Create dedup record for "merged" pivots
Do not create dedup records for group that have more than 20 different acceptance date
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@ -1,130 +1,187 @@
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package eu.dnetlib.dhp.oa.dedup;
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package eu.dnetlib.dhp.oa.dedup;
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import java.lang.reflect.InvocationTargetException;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.dedup.model.Identifier;
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import eu.dnetlib.dhp.oa.dedup.model.Identifier;
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import eu.dnetlib.dhp.oa.merge.AuthorMerger;
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import eu.dnetlib.dhp.oa.merge.AuthorMerger;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import org.apache.commons.beanutils.BeanUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.*;
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import scala.Tuple2;
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import scala.Tuple2;
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import scala.Tuple3;
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import scala.collection.JavaConversions;
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import java.util.*;
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import java.util.stream.Stream;
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public class DedupRecordFactory {
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public class DedupRecordFactory {
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public static final class DedupRecordReduceState {
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public final String dedupId;
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protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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public final ArrayList<String> aliases = new ArrayList<>();
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private DedupRecordFactory() {
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public final HashSet<String> acceptanceDate = new HashSet<>();
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}
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public static <T extends OafEntity> Dataset<T> createDedupRecord(
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public OafEntity entity;
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final SparkSession spark,
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final DataInfo dataInfo,
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final String mergeRelsInputPath,
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final String entitiesInputPath,
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final Class<T> clazz) {
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long ts = System.currentTimeMillis();
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public DedupRecordReduceState(String dedupId, String id, OafEntity entity) {
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this.dedupId = dedupId;
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this.entity = entity;
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if (entity == null) {
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aliases.add(id);
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} else {
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if (Result.class.isAssignableFrom(entity.getClass())) {
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Result result = (Result) entity;
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if (result.getDateofacceptance() != null && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
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acceptanceDate.add(result.getDateofacceptance().getValue());
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}
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}
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}
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}
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// <id, json_entity>
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public String getDedupId() {
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Dataset<Row> entities = spark
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return dedupId;
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.read()
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}
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.schema(Encoders.bean(clazz).schema())
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}
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.json(entitiesInputPath)
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private static final int MAX_ACCEPTANCE_DATE = 20;
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.as(Encoders.bean(clazz))
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.map(
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(MapFunction<T, Tuple2<String, T>>) entity -> {
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return new Tuple2<>(entity.getId(), entity);
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},
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
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.selectExpr("_1 AS id", "_2 AS kryoObject");
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// <source, target>: source is the dedup_id, target is the id of the mergedIn
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private DedupRecordFactory() {
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Dataset<Row> mergeRels = spark
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}
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.read()
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.load(mergeRelsInputPath)
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.where("relClass == 'merges'")
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.selectExpr("source as dedupId", "target as id");
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return mergeRels
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public static Dataset<OafEntity> createDedupRecord(
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.join(entities, "id")
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final SparkSession spark,
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.select("dedupId", "kryoObject")
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final DataInfo dataInfo,
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.as(Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
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final String mergeRelsInputPath,
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.groupByKey((MapFunction<Tuple2<String, T>, String>) Tuple2::_1, Encoders.STRING())
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final String entitiesInputPath,
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.reduceGroups(
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final Class<OafEntity> clazz) {
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(ReduceFunction<Tuple2<String, T>>) (t1, t2) -> new Tuple2<>(t1._1(),
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reduceEntity(t1._1(), t1._2(), t2._2(), clazz)))
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.map(
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(MapFunction<Tuple2<String, Tuple2<String, T>>, T>) t -> {
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T res = t._2()._2();
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res.setDataInfo(dataInfo);
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res.setLastupdatetimestamp(ts);
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return res;
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},
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Encoders.bean(clazz));
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}
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public static <T extends OafEntity> T reduceEntity(
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final long ts = System.currentTimeMillis();
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String id, T entity, T duplicate, Class<T> clazz) {
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final Encoder<OafEntity> beanEncoder = Encoders.bean(clazz);
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final Encoder<OafEntity> kryoEncoder = Encoders.kryo(clazz);
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int compare = new IdentifierComparator()
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// <id, json_entity>
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.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
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Dataset<Row> entities = spark
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.read()
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.schema(Encoders.bean(clazz).schema())
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.json(entitiesInputPath)
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.as(beanEncoder)
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.map(
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(MapFunction<OafEntity, Tuple2<String, OafEntity>>) entity -> {
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return new Tuple2<>(entity.getId(), entity);
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},
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Encoders.tuple(Encoders.STRING(), kryoEncoder))
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.selectExpr("_1 AS id", "_2 AS kryoObject");
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if (compare > 0) {
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// <source, target>: source is the dedup_id, target is the id of the mergedIn
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T swap = duplicate;
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Dataset<Row> mergeRels = spark
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duplicate = entity;
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.read()
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entity = swap;
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.load(mergeRelsInputPath)
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.where("relClass == 'merges'")
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.selectExpr("source as dedupId", "target as id");
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return mergeRels
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.join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left")
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.select("dedupId", "id", "kryoObject")
