2021-11-09 11:25:41 +01:00
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package eu.dnetlib.dhp.bypassactionset.fos;
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2021-11-08 16:44:19 +01:00
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
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2021-11-09 11:25:41 +01:00
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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2021-11-08 16:44:19 +01:00
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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.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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2021-11-09 11:25:41 +01:00
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import org.jetbrains.annotations.NotNull;
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2021-11-08 16:44:19 +01:00
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
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2021-11-08 16:44:19 +01:00
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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2021-11-09 11:25:41 +01:00
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public class PrepareFOSSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
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2021-11-08 16:44:19 +01:00
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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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PrepareFOSSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bypassactionset/distribute_fos_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 = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String sourcePath = parser.get("sourcePath");
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log.info("sourcePath: {}", sourcePath);
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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 -> {
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removeOutputDir(spark, outputPath);
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distributeFOSdois(
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spark,
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sourcePath,
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outputPath
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);
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});
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}
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private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
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Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
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fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
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List<FOSDataModel> fosList = new ArrayList<>();
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final String level1 = v.getLevel1();
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final String level2 = v.getLevel2();
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final String level3 = v.getLevel3();
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Arrays.stream(v.getDoi().split("\u0002")).forEach(d ->
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fosList.add(FOSDataModel.newInstance(getIdentifier(d), level1, level2, level3)));
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return fosList.iterator();
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}, Encoders.bean(FOSDataModel.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.json(outputPath);
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}
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2021-11-09 11:25:41 +01:00
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2021-11-08 16:44:19 +01:00
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}
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