94 lines
2.8 KiB
Java
94 lines
2.8 KiB
Java
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_FOS_DELIMITER;
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import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
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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.Optional;
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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.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 eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class GetFOSSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetFOSSparkJob.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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GetFOSSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_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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// the path where the original fos csv file is stored
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final String sourcePath = parser.get("sourcePath");
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log.info("sourcePath {}", sourcePath);
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// the path where to put the file as json
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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final String delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.orElse(DEFAULT_FOS_DELIMITER);
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SparkConf sconf = new SparkConf();
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runWithSparkSession(
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sconf,
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isSparkSessionManaged,
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spark -> {
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getFOS(
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spark,
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sourcePath,
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outputPath,
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delimiter);
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});
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}
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private static void getFOS(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
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Dataset<Row> fosData = 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(sourcePath);
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fosData.map((MapFunction<Row, FOSDataModel>) r -> {
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FOSDataModel fosDataModel = new FOSDataModel();
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fosDataModel.setDoi(r.getString(0).toLowerCase());
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fosDataModel.setOaid(r.getString(1).toLowerCase());
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fosDataModel.setLevel1(r.getString(2));
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fosDataModel.setLevel2(r.getString(3));
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fosDataModel.setLevel3(r.getString(4));
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fosDataModel.setLevel4(r.getString(5));
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fosDataModel.setScoreL3(String.valueOf(r.getDouble(6)));
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fosDataModel.setScoreL4(String.valueOf(r.getDouble(7)));
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return fosDataModel;
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}, Encoders.bean(FOSDataModel.class))
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.write()
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.mode(SaveMode.Overwrite)
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.json(outputPath);
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}
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}
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