126 lines
3.6 KiB
Java
126 lines
3.6 KiB
Java
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package eu.dnetlib.dhp.countrypropagation;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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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 eu.dnetlib.dhp.schema.oaf.Country;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import scala.Tuple2;
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public class SparkCountryPropagationJob {
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private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob.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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SparkCountryPropagationJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_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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String sourcePath = parser.get("sourcePath");
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log.info("sourcePath: {}", sourcePath);
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String preparedInfoPath = parser.get("preparedInfoPath");
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log.info("preparedInfoPath: {}", preparedInfoPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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execPropagation(
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spark,
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sourcePath,
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preparedInfoPath,
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outputPath,
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resultClazz);
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});
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}
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private static <R extends Result> void execPropagation(
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SparkSession spark,
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String sourcePath,
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String preparedInfoPath,
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String outputPath,
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Class<R> resultClazz) {
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log.info("Reading Graph table from: {}", sourcePath);
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Dataset<R> res = readPath(spark, sourcePath, resultClazz);
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log.info("Reading prepared info: {}", preparedInfoPath);
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Dataset<ResultCountrySet> prepared = spark
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.read()
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.json(preparedInfoPath)
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.as(Encoders.bean(ResultCountrySet.class));
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res
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.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
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.map(getCountryMergeFn(), Encoders.bean(resultClazz))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputPath);
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}
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private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {
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return t -> {
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Optional.ofNullable(t._2()).ifPresent(r -> {
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t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet()));
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});
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return t._1();
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};
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}
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private static List<Country> merge(List<Country> c1, List<CountrySbs> c2) {
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HashSet<String> countries = c1
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.stream()
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.map(Qualifier::getClassid)
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.collect(Collectors.toCollection(HashSet::new));
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return c2
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.stream()
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.filter(c -> !countries.contains(c.getClassid()))
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.map(c -> getCountry(c.getClassid(), c.getClassname()))
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.collect(Collectors.toList());
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}
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}
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