164 lines
5.0 KiB
Java
164 lines
5.0 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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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.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.eosc.model.Provenance;
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import eu.dnetlib.dhp.eosc.model.RelType;
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import eu.dnetlib.dhp.eosc.model.Result;
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import eu.dnetlib.dhp.schema.oaf.*;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 12/01/23
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*/
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public class SparkSelectRelation implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkSelectRelation.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkSelectRelation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/eosc_input_relationdump_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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Optional<String> rs = Optional.ofNullable(parser.get("removeSet"));
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final Set<String> removeSet = new HashSet<>();
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if (rs.isPresent()) {
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Collections.addAll(removeSet, rs.get().split(";"));
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}
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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selectSubset(spark, inputPath, outputPath, removeSet);
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});
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}
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private static void selectSubset(SparkSession spark, String inputPath, String outputPath, Set<String> removeSet) {
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter(
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(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference()
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&& !removeSet.contains(r.getRelClass()));
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Dataset<Tuple2<String, String>> resultIds = Utils
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.readPath(spark, outputPath + "/publication", Result.class)
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.map(
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(MapFunction<Result, Tuple2<String, String>>) p -> new Tuple2<>(p.getId(), p.getType()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
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.union(
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Utils
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.readPath(spark, outputPath + "/dataset", Result.class)
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.map(
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(MapFunction<Result, Tuple2<String, String>>) d -> new Tuple2<>(d.getId(), d.getType()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING())))
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.union(
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Utils
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.readPath(spark, outputPath + "/software", Result.class)
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.map(
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(MapFunction<Result, Tuple2<String, String>>) s -> new Tuple2<>(s.getId(), s.getType()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING())))
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.union(
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Utils
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.readPath(spark, outputPath + "/otherresearchproduct", Result.class)
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.map(
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(MapFunction<Result, Tuple2<String, String>>) o -> new Tuple2<>(o.getId(), o.getType()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING())));
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// select result -> result relations
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Dataset<Relation> relResultResult = relation
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.joinWith(resultIds, relation.col("source").equalTo(resultIds.col("_1")))
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.map(
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(MapFunction<Tuple2<Relation, Tuple2<String, String>>, Relation>) t2 -> t2._1(),
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Encoders.bean(Relation.class));
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relResultResult
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.joinWith(resultIds, relResultResult.col("target").equalTo(resultIds.col("_1")))
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.map((MapFunction<Tuple2<Relation, Tuple2<String, String>>, eu.dnetlib.dhp.eosc.model.Relation>) t2 -> {
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eu.dnetlib.dhp.eosc.model.Relation relNew = new eu.dnetlib.dhp.eosc.model.Relation();
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Relation rel = t2._1();
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relNew
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.setSource(
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rel.getSource());
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relNew
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.setTarget(
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rel.getTarget());
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relNew
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.setReltype(
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RelType
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.newInstance(
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rel.getRelClass(),
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rel.getSubRelType()));
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relNew.setTargetType(t2._2()._2());
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Optional<DataInfo> odInfo = Optional.ofNullable(rel.getDataInfo());
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if (odInfo.isPresent()) {
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DataInfo dInfo = odInfo.get();
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if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() &&
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Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
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relNew
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.setProvenance(
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Provenance
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.newInstance(
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dInfo.getProvenanceaction().getClassname(),
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dInfo.getTrust()));
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}
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}
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return relNew;
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}, Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputPath + "/relation");
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}
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}
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