package eu.dnetlib.dhp.oa.dedup; import java.util.Collection; import java.util.Iterator; import java.util.List; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; public class DedupRecordFactory { protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); private DedupRecordFactory() { } public static Dataset createDedupRecord( final SparkSession spark, final DataInfo dataInfo, final String mergeRelsInputPath, final String entitiesInputPath, final Class clazz) { long ts = System.currentTimeMillis(); // Dataset> entities = spark .read() .textFile(entitiesInputPath) .map( (MapFunction>) it -> { T entity = OBJECT_MAPPER.readValue(it, clazz); return new Tuple2<>(entity.getId(), entity); }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); // : source is the dedup_id, target is the id of the mergedIn Dataset> mergeRels = spark .read() .load(mergeRelsInputPath) .as(Encoders.bean(Relation.class)) .where("relClass == 'merges'") .map( (MapFunction>) r -> new Tuple2<>(r.getSource(), r.getTarget()), Encoders.tuple(Encoders.STRING(), Encoders.STRING())); return mergeRels .joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner") .map( (MapFunction, Tuple2>, Tuple2>) value -> new Tuple2<>( value._1()._1(), value._2()._2()), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))) .groupByKey( (MapFunction, String>) Tuple2::_1, Encoders.STRING()) .mapGroups( (MapGroupsFunction, T>) (key, values) -> entityMerger(key, values, ts, dataInfo, clazz), Encoders.bean(clazz)); } public static T entityMerger( String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) throws IllegalAccessException, InstantiationException { T entity = clazz.newInstance(); entity.setDataInfo(dataInfo); final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); entities .forEachRemaining( t -> { T duplicate = t._2(); entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; if (r1.getAuthor() != null && !r1.getAuthor().isEmpty()) authors.add(r1.getAuthor()); if (r1.getDateofacceptance() != null) dates.add(r1.getDateofacceptance().getValue()); } }); // set authors and date if (ModelSupport.isSubClass(entity, Result.class)) { ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setAuthor(AuthorMerger.merge(authors)); } entity.setId(id); entity.setLastupdatetimestamp(ts); entity.getDataInfo().setDeletedbyinference(false); return entity; } }