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package eu.dnetlib.data.mapreduce.hbase.broker.enrich;
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import java.io.IOException;
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import java.math.BigDecimal;
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import java.util.Map;
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import java.util.Set;
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import com.google.common.base.Function;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.mapreduce.Algorithms;
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import eu.dnetlib.data.mapreduce.JobParams;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.pace.config.DedupConfig;
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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.MapDocument;
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import eu.dnetlib.pace.model.ProtoDocumentBuilder;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.math.util.MathUtils;
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import org.apache.hadoop.hbase.client.HTable;
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import org.apache.hadoop.hbase.client.Result;
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import org.apache.hadoop.hbase.client.ResultScanner;
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import org.apache.hadoop.hbase.client.Scan;
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import org.apache.hadoop.hbase.filter.FilterList;
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import org.apache.hadoop.hbase.filter.FilterList.Operator;
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import org.apache.hadoop.hbase.filter.PrefixFilter;
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
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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.Reducer;
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import static eu.dnetlib.data.mapreduce.util.OafHbaseUtils.getPropertyValues;
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/**
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* Created by claudio on 20/02/2017.
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*/
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public abstract class AbstractEnrichmentReducer extends Reducer<ImmutableBytesWritable, ImmutableBytesWritable, Text, Text> {
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protected DedupConfig dedupConf;
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protected static final int LIMIT = 1000;
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protected static final int SCORE_DECIMALS = 2;
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protected Map<String, String> dsTypeMap = Maps.newHashMap();
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protected Set<String> dsWhitelist = Sets.newHashSet();
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protected Set<String> dsBlacklist = Sets.newHashSet();
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// This is for EuropePMC. They expose OA abstracts, but we want to identify real OA publications. WTF.
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protected Set<String> untrustedOaDsList = Sets.newHashSet();
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// White list for datasource typologies.
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protected Set<String> dsTypeWhitelist = Sets.newHashSet();
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/**
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* lower bound for trust scaling
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*/
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protected double scaleLB;
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protected abstract String counterGroup();
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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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System.out.println("LIMIT: " + LIMIT);
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dsWhitelist.addAll(getPropertyValues(context, "broker.datasource.id.whitelist"));
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dsBlacklist.addAll(getPropertyValues(context, "broker.datasource.id.blacklist"));
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dsTypeWhitelist.addAll(getPropertyValues(context, "broker.datasource.type.whitelist"));
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untrustedOaDsList.addAll(getPropertyValues(context, "broker.datasource.untrusted.oa.list"));
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dsTypeMap = getDsTypeMap(context, dsTypeWhitelist);
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System.out.println("datasource whitelist: " + dsWhitelist);
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System.out.println("datasource blacklist: " + dsBlacklist);
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System.out.println("datasource OA list: " + untrustedOaDsList);
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System.out.println("datasource type whitelist: " + dsTypeWhitelist);
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final String dedupConfJson = context.getConfiguration().get(JobParams.DEDUP_CONF);
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System.out.println("got dedup conf: " + dedupConfJson);
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dedupConf = DedupConfig.load(dedupConfJson);
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System.out.println("parsed dedup conf: " + dedupConf.toString());
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scaleLB = dedupConf.getWf().getThreshold() - 0.01;
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}
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protected Map<String, String> getDsTypeMap(final Context context, final Set<String> dsTypeWhitelist) throws IOException {
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System.out.println("loading datasource typology mapping");
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final Map<String, String> dsTypeMap = Maps.newHashMap();
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final Scan scan = new Scan();
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final FilterList fl = new FilterList(Operator.MUST_PASS_ALL);
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fl.addFilter(new PrefixFilter(Bytes.toBytes("10")));
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scan.setFilter(fl);
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scan.addFamily(Bytes.toBytes("datasource"));
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final String tableName = context.getConfiguration().get("hbase.mapred.inputtable");
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System.out.println(String.format("table name: '%s'", tableName));
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try (final HTable table = new HTable(context.getConfiguration(), tableName); final ResultScanner res = table.getScanner(scan)) {
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for (final Result r : res) {
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final byte[] b = r.getValue(Bytes.toBytes("datasource"), Bytes.toBytes("body"));
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if (b != null) {
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final Oaf oaf = Oaf.parseFrom(b);
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final String dsId = StringUtils.substringAfter(oaf.getEntity().getId(), "|");
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final String dsType = oaf.getEntity().getDatasource().getMetadata().getDatasourcetype().getClassid();
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if (dsTypeWhitelist.contains(dsType)) {
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//System.out.println(String.format("dsId '%s', dsType '%s'", dsId, dsType));
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dsTypeMap.put(dsId, dsType);
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}
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}
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}
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}
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System.out.println("datasource type map size: " + dsTypeMap.size());
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return dsTypeMap;
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}
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protected float similarity(final Oaf oa, final Oaf ob) {
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final MapDocument a = ProtoDocumentBuilder.newInstance(oa.getEntity().getId(), oa.getEntity(), dedupConf.getPace().getModel());
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final MapDocument b = ProtoDocumentBuilder.newInstance(ob.getEntity().getId(), ob.getEntity(), dedupConf.getPace().getModel());
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final ScoreResult sr = new PaceDocumentDistance().between(a, b, dedupConf);
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final float score = (float) Algorithms.scale(sr.getScore(), scaleLB, 1, 0, 1);
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return MathUtils.round(score, SCORE_DECIMALS, BigDecimal.ROUND_HALF_DOWN);
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}
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protected Function<ImmutableBytesWritable, Oaf> oafDeserialiser() {
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return new Function<ImmutableBytesWritable, Oaf>() {
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@Override
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public Oaf apply(final ImmutableBytesWritable input) {
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try {
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return Oaf.parseFrom(input.copyBytes());
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} catch (final InvalidProtocolBufferException e) {
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throw new IllegalArgumentException(e);
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}
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}
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};
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}
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}
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