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