafRelDecoder;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.transform.OafEntityMerger;
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import eu.dnetlib.pace.config.DedupConfig;
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import org.apache.commons.lang.StringUtils;
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import org.apache.hadoop.hbase.client.Durability;
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import org.apache.hadoop.hbase.client.Put;
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import org.apache.hadoop.hbase.client.RetriesExhaustedWithDetailsException;
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
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import org.apache.hadoop.hbase.mapreduce.TableReducer;
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import org.apache.hadoop.hbase.regionserver.NoSuchColumnFamilyException;
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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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public class DedupBuildRootsReducer extends TableReducer<Text, ImmutableBytesWritable, ImmutableBytesWritable> {
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private enum OafPatch {
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rootToEntity, entityToRoot
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}
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private DedupConfig dedupConf;
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private RelClasses relClasses;
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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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dedupConf = DedupConfig.load(context.getConfiguration().get(JobParams.DEDUP_CONF));
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System.out.println("dedup buildRoots reducer\n\nwf conf: " + dedupConf.toString());
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final String relClassJson = context.getConfiguration().get("relClasses");
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System.out.println("relClassesJson:\n" + relClassJson);
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relClasses = RelClasses.fromJSon(relClassJson);
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System.out.println("relClasses:\n" + relClasses);
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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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// ensures we're dealing with a root, otherwise returns
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if (!DedupUtils.isRoot(key.toString())) {
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System.err.println("aborting DedupBuildRootsReducer, found non-root key: " + key);
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context.getCounter("DedupBuildRootsReducer", "aborted").increment(1);
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return;
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}
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final byte[] rowkey = Bytes.toBytes(key.toString());
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final List<Oaf> entities = Lists.newArrayList();
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for (final Oaf oaf : toOaf(values)) {
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switch (oaf.getKind()) {
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case entity:
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entities.add(oaf);
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break;
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case relation:
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handleRels(context, rowkey, oaf);
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break;
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default:
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break;
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}
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}
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// build and emit the root body
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final Oaf.Builder builder = OafEntityMerger.merge(dedupConf, key.toString(), entities);
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if (entities.size() < JobParams.MAX_COUNTERS) {
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context.getCounter(dedupConf.getWf().getEntityType() + " root group size", lpad(entities.size())).increment(1);
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} else {
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context.getCounter(dedupConf.getWf().getEntityType() + " root group size", "> " + JobParams.MAX_COUNTERS).increment(1);
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}
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emit(builder.getEntity().getType().toString(),
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context, rowkey, dedupConf.getWf().getEntityType(), DedupUtils.BODY_S, builder.build().toByteArray(), "root");
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}
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private Iterable<Oaf> toOaf(final Iterable<ImmutableBytesWritable> values) {
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return Iterables.transform(values, OafHbaseUtils.oafDecoder());
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}
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private void handleRels(final Context context, final byte[] rowkey, final Oaf oaf) throws IOException, InterruptedException {
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// emit relation from the root to the related entities
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OafDecoder decoder = rootToEntity(rowkey, oaf);
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emit("emit relation from the root to the related entities",
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context, rowkey, decoder.getCFQ(), decoder.relTargetId(), decoder.toByteArray(), "[root -> entity]");
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// emit relation from the related entities to the root
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decoder = entityToRoot(rowkey, oaf);
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byte[] revKey = Bytes.toBytes(decoder.relSourceId());
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emit("emit relation from the related entities to the root",
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context, revKey, decoder.getCFQ(), new String(rowkey), decoder.toByteArray(), "[entity -> root]");
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// mark relation from the related entities to the duplicate as deleted
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decoder = markDeleted(oaf, true);
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revKey = Bytes.toBytes(decoder.relSourceId());
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emit("mark relation from the related entities to the duplicate as deleted",
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context, revKey, decoder.getCFQ(), decoder.relTargetId(), decoder.toByteArray(), "mark deleted [dup -> entity]");
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// mark relation from the related entities to the duplicate as deleted
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decoder = markDeleted(oaf, false);
