121 lines
3.9 KiB
Java
121 lines
3.9 KiB
Java
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.Collection;
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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.MapGroupsFunction;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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.oa.dedup.model.Identifier;
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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.oaf.*;
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import scala.Tuple2;
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public class DedupRecordFactory {
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private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
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protected static final ObjectMapper OBJECT_MAPPER = new 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,
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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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// <id, json_entity>
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Dataset<Tuple2<String, T>> entities = spark
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.read()
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.textFile(entitiesInputPath)
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.map(
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(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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},
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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(
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(MapFunction<Relation, Tuple2<String, String>>) r -> new Tuple2<>(r.getSource(), r.getTarget()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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return mergeRels
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.joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner")
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.map(
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(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, Tuple2<String, T>>) value -> new Tuple2<>(
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value._1()._1(), value._2()._2()),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
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.groupByKey(
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(MapFunction<Tuple2<String, T>, String>) entity -> entity._1(), Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<String, T>, T>) (key,
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values) -> entityMerger(key, values, ts, dataInfo, clazz),
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Encoders.bean(clazz));
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}
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public static <T extends OafEntity> T entityMerger(
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String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
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throws IllegalAccessException, InstantiationException {
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T entity = clazz.newInstance();
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final Collection<String> dates = Lists.newArrayList();
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final List<List<Author>> authors = Lists.newArrayList();
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final List<Identifier<T>> bestPids = Lists.newArrayList(); // best pids list
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entities
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.forEachRemaining(
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t -> {
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T duplicate = t._2();
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// prepare the list of pids to use for the id generation
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bestPids.add(Identifier.newInstance(duplicate));
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entity.mergeFrom(duplicate);
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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Result r1 = (Result) duplicate;
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if (r1.getAuthor() != null && r1.getAuthor().size() > 0)
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authors.add(r1.getAuthor());
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if (r1.getDateofacceptance() != null)
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dates.add(r1.getDateofacceptance().getValue());
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}
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});
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// set authors and date
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if (ModelSupport.isSubClass(entity, Result.class)) {
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((Result) entity).setDateofacceptance(DatePicker.pick(dates));
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((Result) entity).setAuthor(AuthorMerger.merge(authors));
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}
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entity.setId(IdGenerator.generate(bestPids, id));
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entity.setLastupdatetimestamp(ts);
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entity.setDataInfo(dataInfo);
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return entity;
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}
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}
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