124 lines
4.0 KiB
Java
124 lines
4.0 KiB
Java
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.Arrays;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import org.apache.commons.cli.ParseException;
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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.FlatMapFunction;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 29/02/24
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*/
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public class MapOCIdsInPids implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
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private static final String DELIMITER = ",";
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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MapOCIdsInPids.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json"))));
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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("inputPath");
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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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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> mapIdentifiers(spark, inputPath, outputPath));
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}
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private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
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Dataset<COCI> coci = spark
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.read()
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.textFile(inputPath + "/JSON")
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.map(
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(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
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Encoders.bean(COCI.class));
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Dataset<Tuple2<String, String>> correspondenceData = spark
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.read()
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.format("csv")
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.option("sep", DELIMITER)
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.option("inferSchema", "true")
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.option("header", "true")
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.option("quotes", "\"")
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.load(inputPath + "/correspondence/omid.zip")
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.repartition(5000)
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.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
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String ocIdentifier = r.getAs("omid");
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String[] correspondentIdentifiers = ((String) r.getAs("id")).split(" ");
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return Arrays
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.stream(correspondentIdentifiers)
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.map(ci -> new Tuple2<String, String>(ocIdentifier, ci))
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.collect(Collectors.toList())
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.iterator();
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}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<COCI> mappedCitingDataset = coci
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.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left")
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.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
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String correspondent = t2._2()._2();
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t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
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t2._1().setCiting(correspondent.substring(correspondent.indexOf(":") + 1));
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return t2._1();
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}, Encoders.bean(COCI.class));
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mappedCitingDataset
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.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
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.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
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String correspondent = t2._2()._2();
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t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
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t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
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return t2._1();
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}, Encoders.bean(COCI.class))
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.json(outputPath);
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}
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}
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