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revKey = Bytes.toBytes(decoder.relSourceId());
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emit("mark relation from the related entities to the duplicate as deleted",
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context, revKey, decoder.getCFQ(), decoder.relTargetId(), decoder.toByteArray(), "mark deleted [entity -> dup]");
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}
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private void emit(final String msg, final Context context, final byte[] rowkey, final String family, final String qualifier, final byte[] value, final String label)
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throws IOException, InterruptedException {
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final Put put = new Put(rowkey).add(Bytes.toBytes(family), Bytes.toBytes(qualifier), value);
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put.setDurability(Durability.SKIP_WAL);
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try {
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context.write(new ImmutableBytesWritable(rowkey), put);
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} catch (RetriesExhaustedWithDetailsException | NoSuchColumnFamilyException e) {
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System.err.println(
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String.format("%s, rowkey %s, family %s, qualifier %s",
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msg, new String(rowkey), family, qualifier));
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throw new RuntimeException(e);
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}
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context.getCounter(family, label).increment(1);
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}
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// /////////////////
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private OafDecoder rootToEntity(final byte[] rootRowkey, final Oaf rel) {
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return patchRelations(rootRowkey, rel, OafPatch.rootToEntity);
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}
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private OafDecoder entityToRoot(final byte[] rootRowkey, final Oaf rel) {
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return patchRelations(rootRowkey, rel, OafPatch.entityToRoot);
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}
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private OafDecoder markDeleted(final Oaf rel, final boolean reverse) {
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return deleteRelations(rel, reverse);
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}
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// patches relation objects setting the source field with the root id
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private OafDecoder patchRelations(final byte[] rootRowkey, final Oaf rel, final OafPatch patchKind) {
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final String id = new String(rootRowkey);
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final OafRelDecoder decoder = OafRelDecoder.decode(rel.getRel());
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final Oaf.Builder builder = Oaf.newBuilder(rel);
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builder.getDataInfoBuilder().setInferred(true).setDeletedbyinference(false);
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switch (patchKind) {
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case rootToEntity:
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// builder.getDataInfoBuilder().setInferenceprovenance("dedup (BuildRoots p:rootToEntity)");
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builder.getRelBuilder().setSource(id);
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break;
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case entityToRoot:
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final String relClass = rel.getRel().getRelClass();
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/*
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if(StringUtils.isBlank(relClass)) {
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throw new IllegalStateException(String.format("missing relation term for %s in row %s", rel.getRel().getRelType().name(), id));
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}
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*/
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final String inverse = relClasses.getInverse(relClass);
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if(StringUtils.isBlank(inverse)) {
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throw new IllegalStateException(String.format("missing inverse relation for %s in row %s", relClass, id));
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}
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builder.setRel(decoder.setClassId(inverse));
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// builder.getDataInfoBuilder().setInferenceprovenance("dedup (BuildRoots p:entityToRoot)");
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builder.getRelBuilder().setSource(builder.getRel().getTarget());
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builder.getRelBuilder().setTarget(id);
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break;
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default:
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break;
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}
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return OafDecoder.decode(builder.build());
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}
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private OafDecoder deleteRelations(final Oaf rel, final boolean reverse) {
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final Oaf.Builder builder = Oaf.newBuilder(rel);
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// builder.getDataInfoBuilder().setInferenceprovenance("dedup (BuildRoots d: " + reverse + ")");
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builder.getDataInfoBuilder().setDeletedbyinference(true);
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if (reverse) {
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final OafRelDecoder decoder = OafRelDecoder.decode(rel.getRel());
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builder.setRel(decoder.setClassId(relClasses.getInverse(rel.getRel().getRelClass())));
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// swap source and target
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final String tmp = builder.getRel().getSource();
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builder.getRelBuilder().setSource(builder.getRel().getTarget());
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builder.getRelBuilder().setTarget(tmp);
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}
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return OafDecoder.decode(builder.build());
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}
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private String lpad(final int s) {
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return StringUtils.leftPad(String.valueOf(s), 5);
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}
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}
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