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.as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder))
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.map((MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(t._1(), t._2(), t._3()), Encoders.kryo(DedupRecordReduceState.class))
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.groupByKey((MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
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.reduceGroups(
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(ReduceFunction<DedupRecordReduceState>) (t1, t2) -> {
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if (t1.entity == null) {
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t2.aliases.addAll(t1.aliases);
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return t2;
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}
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if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
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t1.acceptanceDate.addAll(t2.acceptanceDate);
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}
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t1.aliases.addAll(t2.aliases);
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t1.entity = reduceEntity(t1.entity, t2.entity);
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return t1;
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}
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)
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.flatMap
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((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
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String dedupId = t._1();
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DedupRecordReduceState agg = t._2();
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if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) {
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return Collections.emptyIterator();
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}
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return Stream.concat(Stream.of(agg.getDedupId()), agg.aliases.stream())
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.map(id -> {
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try {
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OafEntity res = (OafEntity) BeanUtils.cloneBean(agg.entity);
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res.setId(id);
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res.setDataInfo(dataInfo);
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res.setLastupdatetimestamp(ts);
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return res;
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} catch (Exception e) {
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throw new RuntimeException(e);
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}
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}).iterator();
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}, beanEncoder);
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}
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private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) {
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if (duplicate == null) {
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return entity;
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}
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}
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entity.mergeFrom(duplicate);
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entity.setId(id);
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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int compare = new IdentifierComparator<>()
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Result re = (Result) entity;
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.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
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Result rd = (Result) duplicate;
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List<List<Author>> authors = new ArrayList<>();
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if (compare > 0) {
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if (re.getAuthor() != null) {
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OafEntity swap = duplicate;
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authors.add(re.getAuthor());
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duplicate = entity;
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}
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entity = swap;
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if (rd.getAuthor() != null) {
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}
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authors.add(rd.getAuthor());
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}
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re.setAuthor(AuthorMerger.merge(authors));
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entity.mergeFrom(duplicate);
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}
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return entity;
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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}
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Result re = (Result) entity;
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Result rd = (Result) duplicate;
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public static <T extends OafEntity> T entityMerger(
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List<List<Author>> authors = new ArrayList<>();
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String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
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if (re.getAuthor() != null) {
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throws IllegalAccessException, InstantiationException, InvocationTargetException {
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authors.add(re.getAuthor());
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T base = entities.next()._2();
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}
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if (rd.getAuthor() != null) {
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authors.add(rd.getAuthor());
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}
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while (entities.hasNext()) {
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re.setAuthor(AuthorMerger.merge(authors));
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T duplicate = entities.next()._2();
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}
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if (duplicate != null)
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base = reduceEntity(id, base, duplicate, clazz);
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}
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base.setDataInfo(dataInfo);
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return entity;
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base.setLastupdatetimestamp(ts);
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}
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return base;
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public static <T extends OafEntity> T entityMerger(
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}
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String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) {
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T base = entities.next()._2();
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while (entities.hasNext()) {
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T duplicate = entities.next()._2();
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if (duplicate != null)
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base = (T) reduceEntity(base, duplicate);
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}
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base.setId(id);
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base.setDataInfo(dataInfo);
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base.setLastupdatetimestamp(ts);
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return base;
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}
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}
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}
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@ -611,7 +611,7 @@ public class SparkDedupTest implements Serializable {
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assertEquals(91, pubs.count());
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assertEquals(91, pubs.count());
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assertEquals(47, sw_deduprecord);
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assertEquals(47, sw_deduprecord);
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assertEquals(97, ds_deduprecord);
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assertEquals(97, ds_deduprecord);
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assertEquals(93, orp_deduprecord);
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assertEquals(92, orp_deduprecord);
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verifyRoot_1(mapper, pubs);
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verifyRoot_1(mapper, pubs);
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@ -751,7 +751,7 @@ public class SparkDedupTest implements Serializable {
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assertEquals(100, datasource);
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assertEquals(100, datasource);
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assertEquals(196, softwares);
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assertEquals(196, softwares);
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assertEquals(389, dataset);
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assertEquals(389, dataset);
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assertEquals(521, otherresearchproduct);
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assertEquals(520, otherresearchproduct);
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// System.out.println("publications = " + publications);
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// System.out.println("publications = " + publications);
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// System.out.println("organizations = " + organizations);
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// System.out.println("organizations = " + organizations);
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