116 lines
3.3 KiB
Java
116 lines
3.3 KiB
Java
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package eu.dnetlib.dhp.actionmanager.opencitations;
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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.IOException;
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import java.io.Serializable;
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import java.util.Arrays;
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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.*;
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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.opencitations.model.COCI;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class ReadCOCI implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ReadCOCI.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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ReadCOCI.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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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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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String workingPath = parser.get("inputPath");
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log.info("workingPath {}", workingPath);
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SparkConf sconf = new SparkConf();
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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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final String delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.orElse(DEFAULT_DELIMITER);
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runWithSparkSession(
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sconf,
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isSparkSessionManaged,
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spark -> {
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doRead(
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spark,
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workingPath,
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fileSystem,
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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 doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
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String outputPath,
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String delimiter) throws IOException {
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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new Path(workingPath), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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log.info("extracting file {}", fileStatus.getPath().toString());
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Dataset<Row> cociData = 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(fileStatus.getPath().toString())
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.repartition(100);
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cociData.map((MapFunction<Row, COCI>) row -> {
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COCI coci = new COCI();
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coci.setCiting(row.getString(1));
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coci.setCited(row.getString(2));
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coci.setOci(row.getString(0));
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return coci;
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}, Encoders.bean(COCI.class))
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.filter((FilterFunction<COCI>) c -> c != null)
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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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fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
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}
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}
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}
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