forked from D-Net/dnet-hadoop
112 lines
3.2 KiB
Java
112 lines
3.2 KiB
Java
|
|
||
|
package eu.dnetlib.dhp.actionmanager.opencitations;
|
||
|
|
||
|
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
|
||
|
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
|
||
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||
|
|
||
|
import java.io.IOException;
|
||
|
import java.io.Serializable;
|
||
|
import java.util.Optional;
|
||
|
|
||
|
import org.apache.commons.io.IOUtils;
|
||
|
import org.apache.hadoop.conf.Configuration;
|
||
|
import org.apache.hadoop.fs.FileSystem;
|
||
|
import org.apache.hadoop.fs.LocatedFileStatus;
|
||
|
import org.apache.hadoop.fs.Path;
|
||
|
import org.apache.hadoop.fs.RemoteIterator;
|
||
|
import org.apache.spark.SparkConf;
|
||
|
import org.apache.spark.api.java.function.MapFunction;
|
||
|
import org.apache.spark.sql.*;
|
||
|
import org.slf4j.Logger;
|
||
|
import org.slf4j.LoggerFactory;
|
||
|
|
||
|
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
|
||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||
|
|
||
|
public class ReadCOCI implements Serializable {
|
||
|
|
||
|
private static final Logger log = LoggerFactory.getLogger(ReadCOCI.class);
|
||
|
|
||
|
public static void main(String[] args) throws Exception {
|
||
|
String jsonConfiguration = IOUtils
|
||
|
.toString(
|
||
|
ReadCOCI.class
|
||
|
.getResourceAsStream(
|
||
|
"/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json"));
|
||
|
|
||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||
|
parser.parseArgument(args);
|
||
|
|
||
|
final String outputPath = parser.get("outputPath");
|
||
|
log.info("outputPath: {}", outputPath);
|
||
|
|
||
|
final String hdfsNameNode = parser.get("nameNode");
|
||
|
log.info("nameNode: {}", hdfsNameNode);
|
||
|
|
||
|
final String inputPath = parser.get("sourcePath");
|
||
|
log.info("input path : {}", inputPath);
|
||
|
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
||
|
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||
|
|
||
|
Configuration conf = new Configuration();
|
||
|
conf.set("fs.defaultFS", hdfsNameNode);
|
||
|
|
||
|
FileSystem fileSystem = FileSystem.get(conf);
|
||
|
SparkConf sconf = new SparkConf();
|
||
|
|
||
|
final String delimiter = Optional
|
||
|
.ofNullable(parser.get("delimiter"))
|
||
|
.orElse(DEFAULT_DELIMITER);
|
||
|
|
||
|
runWithSparkSession(
|
||
|
sconf,
|
||
|
isSparkSessionManaged,
|
||
|
spark -> {
|
||
|
doRead(
|
||
|
spark,
|
||
|
fileSystem,
|
||
|
inputPath,
|
||
|
outputPath,
|
||
|
delimiter);
|
||
|
});
|
||
|
}
|
||
|
|
||
|
public static void doRead(SparkSession spark, FileSystem fileSystem, String inputPath, String outputPath,
|
||
|
String delimiter) throws IOException {
|
||
|
|
||
|
RemoteIterator<LocatedFileStatus> iterator = fileSystem
|
||
|
.listFiles(
|
||
|
new Path(inputPath), true);
|
||
|
|
||
|
while (iterator.hasNext()) {
|
||
|
LocatedFileStatus fileStatus = iterator.next();
|
||
|
|
||
|
Path p = fileStatus.getPath();
|
||
|
String p_string = p.toString();
|
||
|
Dataset<Row> cociData = spark
|
||
|
.read()
|
||
|
.format("csv")
|
||
|
.option("sep", delimiter)
|
||
|
.option("inferSchema", "true")
|
||
|
.option("header", "true")
|
||
|
.option("quotes", "\"")
|
||
|
.load(p_string);
|
||
|
|
||
|
cociData.map((MapFunction<Row, COCI>) row -> {
|
||
|
COCI coci = new COCI();
|
||
|
coci.setOci(row.getString(0));
|
||
|
coci.setCiting(row.getString(1));
|
||
|
coci.setCited(row.getString(2));
|
||
|
return coci;
|
||
|
}, Encoders.bean(COCI.class))
|
||
|
.write()
|
||
|
.mode(SaveMode.Overwrite)
|
||
|
.option("compression", "gzip")
|
||
|
.json(outputPath + "/" + p_string.substring(p_string.lastIndexOf("/") + 1));
|
||
|
}
|
||
|
|
||
|
}
|
||
|
|
||
|
}
|