[SDG-FOS] alternative way to get input data to avoid OOM error while getting csv
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a706ba0c08
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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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_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.setLevel1(r.getString(1));
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fosDataModel.setLevel2(r.getString(2));
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fosDataModel.setLevel3(r.getString(3));
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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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@ -1,80 +0,0 @@
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.Serializable;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.zip.GZIPInputStream;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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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 static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
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public class GetInputData implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetInputData.class);
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public static void main(final 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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Objects
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.requireNonNull(
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GetInputData.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"))));
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parser.parseArgument(args);
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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 hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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final String classForName = parser.get("classForName");
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log.info("classForName {}", classForName);
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final char delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.map(s -> s.charAt(0))
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.orElse(DEFAULT_DELIMITER);
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log.info("delimiter {}", delimiter);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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new GetInputData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
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}
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public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
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throws IOException, ClassNotFoundException {
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// reads the csv and writes it as its json equivalent
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try (InputStreamReader reader = new InputStreamReader(new GZIPInputStream(fs.open(new Path(inputPath))))) {
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eu.dnetlib.dhp.common.collection.GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
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}
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}
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}
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@ -0,0 +1,91 @@
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_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.FilterFunction;
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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.actionmanager.createunresolvedentities.model.SDGDataModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class GetSDGSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetSDGSparkJob.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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GetSDGSparkJob.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_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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getSDG(
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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 getSDG(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
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Dataset<Row> sdgData = 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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sdgData.map((MapFunction<Row, SDGDataModel>) r -> {
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SDGDataModel sdgDataModel = new SDGDataModel();
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sdgDataModel.setDoi(r.getString(0).toLowerCase());
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sdgDataModel.setSbj(r.getString(1));
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return sdgDataModel;
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}, Encoders.bean(SDGDataModel.class))
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.filter((FilterFunction<SDGDataModel>) sdg -> sdg.getSbj() != null)
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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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@ -1,48 +1,47 @@
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
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import com.opencsv.bean.CsvBindByPosition;
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
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import java.io.Serializable;
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public class SDGDataModel implements Serializable{
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import com.opencsv.bean.CsvBindByPosition;
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@CsvBindByPosition(position = 0)
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public class SDGDataModel implements Serializable {
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@CsvBindByPosition(position = 0)
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// @CsvBindByName(column = "doi")
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private String doi;
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private String doi;
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@CsvBindByPosition(position = 1)
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@CsvBindByPosition(position = 1)
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// @CsvBindByName(column = "sdg")
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private String sbj;
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public SDGDataModel() {
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private String sbj;
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}
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public SDGDataModel() {
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public SDGDataModel(String doi, String sbj) {
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this.doi = doi;
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this.sbj = sbj;
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}
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}
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public SDGDataModel(String doi, String sbj) {
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this.doi = doi;
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this.sbj = sbj;
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public static SDGDataModel newInstance(String d, String sbj) {
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return new SDGDataModel(d, sbj);
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}
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}
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public String getDoi() {
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return doi;
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}
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public static SDGDataModel newInstance(String d, String sbj) {
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return new SDGDataModel(d, sbj);
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}
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public void setDoi(String doi) {
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this.doi = doi;
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}
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public String getDoi() {
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return doi;
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}
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public void setDoi(String doi) {
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this.doi = doi;
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}
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public String getSbj() {
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return sbj;
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}
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public String getSbj() {
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return sbj;
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}
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public void setSbj(String sbj) {
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this.sbj = sbj;
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}
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public void setSbj(String sbj) {
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this.sbj = sbj;
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}
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}
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