forked from D-Net/dnet-hadoop
96 lines
4.2 KiB
Java
96 lines
4.2 KiB
Java
package eu.dnetlib.dhp.oa.dedup;
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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 com.google.common.collect.Lists;
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import eu.dnetlib.dhp.schema.common.EntityType;
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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.pace.config.DedupConfig;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.api.java.function.PairFunction;
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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.SparkSession;
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import scala.Tuple2;
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import java.util.Collection;
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import java.util.Iterator;
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public class DedupRecordFactory {
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protected static final ObjectMapper OBJECT_MAPPER = new com.fasterxml.jackson.databind.ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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public static <T extends OafEntity> Dataset<T> createDedupRecord(
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final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final Class<T> clazz, final DedupConfig dedupConf) {
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long ts = System.currentTimeMillis();
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//<id, json_entity>
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Dataset<Tuple2<String, T>> entities = spark.read()
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.textFile(entitiesInputPath)
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.map((MapFunction<String, Tuple2<String, T>>) it -> {
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T entity = OBJECT_MAPPER.readValue(it, clazz);
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return new Tuple2<>(entity.getId(), entity);
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}, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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//<source, target>: source is the dedup_id, target is the id of the mergedIn
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Dataset<Tuple2<String, String>> mergeRels = spark
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.read()
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.load(mergeRelsInputPath)
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.as(Encoders.bean(Relation.class))
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.where("relClass == 'merges'")
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.map((MapFunction<Relation, Tuple2<String, String>>)
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r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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//<dedup_id, json_entity_merged>
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return mergeRels.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer")
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.filter((FilterFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>>) value -> value._2() != null)
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.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, T>)
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value -> value._2()._2(), Encoders.kryo(clazz))
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.groupByKey((MapFunction<T, String>) value -> value.getId(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, T, T>)
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(key, values) -> entityMerger(key, values, ts, clazz), Encoders.bean(clazz));
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}
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private static <T extends OafEntity> T entityMerger(String id, Iterator<T> entities, final long ts, Class<T> clazz) {
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try {
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T entity = clazz.newInstance();
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entity.setId(id);
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if (entity.getDataInfo() == null) {
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entity.setDataInfo(new DataInfo());
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}
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entity.getDataInfo().setTrust("0.9");
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entity.setLastupdatetimestamp(ts);
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final Collection<String> dates = Lists.newArrayList();
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entities.forEachRemaining(e -> {
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entity.mergeFrom(e);
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if (ModelSupport.isSubClass(e, Result.class)) {
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Result r1 = (Result) e;
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Result er = (Result) entity;
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er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
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if (er.getDateofacceptance() != null) {
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dates.add(r1.getDateofacceptance().getValue());
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}
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}
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});
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if (ModelSupport.isSubClass(entity, Result.class)) {
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((Result) entity).setDateofacceptance(DatePicker.pick(dates));
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}
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return entity;
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} catch (IllegalAccessException | InstantiationException e) {
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throw new RuntimeException(e);
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}
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}
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}
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