package eu.dnetlib.dedup.sx; import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; public class SparkPropagateRelationsJob { enum FieldType { SOURCE, TARGET } static final String SOURCEJSONPATH = "$.source"; static final String TARGETJSONPATH = "$.target"; public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( SparkPropagateRelationsJob.class .getResourceAsStream( "/eu/dnetlib/dhp/sx/dedup/dedup_propagate_relation_parameters.json"))); parser.parseArgument(args); final SparkSession spark = SparkSession .builder() .appName(SparkUpdateEntityJob.class.getSimpleName()) .master(parser.get("master")) .getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String relationPath = parser.get("relationPath"); final String mergeRelPath = parser.get("mergeRelPath"); final String targetRelPath = parser.get("targetRelPath"); final Dataset merge = spark .read() .load(mergeRelPath) .as(Encoders.bean(Relation.class)) .where("relClass == 'merges'"); final Dataset rels = spark.read().load(relationPath).as(Encoders.bean(Relation.class)); final Dataset firstJoin = rels .joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer") .map( (MapFunction, Relation>) r -> { final Relation mergeRelation = r._2(); final Relation relation = r._1(); if (mergeRelation != null) relation.setSource(mergeRelation.getSource()); return relation; }, Encoders.bean(Relation.class)); final Dataset secondJoin = firstJoin .joinWith(merge, merge.col("target").equalTo(firstJoin.col("target")), "left_outer") .map( (MapFunction, Relation>) r -> { final Relation mergeRelation = r._2(); final Relation relation = r._1(); if (mergeRelation != null) relation.setTarget(mergeRelation.getSource()); return relation; }, Encoders.bean(Relation.class)); secondJoin.write().mode(SaveMode.Overwrite).save(targetRelPath); } private static boolean containsDedup(final String json) { final String source = DHPUtils.getJPathString(SOURCEJSONPATH, json); final String target = DHPUtils.getJPathString(TARGETJSONPATH, json); return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup"); } private static String replaceField(final String json, final String id, final FieldType type) { ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); try { Relation relation = mapper.readValue(json, Relation.class); if (relation.getDataInfo() == null) relation.setDataInfo(new DataInfo()); relation.getDataInfo().setDeletedbyinference(false); switch (type) { case SOURCE: relation.setSource(id); return mapper.writeValueAsString(relation); case TARGET: relation.setTarget(id); return mapper.writeValueAsString(relation); default: throw new IllegalArgumentException(""); } } catch (IOException e) { throw new RuntimeException("unable to deserialize json relation: " + json, e); } } }