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.common.collection.GetCSV;
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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 java.io.*;
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import java.util.Objects;
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import java.util.Optional;
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public class GetFOSData implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
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public static final char DEFAULT_DELIMITER = '\t';
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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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GetFOSData.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bypassactionset/get_fos_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 inputPath = parser.get("inputPath");
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log.info("inputPath {}", inputPath);
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//the path where to put the file as json
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final String outputFile = parser.get("outputFile");
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log.info("outputFile {}", outputFile);
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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 GetFOSData().doRewrite(inputPath, outputFile, 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(fs.open(new Path (inputPath)))) {
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GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
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}
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}
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}
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